2018-2019
AREAS OF STUDY
MOLECULAR BIOLOGY GENETICS DIABETES CELL BIOLOGY GENE THERAPY CHEMICAL BIOLOGY CANCER BIOLOGY DNA DAMAGE/REPAIR STRUCTURAL BIOLOGY STEM CELL BIOLOGY PROTEOMICS IMMUNOLOGY NEUROSCIENCES RNA BIOMEDICAL INFORMATICS
DEAN’S WELCOME
Thank you for your interest in the Irell & Manella Graduate School of Biological Sciences at City of Hope. City of Hope National Medical Center and Beckman Research Institute of City of Hope offer a unique and challenging research and learning environment for graduate education. Both basic science and translational biomedical research flourish here, in a collegial atmosphere where cross- communication thrives and basic science findings are John Rossi, Ph.D. often applied to the cure of life-threatening diseases. Our faculty members have made major contributions in the basic biological sciences and biomedicine. They are widely recognized as leaders in their fields. Our diverse students, from the United States, Canada, Argentina, India, Iran, Korea, China, Burma, Thailand, Bulgaria, France, Russia, Malaysia and Taiwan, bring to our campus a wealth of interests, experience, enthusiasm, potential and creativity. City of Hope’s interdisciplinary research programs provide students with many opportunities to enrich their graduate education by interacting with other graduate students, postdoctoral fellows and faculty members outside of their own areas of specialization. City of Hope has a strong track record in training both predoctoral students and postdoctoral fellows. Our Ph.D. graduates go on to a prestigious postdoctoral fellowship or a biotechnology or academic position, after receiving many excellent offers. We are excited to begin a new joint masters program with the Keck Graduate Institute (KGI), a Master of Science in Translational Medicine. Over the years, our relationship with KGI has grown from research collaborations to a certificate in Bioscience Management. This new development allows students to benefit from KGI’s curriculum in science and business, and the translational research opportunities on the City of Hope campus. This catalog contains all of the necessary information about applying to the graduate school. Please contact us if you have any questions. We encourage you to visit our beautiful campus to learn more about this exciting opportunity for graduate training at City of Hope.
John J. Rossi, Ph.D. Lidow Family Research Chair Morgan and Helen Chu Dean’s Chair Dean, Irell & Manella Graduate School of Biological Sciences City of Hope
TABLE OF CONTENTS
Introduction ...... 1 Mark LaBarge...... 73 Academic Programs ...... 2 Peter P. Lee...... 74 Research Departments ...... 3 Ren-Jang Lin...... 75 Facilities...... 6 Ph.D. Admissions ...... 9 Yilun Liu...... 76 Ph.D. Requirements...... 10 Qiang Lu ...... 77 Ph.D. Course Offerings...... 12 Ke Ma...... 78 Core Course Descriptions ...... 13 Linda Malkas...... 79 Students...... 14 Edwin R. Manuel...... 80 Student Life ...... 16 Alumni — Life After Graduation...... 18 Jeannine McCune...... 81 Master’s Program...... 20 Marcia M. Miller ...... 82 Faculty...... 2 1 Kevin V. Morris...... 83 Karen S. Aboody...... 22 Markus Müschen...... 84 David K. Ann...... 23 Behnam Badie...... 24 Rama Natarajan ...... 85 Adam M. Bailis...... 25 Susan Neuhausen ...... 86 Michael E. Barish...... 26 Edward M. Newman...... 87 Jacob Berlin...... 27 Vu Ngo ...... 88 Mark Boldin ...... 28 Timothy R. O’Connor...... 89 Christine Brown...... 29 John Burnett...... 30 Javier Gordon Ogembo...... 90 Edouard M. Cantin...... 31 Flavia Pichiorri...... 91 Nadia Carlesso...... 32 Christiane Querfeld...... 92 Daniela Castanotto...... 33 Helena Reijonen...... 93 Wing-Chun “John” Chan...... 34 Russell C. Rockne ...... 94 Saswati Chatterjee...... 35 Ammar Chaudhry...... 36 Andrei S. Rodin...... 95 Ching-Cheng Chen ...... 37 Bart O. Roep...... 96 Chun-Wei David Chen...... 38 Steven T. Rosen...... 97 Jianjun Chen ...... 39 John J. Rossi ...... 98 Mike Y. Chen ...... 40 Shiuan Chen...... 41 Paul M. Salvaterra...... 99 WenYong Chen ...... 42 Dustin E. Schones ...... 100 Yuan Chen ...... 43 Victoria Seewaldt...... 101 Zhen (Jen) Chen...... 44 Binghui Shen ...... 102 Warren Chow...... 45 Yanhong Shi...... 103 Jessica Clague DeHart...... 46 Sangeeta Dhawan...... 47 Ben Hung-Ping Shih ...... 104 Don J. Diamond...... 48 John E. Shively...... 105 Richard W. Ermel...... 49 Christopher Sistrunk...... 106 Mingye Feng...... 50 Steven S. Smith...... 107 Yuman Fong...... 51 Jeremy M. Stark...... 108 Stephen J. Forman ...... 52 Patrick T. Fueger ...... 53 Cy A. Stein...... 109 Carlotta A. Glackin...... 54 Zijie (ZJ) Sun...... 110 Robert J. Hickey...... 55 Zuoming Sun ...... 111 David A. Horne ...... 56 Timothy W. Synold...... 112 Wendong Huang ...... 57 John Termini ...... 113 Susanta Hui...... 58 Janice M. Huss...... 59 Debbie C. Thurmond ...... 114 Keiichi Itakura ...... 60 Nagarajan Vaidehi ...... 115 Rahul Jandial...... 61 Qiong (Annabel) Wang...... 117 Lei Jiang...... 62 Leo Wang...... 117 Jeremy Jones ...... 63 Tijana Jovanovic-Talisman ...... 64 Jeffrey N. Weitzel ...... 118 Michael Kahn...... 65 John C. Williams...... 119 Markus Kalkum...... 66 Yanzhong (Frankie) Yang ...... 120 Rick Kittles...... 67 Jiing-Kuan Yee ...... 121 Marcin Kortylewski ...... 68 Hua Yu ...... 122 Hsun Teresa Ku ...... 69 Ya-Huei Kuo ...... 70 Xiaochun Yu...... 123 Larry W. Kwak...... 71 John A. Zaia ...... 124 Keane Lai...... 72 Defu Zeng...... 125
INTRODUCTION
INTRODUCTION
City of Hope was founded in 1913 in Duarte, California, by a imaging, interfering RNAs and HIV treatment, total synthesis small group of working-class men and women who believed of complex and therapeutic natural products, mechanisms of in helping those less fortunate than themselves. From humble drug action, neurogenesis, stem cell therapy, DNA repair and beginnings — two cottages erected on 10 acres of desert radiation, and the immunobiology of viral infection. — City of Hope has expanded to a 114-acre, 115-building Investigating the biology, biological chemistry and pathology campus landscaped with plants, trees and more than 2,000 of cancer and diabetes, our researchers have also explored rose bushes. In this healing setting, over 600 physicians and the emerging links between the diseases. By identifying scientists collaborate to discover, develop and implement opportunities at the cellular and molecular level, they innovative strategies for the prevention and treatment of continue developing breakthrough approaches for predicting, cancer and other catastrophic diseases. preventing, diagnosing, treating and curing these and other City of Hope is recognized worldwide for its patient care, serious diseases. innovative science and translational research, which rapidly The DMRI builds on City of Hope’s long and impressive history turns laboratory breakthroughs into promising new therapies. of groundbreaking discoveries in the field of Diabetes. The We helped launch the biotech industry with the development institute is focused on advancing islet cell transplantation of technologies that led to the first synthetic human insulin and and related treatments for type 1 diabetes, understanding human growth hormone. Our goal is to shorten the time from the genetic and molecular signaling mechanisms that lead scientific breakthroughs to effective new treatments. We strive to diabetes and its complications, and understanding the to find a seamless and fruitful collaboration of basic science, structure and functions of nuclear receptors in order to clinical research and patient care that powers important design drugs that can prevent activation of undesirable genes. advances in medical progress. Our collaborative pursuits Arthur Riggs, Ph.D., the Samuel Rahbar Chair in Diabetes & extend beyond City of Hope. We frequently conduct clinical Drug Discovery, chair of the DMRI, is a pioneer in diabetes trials in partnership with government agencies and other research. He is recognized for this work in synthesizing human academic centers, ensuring that patients here and elsewhere insulin, which largely replaced animal-derived (porcine or receive the potential benefit of promising investigative bovine) insulin and became the standard of care for diabetes therapies as quickly as possible. worldwide. City of Hope’s Department of Clinical Diabetes, Endocrinology & Metabolism is also renowned for its islet cell The campus is located in the San Gabriel Valley, surrounded transplantation program, which offers an increasingly viable by one of the greatest concentration of scientific and cultural treatment option for type 1 diabetes. centers in the United States. Just 10 miles east of Pasadena and 22 miles northeast of Los Angeles in the San Gabriel CAMPUS VISITS AND TOURS Mountains, the campus is located in close proximity to a The beauty of City of Hope’s campus must be experienced in variety of recreational activities, from sunning at the beach person. Visitor Services offers tours to prospective students to hiking in the desert to skiing in the mountains. and their families. The tours last about one hour. Reservations There are two research institutes on the City of Hope campus, are required and may be arranged by calling 626-218-2471. Beckman Research Institute and the Diabetes & Metabolism Research Institute (DMRI). The graduate students are able to study with faculty in each, covering a wide range of topics.
Beckman Research Institute of City of Hope was the first of five Beckman Institutes to be founded, and has held a National Cancer Institute Cancer Center Support Grant for over 30 years. Encompassing over 60 years of expertise in basic science, Beckman Research Institute also houses research done at City of Hope prior to the establishment of the institute by Arnold and Mabel Beckman in 1983. Research areas include diabetes progression and treatment, immunology and
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 1 ACADEMIC PROGRAMS
Ph.D. PROGRAM The Irell & Manella Graduate School of Biological Sciences laboratory rotations, seminars, journal club and scholarly was founded in 1994 with an incoming class of four students, research leading to the Ph.D. in biological sciences. Graduate and the first doctoral degree was conferred in 1997. Since then, work provides ample opportunities for specific training in the the graduate school has grown steadily to over 90 students development of biomedical models and research methodology, and 110 faculty members. The mission of the Irell & Manella as well as in other areas important for ACLAM board Graduate School of Biological Sciences of City of Hope is to certification. The training program also includes a full spectrum train students in an academically stimulating, collaborative of clinical rounds, seminars and special projects pertaining to and diverse environment to apply their creativity, curiosity laboratory animal medicine. and talents to advance understanding of the complexities Apply to: of the life sciences and to apply research discoveries to the Richard W. Ermel, D.V.M., M.P.V.M., Ph.D. cures for diseases. Director/Professor – Division of Comparative Medicine The program provides students with a solid educational Beckman Research Institute of City of Hope foundation and a research environment that encourages [email protected] independent thought and challenges current dogma. The program offers coursework to establish a framework for TRAINING PROGRAM IN BIOSCIENCE MANAGEMENT understanding the complexities of scientific problems, research The Irell & Manella Graduate School of Biological Sciences opportunities with investigators who have integrated the latest in collaboration with the Keck Graduate Institute (KGI) of technologies into their research projects, and professional the Claremont Colleges is proud to offer a Management forums where students can share ideas with colleagues. Training Program for graduate students and postdoctoral Students receive a stipend of $33,000 and health insurance fellows. Advanced graduate students and postdocs, with the (medical, dental and vision). Students must pay a student fee permission of their research advisor, receive full scholarships to of $150 per year. take business-related courses at KGI and to earn a certificate in bioscience management. The program is designed to RESIDENCY AND GRADUATE TRAINING PROGRAM IN prepare students for intellectually challenging careers in the LABORATORY ANIMAL MEDICINE private sector. The Beckman Research Institute of City of Hope and University Required courses include marketing, finance, strategy, of Southern California Residency and Graduate Training accounting and organizational behavior. This program provides Program in Laboratory Animal Medicine is a five-year program excellent preparation for careers in biotechnology and whose overall objective is to provide postdoctoral (D.V.M.) pharmaceutical companies as science and disease concepts trainees (laboratory animal medicine fellows) with intellectual are integrated with management and industry. depth and breadth, and appropriate clinical and research training in laboratory animal medicine, laboratory animal/ VETERANS comparative pathology and comparative medicine. The training The Irell & Manella Graduate School of Biological Sciences is program is designed and managed to support preparation approved for the training of veterans and eligible persons under toward American College of Laboratory Animal Medicine the provisions of Title 38, United States Code. Contact Kate (ACLAM) board certification and to prepare individuals for Sleeth, Ph.D., for additional information at 626-471-3667. academic careers in the biomedical sciences and comparative medicine through completion of the Doctor of Philosophy ACCREDITATION (Ph.D.) degree in the City of Hope Irell & Manella Graduate City of Hope’s Irell & Manella Graduate School of Biological School of Biological Sciences. Sciences is accredited by the Western Association of School Residency training includes clinical laboratory animal medicine, and Colleges Senior College and University Commission. laboratory animal resources and facilities management, Contact the Commission at 985 Atlantic Ave., #100, Alameda, comparative and diagnostic laboratory animal pathology, CA 94501 or call 510-748-9001 for questions about the and methods and practice of biomedical research. Graduate accreditation of City of Hope’s Irell & Manella Graduate School training consists of a combination of graduate course work, of Biological Sciences.
2 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES RESEARCH DEPARTMENTS
CANCER BIOLOGY DIABETES COMPLICATIONS AND METABOLISM The Department of Cancer Biology focuses on understanding The Department of Diabetes Complications & Metabolism is the basic mechanisms of genetics, gene expression and at the forefront of research on the complications of diabetes function, signaling pathways, mutagenesis, DNA repair and and metabolic diseases. This department uses state-of- epigenetics as they relate to the development and progression the-art computational and systems biology data-analysis of cancer. Researchers collaborate with clinical and basic methods, genomic and epigenomic profiling approaches; novel research programs within City of Hope and with other centers transgenic mouse models; and translational approaches with nationally and internationally. With a strong foundation in small molecules and modified nucleotides in animal models basic research methodology, department scientists are working and humans in its quest to advance the field of diabetes, to bring to light new insights that one day could produce novel obesity, diabetic complications and metabolic diseases therapies for a wide range of genetic diseases. They also seek research. Several investigators are examining the role of to develop novel translational cancer research in the areas of epigenetic mechanisms in these pathologies. Researchers are tumor biology, biomedical informatics and cancer prevention also studying the molecular links between diabetes, obesity and diagnosis. and cancer, and mechanisms by which aberrant metabolism leads to cancer. The department offers scientists and CANCER GENETICS AND EPIGENETICS trainees a multidisciplinary environment in these scientific The Department of Cancer Genetics and Epigenetics research areas. focuses on discovering the fundamental mechanisms DIABETES IMMUNOLOGY of DNA replication and DNA damage repair during cell growth. Efficient DNA replication and damage responses are The Department of Diabetes Immunology is dedicated to important for maintaining genome integrity and for preventing studying immune system mechanisms and their impact cancer development, but it also helps to protect cancer cells on diabetes development and control — particularly type 1 from the effects of radiation and chemotherapy. diabetes, which is triggered by an autoimmune reaction against a person’s own insulin-producing beta cells in the pancreas. A DEVELOPMENTAL AND STEM CELL BIOLOGY better understanding of these mechanisms can lead to better Study of the nervous system has a long history at prevention, detection and treatment strategies for people City of Hope, which was one of the first institutions in with, or at-risk for, type 1 diabetes, significantly improving their North America to establish a neurobiology research clinical outcomes and quality of life while reducing the risk of department. The Department of Developmental and Stem serious complications. Cell Biology offers a multidisciplinary research and training environment in neurobiology, with a particular focus on developmental aspects of the nervous system. Research in the department encompasses molecular and cellular neurobiology, genetics and neurophysiology, with ongoing studies in neurogenesis and synaptogenesis, migration and specification, degeneration and embryonic stem cell differentiation. Researchers in the department collaborate with colleagues in other basic science departments and divisions, as well as clinical researchers in neuro-oncology programs focusing on cancer immunotherapy and neurosurgery. The Department of Developmental and Stem Cell Biology spans a broad range of research interests which include early electrical activity in the developing hippocampus and cortex, regulation of transmitter phenotype, studying the nuclear receptors that control generation and differentiation of neural lineage stem cells in the adult nervous system.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 3 RESEARCH DEPARTMENTS
HEMATOLOGIC MALIGNANCIES TRANSLATIONAL SCIENCE MATHEMATICAL ONCOLOGY The focus of the Department of Hematologic Malignancies City of Hope’s Division of Mathematical Oncology is dedicated Translational Science is to improve the understanding of to outsmarting cancer by combining the multidisciplinary leukemia stem cells in order to develop cures for leukemia expertise of physicians, scientists and mathematicians. The and other hematologic malignancies. Leukemia stem cells and division has a unique combination of clinical care, scientific progenitor cells differ significantly from mature leukemia cells research and mathematical expertise enhances overall and, of course, from normal hematopoietic stem cells. Because understanding of cancer development, growth, evolution and recent studies have demonstrated that leukemia stem cells reaction to treatment — ultimately helping the care team to actually cause leukemia, the objective must now be to eradicate predict, control and thwart malignancy on both a global scale leukemia stem cells, rather than just the regular, mature (by improving evidence-based standards of care) and an leukemia cells addressed by current therapies. Eradication of individual level (by personalizing treatment using quantifiable the leukemia stem cells may actually produce cures. patient and disease factors.) The goal is to investigate mechanisms of regulation of MOLECULAR AND CELLULAR BIOLOGY normal hematopoietic stem cell growth by the marrow microenvironment, the cellular and molecular mechanisms Research interests in the Department of Molecular and underlying stem cell transformation in patients with leukemias, Cellular Biology include an array of biological systems and assessment of the effects of therapeutic interventions on problems, but the unifying theme is mechanisms regulating malignant stem cells, and preclinical and clinical development expression of genetic information at both the transcriptional of innovative, mechanism-based therapeutic interventions level (where DNA directs the synthesis of RNA) and the directed against malignant stem cells. post-transcriptional level (meaning how genes control protein synthesis from newly transcribed RNAs). IMMUNO-ONCOLOGY MOLECULAR AND CELLULAR ENDOCRINOLOGY Researchers in the Department of Immuno-Oncology are pioneering medical science that harnesses the power of the The Department of Molecular & Cellular Endocrinology is body’s own immune system to fight cancer. Immunotherapy is pioneering efforts to investigate biological mechanisms a formidable weapon against cancer because of its potential to involved with type 1 and type 2 diabetes development and exploit the body’s natural defenses against infection. substances that promote or interfere with those processes. The findings can lead to potential therapies that can reverse or Two cancer immunotherapies currently in use are T cell prevent the onset of these diseases, as well as diagnostic tools therapy, which uses specialized cells produced by the immune that can detect each disease type earlier. system to target and kill cancer cells, and immune checkpoint blockade, which modulates/enhances the immune system to The department conducts cellular, animal model and human attack and kill tumor cells. These therapies are effective for tissue research with a multidisciplinary staff that includes some patients with metastatic cancer. They also offer renewed molecular and cellular biology, physiology, biochemistry and hope to people who have exhausted other treatment options. pharmacology expertise. Scientists in the Department of Immuno-Oncology foresee a much larger role for immunotherapy in the battle against cancer. They intend to move immunotherapy forward to the front lines by making it a highly effective primary treatment option, capable of producing more powerful, less toxic cures. Our scientists are working to further enhance the efficacy of these novel treatments, and to apply them to patients with early-stage cancer to eliminate microscopic residual disease which can lead to cancer recurrence, even after chemotherapy, radiation therapy and surgery have been successful.
4 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES RESEARCH DEPARTMENTS
MOLECULAR IMAGING AND THERAPY SYSTEMS BIOLOGY The Department of Molecular Imaging and Therapy continues The Department of Systems Biology aims to understand its original vision, with a dual focus on both immunology and the complex biological systems involved in signal structural biology. The unique combination of biological and transduction and in the transcriptional, epigenetic and structural studies and the intensive exploration of structure- metabolic regulation of hematological malignancies, function relationships have created a thriving, productive leukemia and lymphoma. By integrating data on signal environment that has encouraged fruitful collaboration among transduction, transcriptional and metabolic activity at the investigators. The research in the department is focused on the single-cell level with clinical information and drug-resistance role of T cells in immunity, computational approaches to study profiles from clinical trials, our computational analyses can the structure, function and dynamics of G-protein coupled extract features of drug-resistance and relapse in leukemia receptors, and determining the role of CEACAM1 in T cell and lymphoma based on machine learning tools that are activation and mammary epithelial cell polarization. commonly used in face recognition systems. With a focus on hematological malignancies, primary research interests MOLECULAR MEDICINE of the department include oncogenic B cell receptor signaling The Department of Molecular Medicine investigates the in B-lineage leukemia and lymphoma, molecular genetics of mechanisms underlying cancer and other diseases to develop B cell chronic lymphocytic leukemia, genetic engineering of novel molecular therapeutics. The mission of the department epigenetic writers and erasers in MLL-rearranged leukemias, includes identifying new molecular targets for cancer noncoding RNAs and RNA-modifications in malignant therapy, developing small synthetic molecules and natural transformation of leukemia and lymphoma, feedback control product derivatives to address these therapeutic targets, and of oncogenic signaling in B cell malignancies, and metabolic evaluating genomic markers for predicting cancer risk and control of clonal selection and evolutionary fitness in response to therapy. To accomplish these objectives, molecular heterogeneous leukemia and lymphoma populations. medicine researchers employ leading-edge approaches and TRANSLATIONAL RESEARCH AND CELLULAR THERAPEUTICS technologies. These include high throughput screening of medicinal plant extracts and chemical compound libraries, The Department of Translational Research and Cellular organic and bioorganic synthesis, and analyzing the genetic Therapeutics has translated landmark scientific discoveries basis for disease using functional genomics, proteomics, into treatments that have improved the lives of diabetic microarray gene expression profiling and protein X-ray patients around the world. The department has efforts in crystallography. The research in the department focuses on the the fight against diabetes simultaneously on multiple fronts: developing and synthesis of molecular-targeted anti-cancer from developmental research starting in our laboratories to agents, identifying STAT proteins as new molecular targets clinical investigations to innovative patient care. The research for cancer therapy, and using X-ray crystallography to study focus is on stem cell biology and development, translational protein-protein and drug-protein interactions for the design of immunology, islet isolation and distribution, islet quality novel therapeutic agents for the treatment of cancer. assessment, islet imaging, islet encapsulation and isolation, and new drug discoveries. POPULATION SCIENCES The Department of Population Sciences’ mission is to make scientific progress in understanding what causes cancer, how to prevent people from getting cancer, the health problems that can occur as a result of being treated for cancer, ways to reduce the burden of cancer and its after-effects for all people, and to improve the overall quality of life of cancer survivors.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 5 FACILITIES
ANALYTICAL CYTOMETRY CORE CLINICAL PROTOCOL MANAGEMENT CORE The Analytical Cytometry Core provides researchers with high- The Clinical Protocol Management Core provides expertise in quality flow cytometry instrumentation, as well as expertise the areas of protocol administration and data management to in analyzing and/or sorting sample populations of interest the investigators of the comprehensive cancer center. The staff via interpretation of their physical fluorescent and/or light- assists with screening patients for eligibility, managing studies, scattering properties. collecting study data, monitoring regulatory compliances, IRB submissions and participating in training. ANALYTICAL PHARMACOLOGY CORE COMPREHENSIVE METABOLIC PHENOTYPING The Analytical Pharmacology Core encourages and facilitates The Comprehensive Metabolic Phenotyping Core provides collaborative research between basic scientists and clinicians sophisticated metabolic testing in mouse models. Among the by conducting pharmacokinetic studies for both chemotherapy core equipment are an EchoMRI for body composition analysis, clinical trials and peer-reviewed preclinical studies. a TSE Systems LabMaster/PhenoMaster system for assessing food and water consumption, locomotor activity and energy ANIMAL RESOURCES CENTER expenditure, a rodent treadmill for forced exercise studies, City of Hope maintains a centralized animal care and use running wheels in the TSE system for voluntary exercise program, which is registered by the United States Department studies, and two Seahorse systems for metabolic experiments of Agriculture and accredited by the Association for in cells and tissues. Assessment and Accreditation of Laboratory Animal Care International. The mission of the Animal Resources Center is CYTOGENETICS to enhance excellence in research and teaching through the The Cytogenetics Core Laboratory provides classic and provision of high quality animal care consistent with the Public molecular cytogenetics (fluorescence in-situ hybridization, or Health Service Policy on Humane Care and Use of Laboratory FISH). FISH testing has proved invaluable as a diagnostic tool Animals, the Guide for the Care and Use of Laboratory in many types of malignancies, and is useful in determining Animals, the Animal Welfare Act, and other applicable state both prognosis and course of treatment. and local regulations. DRUG DISCOVERY AND STRUCTURAL BIOLOGY BIOSTATISTICS AND MATHEMATICAL ONCOLOGY The Drug Discovery and Structural Biology (DDSB) Core was The Biostatistics and Mathematical Oncology Core established to both technically and scientifically facilitate collaborates across basic (statistical methods, genomics), drug discovery efforts consistent with the translational translational (animal models, cell migration, pharmacokinetic research goals of City of Hope. Two important points of focus modeling), clinical (clinical trials, diagnostics, biomarkers) and for the DDSB are chemical biology probes and discovery of population-oriented (epidemiology) research. They support the cancer drugs in the area of molecular-targeted therapeutics. The core’s services are impressively diverse but also highly information collection, classification, storage, dissemination, convergent. The core is comprised of four major service integration and visualization needs of our investigators. components: high throughput screening, biopolymer synthesis, CENTER FOR APPLIED TECHNOLOGY DEVELOPMENT small molecule synthesis and X-ray crystallography. These disciplines work together in a complementary and cohesive To help bring new discoveries and developments to market, manner to provide a full array of early-phase drug discovery the Sylvia R. & Isador A. Deutch Center for Applied Technology services and chemical probes for biological systems. Development provides both internal and external entities licensing services and patent documentation. ELECTRON MICROSCOPY AND ATOMIC FORCE MICROSCOPY CORE CENTER FOR BIOMEDICINE & GENETICS The Electron Microscopy and Atomic Force Microscopy Our Center for Biomedicine & Genetics manufactures Core provides imaging at far greater resolution than light promising new genetic and cellular agents created by microscopy allowing ultrafine details of cells to be revealed researchers for use in clinical trials. We are uniquely equipped and macromolecular structures to be solved. It assists to evaluate therapies swiftly and move lifesaving drugs into the with all aspects of studies brought to the lab, including marketplace with great speed. experimental design, specimen preparation, data collection and image analysis.
6 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES FACILITIES
GMP MANUFACTURING MASS SPECTROMETRY AND PROTEOMICS CORE The GMP Manufacturing Core facility at City of Hope offers The Mass Spectrometry and Proteomics Core provides high- both biological and chemical GMP manufacturing capabilities. quality analysis of biomolecules. Notable capabilities include: The biological facilities consist of the Biologics & Cellular purified proteins can be rapidly identified, relative protein GMP Manufacturing Center, comprising the Center for expression levels can be determined for lysates of whole Biomedicine & Genetics and the Cell Therapy Production cells or subcellular organelles, and absolute levels of specific Center. The Chemical GMP Synthesis Facility is a stand-alone peptide components in complex biological samples can be operation providing state-of-the-art biopolymer and small determined via multidimensional separation and MS analysis. molecule manufacturing. City of Hope is the only cancer center in the U.S. to provide both biological and chemical MULTI-OMICS MASS SPECTROMETRY GMP manufacturing at a single institution. These facilities AND BIOMARKER DISCOVERY provide process development, regulatory support, and cGMP- The Multi-omics Mass Spectrometry and Biomarker Discovery compliant clinical-grade production of CAR T cell products, Core Facility provides mass spectrometry (MS)-based multi- stem cell-based regenerative medicine products, monoclonal omics technology to support research on cancer pathogenesis, antibodies, lentiviral vectors, vaccines, and complex molecules cancer biomarkers, novel anti-cancer agents and diagnostic including, biopolymers (peptides, siRNA-aptamers, DNA- studies. The multi-omics approaches provided encompass peptide hybrids), nanomaterials and natural products. high-quality MS services for proteomics, deep proteomics, peptidomics, glycomics, lipidomics, metabolomics, quantitative GRAFF MEDICAL AND SCIENTIFIC LIBRARY phosphoproteomics and small molecule analyses. The Graff Medical and Scientific Library serves the information needs of the City of Hope community. It furnishes materials MULTI-SCALE TRANSLATIONAL RESEARCH and services that support the institution’s clinical, scientific The Multi-Scale Translational Research Core facilitates and educational mission. The Graff Library offers an expansive research that integrates analyses made at several different collection of scientific and biomedical journals and online scales — populations, individuals, cells and microenvironment, databases, as well as a wide array of other services. There omics, and analytes — to provide greater insight into cancer. are study spaces and a computer lab with internet/intranet- Historically, scientists have studied cancer at only one of accessible workstations and printers. A copy room allows both these scales at a time, focusing on a large epidemiological black-and-white and color printing and the creation of .pdf files. study, or drug response in an individual, or the effects of a INTEGRATIVE GENOMICS AND BIOINFORMATICS particular DNA mutation, for example. Recently, there has been a push to use computational analysis to integrate data The Integrative Genomics and Bioinformatics Core combines from many scales into multiscale models of cancer and other the expertise and instrumentation of two National Cancer subjects. This move complements the precision medicine Institute supported facilities — the Functional Genomics/ initiative recently launched by the National Institutes of Health, Genomic Sequencing Core and the Bioinformatics Core — to which calls for the use of multiscale models and the provide an integrated array of services for genomics and integration of multiscale data to improve treatment and informatics. The core accomplishes this goal using state- care for the individual. of-the-art genome technologies and innovative analytical methods supported by a dedicated team of instrument The core supports investigators and projects seeking to operators and bioinformaticians. integrate data at several scales and apply multiscale modeling techniques. It builds on the large cohorts established by the LIGHT MICROSCOPY/DIGITAL IMAGING earlier Population Sciences Survey Core, allowing them to be The Light Microscopy Digital Imaging Core makes available leveraged for multiscale studies that incorporate geospatial the latest research platforms for automated microscopy risk information, images and cell signaling data in mouse and experiments, for advanced observation techniques, and for human tissues, among other data. sophisticated digital image processing and analysis. The imaging stations are fully outfitted with software for 3D rendering, quantification and analysis.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 7 FACILITIES
NUCLEAR MAGNETIC RESONANCE CORE STEMM CELL CORE The main focus of the Nuclear Magnetic Resonance (NMR) The Stem Cell Core facility aims to accelerate stem cell Core is to apply high resolution NMR spectroscopy to the research by providing critical stem cell resource and structural characterization of biomolecules, small organic technical support. The core provides customized service for compounds, natural products and biomolecular complexes, disease-specific human iPSC derivation, characterization, including protein-protein, protein-nucleic acid and and genetic correction. Human iPSCs are valuable tools protein-ligand complexes. for disease modeling, drug discovery and preclinical therapeutic development. PATHOLOGY CORE VIRAL VECTOR AND GENE EDITING CORE The Pathology Core provides histologic processing of tissues including paraffin embedding, sectioning, and hematoxylin and The Viral Vector and Gene Editing Core develops gene editing eosin staining of human tissue, animal tissue and preparations tools for manipulating mammalian genomes and delivers these from cell lines. The facility also performs and interprets tools into cells using viral vectors. immunohistochemistry for the detection of cell products in normal and disease states.
SMALL ANIMAL STUDIES The small animal studies core provides services for basic and translational preclinical studies in cancer biology, anti-cancer drug development and stem cell therapeutic development. The small animal imaging available is bioluminescence/ fluorescence optical imaging and PET/SPECT/CT trimodal scanning. The animal tumor models established patient- derived xenograft models to develop next-generation humanized mouse models for research in cancer immunotherapy and in vivo drug metabolism/toxicity studies.
8 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES P h .D. ADMISSIONS
Ph.D. ADMISSIONS students whose native language is not English. The school code Admission to study at the Irell & Manella Graduate School for the TOEFL is 2268. of Biological Sciences is offered to students who are curious Colleges and universities must mail official transcripts directly about science and demonstrate strong undergraduate training to the graduate school office. in biochemistry, chemistry, biology or a related biomedical Supplemental materials should be sent directly from the field. Students lacking preparation in a particular subject, institutions and testing agencies, but we will also process your but otherwise qualified, may be admitted and given the application if all of the supplemental materials are sent initially opportunity to strengthen their background by taking the to your address in officially sealed envelopes and then you appropriate courses. place all the supplemental documents (still in their officially The graduate school strongly encourages applications from sealed envelopes) in a larger envelope and send them directly students regardless of national or ethnic origin, sex, sexual to our office at one time. Your application will be evaluated orientation, marital status, race, age, color, citizenship only if all the materials have been received. or disability. Applications must be submitted online at As preparation for graduate studies, it is recommended https://apply.gradschool.cityofhope.org. that applicants have a minimum of 35 semester hours There is no application fee. The application deadline is (undergraduate or combined with master studies) in biology January 1. Orientation and classes begin in mid-August. and/or chemistry. We expect that these 35 hours will include For information, please contact: basic undergraduate (or advanced) courses in Chemistry, City of Hope Cell Biology, Biochemistry, and Genetics or Molecular Irell & Manella Graduate School of Biological Sciences Biology. Students with an educational background primarily Graduate School Office in Chemistry would be expected to at least have course work 1500 East Duarte Road in Biochemistry. To be competitive, applicants should have at Duarte, CA 91010 least a 3.0 grade point average (GPA) on a 4.0 point scale from Tel: 877-715-GRAD their undergraduate and/or masters studies, but this is not a Email: [email protected] formal requirement. The graduate school has decided to make CityofHope.org/grad-school the submission of GRE score both for the general and subject- specific exam optional. However, we will still consider GRE scores if they are submitted, and such scores may be helpful for applicants with weaknesses in their prior academic records. In addition to academic achievement, the Admissions Committee also evaluates an applicant’s potential for scientific achievement through letters of recommendation, a personal statement of his/her experience, goals, prior research experience, GRE scores and TOEFL scores, if applicable. A minimum of three letters of recommendation are required. Recommenders should provide evidence of the applicant’s potential to conduct significant research. Letters should be submitted through the online system by registering your recommenders’ names and email addresses. The recommender will then receive instructions on how to upload and submit a recommendation electronically. Recommendations will also be accepted by email or mail. Official scores must be sent by ETS to the graduate school office. The school code for Irell & Manella Graduate School of Biological Sciences is 4076. The TOEFL test is required for all Kathleen Elison teaching visiting local elementary school students.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 9 P h .D. REQUIREMENTS
Ph.D. REQUIREMENTS The Irell & Manella Graduate School of Biological Sciences grants a Ph.D. degree upon completion of all of the requirements, which include coursework, lab rotations, qualifying examinations, dissertation research and dissertation defense. Each requirement is described in more detail below. Students devote full time to study and research. The number of years to graduate depends on the student’s prior training and the dissertation project chosen. During the first year, students must complete the core curriculum, which is comprised of lecture courses and lab rotations. There are eight courses taken during the first year: Biochemistry and Structural Biology, Principles of Gene Expression, Cell Biology, Biostatistics and Computational Biology, Fundamentals of Scientific Research, Responsible Conduct of Research, Rigor and Reproducibility and Concepts in Molecular Genetics Lab. Core courses are described below. Students must achieve a grade of A or B in order to receive Chemistry: Drug Delivery, Neurosciences, Virology, RNA, credit in a course. Stem Cell Biology, and DNA Repair, Epigenetics and Cancer. Students are expected to spend half of their time on In consultation with the associate deans and their advisers, coursework and half of their time in the rotation labs. Students students may choose additional courses and/or tutorials. are required to take three rotations to increase their exposure Students must have passed all relevant requirements prior to to different laboratories and select a thesis laboratory that taking the qualifying examinations. There are two qualifying matches their research interest. By the end of the first year, all examinations, one focused on research distinct from a students should have achieved a broad-based understanding student’s thesis research and one focused on the student’s of biology through the didactic coursework, lab rotations and thesis research. The goals of these exams are to rigorously scientific seminars. test the ability of the student to design and write a research Elective courses are offered on a two-year cycle in the plan, present the proposal in a formal seminar and discuss the following areas: Comparative Medicine, Cancer Biology, material presented. The written proposal should be in the style Cancer Metabolism, Epigenomics, Immunology, Medicinal of a National Institutes of Health grant application. After the proposal is approved by the Graduate Oversight Committee and/or the qualifying exam committee, the student must defend the proposal orally. Students are required to pass both qualifying examinations for advancement to doctoral candidacy. Students are required to take journal clubs and leading edge lectures throughout their training which enriches their education. Beginning in year three, an annual thesis committee meeting is required. This will help the student remain on track and bring his/her thesis project to a successful and timely completion. The final requirements for the doctoral degree are the thesis manuscript and the oral defense in front of a panel of faculty members, an external expert in the field and the entire City of Hope community. The diagram on the next page outlines the progression through coursework, qualifying exams, thesis work and graduation.
10 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES P h .D. REQUIREMENTS
PATH TO GRADUATION
Fall Trimester Spring Trimester Summer Trimester (September — December) (January — April) (May — August)
Responsible Conduct Fundamentals of of Research Cell Biology Scientific Research Concepts in Molecular Biostatistics and Genetics Lab Computational Biology Rigor and Reproducibility Biochemistry and Structural Biology Scientific Writing A Principles of Gene Expression Rotation 4 Rotation 1 Rotation 2 Rotation 3 (Optional)
Leading-edge Lecture (two per year) Qual. Exam part 1 — Research Proposal due end of November
Scientific Writing B
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 11 P h .D. COURSE OFFERINGS
CITY OF HOPE Ph.D. COURSES
BIOSCI500 Responsible Conduct of Research [R] BIOSCI501 Rigor and Reproducibility [R] BIOSCI502 Introduction to Grant Writing [R] BIOSCI505 Concepts in Molecular Genetics Laboratory [R] BIOSCI510 Biochemistry and Structural Biology [R] BIOSCI530 Cell Biology [R] BIOSCI544 Biostatistics and Computational Biology BIOSCI550 Fundamentals of Scientific Research [R] BIOSCI560 Laboratory Rotation I [R] BIOSCI561 Laboratory Rotation II [R] BIOSCI562 Laboratory Rotation III [R]
BIOSCI600A Fundamentals of Scientific Writing (R) BIOSCI600B Writing of Research Proposals (R) BIOSCI601 Ethical Issues in Stem Cell Biology and Medicine (E) BIOSCI610 Advanced Topics in Comparative Medicine: The Mouse in Biomedical Research BIOSCI611 Advanced Topics in Comparative Medicine: Animal Models in Biomedical Research [E] BIOSCI615 Advanced Comparative Medicine I [E] BIOSCI616 Advanced Comparative Medicine II [E] BIOSCI620 Advanced Cancer Biology [E] BIOSCI625 Advanced Immunology [E] BIOSCI630 Advanced Neurosciences [E] BIOSCI635 Advanced Virology [E] BIOSCI640 Advanced Stem Cell Biology [E] BIOSCI645 Advanced Stem Cell Research and Medicine [E] BIOSCI650 Advanced RNA [E] BIOSCI655 Advanced DNA Repair, Epigenetics and Cancer [E] BIOSCI660 Advanced Epigenomics [E] BIOSCI665 Advanced Cancer Metabolism [E] BIOSCI680 Advanced Topics in Medicinal Chemistry: Drug Delivery [E]
BIOSCI700-711 Various Journal Clubs BIOSCI730 Leading-edge Lecture Seminar [E] BIOSCI740 Lab Research [R] - after lab rotations and before advancement to candidacy BIOSCI760 Independent Study [E]
BIOSCI800 Research for Dissertation [R] - prerequisite: advancement to candidacy
R = required; E = elective Students are required to take two electives after the first year of study. Students in the Residency/Graduate Training Program in Laboratory Animal Medicine track are required to take BIOSCI615 and BIOSCI616B and one elective.
12 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES CORE COURSE DESCRIPTIONS
BIOCHEMISTRY AND STRUCTURAL BIOLOGY CELL BIOLOGY B510 — 3 CREDITS B530 — 3 CREDITS This course covers several areas of biochemistry congruent This course is divided into three sections: (i) cell structure and with teaching faculty members’ areas of interest and expertise. interactions; (ii) signal transduction and cell physiology; and The course is divided into two halves, with the first half (iii) development, stem cell biology and virus-cell interactions. focusing on structural and functional aspects of nucleic Topology of the cell, including cytoskeleton structures, is acids and proteins, and the second half on the structural and discussed as a prelude to understanding protein trafficking. functional aspects of carbohydrates, lipids, enzyme kinetics, The basics of innate immunity also will be covered, from the biomolecules and metabolic diseases. cells involved to the pattern recognition receptors and the pathogen they recognize. Course Coordinators: Markus Kalkum, Ph.D. Course Coordinator: John E. Shively, Ph.D. PRINCIPLES OF GENE EXPRESSION B520 — 3 CREDITS BIOSTATISTICS AND COMPUTATIONAL BIOLOGY This course delves into the key concepts of molecular biology B544 — 3 CREDITS using seminal papers as the source material. Students will The learning objective of this course is to understand statistical study the biological problems addressed in the papers and and computational methods that would aid the student in the experimental approaches used to examine them. The analyzing big data. We have combined Biostatistics and logical framework used to interpret the data and reach key Computational Molecular Biology to make one integrated conclusions will be highlighted. The class format will develop course that covers the statistical methods and their scientific reading, writing and presentation skills. Subjects applications to analyze biological data. Following this, the covered include: DNA and the gene, transcription, RNA students will then be given an introduction to the range mediated gene regulation, protein synthesis and processing, and human variation and disease. of computational methods used to analyze various types biological data, ranging from sequence data to atomistic and Course Coordinators: Ren-Jang Lin, Ph.D., tissue level modeling. The statistical methods will be reinforced and Jeremy M. Stark, Ph.D. by tying in their applications in the computational biology part of the course. Hands on in silico laboratory sessions are an CONCEPTS IN MOLECULAR GENETICS LABORATORY B505 — 2 CREDITS integral part of this course and will be used as often as needed. This course will introduce and demonstrate core genetic and Course Coordinator: Nagarajan Vaidehi, Ph.D. molecular biological concepts using the budding yeast system. The course will also focus on the development of the skills FUNDAMENTALS OF SCIENTIFIC RESEARCH necessary for culturing and manipulating microorganisms, B550 — 4 CREDITS as well as the manipulation of genetic material, which are This course uses the primary literature to develop skills essential for biomedical laboratory investigation. Hands-on in scientific reading, writing, critique and debate. The first demonstration of the behavior of an organism at the genetic part emphasizes the components of a research paper. and molecular levels will develop a more comprehensive Students analyze each component in selected papers, write understanding of the basic concepts discussed in Principles an essay about their analysis and defend their ideas during of Gene Expression. Subjects covered include, genotype and class discussion. The second part trains students to design phenotype, dominance and recessiveness, complementation experiments to advance understanding of current research and epistasis. Laboratory skills introduced include, sterile questions. Students learn to generate hypotheses, select technique, quadrant streaking, serial dilutions, plating of cells, methods, and describe and interpret data which they defend plasmid purification and characterization, and transformation. both in writing and in class discussion. Course Coordinator: Glenn Manthey, Ph.D. Course Coordinators: Timothy R. O’Connor, Ph.D., and Jeremy M. Stark, Ph.D.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 13 STUDENTS
Ying Qing Roberto Gutierrez
My name is Ying Qing My name is Roberto and I joined the Irell and Gutierrez, and I’m a second Manella Graduate School year graduate student at the of Biological Sciences of Irell & Manella Graduate City of Hope almost a School of Biological Sciences year ago. I completed my at City of Hope. My first clinical medical training and exposure to academic obtained my M.D. degree research came after I at Shandong University, transferred from community China. During my clinical college to the University of rotations as an intern, I California Riverside. gained great interest in Although I was a biomedical research as I biochemistry major, I realized what doctors could performed my do for patients, especially patients with cancers, was still undergraduate research in a neuroscience lab to further rather limited. Therefore, I decided to pursue a career with expand my knowledge in other scientific fields. As an the combination of basic research and clinical practice on undergraduate, my research was focused on understanding the oncology. My first research experience as an undergraduate health effects of environmental toxicants on nervous and other was to study the effect of the phytochemical sulforaphane physiological systems. After I graduated from UCR, I decided on chemoprevention of colorectal cancer and its epigenetic to further my education by beginning my graduate studies at mechanism. This experience made me feel the need to be City of Hope. I chose City of Hope because the research systematically trained in a Ph.D. program and prompted me performed here can directly impact patients’ lives. In addition, to enter the Cancer and Cell Biology program at University the research here is driven by a strong collaborative of Cincinnati. After doing three rotations, I joined Dr. Jianjun environment, thus making it an excellent place for scientists to Chen’s lab to study the genetic/epigenetic regulations in conduct ground breaking research. leukemogenesis. When Dr. Chen became a faculty member at After I completed the first year courses, I decided to perform City of Hope, I did some research about the Irell and Manella my thesis work in the lab of Dr. Timothy O’Connor. His Graduate School of Biological Sciences of City of Hope, research focuses on understanding how DNA repair pathways and learned that City of Hope has a highly collaborative function in maintaining genomic stability by eliminating DNA environment and has made great contributions in the field of damage. My project focuses on determining the role of direct translational medicine that turns research findings here into reversal repair proteins during removal of alkylation-induced clinical therapies rapidly. Based on these reasons, I decided DNA damage caused by chemotherapy. The goal of this project to join the Irell and Manella Graduate School of Biological is to understand how different DNA repair mechanism work Sciences to pursue my Ph.D. study. together to remove DNA damage caused by chemotherapeutic The courses I took as a first year student at City of Hope agents. City of Hope gives me the opportunity to combine are closely related to the current hot research topics and my interest in performing basic research, while still having an techniques, and prepared me well to conduct my own research. impact in a clinical setting. I was trained intensively to critically evaluate work reported As a second year graduate student, I am excited to further my in the literature, to design experiments to test my hypothesis understanding of cancer biology, and continue my research. based on literature, and to write scientifically to communicate The small size of the graduate program allows for more my research to the scientific community. Under the guidance interaction between students with professors. The advanced of Dr. Jianjun Chen, my dissertation research aims to illustrate courses are even smaller, allowing for one-on-one interactions the potential link between metabolic alteration and epigenetic with well-established experts in the field of cancer biology, regulation in leukemogenesis and to potentially exploit this immunology and diabetes. In addition, this program offers link as a therapeutic strategy for leukemia. I am extremely a range of great research core facilities. Altogether, the excited about my research and look forward to obtaining environment at City of Hope allows graduate students to research results that are beneficial to the clinical treatments of form professional relationships with faculty, and to perform leukemia, as well as to the scientific world. competitive research using the most up-to-date technology. Ultimately, I strive to become a professor at a competitive teaching institution, where I will mentor students in the sciences.
14 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES STUDENTS
Kathleen Lennon John Murad
My name is Katie Lennon, My name is John P. Murad, and I am a third year I am currently a 4th year graduate student in the lab graduate student, and I work of Tijana Jovanovic-Talisman for Dr. Stephen Forman in from the department of the Department of Immuno- Molecular Medicine. My Oncology in the T Cell love for science blossomed Therapeutics Research Lab. in middle and high My undergraduate work school. I went on to study was done at California State Biochemistry during my Polytechnic University in undergraduate education Pomona where I graduated at University of California with a B.S. in Chemistry. In San Diego (UCSD). During pursuit of my interests in my second year, my mom science and biology, I got was diagnosed with breast cancer. I took care of her while she my M.S. in pharmaceutical sciences from Western University underwent chemotherapy and had a mastectomy. Through talking with her doctors and researching her treatment, I of Health Sciences in Pomona. During my master’s, I did learned that a chemically engineered humanized antibody, research in the cardiovascular field, researching new methods Herceptin, saved my mom. This deeply personal experience of treating deadly thrombosis events via monoclonal antibody illuminated the critical importance of discovering cancer therapy. The research experience in my master’s helped me mechanisms and developing new therapies. After graduation, get connected with research opportunities at City of Hope as a I began working in a research laboratory at the UCSD Moores research assistant working on tumor immunology. Cancer Center. During this time, I learned about City of Hope I chose the Irell and Manella Graduate School of Biological and the groundbreaking research performed here including Sciences at City of Hope because, as a research assistant, the development of the technology for the artificial synthesis I realized City of Hope offered a great opportunity to learn of humanized monoclonal antibodies, which led to the more in the fields of cancer biology, immunology, and how development of Herceptin and I decided to apply. to be a better scientist. The unique translational capacity of To pursue my interest in understanding the biochemical the research being done at City of Hope was a strong reason processes by which people develop cancer, I joined the lab I was interested in the graduate program. As such, I currently of Dr. Tijana Jovanovic-Talisman. Her research utilizes super- work on developing and improving chimeric antigen receptor resolution microscopy to investigate nano-scale protein- (CAR) T cell therapies for multiple solid tumor types. I work protein interactions and how these many be altered in cancer. on understanding the cellular and extracellular components of My doctoral project investigates the mechanism of Nuclear the tumor microenvironment on suppression of the immune Pore Complex mediated transport, which is rapid, highly system, and impact on CAR T cell therapy. I am fortunate to selective and misregulated in cancer development. work on CAR T cell products for prostate cancer, As a graduate student at City of Hope, small class sizes have breast-to-brain metastasis, ovarian cancer and pancreatic fostered mentorship from faculty members, administrators, cancer, and excited to see the progress of some of these and scientific writing professionals. The courses and products scheduled to become clinical candidates for ongoing mentorship have encouraged me to present my work as trials here at City of Hope. posters and talks, write grants and scientific papers, and City of Hope has been an extremely collaborative and friendly pursue teaching and mentorship roles within the graduate place to conduct research. The core facilities have allowed me school and affiliated summer research programs. I have also had leadership roles within the graduate school as recruitment an opportunity to use the latest biotechnology to help improve co-chair, vice-president, and as the director for the second my research. Furthermore, the abundance of quality professors, annual Graduate Student Research Symposium. scientists and medical doctors provide a great resource for my questions on how to improve research for clinical benefit My dream is to become an independent researcher, elucidating of patients. My future aspiration is to continue to be involved biochemical mechanisms of cancer progression. Additionally, in the immunotherapy field as a senior scientist, in academia I am interested in finding novel diagnostic techniques utilizing or industry, helping to improve and develop novel cancer cancer biomarkers. Ultimately, my most important goal, immune therapeutics. which is fostered and shared by City of Hope, is to improve patient outcomes.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 15 STUDENT LIFE
STUDENT HOUSING RECREATIONAL ACTIVITIES Living in student housing connects you to our vibrant campus and all of its resources. Each house or apartment has unique qualities based on its architecture, size and location, and your living experience is ultimately shaped by the residents who live there. Each residence’s personality changes every year based on the residents’ contributions to their community. First-year students may choose to live in on campus housing, which ranges from $625 to $975 a month. Housing is also available within the immediate area at a cost of approximately $800 to $1,400. Students may express their interest in student housing by filling out an ‘Application for Occupancy’ form which is Graduate students attending the annual Research Staff Organization available on the website or in the Office of Graduate Education. Meeting at Lake Arrowhead The housing lease is an 11-month term starting the day you move in through July 31. Southern California is at the center of local tourism and the entertainment industry, where each year millions of tourists Each room is supplied with a bed, desk, desk drawers, chair visit Disneyland, Magic Mountain, Universal Studios and and dresser. Additional room furnishings may be supplied, television studios. The area is a thriving cultural center, with depending on the type of room being rented. In addition to such wonderful museums as the Getty Center, Norton Simon bedrooms, each apartment or house contains a living room, Museum, Huntington Library, Museum of Contemporary dining area and kitchen. The living area is furnished with Art and the California Science Center. Jazz, rock and stand- a couch, chair, coffee table and television. The dining area up comedy clubs are sprinkled throughout the area. Nearby contains a table and chairs. The kitchen is supplied with dishes, Pasadena hosts the Rose Parade on New Year’s Day and utensils, pots and other kitchen supplies. Each of the houses exciting street life in Old Town Pasadena. Sports fans can contains a washer/dryer, and the apartments share a washer/ enjoy professional baseball (Dodgers and Angels), basketball dryer. Additional appliances and furnishings may be supplied, (Lakers and Clippers), football (Chargers and Rams), hockey depending on the unit rented. (Kings and Ducks) and soccer (Galaxy), as well as outstanding collegiate teams. In this ethnically diverse region, one can explore the food and culture of peoples from different countries. Likewise, the City of Hope campus has an international, cosmopolitan atmosphere, attracting talented scientists from all over the world who feel at home here. Additionally, Southern California is home to many great universities, and our faculty members collaborate with colleagues at nearby Caltech, University of Southern California and University of California Los Angeles. Nestled in the foothills of the San Gabriel Mountains, Duarte is a serene community. The subtropical and semi-arid climate offers year-round outdoor activity. The San Gabriel Mountains are lined with hundreds of miles of hiking and mountain biking trails. An hour’s drive in different directions can take you to ocean beaches, snow skiing or desert camping. Many of our students and faculty are avid outdoorsmen, and several ride their bikes to work.
16 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES STUDENT LIFE
STUDENT SUCCESS City of Hope students have won a number of fellowships, Graduation Rate: 81 percent awards and prizes. While working with John Rossi, Ph.D., Time to Degree: 5.5 years the Helen & Morgan Chu Dean’s Chair of the Irell & Manella Graduate School of Biological Sciences, Daniel Kim (pictured By the time he or she graduates, the typical student below) won the National Academy of Sciences’ Cozzarrelli has published three scientific papers and attended two Prize for his 2008 scientific conferences. first-author, graduate Students are encouraged to present their research at national student paper and international meetings, including Germany, Italy, England, selected as the Hong Kong, Shanghai and British Columbia. One of the most outstanding students wrote, “I recently presented a poster at a national contribution in the conference and was pleasantly surprised at the response generated biological sciences from my work. Presenting work at a specialized conference where published last year many scientists understand and appreciate your work is a very in the Proceedings of rewarding experience.” the National Academy of Sciences USA. Six PNAS papers received the Cozzarrelli Prize out of 3,500 published. Kim is the second City of Hope graduate student whose research has been honored by PNAS. The first was Jing Song, whose thesis advisor was Yuan Chen, Ph.D. A 2008 PLoS Genetics paper by students Seung-Gi Jin and Cai Guo, with Professor Gerd Pfeifer, Ph.D., previously the Lester M. and Irene C. Finkelstein Chair in Biology, was selected for the prestigious Faculty of 1000 database of important publications. A 2010 Nucleic Acids Research paper by Seung-Gi Jin (alumnus), Swati Kadam (student) and Pfeifer, also was selected for the prestigious Faculty of 1000 database of important publications. A 2013 Molecular Cell paper by student Michael Reid in the lab The Irell & Manella Graduate School of Biological Sciences graduating of Mei Kong, Ph.D., was also selected for the Faculty of 1000 students of June 2018 database of key publications.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 17 ALUMNI — LIFE AFTER GRADUATION
Amy Cook, Ph.D. Shuo Gu, Ph.D.
Amy M. Cook, Ph.D. I joined the Graduate School moved to California from of Biological Sciences at Wisconsin to earn an City of Hope in 1998 after undergraduate degree obtaining a Bachelor of in biology at Pepperdine Science degree in molecular University. After receiving biology from Tsinghua acceptances to several University, China. I joined doctoral programs across Professor John Rossi’s the country, Amy chose laboratory to study how City of Hope’s graduate small RNA molecules program because of its could be used as antiviral excellent reputation therapeutic agents in for translational cancer developing gene therapy research. Joining the lab approaches combating HIV. of Ravi Bhatia, M.D., to I continued my passion on conduct research in hematology and cancer stem cell biology, designing better RNA-based gene silencing tools during my her thesis work involved targeting the leukemic stem cell postdoctoral training in the laboratory of Professor Mark Kay at population with a novel small molecule inhibitor involving Stanford University Medical School, Palo Alto. the JAK/STAT pathway. During her time in the graduate Both my Ph.D. and postdoctoral research focused on program, Amy founded the Beckman Pub, a communal the mechanisms of RNA interference pathway, and their gathering developed in an effort to foster cross-disciplinary applications in gene therapy. I demonstrated that active communication and interaction among scientists, which translation impeded miRNA-RISC target mRNAs association, is still active today. After completing her Ph.D. in 2011, found the Ago loading process is dictated by miRNA duplex Amy continued her postdoctoral training in the Bhatia instability, as well as the Ago-PAZ domain. I also established lab before being recruited to the Office of Philanthropy at a “loop-counting” rule governing the preciseness of Dicer City of Hope in 2015. She currently holds the title of Director processing which is critical for miRNA biogenesis and function. of Development. Fulfilling a unique role as a scientific liaison The above key findings have been published in high-profile to the Philanthropy team, Amy represents the Hematologic scientific journals (Cell, Nature Structural & Molecular Biology, Malignancies and Stem Cell Transplantation Institute and PNAS and Current Biology) and presented at international works with philanthropists to support City of Hope’s research conferences. Applying insights gained through these and treatment for leukemia, lymphoma and myeloma. She mechanistic studies, I was able to design more efficient shRNAs leverages her unique perspective as a scientist to help others with less off-targeting effects in an HCV infection model. understand how City of Hope’s cutting-edge research drives In 2014, I joined the intramural research program of National our mission to cure life threatening disease like cancer Cancer Institute (NCI), National Institutes of Health (NIH) as a and diabetes. Stadtman principal investigator at the RNA Biology Laboratory. “I knew I made the right choice in joining the doctoral program As the head of the RNA Mediated Gene Regulation Section, I at City of Hope because each person I met when I walked lead a lab studying the mechanisms of miRNA biogenesis, post- through the door, from the scientists to the clinicians to transcriptional modifications, turnover and biological functions the students, were all as deeply passionate as I was about in mammalian systems. This information will then be used to accelerating cancer research from ‘bench to bedside’. I develop novel RNA-based approaches in cancer treatments. especially enjoyed my time under the mentorship of Ravi I chose City of Hope graduate school because of its emphasis Bhatia, whose support and encouragement was unparalleled. I on translational research. I great appreciate the mentorship by stretched myself more at City of Hope than I imagined possible, Dr. John Rossi. His research program is a perfect example of and I’m deeply proud to continue to serve the institution today.” how cutting-edge basic research leads to novel solutions to life-threatening illnesses. I owe my career to his guidance as well as the rigorous training I received from the City of Hope Ph.D. program.
18 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES ALUMNI — LIFE AFTER GRADUATION
Mausumee Guha, Ph.D. James Finlay, D.V.M., Ph.D.
Mausumee Guha, Ph.D., James Finlay, D.V.M, Ph.D., DABT (Diplomat of grew up in the city of Duarte the American Board of with City of Hope just down Toxicology), earned a the street from his high Master’s degree in Biology school. In fact, he organized from California State a blood drive as a service Polytechnic University, project at City of Hope Pomona prior to joining the for his Eagle Scout project Irell and Manella Graduate in 1997. Finlay earned his School of Biological Sciences. Bachelor of Science from She conducted her graduate Brigham Young University work in the laboratory of (2005) and his Doctor of Dr. Rama Natarajan. She Veterinary Medicine from had the privilege of being Michigan State University the first graduate student in the newly constructed Gonda College of Veterinary North Diabetes Building and her thesis work was focused Medicine (2009) prior to joining the graduate program at on “Molecular and Cellular Mechanisms of Hyperglycemia”. the City of Hope. While concurrently enrolled in the Irell & Upon completion of her Ph.D., Mausumee received a Scripp’s Manella Graduate School of Biological Sciences, he also was postdoctoral fellowship and a National Heart Lung Institute working to complete a veterinary residency specializing in fellowship to work under the guidance of Dr. Nigel Mackman at The Scripps Research Institute, La Jolla on “LPS and Laboratory Animal Medicine under the direction of Richard Tissue Factor Signaling Mechanisms.” Following her passion Ermel, D.V.M, M.P.V.M., Ph.D. He joined that laboratory of to develop safe and efficacious novel drugs for patients, Carlotta Glackin, Ph.D., where he performed in vitro and in vivo Mausumee has worked for the past 16 years in small, mid-sized studies on the effects of siRNA silencing of a protein called and large pharmaceutical companies, including Astra Zeneca, Twist that is upregulated in many types of cancer. During this Bristol Meyers Squibb and now Pfizer. Although her graduate training period, Finlay received funding from the Parvin Family, and postdoctoral training was focused on pharmacology and as well as the American Association for Laboratory Animal molecular mechanisms, she wanted to understand the safety Science. Also during this time, he published three first author aspects of drug development and pursued extensive training in publications and co-authored several other papers. toxicology. Currently she is employed as a Drug Safety Team Following completion of his graduate degree and residency at Lead at Pfizer and as the nonclinical lead, has contributed to City of Hope he accepted a position as Clinical Veterinarian at several successful novel NDA and BLA filings. Her experience the University of Southern California in 2015. In 2017, Finlay spans across a wide variety of therapeutic modalities (small completed all the requirements to become a Diplomate of the molecules, antisense and biologics) and therapeutic areas American College of Laboratory Animal Medicine. In 2018, he of expertise, including oncology, neuroscience, virology, returned to City of Hope as an Assistant Research Professor metabolic and cardiovascular disease and inflammation. She is and Clinical Veterinarian. In his current role he serves as experienced in successfully progressing compounds from early director of the Veterinary Services Program within the Center development to registration, and also in providing life‑cycle for Comparative Medicine. He enjoys getting to work closely management support. with City of Hope researchers, graduate students and rotating “City of Hope and the graduate school faculty provided an veterinary students on a daily basis. Finlay continues to extremely supportive and encouraging environment. As my serve as an on-call veterinarian for the California Institute of mentor, Rama was instrumental in making sure that I became Technology in Pasadena, California. a proficient and independent scientist and her caring nature ensured my well-being during the stressful periods. The “I could not have imagined a more supportive and nurturing laboratory members and Dr. Jerry Nadler made me feel extra environment. The expectations were very high, but the special. Due to the small size of the graduate program, my tools and faculty were in place to allow one to meet fellow graduate students were like family and we always those expectations”. supported each other. My graduate training has allowed me to be a creative and successful drug developer.”
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 19 MASTER’S PROGRAM
M.S. IN TRANSLATIONAL MEDICINE PROGRAM CAPSTONE — MASTER’S RESEARCH THESIS The Master of Science in Translational Medicine is a two-year First Year — Fall Semester KGI-Irell and Manella Graduate School of Biological Sciences • Training in responsible conduct of research (RCR) at City of Hope (IMGS) joint program. Graduates will be First Year — Spring Semester uniquely positioned to begin research laboratory careers in the • Training in biomedical research techniques and specialize biotechnology/pharmaceutical industry, clinical or academic equipment within City of Hope Share Resource Facilities laboratories, or pursue further education at the doctoral level, (every Friday) medical education or both. This program is aimed at providing • Literature study and discussion with IMGS faculty to broadly students with an applied research experience and an in-depth define a thesis research project understanding of how to translate basic research into medical products from the perspectives of both academic research Second Year — Summer (discovery) and downstream commercial development. • Develop thesis project, establish thesis mentor and thesis committee MS IN TRANSLATIONAL MEDICINE PROGRAM • T raining in Concepts in Molecular Genetics Lab LEARNING OUTCOMES: Second Year — Fall Semester • Complete proposal outline (Hypothesis, Goal and Specific • Generate hypothesis and perform hypothesis-driven research Aims) for thesis committee approval • Design research and methodology, and analyze and report • Independent research in mentor’s laboratory data results • C omplete and present preliminary thesis (all sections except • Assess the literature, identify knowledge gaps, and convey Results, Discussion and Methods) to thesis committee findings to the scientific community • Lead discussion on a topic at KGI (every Friday) • Plan the translation of basic science and engineering Second Year — Spring Semester discoveries into products and processes that benefit society • Independent research in mentor’s laboratory • Communicate effectively in an industry environment • C omplete remaining thesis sections; thesis submission and composed of scientists, engineers and business professionals thesis defense • Adhere to ethical principles in research, development, and • Public presentation/research symposium at KGI business issues inherent in the bioscience industries • L ead discussion on a topic at KGI (every Friday) • Tackle complex problems and contribute productively on an interdisciplinary team pursuing a variety of research-oriented INDEPENDENT RESEARCH (IMGS) careers related to medicine. During the independent research, students will be working closely with research staff, postdocs, or Ph.D. students and In year one, students will take rigorous graduate-level courses will give an oral presentation on their work at the end of the in applied biomedical sciences offered by KGI-a pioneer of school year. the professional science master’s degree. In the second year, students will produce cutting-edge research that discovers ADMISSIONS REQUIREMENTS fundamental mechanisms of diseases and develops novel The MS program practices rolling admissions. Admissions therapeutic strategies at IMGS, a world-class biomedical requirements are similar to the Ph.D. Program, but two letters research institute with expertise in therapeutics, population of recommendation is sufficient. GRE is required for the MS science, and stem cell research. admissions but may be substituted with MCAT or GMAT. TOEFL is required for all applicants whose native language is CURRICULUM not English. First Year • Core Science — 12 units KGI-IMGS PROGRAM DIRECTORS • Professional Development — 3 units Anastasia Levitin, Ph.D. • Advanced Technical Course — 18 units Research Assistant Professor, Program Director, M.S. KGI School of Applied Life Sciences Second Year • Research Thesis Capstone (Summer, Fall and Spring) — 30 units Yilun Liu, Ph.D. Associate Professor, Associate Chair, Total: 63 units Department of Cancer Genetics and Epigenetics Beckman Research Institute, City of Hope Apply through the KGI application system at https://keckgrad.force.com/ERx_Forms__Portal_Register
20 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Graduate School of Biological Sciences FACULTY Karen S. Aboody, M.D. Professor, Department of Developmental and Stem Cell Biology, Division of Neurosurgery
NEURAL STEM CELLS — THERAPEUTIC APPLICATIONS
My translational research laboratory focuses on neural stem There are many exciting directions of investigation to pursue cells (NSCs) and their therapeutic applications for primary in order to better understand stem cell function, with a wide and metastatic tumors. Our novel findings have demonstrated array of potential clinical applications to explore. Our lab offers the inherent tumor-tropic property of NSCs, and their use as a unique experience for interested students to be exposed to cellular delivery vehicles to effectively target and disseminate many laboratory techniques, including small animal surgeries, therapeutic agents to invasive tumors, including brain tumors tissue processing and immunocytochemistry, fluorescent and metastatic neuroblastoma, breast and ovarian carcinomas. microscopy, xenogen imaging, molecular biology, PCR, cell Their capacity for tracking infiltrating tumor cells and localizing culture and flow cytometry studies. to distant microtumor foci make NSCs a novel and attractive gene therapy vehicle with tremendous clinical potential. Our SELECTED PUBLICATIONS current research focuses on modifying human NSCs to deliver • Mooney, R., Weng, Y., Tirughana-Sambandan, R., Garcia, different therapeutic agents to tumor sites in animal models. E., Valenzuela, V., Aramburo, S., Annala, A.J., Berlin, J.M.*, Current strategies include delivery of prodrug activating and Aboody, K.S.* Neural stem cells improve intracranial enzymes, HER2 antibody, and nanoparticles for small molecule nanoparticle retention and tumour-selective distribution. drug delivery and thermoablative therapy (in collaboration with Future Oncol. 10: 401-415, 2014. *PIs contributed equally. the Berlin laboratory). • Aboody, K.S., Najbauer, J., Metz, M.Z., D’Apuzzo, M., Gutova, In 2013, we completed a first-in-human NSC-mediated M., Annala, A.J., Synold, T.W., Couture, L.A., Blanchard, S., therapeutic clinical safety study for recurrent glioma patients. Moats, R.A., Garcia, E., Aramburo, S., Valenzuela, V., Frank, Patients receive cytosine deaminase (CD) expressing R.T., Barish, M.E., Kim, S.U., Badie, B., and Portnow, J. Neural NSCs into the brain at the time of surgery, followed by oral stem cell-mediated enzyme-prodrug therapy for glioma: 5-Fluorocytosine which crosses the blood brain barrier and Preclinical studies. Sci. Trans. Med. 5 (184), 2013. gets converted by the CD to the active chemotherapeutic • Metz, M.Z.*, Gutova, M.*, Lacey, S.F., Abramyants, Y., Vo, T., agent 5-Fluorouracil, killing surrounding dividing tumor cells. Gilchrist, M., Ghoda, L.Y., Barish, M.E., Brown, C.E., Najbauer, In effect, the NSCs serve as a platform for tumor-localized J., Potter, P.M., Portnow, J., Synold, T.W., and Aboody, K.S. chemotherapy, which should also minimize toxicity to normal Neural stem cell-mediated delivery of irinotecan-activating tissues. A phase 1 study was initiated in October 2014 and carboxylesterases to glioma: Implications for clinical use. is ongoing. In 2010, we were granted an $18 million CIRM Stem Cells Transl. Med.2: 983-992, 2013. Disease Team Award to move a more potent enzyme/prodrug • Gutova, M., Frank, J.A., D’Apuzzo, M., Khankaldyyan, V., therapeutic toward clinical trials. Collaborators include the Gilchrist, M., Annala, A.J., Metz, M.Z., Abramyants, Y., Synold lab for pharmacology, the Barish lab for 3-D tumor Herrmann, K.A., Ghoda, L.Y., Najbauer, J., Brown, C.E., reconstruction, the Forman lab (C Brown) for xenogen Lesniak, M.S., Barish, M.E., Aboody, K.S.*, and Moats, R.A.* imaging and tumor modeling, and the Moats lab at Children’s (*PIs contributed equally) MRI tracking of ferumoxytol- Hospital Los Angeles (CHLA) for MRI imaging. We also labeled human neural stem cells: Studies leading to clinical work closely with our clinical principal investigator, Dr. Jana use. Stem Cells Trans. Med. 2: 766-775, 2013. Portnow, the Center for Biomedicine & Genetics and the Office of IND Development and Regulatory Affairs. We recently initiated a second phase 1 first-in-human brain tumor study of CE-producing NSCs + Irinotecan to generate the potent topoisomerase 1 inhibitor SN-38. We are also funded by a $5 million NIH-U01 (in collaboration with CHLA and St. Jude) to move this same product to clinical trial for pediatric patients with metastatic neuroblastoma by 2018.
22 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES David Ann, Ph.D. Professor and Associate Chair, Department of Diabetes Complications and Metabolism Associate Dean of Admissions, Irell & Manella Graduate School of Biological Sciences
CANCER METABOLISM, MITOCHONDRIAL BIOLOGY
My lab are actively involved in investigating cancer metabolism: of tumors via multiple mechanisms. Defects in basal 1) Rethinking Urea Cycle: An effective nutrient-restriction autophagy limit the recycling of intracellular constituents. cancer therapy has not been fully exploited and it lacks Despite our understanding of the pro-survival role of studies addressing the underlying mechanism for developing autophagy, how nutrient deprivation, caused by compromised such a selective amino acid restrictive therapy. Although autophagy, affects tumor progression is poorly understood. all cancers have undergone extensive genetic, epigenetic We demonstrate that conditional impairment of the autophagy and post-translational alterations, accumulating evidence gene Atg5 (Atg5-KO) extends the survival of KRASG12Vdriven has portrayed a common phenomenon of intrinsic arginine tumor-bearing mice by 38 percent. Atg5-KO tumors spread restriction that multiple tumor cells become auxotrophic more slowly during late tumorigenesis, despite a faster onset. for arginine and become sensitive to arginine restriction Atg5-KO tumor cells displayed reduced mitochondrial function, as endogenous arginine, synthesized from citrulline with increased mitochondrial fragmentation and asparagine aspartate by argininosuccinate synthetase1 (ASS1) and deficiency. Silencing Atg5 or asparagine synthetase (ASNS) argininosuccinate lyase (ASL), is not sufficient to support the caused a similar reduction of cell migration and invasion, which increased demand in highly proliferating tumor cells. Based on was rescued by asparagine supplementation or knockdown of this feature, we propose to develop dietary arginine restriction the mitochondrial fission protein MFF. Human cancer-derived as a nonpharmacological extrinsic arginine restriction strategy data demonstrate that ASNS overexpression is a signature for against all types of cancer cells. We have demonstrated that poor distal metastasis-free survival. arginine depletion damages mitochondrial activity, leading to chromatophagy and mitophagy in both breast and prostate SELECTED PUBLICATIONS cancer cells. Moreover, several recent reports have identified • Changou, C.A., Chen. Y.R., Xing, L., Yen, Y., Chuang, F.Y.S., arginine as a critical amino acid for inducing mTORC1 signaling Cheng, R.H., Bold, R.J., Ann, D.K.,* and Kung, H.J.* 2014) and it is required for aberrant growth factor-induced mTOR Arginine starvation-associated atypical cellular death pathway often found in tumor cells. Together, these studies involves mitochondrial dysfunction, nuclear DNA leakage put arginine in the driver’s seat for tumor cell proliferation. and chromatin autophagy. Proc Natl Acad Sci USA. 111: 14147 We focus on whether arginine restriction deranges the (*: co-corresponding author). PMID: 25122679. PMCID: mitochondrial biology, altering epigenetic modification PMC4191793. homeostasis, whether arginine restriction plays a dual role • Cheng, C.T., Kuo, C.Y., Ouyang, C., Li, C.F., Chung, Y., in cancer, whether intrinsic arginine restriction facilitates Chan DC, Kung, H.J., and Ann, D.K. (2016) Metabolic tumorigenesis and external arginine restriction limits Stress-Induced Phosphorylation of KAP1 Ser473 Blocks tumor progression in the context of ASS1 silencing, and will Mitochondrial Fusion in Breast Cancer Cells. sustained arginine restriction promote irreversible chromatin Cancer Res. 76: 5006. PMID: 27063096. modifications (chromatin closing) that cannot be reversed • Wang, L.Y., Hung, C.L., Chen, Y.R., Yang, J.C., Wang, J., when arginine levels are normalized to remain unanswered. Campbell, M., Izumiya, Y., Chen, H.W., Wang, W.C., Ann, 2) Autophagy and Tumor Metabolism. Cancer cells undergo a D.K., and Kung, H.J. (2016) KDM4A Coactivates E2F1 to Regulate the PDK-Dependent Metabolic Switch between multifaceted rewiring of cellular metabolism to maximize their Mitochondrial Oxidation and Glycolysis. Cell Report. 16: 3016. macromolecule biosynthesis for growth. Although the Warburg PMID: 27626669 PMCID: PMC5024724. effect has been extensively studied, the broad biological implications and clinical relevance of most metabolic rewiring • Lin, H.H., Chung, Y., Cheng, C.T., Ouyang, C., Fu, Y., Sadeghi, are unclear. Among them, autophagy is a catabolic process M., Vonderfecht, S., Chu, P., Kung, H.J., Li, C.F., Limesand, that uses the cell’s lysosomal system to degrade its own K.H., and Ann, D.K. (2018) Autophagy Coordinates components including cytoplasmic organelles and proteins. In Asparagine Availability and Mitochondrial Activity to Permit the last decade, it has been established that autophagy plays Oncogenic KRAS-driven Tumor. Autophagy (in press). important and complicated roles in the onset and progression
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 23 Behnam Badie, M.D. Professor and Chief, Department of Surgery, Division of Neurosurgery Director, Brain Tumor Program
GLIOMA RESEARCH
Glioma-associated macrophages: My group was one of the first Surgical devices for drug delivery: To enhance the delivery of to identify and characterize the function of glioma-infiltrating antitumor agents like nanoparticles and engineered cells, I’m microglia and macrophages in brain tumors. We demonstrated leading the development of minimally-invasive devices that the heterogeneity of this cell population, their inactivation allow for both tumor resection and delivery of agents directly as innate immune cells and their potential role in local into brain tumors. Feasibility animal studies with these devices immunosuppressive tumor microenvironment. These initial have been completed and clinical-grade prototypes will be reports provided the foundation for future investigations in developed in 2017. understanding the role of pattern-recognition receptors (such as RAGE and TLR9) and developing nanoparticles to activate SELECTED PUBLICATIONS these cells as a therapeutic approach. • Wang, H., Zhang, L. Zhang, I.Y., Chen, X., Da Fonseca, A., Receptor for advanced glycation endproducts (RAGE) is a Wu, S., Ren, H., Badie, S., Sadeghi, S., Ouvang, M., Warden, multiligand pattern-recognition receptor that is expressed on a C.D., and Badie, B. S100B Promotes Glioma Growth through number of cells and plays a role in the pathogenesis of diabetes Chemoattraction of Myeloid-Derived Macrophages. and neurodegenerative disorders. My group was the first to Clin Cancer Res. 2013. evaluate the expression of this receptor on glioma-associated • Chen, X., et al. (2014). “RAGE expression in tumor- macrophages and study its interaction with its ligands in associated macrophages promotes angiogenesis in glioma.” experimental gliomas. We showed that expression of RAGE Cancer Res 74(24): 7285-7297. and S100B (one of its ligands) can promote tumor growth and angiogenesis. This work is being pursued to develop novel • Zhao, D., Alizadeh, D., Zhang, L., Liu, W., Farrukh, O., Manuel, inhibitors of this pathway as a potential glioma therapy. E., Diamond, D.J., and Badie, B. Carbon Nanotubes Enhance CpG Uptake and Potentiate Anti-Glioma Immunity. Clin Development of nanoparticles for glioma immunotherapy: Cancer Res. 2011. (Impact Factor: 8.2) PMCID: PMC3041854 building on our understanding of glioma-associated microglia and macrophages, my group has developed nanoparticles to • Fan, H., Zhang, I.Y., Chen, X., Zhang, L., Wang, H., Carvalho target and stimulate pattern recognisiton receptors like TLR9 da Fonseca, A.C., Manuel, E.R., Diamond, D.J., Raubitschek, in these cells. We were the first to demonstrate the utility of A.A., Badie, B. Intracerebral CpG Immunotherapy with carbon nanotubes as carries of immunostimulatory CpG for Carbon Nanotubes Abrogates Growth of Subcutaneous glioma immunotherapy. Melanomas in Mice. Clin Cancer Res. 2012. (Impact Factor: 8.2) PMCID: PMC3483143 Cell-based therapies for gliomas: As a neurosurgeon with interest in neuro-oncology, I have been the PI or co-principal investigator on a number of first-in human clinical trials investigating the role of engineered neural stem cells and chimeric receptor antigen (CAR) T cell therapy for human glioblastoma. Two of these treatments were developed at City of Hope. I was the PI on a phase I clinical trial that evaluates the safety of anti-IL-13Rα2 engineered T-cell in patients with glioblastoma (City of Hope IRB 07082, IND 14194, NCT01082926) and a co-Investigator in the first-in- human clinical trial that is evaluating the role of neural stem cells in these patients (IRB 08002, IND 14041, NCT01172964). These trials were a culmination of collaborative work between our brain tumor team, our scientists and our regulatory staff at City of Hope.
24 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Adam M. Bailis, Ph.D. Associate Professor, Department of Molecular and Cellular Biology Associate Dean of Professional Development, Irell & Manella Graduate School of Biological Sciences
HOMOLOGOUS RECOMBINATION, GENOME STABILITY AND THE DEVELOPMENT OF TARGETED CANCER THERAPEUTICS
Genome instability in the form of mutations, loss of broken chromosomes in heterozygosity, and chromosomal rearrangements fuels budding yeast. Further, this tumorigenesis. These genetic changes result from endogenous repair is not required for processes, such as DNA replication failure, oxidative the viability of yeast cells, metabolism and age-related telomere erosion, as well as providing the opportunity exposure to exogenous agents, such as chemotherapeutic to distinguish between chemicals, and radiation. A broad array of DNA repair compounds that affect mechanisms addresses this damage in human cells and HsRAD52 function and maintains genome stability. Therefore, the balance between general cellular poisons. DNA damage and DNA repair is a critical determinant of This system is being used genome stability and cancer susceptibility in humans. for the high-throughput screening of compound Figure 1: Luminescence assay The homologous recombination (HR) apparatus is essential for HsRAD52-dependent HR – libraries for inhibitors for life in human cells, indicative of its critical role in the repair Endonuclease cutting at the HO site of HsRAD52 function in (black box) adjacent to the HIS3 locus of endogenous DNA damage. HR factors, such as BRCA1 and cells (Figure 1), and to on yeast chromosome XV initiates BRCA2 are also important tumor suppressors reflecting their repair by HR with a donor sequence on study their effects at the prominent role in genome stabilization. Studying the function chromosome III. Repair by HsRAD52- molecular level in order to dependent HR (black arrow) results in of these factors in HR is critical for understanding their role in develop them into effective the creation of a HIS3-luc fusion gene, genome stabilization and tumor suppression. However, loss of expression of a luciferase reporter chemotherapeutic drugs. HR function in human cells limits viability creating a substantial protein, and a luminescence signal upon addition of luciferin. Inhibitors of barrier to study. In order to study the human HR apparatus in a HsRAD52 block creation of the HIS3- living system we have expressed human HR genes in budding luc fusion gene, and creation of the yeast cells lacking the homologous genes, creating humanized luminescence signal. yeast. These strains permit the unrestricted study of the SELECTED PUBLICATIONS human HR apparatus in a living system. • Manthey, G.M., Clear, A.D., Liddell, L.C., Negrito, M.C., Many breast cancers are found to be defective for BRCA1 and and Bailis, A.M. Homologous recombination in budding BRCA2. In human cells that possess such defects, reducing yeast expressing the human RAD52 gene reveals a Rad51- the level of the DNA repair protein, HsRAD52, is lethal, even independent mechanism of conservative double-strand though reducing its level in normal cells has few effects. The break repair. Nucleic Acids Res. 45: 1879-1888, 2017. lethality that arises when levels of HsRAD52 are reduced in • Liddell, L.C., Manthey, G.M., Owens, S.N., Fu, B.X., and Bailis, BRCA-defective tumor cells indicates HsRAD52 would be an A.M. Alleles of the homologous recombination gene, RAD59, excellent target for chemotherapeutic assault as it would kill identify multiple responses to disrupted DNA replication in the tumors without affecting non tumor cells. Such a strategy Saccharomyces cerevisiae.BMC Microbiol. 13: 229, 2013 would revolutionize breast cancer treatment by replacing drugs that cause side effects that are often permanent with drugs • Ding, Y.C., Adamson, A.W., Steele, L., Bailis, A.M., John. E.M., that are more targeted to the tumor and much better tolerated. Tomlinson, G., and Neuhausen, S.L. Discovery of mutations However, the same attributes that make HsRAD52 an excellent in homologous recombination genes in African-American chemotherapeutic target also make it difficult to develop women with breast cancer. Fam. Cancer 17:187-195, 2018 drugs against, as killing BRCA-defective cells and having little effect on normal cells provide little opportunity for study. This is addressed by our recent discovery that HsRAD52 repairs
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 25 Michael E. Barish, Ph.D. Professor and Chair, Department of Developmental and Stem Cell Biology
PHYSIOLOGICAL AND IMAGING STUDIES OF BRAIN TUMORS
Malignant brain tumors are essentially incurable effort is quantitative assessment of NSC migration to tumor despite extensive efforts to develop aggressive surgical, foci and spatial distributions through different tumor regions chemotherapeutic and radiological treatments. Therapeutic (tumor mass, invading edge, disseminating cells and cell failure is largely attributable to the presence of engrafted groups). Recent results suggest the presence of inflammatory microfoci seeded by infiltrating glioma cells. Our research is processes and expression of mesenchymal markers in areas concerned with the origins of these small disseminated tumor of denser NSC accumulations. Our observations suggest that foci (“tumor initiating cells” and “cancer stem cells”) and their in vivo NSC homing to tumor cells emerges from reciprocal role as homing targets for neural stem cells. interactions of tumor and surrounding brain cells to produce a conducive microenvironment. We hypothesize that this a) Brain tumor cell niches and their role in dissemination microenvironment recapitulates in some important ways the and progression. In collaboration with Christine E. Brown, normal environment of the developing brain to which the NSCs Ph.D. (Immuno-Oncology/Hematology-HCT), we are using characterized patient-derived brain tumor cell lines developed are responding appropriately. at City of Hope to probe the relationships between tumor cell SELECTED PUBLICATIONS migration and proliferation, and structures harboring brain tumor cells, including vasculature and white matter tracts. • Brown, C.E., Aguilar, B., Starr, R., Yang, X., Chang, W.C., Of particular interest is the role of the microenvironment in Weng, L., Chang, B., Sarkissian, A., Brito, A., Sanchez, J.F., defining the phenotypes of resident tumor cells, including Ostberg, J.R., D’Apuzzo, M., Badie, B., Barish, M.E., and expression of stem cell characteristics and tumor progression. Forman, S.J. (2018). Optimization of IL13Rα2-targeted chimeric antigen receptor T cells for improved anti-tumor We are using large-field imaging techniques to visualize the efficacy against glioblastoma. Molecular Therapy 26: 31-44. disseminating edges of patient-derived tumor xenografts, and PMID: 29103912 the spatial relationships of migrating tumor cells and sites of proliferation and engraftment. We observe that in different • Barish, M.E., Herrmann, K., Tang, Y., Herculian, S.A., Metz, brain regions, migrating and proliferating tumor cells emerging M., Aramburo, S., Revathiswari, T., Gutova, M., Annalla, A., Moats, R.A., Goldstein, L., Rockne, R.C., Gutierrez, J., Brown, from the same implantation are found in close proximity C.E., Ghoda, L.Y., and Aboody, K.S. (2017). Human neural to particular structures, and that expression of cell surface stem cell biodistribution and predicted tumor coverage by markers and signaling receptors appears to vary with the a diffusible therapeutic in a mouse glioma model. Stem Cells microenvironment. These observations indicate phenotypic Translational Medicine 6: 1522-1532. PMCID: PMC5689763 plasticity that may reflect current notions about the ephemeral nature of tumor-initiating cancer stem cells in glioblastoma. • Brown, C.E., Alizadeh, D., Starr, R., Weng, L., Wagner, J.R., Naranjo, A., Ostberg, J.R., Blanchard, M.S., Kilpatrick, J., b) Mechanisms by which neural stem cells (NSCs) natively Simpson, J., Kurien, A., Priceman, S.J., Wang, X., Harshbarger, home to, recognize and actively bind tumor cells. In rodent T.L., D’Apuzzo, M., Ressler, J.A., Jensen, M.C., Barish, M.E., models, immortalized NSCs, introduced into the brain Chen, M., Portnow, J., Forman, S.J., and Badie, B. (2016). parenchyma or circulating blood, will home to orthotopically Regression of glioblastoma after chimeric antigen receptor implanted human glioma cells. Our research interest is to T-cell therapy. New England Journal of Medicine 375: 2561- understand mechanisms of NSC homing and binding to 2569. PMCID: PMC5390684 tumor cells, and to optimize these processes to develop more effective anti-cancer therapies. • Li, Z., Oganesyan, D., Mooney, R., Rong, X., Christensen, M.J., Shahmanyan, D., Perrigue, P.M., Benetatos, J., Tsaturyan, L., In collaboration with Karen S. Aboody, M.D. (Developmental Aramburo, S., Annala, A.J., Lu, Y., Najbauer, J., Wu, X., Barish, and Stem Cell Biology/Neurosurgery), we are investigating M.E., Brody, D.L., Aboody, K.S., and Gutova, M. (2016). mechanisms by which NSCs migrate to brain tumor cells L-MYC expression maintains self-renewal and prolongs and subsequently bind to and encircle them. Again, using multipotency of primary human neural stem cells. Stem Cell large-scale imaging techniques we have visualized rapid Reports 7: 483-495. PMCID: PMC5031988 NSC invasion of pre-existing orthotopic tumors. One major
26 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Jacob Berlin, Ph.D. Associate Professor, Department of Molecular Medicine
NANOPARTICLES FOR THE DIAGNOSIS AND TREATMENT OF CANCER
My research group is focused on the application of • Liu, A.T., and Berlin, J.M.* Impact of Cross-Linker Valency on nanomaterials for the diagnosis and treatment of cancer. Gold Nanoparticle Aggregate Formation and Cellular Uptake. As part of City of Hope’s “bench-to-bedside” continuum, Langmuir, 2017, 33, 14358–14365 we are committed to developing novel therapies that will • Van Haute, D.*, and Berlin, J.M.* Challenges In Realizing improve patient outcomes. City of Hope is a world leader Selectivity For Nanoparticle Biodistribution And Clearance: in clinical trials, and with on-campus facilities capable of Lessons From Gold Nanoparticles. Ther. Deliv., 2017, 8, producing materials suitable for clinical trial use, our lab is 763–774 focused on getting nanoparticle treatments into the clinic in a • Tiet, P.*, and Berlin, J. M.* Exploiting Homing Abilities Of rapid manner. Cell Carriers: Targeted Delivery Of Nanoparticles For Cancer Therapy. Biochemical Pharmacology, 2017, 145, 18–26 Selective drug action on cancerous cells is the future of cancer therapy. Current targeting methodologies for nanoparticles • Cao, P., Mooney, R., Tirughana, R., Abidi, W., Aramburo, usually result in an increase in tumor accumulation relative S., Flores, L., Gilchrist, M., Nwokafor, U., Haber, T., Tiet, P., to nontargeted particles, but the majority of both classes Annala, A.J., Han, E., Dellinger, T., Aboody, K.S.*, and Berlin, accumulate in the liver and spleen. J.M.* Intraperitoneal Administration of Neural Stem Cell– Nanoparticle Conjugates Targets Chemotherapy to Ovarian We are broadly interested in developing new drug delivery Tumors. Bioconjugate Chem., 2017, 28,1767–1776. constructs that overcome this challenge. Our efforts fall into • Van Haute, D., Longmate, J. M., and Berlin, J. M.* Controlled four general categories: Assembly of Biocompatible Metallic Nanoaggregates Using 1. Using nanoparticle aggregates to understand what controls a Small Molecule Crosslinker. Adv. Mater, 2015, 27, 5158– cell and organ uptake of nanoparticles in order to design 5164. systems with improved tumor targeting • White, E. E., Pai, A., Weng, Y., Suresh, A. K., Van Haute, D., Pailevanian, T., Alizadeh, D., Hajimiri, A.,* Behnam Badie, B.,* 2. Neur al stem cell-nanoparticle conjugates where the and Berlin, J. M.* Functionalized Iron Oxide Nanoparticles for targeting is controlled by the tumor tropic stem cells and the Controlling the Movement of Immune Cells. Nanoscale, 2015, nanoparticles are used for therapy delivery (in collaboration 7, 7780-7789. with the Aboody lab) • Mooney, R.*, Roma, L., Zhao, D., Van Haute, D., Garcia, E., 3. Local injections of nanoparticles for targeted Kim, S. U., Annala, A., Aboody, K., and Berlin, J.M.* Neural immunotherapy. Current applications include IP injection for Stem Cell-Mediated Intratumoral Delivery of Gold Nanorods ovarian cancer and intracranial injection for brain cancer Improves Photothermal Therapy. ACS Nano, 2014, 8, 12450- (in collaboration with the Badie Lab) 12460. 4. Developing a platform for next generation high throughput • Mooney, R.*, Weng, Y., Tirughana-Sambandan, R., Garcia, screening to dramatically improved discovery of ligands and E., Hernandez, V., Aramburo, S., Annala, A., Berlin, J.M.*, and Aboody, K. Neural stem cells improve intracranial drug candidates for a wide array of targets nanoparticle retention and tumor-selective distribution. Future Oncology 2014, 10, 401-415. SELECTED PUBLICATIONS • Alizadeh, D., White, E.E., Sanchez, T. C., Liu, S., Zhang, L., • Schnarr, K., Mooney, R., Weng, Y., Zhao, D., Garcia, E., Badie, B.*, and Berlin, J.M.* Immunostimulatory CpG on Annala, A. J., Kim, S. U., Aboody, K. A.*, and Berlin, J. Carbon Nanotubes Selectively Inhibits Migration of Brain M.* Gold Nanoparticle-Loaded Neural Stem Cells for Tumor Cells. Bioconjugate Chemistry, 2018, Just Accepted. Photothermal Ablation of Cancer. Adv. Healthcare Mater. 2013, 2, 976–982. § Selected for the cover • Van Haute, D., Liu, A.T., and Berlin, J.M.* Coating Metal Nanoparticle Surfaces with Small Organic Molecules Can Reduce Nonspecific Cell Uptake. ACS Nano, 2018, 12, 117–127
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 27 Mark Boldin, M.D., Ph.D. Associate Professor, Department of Molecular and Cellular Biology
CONTROL OF MAMMALIAN HEMATOPOIESIS, IMMUNITY AND CANCER BY REGULATORY RNAS
The immune response to pathogens is a highly evolved and expression of TRAF6 and IRAK1, two adapter proteins that complex biological reaction that requires an orchestrated function in a signaling hub that connects immune receptors to action of numerous immune cell types, guided by a continuous NF-kB activation. flow of cell communication cues in the form of cytokines Current research in our laboratory is defining the contribution and secondary messengers. Too much or too little of this of both miRNAs and long noncoding RNAs to the regulation response can have dire consequences for the organism, as of gene expression during hematopoiesis and the activation of exemplified by a wide spectrum of human immune disorders, immune responses. Besides being fundamentally important, from autoimmunity to immunodeficiency and even cancer. The this work potentially could lead to the creation of novel precise execution and coordination of different steps during the pharmacological strategies for the treatment of immune- immune response requires the activation of intricate genetic mediated diseases and cancer. programs that are driven by a myriad of cell surface receptors and transcription factors. SELECTED PUBLICATIONS Until recently, the complexity of gene regulation during the • Magilnick, N., and Boldin, M.P. Molecular Moirai: Long immune response was considered mostly from the perspective Noncoding RNA Mediators of HSC Fate. Curr Stem Cell Rep, of protein-coding genes. However, the discovery of microRNAs 2018. (miRNAs) and the advent of high throughput sequencing technologies have revolutionized our understanding of gene • Magilnick, N., Reyes, E.Y., Wang, W.L., Vonderfecht, S.L., control. It is clear today that the human genome is pervasively Gohda, J., Inoue, J.I., and Boldin, M.P. miR-146a-Traf6 regulatory axis controls autoimmunity and myelopoiesis, transcribed and produces a staggering number of non-protein- but is dispensable for hematopoietic stem cell homeostasis coding transcripts, including miRNAs, siRNAs, piRNAs and and tumor suppression. Proc Natl Acad Sci USA, 114: long noncoding RNAs. These RNA molecules operate as E7140-E7149, 2017. critical regulators of other functional elements in the genome, especially protein-coding genes, and are known to control • Kramer N.J., Wang, W.L., Reyes, E.Y., Kumar, B., Chen, C.C., diverse biological processes. Understanding the biology and Ramakrishna, C., Cantin, E.M., Vonderfecht, S.L., Taganov, molecular mode of action of noncoding RNAs that govern K.D., Chau, N., and Boldin, M.P. Altered lymphopoiesis and development and functioning of the immune system is the immunodeficiency in miR-142 null mice. Blood 125:3720- long-term goal of our laboratory. 30,2015. A few years ago, we hypothesized that miRNAs comprise a • Boldin, M.P., and Baltimore, D. miRNAs, new effectors and novel layer of regulation of the innate immune response and regulators of NF-kB. Immunol. Rev. 246: 205-20, 2012. have carried out a systematic effort to identify miRNAs that • Boldin, M.P., Taganov, K.D., Rao, D. S., Yang, L., Zhao, J. L., are involved in the mammalian response to microbial infection. Kalwani, M., Garcia-Flores, Y., Luong, M, Devrekanli, A., We identified three miRNA genes (miR-146a, miR-132 and Xu, J., Sun, G., Tay, J., Linsley, P.S., and Baltimore, D. miR- miR-155), whose expression is sharply upregulated in response 146a is a significant molecular brake on autoimmunity, to bacterial lipopolysaccharide and studied the function of one myeloproliferation, and cancer in mice. J. Exp. Med. 208: of them, miR-146a, in depth. Using a loss-of-function genetic 1189-201, 2011. approach, we found that miR-146a serves as an essential molecular brake on both inflammation and cancer. Mice that • Lu, L-F., Boldin, M.P., Chaudhry, A., Lin, L-L., Taganov, K.D., lack the miR-146a gene develop an autoimmune disorder as Yoshimura, A., Baltimore, D., and Rudensky, A.Y. Function of well as frank tumors in the secondary lymphoid organs. Our miR-146a in controlling Treg cell-mediated regulation of Th1 molecular studies suggest that this miRNA acts as a negative responses. Cell 142:914-29, 2010. feedback regulator of the innate immune response by silencing
28 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Christine Brown, Ph.D. Heritage Provider Network Professor in Immunotherapy Associate Director, T Cell Therapeutics Research Laboratory Departments of Hematology & Hematopoietic Cell Transplantation and Immuno-Oncology
DEVELOPING CHIMERIC ANTIGEN RECEPTOR T CELLS FOR MALIGNANT BRAIN TUMORS
The research program of Christine Brown, Ph.D., aims to SELECTED PUBLICATIONS advance the application of chimeric antigen receptor (CAR) T • Wang, D., Aguilar, B., Starr, R., Alizadeh, D., Brito, A., cell therapy for the treatment of malignant brain tumors. CARs Sarkissian, A., Ostberg, J.R., Forman, S.J., and Brown, C.E. are synthetic immune receptors composed of a tumor targeting Glioblastoma-Targeted CD4+ CAR-T cell outperform CD8+ domain and signaling components of the T cell receptor, which cells for Sustained Effector Function and Superior Antitumor function together to reprogram T cells to recognize and destroy Activity. JCI Insight. (2018) In press malignant cells. • Brown, C.E., Aguilar, B., Starr, R., Yang, X., Chang, W.C., The lead program focuses on optimizing IL13R 2-targeted α Weng, L., Chang, B., Sarkissian, A., Brito, A., Sanchez, J.F., CAR T cells. Preclinical studies have delineated an optimal Ostberg, J.R., D’Apuzzo, M., Badie, B., Barish, M.E., and CAR design, developed manufacturing strategies to maintain a Forman, S.J. Optimization of IL13Rα2-Targeted Chimeric less-differentiated T cell product, and evaluated routes of T cell Antigen Receptor T Cells for Improved Anti-tumor Efficacy delivery to most effectively eliminate infiltrative brain tumors. against Glioblastoma. Mol Ther 26, 31-44 (2018). The team’s scientific progress in this area has led to the initiation of a first-in-human clinical trial evaluating IL13Rα2- • Priceman, S.J., Tilakawardane, D., Jeang, B., Murad, J.P., CAR T cells for treatment of glioblastoma, an effort showing Park, A.K., Chang, W.C., Ostberg, J.R., Neman, J., Jandial, R., preliminary evidence for promising anti-tumor effects. Portnow, J., Forman, S.J., and Brown, C.E. Regional Delivery of Chimeric Antigen Receptor-Engineered T Cells Effectively The laboratory of Dr. Brown also continues to define and Targets HER2+ Breast Cancer Metastasis to the Brain. Clin implement CAR T cell advancements to overcome barriers to Cancer Res 24, 95-105 (2018). therapeutic success. For instance, to address the challenge of tumor heterogeneity, the group is focused on boxing in tumor • Brown, C.E., Alizadeh, D., Starr, R., Wagner, J.R., Naranjo, antigen escape by simultaneously targeting several tumor A., Ostberg, J.R., Blanchard, M.S., Kilpatrick, J., Simpson, antigens, including IL13Rα2, HER2, EGFR, and chlorotoxin J., Kurien, A., Priceman, S.J., Wang, X., Harsharger, T.L., receptors. Another critical barrier often limiting CAR T cell D’Apuzzo, M., Ressler, J.A., Jensen, M.C., Barish, M.E., Chen, therapeutic success is the hostile tumor microenvironment M., Portnow, J., Forman, S.J., and Badie, B. (2016) Regression that functions to subdue immune anti-tumor responses. The of Glioblastoma after Chimeric Antigen Receptor T-Cell team is developing mouse models that better reflect the Therapy. N Engl J Med 375, 2561-2569 (2016). suppressive immune landscape in order to better evaluate approaches to overcome these suppressive pathways. As part of the T Cell Therapeutics Research Laboratory, Brown and team work with a talented group of scientists developing and optimizing CAR T cell therapy for a wide range of cancers. This collaborative research group, through rigorous scientific discovery and optimization, aims to rapidly translate promising new CAR T cell therapies to patients.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 29 John Burnett, Ph.D. Assistant Professor, Center for Gene Therapy
DEVELOPMENT OF GENE AND RNA THERAPIES FOR ACQUIRED DISEASES AND GENETIC DISORDERS
The laboratory of John Burnett, Ph.D., focuses on applying latency by altering the epigenetic state of the virus through the principles from molecular biology to engineer advanced TGA process. In a related strategy, we are using the CRISPR/ biological therapeutics for genetic and infectious diseases. Cas9 RNA-guided genome editing (RGEN) system to disrupt Our research interest includes strategies to achieve targeted the integrated HIV genome in infected cells. In contrast to delivery with specialized RNA aptamers, gene-specific the siRNA-based approach, which aimed to reactivate latent inhibition (or activation) with siRNAs, constitutive or inducible infections, the RGEN approach aims to induce mutations or gene expression with viral vectors, and the manipulation of deletions in the HIV genome in latently infected cells. genomes with targeted gene-editing strategies. Another aspect of the Burnett lab is the application of The canonical cellular process of RNA interference (RNAi) oligonucleotide-based and targeted genome editing uses small RNAs in a complex with Argonaute proteins to technologies to treat diseases caused by mitochondrial DNA induce silencing of messenger RNA (mRNA) through post- mutations (mtDNA) — inherited diseases that currently transcriptional gene silencing (PTGS). However, recent have no treatments or cures. By designing the CRISPR/Cas9 evidence shows that Argonaute-associated small RNAs system against mtDNA mutations, and by engineering the can induce chromatin remodeling at promoters that share system to traffic to the mitochondrial matrix, we aim to disrupt sequence complementarity. In a recent investigation of the pathogenic mtDNA mutations and restore the proliferation of TGA mechanism, we observed the additional requirement wild-type mtDNA. The ability to manipulate mtDNA has great of a cis-acting long noncoding RNA (lncRNA). However, the biomedical value, particularly because DNA transformation molecular requirements of TGA are still being uncovered, and of this organelle in mammals remains unsolved. This project we are currently investigating whether known lncRNAs that offers a novel approach for correcting genetic mitochondrial epigenetically regulate gene promoters can be targeted by disorders in patients, for which there are no effective a TGA mechanism. This work has therapeutic relevance for treatments or cures. developing new treatments for hepatocellular carcinoma and HIV latency. SELECTED PUBLICATIONS Current anti-HIV antiretroviral therapies are noncurative, • Zhang, X. Li, H. Burnett, J.C.*, and Rossi, J.J.* The role of antisense long non-coding RNA in small RNA-triggered gene and the complete elimination of HIV-1 in a patient will likely activation. RNA. 20(12): 1916-1928. PMCID: PMC4238356, require novel clinical approaches to purge the reservoir of 2014. *Corresponding authors latently infected cells. In an effort to establish a functional cure for HIV/AIDS, we are focused on developing strategies for • Burnett, J.C., Lim, K.I., Calafi, A., Rossi, J.J., Schaffer, D.V., and Arkin, A.P. “Combinatorial latency reactivation for HIV-1 eradicating HIV latency RNA-based gene therapy and targeted subtypes and variants.” Journal of Virology 84(12): 5958-74. genome engineering. One strategy utilizes aptamers, which PMCID: PMC2876650, 2010. are single-stranded nucleic acids with stable 3-D shapes that • Burnett, J.C., Miller-Jensen, K., Shah, P.S., Arkin, A.P., and bind to molecular targets, such as proteins or other nucleic Schaffer, D.V. “Control of stochastic gene expression by acids, with high affinity and specificity. Such RNA aptamers host factors at the HIV promoter.” PLoS Pathogens 5(1): can be conjugated with small interfering RNAs (siRNAs) e1000260. PMCID: PMC2607019, 2009. to create multifunctional biomolecules that are specifically • Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P., internalized into target cells and modulate expression of and Schaffer, D.V. “Stochastic gene expression in a lentiviral target genes by RNA interference (RNAi). These aptamer- positive-feedback loop: HIV-1 Tat fluctuations drive siRNA conjugates can be used to induce post-transcriptional phenotypic diversity.” Cell 122(2): 169-82, 2005. gene silencing (PTGS) of host genes that are required for the establishment and persistence of HIV latency. Alternatively, aptamer-siRNA molecules can be designed to reactivate HIV
30 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Edouard M. Cantin, Ph.D. Professor, Department of Molecular Imaging and Therapy
HERPES SIMPLEX VIRUS INFECTIONS IN THE NERVOUS SYSTEM
Herpes simplex virus (HSV) is a ubiquitous human pathogen HSV establishes lifelong latent infections in the sensory ganglia associated with mild disease as in cold sores. Less frequent from which it periodically reactivates to cause recurrent are more serious diseases like herpes keratitis, a leading disease and spread in the population. Understanding the cause of blindness, and herpes encephalitis (HSE), a mechanisms regulating latency is critical for devising strategies debilitating neurological disease with relatively high mortality to interfere with latency and reactivation. To this end, we and morbidity. Susceptibility to HSV disease is genetically have exploited IVIG to develop a novel model of latency controlled, and our studies indicate that a complex genetic establishment in immunodeficient Rag mice. By combining this system determines resistance or susceptibility to fatal HSE model with the use of dual fluorescent Protein Cre-reporter in C57BL/6 and 129S6 mice respectively. Resistance is mice we have developed a powerful strategy to genetically also strongly influenced by sex such that females are more mark and isolate HSV infected neurons and discriminate resistant than males. Using a variety of approaches including reactivated from nonreactivated neurons, which will facilitate bone marrow transplantation, in vivo siRNA gene silencing, deciphering molecular and immunological mechanisms flow cytometry analysis of brain infiltrating cells and MRI regulating latency. imaging, we determined that fatal HSE resulted primarily from unrestrained inflammatory responses in the central SELECTED PUBLICATIONS nervous system (CNS) rather than from virus cytopathology. • Ramakrishna, C., Newo, A.N.S, Shen, Y.-W., and An important finding was that once CNS inflammation Cantin, E. 2011. Passively administered pooled human immunoglobulins exert IL-10 dependent anti-inflammatory was initiated the antiviral drug Acyclovir was ineffective in effects that protect against Fatal HSV encephalitis. PLoS preventing mortality despite early and sustained inhibition of Pathog 7: e1002071, 2011. virus replication. • Lundberg, P., Ramakrishna, C., Brown, J., Tyszka, J.M., Intravenous immunoglobulin (IVIG) is a clinical product Hamamura, M., Hinton, D.R., Kovats, S., Nalcioglu, O., Weinberg, K., Openshaw, H., and Cantin, E.M. The immune comprised of pooled human IgG collected from thousands of response to herpes simplex virus type 1 infection in donors. Initially, IVIG was used to treat primary and secondary susceptible mice is a major cause of CNS pathology resulting immunodeficiencies but its use has expanded to include in fatal encephalitis. J. Virol. 82: 7078-7088, 2008. treatment for a host of other autoimmune and systemic • Lundberg, P., Welander, P.V., Edwards, C.K., III, van Rooijen, inflammatory diseases due to its potent anti-inflammatory and N., and Cantin, E. Tumor necrosis factor (TNF) protects immunomodulatory properties. IVIG protects against fatal HSE resistant C57BL/6 mice against herpes simplex virus- induced encephalitis independently of signaling via TNF by preventing hyper-inflammatory CNS responses through receptor 1 or 2. J. Virol. 81: 1451-146, 2007. a mechanism(s) independent of virus specific antibodies that includes induction of regulatory T cells and monocytes, • Amarzguioui, M., Lundberg, P., Cantin, E., Hagstrom, J., Behlke, M.A., and Rossi, J.J. Rational design and in vitro and which confer long-term protection. We confirmed a report in vivo delivery of Dicer substrate siRNA. Nat. Protoc. 1: 508- that sialylated IgGs (sIgG) present in limiting amount in 517, 2006. IVIG can mediate its anti-inflammatory activity, and we have • Openshaw, H. and Cantin, E.M. Corticosteroids in herpes uncovered another sIgG independent mechanism. Further simplex virus encephalitis. J. Neurol. Neurosurg. Psychiatry 76: studies of IVIG’s mechanism(s) of action, including a novel 1469, 2005. capacity to block intracellular virus replication, are underway. • Lundberg, P., Welander, P., Openshaw, H., Nalbandian, C., These ongoing studies are clinically relevant with a strong Edwards, C., Moldawer, L., and Cantin, E. A locus translational potential. on mouse chromosome 6 that determines resistance to herpes simplex virus also influences reactivation, while an unlinked locus augments resistance of female mice. J. Virol. 77: 11661-11673, 2003.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 31 Nadia Carlesso, M.D., Ph.D. Professor, Department of Hematological Malignancies Translational Science Associate Director of Basic Research, Gehr Family Center for Leukemia Research
BIOLOGY OF LEUKEMIA DEVELOPMENT AND RELAPSE
Our laboratory studies the molecular mechanisms driving HSC and its niche as regulators of innate immunity. We found normal stem cell differentiation and malignant transformation that TNFα, LPS, and gram-negative bacteria upregulate the in the hematopoietic system. More specifically we are expression of the Notch ligand J2 on BM endothelial cells investigating how the interactions between the bone marrow (EC), suggesting a microenvironment-hematopoietic cells microenvironment and the hematopoietic stem and progenitor interaction, where EC act as a sensor of stress and, in turn, cells shape their cell fate decisions. We are interested in regulate stem/progenitor cell response. We were the first defining: a) how Notch signaling guides and affects the to discover that the BM responds to severe sepsis with a reciprocal interactions between normal or malignant stem dysfunctional expansion of the hematopoietic stem cell (HSC) cells and their niches; b) Notch signaling and its interplay population associated with their loss of stem cell self-renewal with the Toll receptors and NF-κB pathways; and c) how this and ability to differentiate toward the myeloid lineage, resulting crosstalk is involved in the link between inflammation, aging in fatal neutropenia. By using the TLR4 adaptors MyD88 and leukemia development. To address these questions, we and TRIF knock-out mice, we further identified the unique are using complementary approaches including in vivo models role of the TLR4/TRIF-dependent pathway in mediating an of sepsis and leukemia, xenograft models and in vivo multi- irreversible damage to the HSC during inflammation. We are model imaging. The long-term goal of our research is to exploit pursuing these studies to define therapeutic strategies aimed basic insights in hematopoietic stem cell biology to identify at protecting HSC from inflammation-mediated injury. therapeutic targets and test drugs that will target leukemia Targeting SKP2 in normal and malignant hematopoiesis. cells and the inflamed microenvironment. We discovered that Notch signaling directly induces cell cycle entry by upregulating SKP2. We are currently investigating the role of the Notch/SKP2/p27 axis on the regulation of normal HSC and leukemia. We found that this pathway is not only involved in cell cycle regulation, but also directly regulates cell metabolism and senescence. Inhibition of SKP2 inhibits lymphoid leukemia. We are currently screening SKP2 inhibitors as therapeutic targets in relapse T-ALL.
SELECTED PUBLICATIONS • Bi, P., Shan, T., Yang, X., Liu, W., Liang, X.-R., Wang, J., Li, J., Inflammation and Leukemogenesis: Targeting the inflamed Carlesso, N., Liu, X., and Kuang, S. Notch signaling regulates microenvironment in myeloid leukemias. Notch signaling adipose browning and energy metabolism. Nature Medicine, influences cell fate decisions during normal and malignant 2014 Jul 20 hematopoiesis, and it can function either as a tumor • Wang, L., Zollman, A., and Carlesso N. Using Intravital suppressor or as an oncogene, depending on the cellular Fluorescent Microscopy (IVFM) of the Calvarium to Study the context. We have found that Notch signaling controls the Dynamic Track of Myeloid Expansion in Mouse Bone Marrow tone of inflammation in the bone marrow (BM) niche and that Microenvironment. JoVE, 2016 silencing of Notch signaling in the endothelium or BM stromal • Zhang, H., Rodriguez, S., Wang, L., Wang, S., Serezani, H., cells trigger a chronic inflammatory state resulting ultimately Kapur, R., Cardoso, A.A., and Carlesso, N. Sepsis Induces in a myeloproliferative disease (MPN). We found that miR-155 Hematopoietic Stem Cell Exhaustion and Myelosuppression links Notch signaling with NF-κB activation and plays a pivotal through Distinct Contributions of TRIF and MYD88. Stem Cell role in the development of MPN disease. We are currently Reports. 2016 Jun 14; 6(6):940-56 studying the impact of chronic inflammation and miR155 in leukemia initiation, progression or relapse, by using mouse models and patient samples.
32 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Daniela Castanotto, Ph.D. Research Professor, Department of Medical Oncology & Therapeutics Research
THERAPEUTIC TARGETING OF CANCER GENES USING SMALL MODIFIED NUCLEIC ACIDS
Considerable progress has been made in the design and of drugs to increase nucleic acid uptake in tumor cells using delivery of short, potentially therapeutic nucleic acids. human spheroids (see below) and mice as model systems. Chemical modifications have improved absorption, These studies are currently being extended to different types distribution and metabolism, while at the same time reducing of cancer. toxicity. Nevertheless, critical aspects of the cellular, tumor pharmacology and delivery properties of these agents are not well understood. The delivery and the cellular uptake of these potentially therapeutic molecules are not adequate to provide the desired outcome. Despite numerous clinical trials and thousands of trial participants accrued onto studies, we still do not have a marketed antisense oligonucleotide (ON) or siRNA for a cancer indication. Our research program focuses on understanding cellular mechanisms of gene regulation and how to manipulate those using small RNA and/or DNA molecules. We place a particular emphasis on how to overcome the barriers of delivery and cellular uptake, which have thwarted clinical cancer treatment with siRNAs or ONs from becoming a reality. We have found that both, siRNAs and ONs can be designed to highjack cellular pathways and can be directed to function in specific cellular compartments. By combining different strategies, two separate SELECTED PUBLICATIONS siRNAs or ONs can become synergistic [an example is shown • Castanotto, D., Zhang, X., Alluin, J., Zhang, Y., Rüger, J., below, in which the siRNA-1 and the siRNA-2 both target the Armstrong, B., Rossi, J., Riggs, A., and Stein CA. A Stress- same site in the luciferase gene, but show greater activity when Induced Response Complex (SIRC) shuttles oligos and combined (last panel)]. miRNAs to the nucleus. Proc. Natl, Acad. Sci. (2018) • Castanotto, D., Lingeman, R., Riggs, A., and Rossi, J. CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs. Proc. Natl, Acad. Sci. 106(51):21655-21659. (2009). • Castanotto, D., Lin, M., Kowolik, C., Wang, L., Ren, X., Soifer, H., Koch, T., Hansen, B., Armstrong, B., Wang, Z., Bauer, P., Rossi, J., and Stein, C.A. A Cytoplasmic Pathway for Gapmer Antisense-Mediated Gene Silencing in Mammalian Cells. Nucleic Acids Res. 43(19):9350-61 (2015). • Zhang, X., Castanotto, D., Shemi, A., and Stein, C.A. Ammonium and arsenic trioxide are potent, inexpensive facilitators of oligonucleotide functions when delivered by We use ONs to modulate miRNA function and to alter gymnosis. Nucleic Acids Res. 46(7): 3612–3624 (2018). transcription, splicing and RNA stability of cellular genes. To • Castanotto, D., and Rossi J. The promises and pitfalls of RNA- summarize, our projects investigate both, the mechanisms interference-based therapeutics. Nature, 457(7228): 426-433 of ONs and siRNAs and the role that specific oncogenes (2009). play in the development of cancer. We also explore the use
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 33 Wing-Chung (John) Chan, M.D. Dr. Norman & Melinda Payson Professor in Hematologic Cancers Professor, Department of Pathology
THE FUNCTIONAL GENOMICS OF LYMPHOMA
This area includes the gene expression profiling study • Küçük, C., Jiang, B1, Hu, X., Zhang, W., Chan, J.K., Xiao, W., performed by our consortium: Lymphoma/Leukemia Molecular Lack, N., Alkan, C., Williams, J.C., Avery, K.N., Kavak, P., Scuto, Profiling Project supported by the SPECS Initiative, with the A., Sen, E., Gaulard, P., Staudt, L., Iqbal, J., Zhang, W., Cornish, goal of constructing robust classifiers and prognosticators A., Gong, Q., Yang, Q., Sun, H., d’Amore, F., Leppä, S., Liu, W., Fu, K., de Leval, L., McKeithan, T., and Chan, W.C. Activating for non-Hodgkin lymphoma. This has provided large data and mutations of STAT5B and STAT3 in lymphomas derived from tissue resources for other areas of investigation, including the γδ-T or NK cells. Nat Commun. 2015 Jan 14;6:6025. molecular pathogenesis of lymphoma, as well as therapeutic target discovery. We are also performing microRNA expression • Iqbal, J., Wright, G., Wang, C., Rosenwald, A., Gascoyne, R.D., Weisenburger, D.D., Greiner, T.C., Smith, L., Guo, S., Wilcox, profiling and DNA methylation analysis on selected lymphoma R.A., Teh, B.T., Lim, S.T., Tan, S.Y., Rimsza, L.M., Jaffe, E.S., subtypes to determine their role in the pathogenesis of Campo, E., Martinez, A., Delabie, J., Braziel, R.M., Cook, J.R., these lymphomas and their possible use in diagnosis Tubbs, R.R., Ott, G., Geissinger, E., Gaulard, P., Piccaluga, P.P., and prognostication. Pileri, S.A., Au, W.Y., Nakamura, S., Seto, M., Berger, F., de Leval, L., Connors, J.M., Armitage, J., Vose, J., Chan, W.C.+, Molecular pathogenesis of lymphoma and and Staudt, L.M. Gene expression signatures delineate biologic and prognostic subgroups in peripheral T-cell experimental therapeutics lymphoma. Blood 123: 2915-2913, 2014. This program is directed mainly at T cell lymphoma and +Co-corresponding author. the transformation of follicular lymphoma. Our goal is to • Bouska, A., McKeithan, T.W., Deffenbacher, K.E., Lachel, C., obtain detailed molecular genetic information on these Wright, G.W., Iqbal, J., Smith, L.M., Zhang, W., Kucuk, C., lymphomas, using high resolution array CGH techniques and Rinaldi, A., Bertoni, F., Fitzgibbon, J., Fu, K., Weisenburger, next generation sequencing. We will construct models of D.D., Greiner, T.C., Dave, B.J., Gascoyne, R.D., Rosenwald, A., molecular pathogenesis and genetic progression and discover Ott, G., Campo, E., Rimsza, L.M., Delabie, J., Jaffe, E.S., Braziel, possible therapeutic targets to develop novel therapeutic R.M., Connors, J.M., Staudt, L.M., and Chan, W.C. Genome- approaches. We will also investigate the contribution of wide copy number analyses reveal genomic abnormalities the tumor microenvironment to the pathogenesis of these involved in transformation of follicular lymphoma. Blood 123: lymphomas and how to modify it to provide synergistic effects 1681-1690, 2014. to treatments aiming at the lymphoma cells. • Rohr J., Guo, S., Huo, J., Bouska, A,. Lachel, C., Li, Y., Simone, We are also actively engaged in the development and P.D., Zhang, W., Gong, Q., Wang, C., Cannon, A., Heavican, refinement of molecular assays in the diagnosis of lymphomas T., Mottok, A., Hung, S., Rosenwald, A., Gascoyne, R., Fu, K., and leukemias and in the detection of molecular characteristics Greiner, T.C., Weisenburger, D.D., Vose, J.M., Staudt, L.M., Xiao, W., Borgstahl, G.E., Davis, S., Steidl, C., McKeithan, T., of individual tumors that would inform us of the best and most Iqbal, J., and Chan, W.C. Recurrent activating mutations of targeted therapies for the patient. CD28 in peripheral T-cell lymphomas. Leukemia. 30(5):1062- 70, 2016. SELECTED PUBLICATIONS • Bouska, A., Zhang, W., Gong, Q., Iqbal, J., Scuto, A., Vose, • Wang, C., McKeithan, T.W., Gong, Q., Zhang, W., Bouska, A., J., Ludvigsen, M., Fitzgibbo,n J., Fu, K., Weisenburge,r D.D., Rosenwald, A., Gascoyne, R.D., Wu, X., Wang, J., Muhammad, Greiner, T.C., Gascoyne, R.D., Rosenwald, A., Ott, G., Campo, Z., Jiang, B., Rohr, J., Cannon, A., Steidl, C., Fu, K., Li, Y., E., Rimsza, L.M., Delabie, J., Jaffe, E.S., Braziel, R.M., Connors, Hung, S., Weisenburger, D.D., Greiner, T.C., Smith, L., Ott, G., J.M., Wu, C.I., Staudt, L.M., D‘Amore, F., McKeithan, T.W., and Rogan, E.G., Staudt, L.M., Vose, J., Iqbal, J., and Chan, W.C. Chan, W.C. Combined copy number and mutation analysis IDH2R172 mutations define a unique subgroup of patients identifies pathways associated with transformation of with angioimmunoblastic T-cell lymphoma. Blood. 2015 Oct follicular lymphoma. Leukemia. 31(1):83-91, 2017. 8;126(15):1741-52.
34 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Saswati Chatterjee, Ph.D. Professor, Department of Surgery
ADENO-ASSOCIATED VIRUS VECTORS FOR STEM CELL GENE THERAPY
My research group studies gene-based therapies for inherited SELECTED PUBLICATIONS and acquired diseases. We recently discovered a family • Mroske, C, Rivera, H., Ul-Hasan, T., Chatterjee, S., and Wong, of novel adeno-associated viruses from healthy human K.K. Jr. A Capillary Electrophoresis Sequencing Method hematopoietic stem cells, known as AAVHSCs. We have for the Identification of Mutations in the Inverted Terminal derived gene delivery vectors based on these novel viruses. Repeats of Adeno-Associated Virus. Human Gene Therapy These novel gene transfer vectors have unique properties and Methods 2012 Apr;23(2):128-36. Epub 2012 May 21. target tissues including the liver and muscle in vivo. They also cross the blood brain barrier and can deliver therapeutic genes • Song, L., Kauss, M.A., Kopin, E., Chandra, M., Ul-Hasan, T., Miller, E., Jayandharan, G.R., Rivers, A.E., to the central nervous system. In addition, due to their stem Aslanidi, G.V., Ling, C., Li, B., Ma, W., Li, X., Andino, L.M., cell origin, vectors derived from these novel AAVHSCs target Zhong, L., Tarantal, A.F., Yoder, M.C., Wong, K.K. Jr, Tan, M., stem cells very efficiently. These characteristics make them Chatterjee, S., and Srivastava, A. Optimizing the transduction very attractive for systemic delivery of therapeutic genes to efficiency of capsid-modified AAV6 serotype vectors in multiple organs, particularly for the treatment of multi-organ primary human hematopoietic stem cells in vitro and in a diseases such as inborn errors of metabolism. We are pursuing xenograft mouse model in vivo. Cytotherapy. 8;15(8):986-98, novel therapies based on these properties of the AAVHSCs. 2013. More recently, we have developed a non-nuclease gene editing platform based upon AAVHSCs that functions highly efficiently • Smith, L.J., Ul-Hasan, T., Carvaines, S.K., Van Vliet, K., Yang, in vivo and in primary cells and leave very few detectable E., Wong, K.K., Agbandje-McKenna, M., and Chatterjee, genomic scars. We are currently pursuing both preclinical S. Structure and Gene Transfer Properties of Human Stem therapeutic applications of this technology as well as studying Cell-Derived AAV. Mol Ther. 2014 Sep;22(9):1625-34. doi: 10.1038/mt.2014.107. Epub 2014 Jun 13. PMID: 24925207 the basic underlying molecular mechanisms. • Smith, L.J., Wright, J.B., Atallah, G., St Martin, T., Ul-Hasan, T., Chandra, M., Fong, A., Fong, Y., Wong, K.K., and Chatterjee, S. A Novel Efficient Exclusively Homologous Recombination-Based Genome Editing Platform. In Review.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 35 Ammar Chaudhry, M.D. Director, Precision Imaging Lab Associate Director of Research, Radiology and Imaging Informatics Assistant Professor, Department of Diagnostic and Interventional Radiology
INTEGRATION OF ADVANCED IMAGING, RADIOBIOGENOMICS AND ARTIFICIAL INTELLIGENCE-MACHINE LEARNING TO DEVELOP PRECISION IMAGING
Lab and study information The precision imaging lab of Ammar Chaudhry, M.D., is dedicated to advancing the fields of radiology and imaging informatics science through basic science and translational research. With the ultimate goal of optimizing patient care through groundbreaking research, Chaudhry and his colleagues are pioneering and applying new medical imaging techniques PET-MRI evaluation of GBM patient treated with CAR T-cell therapy identified as pseudo progression. Fifty day post-operative PET-MRI demonstrates (A) increased metabolic (e.g. fMRI, PET-MRI, immunoPET, etc.) in the field of oncology activity along the posterior surgical margins which demonstrated (B) irregular nodular and metabolic disorders. As a translational researcher, the enhancement on the post-contrast series. (C) PET-MRI fusion. Findings are worrisome for progressive disease, however, given immunotherapy, pseudoprogression is in the overarching aim of Chaudhry’s work has been development of differential diagnosis. more accurate noninvasive diagnostic techniques that can be used as screening exams or prediction models for tumor biology (imaging biomarkers; imaging phenotype- genotype correlation). Chaudhry has been a principal investigator/co-PI on several funded studies, published over 30 articles in peer-reviewed scientific journals, authored several books chapters and is a reviewer for seven medical journals. While working with other subspecialists, Dr. Chaudhry’s team is collaborating and promoting preclinical and clinical multimodality approach to diagnosing and effectively treating oncologic and metabolic SELECTED PUBLICATIONS disorders. These collaborations are paving the way for advent • Chaudhry AA, Gul M, Chaudhry Ab. Utility of CT Lung and application of advanced molecular imaging. These Cancer Screening and the Management of CT Screen- advances have led to the emergence of our Radiobiogenomics Detected Findings. Journal of Thoracic Disease. March, 2018. and Imaging Informatics team which is working toward synthesizing big data accrued from radiological and biological • Chaudhry AA, Gul M, Gould E, et al Utility of Positron (genomic, proteomics, transcriptomics, etc.) sources with Emission Tomography-Magnetic Resonance in ultimate goal of bring precision imaging and precision medicine Musculoskeletal Imaging. World Journal of Radiology. to our patients. March 2016; 8(3):268-274. • Chaudhry AA, Gul M, Chaudhry Ab, Dunkin J. Qualitative Assessment of Diffusion Weighted Imaging and Susceptibility Weighted Imaging of CNS Myeloid Sarcoma. J Computer Assist Tomography. Jan-Feb 2016; 40 (1): 61-6.
• Chaudhry AA, Huston B, Grechushkin V, Kim C, Pena A, Hoshmand M, Chaya Y, Moore W, Bilfinger T. Characteristic CT Findings after Percutaneous Cryoablation Treatment of Malignant Lung Nodules. MEDICINE. Oct 2015; 94(42):e1672.
49 year old male with GBM underwent surgical resection and chemoradiation. Intravenous contrast was contraindicated due to patients renal failure. PET- MRI demonstrates treatment related changes without evidence of local or satellite recurrence.
36 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Ching-Cheng Chen, Ph.D. Assistant Professor, Division of Hematopoietic Stem Cell and Leukemia Research
CELLULAR AND MOLECULAR CHARACTERIZATION OF THE HEMATOPOIETIC NICHE
My research interests focus on the cellular and molecular indicated that fasting-induced reduction of serum IGF1 interactions between bone marrow (BM) microenvironment levels rejuvenates HSCs, and leads to more balanced lineage with normal or malignant hematopoietic stem cells (HSCs). differentiation. However, as fasting can activate multiple The goal of my group is to use knowledge gained to develop stress response pathways, it remains unclear what are novel therapeutic approaches that will i. (specifically target the IGF1 specific contributions to fasting-induced HSC leukemia cells or the modified niches that support them or ii.) rejuvenation. Thus, our objective is to identify regulatory improve engraftment and reconstitution capabilities of HSCs. pathways activated in HSCs when exposed to low levels of IGF1 that promote HSC self-renewal and regeneration. The current projects in our laboratory are:
1) To understand how leukemia cells and AML derived SELECTED PUBLICATIONS exosomes manipulate the BM microenvironment • Kumar, B., Garcia, M., Weng, L., Jung, X., Murakami, J. L., to facilitate their own growth and suppress Hu, X., McDonald, T., Lin, A., Kumar, A. R., DiGiusto, D. L., normal hematopoiesis. Stein, A. S., Pullarkat, V. A., Hui, S. K., Carlesso, N., Kuo, Y. Aggressive approaches for treating acute myeloid leukemia H., Bhatia, R., Marcucci, G., and Chen, C. C. Acute myeloid (AML) include chemotherapy and bone marrow (BM) leukemia transforms the bone marrow niche into a leukemia- transplantation. Even with state-of-the-art therapy, relapses permissive microenvironment through exosome secretion. occur often. Most adult AML patients die from the disease, Leukemia 32:575-587. doi: 10.1038/leu.2017.259. PubMed and the overall five-year relative survival rate is only PMID: 28816238; PMCID: PMC5843902. (2018) approximately 20%. Treatment failure is likely due to the presence of a population of leukemia cells that are resistant • Hu, X., Garcia, M., Weng, L., Jung, X., Murakami, J. L., Kumar, to treatment. These cells may be sheltered by the BM B., Warden, C. D., Todorov, I., and Chen, C. C. Identification microenvironment (niche), where they are protected from of a common mesenchymal stromal progenitor for the adult chemotherapy. Furthermore, there is evidence that leukemia haematopoietic niche. Nat Commun. 7:13095. doi: 10.1038/ cells not only co-opt normal niche signals, they also modify ncomms13095. PubMed PMID: 27721421. (2016) the cellular and molecular components of the niche to • Weng, L., Hu, X., Kumar, B., Garcia, M., Todorov, I., promote their own survival at the expense of normal HSCs. Jung, X., Marcucci, G., Forman, S. J., and Chen, C. C. As yet, the identity of the niche cells and secreted factors that facilitate leukemia cell growth and survival is unclear. Identification of a CD133-CD55- population functions as The objective of our group is to define the mechanisms a fetal common skeletal progenitor. Sci Rep. 6:38632. doi: that AML cells use to alter the BM niche and support their 10.1038/srep38632. PubMed PMID: 27929130; PMCID: own growth. PMC5144148. (2016) 2) T o develop a comprehensive understanding of how HSCs • Kumar, B., Garcia, M., Murakami, J. L., and Chen, C. C. adapt to microenvironment stress and activate mechanisms Exosome-mediated microenvironment dysregulation in that promote hematopoietic stem cell self-renewal leukemia. Biochim Biophys Acta. 1863:464-470. doi: 10.1016/j. and regeneration. bbamcr.2015.09.017. PubMed PMID: 26384870. (2016) Hematopoietic cell transplantation (HCT) is a highly • Murakami, J. L., Xu, B., Franco, C. B., Hu, X., Galli, S. J., effective treatment, and often the only potentially curative Weissman, I. L., and Chen, C. C. Evidence that beta7 option, for a variety of hematological malignancies. The Integrin Regulates Hematopoietic Stem Cell Homing and success of HCT depends on the ability of donor cells, Engraftment Through Interaction with MAdCAM-1. Stem especially HSCs to regenerate and repopulate in the Cells Dev. 25:18-26. doi: 10.1089/scd.2014.0551. PubMed recipient. Insulin-like growth factor-1 (IGF1) signaling PMID: 26422691; PMCID: PMC4692116. (2016) regulates critical biological processes important for stem cell homeostasis across species. Recent studies have
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 37 Chun-Wei (David) Chen, Ph.D. Assistant Professor, Department of Systems Biology Director, Division of Epigenetics and Transcriptional Engineering
HIGH THROUGHPUT GENETIC SCREENS, EPIGENETIC MECHANISMS IN LEUKEMIA AND CANCERS
High throughput CRISPR screen in leukemia and cancers Dr. Chen received his postdoctoral training in the Children’s For de novo therapeutic target discovery, the laboratory of Hospital Boston/Harvard Medical School. Prior to joining Chun-Wei Chen, Ph.D., developed a complete pipeline from City of Hope, Chen served as a senior research scientist at sgRNA library design, cloning, QC, screen in cancer models, Memorial Sloan-Kettering Cancer Center, and an instructor high throughput CRISPR sequencing and data analyses at Dana-Farber Cancer Institute/Harvard Medical School. His laboratory at City of Hope is currently funded by a five-year Oligo array start-up package and a National Institutes of Health K99/ R00 Award.
SELECTED PUBLICATIONS CRISPR Library • Chen, C.W., Koche, R., Sinha, A., Deshpande, A., Zhu, N., Eng, R., Doench, J., Xu, H., Chu., S., Qi, J., Wang, X., Delaney, C., Bernt, K.M., Root, D.E., Hahn, W.C., Bradner, J.E., and Armstrong, S.A. DOT1L Inhibits SIRT1-mediated Epigenetic Silencing to Maintain Leukemic Gene Expression in MLL- rearranged Leukemia. Nature Medicine. 2015; 21; 335-343. HiSeq Screen • Deshpande, A.J., Deshpande, A.A., Sinha, A.U., Chen, L., Chang, J., Cihan, A., Fazio, M., Chen, C.W., Zhu, N., Koche, R., Epigenetic networks in leukemia and cancers Dzhekieva, L., Ibáñez, G., Dias, S., Banka, D., Krivtsov, A., Luo, Using the epigenetic tools including ChIP-seq, ATAC-seq M., Roeder, R.G., Bradner, J.E., Bernt, K.M., and Armstrong, and combined with high throughput genetic screens, Chen’s S.A. AF10 Regulates Progressive H3K79 Methylation and laboratory aims to define the epigenetic circuities that drive Hox Gene Expression in Diverse AML Subtypes. Cancer Cell. tumorogenesis and drug resistance in leukemia and cancers. 2014; 26(6); 896-908. Understanding these mechanisms will allow developing next generation therapeutics (including combinational therapies) • Xu, H., Valerio, D.G., Eisold, M.E., Sinha, A., Koche, R.P., Hu, to better suppress the biggest challenge in current clinical W., Chen, C.W., Chu, S.H., Brien, G.L., Hsieh, J.J., Ernst, P., oncology, e.g., relapsed and refractory cancers in patients. and Armstrong, S.A. NUP98-fusion Proteins Interact with the NSL and MLL1 Complexes to Drive Leukemogenesis. Cancer Cell. 2016; 30(6):863-878.
• Lee, S.C.W., Dvinge, H., Kim, E., Cho, H., Micol, J.B., Chung, Y.R., Durham, B.H., Yoshimi, A., Kim, Y.J., Thomas, M., Lobry, C., Chen, C.W., Pastore, A., Taylor, J., Wang, X., Krivtsov, A, Armstrong, S.A., Palacino, J., Buonamici, S., Smith, P.G., Bradley, R.K., and Abdel-Wahab, O. Modulation of Splicing Catalysis for Therapeutic Targeting of Leukemias with Spliceosomal Mutations. Nature Medicine. 2016; 22(6):672-8.
• Wang, S.P., Tang, Z., Chen, C.W., Shimada, M., Koche, Precision epigenome editing R.P., Wang, L.H., Nakadai, T., Chramiec, A., Krivstov, A.V., Chen’s laboratory is developing the leading-edge technology Armstrong, S.A., and Roeder, R.G. A UTX-MLL4-p300 for loci-specific epigenome editing. This project is funded by Transcriptional Regulatory Network Coordinately Shapes the NCI-K99/R00 award. Active Enhancer Landscapes for Eliciting Transcription. Molecular Cell. 2017; 67(2):308-321.
38 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Jianjun Chen, Ph.D. Simms/Mann Family Foundation Chair in Systems Biology Professor and Vice Chair, Department of Systems Biology Faculty Member of the Gehr Family Center for Leukemia Research
FUNCTION, MECHANISM AND THERAPEUTIC POTENTIALS OF RNA/DNA EPIGENETICS IN CANCER
The laboratory of Jianjun Chen, Ph.D., has been working and cancer biology. TET (Ten-Eleven Translation) proteins on both genetic and especially epigenetic (e.g., RNA/DNA (TET1/2/3) are a group of methylcytosine dioxygenases that modification) changes in cancer-related protein-coding and can convert 5mC into 5hmC, leading to active or passive DNA noncoding genes (e.g., microRNAs) in tumorigenesis and drug demethylation. Our recent studies demonstrated that TET1 response for many years. We have systematically studied the plays an indispensable oncogenic role in the development of biological functions and underlying mechanisms of genetic certain subtypes of AMLs by promoting expression of a group and epigenetic regulators in leukemia and other cancers. We of critical oncogenic targets such as HOXA genes, MEIS1, have also made important progress in translational research in PBX3 and FLT3. Previously, it was commonly believed that all leukemia as evidenced by establishment of novel prognostic three TET genes function as tumor suppressors in all cancers; systems for outcome prediction and risk stratification and thus, our studies have challenged this prevailing concept by development of novel targeted therapy strategies and tools. demonstrating the critical oncogenic role of TET1 in AML. We Our long-term goal is to further advance our understanding have also shown that TET1 can negatively regulate expression of cancer biology, and acute myeloid leukemia (AML) in of a set of tumor-suppressor genes such as miR-22. particular, and to translate our discoveries from basic research Collectively, our studies shed new light into the functional into clinical application. importance of DNA modification machinery in normal and RNA epigenetics research malignant biological process. Moreover, we showed recently In recent years, we have been working on understanding of the that TET1 is a direct target of STAT3/5 and targeting STAT/ functions and underlying molecular mechanisms of TET1 signaling by small-molecule inhibitor compounds holds N6-methyladenosine (m6A) modification, the most abundant great therapeutic potential to treat AML. internal modification in messenger RNAs (mRNAs), and the associated machinery including ‘writers’ (e.g., METTL3, SELECTED PUBLICATIONS METTL14 and WTAP), ‘erasers’ (e.g., FTO, and ALKBH1/5) and • Su, R., Dong, L., Li, C., Nachtergaele, S., Wunderlich, M., Qing, ‘readers’ (e.g., IGF2BP1/2/3, YTHDF1/2/3, and YTHDC1/2) Y., Deng, X., Wang, Y., Weng, X., Hu, C., Yu, M., Skibbe, J., in normal development and tumorigenesis as well as in Dai, Q., Zou, D., Wu, T., Yu, K., Weng, H., Huang, H., Ferchen, drug response/resistance of cancer (especially AML). Our K., Qin, X., Zhang, B., Qi, J., Sasaki, A.T., Plas, D., Bradner, J.E., studies have demonstrated the functional importance of RNA Wei, M., Marcucci, G., Jiang, X., Mulloy, J., He, C., and Chen, epigenetics in normal and malignant hematopoiesis and in drug J. R-2HG exhibits anti-tumor activity by targeting FTO/m6A/ response of leukemia, as well as in other cancers, which may MYC/CEBPA signaling. Cell. 2018 Jan 11;172(1-2):90-105. lead to the development of more effective novel therapeutic strategies to treat leukemia and other cancers. For instance, • Weng., H., Huang, H., Wu, H., Qin, X. Zhao, B.S., Dong, we showed that FTO plays a critical oncogenic role in AML L., Shi, H., Skibbe, J., Shen, C., Hu, C., Sheng, Y., Wang, Y., as an m6A demethylase. Subsequently, we reported that by Wunderlich, M., Zhang, B., Dore, L., Su, R., Deng, X., Ferchen, targeting the FTO/MYC/CEBPA signaling, R-2-hydroxyglutarate K., Li, C., Sun, M., Lu, Z., Jiang, X., Marcucci, G., Mulloy, J., (R-2HG), which is produced at high levels by mutant IDH1/2 Yang, J., Qian, Z. Wei, M., He, C., and Chen, J. METTL14 enzymes and was reported previously as an oncometabolite, Inhibits Hematopoietic Stem/Progenitor Differentiation and actually exhibits a broad and intrinsic anti-tumor activity in Promotes Leukemogenesis via mRNA m6A Modification. Cell leukemia and brain tumor. We also demonstrated METTL14 Stem Cell. 2018 Feb 1;22(2):191-205. as an oncoprotein in AML. Furthermore, we have identified IGF2BP1/2/3 proteins as a novel family of m6A readers that • Huang, H., Weng, H., Sun, W., Qin, X., Shi, H., Wu, H., Zhao, recognize thousands of RNA transcripts and promote the B.S., Mesquita, A., Liu, C., Yuan, C.L., Hu, Y.C., Hüttelmaier, stability and storage of the targets (e.g., MYC). S., Skibbe, J., Su, R., Deng, X., Dong, L., Sun, M., Li, C., Nachtergaele, S., Wang, Y., Hu, C., Ferchen, K., Greis, K.D., DNA epigenetics research Jiang, X., Wei, M., Qu, L., Guan, J.L., He, C., Yang, J., and We have also been working on DNA epigenetics (i.e., DNA Chen, J. Nature Cell Biology. 2018 Mar;20(3):285-295. methylation and demethylation) in normal biological process
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 39 Mike Y. Chen, M.D., Ph.D. Associate Professor, Division of Neurosurgery
CBX MEDIATED EPIGENETIC CONTROL OF GLIOBLASTOMA EPITHELIAL TO MESENCHYMAL CELL TRANSITION
Our lab is currently investigating the effect of dysregulation SELECTED PUBLICATIONS of histone mediated epigenetic pathways in glioblastoma • Chen, M.Y., Lin, J., Graf, M.R., Holt, S.E., Chan, D.C., Clark, multiforme. Specifically, we have discovered that Chromobox A.J., VanMeter, T.E., Chidambaram, A., Fillmore, H.L., proteins, key components of the Polycomb repressive complex and Broaddus, W.C. Differential Cell Death Effects in 1, are aberrantly expressed in glioblastoma when compared Glioblastoma after Drug- Induced DNA Damage Laboratory to normal brain and lower grades of other astrocytomas. We Investigation. J Spine Neurosurg 2016 5:6 hypothesize that dysregulation causes glioblastomas and • Zou, Z., Yin, Y., Chen, L., Hsu, J.L., Yang, F., Jove, R., Jandial, other cancers to under a form of epithelial to mesenchymal R., Li, G., and Chen, M. Convection-Enhanced Delivery cell transition. Our studies are particularly interesting as they of Sorafenib Suppresses Tumor Progression in a Murine coincide with recent reports that H3K27 mutations potentially Model of Brain Melanoma through the Inhibition of Signal drive the development of maintenance of the majority of Transducer and Activator of Transcription 3. Journal of pediatric glioblastomas. Neurosurgery. 2016: 124(5), 1310-8.
Another project that we are working on, “Effect of pulsed • Li, G., Warden, C., Zou, Z., Neman, J., Jain, A., Jandial, R., and electromagnetic fields on cancer cell chemosensitivity,” is Chen, M. Altered expression of Polycomb group genes in examining the effect of pulsed electromagnetic fields on glioblastoma multiforme. PlosOne 2013 8(11):e80980 chemosensitivity of cancer cells. Alternating electrical fields have recently been shown to be an effective therapy for glioblastomas in phase 3 clinical trials. Our in vitro and in vivo data suggest that pulsed electromagnetic fields can also cause apoptosis in cancer cells. We are presently investigating the dose response curves and potential mechanisms of the effect.
40 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Shiuan Chen, Ph.D. Lester M. and Irene C. Finkelstein Chair in Biology Professor and Chair, Department of Cancer Biology
HORMONES AND CANCER
A major focus of this laboratory is to investigate the roles therapy-associated declines in myeloid-derived suppressor of aromatase in breast cancer development. In estrogen- cells (MDSCs) (Twardowski, et al., Cancer, 2015). A reverse dependent breast tumors, estrogen binds to the estrogen translational research is initiated to examine the effect of receptor protein and induces the expression of peptide growth mushroom intake on MDSC levels in mice. The team planning factors that are responsible for the proliferative responses of a new trial to verify the finding from the first trial. cancer cells. Aromatase is an enzyme that converts androgen Chen and Susan L. Neuhausen, Ph.D., obtained a multi-PI to estrogen. Since aromatase is the enzyme responsible for National Institutes of Health grant to evaluate the impact the synthesis of estrogen and estrogen can have a major effect of exposure to endocrine disrupting chemicals (EDCs) on in the development of breast cancer, an abnormal expression the risk of breast cancer development during an important of aromatase in breast cancer cells and/or surrounding period of susceptibility, the menopausal transition. The team adipose stromal cells has a significant influence on breast is interrogating two chemicals that have been recognized tumor development. as major health concerns: polybrominated diphenyl ethers Patient-derived tumor xenografts (PDXs) have been generated (PBDEs) and bisphenol A (BPA), a commonly used component in Chen’s laboratory as models for ER+ and triple-negative in food-grade plastics. A transdisciplinary approach is being breast cancers. The Chen laboratory characterized ten ER+ used that includes cell culture, mouse models and samples PDX mouse models and found that, consistent with their more collected from women during the menopausal transition. aggressive clinical characteristics, the intake rate of ER+HER2+ The approach involves using Dr. Chen’s AroER-Tri screen to tumors was higher than ER+HER2- tumors; and ER+HER2- interrogate EDC mechanisms; determine the effects of EDCs tumors were divided into two types by luminal A/B signature, in women during menopausal transition on the estrogenic which was also associated with the rate of PDX intake. In activity and the epigenome; and test the effects of EDCs on addition, eight lines of triple-negative breast cancer have been the development of mammary lesions in a mouse model of generated. Several projects have been developed using these menopause. In addition, with their community partners, the PDX lines, including biomarker analysis of estrogen-stimulated team is also providing a web-based resource on the role of and –suppressed ER+ PDXs, molecular characterization and exposures on development of breast cancer. drug test of AR+ triple-negative breast cancers and drug responses of ER+/HER2+ cancers. SELECTED PUBLICATIONS The Chen laboratory has a long-standing interest in the • Hsu, P.Y., Wu, V.S., Kanaya, N., Petrossian, K., Hsu, H.K., development of natural products as alternatives to and in Nguyen, D., Schmolze, D., Kai, M., Liu, C.Y., Lu, H., Chu, conjunction with conventional Western medicines, including P., Vito, C.A., Kruper, L., Mortimer, J., and Chen, S. Dual the potential role of plant-derived phytochemicals in prostate mTOR kinase inhibitor MLN0128 sensitizes HR+/HER2+ cancer prevention, risk of recurrence and therapy. Based on breast cancer patient-derived xenografts to trastuzumab or earlier work in our laboratory, Chen, Przemyslaw Twardowski, fulvestrant. Clin Cancer Res, 24: 395-406, 2018. M.D., Paul Frankel, Ph.D., Timothy Synold, Pharm.D., and Sumanta Pal, M.D., conducted a phase 1 trial of white button mushroom (WBM) powder in patients with biochemically recurrent prostate cancer, examining the effects of WBM powder on serum PSA levels and determined the tolerability and biological activity of WBM. Two patients experienced complete responses (CR; decline in PSA to undetectable levels) and two patients experienced partial responses (PR). Patients with CR and PR demonstrated higher levels of baseline interleukin-15 than nonresponders and this group had
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 41 WenYong Chen, Ph.D. Associate Professor, Department of Cancer Biology
EPIGENETICS, CANCER AND AGING
Epigenetic modifications play important roles in many SELECTED PUBLICATIONS normal biological processes, such as development, stem cell • Roth, M., Wang, Z., and Chen, W,Y. SIRT1 and LSD1 differentiation and aging, as well as in disease settings such competitively regulate KU70 functions in DNA repair and as cancer. We are interested in understanding the biology mutation acquisition in cancer cells. Oncotarget 2016, of cancer involving epigenetic regulation of tumorigenesis 50195-50214. and cancer drug resistance. One area of our research is to • Wang, Z., Chen, C.C., and Chen, W.Y. (2015) CD150 - side delineate the roles of sirtuin 1 (SIRT1) in normal hematopoietic population defines leukemia stem cells in a mouse model stem cells and leukemic stem cells. SIRT1 is a mammalian of chronic myelogenous leukemia in BABL/c mice and is stress-response gene encoding an NAD-dependent protein depleted by genetic loss of SIRT1. Stem Cells. 33:3437-3451, lysine deacetylase that plays diverse roles in regulating 2015 metabolism, aging and cancer. We have shown that SIRT1 is activated by oncogenic transformation of hematopoietic stem • Wang, Z., Liu, Z., Wu, X., Chu, S., Wang, J.H., Yuan, H., Roth, cells, and promotes leukemogenesis and drug resistance of M., Yuan, Y.C., Bhatia, R., and Chen, W.Y. ATRAinduced leukemic stem cells to chemotherapeutic agents. Our studies cellular differentiation and CD38 expression inhibits suggest that SIRT1 is a promising therapeutic target for acquisition of BCR-ABL mutations for CML acquired treatment of leukemia and perhaps other malignancies. resistance. PloS Genet. 10: e1004414, 2014. Another area of our research is to understand the mechanisms • Roth, M., and Chen, W.Y. Sorting out functions of sirtuins in of mutation acquisition for cancer drug resistance. We cancer. Oncogene. 27: 1609-1620, 2014. have developed a mammalian model system of mutation • Wang, Z., Yuan, H., Roth, M., Stark, J., Bhatia, R., and Chen, acquisition using chronic myeloid leukemia (CML) cells, and W.Y. SIRT1 promotes error-prone DNA damage repair and shown that resistant BCR-ABL genetic mutations can be acquisition of genetic mutations in CML cells. Oncogene 32: acquired de novo in CML cells in response to treatment with 589-598, 2013. tyrosine kinase inhibitors. The de novo mutation acquisition in these leukemia cells involves multiple processes, particularly • Li, L., Wang, L., Li, L., McDonald, T., Ho, Y., Holyoake, T., error-prone DNA damage repair and regulation of such repair Chen, W.Y.#, and Bhatia, R.#. Activation of p53 by SIRT1 by SIRT1 and other epigenetic factors. Further elucidating inhibition enhances elimination of CML leukemia stem cells mechanisms of mutation acquisition may help devise novel in combination with Imatinib. Cancer Cell 21:266-281, 2012. therapeutic strategies for cancer and prevent disease relapse. (#co-corresponding authors)
The third area of our research is on NAD metabolism in • Yuan, H., Wang, Z., Li, L., Zhang, H., Modi, H., Horne, D., cancer. A number of cellular enzymes including mammalian Stark, J., Bhatia, R.#, and Chen, W.Y.#. Activation of stress sirtuins depend on the cofactor NAD for enzymatic activity. response gene SIRT1 by BCR-ABL promotes leukemogenesis. We have shown that alteration of NAD metabolism through Blood 119: 1904-1914, 2012. (#co-corresponding authors) increasing salvage biosynthesis by NAMPT promotes prostate cancer cell survival and stress resistance and that stimulating • Wang, B., Hasan, K.M., Alvarado, E., Yuan, H., Wu, H., and differentiation of leukemia cells by increasing expression of Chen, W.Y. NAMPT over-expression in prostate cancer and CD38, a cellular NADase, inhibits drug resistance of leukemia its contribution to tumor cell survival and stress response. cells. Thus alteration of NAD metabolism has important Oncogene 30: 907-921, 2011. implication in cancer.
42 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Yuan Chen, Ph.D. Professor, Department of Molecular Medicine
UBIQUITIN-LIKE MODIFICATIONS
The long-term objective of my laboratory is to identify novel metabolic activities. Our goal is to provide information on mechanisms that can be targeted for developing innovative cellular pathways and to discover biomarkers for diagnosis, as treatments for cancer and other life-threatening human well as prognosis assessment in cancer therapy. diseases that lack a cure. Our current research focus is Application of NMR methods in drug discovery ubiquitin-like (Ubl) modifications, the regulation of which We are collaborating with several other laboratories with influences major oncogenic pathways, such as c-Myc and expertise in synthetic chemistry, molecular biology and KRas-dependent oncogenesis. Even though more than medical oncology to develop new therapeutics for cancer. 1,000 enzymes are involved in catalyzing Ubl modifications, State-of-the-art NMR methods are employed to provide in comparison to several hundred kinases involved in information on protein-ligand interactions at an atomic phosphorylation, Ubl modifications have been poorly explored resolution, information that is critical for the rational design of for therapeutic development. This is in contrast to the new therapeutics. development of over 30 kinase inhibitors as drugs. Thus, Ubl modifications are an untapped resource for potential new drug SELECTED PUBLICATIONS targets. We employ a multidisciplinary approach including chemical, biochemical, molecular and cellular biological • Alontaga, A.Y., Li, Y., Chen, C., Ma, C., Malany, S., Key, D.E., approaches, and animal models in our studies. Specific Sergienko, E., Sun, Q., Whipple, D.A., Matharu, D.S., Li, B., Vega, R., Li, Y., Schoenen, F.J., Blagg, B.J., Chung, T.D.Y., research programs are outlined below. and Chen, Y. Design of High Throughput Screening Assays The role of SUMOylation in oncogenesis and Identification of a SUMO1-Specific Small Molecule Post-translational modifications by the small ubiquitinlike Chemotype Targeting the SUMO-Interacting Motif-Binding modifiers (SUMO) are important in oncogenesis and cellular Surface. ACS Combinatorial Science, 17(4):239-46, 2015. response to DNA damage. Recent findings indicate that • Chen, C.H., Namanja, A.T., and Chen, Y. Conformational the key oncogenic pathways driven by Myc and K-Ras are flexibility and changes underlying activation of the SUMO- dependent on, or addicted to, SUMOylation. For example, specific protease SENP1 by remote substrate binding. Nat knocking down of the gene encoding the catalytic subunit of Commun. 5:4968, 2014. the SUMO activating enzyme (SAE), SAE2, has the strongest • Madu, I.G., Namanja, A.T., Su, Y., Wong, S., Li, Y.J., and Chen, synthetic lethal interaction with Myc hyperactivation. We Y. Identification and Characterization of a New Chemotype are investigating the molecular mechanisms underlying the of Noncovalent SENP Inhibitors. ACS Chem Biol. 8(7):1435- synthetic lethality of SUMOylation with Myc hyperactivation 41, 2013. and K-Ras mutations. In addition, we are investigating the structure-activity relationship of how the inhibitors interact • Zhang, X., Yue, P., Page, B.D., Li, T., Zhao, W., Namanja, A.T., with the SAE and inhibit its enzymatic activity, and use this Paladino, D., Zhao, J., Chen, Y., Gunning, P.T., and Turkson, J. information to guide further improvement of the inhibitors. Orally bioavailable small-molecule inhibitor of transcription factor Stat3 regresses human breast and lung cancer These studies could potentially improve treatment of many xenografts. Proc Natl Acad Sci U S A. 109(24):9623-8, 2012. cancers, as overexpression of Myc is estimated to contribute to 70 percent of all human cancers and K-Ras is also frequently • Cano, K.E., Li, L., Bhatia, S., Bhatia, R., Forman, S.J., and Chen, mutated in human cancers. Y. NMR-Based Metabolomic Analysis of the Molecular Pathogenesis of Therapy-Related Myelodysplasia/Acute NMR-based metabolomics Myeloid Leukemia. J Proteome Res, 10(6):2873-81, 2011. Metabolic activity is a reflection of cellular functions and thus inform on changes of cellular functions due to disease states. As such, many diagnostic tests use metabolites biomarkers. Our laboratory utilizes nuclear magnetic resonance (NMR) spectroscopy, in combination with cell biology methods, as tools for metabolomic studies — that is, global analysis of
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 43 Zhen (Jen) Chen, BMed, Ph.D. Assistant Professor, Department of Diabetes Complications and Metabolism
NONCODING RNA IN EPIGENETIC CONTROL AND ENDOTHELIAL STRESS RESPONSES
Uniquely positioned at the interface between blood and SELECTED PUBLICATIONS tissues, the vascular endothelium integrates environmental • Miao, Y., Ajami, N., Huang, T.-S., Lin, F.-M., Lou, C.-H., Li, S., (e.g. oxygen level), mechanical (e.g. hemodynamic flow), Kang, J., Munkacsi, H., Wang, Y.-T., Maurya, M., Gupta, S., and pharmacological (e.g. chemotoxic drugs) factors to Chien, S., Subramaniam, S., and Chen, Z. Long Non-Coding maintain the blood circulation to local tissues as well as RNA LEENE Promotes Chromatin Remodeling to Enhance organs throughout the body. Under various stress conditions, Endothelial Nitric Oxide Synthase. Nat Comm. 2018. endothelial cells (EC) undergo biological and functional • Shang, F., Wang, S.-C., Hsu, C.-Y., Miao, Y., Martin, M., Yin, changes. In normal vasculature, EC are chronically subjected Y., Wu, C.-C., Wang, Y.-T., Wu, G., Chien, S., Huang, H.-D., to laminar vs. disturbed flow, predisposing certain regions for Tarng, D.-C., Shiu, Y.-T., Cheung, A.K., Huang, P.-H., Chen, atherosclerosis. In the context of cancer, hypoxia promotes EC Z, and Shyy, J. Y.-J. MicroRNA-92a mediates endothelial angiogenesis to facilitate tumorigenesis. As an undesirable but dysfunction in chronic kidney disease. J. Am. Soc. Nephrol. common consequence, chemotherapies damage EC, increasing 2017. (*Co-corresponding author) cardiovascular risks despite their efficacy in treating cancer. • Ajami, N.E., Gupta, S., Mauraya, M.R., Nguyen, P., Li, J., Shyy Under diabetic conditions, these pathological processes can be J. Y.-J., Chen, Z., Chien, S., and Subramaniam, S. Systems exacerbated due to the pro-inflammatory milieu. Biology Analysis of Longitudinal Functional Response of Our research interest is to understand how EC responds to Endothelial Cells to Shear Stress. Proc Natl Acad Sci USA. stress conditions at the molecular, cellular and systems levels, 2017. (*Co-corresponding author) and how these mechanisms contribute to vascular health • Guo, W., Liu, W., Chen, Z., Gu, Y., Peng, S., Shen, L., Shen, Y., and disease. We integrate multiscale-omics (e.g. RNA-seq, Wang, X., Fent, G.-S., Sun, Y., and Xu, Q. Tyrosine phosphatase CLIP-seq, ChIP-seq), bioinformatics, systems biology, vascular SHP2 negatively regulates NLRP3 inflammasome activation via biology and cancer biology approaches to investigate the ANT1-dependent mitochondrial homeostasis. Nat Comm. 2017. epigenetic regulatory mechanisms in endothelial biology, with • Chen, Z, Li., S, Shyy, J.Y. Subramaniam, S, and Chien, S. a focus on noncoding RNA, e.g. miRNA and long noncoding Epigenetic Regulation: A New Frontier for Biomedical RNA. We aim to identify key molecules and pathways that Engineers. Annu Rev Biomed Eng. 2017. can be used as diagnostic markers and/or preventive and therapeutic targets to guide precision medicine for patients • Chen, Z.*, Wen, L., Martin, M., Hsu, C.Y., Fang, L., Lin, F.M., with cardiovascular disorders and cancer. Lin, T.Y., Geary, M.J., Geary, G., Zhao, Y., Johnson, D.A., Chien, S., Huang, H.D., Miller, Y.I., Huang, P.H., and Shyy, Our ongoing projects include: J.Y. Oxidative stress activates endothelial innate immunity • miRNA-mediated crosstalk between endothelium and through SREBP2 transactivation of miR-92a. Circulation. adipose tissue in obesity and diabetes 2015. (*co-corresponding) • lncRNAs and chromatin remodeling in endothelial • Cooke, J.P., and Chen, Z. A Compendium on Peripheral dysfunction and diabetic complicatiions Arterial Disease. Circ Res. 2015. • Chemotoxic drug-modulated transcriptome and epigenome in endothelial-mesenchymal transition and pulmonary fibrosis
44 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Warren Chow, M.D. Clinical Professor, Department of Medical Oncology & Therapeutics Research
CELL SIGNALING AND CANCER
Our laboratory is pursuing three different cancer-focused SELECTED PUBLICATIONS research projects. Firstly, we are interested in studying the • Guan, M., Fousek, K., Jiang, C., Guo, S,. Synold, T., Xi, B., epigenetic changes related to the “lipogenic phenotype” of Shih, C-C., and Chow, W.A. Nelfinavir induces liposarcoma cancer. Here, cancers develop adipogenic-like properties, apoptosis through inhibition of regulated intramembrane and generate excess fatty acids and lipids for membrane proteolysis of SREBP-1 and ATF6. Clin Cancer Res biosynthesis and lipid-based protein modifications. We 2011;17:1796-1806. have shown a substantial link between acquisition of the “lipogenic phenotype” and epigenetic dysregulation in • Pan, J., Mott, M., Xi, B., Hepner, E., Guan, M., Fousek, K., cancers. Secondly, we have identified several genes that Magnusson, R., Tinsley, R., Valdes, F., Frankel, P., Synold, T., are up- and downregulated in rare subtypes of carcinomas, and Chow, W.A. Phase I study of nelfinavir in liposarcoma. called carcinosarcomas, which we believe are important in Cancer Chemo Pharm 2012;70:791-9. the epithelial-to-mesenchymal transition (EMT). We are • Guan, M., Fousek, K., and Chow, W.A. Nelfinavir inhibits investigating the function of these genes in EMT transition. regulated intramembrane proteolysis of SREBP-1 and ATF6 in Finally, we are developing novel pediatric translocation castration-resistant prostate cancer. FEBS J 2012;279:2399- associated sarcoma mouse models using the considerable 411. power of newer gene-editing techniques to study • Zhang, K., Chu, K., Wu, X., Gao, H., Wang, J., Yuan, Y,C., sarcomagenesis and novel therapeutics. Loera, S., Ho, K., Wang, Y., Chow, W., Un, F., Chu, P., and Yen, Y. Amplification of FRS2 and Activation of FGFR/FRS2 Signaling Pathway in High-Grade Liposarcoma. Cancer Res. 2013;73:1298-307.
• Eroglu, Z., Tawbi, H.A., Hu, J., Guan, M., Frankel, P.H., Ruel, N., Wilczynski, S., Christensen, S., Gandara, D.R., and Chow, W.A. A randomized phase II trial of AZD6244 alone and AZD6244 plus temsirolimus for soft-tissue sarcomas. Br J Cancer 2015;112:1644-1651.
• Guan, M., Su, L., Yuan, Y-C., Li, H., and Chow WA. Nelfinavir and its analogs inhibit proliferation of castration-resistant prostate cancer through inhibition of sit-2 protease cleavage. Scientific Rep. DOI: 10.1038/srep09698, 2015.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 45 Jessica Clague DeHart, Ph.D., M.P.H. Assistant Professor, Divisions of Biomarkers of Early Detection and Prevention
IDENTIFYING MOLECULAR MECHANISMS OF EXERCISE FOR CANCER PREVENTION, SURVIVORSHIP AND NUTRITION
Exercise and breast cancer in the U.S., yet there are no published exercise trials combining Exercise is the single most modifiable factor for decreasing quality-of-life data with molecular markers for ovarian cancer breast cancer development and recurrence. Among patients. Currently, the standard treatment is aggressive epidemiologic studies, exercise reduces risk of invasive surgical debulking followed by chemotherapy. Even with recent breast cancer by 20 to 40 percent. Despite the wealth of improvements, this regime fails to produce remission in over epidemiologic data showing an inverse association between 70 percent of patients with ovarian cancer. Further, patients exercise and breast cancer development, we do not understand report severe side effects, including nausea, vomiting, swelling the molecular mechanisms that account for this association. in the extremities, peripheral neuropathy and fatigue, all causing Without this knowledge, we cannot develop a prescription of a substantial decline in quality of life. The evidence that exercise recommendations identifying the optimal duration and intensity could decrease treatment-related symptoms and influence of activity needed to achieve a benefit. clinical outcomes for other cancers indicates that well-designed exercise trials for ovarian cancer patients are sorely needed. Our team of epidemiologists, molecular biologists and oncologists is conducting intervention trials to assess the Therefore, we are investigating the impact of exercise effects of exercise on molecular mechanisms among women “prehabilitation” on DNA repair mechanisms — known to be prior to or who have had breast cancer. Our goal is to identify targeted by platinum therapy — among ovarian cancer patients the minimum dose of exercise necessary to elicit biological currently on treatment. Women randomized to the exercise effects in order to develop tailored recommendations that not regimen have one-on-one training with physical therapists only prevent disease but are feasible for the average woman before each platinum therapy session. We hope to show that to maintain. exercise before therapy not only increases quality of life, but decreases negative side effects and symptoms related to In our Curves exercise study, postmenopausal breast cancer treatment and increases the treatments effectiveness. survivors are randomized to either 16 weeks of exercise at a community based exercise facility or 16 weeks of no exercise Nutrition and breast cancer survivorship (control arm). Four molecular mechanisms are investigated: Breast cancer survivors have a high prevalence of metabolic DNA repair capacity, circulating cytokines and chemokines, dysfunction — characterized by high glucose levels and weight telomerase activity and RNA-seq. These mechanisms are gain. Regardless of menopausal status, overweight and obese hypothesized to perform more favorably after 16 weeks of women are at increased risk for developing breast cancer and exercise training, thus giving some insight into how exercise those who are diagnosed with breast cancer experience adverse may be preventing breast cancer recurrence. cancer-related outcomes. The underlying principle of the Pancreatic Nutrition Program is that bio-individualized healthy In a second eight-month study, women with no history of food choices — eating the correct foods and food combinations cancer or diabetes are randomized to one of four community- for an individual’s body — can minimize fluctuations in insulin based exercise programs — walking, Curves, Zumba and by keeping blood glucose regulated (70-100 mg/dL) and this CrossFit — for four months. Then, the same molecular will promote sustained weight loss, improved health and quality mechanisms are measured as above in order to compare of life. baseline levels between women with and without a history of cancer. Changes in molecular levels over the four-month Our six-month “Pancreatic Nutrition Program (PNP): A Novel intervention are compared between exercise groups. For the Weight Reduction Program for Breast Cancer Survivors” additional four months, women get to choose their exercise study aims to test the effect of the PNP on weight loss, program and we will compare results/adherence between glucose, insulin resistance, body composition, body chemistry, randomization and choice. physical fitness, inflammation and quality of life. Through the comparison of real-time glucometer data and food journals, Exercise and ovarian cancer nutrition plans are individualized to regulate glucose levels. Exercise is an under-used and under-encouraged area of treatment for patients with ovarian cancer. Epithelial ovarian cancer is the leading cause of gynecologic cancer death and the fifth most common cause of cancer mortality among women
46 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Sangeeta Dhawan, Ph.D. Assistant Professor, Department of Translational Research and Cellular Therapeutics and Department of Diabetes Complications and Metabolism
EPIGENETIC REGULATION OF BETA CELLS IN HEALTH AND DIABETES. DEVELOPMENTAL AND REGENERATIVE BIOLOGY
The lab of Sangeeta Dhawan, PhD., focuses on understanding chromatin structure. Loss of CTCF in beta cells leads to their the biology of insulin producing beta cells. Both type 1 and apoptosis, resulting in a deficit of beta-cells and ultimately type 2 diabetes are associated with the loss of beta cells, causing diabetes in mice. The accompanying photo shows a making the replenishment of beta cells a critical therapeutic severe loss of beta cells in the CTCF knockout mice compared goal. Approaches to this end include generating beta cells to controls. from stem cells, as well as protecting and regenerating the Epigenetic dysregulation in diabetic beta cells endogenous beta cells. The successful outcome of each Our work shows that of these approaches demands the generation of abundant diabetic beta cells lose numbers of functional beta cells that are survival competent their fully differentiated in the diabetic milieu. In pursuit of this goal, we study the characteristics and begin epigenetic mechanisms that regulate the formation, function, to resemble fetal beta regeneration and survival of pancreatic beta cells during cells (which are not yet development, and under circumstances that warrant the completely differentiated). repair/regeneration of beta cells. Equally important, we are We recently made the exciting discovery that diabetic dedicated to understanding the mechanistic changes that beta cells undergo profound changes in their epigenetic are responsible for the failure of beta cells in diabetes. Our landscape, which propel the disruption of beta cell function motivation to determine the epigenetic regulation of beta-cells and identity, thus recapitulating a few specific hallmarks of comes from the central role that a cell’s environment plays in fetal beta cells. Case in point, there is a severe loss of DNA shaping its behavior; and epigenetic mechanisms serve as the hydroxymethylation (hmC), an epigenetic signature related primary means by which a cell changes its gene expression to to DNA methylation, in the diabetic beta cells (accompanying adapt to changes in the cellular environment. The following photo). These studies provide novel clues towards examples illustrate the critical role of epigenetic mechanisms understanding diabetes pathogenesis. in keeping beta cells healthy. SELECTED PUBLICATIONS DNA methylation: the epigenetic safeguard of beta cells identity and function • Rodnoi, P., Rajkumar, M., Md Moin, A.S., Georgia, S.K., Butler, A.E., and Dhawan, S. Neuropeptide Y expression marks Beta cells need intact partially differentiated beta-cells in mice and humans. JCI DNA methylation, a key Insight. 2017; 2(12). epigenetic mechanism, to express and secrete • Dhawan, S., Dirice, E., Kulkarni, R.M., and Bhushan, A. Inhibition of TGF-β Signaling Promotes Human Pancreatic insulin in response to β-Cell Replication. Diabetes. 2016; 65(5):1208-18. glucose. We have shown that loss of specific enzymes either establish or maintain DNA • Dhawan, S., Dirice, E., Kulkarni, R.M., and Bhushan, A. (2015) DNA methylation directs functional maturation. Of methylation (DNA methyltransferases, DNMTs) in beta cells, pancreatic beta cells. Journal of Clinical Investigation. 125(7): can lead them to lose their function, or result in the conversion 2851-2860. of beta cells into alpha cells (which make glucagon). The • Zhou, X., Dhawan, S., Fu H., Kundu, S., Kim, S.K., and picture above shows that beta-cells are replaced by alpha cells Bhushan, A. (2013) Polycomb and trithorax regulation of in the DNMT knockout. Ink4a to regenerate beta cells. Journal of Clinical Investigation. Epigenetic regulation of 123 (11): 4849-4858. beta cell survival • Papizan, J.B., Singer, R.A*., Tschen, S.I.*. Dhawan, S*., Friel, We recently found a novel J.M., Hipkins, S.B., Magnuson, M.A., Bhushan, A., and Sussel., regulator of beta cell L. (2011) Nkx2.2 repressor complex regulates islet beta cell survival, CTCF, which is an specification and prevents beta to alpha cell reprogramming. epigenetic regulator of 3D Genes and Development. 25(21): 2291-2305.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 47 Don J. Diamond, Ph.D. Professor, Department of Immuno-Oncology
TRANSLATIONAL RESEARCH IN CANCER VACCINES
The Diamond Laboratory is developing therapeutic and vaccine ConVax, is a highly innovative construct expressing seven strategies to combat hematologic malignancy (HM), solid different CMV antigens that has already been tested in mice tumors and herpes viruses. A comprehensive program of and shown strong neutralizing antibodies stimulation. Helocyte developing molecular vaccines is ongoing using peptide, viral Inc. will fund studies that bring us to the point where we are in a and bacterial vectors. Mouse models of HM and pancreatic position to file an investigational new drug application with the adenocarcinoma are being used to evaluate our strategies for Food and Drug Adminstration. clinical application. We are pursuing a novel approach that IDO Pathway Inhibition – Indoleamine 2,3-deoxygenase is an uses attenuated salmonella encoding a short hairpin RNA to important immunosuppressive molecule that tumors and the decrease the expression of molecules contributing to tumor endogenous immune system express, defeating the ability of rejection and controlling metastasis. the immune response to eliminate the tumor. Our laboratory MVA as a platform for vaccine delivery developed an approach to silence the IDO protein expression p53 — We are using a vaccine delivery platform that is based using an shRNA. We found that salmonella is a convenient on a highly attenuated virus referred to as modified vaccinia and efficient platform for its delivery into tumors, yet it can be Ankara or MVA. This crippled virus was developed in Europe administered systemically making it a very versatile therapeutic. in the 1970s as a safer alternative to the licensed vaccine for Using bioluminescent pancreatic cancer models, we are able to smallpox infection. We have successfully immunized advanced employ advanced imaging techniques to follow our therapeutic cancer patients with the clinical-grade viral vaccine, and strategies in which our salmonella vector is combined with a continue to dose-escalate and investigate immune correlates proprietary adjuvant that causes remarkable complete rejection of protection and determine if the vaccine controls disease of transplantable tumors. We are also developing a mouse progression. We are conducting pilot phase 1b clinical trials to model using the CRISPR-Cas technology that will be a valuable test efficacy of the vaccine as a multimodal therapy with new tool to study human IDO expression modulated by an shRNA immunologic checkpoint inhibitors. We are starting a clinical specific for the human protein. When completed, it will be a trial in advanced ovarian cancer combining the p53 MVA unique translational advance for this therapeutic strategy to be vaccine with pembroluzimab (anti-PD1). The vaccine combined evaluated in the clinic in cancer patients. with pembrolizumab (anti-PD1) caused a complete pathologic dermal response in an end stage triple negative breast cancer SELECTED PUBLICATIONS patient. Her story can be viewed in the following newscasts: • La Rosa, C., Longmate, J., and Martinez, J., et al. MVA vaccine http://losangeles.cbslocal.com/2016/12/27/ground-breaking-breast- encoding CMV antigens safely induces durable expansion of cancer-drug-gives-terminally-ill-woman-a-chance-to-survive/ CMV-specific T cells in healthy adults. Blood 129(1):114-125, 2017. PMID: 27760761 http://abc7.com/health/woman-battling-breast-cancer-gets- miracle-treatment-from-city-of-hope/1656854/ • Chiuppesi, F., Kaltcheva, T., Zhuo, M., Barry, P.A., Diamond, D.J., and Wussow, F. Identification of a continuous CMV — We have approval from the National Cancer Institute neutralizing epitope within UL128 of human cytomegalovirus. to produce clinical-grade MVA vaccine targeting the herpes J Virol 91(6):e01857-16, doi: 10.1128/JVI.01857-16, 2017. virus cytomegalovirus (CMV), a major post-transplant PMID: 28077639. complication of leukemia and lymphoma patients. We are producing this molecular vaccine in the City of Hope clinical • Hardwick, N., Frankel, P., Ruel, C. Kilpatrick, J., Tsai, W., Kos, manufacturing facility. We initiated vaccinating transplant F., Kaltcheva, T., Leong, L., Morgan, R., Tinsely, R., Eng, M., recipients in 2015 and full accrual occurred in the fourth quarter Ellenhorn, J., Diamond, D.J., and Cristea, M.A. Phase 1 study of 2017. Data will be unblinded in the fourth quarter of 2018. of p53MVA vaccine and gemcitabine in platinum-resistant epithelial ovarian cancer: Safety and assessment of clinical Congenital CMV — A new human CMV vaccine to prevent benefit associated with p53-reactive T cells. Clin Cancer Res, congenital infection is being developed with support from a 3/15/2018; 24(6):1315-1325, PMID: 29301826. four-year National Institutes of Health grant and the start- up company, Helocyte Inc., of which City of Hope and the Diamond lab have equity stakes. The new vaccine, coined
48 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Richard W. Ermel, D.V.M., M.P.V.M., Ph.D. Professor and Director, Center for Comparative Medicine Director, Animal Resources Core Director, Animal Care Program Director, Residency and Graduate Training Program in Laboratory Animal Medicine COMPARATIVE MEDICINE
The Center for Comparative Medicine (CCM), an academic Collaborative research to determine the anti-cancer potential and clinical center within Beckman Research Institute of of readily available and affordable natural compounds alone City of Hope, is delegated the oversight of all animal care and in combination using cell culture, xenograft rodent models, and use at City of Hope and Beckman Research Institute. The and comparative oncology (canine clinical trials) methods and CCM contributes to the City of Hope and Beckman Research approach. The primary research objective is to determine the Institute research missions by: providing excellent quality anti-cancer effects of cardiac glycosides and related compounds and humane animal care; providing comparative medicine, on human and canine cancers in cell culture assays and rodent laboratory animal science and veterinary medicine expertise xenograft models and to evaluate their therapeutic potential. through teaching and consultation; promoting animal welfare Collaborative research on the effect of novel inhibitors of and improving the quality and integrity of animal based advanced glycation endpoint (AGE) to prevent arterial biomedical and translational research; and by fulfilling the stiffening and improve arterial elasticity and compliance in a CCM mission, advancing animal and human health through streptozotocin (STZ)-induced diabetic Sprague Dawley rat excellent service, education and research with compassion and model. The primary research objective is to determine the respect for all species. effect of AGE inhibitors on the mechanical properties of the The CCM consists of academic programs (graduate and arterial system in STZ-induced diabetic Sprague Dawley rats professional teaching programs, residency and graduate based on the aortic input impedance analysis. training program in laboratory animal medicine, and Collaborative research on the oral administration of antibiotics independent and collaborative research programs) and animal and analgesics in rodents. The primary research objective is to model shared resources/cores/programs which provide determine the effect of antibiotic and analgesic compounding technical expertise and services. The City of Hope and and administration of different formulations in rodents. Beckman Research Institute CCM laboratory animal care and use program is accredited by the Association for Assessment Collaborative research to develop new diagnostic techniques and Accreditation of Laboratory Animal Care International, for infectious diseases of laboratory animals. The primary approved by the National Institutes of Health Office of research objective is to develop service-directed applied Laboratory Animal Welfare and registered by the United States diagnostic and clinical pathology research in conjunction Department of Agriculture. The CCM research mission is to with the initiation of an in-house rodent diagnostic/clinical engage in collaborative and independent service-directed pathology laboratory. applied research in laboratory animal science and comparative medicine. Areas of research emphasis include: development of SELECTED PUBLICATIONS new biomodels (animal models of human disease), refinement • Finlay, J., Liu, X., Ermel, R., and Adamson, T. Maternal weight of laboratory animal research environments and techniques, gain as a predictor of litter size in Swiss Webster, C57BL/6J, study of spontaneous and induced animal diseases and/ and BALB/cJ mice. JAALAS 54 (6):694-699, 2015. or zoonotic diseases (diseases transmitted from animals • Satheesan, S., Figarola, J., Dabbs, T., and Ermel, R.W. Effects to humans), development of new diagnostic techniques for of a new advanced glycation inhibitor, LR-90, on mitigating infectious/immune mediated diseases, and development of arterial stiffening and improving arterial elasticity and therapeutic protocols/intervention and prevention strategies compliance in a diabetic rat model: aortic impedance for animal and human diseases. analysis. British J. Pharmacol. 171: 3103-3114, 2014. Recent research projects have included the following: • Chomel, B.B., Ermel, R.W., Kasten, R.W., Henn, J.B., Fleischman, D.A., and Chang, C. Experimental infection of Collaborative research to determine the effects of the dogs with various Bartonella species or subspecies isolated microbiome on health and disease using rodent models and from their natural reservoir. Vet. Microbiol. 168: 169-176, naked mole rat model. The primary objective is to advance the 2014. understanding of the microbiome in health and disease.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 49 Mingye Feng, Ph.D. Assistant Professor, Department of Immuno-Oncology
MACROPHAGE-MEDIATED TUMOR IMMUNOSURVEILLANCE IN CANCER DEVELOPMENT AND METASTASIS
The ability to escape from surveillance by the immune system SELECTED PUBLICATIONS is regarded as one of the essential hallmarks of cancer cells. • Weiskopf, K., Schnorr, P.J., Pang, W.W., Chao, M.P., Chhabra, While the functions of lymphocytes (T, B and NK cells) in tumor A., Seita, J., Feng, M., and Weissman, I.L. Myeloid Cell immunosurveillance have been studied for decades, the roles Origins, Differentiation, and Clinical Implications, Microbiol of macrophages on tumor cell elimination have only begun to Spectr, 2016 Oct; 4(5). be explored. Macrophages detect and eliminate tumor cells via a process of macrophage-mediated cell phagocytosis called • Feng, M., Chen, J.Y., Weissman-Tsukamoto, R., Volkmer, “programmed cell removal” (PrCR). Recent studies showed J.P., Ho, P.Y., McKenna, K.M., Cheshier, S., Zhang, M., Guo, that blockade of a “don’t eat me” signal CD47 on malignant N., Gip, P., Mitra, S.S., and Weissman, I.L. Macrophages eat hematopoietic and various solid tumor cells enabled their cancer cell using their own calreticulin as a guide: roles of phagocytosis by macrophages and prevented their engraftment TLR and Btk, Proc Natl Acad Sci USA, 2015 Feb 17; 112(7): in mice lacking T, B and NK cells, indicating a key role of 2145-50. macrophages in tumor surveillance and elimination. While • Feng, M., and Rao, R. New insights into store-independent inducing macrophage-mediated immunosurveillance holds Ca2+ entry: secretory pathway calcium ATPase in normal considerable promise for the treatment of various cancers, its physiology and cancer. Int J Oral Sci, 2013 Jun; 5 (2): 71-4. underlying mechanism remains largely unknown. • Leitch, S*, Feng, M.*, Muend, S., Braiterman, L.T., Hubbard, My laboratory is focused on three fundamental questions: A.L., and Rao, R. Vesicular distribution of Secretory Pathway First, how do macrophages recognize tumor cells and target Ca2+-ATPase isoform1 (SPCA1) and a role in manganese them for phagocytosis? Second, at different stages of cancer detoxification in liver-derived polarized cells, Biometals, 2011 development, do macrophages exert multiple layers of extrinsic Feb; 24 (1): 159-70. (*equal contribution) PrCR pressure to tumor cells and how do tumor cells react and develop self-protective mechanisms? Third, what are the • Feng, M., Grice, D.M., Faddy, H.M., Nguyen, N., Leitch, S., intrinsic regulatory programs in macrophages that regulate their Wang, Y., Muend, S., Kenny, P.A., Sukumar, S., Roberts- functions in PrCR? Thomson, S.J., Monteith, G.R., and Rao, R. Store-independent Our overall objective is to combine in vitro and in vivo activation of Orai1 by SPCA2 in mammary tumors, Cell, 2010 approaches to explore the underlying mechanisms of Oct 1; 143 (1): 84-98. macrophage-mediated immunosurveillance and its therapeutic • Xiang, M., Feng, M., Muend, S., and Rao, R. A human Na+/ potential. The identification and understanding of such H+ antiporter sharing evolutionary origins with bacterial important mechanisms should shed light on the basic NhaA may be a candidate gene for essential hypertension. mechanisms of tumor cell immune evasion, and enable the Proc Natl Acad Sci USA. 2007 Nov 20; 104 (47): 18677-81. development of novel anti-cancer immunotherapies.
50 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Yuman Fong, M.D., D.Sc. (Hon) The Sangiacomo Family Chair in Surgical Oncology Professor and Chair, Department of Surgery
TARGETING CANCER USING GENETICALLY MODIFIED VIRUSES
The laboratory of Yuman Fong, M.D., D.Sc. (Hon), and Nanhai SELECTED PUBLICATIONS Chen, Ph.D., the Heritage Provider Network Professor in Gene • Bennett, J.J., Tjuvajev, J., and Johnson, P., et al. Positron Therapy, studies the use of genetically modified viruses for emission tomography imaging for herpes virus infection: the killing of cancer. Fong was one of the first investigators Implications for oncolytic viral treatments of cancer. Nat to administer engineered viruses into the blood stream of Med. Jul 2001;7(7):859-863. humans for treatment of cancer. He is active at coordinating trials of such novel viruses. His group has also studied many • Jun, K.H., Gholami, S., and Song, T.J., et al. A novel oncolytic non-invasive methods of imaging and tracking viral vector for viral therapy and imaging technique for gastric cancer using use in clinical trials, including optical and positron emission a genetically engineered vaccinia virus carrying the human tomography imaging. sodium iodide symporter. Journal of Experimental & Clinical Cancer Research. Jan 02 2014;33:2. Since coming to the City of Hope in 2014, the Fong-Chen laboratory has generated new families of chimeric viruses • Gholami, S., Chen, C.H., and Lou, E., et al. Vaccinia virus GLV- (hope oncolytic viruses, HOVs) for preclinical studies with the 1h153 in combination with 131I shows increased efficiency goal of taking a number of these into human clinical trials. In in treating triple-negative breast cancer. FASEB J. Feb particular, Fong’s group is working on novel viruses with much 2014;28(2):676-682. increased tropism, potency and specificity in killing chemo- and radio-therapy resistant tumors. They have armed many • Gholami, S., Chen, C.H., and Belin, L.J., et al. Vaccinia virus of these viruses with additional payload, such as the ability to GLV-1h153 is a novel agent for detection and effective local locally produce check point inhibition and to synergize with control of positive surgical margins for breast cancer. Breast viral oncolysis in cancer killing while decreasing systemic auto- Cancer Research. Mar 18 2013;15(2):R26. immune adverse effects. • Ady, J.W., Desir, S., and Thayanithy, V., et al. Intercellular communication in malignant pleural mesothelioma: properties of tunneling nanotubes. Frontiers in Physiology. 2014;5:400.
• Ady, J.W., Heffner, J., and Mojica, K., et al. Oncolytic immunotherapy using recombinant vaccinia virus GLV-1h68 kills sorafenib-resistant hepatocellular carcinoma efficiently. Surgery. Aug 2014;156(2):263-269.
• Gholami, S., Chen, C.H., and Gao, S., et al. Role of MAPK in oncolytic herpes viral therapy in triple-negative breast cancer. Cancer Gene Ther. Jul 2014;21(7):283-289.
• Warner, S.G., Haddad, D., and Au, J., et al. Oncolytic herpes simplex virus kills stem-like tumor-initiating colon cancer cells. Molecular Therapy Oncolytics. 2016;3:16013.
• Kelly, K.J., Wong, J., and Gonen, M., et al. Human Trial of a Genetically Modified Herpes Simplex Virus for Rapid Detection of Positive Peritoneal Cytology in the Staging of Pancreatic Cancer. EBioMedicine. May 2016;7:94-99.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 51 Stephen J. Forman, M.D. Francis & Kathleen McNamara Distinguished Chair in Hematology and Hematopoietic Cell Transplantation Director, T Cell Therapeutics Research Laboratory
T CELL IMMUNOTHERAPY FOR TREATMENT OF CANCER
Harnessing the power and specificity of the immune system to At this time, our novel preclinical research has been translated directly target and eliminate malignant disease is emerging as to ongoing phase 1 clinical trials in patients with glioblastoma, a promising clinical approach. Our laboratory is focused on the breast cancer, leukemia and lymphoma. development of antigen-specific adoptive T cell immunotherapy for the treatment of cancer by the use of T cells that have SELECTED PUBLICATIONS been genetically modified to express a chimeric antigen • Wang, X., Walter, M., Urak, R., Weng, L., Huynh, C., Lim, receptor (CAR, see figure) which allows for the targeting of L., Wong, C.W., Chang, W.C., Thomas, S.H., Sanchez, J.F., antigens on tumor cells in an HLA independent manner. The Yang, L., Brown, C.E., Pichiorri, F., Htut, M., Krishnan, A.Y., laboratory is studying ways to enhance the ability of CAR+ and Forman, S.J. Lenalidomide Enhances the Function of T cells to recognize tumor CS1 Chimeric Antigen Receptor-Redirected T Cells Against cells in patients, mediate Multiple Myeloma. Clin Cancer Res. 1;24(1):106-119, 2018. an anti-tumor response and • Priceman, S.j., Tilakawardane, D., Jeang, B., Aguilar, B., Tumor become part of the adaptive Murad, J.P., Park, A.K., Chang, W.C., Ostberg, J.R., Neman, J., Targeting immune system, resulting Jandial, R., Portnow, J., Forman, S.J., and Brown, C.E. Regional Domain in an ongoing anti-tumor Delivery of Chimeric Antigen Receptor-Engineered T Cells response. Our focus has been Effectively Targets HER2+ Breast Cancer Metastasis to the Brain. Clin Cancer Res. 1;24(1):95-105, 2018. on genetically engineering T cells that can recognize B • Priceman, S.J., Gerdts, E.A., Tilakawardane, D., Kennewick, cell malignancies (CD19), K.T., Murad, J.P., Park, A.K., Jeang, B., Yamaguchi, Y., Yang, and myeloid leukemias (IL-3 X., Urah, R., Weng, L., Chang, W.C., Wright, S., Pal, S., receptor), as well as solid Reiter, R.E., Wu, A.M., Brown, C.E., and Forman, S.J. Co- stimulatory signaling determines tumor antigen sensitivity tumors such as glioblastoma and persistence of CAR T cells targeting PSCA+ metastatic multiforme (IL-13Rα2 and prostate cancer. Oncoimmunology. 16;7(2):e1380764, 2017. HER2), breast cancer (HER2), T cell prostate cancer (PSCA), and • Brown, C.E., Alizadeh, D., Starr, R., Weng, L., Wagner, J.R., “KILL” ovarian cancer (TAG-72). Naranjo, A., Ostbert, J.R., Blanchard, M.S., Kilpatrick, J., Simpson, J., Kurien, A., Priceman, S.J., Wang, X., Harshbarger, Signal In addition to developing T.L., D’Apuzzo, M., Ressler, J.A., Jensen, M.C., Barish, M.E., T cell-based therapies Chen, M., Portnow, J., Forman, S.J., and Badie, B. Regression for treatment of human disease, our laboratory conducts of Glioblastoma after Chimeric Antigen Receptor T-Cell experiments focused on understanding the impact of the tumor Therapy. N Engl J Med. 29;375(26):2561-9, 2016. microenvironment on T cell function and persistence. This has • Jonnalagadda, M., Mardiros, A., Urak, R., Wang, X., Hoffman, been accomplished by further genetic modification of the T L.J., and Bernanke, A., et al. Chimeric antigen receptors cells or combining them with other therapeutic strategies that with mutated IgG4 Fc spacer avoid Fc receptor binding and reduce the immunosuppressive environment and facilitate the improve T cell persistence and anti-tumor efficacy. Mol. Ther. effectiveness of adoptively transferred antigen-specific cells. 23:757-768, 2015. Our lab continues to conduct studies to determine the optimal • Mardiros, A., Dos Santos, C., McDonald, T., Brown, C.E., T cell population for use in adoptive therapy. One T cell Wang, X., and Budde, L.E., et al. T cells expressing CD123- population of interest, comprised of naive and memory T cells specific chimeric antigen receptors exhibit specific cytolytic (Tn/mem), is intrinsically programmed for persistence following effector functions and antitumor effects against human acute myeloid leukemia. Blood 122: 3138-3148, 2013. adoptive transfer and is capable of repopulating functional immunologic memory. We have thus developed a GMP • Prosser, M.E., Brown, C.E., Shami, A.F., Forman, S.J., and manufacturing platform, involving the isolation of Tn/mem cells, Jensen, M.C. Tumor PD-L1 co-stimulates primary human lentiviral transduction to direct CAR expression, and expansion CD8(+) cytotoxic T cells modified to express a PD1:CD28 to clinically relevant cell numbers for adoptive transfer chimeric receptor. Mol. Immunol. 51: 263-272, 2012. to humans.
52 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Patrick T. Fueger, Ph.D. Associate Professor, Department of Molecular and Cellular Endocrinology Director, Comprehensive Metabolic Phenotyping Core
RESTORATION OF GLUCOSE HOMEOSTASIS BY FORTIFYING FUNCTIONAL BETA CELL MASS
The mission of the the laboratory of Patrick Fueger, Ph.D., In addition to our work in the beta cell, we have been is to identify molecular mechanisms regulating glucose investigating how Mig6 in the liver contributes to the homeostasis during health and disease (e.g., diabetes). In the pathogenesis of type 2 diabetes and fatty liver disease. We healthy state, glucose homeostasis is primarily maintained have identified that mice lacking hepatic Mig6 have improved by the intricate balance of the glucoregulatory hormones glucose homeostasis during obesity and decreased hallmarks insulin and glucagon. Type 1 diabetes mellitus results from of fatty liver disease. the autoimmune destruction of pancreatic beta cells, which produce insulin. Currently, the only available cure for type SELECTED PUBLICATIONS 1 diabetes is pancreatic or islet transplantation. A primary • Chen, Y.C., Colvin, E.S., Griffin, K.G., Maier, B.M., and Fueger, limitation of these bona fide cures is the limited availability P.T. Mig6 haploinsufficiency protects against chemically- of pancreata and pancreatic islets from cadaver donors. induced diabetes, Diabetologia, 57(10):2066-75, 2014. Moreover, islet transplants are compromised by the rapid decline in beta cell mass that occurs immediately following • Chen, Y.C., Colvin, E.S., Maier, B.F., Mirmira, R.G., and transplantation. Because of this bottleneck in islet availability, Fueger, P.T. Mitogen inducible gene 6 triggers apoptosis much work has been performed with the goal of finding and exacerbates ER stress-induced beta cell death. Mol an alternative source of insulin-producing cells as well as Endocrinol, 27:62-171, 2013. establishing methods to stimulate proliferation of islets • Colvin, E.S., Ma, H.Y., Chen, Y.C., Hernandez, A.M., and harvested for transplantation. The focus of my research Fueger, P.T. Glucocorticoid-induced suppression of beta program addresses the critical need to establish methods to cell proliferation is mediated by Mig6. Endocrinology, increase functional pancreatic islet mass. 154(3):1039-1046, 2013 The projects currently being conducted in the laboratory are directed toward identifying novel beta growth factors, elucidating their signaling pathways, and translating these discoveries into animal transplantation and/or beta cell expansion models. In addition, we are attempting to minimize deficits in functional beta cell mass that occur in diabetes by abrogating cell death and boosting cellular repair mechanisms within the beta cells themselves. We are particularly interested in feedback control mechanisms and how these pathways become dysregulated during diabetes. Recently, we have been examining the endogenous EGF receptor feedback inhibitor Mig6 (aka. errfi1, Gene 33, or RALT). Interestingly, Mig6 is induced in beta cells by the milieu of both type 1 and type 2 diabetes, where it suppresses cellular proliferation, survival and repair mechanisms. We are actively investigating the extent to which suppressing the expression or function of Mig6 can prevent and/or rescue animal models from both major forms of diabetes.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 53 Carlotta A. Glackin, Ph.D. Associate Professor, Department of Developmental and Stem Cell Biology
UNDERSTANDING GENE REGULATION FROM STEM CELLS
The long-term objectives of my laboratory are to understand 1) filling a much needed gap in understanding of how Twist1 the basic molecular mechanisms underlying the functional promotes EMT and invasive properties of drug resistant breast properties of TWIST1 in cancer cells and to develop novel and ovarian cancer stem cells; 2) enabling further development TWIST1 inhibitors and screening tools for targeting TWIST1 of RNAi-based gene silencing therapeutics for a variety of in breast and ovarian cancer models. We and others have transcription factor targets for breast and ovarian cancers; published extensive studies addressing the EMT process and 3) potentially leading to a novel siTwist-based therapy (epithelial-mesenchymal transition) and the functional for breast cancer and EOC that would significantly improve role of TWIST in cancer cell invasion, angiogenesis and survival of cancer patients. metastasis. TWIST1-mediated regulation of downstream target genes, including SLUG and SNAIL, has been shown to SELECTED PUBLICATIONS correlate with EMT and chemotherapy resistance in breast • Roberts, C.M., Loeza, J., Dellinger, T., Williams, J.C., and cancer. Knockdown of SNAIL and SLUG results in increased Glackin C.A. Disruption of TWIST1-RELA binding by sensitivity of tumor cells to chemotherapy accompanied by mutation and competitive inhibition to validate the TWIST1 a reduction in the invasive phenotype, suggesting that the WR domain as a therapeutic target, BMC Cancer (2017) pathways activating EMT may be shared with those that confer 17:184DOI 10.1186/s12885-017-3169-9 chemotherapy resistance. Drug-resistant breast cancer cells pose a particularly difficult challenge to treatment because • Roberts, C.M., Lowe, G., Finlay, Tamanoi, F., Zink, J., Dellinger, they are chemoresistant and often metastasize. Targeting EMT T., and Glackin, C.A. HYPERLINK “https://www.ncbi.nlm.nih. by inhibiting TWIST in this population of breast cancer cells gov/pubmed/27890656” Nanoparticle delivery of siRNA may therefore sensitize them to further drug treatment. against TWIST to reduce drug resistance and tumor growth in ovarian cancer models.Nanomedicine. 2016 Nov 25. pii: We are developing TWIST1 inhibitors as therapeutic agents S1549-9634(16)30202-7. doi: 10.1016/j.nano.2016.11.010. for treating breast cancer by using a gene silencing approach [Epub ahead of print] PMID:27890656 using nanoparticles developed by our collaborators in the Rossi group at City of Hope, and in collaboration with Dr. • Roberts, C.M., Tran, M.A., Pitruzzello, M.C., Wen, W., Loeza, Ling Peng (director, Centre Interdisciplinaire de Nanoscience J., Dellinger, T., Mor, G., and Glackin, C.A. TWIST1 drives de Marseille, France), using Poly Amido Amine dendrimers, cisplatin resistance and cell survival in an ovarian cancer as well as nanoparticle approaches developed by our model, via upregulation of GAS6, L1CAM, and Akt signalling” collaborators at UCLA, Drs. Jeff Zink and Fuyu Tamanoi Scientific Reports 2016 Nov 23;6:37652. doi: 10.1038/ using Mesoporous silica nanoparticles as efficient delivery srep37652.PMID:27876874 vehicles for anti-cancer drugs and molecular cargo. This year, • Wen, W., Lowe, G., Roberts, C.M., Finlay, J., Han, E.S., my group has developed a novel mRNA inhibitor therapy, Glackin, C.A., and Dellinger, T.H. Pterostilbene, a natural MSN-HA-siTWIST, against TWIST protein, delivered by phenolic compound, synergizes the antineoplastic effects nanoparticle carriers targeting cancer stem cells (CSC) to of megestrol acetate in endometrial cancer. Sci Rep. 2017 reverse chemoresistance. When combined with standard Oct 6;7(1):2754. doi: 10.1038/s41598-017-12922-2. therapy it significantly improves survival in drug-resistant PMID:28986550 ovarian and breast cancer patients. It is the first and only therapy to: 1) target and silence TWIST, the master regulator • Camp-Dotlic, E., Zannettino, A., Glackin, C., and of EMT, and thus inhibit metastasis and angiogenesis; 2) Gronthos, S. Tyrosine kinase receptor c-ros-oncogene 1 treat chemoresistant triple-negative breast cancer and inhibition alleviates aberrant bone formation of TWIST-1 epithelial ovarian cancer (EOC) when combined with standard haploinsufficient calvarial cells from Saethre-Chotzen chemotherapy; 3) specifically inhibit the EMT process in syndrome patients. Journal of Cellular Physiology accepted on CSCs; and 4) be applicable to many other cancer types that 23-Feb-2018. develop chemoresistance in CSCs. Our preliminary “proof of • Sanchez-Salcedo, S., Shahin, SA, ,Carlotta A. Glackin*, and concept” studies demonstrate efficacy when combined with Zink, J.I.* Mesoporous core-shell silica nanoparticles with chemotherapy in mouse models of breast and ovarian cancer. anti-fouling properties for ovarian cancer therapy. Chemical Taken together, successful completion of these studies will Engineering Journal (2017), https://doi.org/10.1016/j. contribute to reducing the burden of EOC in many ways by: cej.2017.12.116
54 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Robert J. Hickey, Ph.D. Associate Professor, Department of Molecular Medicine
IDENTIFICATION AND CLINICAL TRANSLATION OF MOLECULAR SIGNATURES OF DISEASE
My laboratory is divided into both a basic science and a assays. They therefore can be used to better explore the nature clinical applications work group. We are primarily a protein of the PCNA-binding partner interaction and subsequently chemistry/molecular biology group with interests that are improve our mechanistic understanding of PCNA dependent focused toward identifying the mechanisms mediating the cellular processes. development and progression of cancer. We also have a In addition to our studies on the DNA synthesome and strong interest in identifying distinct molecular signatures PCNA, my group is also interested in examining patient fluid that are indicative of the presence of cancer and that provide and tissue specimens for the presence of unique molecular a useful target for selectively killing cancer without harming signatures that correlate with the presence of disease noncancer cells. Specifically, we have used our skills in protein (especially cancer). Toward this end we have identified chemistry to identify and isolate, to essential homogeneity, glycomic and proteomic signatures of breast, prostate and the intact cellular DNA synthetic apparatus of both cancer esophageal cancer, and are developing projects with several and noncancer cells. We have termed this apparatus the clinical investigators with the goal of identifying molecular DNA synthesome, because it is a highly organized functional markers that have diagnostic and or prognostic value, and/or complex of several dozen polypeptides that act in concert to can serve as efficacy markers following treatment. We use a orchestrate the DNA synthetic process, and mediate aspects variety of technologies to accomplish these goals, including: of the DNA repair processes carried out by cells. various forms of mass spectrometry, 1D and 2D-PAGE Our discovery that the DNA synthetic fidelity of the DNA (including DIGE), column chromatography (including FPLC synthesome is consistently lower in cancer vs. noncancer cells and nano-flow HPLC 0, robotic sample handling, ELISA led to our observation that several of the components of the development, IHC/IF, antibody development, molecular cancer cell’s DNA synthesome were structurally distinct from cloning, gene expression systems, cell culture and a host their counterparts in the noncancer cell’s DNA synthesome. of other techniques.) Our ultimate goals in these sets of One of these altered components, identified as the protein studies are to identify disease specific therapeutic efficacy proliferating cell nuclear antigen (PCNA), was examined and/or diagnostic biomarkers, and then develop clinically in detail by our group and shown to undergo epigenetic useful biomarker assays that can be readily validated and modification in the cancer cell. This cancer cell associated subsequently incorporated into the clinical laboratory under PCNA, or caPCNA, contributed to the increased mutation the current standard-of-care. frequency exhibited by cancer cells. Localization of some of the epigenetic alterations to a very short region within the cancer SELECTED PUBLICATIONS cell’s PCNA enabled the development of a cancer selective • Sandoval, J.A., Malkas, L.H., and Hickey, R.J. Clinical antibody, which we subsequently showed facilitates the significance of serum biomarkers in pediatric solid identification of cancer in patient biopsy specimens. We also mediastinal and abdominal tumors. Int. J. Mol. Sci. 13: 1126- showed that this same peptide region of the cancer cell’s PCNA 1153, 2012. could interact with traditional PCNA binding partner proteins, leading to the selective killing of cancer cells and subsequently • Summers, K.C., Shen, F., Sierra Potchanant, E.A., Phipps, E.A., enabling the development of small molecule inhibitors of PCNA Hickey, R.J., and Malkas, L.H. Prosphorylation: The molecular function. Several of these same small molecule inhibitors of switch of double-strand break repair. Int. J. Proteomics 373816 the function of the cancer cell’s PCNA also exhibited a cancer Epub, 2011. selective cytotoxicity, while exhibiting little or no cytotoxicity toward noncancer cells. In addition to their potential anti- cancer therapeutic properties, these same small molecule inhibitors of PCNA function can also serve as highly specific molecular probes of PCNA, binding partner interaction in both malignant and nonmalignant cells, as well as in in vitro
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 55 David A. Horne, Ph.D. Vice Provost and Associate Director, Beckman Research Institute of City of Hope Professor, Department of Molecular Medicine
DEVELOPING NATURAL PRODUCTS AS NOVEL ANTI-CANCER AGENTS
Natural products possess a long and storied history in the discovery of lead compounds and important medicines for the treatment of human disease. This is particularly notable in the area of cancer research, where, according to data published by the National Cancer Institute, 74 percent of the small-molecule chemical entities introduced as new drugs worldwide from 1981 to 2001 can be traced to or were inspired by natural products. Moreover, natural products synthesis is an integral part of the drug development process. Pharmacophore identification, optimization of lead compounds and creating novel structural scaffolds inspired by nature are achieved by synthetic means. An integral aspect of our research program at City of Hope involves the application of complex molecule synthesis to the generation and development of novel therapeutic agents From nature to the laboratory for the molecular-targeted treatment of cancer and related conditions. Our research interests in general lie in developing SELECTED PUBLICATIONS new synthetic methods and strategies for the total synthesis • Li, Y.J., Perkins, A.L., Su, Y., Ma, Y., Colson, L., Horne, D.A., of architecturally complex biologically active natural products, and Chen, Y. Gold nanoparticles as a platform for creating a particularly from marine sources. One such natural product multivalent poly-SUMO chain inhibitor that also augments that is currently under development is grossularine. This ionizing radiation Proc. Natl. Acad. Sci. 109: 4092-4097, 2012. metabolite shows potent anti-cancer properties against • Ma, Y., Kowolik, C.M., Swiderski, P.M., Kortylewski, M.,Yu, H., solid tumors and is derived from the tunicate (sea squirt) Horne, D.A., Jove, R., Caballero, O.L., Simpson, A. J. G., Lee, Dendrodoa grossularia. That this metabolite is only produced F.-T., Pillay, V., and Scott, A.M. Humanized Lewis-Y specific antibody based delivery of STAT3 siRNA. ACS Chem. Bio. 6: in very minute quantities has hampered further development. 962-970, 2011. Our lab has completed a total synthesis of grossularine-1 and prepared a focused library of α-carboline analogs upon • Buettner, R., Corzano, R., Rashid, R., Lin, J.-P., Senthil, M., Hedvat, M., Schroeder, A., Mao, A., Herrmann, A., Yim, J., which grossularine is structurally based. The α-carboline Li, H.-Z., Yuan, Y.-C., Yakushijin, K., Yakushijin, F., Vaidehi, N., hetercyclic framework is unique among natural products and Moore, R., Gugiu, G., Lee, T.D., Yip, R., Chen, Y., Jove, R., Horne, represents a new pharmacophore for anti-cancer activity. The D., and Williams, J.C. Alkylation of cysteine 468 in Stat3 synthesis is highly efficient, allowing access to gram quantities defines a novel site for therapeutic development. ACS Chem. Biol. 6: 432-443, 2011. of synthetic material for biological evaluation. Our group has recently demonstrated that grossularines have potent anti- • Xie, J., Ma, Y., and Horne, D.A. Asymmetric synthesis of the core structure of leucosceptroids A and B. J. Org. Chem. 76: cancer activity against DU145 prostate cells. In vivo studies are 6169-6176, 2011. currently in progress, as well as molecular • Lee, H., Deng, J., Kujawski, M., Yang, C., Liu, Y., Herrmann, target identification. A., Kortylewski, M., Horne, D., Somlo, G., Forman, S., Jove, R., and Yu, H. STAT3-induced S1PR1 expression is crucial for persistent STAT3 activation in tumors. Nature Medicine 16: 1421-1428, 2010.
56 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Wendong Huang, Ph.D. Professor, Department of Diabetes Complications and Metabolism
METABOLIC REGULATION, DIABETES AND CANCER
We are interested in the molecular pathways regulating SELECTED PUBLICATIONS metabolism and their roles in diabetes and cancer. One • Gu, Y., Zhang, J., Ma, X., Kim, B., Wang, H., Li, J., Pan, Y., Xu, particular direction is functional studies of a group of nuclear Y., Ding, L., Yang, L., Guo, C., Wu, X., Wu, J., Wu, K., Gan, receptors in both normal and disease conditions. Nuclear X., Li, G., Li, L., Forman, S., Chan, W., Xu, R., and Huang, W. receptors are a special group of transcriptional factors that are (2017) Stabilization of c-Myc protein by CAMKIIγ promotes activated by their cognate ligands. Studies in this area have T-cell lymphoma. Cancer Cell 32:115-128. generated significant impact in many human diseases such as • Ma, X., Meng, Z., Jin, L., Xiao, Z., Wang, X., Tsark, W., Ding, obesity, diabetes and cancer. L., Guy, Y., Zhang, J., Kim, B., He, M., Gan, X., Shively, J., A second approach to address our research interest is focused Yu, H., Xu, R., and Huang, W. (2017) CAMK2γ in intestinal on the identification of novel molecular pathways from both epithelial cells modulates colitis-associated colorectal genetic and epigenetic approaches in diabetes and cancer. carcinogenesis via enhancing STAT3 activation. Oncogene Moreover, we have screened and identified small chemical 36(28):4060-4071. compounds to treat diabetes and cancer. • Meng Z., Max., Du, J., Wang, X., He, M., Gu, Y., Zhang, J., By using both genetically engineered mouse models and Han, W., Fang, Z., Gan, X., Van Ness, C., Fu, X., Schones, molecular pharmacological tools, our long-term goal is to D.E., Xu, R., and Huang, W. (2016) CAMK2γ Antagonizes identify novel components in signaling pathways that will mTORC1 Activation during Hepatocarcinogenesis. Oncogene provide new targets for drug discovery. 36(17):2446-2456. The current research projects in my laboratory focus on: • Ding., L., Sousa, K.M., Jin, L., Dong, B., Kim, B.W., Ramirez R., Xiao, Z., Gu, Y., Yang. Q., Wang, J., Yu, D., Pigazzi, A., 1. Identification of novel signal molecules and signaling Schones, D., Yang, L., Moore, D., Wang, Z., and Huang, W. pathways that regulate metabolism in diabetes and cancer (2016) Vertical Sleeve Gastrectomy Activates GPBAR-1/ 2. Epigenetic mechanisms in diabetes and cancer TGR5 to Sustain Weight Loss, Improve Fatty Liver, and Remit 3. Molecular mechanisms of metabolic surgery in Insulin Resistance in Mice. Hepatology. 64(3):760-73. diabetes treatment • Fu, X.H., Dong, B.N., Tian, Y., Lefebvre, P., Meng, Z., Wang, X., Pattou, F., Han, W., Wang, X., Lou, F., Jove, R., Staels, B., Moore, D.D., and Huang, W. (2015) MiR-26a regulates insulin sensitivity and metabolism of glucose and lipids. J. Clin. Invest. 125(6):2497-509.
• Fu, X.H., Jin, L., Wang, X.C., Hu, J.K., Zheng, X.W., Tsark, W.M., Riggs, A.D., Ku, H.T., and Huang, W. (2013) MiR-26a targets TET enzymes and is regulated during pancreatic cell differentiation. Proc Natl Acad Sci. 110(44):17892-7.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 57 Susanta Hui, Ph.D. Professor, Department of Radiation Oncology Director of Radiation Research Director of Small Animal Imaging Core
MOLECULAR IMAGING AND THERAGNOSTICS
The lab of Susanta Hui, Ph.D., has a primary focus to develop discovered preferential niches for AML invasion in the skeletal multimodal molecular image guided personalized, precise and system as shown in figure. This discovery led to develop translational radiation medicine. The laboratory developed next generation targeted therapy for pre-clinical and will be several multimodal imaging processes such as PET, Optical, translated into clinical studies. MRI, CT which provided a platform not only to characterize Our interdisciplinary team developed a global health consortium tumors and tumor invasion to distant sites (metastasis), it and works towards theranostics by combining molecular also offered a new understanding of how macro and micro information and functional image guidance with therapy such tumor microenvironment may provide shelter to resistant as TMI to accelerate personalized medicine globally. In this disease. Therefore, spatial and temporal knowledge, consortium, there are several countries participating in clinical often ignored, become key features to unravel complex and basic research associated with leukemia, targeted radiation, dynamics and evolution of cancer resistance in the dynamic and bone marrow microenvironment. physiological system. The lab also focuses in depth on understanding the science SELECTED PUBLICATIONS of physical biology in oncology though multidisciplinary and • Hui, S., et al. Early assessment of dosimetric and biological translational approaches in preclinical and clinical studies. differences of total marrow irradiation versus total body Specifically, the lab seeks to understand i) How the bone and irradiation in rodents. Radiotherapy and oncology. Radiother marrow environment (BME) respond to radiation treatment, ii) Oncol. 2017 Sep;124(3):468-474.). PMID: 28778346, How macro- and micro- BME and malignant cell (hematologic PMCID: PMC5624834 and metastatic) influence each other to survive. In that, our • Hui, S., et al. Dose Escalation of Total Marrow Irradiation in work focuses on understanding the role of bone marrow High-Risk Patients Undergoing Allogeneic Hematopoietic adipocyte and the molecular mechanism of adipocyte and Stem Cell Transplantation. Biol Blood Marrow Transplant 23 leukemia interaction in preclinical models. Current clinical (2017) 1110–1116. PMID: 28396164, PMCID:PMC5531195 studies will detect if there are preferential locations of leukemia niche and its association with adipocyte and other component • Magome, T., et al. Whole body distribution of leukemia of BME, iii) Our laboratory has and functional total marrow irradiation based on FLT-PET and dual energy CT. Mol Imaging. 2017. PMID: 28948859, successfully created bioengineered PMCID: PMC5624344 tissue mimicking bone and marrow system. This is current used for • Kumar, B., et. al. Acute myeloid leukemia transforms long culture and manipulate stem the bone marrow niche into a leukemia-permissive cells, iv) Laboratory discovered microenvironment through aberrant exosome secretion. targeted marrow irradiation (TMI) Leukemia 2017. PMID: 28816238 and successfully implemented the • Kaveh, K., et. al, Combination therapeutics of Nilotinib and clinical treatment management of radiation in Acute Lymphoblastic Leukemia as an effective hematological malignancies which method against drug-resistance. PLOS Computational is now globally accepted. Further Biology 2017; 13(7): e1005482. PMID: 28683103, PMCID: effort is ongoing for comprehensive PMC5500007 understanding of the role of targeted radiation in the donor marrow homing and engraftment. v) Our laboratory recently developed 64Cu- anti-CD33-DOTA PET-CT imaging Figure: 64Cu-anti-CD33- in the humanized acute myeloid DOTA PET-CT of humanized AML leukemia (AML) mouse model and
58 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Janice M. Huss, Ph.D. Associate Professor, Department of Molecular and Cellular Endocrinology
THE ROLE OF ORPHAN NUCLEAR RECEPTORS IN CARDIAC AND SKELETAL MUSCLE BIOLOGY
Our laboratory investigates how the nuclear receptor • Huss, J.M., Garbacz, W., and Xie, W. Constitutive activities (NR) superfamily of transcription factors regulates energy of estrogen-related receptors: Transcriptional regulation metabolism and growth in skeletal muscle. Genome-wide of metabolism by ERRα and ERRγ in health and disease. target gene identification using chromatin immunoprecipitation Biochimica et Biophysica Acta-Molecular Basis of Disease. 1852:1912-1927, 2015. and next-generation sequencing (RNA-seq) have shown that the estrogen-related receptor (ERR) family of orphan • Labarge, S., McDonald, M., Smith-Powell, L., Auwerx, J., and NRs are involved in regulating genes involved in muscle Huss J.M. Estrogen-related receptor-α (ERRα) deficiency in contractile function, mitochondrial oxidative pathways and skeletal muscle impairs regeneration in response to injury. glucose/glycogen metabolism. We employ primary skeletal FASEB Journal. 28(3):1082-1097, 2014. myocyte models to investigate the upstream signaling • Murray, J., Auwerx, J., and Huss, J.M. Impaired myogenesis pathways that regulate ERR activity and the mechanisms in estrogen-related receptor γ (ERRγ)-deficient skeletal by which ERRs coordinate expression of their target gene myocytes due to oxidative stress. FASEB Journal. 27(1):135- programs in response to exercise signaling and growth factor 150, 2013. involved in differentiation. We use inducible gain and loss of • Murray, J., and Huss, J.M. The estrogen-related receptor function models to study how muscle-specific modulation alpha (ERRα) regulates skeletal myocyte differentiation via of the ERRα or ERRγ isoforms affects metabolic and growth/ modulation of the ERK MAP kinase pathway. Am. J. Physiol. repair adaptations in response to physiologic stimuli, such as Cell Physiol. 301: C630-645, 2011. exercise, or pathologic states, such as obesity-related type • Cresci, S., Huss, J.M., Beitelshees, A.L., Jones, P.G., Minton, 2 diabetes. Our studies have revealed that the ERR pathway M.R., Dorn, G.W., Kelly, D.P., Spertus, J.A., and McLeod, is a potential therapeutic target for diseases associated with H.L. A PPAΡα promoter variant impairs ERR¬dependnet metabolic dysregulation, including type 2, diabetes, heart transactivation and decreases mortality after acute coronary failure and muscle atrophy. ischemia in patients with diabetes. PLoS One 3;5(9):e12584, 2010. SELECTED PUBLICATIONS • Wende, A.R., Schaeffer, P.J., Parker, G.J., Zechner, C., Han, • Hamilton, A., Ly, J., Corder, K.R., Schaeffer, P.J., and Huss, D.-H., Chen, M.M., Hancock, C., Huss, J.M., McClain, D.A., J.M. Conserved role of avian PPARs in regulating lipid Holloszy, J.O., and Kelly, D.P. A role for the transcriptional metabolism: A mechanistic basis for metabolic plasticity in coactivator PGC-1 in muscle refueling. J. Biol. Chem. 282: migratory birds. General and Comparative Endocrinology. In 36642-36651, 2007. press, 2018. • Huss, J.M., Imahashi, K., Dufour, C.R., Weinheimer, C.J., • Lenz, G., Hamilton, A., Geng, S., Hong, T., Kalkum, M., Courtois, M., Kovacs, A., Giguère, V., Murphy, E., and Kelly, Momand, J., Kane, S.E., and Huss, J.M. t-Darpp activates D.P. The nuclear receptor ERRalpha is required for the IGF-1R signaling to regulate glucose metabolism in bioenergetic and functional adaptation to cardiac pressure trastuzumab-resistant breast cancer cells. Clinical Cancer overload. Cell. Metab. 6: 25-37, 2007. Research. 24(5):1216-1226, 2018. • Garcia-Roves, P.M., Huss, J.M., Han, D.H., Hancock, C.R., • Yu, D.M., Huss, J.M., Li, H., and Forman, B.M. Identification Iglesias-Gutierrez, E., Chen, M.M., and Holloszy, J.O. of novel inverse agonists of estrogen-related receptors Raising plasma fatty acid concentration induces increased ERRγ and ERRβ. Bioorganic and Medicinal Chemistry. biogenesis of mitochondria in skeletal muscle. Proc. Natl. 25:1585–1599, 2017. Acad. Sci. USA 104: 10709-10713, 2007. • Corder, K.R., Russell, D.E., Huss, J.M., and Schaeffer, P.J. • Dufour, C.R., Wilson, B.J., Huss, J.M., Kelly, D.P., Alaynick, Molecular regulation of adiposity in a migrant, the gray W.A., Downes, M., Evans, R.M., Blanchette, M., and Giguère, catbird, Dumetella carolinensis. Journal of Experimental V. Genome-wide orchestration of cardiac functions by the Biology. 219(Pt 21):3391-3398, 2016. orphan nuclear receptors ERRalpha and gamma. Cell. Metab. 5: 345-356, 2007.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 59 Keiichi Itakura, Ph.D. Emeritus Professor, Department of Molecular and Cellular Biology
FUNCTIONS OF MRF-1 AND -2
Mrf-2 in differentiation of mesenchymal stem cells Mrf-1 in carcinogenesis During the study of mechanisms underlying the activation of Our preliminary data showed that expression of Mrf-1mRNA human cytomegalovirus (HCMV), we have cloned modulator was induced under conditions such as heat shock, hypoxia recognition factors (Mrf)-1 and -2 that interact with the and ER stress, and that knockdown of Mrf-1 suppressed cell modulator region of the HCMV major immediate early gene. migration and proliferation in prostate cancer DU145 and These proteins belong to the family of AT-rich interactive LnCAP cells. To investigate functions of Mrf-1 in carcinogenesis domain proteins, which regulate differentiation and gene in vivo, we produced Tramp prostate cancer models with expression in fungi, plants and animals. To study functions Mrf-1KO. Additionally, these mice were castrated to study the of the proteins, we have generated transgenic mice with a interaction between androgen receptor and Mrf-1. Analysis of deletion of Mrf-1 (Mrf-1KO, a gift from Ohsaka University) these mice is in progress. We will further extend this approach and Mrf-2 (Mrf-2KO). In the case of Mrf-1KO, we did not to the PTEN knockout model that is considered to be similar to observe any significant phenotype. The two most significant the human etiology. phenotypes associated with the deletion of Mrf-2 are their leanness and craniofacial bone abnormality in comparison SELECTED PUBLICATIONS to wild type mice. Weight measurement of several organs • Yamakawa, T., Sugimoto, K., Whitson, R.H., and Itakura, revealed that accumulation of fat in white adipocytes was K. Modulator recognition factor-2 regulates triglyceride impaired. To investigate causes for less fat accumulation, we metabolism in adipocytes. Biochem. Biophys. Res. Commun. exploited two in vitro systems; 1) embryonic fibroblasts from 391: 277-281, 2010. Mrf-2KO and wild type mice, and 2) preadipocyte 3T3-L1 cells after knock down of Mrf-2 were induced to differentiate to fat • Chesnokov, V., Sun, C., and Itakura, K. Glucosamine cells. Both the systems, knockout and knockdown of Mrf-2, suppresses proliferation of human prostate carcinoma respectively suppressed differentiation to adipocytes and DU145 cells through inhibition of STAT3 signaling. Cancer reduced the expression various agipogenic genes. Cell Int., 2009. (no volume or page numbers available) In addition to fat and bone abnormality, our collaborators • Yamakawa, T., Whitson, R.H., Li, S.L., and Itakura, K. found abnormality in chondrocytes of Mrf-2 KO mice. Modulator recognition factor-2 is required for adipogenesis Therefore, we reasoned that Mrf-2 plays an important general in mouse embryo fibroblasts and 3T3-L1 cells. Mol. role for differentiation of mesenchymal stem cells. Even Endocrinol. 22: 441-453, 2008. though skeletal muscles in newborn Mrf-2KO mice are normal, we hypothesized that adult muscles could have defects in regeneration. In vitro experiments showed that myoblasts from adult Mrf-2KO mice delayed in differentiation to myotubes in comparison to the wild type mice. In the future, we will investigate more details of how Mrf- 2 regulates gene expression involved in adipogenesis and myogenesis. We also produce tissue specific Mfr-2KO mice to study obesity and muscle regeneration, respectively.
60 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Rahul Jandial, M.D., Ph.D. Associate Professor, Division of Neurosurgery
BRAIN METASTATIC CANCER
It is often unrecognized that 90 percent of deaths from cancer characteristics that may increase their chances of fully occur because of metastasis, and one of the most dangerous developing a colony into a detectable metastasis tumor. areas to which cancer can spread is the brain. This has become This includes expression of functional neurotrophin and particularly relevant for women with breast cancer. The recent neurotransmitter receptors on the breast-to-brain metastases increase in the spread of breast cancer to the brain can be cells. Breast cancer cells can utilize the neurotrophins and attributed partially to the success of new drug therapies neurotransmitters enriched in the brain microenvironment available to control advanced cancer outside of the brain. for successful metastasis. Administration of exogenous Because women are living longer with breast cancer, the brain neurotrophins and neurotransmitters to the breast-to-brain has arisen as the site where the cancer invades, serving as a metastasis cells increases proliferation, migration “sanctuary site” for cancer cells against therapies. This affects and colonization. both afflicted women’s survival and their quality of life. SELECTED PUBLICATIONS Current treatment options are limited to radiation and surgery. Research into brain metastases is in its early stages, and there • Termini, J., Neman, J., and Jandial R. HYPERLINK “http:// are several obstacles in improving treatment options. First, www.ncbi.nlm.nih.gov/pubmed/25035392”Role of the there is inadequate access to fresh specimens from surgery. neural niche in brain metastatic cancer. Cancer Res. 74:4011- Fresh specimens and primary cell lines increase accuracy in the 4015, 2014. study of this disease as compared to the immortalized breast- • Neman, J., Termini, J., Wilczynski, S., Vaidehi, N., Choy, C., to-brain cell lines that have been cultured for years and have Kowolik, CM., Li, H., Hambrecht, AC., Roberts, E., and Jandial, been subjected to many possible mutations. Second, getting R. Human breast cancer metastases to the brain display new drugs into the brain is a challenge because the brain has GABAergic properties in the neural niche. Proc. Natl. Acad. its own unique and robust obstacle that blocks the access Sci. USA. 111: 984-989, 2014. of molecules and drugs, known as the “blood-brain-barrier.” Third, new treatments that can cross the blood-brain-barrier • Neman, J., Choy, C., Kowolik, C.M., Anderson, A., Duenas, have the potential to hurt healthy brain cells in addition to the V.J., Waliany, S., Chen, B.T., Chen, M.Y., and Jandial, R. Co- tumor cells. Lastly, in addition to the lack of potent and specific evolution of breast-to-brain metastasis and neural progenitor therapies targeting a patient’s breast-to-brain metastasis, the cells. Clin. Exp. Metastasis 30: 753-768, 2013. importance of the brain microenvironment in the survival of the • Jandial, R., Neman, J., and Termini, J. Genetic mutations breast cancer cells is poorly understood. According to Paget’s and tissue type lead to heterogeneous metabolic profiles in “seed and soil hypothesis,” the cells that flourish in a foreign tumors. Neurosurgery 70: N20-21, 2012. microenvironment are the cells that readily or have inherent adaptability to that new microenvironment. • Jandial, R., Anderson, A., Choy, C., and Levy, M.L. Our research goals are to overcome obstacles by 1) utilizing Bidirectional microenvironmental cues between neoplastic fresh surgical specimens from patients with breast-to-brain and stromal cells drive metastasis formation and efficiency. metastasis obtained through our neurosurgery department Neurosurgery 70: N12-13, 2012. at City of Hope, 2) identifying the cellular roots of treatment • Hambrecht, A., Jandial, R., and Neman, J. Emerging role of failure, 3) improving agents that selectively attack breast- brain metastases in the prognosis of breast cancer patients. to-brain metastases, and 4) understanding the bidirectional Breast Cancer: Targets and Therapy 3: 79-91, 2011. interactions between the breast cancer cell in the brain microenvironment. Our recent and current research suggests that breast cancer cells that survive and colonize in the brain display “brain-like”
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 61 Lei Jiang, Ph.D. Assistant Professor, Department of Molecular and Cellular Endocrinology
METABOLIC ALTERATION IN DIABETES AND CANCER
Metabolism is a fundamental biological phenomenon. SELECTED PUBLICATIONS Dysregulated metabolism contributes to a variety of • Jiang, L., Boufersaoui, A., Yang, C., Ko, B., Rakheja, D., disease, including cancer and diabetes, which are known as Guevara, G., Hu, Z., and DeBerardinis, R.J. Quantitative metabolic disease. A major goal of my research is to explore metabolic flux analysis reveals an unconventional pathway the coordinated metabolic adaptation under both normal of fatty acid synthesis in cancer cells deficient for the physiological and specific pathological conditions. mitochondrial citrate transport protein. Metab Eng. 2017 Cellular metabolic reactions are compartmented, with their • Jiang, L., Shestov, A.A., Swain, P., Yang, C., Parker, S.J., Wang, own spatial and temporal distribution. Both the adipose tissue of diabetic patients and the tumor of cancer patients Q.A., Terada, L.S., Adams, N.D., McCabe, M.T., Pietrak, B., contain a wide variety of cell types, and their metabolism Schmidt, S., Metallo, C.M., Dranka, B.P., Schwartz, B., and actively communicates with each other, which is another layer DeBerardinis, R.J. Reductive carboxylation supports redox of compartmentation. homeostasis during anchorage-independent growth. Nature. 2016 Metabolites, like citrate and serine, are well known for their nutrient role, and they can also serve as signal molecule • Schell, J.C., Olson, K.A., Jiang, L., Hawkins, A.J., Van Vranken, between the cells and within the subcellular structure. My J.G., Xie, J., Egnatchik, R.A., Earl, E.G., DeBerardinis, R.J., recent study showed that a novel cytosol-to-mitochondria and Rutter, J. A role for the mitochondrial pyruvate carrier citrate transport system mitigates the mitochondrial oxidative as a repressor of the Warburg effect and colon cancer cell stress in the detached cancer cell, and we will look into the growth. Mol Cell. 2014 signaling control between the subcellular organelles. • Yang, C., Ko, B., Hensley, C.T., Jiang, L., Wasti, A.T., Kim, J., In recent years, the metabolic heterogeneity has also been Sudderth, J., Calvaruso, M.A., Lumata, L., Mitsche, M., Rutter, more appreciated with the evolution of analytical tools. J., Merritt, M.E, and DeBerardinis R.J. Glutamine oxidation The integration of mass spec based metabolic tracing and maintains the TCA cycle and cell survival during impaired mathematical bioengineering based modeling prediction will mitochondrial pyruvate transport. Mol Cell. 2014 provide a new angle to understand the metabolic rewiring in diabetes, cancer and other diseases. A better knowledge of the central carbon metabolism, amino acid utilization and nucleic acid synthesis will lead to new diagnostic approach and potential novel drug target.
62 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Jeremy Jones, Ph.D. Associate Research Professor, Department of Medical Oncology & Therapeutics Research
TRANSLATIONAL RESEARCH IN UROLOGIC ONCOLOGY
The lab of Jeremy Jones, Ph.D., focuses on translational SELECTED PUBLICATIONS research in urologic oncology. In the setting of metastatic • Lim, M., Otto-Duessel, M., He, M., Su, L., Nguyen, D., Chin, E., prostate cancer, we are developing androgen receptor (AR) Alliston, T., and Jones, J.O. Ligand-independent and tissue- DNA binding domain inhibitors to control the growth of selective androgen receptor inhibition by pyrvinium. ACS cancers resistant to traditional AR targeted therapies. We Chem Biol. 2014 Mar 21;9(3):692-702. are using liquid biopsy and deep sequencing approaches to identify biomarkers of resistance to the AR targeted • Pal, S.K., Patel, J., He, M., Foulk, B., Kraft, K., Smirnov, D.A., therapies enzalutamide and abiraterone, as well as to identify Twardowski, P., Kortylewski, M., *Bhargave, V., and *Jones., mechanisms of resistance and novel drug targets. We are J.O. Identification of mechanisms of resistance to treatment also developing tissue selective AR modulators for prostate with abiraterone acetate or enzalutamide in patients with cancer and other indications. We are working to understand castration resistant prostate cancer. Cancer. 2017 Dec 19. the mechanism by which warfarin reduces the risk of prostate cancer in order to identify molecular targets for prostate • Zhou, Y., Ott-Duessel, M., Copeland, B., He, M., Markel, S., cancer prevention. Likewise, we are working to understand Synold, T., and Jones, J.O. Low testosterone alters levels and the relationship between low systemic testosterone and the transcriptomes of mouse prostate stem cells. Prostate. 2016 increased risk of high grade prostate cancer with the goal of Dec 14. preventing prostate cancer through appropriate androgen • Tew, B.Y., Hong, T., Otto-Duessel, M., Castro, E., Elix, C., He, stimulation. In the setting of metastatic kidney cancer, we are M., Kalkum, M., and Jones, J.O. Vitamin K Epoxide Reductase using deep sequencing approaches to identify novel molecular Regulation of Androgen Receptor Activity. Oncotarget. 2017 targets in patients with sarcomatoid cancer, the most Jan 13. aggressive form of the disease. We are also testing the efficacy of MET inhibitors in models of papillary renal cell carcinoma. • Pal, S.K., Sonpavde, G., Agarwal, N., Vogelzang, N.J., Srinivas, In the setting of bladder cancer, we are working to improve S., Haas, N.B., Signoretti, S., McGregor, B.A., Jones, J., detection of recurrent non-invasive bladder cancer and to Lanman, R.B., Banks, K.C., and Choueiri, T.K. Evolution of understand the mechanism of resistance to Food and Drug Circulating Tumor DNA Profile from First-line to Subsequent Administration-approved fibroblast growth factor receptor- Therapy in Metastatic Renal Cell Carcinoma. Eur Urol. 2017 targeted drugs. In all of these urologic cancers, we are using Oct;72(4):557-564. doi: 10.1016/j.eururo.2017.03.046. Epub circulating tumor cells to predict response to drug treatment 2017 Apr 14. PubMed PMID: 28413127. and to improve patient risk stratification.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 63 Tijana Jovanovic-Talisman, Ph.D. Assistant Professor, Department of Molecular Medicine
SUPER-RESOLUTION IMAGING IN DRUG DISCOVERY
To investigate biological processes that are critical to the Proteinaceous assemblies called nuclear pore complexes progression of cancer and other human diseases we use mediate transport of macromolecules across the nuclear pointillistic super-resolution imaging techniques that offer high envelope. Individual nucleoporins have unique roles in spatial resolution and single-molecule sensitivity. Our research regulation of nucleocytoplasmic transport, and their defects interests lie in the advancement of quantitative nanoscale can often lead to various disease phenotypes including cancer. methods to study important biological mechanisms and in the We aim to elucidate the mechanistic contributions of the development of novel therapeutic and imaging agents with specific nucleoporins during both normal cell function and these powerful techniques. Elucidation of protein organization carcinogenesis by utilizing and developing nanobiological in the plasma membrane will clarify the mechanisms of assays and biophysical tools such as super-resolution signaling networks that regulate cellular function and microscopy. Mechanisms that regulate nucleocytoplasmic communication. Quantitative super-resolution microscopy transport of proteins may ultimately provide novel targets and techniques are used in our lab to investigate the distribution of opportunities for drug development. plasma membrane receptors such as growth factor receptors and G protein coupled receptors in the steady state and upon SELECTED PUBLICATIONS perturbation with various ligands. Over the long-term we • Tobin, S., Cacao, E., Hong, D., Terenius, L., Vukojevic, V., and envision that advanced super-resolution microscopy methods Jovanovic-Talisman, T. Nanoscale effects of ethanol and can be used as a tool for quantitative, high throughput naltrexone on protein organization in the plasma membrane screening of ligands and their receptors on the cell membrane studied by photoactivated localization microscopy (PALM). to develop novel cancer therapeutics that are specific to the PLOS One 9(2), e87225, 2014. disease site. • Sengupta, P*., Jovanovic-Talisman, T.,* Skoko, D., Renz, M., Veatch, S., and Lippincott-Schwartz, J. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8: 969-975, 2011. *Both authors contributed equally.
• Jovanovic-Talisman, T., Tetenbaum-Novatt, J., McKenney, A.S., Zilman, A., Peters, R., Rout, M.P., and Chait B.T. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature 457: 1023-1027, 2009.
64 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Michael Kahn, Ph.D. Professor and Chair, Department of Molecular Medicine
IDENTIFY AND VALIDATE PHARMACOLOGIC TOOLS
Dr. Kahn’s lab utilizes a forward chemical genomic strategy SELECTED PUBLICATIONS to identify and validate novel pharmacologic tools to study • Teo, J.L., Ma, H., Nguyen, C., Lam, C., and Kahn, M. Specific complex signaling pathways in development and disease. inhibition of CBP/beta-catenin interaction rescues defects in Utilizing a proprietary chemical library, which his team neuronal differentiation caused by a presenilin-1 mutation. designed and synthesized, they identified the first specific Proc. Natl. Acad. Sci. USA, 2005, 102(34), 12171-12176 CBP/β-catenin antagonist ICG-001 from a cancer cell-based Wnt signaling screen. During the course of Dr. Kahn’s team’s • Henderson, W.R. Jr., Chi, E.Y., Ye, X., Nguyen, C., Tien, Y.T., investigations with the specific CBP/catenin antagonist ICG- Zhou, B., Borok, Z., Knight, D.A., and Kahn, M. Inhibition of 001, they discovered a very fundamental regulatory event Wnt/beta-catenin/CREB binding protein (CBP) signaling — in both pluripotent and somatic stem cells — that controls reverses pulmonary fibrosis. Proc. Natl. Acad. Sci. USA, 2010, the cell’s decision to either maintain “stemness” or initiate 107(32), 14309-14314 differentiation. This decision is governed by the choice of • Kahn, M. Can we safely target the Wnt pathway? Nature which of the two highly homologous Kat3 coactivators, CBP Reviews. Drug Discovery, 2014, 13(7), 513-532 or p300, the key Wnt signaling component β-catenin partners with to drive transcription. ICG-001 is a selective CBP/β- • Zhao, Y., Masiello, D., McMillan, M., Nguyen, C., Wu, Y., catenin antagonist and the structurally related small molecule Kida, A., Melendez, E., Smbatyan, G., He, Y., Teo, J.L., and YH250, which they developed more recently, is a selective Kahn, M. Specific Inhibition of CBP/Catenin Signaling p300/β-catenin antagonist. His team recently demonstrated Safely Eliminates Drug Resistant Leukemia Initiating Cells. that YH250 stimulates hematopoiesis in lethally or sublethally Oncogene, 2016, 35(28), 3705-3717 irradiated mice. A single administration of YH250, 24 hours • Thomas, P.D., and Kahn, M. Kat3 Coactivators in Somatic post-irradiation can significantly stimulate HSC proliferation, Stem Cells and Cancer Stem Cells: Biological Roles, Evolution improve survival and accelerate peripheral blood count and Pharmacologic Manipulation. Cell Biol. Toxicol., 2016, 32, recovery. Their studies suggest that increased expansion of the 61–81 remaining HSC population via symmetric non-differentiative proliferation is at least part of the mechanism of action. • Zhao, Y., Wu, K., Nguyen, C., Smbatyan, G., Melendez, E., Most recently, his lab has begun investigating the role Higuchi, Y., Chen, Y., and Kahn, M. Small molecule p300/ of selective modulation of Wnt signaling on immune cell Catenin antagonist enhances hematopoietic recovery after biasing and recruitment in chronic inflammatory diseases radiation. PLoS One, e0177245, 2017 (e.g., IBD), obesity and metabolic disease and the tumor • Gang, E., Kim, Y.M, and Kahn, M. CBP/catenin antagonists: microenvironment, utilizing both their highly specific Targeting LSC’s Achilles Heel Exp. Hematol., 52:1-11. doi: pharmacologic tools and genetic models (knockin mouse and 10.1016/2017 CRISPR/Cas9 editing of p300).
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 65 Markus Kalkum, Dr. Rer. Nat. (Ph.D.) Professor, Department of Molecular Imaging and Therapy
EMERGING INFECTIOUS DISEASES, VACCINES AND ADVANCED DIAGNOSTICS
Mass spectrometry and proteomics the proteases secreted by the pathogenic fungus Aspergillus Novel proteomic methods permit us to quantitatively analyze fumigatus upon invasion of host tissues, and hence allows us to the proteome of an organism at a deeper level than what generate novel diagnostic assay for invasive fungal infections. was previously possible. In fact, modern mass spectrometric approaches identify and quantify tens of thousands of proteins within a single sample. My laboratory is pursuing the biological applications of advanced mass spectrometric methodology, exemplified by the following projects: Emerging infectious diseases, vaccines and drug development Invasive fungal infections represent a major challenge to immunosuppressed patients, including cancer patients who received hematopoietic stem cell transplants for the treatment of leukemia or other hematologic malignancies. The disease is associated with high mortality rates >50%. We use mass Figure 1 – X-ray structure ribbon diagram of the peroxiredoxin Asp f3, a vaccine spectrometry to identify molecular candidates for vaccine candidate and potential drug target. and drug development, as well as for molecular imaging, and diagnostic approaches. We have successfully tested recombinant peroxiredoxin Asp f3 from Aspergillus fumigatus SELECTED PUBLICATIONS (Figure 1) as a potent aspergillosis vaccine in vertebrate • Hillmann, F., Bagramyan, K., Straßburger, M., Heinekamp, animals. Similar to immunosuppressed humans, birds often T.’ Hong, T.B.’ Bzymek, K.P.’ Williams, J.C.’ Brakhage, A.A.’ contract and die from invasive fungal infections. Our vaccine is Kalkum, M. The Crystal Structure of Peroxiredoxin Asp f3 currently being investigated for the protection of captive birds Provides Mechanistic Insight into Oxidative Stress Resistance such as penguins, Pacific Eiders and Inca terns in zoological and Virulence of Aspergillus fumigatus. Scientific reports 2016, parks (recently featured on Animal Planet’s “The zoo” episode 6, 33396. 9). Furthermore, we have shown that Asp f3 is required for • Bagramyan, K., Kaplan, B.E., Cheng, L.W., Strotmeier, J., fungal virulence, making it a potential drug target. Rummel, A., and Kalkum, M. (2013). Substrates and controls Detection of neurotoxins and fungal proteases for the quantitative detection of active botulinum neurotoxin in protease-containing samples. Analytical Chemistry, 85(11), The bacterially-produced botulinum neurotoxins (BoNTs) are 5569-5576. the most toxic biological substances known. Their abuse as a biological threat agent is feared, but at the same time BoNTs • Diaz-Arevalo, D., Ito, J.I., and Kalkum, M. (2012), Protective represent important medical drugs for the treatment of various effector cells of the recombinant Asp f3 anti-aspergillosis human diseases. My laboratory is developing molecular vaccine. Frontiers in Microbiology, 3, 299. assays for the rapid and ultrasensitive detection of BoNTs. Our present assay platform, known as the ALISSA (assay with a large immunosorbent surface area), can detect attomolar concentrations of BoNT serotype A in 0.5 mL volumes of complex biological samples such as blood plasma or liquid foods. We use a combination of mass spectrometry and biochemical techniques to expand the scope and robustness of the ALISSA platform for diagnostics. For example, preliminary data suggests that the ALISSA principle can be extended to
66 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Rick A. Kittles, Ph.D. Professor and Director, Division of Health Equities, Department of Population Sciences Associate Director for Health Equities, City of Hope Comprehensive Cancer Center
THE BIOLOGICAL AND SOCIO-CULTURAL CONTEXT OF CANCER DISPARITIES
Use of genetic ancestry in disparities research within the prostate the expression My interest is in understanding the complex issues of several vitamin D–related surrounding race, genetic ancestry, and health disparities. Our genes differ by self-reported race lab focus has been on quantifying and utilizing genetic ancestry and correlate to West African in genomic studies on cancer risk and outcomes; impact of genetic ancestry. We are currently genetic variation across populations in pharmacogenomics, exploring vitamin D signaling in and biomarker discovery and disease gene mapping. Genetic the prostate in order to determine ancestry has strong utility as an index for human biological mechanisms leading to cancer and variation. Also, when ancestry is used to describe genetic potential therapeutic targets. background, it allows for more sophisticated investigation of biological risk factors than just using self-reported race. SELECTED PUBLICATIONS Recently we have shown that naltrexone efficacy for smoking • Conti, D.V., Wang, K., Sheng, cessation varies across African-American individuals with X., Bensen, J.T., Hazelett, D.J., Cook, M.B., Ingles, S.A., different levels of West African genetic ancestry. These results Kittles, R.A., Strom, S.S., Rybicki, B.A., Nemesure, B., Isaacs, suggest that genetic background may partially explain racial W.B., Stanford, J.L., Zheng, W., Sanderson, M., John, E.M., differences in drug response. Park, J.Y., Xu, J., Stevens, V.L., Berndt, S.I., and Haiman, We examine genomic variation using genome-wide C.A. PRACTICAL/ELLIPSE Consortium. (2017) Two Novel approaches (GWAS, admixture mapping, whole genome Susceptibility Loci for Prostate Cancer in Men of African and exome sequencing, and ChIP-Seq). Our lab is currently Ancestry. J Natl Cancer Inst. 109(8). doi: 10.1093/jnci/ following up djx084. PMID: 29117387 on our GWAS • Richards, Z., Batai, K., Farhat, R., Shah, E., Makowski, and admixture A., Gann, P.H., Kittles, R., and Nonn, L. (2017) Prostatic mapping findings compensation of the vitamin D axis in African American on chromosome men. JCI Insight. 2(2):e91054. doi: 10.1172/jci.insight.91054. 8q24 and 5p15. PMID: 28138564 Given the genetic heterogeneity in • Batai, K., Murphy, A.B., Nonn, L., and Kittles, R.A. (2016) African Americans Vitamin D and Immune Response: Implications for Prostate due to admixture Cancer in African Americans. Front Immunol. 7:53. doi: our fine-mapping efforts have been far from routine. We have 10.3389/fimmu.2016.00053. eCollection 2016. Review. had to utilize ancestry informative markers in order to identify PMID: 26941739 and account for differences in ancestral proportions within the • Batai, K., Murphy, A.B., Ruden, M., Newsome, J., Shah, E., population. We have also taken advantage of the increased Dixon, M.A., Jacobs, E.T., Hollowell, C.M., Ahaghotu, C., admixture linkage disequilibrium within these chromosomal and Kittles, R.A. (2016) Race and BMI modify associations regions in order to localize functional variants. of calcium and vitamin D intake with prostate cancer. BMC The role of vitamin D in Pca disparities Cancer. 17(1):64. doi: 10.1186/s12885-017-3060-8. PMID: We have worked extensively on the epidemiology of vitamin D 28103838 deficiency and Pca. Our lab explores genetic and environmental • Bress, A., Kittles, R., Wing, C., Hooker Jr., S.F., and King, A. modifiers of serum and prostatic vitamin D levels. We have (2015) Genetic ancestry as an effect modifier of naltrexone developed genetic risk scores for vitamin D deficiency and in smoking cessation among African Americans: an analysis evaluated the effects of vitamin D deficiency on biopsy of a randomized controlled trial. Pharmacogenet Genomics. outcomes and aggressive clinical features. We have shown that 25(6):305-12. doi: 10.1097. PMID: 25918964
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 67 Marcin Kortylewski, Ph.D. Associate Professor, Department of Cancer Immunotherapeutics and Tumor Immunology
IMMUNE CELLS AS TARGETS FOR CANCER THERAPY
Fighting tumors by activating the immune system to search Our current research goals are: and destroy cancer cells with high precision could overcome A. To unravel the mechanism of therapeutic effects of the problem of serious side effects observed after conventional CpG-STAT3 inhibitors on myeloid leukemia and B cell cancer treatments. Recent advances in the understanding lymphoma cells of interactions between tumors and the immune system B. To identify new tolerogenic transcription factors and/ demonstrated that immune cells accumulated within tumor or miRNAs that promote resistance of solid tumors to tissue are essential therapeutic targets for cancer therapy. radiation therapy Dysfunctional dendritic cells, macrophages and other myeloid cell populations within the tumor microenvironment secrete C. To develop clinically relevant, oligonucleotide strategies for growth factors, promote blood vessel formation and dampen cancer immunotherapy anti-tumor effects of the immune system. Blocking oncogenic and immunosuppressive signaling pathways in tumor- SELECTED PUBLICATIONS associated immune cells can restore the anti-tumor immunity • Mini-review: Kortylewski, M., and Moreira, D. Myeloid inducing complete regression of established tumors. However, cells as a target for oligonucleotide therapeutics: targeting immune cells in the tumor microenvironment turning obstacles into opportunities. Cancer Immunol. poses problems due to the lack of specific therapeutics. Immunother., 66, 2017. We previously developed a novel strategy for cell-selective • Zhao, X., Zhang, Z., Moreira, D., Su, Y.L., Won, H., Adamus, delivery of therapeutic oligonucleotides (such as siRNA, T., Dong, Z., Liang, Y., Yin, H.H., Swiderski, P., Pillai, R.K., miRNA or decoy DNA) into human and mouse dendritic cells, Kwak, L., Forman, S., and Kortylewski, M. B Cell Lymphoma macrophages and B cells. Immunotherapy Using TLR9-Targeted Oligonucleotide Our TLR9-specific oligonucleotides are bifunctional, STAT3 Inhibitors. Mol. Ther. 26, 2018. simultaneously activating immunity and inhibiting • Zhang, Q., Hossain, D.M.S., Duttagupta, P., Moreira, D., tolerogenic signaling, such as STAT3, which results in Zhao, X., Won, H., Buettner, B., Nechaev, S., Majka, M., potent immunostimulatory and anti-tumor activity in mice. Zhang, B., Cai, Q., Swiderski, P., Kuo, Y.H., Forman, S., Such oligonucleotide therapeutics overcome limitations of Marcucci, G., and Kortylewski M. Serum-resistant CpG- current pharmacologic drugs and antibody-based strategies STAT3 decoy for targeting survival and immune checkpoint in targeting undruggable transcription factors which drive signaling in acute myeloid leukemia. Blood, 123, 2016. tumor immune evasion and resistance to standard therapies. e-pub: blood-2015-08-665604; PMID: 26796361. We validated the use of CpG-STAT3 inhibitors against several TLR9-positive human hematologic malignancies • Hossain, D.M.S., Pal, S.K., Moreira, D.F., Duttagupta, P., (myeloid leukemias and B cell lymphomas) and in certain Zhang, Q., Won, H., Jones, J.O., D’Apuzzo, M., Forman, solid tumors (metastatic prostate cancers, head and S.J., and Kortylewski, M. TLR9-Targeted STAT3 Silencing Abrogates Immunosuppressive Activity of Myeloid- neck cancers and glioma). In our most recent studies, we Derived Suppressor Cells from Prostate Cancer Patients. also adapted this strategy for targeting oncogenic and Clin Cancer Res., 21, 3771-3782, 2015. PMID: 25967142 immunomodulatory miRNAs in hematologic malignancies. The first two generations of CpG-STAT3 inhibitors are currently in translation for clinical testing in B cell lymphoma. In the long run, our strategy can become a technology platform for broad application in immunotherapy of human malignancies.
68 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Hsun Teresa Ku, Ph.D. Associate Professor, Department of Translational Research and Cellular Therapeutics
PANCREATIC STEM CELLS
Pancreatic stem and progenitor cells insulin-secreting cells derived from human pluripotent Type 1 diabetes (T1D) occurs when insulin-secreting beta cells stem cells in vitro. This cell population will be a suitable residing in the islets of Langerhans within the pancreas are development candidate for future clinical cell replacement destroyed by autoimmune attacks. End-stage T1D patients can therapy for T1D. However, the maturity of the beta-like cells be effectively managed by allogeneic islet cell transplantation generated from pluripotent stem cells has not yet matched using cadaveric organs. However, a dearth of the available their adult counterpart. Our laboratory is investigating what donor organs limits this promising treatment. One way to factors may enhance the further maturation of the beta-like overcome the donor shortage is to generate therapeutic cells derived from pluripotent stem cells in culture. beta-like cells from stem cells that have the capacity to self- renew and to differentiate into beta-like cells in a culture dish. SELECTED PUBLICATIONS The goal of our laboratory is to understand the biology of • Jin, L., Feng, T., Shih, H.P., Zerda, R., Luo, A., Hsu,J., pancreatic stem cells and manipulate these cells to advance Mahdavi, A., Sander, M., Tirrell, D.A., Riggs, A.D., and Ku, cell-replacement therapy for patients with T1D. H.T. Colony-forming cells in the adult mouse pancreas are expandable in Matrigel and form endocrine/ acinar Identification and characterization of stem and progenitor colonies in laminin hydrogel, Proc Natl Acad Sci USA, 110 cells in the adult pancreas (2013) 3907-3912. Whether stem and progenitor cells exist in the adult pancreas • Jin, L., Feng, T., Zerda, R., Chen, C.C., Riggs, A.D., and Ku, is highly controversial. To address this question, our laboratory H.T. In Vitro Multilineage Differentiation and Self- Renewal has devised colony assays that allow quantitative analyses of of Single Pancreatic Colony-Forming Cells from Adult adult pancreatic progenitor cells in a culture dish. We have C57Bl/6 Mice, Stem Cells Dev, 23 (2014) 899-909. named these cells “pancreatic colony-forming units (PCFUs)” • Ghazalli, N., Mahdavi, A., Feng, T., Jin, L., Kozlowski, M.T., because they are able to form colonies in 3-D space in Hsu, J., Riggs, A.D., Tirrell, D.A., and Ku, H.T. Postnatal methycellulose-containing semisolid media. Methylcellulose Pancreas of Mice Contains Tripotent Progenitors Capable is a viscous, biologically-inert material. Our colony assays of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro, allow single cell analysis to discern whether a progenitor cell Stem Cells Dev, 24 (2015) 1995-2008. is multipotent, oligopotent or monopotent. Using pancreatic • Jin, L., Gao, D., Feng, T., Tremblay, J., Quijano, J., Wedeken, colony assays, we found that adult PCFUs are a minor L., Luo, A., Hsu, J., Mahdavi, A., Ghazalli, N., Tirrell, D.A., population (~1% of total pancreatic cells) in the adult murine Riggs, A.D., and Ku, H.T. Cells with surface expression of pancreas. PCFUs can self-renew and differentiate into the CD133 high CD71 low are enriched for tripotent colony- three major cell lineages in the pancreas: endocrine, acinar forming progenitor cells in adult murine pancreas, Stem Cell Res, 16 (2016) 40-53. and ductal cells. The endocrine, insulin-secreting, beta-like cells generated from the adult PCFUs in culture are functional • Wedeken, L., Luo, A., Tremblay, J.R., Rawson, J., Jin,L., in glucose- stimulated insulin secretion. Collectively, these Gao, D., Quijano, J., and Ku, H.T. Adult Murine Pancreatic Progenitors Require Epidermal Growth Factor and results suggest that PCFUs from adult pancreas are stem-like Nicotinamide for Self-Renewal and Differentiation in a cells. Several important questions remain to be investigated. Serum- and Conditioned Medium-Free Culture. Stem Cells For example, what are the cellular and molecular mechanisms Dev. 2017 Apr 15;26(8):599-607. by which adult PCFUs regulate self-renewal and differentiation, • Ghazalli, N., Wu, X., Walker, S., Trieu, N., Hsin, L.-Y., Choe, can one purify adult PCFUs to homogeneity, and can PCFUs J., Chen, C., Hsu, J., LeBon, J., Kozlowski, M.T., Rawson, reconstitute adult pancreas in vivo after injury? Studies are J. Tirrell, D.A., Yip, M.L.R. and Ku, H.T. Glucocorticoid underway in our laboratory to address these questions. signaling enhances expression of glucose-sensing Pluripotent Stem Cell Therapy for Type 1 Diabetes molecules in immature pancreatic beta-like cells derived from murine embryonic stem cells in vitro. Stem Cells Dev. We have established a potentially cost-effective differentiation 2018 In Press. protocol, and generated a population of glucose-responsive,
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 69 Ya-Huei Kuo, Ph.D. Associate Professor, Division of Hematopoietic Stem Cell and Leukemia Research
MOLECULAR GENETICS OF HEMATOPOIETIC STEM CELLS AND LEUKEMIA STEM CELLS
Acute myeloid leukemia (AML) is the most common type • Qi, J., Singh, S., Hua, W.K., Cai, Q., Chao, S-W,, Li, L., Liu, H., of leukemia in adults with more than 21,000 new cases Ho, Y., McDonald, T., Lin, A., Marcucci, G., Bhatia, R., Huang, diagnosed in the United States each year. Despite considerable W-J., Chang, C-I., and Kuo, Y.H. (2015) HDAC8 inhibition specifically targets inv(16) acute myeloid leukemia stem improvement of survival rates for patients with leukemia over cells by restoring p53 acetylation. Cell Stem Cell 17:5, 597- the past 50 years, the overall five-year relative survival rate 610, PMID: HYPERLINK “tel:26387755” 26387755; PMCID: for AML patients is only approximately 20 percent. Leukemia PMC4636961 (Cover) stem cells (LSCs) are now recognized as the critical “seeds” • Kuo, Y.H., Zaidi, S.K., Gornostaeva, S., Komori, T., Stein, G.S., of leukemia, and represent a fundamental challenge thought and Castilla, L.H. (2009) Runx2 induces acute myeloid to underlie poor outcome due to their relative resistance to leukemia in cooperation with Cbfb-SMMHC in mice. Blood standard chemotherapy. Our long-term goal is to elucidate the 113(14): 3323-32. molecular mechanism(s) regulating the maintenance of LSCs, • Li, L., Osdal, T., Ho, Y., Chun, S., McDonald, T., Agarwal, P., to understand how they differ from normal hematopoietic stem Lin, A., Chu, S., Qi, J., Li, L., Hsieh, Y-T., Dos Santos, C., Yuan, cells and to develop novel LSC-targeted therapeutics. H., Popa, M., Gjertsen, B.T., Kuo, Y.H., Chen, W., Lain, S., McCormack, E., and Bhatia, R. (2014) SIRT1 activation by Using a genetic mouse model of a common chromosome a c-MYC Oncogenic Network Promotes the Maintenance aberration found in AML patients, known as inv(16), we and Drug Resistance of Human FLT3-ITD Acute Myeloid have shown that leukemia arises as a result of a multistep Leukemia Stem Cells. Cell Stem Cell 15(4): 431-46. transformation process involving mutations that disrupt • Kortylewski, M., and Kuo, Y.H. (2014) Push and release: hematopoietic differentiation, and those that deregulate TLR9 activation plus STAT3 blockade for systemic antitumor proliferation and self-renewal programs. Our current research immunity. OncoImmunology 3(1): e27441. efforts are directed toward understanding the molecular • Hossain, D.M., Dos Santos, C., Zhang, Q., Kozlowska, A., Liu, pathways and functional mediators regulating normal H., Gao, C., Moreira, D., Swiderski, P., Jozwiak, A., Kline, J., Forman, S., Bhatia, R., Kuo, Y.H., and Kortylewski, M. (2014) hematopoiesis, as well as those underlying leukemogenesis Leukemia cell-targeted STAT3 silencing and TLR-9-triggering using a combination of genetics, genomics, biochemistry, generate systemic antitumor immunity. Blood 123(1): 15-25. proteomics, molecular biology and cellular biology approaches. • Dos Santos, C. McDonald, T., Ho, Y.W., Liu, H., Lin, A., We use defined genetic mouse models as an experimental Forman, S.J., Kuo, Y.H., and Bhatia, R. (2013) The Src and system to identify molecular pathways and targets, and c-Kit kinase inhibitor dasatinib enhances p53-mediated primary cells from AML patients to validate the findings and targeting of human acute myeloid leukemia stem cell by perform further translational and preclinical studies. We chemotherapeutic agents. Blood 122(11): 1900-13. believe that a comprehensive understanding of oncogenic • Jeannet, R., Cai, Q., Liu, H., Vu, H., and Kuo, Y.H. Alcam mechanisms will enable rational design and selection of regulates long-term hematopoietic stem cell engraftment and self-renewal. Stem Cells 31: 560-571, 2013. improved cancer treatments. • Pulikkan, J.A., Madera, D., Xue, L., Bradley, P., Landrette, SELECTED PUBLICATIONS S.F., Kuo, Y.H., Abbas, S., Zhu, L.J., Valk, P., and Castilla, L.H. THPO/MPL participates in initiating and maintaining RUNX1- • Cai, Q., Jeannet, R., Hua, W.K., Cook, G.J., Zhang, B., Qi, J., ETO acute myeloid leukemia via PI3K/AKT signaling. Blood Liu, H., Li, L., Chen, C.C., Marcucci, G., and Kuo, Y.H. (2016) 120(4):868-879, 2012. CBFβ-SMMHC creates aberrant megakaryocyte-erythroid progenitors prone to leukemia-initiation in mice. Blood • Kuo, Y.H., Zaidi, S.K., Gornostaeva, S., Komori, T., Stein, G.S., 128(11): 1503-15. and Castilla, L.H. Runx2 induces acute myeloid leukemia in cooperation with Cbfβ-SMMHC in mice. Blood 113: 3323- • Kuo, Y.H., Qi, J., and Cook, G.J. (2016) Regain control of p53: 3332, 2009. targeting leukemia stem cells by isoform-specific HDAC • Kuo, Y.H., Gerstein, R.M., and Castilla, L.H. CbfbSMMHC inhibition. Exp Hematol. 44(5):315-21. impairs differentiation of common lymphoid progenitors and • Zhang, Q., Hossain, D.M., Duttagupta, P., Moreira, D., Zhao, reveals an essential role for RUNX in early B cell development. X., Won, H., Buettner, R., Nechaev, S., Majka, M., Zhang, B., Blood 111: 1543-1551, 2008. Cai, Q., Swiderski, P., Kuo, Y.H., Forman, S., Marcucci, G., and • Kuo, Y.H., Landrette, S.F., Heilman, S.A., Perrat, P.N., Garrett, Kortylewski, M. (2016) Serum-resistant CpG-STAT3 decoy L., Liu, P.P., Le Beau, M.M., Kogan, S.C., and Castilla, L.H. for targeting survival and immune checkpoint signaling in Cbfb-SMMHC induces distinct abnormal myeloid progenitors acute myeloid leukemia. Blood 127(13):HYPERLINK “tel:1687- able to develop acute myeloid leukemia. Cancer Cell 9: 57-68, 700” 1687-700. 2006.
70 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Larry W. Kwak, M.D., Ph.D. Vice President and Deputy Director, Comprehensive Cancer Center Director, Toni Stephenson Lymphoma Center Dr. Michael Friedman Professor in Translational Medicine Professor, Department of Hematology & Hematopoietic Stem Cell Transplantation
HEMATOLOGIC MALIGNANCIES AND STEM CELL TRANSPLANTATION INSTITUTE, TONI STEPHENSON LYMPHOMA CENTER
Larry W. Kwak, M.D., Ph.D., is an internationally recognized we isolated after many rounds of screening depleted MDSC physician scientist who is well known for pioneering bench- in the tumors of mice more effectively than other available to-bedside translational development of cancer vaccine antibodies, and importantly, treatment resulted in marked strategies. Kwak’s key scientific accomplishments include: inhibition of tumor growth. Preliminary experiments suggest 1) identification of GM-CSF as an integral component to that this same marker is also a target on human MDSC, making enhance the potency of lymphoma vaccines in laboratory clinical application likely. models, 2) pioneering clinical trials of a cancer vaccine which elicited lymphoma-specific T cell responses and molecular SELECTED PUBLICATIONS remissions associated with favorable clinical outcomes, and 3) • Kwak, L.W., Campbell, M.J., Czerwinski, D.K., Hart, S., Miller, championing the technology transfer of a unique personalized R.A., and Levy, R. Induction of immune responses in patients lymphoma vaccine from academic laboratory to commercial with B-cell lymphoma against the surface-immunoglobulin sector and completion of a positive phase 3 controlled trial. idiotype expressed by their tumors. New England Journal of Kwak’s research has led to the invention of a novel genetic Medicine 327(17):1209-15, 1992. vaccine delivery platform targeting antigen delivery to antigen • Bendandi, M., Gocke, C.D., Kobrin, C.B., Benko, F.A., Sternas, presenting cells to elicit potent T cell immunity. This discovery L.A., Pennington, R., Watson, T.M., Reynolds, C.W., Gause, grew out of our desire to develop a DNA vaccine which did not B.L., Duffey, P.L., Jaffe, E.S., Creekmore, S.P., Longo, D.L., require protein expression. Specifically, lymphoma antigen, and Kwak, L.W. Complete molecular remissions induced genetically fused to a proinflammatory chemokine, elicited by patient-specific vaccination plus granulocyte-monocyte potent anti-tumor immunity in animal tumor models. colony-stimulating factor against lymphoma. Nature Medicine 5(10):1171-7, 1999.
• Biragyn, A., Tani, K., Grimm, M.C., Weeks, S., and Kwak, L.W. Genetic fusion of chemokines to a self tumor antigen induces protective, T-cell dependent antitumor immunity. Nature Biotechnology 17(3):253-8, 1999.
• Biragyn, A., Ruffini, P.A., Leifer, C.A., Klyushnenkova, E., Shakhov, A., Chertov, O., Shirakawa, A.K., Farber, J.M., Segal, D.M., Oppenheim, J.J., and Kwak, L.W. Toll like receptor 4 Currently, Kwak’s laboratory is focused on discovering a marker activation of dendritic cells mediated by the endogenous that will allow depletion of an elusive suppressor cell type, antimicrobial peptide B-defensin-2. Science 298:1025-9, termed myeloid-derived suppressor cells (MDSC) in tumor 2002. microenvironments. MDSC are rare, but potent cells which are • Qin, H., Lerman, B., Sakamaki, I., Wei, G., Cha, S.C., Rao, capable of infiltrating most human cancers and suppressing S.S., Qian, J., Hailemichael, Y., Nurieva, R., Dwyer, K.C., Roth, the immune response in the tumor microenvironment. Because J., Yi, Q., Overwijk, W.W., and Kwak, L.W. Generation of these cells share surface markers with normal blood cells, it is a new therapeutic peptide that depletes myeloid-derived difficult to remove them from the body. Our team discovered suppressor cells in tumor-bearing mice. Nature Med. a way to eliminate such suppressive cells by using therapeutic 20(6):676-81, 2014. peptides that do not harm other vital cells. We invented a new technology adapting a random peptide phage library to mass- screen for peptides that bound only to MDSC. The peptides
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 71 Keane Lai, M.D. Associate Clinical Professor, Departments of Pathology and Molecular Medicine
LIVER CANCER AND PANCREATIC CANCER
The research laboratory of Keane Lai, M.D., has as its primary via a Wnt Positive-Signaling Loop by Stabilization of Low- focus studies on the molecular mechanisms underlying the Density Lipoprotein-Receptor-Related Proteins 5 and 6. development of hepatocellular carcinoma (HCC)/liver cancer Gastroenterology 152(6):1477-1491, 2017. PubMed PMID: and pancreatic ductal carcinoma (PDAC)/pancreatic cancer. 28143772. (*Co-first author.) The Lai Lab is particularly interested in dissecting the role of the Wnt/β-catenin signaling pathway (and related signaling • Manegold, P.*, Lai, K.K.Y.*, Wu, Y., Teo, J.L., Lenz, H.J., Genyk, pathways) and identifying novel therapeutic targets to combat Y.S., Pandol, S.J., Wu, K., Lin, D.P., Chen, Y., Nguyen, C., HCC and PDAC which are highly lethal cancers. Zhao, Y., and Kahn, M. Differentiation Therapy Targeting the Stearoyl-CoA desaturase (SCD) promotes liver cancer β-Catenin/CBP Interaction in Pancreatic Cancer. Cancers development via a Wnt/β-catenin/SCD feedback loop 10(4). pii: E95, 2018. PubMed PMID: 29596326. (*Co-first Stearoyl-CoA desaturase (SCD), which encodes for a critical author.) and essential enzyme used to generate bioreactive mono- • Xu, J.*, Lai, K.K.*, Verlinsky, A., Lugea, A., French, unsaturated fatty acids (MUFA), is a Wnt/β-catenin target S.W., Cooper, M., Ji, C., and Tsukamoto, H. Synergistic gene. Scd2 knockdown in liver tumor-initiating cells (TICs), also known as cancer stem cells, inhibits proliferation and steatohepatitis by moderate obesity and alcohol in mice self-renewal in vitro, and prevents TIC-initiated tumorigenesis despite increased adiponectin and p-AMPK. J Hepatol in mice. SCD-induced liver cancer development occurs via a 55:673-82, 2011. PubMed PMID:21256905. (*Co-first novel mechanism by which SCD facilitates a positive feedback author.) loop for β-catenin via MUFA-dependent LRP6 expression, • Lai, K.K., Jin, M., Yuan, S., Larson, M.F., Dominitz, J.A., and which serves to activate oncogenic TICs. SCD is thus a novel Bankson, D.D. An improved reflexive testing algorithm therapeutic target for liver cancer. for hepatitis C infection utilizing signal-to-cutoff ratios of Therapeutically targeting the β-Catenin/CBP interaction in an anti-HCV antibody assay. Clin Chem 57:1050-6, 2011. pancreatic cancer PubMed PMID: 21566071. To investigate Wnt-mediated carcinogenesis in pancreatic cancer, the specific small molecule CBP/β-catenin antagonist, • Lai, K.K.*, Shang, S.*, Lohia, N., Booth, G.C., Masse, D.J., ICG-001 (identified by collaborator Michael Kahn), has been Fausto, N., Campbell, J.S., and Beretta, L. Extracellular used to examine its effects in human pancreatic cancer cells matrix dynamics in hepatocarcinogenesis: a comparative and in both an orthotopic mouse model and a human patient- proteomics study of PDGFC transgenic and Pten null mouse derived xenograft model of pancreatic cancer. K-Ras activation models. PLoS Genet 7(6):e1002147, 2011. PubMed PMID: increases the CBP/ -catenin interaction in pancreatic cancer; β 21731504. (*Co-first author.) ICG-001 specific antagonism of the CBP/β-catenin interaction sensitizes pancreatic cancer cells and tumors to gemcitabine • Lai, K.K., Kolippakkam, D., and Beretta, L. Comprehensive treatment. These therapeutic effects are associated with and quantitative proteome profiling of the mouse liver increases in the expression of let-7a microRNA; suppression of and plasma. Hepatology 47:1043-51, 2008. PubMed K-Ras and survivin; and the elimination of drug-resistant cancer PMID:18266228. stem/tumor-initiating cells. • Pal, S., Sullivan, D.G., Kim, S., Lai, K.K.Y., Kae, J., Cotler, SELECTED PUBLICATIONS S.J., Carithers Jr., R.L., Wood, B.L., Perkins, J.D., and • Lai, K.K.Y.*, Kweon, S.M.*, Chi, F.*, Hwang, E.*, Kabe, Y., Gretch D.R. Productive replication of hepatitis C virus Higashiyama, R., Qin, L., Yan, R., Wu, R.P., Lai, K., Fujii, N., in perihepatic lymph nodes in vivo: implications of HCV French, S., Xu, J., Wang, J.Y., Murali, R., Mishra, L., Lee, J.S., lymphotropism. Gastroenterology 130:1107-16, 2006. PubMed Ntambi, J.M., and Tsukamoto, H. Stearoyl-CoA Desaturase PMID:16618405. Promotes Liver Fibrosis and Tumor Development in Mice
72 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Mark LaBarge, Ph.D. Professor, Department of Population Sciences Deputy Director of Center for Cancer and Aging Research
THE CELL AND TISSUE BIOLOGY OF AGING AND CANCER SUSCEPTIBILITY
The team of Mark LaBarge, Ph.D., specializes in developing SELECTED PUBLICATIONS human cell systems for understanding why aging is a major risk • Pelissier Vatter, F.A., Schapiro, D., Chang, H., Borowsky, factor for breast cancer. The objectives of his research program A.D., Lee, J.K., Parvin, B., Stampfer, M.R., LaBarge, M.A., are to generate a comprehensive understanding of the micro- Bodenmiller, B., and Lorens’ J.B. Cell Rep. 2018 Apr environmental and tissue-level changes in breast that arise 24;23(4):1205-1219. doi: 10.1016/j.celrep.2018.03.114. PMID: with age, and then develop a functional understanding of how 29694896 those changes alter mammary gland homeostasis, contribute to breast tumor genesis and modulate activity of therapeutics. • Lin, C.H., Jokela, T., Gray, J., and LaBarge, M.A. Cell Rep. 2017 Oct 10;21(2):533-545. doi: 10.1016/j.celrep.2017.09.058. A cornerstone of their approach involves the use of a growing PMID: 29020637 collection of primary human mammary epithelial cell (HMEC) strains, dubbed the HMEC Aging Resource, that were derived • Miyano, M., Sayaman, R.W., Stoiber, M.H., Lin, C.H., from reduction mammoplasty, mastectomy and peripheral Stampfer, M.R., Brown, J.B., and LaBarge, M.A. Aging tumor dissections. They explore the functional impact of (Albany NY). 2017 Oct 9;9(10):2026-2051. doi: 10.18632/ aging on various lineages of HMEC, at different stages of aging.101298. PMID: 29016359 cancer progression, by probing them with combinatorial • Pelissier, F.A., Garbe, J.C., Ananthanarayanan, B., Miyano, bioengineered culture substrata and measuring outcomes M., Lin, C., Jokela, T., Kumar, S., Stampfer, M.R., Lorens, quantitatively with imaging and molecular analyses. In doing J.B., and LaBarge, M.A. Cell Rep. 2014 Jun 26;7(6):1926-39. so, they continue to derive a catalog of micro-environmental, doi: 10.1016/j.celrep.2014.05.021. Epub 2014 Jun 5. PMID: epigenetic, genetic, cellular, and tissue-level changes that occur 24910432 normally with age, and are trying to determine mechanistically which of those changes increase the vulnerability of older • Garbe, J.C., Pepin, F., Pelissier, F.A., Sputova, K., Fridriksdottir, women to breast cancer. Put differently, they are deriving a A.J., Guo, D.E., Villadsen, R., Park, M., Petersen, O.W., growing list of potential therapeutic targets and biomarkers of Borowsky, A.D., Stampfer, M.R., and Labarge, M.A. Cancer breast aging and breast cancer susceptibility. Res. 2012 Jul 15;72(14):3687-701. doi: 10.1158/0008-5472. CAN-12-0157. Epub 2012 May 2. PMID: 22552289 LaBarge says his dream is to identify primary breast cancer prevention modalities that are so safe, they become commonplace.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 73 Peter P. Lee, M.D. Billy and Audrey L. Wilder Professor in Cancer Immunotherapeutics Professor, Department of Hematology & Hematopoietic Cell Transplantation Chair, Department of Immuno-Oncology
THE IMPACT OF CANCER ON IMMUNE FUNCTION
The focus of my research is on understanding how cancer SELECTED PUBLICATIONS impacts host immune responses in patients, with the goal • Chung, B., Esmaeili, A.A., Gopalakrishna-Pillai, S., Murad, J.P., of developing novel treatments to restore/enhance immune Andersen, E.S., Kumar Reddy, N., Srinivasan, G., Armstrong, function in cancer patients. My group utilizes state-of-the- B., Chu, C., Kim, Y., Tong, T., Waisman, J., Yim, J.H., Badie, B., art technologies – such as high-dimensional flow cytometry, and Lee, P.P. NPJ Breast Cancer. 2017 Mar 2;3:6. doi: 10.1038/ quantitative spatial image analysis and next-generation s41523-017-0008-8. eCollection 2017. PMID: 28649646 genomics – to dissect the complex interplay between immune/ stromal cells and cancer cells within tumors, tumor-draining • Wang, L., Miyahira, A.K., Simons, D.L., Lu, X., Chang, A.Y., lymph nodes (TDLNs) and blood. Through image analysis of Wang, C., Suni, M.A., Maino, V.C., Dirbas, F.M., Yim, J., breast tumors and TDLNs, we have found that immune cell Waisman, J., and Lee, P.P. Cancer Res. 2017 Mar 1;77(5):1119- populations, as well as their spatial distributions and clustering 1126. doi: 10.1158/0008-5472.CAN-16-1373. Epub 2016 Nov patterns, have strong correlation with clinical outcome. My 22. PMID: 27879265 group has also shown that lymphocytes from patients with • Munson, D.J., Egelston, C.A., Chiotti, K.E., Parra, Z.E., Bruno, breast cancer, melanoma and colorectal cancer develop T.C., Moore, B.L., Nakano, T.A., Simons, D.L., Jimenez, G., immune signaling defects that blunt their proliferation and Yim, J.H., Rozanov, D.V., Falta, M.T., Fontenot, A.P., Reynolds, function in vivo. We are currently extending these findings in P.R., Leach, S.M., Borges, V.F., Kappler, J.W., Spellman, P.T., multiple directions, including to other human cancers such as Lee. P,P,, and Slansky, J.E. Proc Natl Acad Sci USA. 2016 Jul prostate cancer and leukemia. A unique focus of my work is 19;113(29):8272-7. doi: 10.1073/pnas.1606994113. Epub 2016 on the impact of heterogeneity within tumors and tumor cell Jun 15. PMID: 27307436 populations, including subpopulations commonly referred to as ‘cancer stem cells,’ on the immune response. We utilize • Stack, E.C., Foukas, P.G., and Lee, P.P. J Immunother computational modeling and network analysis to understand the Cancer. 2016 Feb 16;4:9. doi: 10.1186/s40425-016-0115-3. population dynamics of cancer and immune responses, as well eCollection 2016. No abstract available. PMID: 26885371 as control theory to find novel interventions. As such, my group • Draganov, D., Gopalakrishna-Pillai, S., Chen, Y.R., Zuckerman, is highly interdisciplinary, combining immunology, pathology, N., Moeller, S., Wang, C., Ann, D., and Lee, P.P. Sci Rep. 2015 genomics, bioinformatics, mathematical modeling, computer Nov 10;5:16222. doi: 10.1038/srep16222. PMID: 26552848 science, engineering, network analysis and control systems. • Chang, G.Y., Kohrt, H.E., Stuge, T.B., Schwartz, E.J., Weber, J.S., and Lee, P.P. Cytotoxic T lymphocyte responses against melanocytes and melanoma. J. Transl. Med. 9: 122, 2011.
• Setiadi, A.F., Ray, N.C., Kohrt, H.E., Kapelner, A., Carcamo- Cavazos, V., Levic, E.B., Yadegarynia, S., van der Loos, C., Schwartz, E.J., Holmes, S.P., and Lee, P.P. Quantitative, architectural analysis of immune cell subsets in tumor- draining lymph nodes from breast cancer patients and healthy lymph nodes. PLoS ONE 5(8): e12420. DOI:10.1371/ journal.pone.0012420, 2010.
• Critchley-Thorne, R.J., Simons, D.L., Yan, N., Miyahira, A.K., Dirbas, F.M., Johnson, D.L., Swetter, S.M., Carlson, R.W., Fisher, G.A., Koong, A., Holmes, S., and Lee, P.P. Impaired
74 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Ren-Jang Lin, Ph.D. Professor, Department of Molecular and Cellular Biology Associate Dean for Curriculum, Irell & Manella Graduate School of Biological Sciences
RNA SPLICING, MICRORNA AND GENE SCREENING
RNA splicing factors with disease mutations miR-151a expression group than in the low expression group. Pre-mRNA splicing is catalyzed by the spliceosome and is Moreover, p21/CDKN1A expression is negatively correlated essential for proper gene expression. Spliceosomal mutations with miR-151a expression in many cancers and in no case is are found in human diseases; however, their pathological there a positive correlation. The importance of dysregulating roles are not understood. We are investigating two splicing miR-151a and p21 in cancer is being evaluated. The utility of factors (SRSF2 and ZRSR2) associated with myelodysplastic our microRNA-specific CRISPR library remains to be further syndromes (MDS). SRSF2 is an RNA-binding protein critical explored. for constitutive and alternative splicing, and its proline-95 is often mutated in MDS patients. We reported that SRSF2-P95 SELECTED PUBLICATIONS mutants cause a MDS-linked splicing change in CDC25C, • Liu, J., Geng, A., Wu, X., Lin, R.-J., and Lu, Q. (2017) a cell cycle phosphatase, which is ATM independent. How Alternative RNA splicing associated with mammalian SRSF2-P95 causes CDC25C alternative splicing and what role neuronal differentiation. Cereb Cortex 2017 June 23:1-7. CDC25C splice isoforms play remain to be elucidated. ZRSR2 • Liao, J., Lin, J., Lin, D., Zou, C., Kurata, J., Lin, R., He, Z., and is involved in 3’ splice site recognition, and loss-of-function Su, Y. (2017). Down-regulation of miR-214 reverses erlotinib mutations are found in this X-linked gene in 10% of MDS resistance in non-small-cell lung cancer through up- patients. We used TALEN to knock out the ZRSR2 gene and regulating LHX6 expression. Sci Rep 7:781. found ZRSR2-KO lines were defective in splicing of U12-type introns with imbalanced cell cycle and elevated autophagy • Skrdlant, L., Stark, J.M., and Lin, R.-J. (2016). Myelodysplasia- upon serum deprivation. These defects were rescued by associated mutations in serine/arginine-rich splicing factor ectopic expression of ZRSR2 or ZRSR1 — a paralog. Splicing SRSF2 lead to alternative splicing of CDC25C. BMC Mol Biol 17:18. perturbation and the involved U12-intron containing genes are being investigated. • Skrdlant, L., and Lin, R.-J. (2016) Characterization of RNA– protein interactions: lessons from two RNA-binding proteins, MicroRNA-specific CRISPR/Cas9 Library and SRSF1 and SRSF2. Methods Mol Biol 1421:1-13. miR-151a function MicroRNAs regulate cellular development, differentiation, • Zang, S. and Lin, R.-J. (2016) Northwestern blot analysis: proliferation, and apoptosis. The importance of microRNAs detecting RNA–protein interaction after gel separation of as cancer markers and targets are widely recognized. We protein mixture. Methods Mol Biol 1421:111-125. have investigated the pathobiological role of microRNA-21 by • Lin, R.-J. (2015) A magnesium-binding nucleotide, a generating knockout cell lines using TALEN. Cells lacking miR- remodeling ATPase, and a wonderful RNA world. RNA 21 were less transformed, more sensitive to genotoxic drugs, 21:680. and increased expression of genes involved in extracellular matrix interactions. To facilitate functional screening of human • Chen, B., Chen, X., Wu, X., Wang, X., Wang, Y., Lin, T. Y., Kurata, J., Wu, J., Vonderfecht, S., Sun, G., Huang, H., Yee, J. microRNAs, we designed a genome-wide microRNA-focused K., Hu, J., and Lin, R.-J. (2015) Disruption of microRNA-21 by sgRNA library based on crispr-Cas9. We used this sgRNA TALEN leads to diminished cell transformation and increased library to identify microRNAs that are involved in regulating expression of cell-environment interaction genes. Cancer Lett cell growth in cancer cell lines. By combining tumor expression 356:506-516. data, we identified several pro-fitness and putative oncogenic microRNAs. We generated miR-151a knockout lines, and • Zang, S., Lin, T. Y., Chen, X., Gencheva, M., Newo, A. N., through RNA-Seq and reporter assays identified de-repression Yang, L., Rossi, D., Hu, J., Lin, S. B., Huang, A., and Lin, R. J. (2014) GPKOW is essential for pre-mRNA splicing in vitro of the p53-p21 pathway. By analyzing TCGA database, we and suppresses splicing defect caused by dominant-negative found miR-151a is overexpressed in 13 of the 14 cancers that DHX16 mutation in vivo. Biosci Rep 34, 841-850. were available of paired tumor and normal tissues. Patient overall survival rates in several cancers are lower in the high
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 75 Yilun Liu, Ph.D. Associate Professor and Associate Chair, Department of Cancer Genetics and Epigenetics Program Director, Master of Science in Translational Medicine, Irell & Manella Graduate School of Biological Sciences HUMAN RECQ HELICASES IN AGING AND CANCER PREVENTION
DNA contains essential genetic information that cells SELECTED PUBLICATIONS transcribe via RNA polymerase II to generate transcripts • Olson, H.C., Davis, L., Kilanitsa, K., Khoo, K., Liu, Y., encoding proteins essential for cellular processes. Therefore, it Knijnenburg, T., and Maizels, N. (2018). Increased levels is critical to ensure that chromosomes remain intact and that of RECQ5 shift DNA repair from canonical to alternative DNA passed on to daughter cells is duplicated correctly to pathways. Nucleic Acids Research (in press). enable cell survival and growth. Unfortunately, DNA strands • Li, M., Xu, X., Chang, C., Zheng, L., Shen, B., and Liu, Y. can be broken following exposure to DNA-damaging agents, (2018). SUMO2 conjugation of PCNA facilitates chromatin and such damage can block replication and transcription, remodeling to resolve transcription-replication conflicts. leading to either apoptosis or to mutagenesis, the latter a Nature Communications 9:2706. precursor of tumorigenesis. DNA can also be broken during normal cellular processes in the absence of exogenous • Liu, Y. (2016) EEPD1: Breaking and rescuing the replication assault. Paradoxically, spontaneous DNA breaks can also be fork. PLoS Genetics 12, e1005742. a consequence of overlapping traffic and collisions between • Xu, X., Wang, J.T., Li, M., and Liu, Y. (2016) TIMELESS the DNA replisomes and transcriptional complexes, events suppresses the accumulation of aberrant CDC45-MCM2-7- that disrupt both replication and transcription and damage GINS replicative helicase complexes on human chromatin. DNA templates. Our research interests focus on how the Journal of Biological Chemistry 291, 22544-22558. human RECQ family helicases, which are important tumor • Li, M., and Liu, Y. (2016) Topoisomerase I in human disease suppressors, maintain genomic integrity. We have established pathogenesis and treatments; Special issue on genome novel models and obtained important mechanistic insights stability. Genomics Proteomics & Bioinformatics 14, 166-171. into (a) how the RECQ4 helicase facilitates efficient DNA • Li, M., Pokaharel, S., Wang, J., Xu, X., and Liu, Y. (2015) replication; (b) how a defect in RECQ4 helicase contributes RECQ5-dependent SUMOylation of DNA topoisomerase I to mitochondrial dysfunction and cancer pathogenesis; (c) prevents transcription-associated genome instability. Nature how the RECQ5 helicase maintains progression of the RNA Communications 6:6720. polymerase II-associated transcription complex to avoid collision with DNA replication machinery; and (d) how RECQ5 • Wang, J.T., Xu, X., Alontaga, A.Y., Chen, Y., and Liu, Y. (2014) avoids DNA breaks caused by naturally aborted topoisomerase Impaired p32 regulation caused by the lymphoma-prone 1 reactions that occur during transcription. While our RECQ4 mutation drives mitochondrial dysfunction. Cell Reports 7, 848-858. expertise is in basic cancer research, our research interests are expanding to explore the translational potential of targeting these enzymes for cancer prevention and treatment.
76 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Qiang Lu, Ph.D. Professor, Department of Developmental and Stem Cell Biology
UNDERSTANDING THE MECHANISMS THAT CONTROL SELF-RENEWAL AND DIFFERENTIATION OF NEURAL PROGENITOR/ STEM CELLS
Neural progenitor/stem cells can self-renew and are capable epigenetic control of the neural progenitor cell state. Our of generating neurons and glia, the major cell types that strategy is to use genetic modification to differentially label constitute the central nervous system. They are fundamentally neural progenitor cells and their immediate neuronal progeny important in the development of a functional nervous system. in the mouse cerebral cortex. This differential labeling The multipotent potential and the ability to self-renew also strategy provides us a platform to achieve co-purification of make them promising candidates in cell-based replacement endogenous neural progenitor cells and their progeny. We can therapy for repairing damaged nerves or treating neurological then apply advanced global genetic and epigenetic analysis to disorders. Under physiological conditions, neural progenitor/ identify candidate regulators and mechanisms with respect stem cells maintain a balance between the two cell states — to the decision of neural progenitor cells to either self-renew self-renewal and differentiation — and can shift the balance or differentiate. in response to environmental cues. Loss of this homeostasis can lead to defects in brain development and may be the SELECTED PUBLICATIONS cause of brain cancers. The long-term goal of our laboratory • Hahn, M.A., Qiu, R.X., Wu, X.W., Li, A.X., Wang, J., Zhang, is to understand the mechanisms that govern self-renewal H.Y., Jui, J., Jin, S.G., Jiang, Y. Pfeifer, G.P., and Lu, Q. Dynamics of 5-hydroxymethylcytosine and chromatin marks and differentiation and to apply this knowledge to developing in mammalian neurogenesis. Cell Reports 3: 291-300, 2013. novel treatments for neural regeneration and brain cancers. We • Wang, J., Zhang, H., Young, A.G., Qiu, R., Argalian, S., Li, study neural progenitor/stem cells using combined molecular, X., Wu, X., Lemke, G., and Lu, Q. Transcriptome analysis of cell biological and genetic approaches. neural progenitor cells by a genetic dual reporter strategy. Stem Cells 29: 1589-600, 2011. Our current research was directed toward identifying molecular determinants important for the self-renewal and • Qiu, R.X., Wang, J., Tsark, W., and Lu, Q. Essential role of differentiation of neural progenitor cells in the mammalian PDZ-RGS3 in the maintenance of neural progenitor cells. Stem Cells 28:1602-1610, 2010. cerebral cortex. During development, neural progenitor cells of the cerebral cortex initially expand within the ventricular • Murai, K., Qiu, R.X., Zhang, H.Y., Wang, J., Wu, C., Neubig, R.R., and Lu, Q. Galpha subunit coordinates with ephrin-B to zone (VZ). As corticogenesis proceeds, they differentiate balance self-renewal and differentiation in neural progenitor into neurons, which migrate out of the VZ into their final cells. Stem Cells 28:1581-1589, 2010. residence in the cortical plate. This developmental progression • Wu, C., Qiu, R.X., Wang, J., Zhang, H.Y., Murai, K., and of cortical neurogenesis provides a particularly good platform Lu, Q. ZHX2 interacts with ephrin-B and regulates neural for studying neural progenitor cell self-renewal, differentiation progenitor maintenance in the developing cerebral cortex. J. and migration. Neurosci. 29: 7404-7412, 2009. Our ongoing studies include two parallel approaches. (1) We • Qiu, R.X., Wang, X.Y., Davy, A., Wu, C., Murai, K., Zhang, H.Y., Flanagan, J.G., Soriano, P., and Lu, Q. Regulation of neural have recently discovered that ephrin-B and heterotrimeric G progenitor cell state by ephrin-B. J. Cell. Biol. 181: 973-983, protein signaling pathways coordinately regulate the balance 2008. between self-renewal and differentiation of neural progenitor • Wang, X.Y., Qiu, R.X., Tsark, W., and Lu, Q. Rapid promoter cells in the developing mouse cerebral cortex. Thus, we are analysis in developing mouse brains and genetic labeling of continuing to investigate the functions and the mechanisms young neurons by DoublecortinDsRed-express. J. Neurosci. of action of the ephrin/Eph family signaling molecules and Res. 85: 3567-3573, 2007. G proteins in neural progenitor/stem cells. (2) We also want to more broadly identify molecules and mechanisms critical for neural progenitor/stem cell regulation, in particular the
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 77 Ke Ma, M.D., Ph.D. Associate Professor, Department of Diabetes Complications and Metabolism
CIRCADIAN CLOCK CONTROL OF METABOLIC TISSUE GROWTH AND FUNCTION
As an evolutionarily-conserved mechanism for time-keeping, investigators, to specifically address how environmental the circadian clock governs diverse aspects of physiological lighting and shiftwork-induced circadian clock disruptions processes entrained by environmental cues to confer fitness lead to metabolic diseases, and its causal relationship with and survival. In addition to the central clock pacemaker development of cancer. The particular focus is on elucidating residing in suprachiasmatic nuclei that drives overt behavioral the genetic, epigenetic and signaling networks underlying rhythms, individual tissue and cell types possess cell- circadian misalignment-induced disease etiology in patients. autonomous clock oscillators. How tissue-intrinsic peripheral Ultimately, we envision our research to decipher temporal clock circuits in adipose depots, skeletal muscle and liver mechanisms in metabolic regulation and tissue growth orchestrates tissue metabolism in accordance with timing processes will uncover novel targeted clock interventions to cues to maintain homeostasis is a major focus of our research. prevent or treat metabolic diseases and cancer. Our modern lifestyle creates frequent conflicts between daily activity cycles and the endogenous clock timing, which SELECTED PUBLICATIONS poses significant risk to the development of metabolic • Nam, D., Yechoor, V.K. and Ma, K. Molecular clock disorders and cancer. In order to uncover circadian etiologies integration of brown adipose tissue formation and function. underlying metabolic dysregulations for targeted therapeutic Adipocyte DOI:10.1080/21623945. 2015;10820153. interventions, we strive to decipher the molecular and signaling • Nam, D., Chatterjee, S., Yin, H., Liu, R., Lee, J., Yechoor, V.K., pathways by which cell-autonomous clock circuits drive and Ma, K. Novel function of Rev-erb α in promoting brown metabolic tissue growth and functional capacity. Combining adipogenesis. Sci Rep. 2015 Jun 10;5:11239. biochemical and molecular/cellular biology approaches with • Nam, D., Guo, B., Chatterjee, S., Chen, M.H., Fang, Z., Nelson, state-of-the art circadian biology tools, we have successfully D., Yechoor, V.K., and Ma, K. The adipocyte clock controls established a unique research program in dissecting the brown adipogenesis through the TGF-β and BMP signaling temporal regulatory mechanisms in distinct adipose depots pathways. J Cell Sci. 2015 May 1;128(9):1835-47 and skeletal muscle critical for the maintenance of whole-body • Chatterjee, S., Nam, D., Guo, B., Kim, J.M., Winnier, G.E., Lee, metabolic homeostasis. J., Berdeaux, R., Yechoor, V.K., and Ma, K. Brain and Muscle Our current projects focus on these following directions Arnt-like 1 is a key regulator of myogenesis. J Cell Sci. 2013 1. W e aim to identify the genetic and epigenetic regulatory May 15;126(Pt 10):2213-24. networks mediating the nutrient-sensing functions of clock in • Guo, B., Chatterjee, S., Li, L., Kim, J.M., Lee, J., Yechoor, V.K., orchestrating metabolic homeostasis. We will further explore Minze, L.J., Hsueh, W., and Ma, K. The clock gene, brain and how dysregulation of these mechanisms may underlie the muscle Arnt-like 1, regulates adipogenesis via Wnt signaling development of obesity and type II diabetes. pathway. FASEB J. 2012 Aug;26(8):3453-63 • Huang, W., Ma, K., Zhang, J., Qatanani, M., Cuvillier, J., Liu, 2. W e will dissect the signaling mechanisms by which the J., Dong, B., Huang, X., and Moore, D.D. Nuclear receptor- cell-autonomous clock circuits coordinates stem/progenitor dependent bile acid signaling is required for normal liver properties to drive tissue development, growth and regeneration. Science. 2006 Apr 14;312(5771):233-6. remodeling processes in adipose tissue and skeletal muscle, • Ma, K., Saha, P.K., Chan., L., and Moore, D.D. Farnesoid X in order to gain insights into how tissue clock-controlled receptor is essential for normal glucose homeostasis. J Clin temporal pathways consequently impact metabolic capacity. Invest. 2006 Apr;116(4):1102-9. 3. The mechanistic insights garnered from animal models and pharmacological interventions will be applied to establish collaborative translational projects with clinical
78 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Linda Malkas, Ph.D. M.T. & B.A. Ahmadinia Professor in Molecular Oncology Professor and Associate Chair, Department of Molecular and Cellular Biology Deputy Director of Basic Research, Comprehensive Cancer Center
THE SELECTIVE TARGETING OF CANCER CELLS
The protein proliferation cell nuclear antigen (PCNA) plays • Smith, S., Li, C., Hickey, R.J., and Malkas, L.H., DNA an important role in the process of DNA replication, repair, Replication: Mammalian (2014) Nature Encyclopedia cell cycle check-point control and other cellular proliferative of Life Sciences: Published Online: 14 NOV 2014; DOI: activities. Different isoforms of PCNA that display both 10.1002/9780470015902.a0001041.pub3 acidic and basic isoelectric points have been demonstrated. • Lingeman, R., Hickey, R.J., and Malkas, L.H., Expression of We observed that a basically charged isoform was present a novel peptide derived from PCNA damages DNA and in nonmalignant cells and tissues (designated nmPCNA). reverses cisplatin resistance. Cancer Chemother Pharmacol. Our analyses also revealed that the basic PCNA isoform 2014 Nov; 74(5):981-93. DOI: 10.1007/s00280-014-2574-x. was also present in malignant cells and tissues; however, an Epub 2014 Sep 5. PMID:25190177 additional acidic form of PCNA was also highly expressed in • Chen, M.C., Zhou, B., Zhang, L., Yuan, Y.C., Un, F., Hu, S., these cells (referred to as the cancer-associated PCNA, or Chou, C.M., Chen, C.H., Wu, K., Wang, Y., Liu, X., Smith, L., caPCNA). An antibody was developed to this region of the Warden, C.D., Liu, Z., Li, H., Su, L., Malkas, L.H., Chung, Y.M., caPCNA that proved to be highly selective for this isoform in Hu, M.C., and Ye,n Y. The Novel Ribonucleotide Reductase cancer cells. We have identified peptides and small molecule Inhibitor COH29 Inhibits DNA Repair In Vitro. Mol (SM) compounds targeting caPCNA that promote cancer cell Pharmacol. 2015 Mar 26. pii : mol.114.094897[epub ahead of cytotoxicity. These agents have the potential ability to block print] PMID: 25814515 the binding of critical proteins that participate in a variety of • Perry, J.J., Ballard, G.D., Albert, A.E., Dobrolecki, L.E., Malkas, caPCNA dependent processes in cancer cells. This disruption L.H., and Hoelz, D.J. Human C6orf211 Encodes Armt1, a in the function of vital cellular processes would render these Protein Carboxyl Methyltransferase that Targets PCNA and SM compounds cytotoxic by themselves or in combination is Linked and to the DNA Damage Response. Cell Rep. 2015 with other anti-cancer chemotherapeutics. Our overarching Mar 3; 10(8):1288-96. doi: 10.1016/j.celrep.2015.01.054. research goal is to develop first-in-class compounds that target Epub 2015 Feb 26. PMID: 25732820 the novel cancer associated protein caPCNA. The selective • Zhang, W., et al., Comparison of RNA-seq and microarray- targeting of cancer cells by directly disrupting the interaction based models for clinical endpoint prediction. Genome Biol. between caPCNA and its natural binding partners would 2015 Jul 25; 16:133. doi: 10.1186/s13059-015-0649-1. PMID: represent a significant advance in the selective targeting of 26109056 [PubMed - in process]; PMCID: PMC4506430 cancer cells. • Gu, L., Chu, P., Lingeman, R., McDaniel, H., Kechichian, SELECTED PUBLICATIONS S., Hickey, R.J. , Liu, Z., Yuan, Y.C., Sandoval, J.A., Fields, G.B., and Malkas, L.H. The Mechanism by Which MYCN • Smith, S.J., Gu, L., Phipps, E.A., Dobrolecki, L.E., Mabrey, K.S., Amplification Confers an Enhanced Sensitivity to a PCNA- Gulley, P., Dillehay, K.L., Dong, Z., Fields, G.B., Chen, Y.R., Derived Cell Permeable Peptide in Neuroblastoma Cells, Ann, D., Hickey, R.J., and Malkas, L.H. A peptide mimicking EBioMedicine. 2015 Dec; 2(12): 1923-1931. Published online a region in proliferating cell nuclear antigen specific to 2015 Nov 10. doi: 10.1016/j.ebiom.2015.11.016. PMCID: key protein interactions is cytotoxic to breast cancer. Mol. PMC4703743 Pharmacol. 87: 263-276, 2015. • Smith, S.J., Hickey, R.J., and Malkas, L.H. Validating the • Dai, H., Liu, J., Hickey, R.J., Bigsby, R.M., Lanner, C., and disruption of proliferating cell nuclear antigen in the Malkas, L.H. Error-promoting DNA synthesis in ovarian development of targeted cancer therapeutics, Cancer Biol cancer cells. Gynecol Oncol. 2013 Oct;131(1):198-206. Ther. 2016; 17(3):310-9, doi:10.1080/15384047:2016.113924 DOI: 10.1016/j.gyno.2013.06.022. Epub 2013 Jul 12. 7. PMCID: PMC4847981 PMD:23851291 • Li, C.M., Miao, Y., Lingeman, R.G., Hickey, R.J., and Malkas, • Gu, L., Smith, S., Li, C., Hickey, R.J., Stark, J., Fields, G.B., Lang, L.H. Purification of a Megadalton DNA Replication Complex W.H., Sandoval, J.A., and Malkas, L.H. A PCNA-derived Cell by Free Flow Electrophoresis. PLoS One. 2016;11(12): Permeable Peptide Selectively Inhibits Neuroblastoma Cell e0169259. Published online 2016 Dec. 30. doi: 10.1371/ Growth, PLoS One. 2014 Apr 11; 9(4): e94773. doi: 10.1371/ journal.pone.0169259. PMCID:PMC5201288 journal.pone.0094773. ecollection 2014. PMID: 24728180; PMCID: PMC3984256.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 79 Edwin R. Manuel, Ph.D. Assistant Professor, Department of Immuno-Oncology
METHODS TO ENHANCE ANTI-TUMOR RESPONSES
Tumor escape from immune recognition is an emerging SELECTED PUBLICATIONS hallmark of cancer that can significantly compromise the • Salazar, M.A., Manuel, E.R., Tsai, W, D’Apuzzo, M., Goldstein, efficacy of current immunotherapeutic strategies. Immune L., Blazar, B.R., and Diamond, D.J. Evaluation of innate suppressive mechanisms within tumor-draining lymph and adaptive immunity contributing to the antitumor nodes and the tumor microenvironment contribute to the effects of PD1 blockade in an orthotopic murine model of ability of tumor cells to escape anti-tumor immunity. In order pancreatic cancer. Oncoimmunology, DOI:10.1080/216240 to study the role of escape mechanisms within the tumor 2X.2016.1160184, 2016 microenvironment, the lab of Edwin R. Manuel, Ph.D., has • Chen, J., Diamond, D.J., and Manuel, E.R. Developing developed a versatile, Salmonella typhimurium (ST)-based effective Salmonella-based approaches to treat pancreatic platform that utilizes shRNA plasmid technology to target cancer. Pacreat. Disord. Ther., 6(1):1-2. 2016 expression of proteins known to contribute to immune suppression. One such protein, indoleamine 2,3-dioxygenase • Manuel, E.R., Chen, J., D’Apuzzo, M., Lampa, M.G., Kaltcheva, T.I., Thompson, C.B., Ludwig, T., Chung, V., and Diamond, (IDO), is overexpressed in a variety of malignancies and has D.J. Salmonella-based therapy targeting indoleamine been shown to induce maturation of regulatory T cells and 2,3-dioxygenase coupled with enzymatic depletion of tumor suppress tumor-reactive immune cells by virtue of its ability to hyaluronan induces complete regression of aggressive deplete the essential amino acid tryptophan. Administration pancreatic tumors. Can. Immuno. Res., 3(9):1096-107. 2015. of ST targeting IDO (shIDO-ST) resulted in significant tumor- specific IDO-silencing and regression in preclinical models of • Manuel, E.R., Blache, C.A., Paquette, R., Kaltcheva, T.I., melanoma, pancreatic cancer and colorectal cancer, which was Ishizaki, H., Ellenhorn, J.D.I., Hensel, M., Metelitsa, L., and dependent on activation of tumoricidal neutrophils. The lab is Diamond, D.J. Enhancement of cancer vaccine therapy by systemic delivery of a tumor targeting Salmonella- currently using the shIDO-ST platform to induce a novel type based Stat3 shRNA suppresses the growth of established of neutrophil with enhanced antigen-presenting cell (APC) melanoma tumors. Cancer Res., 71(12):4183-91. 2011. function and the potential to induce anti-tumor immunity. Another focus of the Manuel lab includes the use of checkpoint inhibitors to improve efficacy of cancer immunotherapies, specifically, therapeutic vaccines encoding tumor-specific antigens. The overall objective of our research program will be to continue to generate novel approaches that overcome tumor escape to elicit potent anti-cancer immune responses, which can then be translated to the clinic for the treatment of aggressive solid and hematologic malignancies.
80 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Jeannine S. McCune, Pharm.D. Professor, Department of Population Sciences and Hematology & Hematopoietic Cell Transplantation
MAKING CANCER DRUGS WORK BETTER THROUGH PRECISION MEDICINE
The research of Jeannine S. McCune, Pharm.D., focuses SELECTED PUBLICATIONS on the clinical pharmacology of anti-cancer agents and • Palmer, J.*, McCune, J.S.*, Perales, M.-A., Marks, D., Bubalo, immunosuppressants. Specifically, she has quantified the J., Mohty, M., Wingard, J.R., Paci, A., Hassan, M., Bredeson, exposure of anti-cancer agents and immunosuppressants C., Pidala, J., Shah, N., Shaughnessy, P., Majhail, N., Schriber, in hematopoietic cell transplant recipients used to treat J., Savani, B.N., and Carpenter, P.A. Personalizing Busulfan- based Conditioning: Considerations from the American malignant and nonmalignant conditions. She is currently Society for Blood and Marrow Transplantation Practice developing mathematical models to identify anti-cancer agent Guidelines Committee. *shared first authorship. Biol Blood plasma exposure effective at treating cancer and modeling Marrow Transplant. 2016 Nov;22(11):1915-1925. doi: 10.1016/j. drug doses and dosing frequencies to optimize efficacy of bbmt.2016.07.013. Epub 2016 Jul 29. PMID: 27481448. cancer prevention and/or treatment. Her work also evaluates • Navarro, S.L., Randolph, T.W., Shireman, L., Raftery, M.D., and constitutional pharmacogenomics and pharmacometabolomics McCune, J.S. Endogenous metabolites predict IV busulfan relevant to drug exposure and drug response. clearance in hematopo9etic cell transplant patients. J Proteome Res 2016 Aug 5;15(8):2802-11. doi: 10.1021/acs. She has received several major National Institutes of Health jproteome.6b00370. PMID: 27350098. grants for personalized medicine with children and adults with cancer, and has over 130 publications in her areas of • McCune, J.S., Bemer, M.J., Baker, K.S., Gamis, A., and interest. She has served as a standing member of the NIH Holford, N.H.G. Busulfan in infant to adult hematopoietic cell transplant recipients: A population pharmacokinetic model Developmental Therapeutics Study Section (September 2009- for initial and Bayesian dose personalization Clinical Cancer June 2013) and Cancer Prevision Study Section (September Research. 2014 Feb 1;20(3):754-63. doi: 10.1158/1078-0432. 2015-present) and is a member of Children’s Oncology CCR-13-1960. Epub 2013 Nov 11. PMID: 24218510. Group trials.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 81 Marcia M. Miller, Ph.D. Professor Emeritus and Associate Chair, Department of Molecular and Cellular Biology Director, Electron Microscopy and Atomic Force Microscopy Core Facility
MOLECULAR IMMUNOGENETICS AND EM/AFM CORE FACILITY
We are interested in the genes that exist in populations as V., Vignal, A., Chow, W., Howe, K., Fulton, J.E., Miller, M.M., the result of pathogen selection over evolutionary time. Such Lovell, P., Mello, C., Wirthlin, M., Mason, A.S., Kuo, R., Burt, genes/alleles exist because they provided protection from D.W., Dodgson, J.B., and Cheng, H.H. 2017. A new chicken genome assembly provides insight into avian genome disease and allowed individuals to survive and reproduce. structure. G3 (Bethesda) 7:109-117. Some of these genes become fixed. Others are polymorphic: that is, different individuals in the population have different • Miller, M.M., and Taylor Jr., R.L. Brief Review of the Chicken alleles, some more effective than others in minimizing disease Major Histocompatibility Complex – the Genes, their Distribution on Chromosome 16 and their Contributions to caused by a particular infection or by transformed cells. We Disease Resistance. Poult. Sci. 95: 375-392, 2016. focus primarily on genes within the major histocompatiblity complex (MHC). The MHC is highly polymorphic in man • Miller, M.M., Robinson, C.M., Abernathy, J., Goto, R.M., and in many other organisms. Particular alleles encoded Hamilton, M.K., Zhou, H., and Delany, M.E. Mapping genes to at MHC loci may, in a sense, be “customized” through chicken microchromosome 16 and discovery of olfactory and scavenger receptor genes near the major histocompatibility evolutionary selection. We would like to understand in detail complex. J. Heredity 105: 203-215, 2014. the relationship between MHC alleles and disease so as to be able to predict immune responses and thereby intervene, when • Zhang, L., Katselis, G., Moore, R.E., Lekpor, K., Goto, R.M., needed, to better harness and direct the powerful immune Lee, T.D., and Miller, M.M. MHC class I target recognition, immunophenotypes and proteomic profiles of natural killer responses that humans and other higher organisms possess. cells within the spleens of day-14 chick embryos. Comp. We are using the chicken as our experimental model. Chickens, Develop. Immunol. 37: 446-456, 2012. just like humans, are challenged by a variety of viral and • Hee, C.S., Gao, S., Loll, B., Miller, M.M., Uchanska-Ziegler, bacterial pathogens. Resistance to several viral diseases has B., Daumke, O., and Ziegler, A. Structure of a classical MHC been genetically mapped to the MHC region. Which genes class I molecule that binds “non-classical” ligands. PloS within the region are responsible and how they protect against Biology 8: 1-12, 2010. disease is mostly unknown. In recent work we were able to • Goto, R.M., Wang Y., Taylor Jr., R.L., Wakenell P.S., identify one locus, BG1, with a major influence in whether Hosomichi, K., Shiina, T., Blackmore, C.S., Briles, W.E., and tumors form following infection with a highly oncogenic Miller, M.M. BG1 has a major role in MHC-linked resistance herpesvirus. Currently we are focused on the nonclassical to malignant lymphoma in the chicken. Proc. Natl. Acad. Sci. chicken YF molecules and their role in recognition of microbes USA. 106: 16740-16745, 2009. that colonize chickens. • Delany, M.E., Robinson, C.M., Goto, R.M., and Miller, M.M. I support investigators helping in the design, execution and Architecture and organization of chicken microchromosome 16: Order of the NOR, MHC-Y and MHC-B subregions. J. interpretation of experiments involving EM, SBEM and AFM in Heredity 100: 507-514, 2009. the well-equipped COH EM and SEM Core facility. • Sherman, M., Goto, R.M., Moore, R.E., Hunt, H.D., Lee, T.D., SELECTED PUBLICATIONS and Miller, M.M. Mass spectral data for 64 eluted peptides and structural modeling define peptide binding preferences • Ahrens, B.J., Li, L., Ciminera, A.K., Chea, J., Poku, E., for class I alleles in two chicken MHC-B haplotypes Bading, J.R., Weist, M.R., Miller, M.M., Colcher, D.M., and associated with opposite responses to Marek’s disease. Shively, J.E. 2017. Diagnostic PET imaging of mammary Immunogenetics 60: 527-541, 2008. microcalcifications using 64Cu-DOTA-alendronate in a rat model of breast cancer. The Journal of Nuclear Medicine. • Hosomichi, K., Miller, M.M., Goto, R.M., Wang, Y., 58(9):1373-1379. Suzuki, S., Kulski, J.K., Nishibori, M., Inoko, H., and Shiina, T. Contribution of mutation, recombination and gene • Warren, W.C., Hillier, L.W., Tomlinson, C., Minxm, P., conversion to chicken Mhc-B haplotype diversity. J. Immunol. Kremitzki, M., Graves, T., Markovic, C., Bouk, N., Pruitt, K., 181: 3393-3399, 2008. Thibaud-Nissen, F., Schneider, V., Mansour, T., Brown, C.T., Zimin, A., Hawken, R., Pyrkosz, A.B., Morisson, M., Fillon,
82 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Kevin V. Morris, Ph.D. Professor and Associate Director, Center for Gene Therapy
CENTER FOR GENE THERAPY
The lab of Kevin V. Morris, Ph.D., is primarily focused on SELECTED PUBLICATIONS understanding the role of RNA in gene expression and cellular • Morris, K.V. The theory of RNA-mediated gene evolution. complexity. Noncoding RNAs have quickly emerged as Epigenetics. 2015 Jan 2;10(1):1-5. PMID:25581873 functional genomic entities involved in controlling gene expression. Both small and long non-coding RNAs have proven • Saayman, S.M., Lazar, D.C., Scott, T.A., Hart, J.R., Takahashi, M., Burnett, J.C., Planelles, V., Morris, K.V., and Weinberg, to be active modulators of transcriptional and epigenetic M.S. Potent and Targeted Activation of Latent HIV-1 Using states, in human cells. We study the role of noncoding RNAs in the CRISPR/dCas9 Activator Complex. Mol Ther. 2015. the evolution of cellular states as well as utilize the inherent PMID:26581162 endogenous noncoding cellular mechanisms to control the expression of genes involved in human diseases ranging from • Saayman, S., Ackley, A., Turner, A.W., Famiglietti, M., Bosque, cancer to HIV-1 to cystic fibrosis. Several experimentally A., Clemson, M., Planelles, V., and Morris K.V. An HIV- designed synthetic biological, small molecule and gene therapy Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription. Molecular Therapy. 2014. based approaches are being employed and developed to NIHMSID#569381. specifically target diseased cells and noncoding regulatory pathways. • Johnsson, P., Ackley, A., Vidarsdottir, L., Lui, W.O., Corcoran, M., Grandér, D., and Morris, K.V. A pseudogene long- noncoding-RNA network regulates PTEN transcription and translation in human cells. Nature Structural Molecular Biology, (2013) PMID 23435381
• Lister, N., Shevchenko, G., Walshe, J.L., Groen, J., Johnsson, P., Vidarsdóttir, L., Grander, D., Ataide, S.F., and Morris, K.V. The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene. Proc Natl Acad Sci USA. 2017 Sep 12;114(37):9942-9947. PMID:28847966
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 83 Markus Müschen, M.D., Ph.D. The Norman and Sadie Lee Foundation Endowed Professor in Pediatrics Howard Hughes Medical Institute Faculty Scholar Chair, Department of Systems Biology Associate Director of Basic Science, Comprehensive Cancer Center
GENETIC TARGET DISCOVERY IN B CELL LEUKEMIA AND LYMPHOMA
Over the past 10 years, the Müschen laboratory has developed SELECTED PUBLICATIONS a multidisciplinary research program to study oncogenic • Xiao, G., Chan, L.N., Klemm, L., Braas, D., Chen, Z., Geng, signaling and clonal evolution in acute lymphoblastic leukemia, H., Cosgun, K.N., Sadras, T., Lee, J., Salgia, R., Ernst, T., the most frequent type of cancer in children and young Hochhaus, A., Jumaa, H., Jiang, X., Weinstock, D.M., Graeber, adults. Applying CRISPR/Cas9-forward genetic screens in T.G., and Müschen. M.B. B cell-specific diversion of glucose PDX models, his drug-discovery program will leverage newly carbon utilization reveals a unique vulnerability in B cell discovered vulnerabilities to broaden treatment options and malignancies. validate a diagnostic test. Cell 173: 644-656 (2018) Role of infection in clonal evolution of B cell leukemia • Shojaee, S., Caeser, R., Buchner, M., Park.,E., Swaminathan, S., In collaboration with Mel Greaves, we demonstrated that the Hurtz, C., Melnick, A., Kornblau, S.M., and Müschen, M. Erk immunoglobulin mutator enzyme AID drives clonal evolution negative feedback control enables pre-B cell transformation towards B-cell leukemia in the context of acute infections and represents a therapeutic target in acute lymphoblastic (Greaves & Müschen, Cancer Discov 2016). In animal models leukemia. Cancer Cell. 28:114-128 (2015) that recapitulate inflammatory stimuli related to infections our group demonstrated the critical role of AID and explained how • Geng, H., Hurtz, C., Druker, B.J., Burger, J.A., Milne, T.A., infection can drive clonal evolution of dormant pre-leukemic Chang, B.H. and Müschen, M. Self-enforcing feedback cells (Swaminathan et al., Nature Immunol 2016). activation between BCL6 and pre-B cell receptor signaling BCL6 mediates a novel form of drug resistance defines a distinct subtype of acute lymphoblastic leukemia. Our group discovered that leukemia cells increased BCL6 levels Cancer Cell. 27: 409-425 (2015) by ~2-3 log orders in response to tyrosine kinase inhibition • Chen, Z., Shojaee, S., Buchner, M., Geng, H., Lee, J.W., (TKI). To test the role of BCL6 in TKI-resistance, our group Klemm, L., Titz, B., Graeber, T.G., Jumaa, H., Reth, M., Weiss, generated a new floxed mouse model for conditional ablation A., Lowell, C.A. and Müschen, M. Signaling thresholds and of Bcl6. Ablation of BCL6 restored drug-sensitivity and negative B-cell selection in acute lymphoblastic leukaemia. prevented recurrence of disease in an in vivo disease model Nature. 521:357-361 (2015). (Duy et al., Nature 2012 and Swaminathan et al., Nature Medicine 2013). • Swaminathan, S., Klemm, L., Park, E., Papaemmanuil, E., Casellas, R., Schatz, D.G., Lieber, M.R., Greaves, M.F., and Discovery of autoimmunity checkpoints as new target in Müschen, M. Mechanisms of clonal evolution in childhood B cell tumors acute lymphoblastic leukemia. Nature Immunol. 16: 766-774 In a series of three recent studies, we discovered that despite (2016) oncogenic transformation, basic mechanisms to eliminate autoreactive B cells are still functional in B cell leukemia • Shojaee, S., Chan, L.N., Buchner, B., Cosgun, K.N., Geng, H., (Shojaee et al., Nature Medicine 2016). Reliable activation of Qiu, Y.H., Zhang, N., Melnick, A., Kornblau, S.M., Graeber, autoimmunity checkpoints and induction of cell death can be T.G., Wu, H., Jumaa, H., and Müschen, M. PTEN is essential achieved by pharmacological hyperactivation of B cell receptor for oncogenic transformation of pre-B cells. Nature Medicine signaling (Chen et al., Nature 2015). 22: 379-387 (2016) • Chan, L.N., Chen, Z., Braas, D., Lee, J.W., Xiao, G., Geng, H., Shojaee, S., Dickins, R.A., Graeber, T.G., and Müschen M. Metabolic gatekeeper function of B-lymphoid transcription factors. Nature 542: 479-483 (2017)
84 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Rama Natarajan, Ph.D. National Business Products Industry Professor in Diabetes Research Professor and Chair, Department of Diabetes Complications and Metabolism
DIABETIC VASCULAR COMPLICATIONS
The major focus of our research is to determine the molecular • Kato, M., Wang, M., Yuan, H., Lanting, L., Putta, S., Gunn, mechanisms involved in the accelerated development of A., Nakagawa, Y., Shimano, H., Rossi, J.J., and Natarajan, R. inflammation, vascular and renal complications under diabetic TGF-beta activates Akt kinase via a microRNA-dependent amplifying circuit targeting PTEN. Nature Cell Biol. 11: 881- conditions. We are examining the role of epigenetics and 889, 2009. noncoding RNAs in diabetic complications, and also how persistence of epigenetic changes can create a “metabolic • Jin, F., Li, Y., Ren, B., and Natarajan, R. PU.1 and C/ EBPa synergistically program distinct response to NF-κB activation memory” that results in long-term malfunction of genes through establishing monocyte-specific enhancers. Proc. and sustained complications even after diabetes patients Natl. Acad. Sci. USA 108:5290-5295, 2011. bring their blood sugar under control. We use state-of-the • Kato, M., Dang, V., Wang, M., Park, J.T., Deshpande, S., art approaches in cell culture, animal and clinical models to Kadam, S., Mardiros, A., Zhan, Y., Oettgen, P., Putta, S., Yuan, examine how these mechanisms enhance vascular and renal H., Lanting, L., and Natarajan R. TGF-β induces acetylation cell growth, and monocyte activation due to altered expression of chromatin and of Ets-1 to alleviate repression of miR-192 of inflammatory cytokines, chemokines and lipids under in diabetic nephropathy. Science Signaling Jun 4;6(278):ra43, diabetic conditions. 2013. We have uncovered key signaling pathways, and gene • Leung, A., Trac, C., Lanting, L., Schones, D.E., and Natarajan, regulation mechanisms that integrate and amplify the R. Novel long non-coding RNAs are involved in cellular response to Angiotensin II-signaling. Circ. Res. 113: 266-278, effects of diabetogenic stimuli in target cells. Additionally, 2013. we have demonstrated the role of specific chromatin histone posttranslational modifications in the epigenetic regulation • Reddy, M.A., Chen, Z., Park, J.T., Wang, M., Lanting, L., Zhang, Q., Bhatt, K., Leung, A., Wu, X., Putta, S., Sætrom, of inflammatory and fibrotic genes under diabetic conditions P., and Natarajan, R. (2014) Regulation of inflammatory and in the phenomenon of “metabolic memory.” We use phenotype in macrophages by a diabetes-induced long genomic profiling approaches to map histone modifications, noncoding RNA. Diabetes. 63:4249-4261, 2014. DNA methylation, binding of chromatin factors at diabetes- • Bhatt, K., Lanting, L., Jia, Y., Yadav, S., Reddy, M.A., Boldin, M., regulated genes and transcriptome changes with techniques and Natarajan, R. 2016. Anti-inflammatory role of miR-146a such as chromatin immunoprecipitation (ChIP)-linked to in the pathogenesis of Diabetic Nephropathy. J. Am. Soc. sequencing, ATAC-sequencing and RNA-sequencing. Nephrol. 27: 2277-2288. PMID:26647423. Another active area is the examination of microRNAs and long • Chen, Z.*, Miao, F.*, Paterson, A.D., Lachin, J.M., Zhang, L., noncoding RNAs (lncRNAs) that regulate the expression of Riggs, A.D., Schones, D.E., Wu, X., Wang, J., Tompkins, J.D., inflammatory and fibrotic genes under diabetic conditions. We Genuth, S.M., and Braffett, B., DCCT/EDIC Research group, discovered novel roles for certain microRNAs and lncRNAs and and Natarajan, R. Epigenomic Profiling reveals an association between persistence of DNA methylation and metabolic their downstream targets in the enhanced inflammation, renal memory in the DCCT/EDIC type 1 diabetes cohort. Proc Natl fibrosis and vascular dysfunction in diabetes. We are studying Acad Sci U S A. 2016 May 24;113(21):E3002-11. microRNA and lncRNA knockout mice and also the therapeutic • Kato, M., Wang, M., Chen, Z., Deshpande, D., Bhatt, K., efficacy of microRNA and lncRNA inhibitors on diabetic kidney Jia, Y., Oh, H.J., Lanting, L., Lai, J.Y.C., O’Connor, C.L., Wu, disease and inflammation in mouse models. Together, these Y.F., Hodgin, J.B., Nelson, R.G., Bitzer, M., and Natarajan, R. approaches could lead to new therapeutic modalities for the (2016) An Endoplasmic Reticulum Stress-regulated lncRNA debilitating complications of diabetes. hosting a microRNA megacluster induces Early features of Diabetic Nephropathy. Nature Communications 7: 12864. DOI: SELECTED PUBLICATIONS 10.1038/ncomms12864 • Das, S., Senapati, P., Chen, Z., Reddy, M.A., Ganguly, R., • Villeneuve, L.M., Reddy, M.A., Lanting, L., Wang, M., Lanting, L., Mandi, V., Bansal, A., Leung, A., Zhang, S., Jia, Y., Meng, L., and Natarajan, R. Epigenetic histone H3 lysine Wu, X., Schones, D.E., and Natarajan, R. (2017) Regulation of 9 methylation in metabolic memory and inflammatory Angiotensin II Actions by Enhancers and Super-enhancers in phenotype of vascular smooth muscle cells in diabetes. Proc. Vascular Smooth Muscle Cells. Nature Communications Nov Natl. Acad. Sci. USA 105: 9047-9052, 2008. 13;8(1):1467. doi: 10.1038/s41467-017-01629-7.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 85 Susan Neuhausen, Ph.D. The Morris & Horowitz Families Professor in Cancer Etiology & Outcomes Research, Professor, Department of Population Sciences
GENETIC EPIDEMIOLOGY OF COMPLEX DISEASES
My research is centered on identifying genes and SELECTED PUBLICATIONS environmental stressors that predispose to disease and affect • Clague, J., Wilhoite, G., Adamson, A., Bailis, A., Weitzel, J.N., disease progression. We are focused primarily on breast, and Neuhausen, S.L. RAD51C germline mutations in breast ovarian and prostate cancers. The current ongoing projects in and ovarian cancer cases from high-risk families. PLoS One: my laboratory are as follows. We are conducting an National Epub 2011 Sep 28. Cancer Institute-funded study to discover breast cancer • Warden, C.D., Adamson, A.W., Neuhausen, S.L., and Wu, X. susceptibility genes in Hispanic women using a combined Detailed comparison of two popular variant calling packages germline and somatic genomics approach. This study involves for exome and targeted exon studies. PeerJ. 2014 Sep whole exome sequencing of Hispanic breast cancer cases and 30;2:e600. PMCID: PMC4184249 controls, validation through sequencing of a subset of genes in an independent set of Hispanic breast cancer cases and • Chai, X., Friebel, T.M., Singer, C.F., Evans, D.G., Lynch, H.T., controls, and DNA and RNA sequencing of breast tumors for Isaacs, C., Garber, J.E., Neuhausen, S.L., Matloff, E., Eeles, R., Tung, N., Weitzel, J.N., Couch, F.J., Hulick, P.J., Ganz, P.A., a subset of genes. In addition, we are conducting a pilot study Daly, M.B., Olopade, O.I., Tomlinson, G., Blum, J.L., Domchek, to investigate the specific molecular subtypes in triple negative S.M., Chen, J., and Rebbeck, T.R. Use of risk-reducing breast cancer tumors of Hispanic women. A second study is surgeries in a prospective cohort of 1,499 BRCA1 and BRCA2 an National Institute of Environmental Health Sciences/NCI- mutation carriers. Breast Cancer Res Treat. 2014 Oct 14. funded study of the effects of environmental chemicals on risk PMCID: PMC4224991 of developing breast cancer during the menopausal transition. Shiuan Chen, Ph.D., and I are using a transdisciplinary • Ding, Y.C., Wu, H., Warden, C., Steele, L., Liu, X., van Iterson, approach integrating in vitro cell line experiments, in vivo M., Wu, X., Nelson, R., Liu, X., Yuan, Y-C., and Neuhausen, S.L. Gene expression differences in prostate cancers between mouse models, and a population-based study of women during young and old men. PLoS Genetics. 2016 12(12): e1006477. the menopausal transition. A third study study is to identify PMCID: PMC5189936 genetic and lifestyle factors that modify risks of developing cancers in women carrying deleterious mutations in BRCA1 and • Ding, Y.C., Adamson, A.W., Steele, L., Bailis, A.M., John, E.M., Tomlinson, G., Neuhausen, S.L. HYPERLINK “https:// BRCA2. We are part of a large international collaboration. Our www.ncbi.nlm.nih.gov/pubmed/28864920” Discovery of lab is exploring the association of variants, including variable mutations in homologous recombination genes in African- number tandem repeats (VNTRs) which affect methylation American women with breast cancer. Fam Cancer. 2018 and expression. For our study of prostate cancers, we are 17(2): 187-195. PMCID: PMC5834346 comparing the transcriptomes of prostate cancers in younger men (diagnosed under age 45 years) and older men (ages 70 to 75 years) to address whether we can identify biomarkers of prostate cancer in younger men that predict cancer aggressiveness and prognosis. The incidence of prostate cancer in younger men is increasing, yet there are little empiric data for urologists to use for risk prediction and treatment decisions. We are using our own generated data and data from The Cancer Genome Atlas (TCGA). The long-term objectives are comprehensive genomic tests for clinical risk assessment and prevention, and precision medicine for treatment.
86 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Edward M. Newman, Ph.D. Associate Professor, Department of Cancer Biology
BIOCHEMICAL PHARMACOLOGY OF ANTI-METABOLITES
The principal area of investigation of the laboratory is SELECTED PUBLICATIONS the biochemistry of anti-neoplastic drugs and potential • Shibata, S.I., Chung, V., Synold, T.W., Longmate, J.A., Suttle, antineoplastic drugs. A.B., Ottesen, L.H., Lenz, H.J., Kummar, S., Harvey, R.D., Hamilton, A.L., O’Neil, B.H., Sarantopoulos, J., Lorusso, P., Drug development of 5-Fluorodeoxycytidine (FdCyd) Rudek, M.A., Dowlati, A., Mulkerin, D.L., Belani, C.P., Gandhi, Initial studies have demonstrated novel metabolic pathways L., Lau, S.C., Ivy, S.P., and Newman, E.M. Phase I Study of for the activation of FdCyd, as compared with the activation of Pazopanib in Patients with Advanced Solid Tumors and Hepatic Dysfunction: A National Cancer Institute Organ approved fluoro-pyrimidine anti-cancer drugs. These studies Dysfunction Working Group Study. Clin Cancer Res. 19, 3631- indicate direct incorporation of FdCyd into DNA and inhibition 3639, 2013. PMID: 23653147. PMCID: PMC3779138 of DNA cytidine methyltransferase. We have completed • Newman, E.M., Morgan, R.J., Kummar, S., Beumer, J.H., a phase 1 (dose-finding) trials of FdCyd both in patients Blanchard, M.S., Ruel, C., El-Khoueiry, A.B., Carroll, M.I., Hou, with advanced solid tumors and in patients with myeloid J.M., Li, C., Lenz, H.J., Eiseman, J.L., and Doroshow, J.H. A malignancies. Based on our data, the National Cancer Institute phase I, pharmacokinetic, and pharmacodynamic evaluation of the DNA methyltransferase inhibitor 5-fluoro-2’- (NCI) is conducting a phase 2 (initial efficacy) trial of FdCyd in deoxycytidine, administered with tetrahydrouridine. Cancer patients with solid tumors of multiple histologies and a phase 1 Chemother Pharmacol. 75, 537-546, 2015. PMID: 25567350. trial of oral FdCyd. PMCID: PMC4344391 Early drug development with phase 1 emphasis • Somlo, G., Frankel, P.H., Arun, B.K., Ma, C.X., Garcia, A.A., Cigler, T., Cream, L.V., Harvey, H.A., Sparano, J.A., Nanda, R., City of Hope was recently awarded a cooperative agreement Chew, H.K., Moynihan, T.J., Vahdat, L.T., Goetz, M.P., Beumer, entitled “Phase I Molecular and Clinical Pharmacodynamic J.H., Hurria, A., Mortimer, J., Piekarz, R., Sand, S., Herzog, J., Trials ET-CTN” to participate in the NCI’s Experimental Van Tongeren, L.R., Ferry-Galow, K.V., Chen, A.P., Ruel, C., Therapeutics Clinical Trials Network. This cooperative Newman, E.M., Gandara, D.R., and Weitzel, J.N. Efficacy of the Poly (ADP-ribose) Polymerase Inhibitor (PARPi) ABT- agreement continues over 25 years of continuous funding. This 888 (veliparib) Alone or in Combination with Carboplatin in grant funds the infrastructure for conducting clinical trials of Germline BRCA1- or BRCA2-Associated Metastatic Breast NCI-sponsored investigational agents of interest to the NCI Cancer California Cancer Consortium Trial NCT01149083. Cancer Therapy Evaluation Program. A consortium of four Clin. Cancer Res. 23, 4066-4076, 2017. PMID: 28356425. PMCID: PMC5540749 institutions (City of Hope, University of Southern California, University of California Davis, and Stanford) participates in • Mohrbacher, A.M., Yang, A.S., Groshen, S., Kummar, S., Gutierrez, M.E., Kang, M.H., Tsao-Wei, D., Reynolds, C.P., these trials, with City of Hope as the coordinating center. Newman, E.M., and Maurer, B.J. Phase I Study of Fenretinide Delivered Intravenously in Patients with Relapsed or Refractory Hematologic Malignancies: A California Cancer Consortium Trial. Clin. Cancer Res. 23, 4550-4555, 2017. PMID: 28420721. PMCID: PMC5559312 • Kirschbaum, M.H., Frankel, P., Synold, T.W., Zain, J., Claxton, D., Tuscano, J., Newman, E.M., Gandara, D.R., and Lara Jr., P.N. A phase II study of vascular endothelial growth factor trap (Aflibercept, NSC 724770) in patients with myelodysplastic syndrome: a California Cancer Consortium Study. Br J Haematol. 180,445-448, 2018. PMID: 27650362. PMCID: PMC5360527.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 87 Vu Ngo, Ph.D. Associate Research Professor, Department of Systems Biology
MOLECULAR TARGETS IN LYMPHOID MALIGNACIES
Cancer cells are often addicted to a transformed state that Novel mechanisms of lymphomagenesis involves multiple signaling pathways. Inactivation of one The neural transcription factor SOX11 is aberrantly expressed pathway is often insufficient to kill cancer cells, but may in MCL, but its functional significance and mechanisms of sensitize them to inhibition of additional pathways, a concept deregulated expression are not known. We have identified known as synthetic lethality. Using a functional genomics and that cyclin D1 plays a key role in regulating SOX11 expression proteomics approaches in mantle cell lymphoma models, our through its ability to alter HDAC1 function. Overexpression of laboratory has identified multiple synthetic lethal interactions cyclin D1 results in HDAC1 eviction from local chromatin and that can be exploited for gaining insights into disease accumulation of active histone mechanisms and therapeutic application. Our specific projects marks (H3K9/14Ac) at the SOX11 are as follows. locus, leading to increased SOX11 transcription. Our goal is to Cyclin D1 and DNA damage response in mantle cell lymphoma unravel the complexity of SOX11 Mantle cell lymphoma (MCL) is an incurable B cell malignancy transcriptional regulation and that is characterized by cyclin D1 overexpression. Elevated to identify potential targets that cyclin D1 levels were strongly associated with aggressive disrupt oncogenic cooperation clinical manifestations. Studies in our laboratory uncovered between cyclin D1 and SOX11. a role for cyclin D1 in preserving genomic stability during DNA replication. We also discovered that cyclin D1 inhibition SELECTED PUBLICATIONS induced activity of molecules that promote tumor survival. To circumvent this tumor protective response, we performed • Mohanty, S.*, Mohanty, A.*, Sandoval, N., Tran, T., Bedell, a synthetic lethal RNA interference (RNAi) screen and V., Wu, J., Scuto, A., Murata-Collins, J., Weisenburger, D.D., and Ngo, V.N. Cyclin D1 depletion induces DNA damage in uncovered multiple targets that play essential roles in the mantle cell lymphoma lines. Leukemia & lymphoma. 2017; DNA damage response pathway. These results confirmed 58(3):676-688. our hypothesis that targeting DNA damage response factors could provide a rational combination with anti-cyclin D1 as an • Mohanty, A., Sandoval, N., Das, M., Pillai, R., Chen, L., Chen, R.W., Amin, H.M., Wang, M., Marcucci, G., Weisenburger, effective strategy for treating mantle cell lymphoma. D.D., Rosen, S.T., Pham, L.V., and Ngo, V.N. CCND1 mutations Overcoming therapy resistance in mantle cell lymphoma increase protein stability and promote ibrutinib resistance The emergence of ibrutinib therapy, which targets the Bruton’s in mantle cell lymphoma. Oncotarget. 2016; 7(45):73558- 73572. tyrosine kinase, has revolutionized the treatment of MCL. However, a third of patients are not responding to this therapy, • Ngo, V.N. Identification of pathogenetically relevant genes necessitating a better understanding of ibrutinib resistance in lymphomagenesis by shRNA library screens. Methods Mol and development of more effective treatment approaches. We Biol. 2013; 971:245-63. found that somatic mutations in cyclin D1 produced a more • Ngo, V.N.*, Young, R.*, Schmitz, R.*, Jhavar, S.*, Xiao, stable protein and promoted ibrutinib resistance in MCL cells. W.*, and Lim, K.H.*, et al. Oncogenically Active MYD88 These results led us to hypothesize that deregulated turnover Mutations in Human Lymphoma. Nature. 470 (7332): 115-9 of cyclin D1 and potentially other oncoproteins may contribute (2011). to therapy resistance of cancer cells. We are actively testing • Ngo, V.N.*, Davis, R.E.*, Lamy, L., Yu, X., Zhao, H., Lenz, G., this hypothesis in many lymphoid tumors. Lam, L., Dave, S., Yang, L., Powell, J., and Staudt, L.M. A Loss- of-function RNA Interference Screen for Molecular Targets in Using a synthetic lethal RNAi screen in an ibrutinib resistant Cancer. Nature. 441 (7089): 106-10. (2006). MCL cell line, we have also identified many targets that increase the antitumor activity of ibrutinib. Preclinical studies are conducted to validate these targets and results from these studies are expected to provide new therapeutic opportunities in MCL.
88 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Timothy R. O’Connor, Ph.D. Professor and Associate Chair, Department of Cancer Biology
DNA REPAIR
Cells have dealt with threats to genomic stability of DNA methylation is minimal, making those cells the best model from both endogenous and exogenous sources by evolving available to study demethylation. We have generated deficient DNA repair systems. We study those systems at a basic level, mouse embryonic stem cell lines with either single or multiple with the ultimate goal of understanding their mechanisms deficiencies to evaluate the mechanism(s) of demethylation. for eventual application in the clinic. Our work covers a broad DNA repair and translational studies area from the formation of DNA damage to the effects on Understanding DNA repair in individuals could provide model organisms. We investigate DNA repair mechanisms in personalized information their response to therapeutic both normal and tumor cells and how those mechanisms can intervention and their possibility to develop resistance to function either for use in therapeutic interventions or to evade therapy. We have collaborated with physicians to study the treatment. We approach our work developing questions and role of DNA repair proteins in cells from patients, to potentially then employing methods that will address those questions. have diagnostic roles and guide therapeutic interventions. Our These are the present major areas in which we are working: ongoing work used assays established in our laboratory to DNA repair and metabolism monitor DNA repair in blood and to examine potential use of ALKBH2 and ALKBH3 proteins remove alkylated bases in a drug combinations in therapy. We are using these methods in reversible manner. The levels of these enzymes in glioblastoma studies that involve leukemia and solid tumors. cells are linked to patient responses to therapy. We have generated mouse models of the ALKBH2 or ALKBH3. We SELECTED PUBLICATIONS demonstrated cells deficient in either of those enzymes protects equally against treatment by alkylating agents, • Luo, L. Z., Gopalakrishna-Pillai, S., Nay, S. L., Park, S. W., but only one of those enzymes protects against mutations. Bates, S. E., Zeng, X., and O’Connor, T. R. (2012). DNA repair in human pluripotent stem cells is distinct from that in non- However, we noted that the mouse embryonic fibroblasts pluripotent human cells. PLoS ONE, 7(3), e30541. deficient in both proteins results in significant loss of repeat sequences eliminating over 1.6 megabases of genomic DNA. • Nay, S.L., Lee, D.H., Bates, S.E., and O’Connor, T.R. Alkbh2 We are currently examining the consequences of that loss and protects against lethality and mutation in primary mouse the possible involvement of amino acid deficiencies that can embryonic fibroblasts. DNA Repair (Amst) 11: 502-510, 2012. occur in tumors in collaboration with the laboratory of Mei • Clark, C.C., Weitzel, J.N., and O’Connor, T.R. Enhancement Kong, Ph.D. of synthetic lethality via combinations of ABT-888, a PARP DNA repair and links to obesity/diabetes and cancer inhibitor, and carboplatin in vitro and in vivo using BRCA1 Patients who are diabetic or obese have a higher risk of and BRCA2 isogenic models. Mol Cancer Ther. 11: 1948-58, 2012. developing certain cancers. Those risks could be linked to certain hormonal responses, but our new work indicates that • Lacoste, S., Bhatia, R., Bhatia, S., and O’Connor, T.R. high levels of glucose increases DNA damage. The increased Granulocytes affect double-strand break repair assays in damage can lead to mutations and ultimately to cancer. We primary human lymphocytes. PLoS One. 9: e93185, 2014. have developed mouse models of mice that develop diabetes • Beharry, A.A., Lacoste, S., O’Connor, T.R., and Kool, E.T. in which we can monitor DNA damage and mutations. To Fluorescence Monitoring of the Oxidative Repair of DNA pursue these studies, we are also using in vitro cell models Alkylation Damage by ALKBH3, a Prostate Cancer Marker. J to examine the role of DNA damage and have created cells Am Chem Soc. 138: 3647-50, 2016. that are deficient in DNA repair pathways in this work. This collaborative effort with Dr. John Termini’s laboratory has • You, C., Wang, P., Nay, S.L., Wang, J., Dai, X., O’Connor, T.R., recently demonstrated that a specific type of DNA damage can and Wang, Y. Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions. be used to provide a more accurate assessment of diabetes ACS Chem Biol., in press, 2016. Excision repair eliminates that is currently available. unique DNA-protein cross links from mammalian cells. J. DNA repair and epigenetics Biol. Chem. 282: 22592-22604, 2007. DNA repair is not only associated with genomic stability, but • Lee, H.W., Lee, H.J., Hong, C.M., Baker, D.J., Bhatia, R., and also has a role in regulating epigenetics. We are currently O’Connor, T.R. Monitoring repair of DNA damage in cell investigating the role of DNA repair proteins and the pathways lines and human peripheral blood mononuclear cells. Anal. in mammalian cells that eliminate DNA methylation at Biochem. 365: 246-259, 2007. the 5 position of cytosine. In mouse embryonic stem cells,
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 89 Javier Gordon Ogembo, Ph.D. Assistant Professor, Department of Immuno-Oncology
ENTRY MECHANISMS AND DEVELOPMENT OF VACCINES AGAINST GAMMA-HERPESVIRUSES
The laboratory of Javier Gordon Ogembo, Ph.D., is focused on • Andersen, M.S., Ericson, E., Lu, S., Richard, M., Gregory, M., elucidating entry mechanisms and infection outcomes of two Ogembo, J.G., Mazor, O., Gorelik, P., Shapiro, N., Sharda, gamma-herpesviruses, Epstein-Barr virus and Kaposi sarcoma- A., and Ghiran, I. Detection of membrane-bound and associated human herpesvirus, with a goal of developing soluble antigens by magnetic levitation. Lab Chip. 2017 Oct prophylactic and therapeutic vaccines. In addition, his 11;17(20):3462-3473. DOI: 10.1039/C7LC00402H PMCID: laboratory has interest in global health research, particularly PMC5642277. understanding the epidemiology of human papillomavirus, • Ogembo, J.G., Muraswki, M.R., McGinnes, L.W., Parcharidou, prevention of cervical cancer through screening of women A., Sutiwisesak, R., Tison, T., Avendano, J., Agnani, D., at high-risk and assessing the acceptability, feasibility and Finberg, R.W., Morrison, T.G., and Fingeroth, J.D. A chimeric optimal delivery strategies of different vaccines in Africa. EBV gp350/220-based VLP replicates the virion B-cell Areas of research attachment mechanism and elicits long-lasting neutralizing • Pathogenesis of human gamma-herpesvirus infections antibodies in mice. J Transl Med. 2015 Feb 6;13(1):50. PMCID: in vitro and in vivo PMC4328182. • Identification of ellularc proteins that interact with gamma • Ogembo, J.G., Milner, D.A., Mansfield, K.G., Rodig, S.J., herpesviruses glycoproteins to mediate productive infection Murphy, G.F., Kutok, J.L., Pinkus, G.S., and Fingeroth, J.D. • Development of candidate vaccines against human SIRPα/CD172a and FHOD1 are unique markers of littoral gamma-herpesviruses cells, a recently evolved major cell population of red pulp of human spleen. J Immunol. 2012 May 1;188(9):4496-505. • Development of monoclonal antibodies as PMCID: PMC3331893. immunotherapeutic and diagnostic reagents • Global health • Ogembo, J.G., Kannan, L., Ghiran, I., Nicholson-Weller, A., Finberg, R.W., Tsokos, G.C., and Fingeroth, J.D. Human SELECTED PUBLICATIONS complement receptor type 1/CD35 is an Epstein-Barr virus receptor. Cell Rep. 2013 Feb 21;3(2):371-85. PMCID: • Perez, E., Foley, J., Tison, T., Silva, R., and Ogembo, J.G. Novel PMC3633082. Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibodies and EBV- • Cholli, P., DeGregorio, G., Manga, S., Kiyang, E., Manjuh, F., specific T-cell responses in immunized mice. Oncotarget. Bradford, L., Wamai, R.G., Ogembo, K.R., Sando, Z., Liu, Y., 2017 Mar 21;8(12):19255-19273. PMCID: PMC5386682. Sheldon, L.K., Nulah, K., Welty, T., Welty, E., and Ogembo, J.G. Screening for cervical cancer among HIV-positive and • Barasa, A., Ye, P., Phelps, M., Arivudainambi, G., Tison, T., and HIV-negative women in Cameroon using simultaneous co- Ogembo, J.G. BALB/c mice immunized with a combination testing with careHPV DNA testing and visual inspection with of virus-like particles incorporating Kaposi sarcoma- acetic acid enhanced by digital cervicography: Findings of associated herpesvirus (KSHV) envelope glycoprotein B initial screening and one-year follow-up. Gynecol Oncol. 2018 and gH/gL induced comparable serum neutralizing antibody Jan;148(1):118-125. PMID: 29153541 activity to UV-inactivated KSHV. Oncotarget. 2017 May 23;8(21):34481-34497. PMCID: PMC5470984.
• Andersen Weiss, E.R., Alter, G., Ogembo, J.G., Henderson, J.L., Tabak, B., Bakiş, Y., Somasundaran, M., Garber, M., Selin, L., and Luzuriaga, K. High EBV load and genomic diversity are associated with generation of gp350 specific neutralizing antibodies following Acute Infectious Mononucleosis. J Virol. 2017 Jan 1;91(1):e01562-16. PMCID: PMC5165192.
90 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Flavia Pichiorri, Ph.D. Associate Professor, Judy and Bernard Briskin Center for Multiple Myeloma Research, Hematologic Malignancies and Stem Cell Transplantation Institute
MOLECULAR PATHOGENESIS OF MULTIPLE MYELOMA
Our laboratory’s primary focus is to investigate the genetic and epigenetic changes in the molecular pathogenesis of multiple myeloma (MM). MM is an incurable plasma cell (PCs) malignancy in which patients accumulate monoclonal immunoglobulin-producing plasma cells within their bone marrow. Worldwide, the incidence of MM is about 86,000 cases annually, with about 63,000 deaths each year. Our group was the first to show that small RNA deregulations due to epigenetic changes are involved in the clonal selection and malignant transformation of PCs. We also showed that TP53 is still functional in MM-PCs and its tumor suppressor activity can be restored by inhibiting the p53 molecular inhibitor MDM2, which we found highly expressed in MM patients can be used as novel non-invasive biomarkers to cells. We recently generated a novel transgenic mouse model stratify MM patients at diagnosis, with the potential to be used that expresses the E3 ubiquitin-protein ligase MDM2 only in to detect early mechanisms of acquired resistance. The study the PCs compartment, in order to develop a mouse model that of extracellular vesicles and immune cellular subsets of MM can better recapitulate the disease and can be used for testing patients resistant and sensitive to therapeutic treatments is novel therapies. currently in progress, as well as molecular target identification. An integral aspect of our research program at City of Hope also involves the preclinical and clinical testing of novel therapeutic SELECTED PUBLICATIONS interventions for MM treatment, including oncolytic viral • Pichiorri, F., Suh, S.S., Ladetto, M., Kuehl, M., Palumbo, T., therapy and antibody therapy. We recently generated a novel Drandi, D., Taccioli, C., Zanesi, N., Alder, H., Hagan, J.P., anti-CD38 drug conjugated antibody to detect and target MM Munker, R., Volinia, S., Boccadoro, M., Garzon, R., Palumbo, bone metastasis. A., Aqeilan, R.I., and Croce, C.M. MicroRNAs regulate critical genes associated with multiple myeloma pathogenesis. Proc Natl Acad Sci USA. 2008 Sep; 105(35):12885-90. • Rocci, A., Hofmeister, C.C., Geyer, S., Stiff, A., Gambella, M., Cascione, L., Guan, J., Benson, D.M., Efebera, Y.A., Talabere, T., Dirisala, V., and Pichiorri, F. Circulating miRNA markers show promise as new prognosticators for multiple myeloma. Leukemia. 2014 Sep;28(9):1922-6. • Harshman, S.W., Canella, A., Ciarlariello, P.D., Agarwal, K., Branson, O.E., Rocci, A., Cordero, H., Phelps, M.A., Hade, E.M., Dubovsky, J.A., Palumbo, A., Rosko, A., Byrd, J.C., Hofmeister, C.C., Benson, D.M. Jr., Paulaitis, M.E., Freitas, M.A., and Pichiorri, F. Proteomic characterization Our research team works very closely with the clinical team of circulating extracellular vesicles identifies novel serum myeloma associated markers. J Proteomics. 2016 Mar 16; to address unmet clinical needs and understand the molecular 136:89-98. changes associated with the clinical response of MM patients enrolled in our investigator initiated phase 1-2 trials. Because • Canella, A., Cordero-Nieves, H., Sborov, D.W., Cascione, L., of the strong translational focus of our laboratory, we also Radomska, H.S., Smith, E., Stiff, A., Consiglia, J., Caserta, E., focus on identifying novel circulating biomarkers to routinely Rizzotto, L., Zanesi, N., Stefano, V., Kaur, B., Mo, X., Byrd, J.C., Efebera, Y.A., Hofmeister, C.C., and Pichiorri F. HDAC screen patients with premalignant disease for early therapeutic inhibitor AR-42 decreases CD44 expression and sensitizes intervention or to drive personalized therapeutic approaches. myeloma cells to lenalidomide. Oncotarget. 2015 Sept 25. Our group has recently demonstrated that extracellular vesicles and circulating small RNAs in the blood of MM
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 91 Christiane Querfeld, M.D., Ph.D Assistant Clinical Professor and Chief, Division of Dermatology Director, Cutaneous Lymphoma Program
IDENTIFYING TUMOR MICROENVIRONMENTS IN CUTANEOUS LYMPHOMA
Cutaneous lymphoma, classified as a non-Hodgkin lymphoma, is a group of lymphoproliferative disorders caused by lymphocytes that are localized in the skin. Our current research focuses on investigations of the biology of cutaneous lymphomas and novel therapies for these diseases, which are being studied in phase 1 and 2 trials. Our newest project is aimed at identifying the contributing elements of the tumor microenvironment in cutaneous T cell lymphoma (CTCL), which should help elucidate the underlying mechanisms that lead to disease progression through maintenance and proliferation of malignant cells in the skin. A longitudinal cutaneous lymphoma database has also been established and maintained for over 200 City of Hope patients, which provides an important tool for ongoing research. These data are also SELECTED PUBLICATIONS being used in collaboration with other centers to develop an • Querfeld, C., Curran, S.A., Leung, S., Myskowski, P.L., international prognostic index. Horwitz, S.M., Halpern, A.C., and Young, J.W. T cells in CTCL Current investigations focus on signaling interactions within have an exhausted phenotype while cutaneous dendritic the tumor microenvironment that create a permissive cells display a normally activated mature phenotype. Blood environment for tumor growth. We have discovered evidence 124: 1695, 2014 for T cell exhaustion, a phenotype that has been observed • Querfeld, C., Wu, X., Sanchez, J., Palmer, J., Motevalli, A., in chronic viral infections and is associated with disease Zain, J., and Rosen, S.T. The miRNA profile of cutaneous progression in hematologic malignancies. Exhausted T cells are T cell lymphoma correlates with the dysfunctional characterized by the presence of immune-inhibitory molecules, immunophenotype of the disease. Blood 128: 4132, 2016 like programmed death-1 (PD-1). In support of this hypothesis, it has been shown that CD4+ T cells from lesions of Sézary • Querfeld, C., Pacheco, T., Foss, F., Halwani, A., Porcu, syndrome, a CTCL subtype, express PD-1. We have isolated cell P.L., Seto, A.G., Landry, M., Jackson, A.L., Pestano, L.A., subsets from the CTCL tumor microenvironment and found Dickinson, B., Rodman, D.M., Gordon, G.S., and Marshall, that both the malignant CD4+ T cells and the tumor-infiltrating W.S. Preliminary results of a phase 1 trial evaluating MRG- CD8+ T cells express PD-1 among other exhaustion markers, 106, a synthetic microRNA antagonist (LNA antimiR) of whereas dendritic cells (DCs) express PD ligands (PDLs). microRNA-155, in patients with CTCL. Blood 128:1829, 2016 We are currently testing the role of PD-L1 signaling in an in • Rubio-Gonzalez, B., Zain, J., Rosen, S.T., and Querfeld, C. vitro co-culture model that combines signal generating cells Tumor microenvironment in mycosis fungoides and Sézary (DCs) with putative signal-receiving cells (CD8+ T cells and syndrome. Curr Opin Oncol 28(1): 88-96, 2016 malignant CD4+ T cells). The findings will help to define new therapeutic targets and potential prognostic markers for CTCL. Confocal microscopy with PD-L1, pSTAT-3 and CD163 expression on skin biopsy section of patient with early stage CTCL. CD163 positive cells (purple) co-expressing PD-L1 (red) and pSTAT3 (green). In many cancers, JAK-STAT signaling is responsible for upregulation of PD-L1 cells. PD-L1 expression within the CTCL environment is correlated with advanced stage of CTCL.
92 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Helena Reijonen, Ph.D. Associate Professor, Department of Diabetes Immunology
AUTOIMMUNITY IN TYPE 1 DIABETES
The role of CD4+ T cells is well established in triggering and SELECTED PUBLICATIONS perpetuating autoimmune process leading to destruction • Ge., X., James, E.A., Reijonen, H., and Kwok, W.W. of the insulin producing beta cells in type 1 diabetes (T1D). Differences in self-peptide binding between T1D-related Our research is focused on the characterization of these susceptible and protective DR4 subtypes. J Autoimmun 2011; autoreactive T cells and their functional properties. We 36(2):155-160. investigate T cells that target proteins expressed in the beta • Oling, V., Reijonen, H., Simell, O., Knip, M., and Ilonen, L. cells of Langerhans islets. We analyze T lymphocytes from the Autoantigen-specific memory CD4+ T cells are prevalent subjects who have a genetic risk but have not progressed to early in progression to type 1 diabetes. Cell Immunol 2012; T1D yet (pre-diabetes) and from the T1D patients. Staging of 273(2):133-139. the autoimmune process and understanding the heterogeneity • Schubert, D.A., Gordo, S., Sabatino Jr., J.J., Vardhana, S., and regulatory factors of the autoimmune process are critical Gagnon, E., Sethi, D.K., Seth, N.P., Choudhuri, K., Reijonen, H., for designing of individualized therapies to treat or prevent Nepom, G.T., Evavold, B.D., Dustin, M.L., and Wucherpfennig, the disease. We are using advanced immunological assays to K.W. Self-reactive human T cell clones form unusual immunological synapses. J Exp Med 2012; 209(2):335-352. study autoantigen specific T cells which are present at a very low frequency in the peripheral blood. We determine their • Burke 3rd, G.W., Vendrame, F., Virdi, S.K., Ciancio, G., Chen, specificity, phenotype and gene expression profiles and their L., Ruiz, P., Messinger, S., Reijonen, H.K., and Pugliese, A. Lessons from pancreas transplantation in type 1 diabetes: correlation with the functional properties. In these projects Recurrence of islet autoimmunity. Curr Diab Rep 2015; we expect to discover new attributes for disease progression, 15(12):121. staging, stratification and monitoring of the treatment effects in the clinical trials. • Azzi, J., Thueson, L., Moore, R., Abdoli, R., Reijonen, H., and Abdi, R. PI3K-gamma deficient NOD-Mice are protected Genetic risk and protection to develop T1D is strongly from diabetes by restoring the balance of regulatory to associated with the presence of certain HLA gene variants. effector T cells. PLoS One, 2017 Jan 12;1 2(1). Individuals with the protective HLA genotype (HLA-DQ0602) • Cerosaletti, K., Barahmand-pour-Whitman, F., Yang,J., have extremely low risk to develop T1D, and those few who DeBerg, H.A., Dufort, M.J., Murray, S.A., Israelsson, E., do, are usually diagnosed at later age. The protective effect of Speake, C., Gersuk, V.H., Eddy, J.A., Reijonen, H., Greenbaum, the HLA-DQ0602 is dominant, and it overrides the effect of C.J., Kwok, W.W., Wambre, E., Prlic, M., Gottardo, R., Nepom, G.T., and Linsley, P.S. Single-Cell RNA Sequencing Reveals the risk associated gene in the same individual. Although the Expanded Clones of Islet Antigen-Reactive CD4+ T Cells protective effect of this gene variant has been known for a long in Peripheral Blood of Subjects with Type 1 Diabetes. The time, the molecular mechanisms of HLA mediated protection Journal of Immunology 2017; Jul1;199(1):323-335. are still unresolved. We have identified T cells recognizing islet autoantigens in the context of the protective HLA-DQ0602. We are investigating how this recognition leads to peripheral immune regulation and whether there are distinct features potentially retaining differentiation to the pathogenic identity. We utilize multi-functional flow cytometry, tetramers, imaging and in-depth transcriptomics to answer these questions. We focus on the cell activation and signaling pathways, bystander suppression and cell to cell interaction. Furthermore, we examine the role of the microenvironment in the T cell lineage commitment, phenotype and cell differentiation.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 93 Russell C. Rockne, Ph.D. Assistant Professor and Director, Division of Mathematical Oncology
MATHEMATICAL ONCOLOGY
I am an applied mathematician who studies cancer as a SELECTED PUBLICATIONS dynamic system with the tools of mathematics. My research • Sahoo, P., Frankel, P., Ressler, J., Gutova, M., Annala, A.J., at the interface of mathematics, imaging, histopathology Badie, B., Portnow, J., Aboody, K.S., Apuzzo, M.D., and and genomics focuses on how to combine information from Rockne, R.C., 2018. Early Changes in Tumor Perfusion from these types of data to improve treatment of individual cancer T1-Weighted Dynamic Contrast-Enhanced MRI following patients based on an improved understanding of how their Neural Stem Cell-Mediated Therapy of Recurrent High- tumors will evolve when confronted with a specific treatment Grade Glioma Correlate with Overall Survival. Stem Cells Int. regimen. My personal research goal is explore the novel 2018, 9. doi:https://doi.org/10.1155/2018/5312426 hypothesis that mathematical models can quantify and predict disease dynamics and recurrence resulting from therapy • Mortimer, J.E., Bading, J.R., Park, J.M., Frankel, P.H., Carroll, in vivo, in individual patients. As such, I consider myself a M.I., Tran, T.T., Poku, E.K., Rockne, R.C., Raubitschek, A.A., “mathematical oncologist.” Shively, J.E., and Colcher, D.M., 2018. Tumor uptake of 64Cu-DOTA-trastuzumab in patients with metastatic breast Mathematical oncology is the science of oncology that cancer. J. Nucl. Med. 59. doi:10.2967/jnumed.117.193888 uses mathematics as the means of discovery. The goal of the Division of Mathematical Oncology is to translate • Rockne, R.C., and Frankel, P., 2017. Mathematical modeling mathematical, physics and evolution based research to in radiation oncology: Translating mathematical models into clinical care. the clinic, in: Wong, J.Y.C., Schultheiss, T.E., Radany, E.H. My work is based upon patient-specific (PS) mathematical (Eds.), Advances in Radiation Oncology. Springer International models of cancer growth and response to therapy. Specifically, Publishing, Cham, Switzerland, pp. 255–271. doi:10.1007/978- I consider how routine and advanced clinical data can be 3-319-53235-6_12 used to parameterize PS models that can provide biological insight and clinically relevant predictions of individual disease behavior, with a focus on imaging data (e.g., MRI, PET, CT). Potential students should have a strong desire for clinically focused, translational research and be prepared for interdisciplinary collaborations involving computational and theoretical mathematicians, experimental biologists and clinicians. A degree in mathematics is not required.
94 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Andrei S. Rodin, Ph.D. Dr. Susumu Ohno Chair in Theoretical Biology Associate Professor, Department of Diabetes Complications & Metabolism
COMPUTATIONAL BIOLOGY, LARGE DATA AND MOLECULAR EVOLUTION
Our two primary research interests are: (1) application of SELECTED PUBLICATIONS computer science-based analysis methodology to large-scale • Rodin, A.S., and Rodin, S.N. Universal genetic code. In “-omics” data, and (2) molecular evolution. Encyclopedia of Genetics. Elsevier, St. Louis, MO, 2012. (1) We are working on developing a comprehensive • Rodin, A.S., Gogoshin, G., Litvinenko, A., and Boerwinkle, E. hierarchical data analysis strategy (that integrates statistical Exploring genetic epidemiology data with Bayesian networks. and machine-learning analysis methods for variable selection In Rao, C.R., Sen, P.K., and Chakraborty, R. eds Handbook of and predictive/descriptive modeling) aimed at genomic data. Statistics. Vol. 28 (Bioinformatics). Elsevier, St. Louis, MO, Due to the complex multifaceted nature of most common 2012. diseases, traditional straightforward statistical approaches • Rodin, A.S., Szathmary, E., and Rodin, S.N. On origin of are ill-suited to dealing with the massive datasets generated genetic code and tRNA before translation. Biology Direct 6:14, by the ongoing biomedical studies – hence the need for a 2011. more sophisticated data analysis approach. Specifically, we have developed and implemented a Bayesian network (BN) • Rodin, A.S., Litvinenko, A., Klos, K., Morrison, A.C., Woodage, modeling framework – BNs being arguably the most promising T., Coresh, J., and Boerwinkle, E. Use of a Random Forests methodology for the systems, or pathway, biology analyses. classifier for variable selection in large-scale genomic association studies. J. Comp. Biol. 16: 1705-1718, 2009. (2) Our molecular evolution research centers around phylogenetic analysis methodology, origin of genetic code and • Rodin, A.S., Szathmary, E., and Rodin, S.N. One ancestor for two codes viewed from the perspective of two translation, biological effects of DNA strand bias and, most complementary modes of tRNA aminoacylation. Biology recently, epigenetic effects in evolution by gene duplication. Direct 4:4, 2009. We are currently working on moving this research in new directions, toward systems biology and information-theoretic • Rodin, A.S., Rodin, S.N., and Carter, C.W. On primordial approaches to early molecular evolution modeling and data sense–antisense coding. J. Mol. Evol. 69:555-567, 2009. analysis, which would, in fact, bridge our two main research • Rodin, S.N., and Rodin, A.S. On the origin of the genetic code: interests. Signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100:341-355, 2008. • Rodin, A.(.S), Mosley Jr., T.H., Clark, A.G., Sing, C.F., and Boerwinkle, E. Mining genetic epidemiology data with Bayesian networks application to APOE gene variation and plasma lipid levels. J. Comp. Biol .12:1-11, 2005. • Rodin, S.N., Parkhomchuk, D.V., Rodin, A.S., Holmquist, G.P., and Riggs, A.D. Repositioning-dependent fate of duplicate genes. DNA Cell Biol. 24:529-542, 2005. • Rodin, A.(S.), and Li, W.-H. A rapid heuristic for finding minimum evolution trees. Mol. Phylogenet. Evol. 16:173-179, 2000. • Rodin, S., Rodin, A.(S.), and Ohno, S. The presence of codon- anticodon pairs in the acceptor stem of tRNAs. Proc. Natl. Acad. Sci. USA 93:4537-4542, 1996.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 95 Bart O. Roep, Ph.D. Chan Soon-Shiong Shapiro Distinguished Chair in Diabetes Professor and Chair, Department of Diabetes Immunology
TRANSLATING CAUSE TO CURE OF TYPE 1 DIABETES
Intensive medical research on type 1 diabetes has changed world experts on beta cell function to help understand why the insight radically. Type 1 diabetes is caused by self- certain beta cells escape immune attack, how they hibernate reactive T cells (not antibodies) that accidentally respond in established disease, and how they can be turned back into to the insulin-producing beta cells in the pancreatic islets action (insulin production) as soon as the cause of the disease of Langerhans, leading to beta cell destruction and insulin- has been dealt with by immunotherapy. This knowledge is dependency. Our recent discoveries revealed that beta cells essential to help protect new beta cells arising in the patient are actively contributing to their own demise. The immune (neogenesis) or transplanted into type 1 diabetes patients from system responds to distressed, ‘unhappy’ beta-cells, rather donors (for instance by islet transplantation or embryonic stem than healthy tissue, under the assumption that something is cell therapy). wrong. This is precisely what the immune system is supposed to do in the case of cancer and infection. Yet, in the case of SELECTED PUBLICATIONS type 1 diabetes, this response to own tissue causes destruction • Kleijwegt, F.S., Laban, S., Duinkerken, G., Joosten, A.M., of the only cells producing the vital insulin that is required Koeleman, B.P., Nikolic, T., and Roep, B.O. Transfer of for proper control of blood glucose. Regrettably, therapy of Regulatory Properties from Tolerogenic to Proinflammatory type 1 diabetes is still limited to treating the consequences Dendritic Cells via Induced Autoreactive Regulatory T Cells. J of the disease (by insulin injection), rather than its cause Immunol, 187(12):6357-64, 2011 (autoimmunity). Given the new awareness that type 1 diabetes • Roep, B.O., et al. The problems and promises of research is far more heterogeneous than previously appreciated, it is into human immunology and autoimmune disease. Nature conceivable that no magic bullet exists as intervention therapy Medicine 18(1):48-53, 2012. for all type 1 diabetes. Instead, understanding the differences • Roep, B.O., et al. BHT-3021 Investigators, Steinman L: in disease between patients creates the important opportunity Plasmid-Encoded Proinsulin Preserves C-Peptide While to assign personalized medicine, much like the new situation in Specifically Reducing Proinsulin-Specific CD8+ T Cells in anti-cancer therapy. Our own studies on immune profiling and Type 1 Diabetes. Science Transl Med 5:191, 2013 genetic barcoding of patients have already identified patient • Van Lummel, M., Duinkerken, G., van Veelen, P.A., de signatures ideally suited for certain intervention strategies, Ru, A., Cordfunke, R., Zaldumbide, A., Gomez Tourino, whereas other patients desire different treatment. I., Arif, S., Peakman, M., Drijfhout, J.W., and Roep, B.O. Post-translational modification of HLA-DQ binding islet We elected to negotiate with the immune system by autoantigens in type 1 diabetes. Diabetes, 63(1):237-47, 2014. sophisticated immunotherapy focusing on the disease-causing • Roep, B.O., and Tree, T.I.M. Immunomodulation in immune component, while leaving immunity against tumor autoimmunity: lessons from type 1 diabetes. Nature Rev and infection unharmed. This type of immune modulation has Endocrinol., 10(4):229-42, 2014. similarities with allergy, in which case we can desensitize the • Beringer, D., Kleijweg, F.S., Wiede, F., van der Slik, A., Loh, patient once the cause of the allergy has been identified. We K.L., Petersen, J., Dudek, N., Duinkerken, G., Laban, S., have now reach the stage in type 1 diabetes that we believe Joosten, A., Vivian, J., Chen, Z., Uldrich, A., Godfrey, D., to know what causes the disease, so we can translate this McCluskey, J., Price, D., Radford, K., Purcell, W., Nikolic, T., knowledge in effective, specific and sensitive immunotherapy Reid, H.H., Tiganis, T., Rossjohn, J., and Roep, B.O. T-cell in type 1 diabetes. We will develop and execute vaccination receptor reversed polarity recognition of a self-antigen MHC. Nature Immunol, 16(11):1153-61, 201 strategies and advance immune cell therapies, reinforcing the patients’ own immune system to keep islet autoimmunity in check. We will also engage our unique knowledge of ways that nature controls immunity, by translating the way that mothers protect their babies during pregnancy and shortly after into effective immune protection against beta-cells. Finally, we will build on the knowledge gained at City of Hope by recruiting
96 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Steven T. Rosen, M.D. Provost and Chief Scientific Officer Director, Comprehensive Cancer Center and Beckman Research Institute of City of Hope Irell & Manella Cancer Center Director’s Distinguished Chair
DEVELOPING NOVEL THERAPIES FOR TREATMENT OF HEMATOLOGIC MALIGNANCIES
8-chloro-adenosine in acute myeloid leukemia Role of p38 in CTCL Relapsed/refractory acute myeloid leukemia (AML) carries Cutaneous T Cell lymphomas (CTCL) are a heterogeneous a poor prognosis. The most effective therapies, including group of hematopoietic malignancies that account for 5 to hematopoietic stem cell transplantation, are frequently too 10 percent of non-Hodgkin lymphomas. The initial disease toxic for an older patient population afflicted with the disease. presentation is characterized by the infiltration of the skin by 8-chloro-adenosine (8-Cl-Ado) is a novel chemotherapeutic malignant clonal CD4+ lymphocytes that possess a mature agent with a unique mechanism of action and has been memory T cell phenotype. However, little is understood about advanced to a phase 1/2 clinical trial in relapsed/refractory the pathogenesis of CTCL. Previous works in our laboratory AML at City of Hope. We and our collaborators have shown demonstrate that p38 as a potential therapeutic target for that, in cells, 8-Cl-Ado is metabolized into the active, the treatment of cutaneous T cell lymphoma. To elucidate the cytotoxic metabolite 8-Cl-ATP. In contrast to most traditional mechanism and achieve a potential cure for CTCL, with the chemotherapeutics, 8-Cl-ATP incorporates predominantly into help of the City of Hope facilities of High Throughput Core mRNA, thereby causing inhibition of transcription. In addition, and Bioinformatics Core, we screen and identify compounds 8-Cl-Ado inhibits ATP synthase activity, thereby diminishing that are specific for p38 inhibitors that would selectively kill endogenous ATP pools. 8-Cl-Ado has particular high efficacy CTCL cells. We also seek to enhance the drug potency by against AML cells that carry the FLT3/ITD mutation, which is synergistically treating with compounds that target other associated with poor clinical outcome. Importantly, 8-Cl-Ado signaling pathways such as by targeting histone deacetylases inhibits activity of the treatment-resistant leukemia stem cell and deubiquitinating enzymes. population, which is one of the major challenges in curing AML. To further enhance the anti-cancer potential of 8-Cl-Ado SELECTED PUBLICATIONS in AML, we are currently developing 8-Cl-Ado combination therapies using targeted therapies, such as BCL-2 and FLT3 • Gandhi, V., et al. (2001) 8-chloro-cAMP and 8-chloro- adenosine act by the same mechanism in multiple myeloma inhibitors. In addition, the anti-cancer activity of 8-Cl-Ado is cells. Cancer Res 61: 5474-5479. being investigated in other cancers. • Chen, L.S., et al. (2009) Inhibition of ATP synthase by Leflunomide in multiple myeloma chlorinated adenosine analogue. Biochem Pharmacol 78: 583- Multiple myeloma (MM) remains an incurable disease 591. and new, effective treatments are needed. Leflunomide is a commercially available oral immunosuppressive agent that • Halgren, R.G., et al. (1998) 8Cl-cAMP cytotoxicity in both steroid sensitive and insensitive multiple myeloma cell lines has been FDA-approved since 1998 for the treatment of is mediated by 8Cl-adenosine. Blood 92: 2893-2898. rheumatoid arthritis. The primary mechanism of action of leflunomide is inhibition of de novo pyrimidine synthesis by • McBrayer, S.K., et al. (2012) Integrative gene expression targeting dihydroorotate dehydrogenase, and thus achieving profiling reveals G6PD-mediated resistance to RNA-directed anti-proliferative effect in B- and T-lymphocytes. Leflunomide nucleoside analogues in B-cell neoplasms. PLoS One 7: e41455. has been investigated for its anti-neoplastic potential in a variety of preclinical tumor models. Recent preclinical studies • Baumann, P., et al. (2009) Dihydroorotate dehydrogenase have demonstrated significant anti-neoplastic activity in inhibitor A771726 (leflunomide) induces apoptosis and MM. In addition, limited clinical experience is suggestive of a diminishes proliferation of multiple myeloma cells. Mol. Cancer Ther 8:366-75. beneficial response when leflunomide is used to treat relapsed/ refractory MM. Considering the favorable toxicity profile and • Sanchez-Vega, B., et al. (2006) Glucocorticoid receptor extensive clinical experience with leflunomide in rheumatoid transcriptional isoforms and resistance in multiple myeloma arthritis, this drug represents a potential new candidate for cells. Mol Cancer Ther 5:3062-70. therapy in multiple myeloma. A phase 1 dose-escalation • Bloom, T., et al. (2012) Cutaneous T-Cell Lymphomas: A trial of leflunomide in patients with relapsed or relapsed/ Review of New Discoveries and Treatments. Current Treatm. refractory MM is currently ongoing at City of Hope. In addition, Options in Oncology 13:102–121. we are currently investigating leflunomide in combination • Bliss-Moreau, M., et al. (2015) Identification of p38beta as with a variety of approved drugs, including steroids, a therapeutic target for the treatment of Sezary syndrome. J immunomodulatory drugs, proteasome- and HDAC inhibitors. Invest. Derm. 135: 599-608.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 97 John J. Rossi, Ph.D. Lidow Research Family Chair Morgan & Helen Chu Dean’s Chair of the Irell & Manella Graduate School of Biological Sciences Professor and Chair, Department of Molecular and Cellular Biology Dean, Irell & Manella Graduate School of Biological Sciences THE BIOLOGY AND APPLICATIONS OF SMALL RNAS
The lab of John J. Rossi, Ph.D., has as its primary focus studies • Hori, S., Herrera, A., Rossi, J.J., and Zhou, J. (2017) Review on the functions and therapeutic applications of small RNAs. - Current advances in aptamers of cancer diagnosis and Within the past two decades there has been an explosion therapy. Cancers J. 10: 1-33 doi:10.3390/cancers10020009 of new findings about the roles that small RNAs play in (review article; not peer-reviewed) biological processes. We now know that RNAs not only encode • Pang, K.M., Castanotto, D., Li, H., Scherer, S., and Rossi, J.J. information for protein translation, but they also can serve as (2017) Incorporation of aptamers in the terminal loop of biological catalysts and gene regulatory agents. The recent shRNAs yields an effective and novel combinatorial targeting discovery of RNA interference in which precursor, double strategy. Nucl. Acid Res. Oct. 25, 17 gkx980, https://doi. stranded RNAs or RNA hairpins are processed to smaller org/10.1093/nar/gkx980 PMCID: PMC5758892. 21 to 23 base duplexes called small interfering RNAs and • Satheesan, S., Li, H., Burnett, J.C., Takahashi, M., Li, S., Wu, microRNAs has revolutionized mammalian cell genetics. S.X., Synold, T.W., Rossi, J.J., and Zhou, J.H. (2018) HIV These small RNAs can be used to inhibit gene expression by replication and latency in a humanized NSG mouse model targeting mRNAs with complementary sequences. We study during suppressive oral combinational ART. J. Virology, 92(7), the mechanism of RNAi at the biochemical level as well as pii: e02118-2117. PMID: 29343582 exploit the therapeutic potential in AIDS and cancer. In addition • Zhou, J.H., Lazar, D., Li, H., Xia, X., Satheesan, S., Charlins, P., to the use of small RNA triggers of the RNAi mechanism, the O’Mealy, D., Akkina, R.,Saayman, S., Weinberg, M.S., Rossi, lab has been developing RNA aptamers for targeted inhibition J.J., and Morris, K.V. (2018) Receptor-targeted aptamer- of HIV replication as well as a cell internalizing delivery vehicle siRNA conjugate-directed transcriptional regulation of HIV-1. for siRNAs in the treatment of HIV infection and cancers. Theranostics, 8(6): 1575-1590. PMID: 29556342. We have evolved and tested aptamers targeting the HIV-1 • Yoon. S., Huang, K.W., Reebye, V., Spalding, D., Przytycka, envelope. These aptamers are dual functional in that they bind T.M., Wan, Y., Swiderski, P., Li, L., Armstrong, B., Reccia, I., to HIV and neutralize infection, but they are also internalized Zacharoulis, D., Dimas, K., Kusano, T., Shively, J., Habib, N., into HIV infected cells that express the envelope on the and Rossi. J.J. (2017) Aptamer drug conjugates (ApDCs) of cell surface. This strategy of cell internalizing, dual function active metabolites of nucleoside analogues and cytotoxic aptamers is being extended to a variety of receptors on agents inhibit pancreatic tumor cell growth. Mol. Ther-Nucleic hematopoieic cells and pancreatic cancer cells. Acids 6(17): 80-88 PMCID: PMC Journal - In Process • Yoon, S., and Rossi, J.J. (2017) Future strategies for the SELECTED PUBLICATIONS discovery of therapeutic aptamers. Expert Opinion 12: 317-319 • Yoon, S., Armstrong, B., Habib, N., and Rossi, J.J. (2017) Blind PMID: 28276706 PMCID: PMC Journal - In Process SELEX approach identifies RNA aptamer that regulate EMT • Voutila, J., Reebye, V., Roberts., T.C., Protopapa, P., and Inhibit metastasis. Mol. Cancer Res. doi 10.1158/1541- Andrikakou, P., Blakey, D.C., Habib, R., Huber, H., Saetrom, 7786.MCR-16-0462 Published April 2017 PMCID: P., Rossi, J.J., and Habib, N.A. (2017) Development an PMC5555160. mechanism of small activating RNA targeting CEBPA, a novel • Song, M-N., and Rossi, J.J. (2017) Molecular mechanisms therapeutic in clinical trials for liver cancer. Mol. Therapy (In of Dicer: endonuclease and enzymatic activity. Biochem. J. Press) 424: 1603-1618 doi: HYPERLINK “https://doi.org/10.1042/ • Xia, X., and Rossi, J.J. (2017) Review - RAFTing towards BCJ20160759” 10.1042/BCJ20160759 PMCID: the shore of nanotherapeutic. Current Drug Delivery (review PMC5415849 article; not peer-reviewed) (In Press) • Zhou, J., and Rossi, J.J. (2017) Aptamers as targeted • Yoon, S., and Rossi, J.J. (2018) Therapeutic potential of small therapeutics: current potential and challenges. HYPERLINK activating RNAs (saRNAs) in human diseases. Curr. Pham. “https://www.ncbi.nlm.nih.gov/pubmed/27807347” \o Biotech. (In Press) “Nature reviews. Drug discovery.” Nat Rev Drug Discov. Jun;16(6):440. doi: 10.1038/nrd.2017.86. Epub 2017 Apr 28. PMCID: PMC5700751
98 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Paul M. Salvaterra, Ph.D. Professor Emeritus, Department of Developmental and Stem Cell Biology
MODELING ALZHEIMER-TYPE NEURODEGENERATION
Neurodegenerative diseases constitute a major health specifically in amyloid beta 42 neurons and found that an problem with no effective treatments. The causes of most increase in an abnormal form of autophagy appears to be the neurodegenerative disorders are unknown, but certain rare key cellular problem. When we undertake similar experiments genetic forms provide important clues to what has gone with the related but nontoxic amyloid beta 40 protein, no wrong. Alzheimer disease (AD) is the most common form of significant pathology or neurology is observed. Importantly, age-related dementia with an estimated 5 million sufferers when we combine amyloid beta 42 expression with in the United States alone. It is estimated that the incidence pharmacological or genetic changes in autophagy function we of AD is more than 50 percent in individuals who live to be can influence the course of neurodegeneration. An increased older than 85. This obviously presents an enormous medical autophagy activity results in a more severe neurodegenerative and economic challenge to society as individuals live longer. phenotype, while downregulation provides a protective First described more than a hundred years ago by the German benefit to animals expressing amyloid beta 42. These types of scientist Alois Alzheimer, to this day the disease is poorly experiments suggest new therapeutic approaches that could understood, untreatable and ranked as the No. 6 be considered in the search for AD treatments. cause of death for individuals in the U.S. (trailing only Our current focus is to extend our initial description of cardiovascular disease and cancer). Alzheimer described the autophagy as a central focus of AD neuropathology, begin neuropathology focusing his attention on characteristic senile to link the aging process to amyloid beta 42 induced plaques and neurofibrillary tangles. Subsequent work revealed neurodegeneration and establish the mechanism for senile the biochemical composition of these brain lesions but not plaque formation. how they are formed or how we can prevent or remove them. In fact, even their contribution to disease phenotypes such as memory loss and dementia is still a subject of controversy. SELECTED PUBLICATIONS Several decades ago new research led to the identification of • Ling, D., Magallanes, M., and Salvaterra, P.M. Accumulation several genes that cause a rare type of aggressive early onset of amyloid-like αβ1-41 in AEL (autophagy-endosomal- AD and provided a strong correlative link with the main protein lysosomal) vesicles: Potential implications for plaque components of senile plaques, the amyloid beta peptides. No biogenesis. ASN Neuro. 2014 Mar 12;6(2). pii: e00139. DOI: 10.1042/AN20130044. convincing explanation, however, has emerged to link amyloid beta accumulation with the cellular or molecular mechanisms • Ling, D., Pike, C.J., and Salvaterra, P.M. Deconvolution of the leading to neurodegeneration. Our current work is designed to confounding variations for reverse transcription quantitative explore this important relationship. real-time polymerase chain reaction by separate analysis of biological replicate data.Anal Biochem. 427: 21-25, 2012. We use a multidisciplinary approach primarily concentrating on understanding amyloid beta pathogenesis in a Drosophila • Ling, D., and Salvaterra, P.M. Autophagy-derived Alzheimer’s model system. It may at first seem silly to use fruit flies to pathogenesis. Alzheimer’s Disease/Book 2, InTech., 2011. understand a human disease like AD but there are a number • Ling, D., and Salvaterra, P.M. Brain aging and Abeta(1-42) of reasons why we made this choice. First among them are the neurotoxicity converge via deterioration in autophagy- numerous scientific advantages to be gained by the advanced lysosomal system: A conditional Drosophila model linking genetic approaches available in Drosophila. Second, flies have Alzheimer’s neurodegeneration with aging. Acta Neuropathol. a relatively short lifespan, so we can easily design experiments 121: 183-191, 2011. to investigate the relationship between normal aging and AD- • Ling, D., and Salvaterra, P.M. Optimization of quantitative like neuropathology and neurodegeneration. PCR data normalization: Selection of internal reference genes Our initial studies have borne out the usefulness of a fly model for Drosophila models of brain aging & neurodegeneration. PLoS ONE 6(3): 1-8, 2011. for AD type neurodegeneration as a way to understand the human condition. Targeted expression of human amyloid beta 42 in specific types of fly neurons leads to obvious neurological problems and age-dependent neurodegeneration. We have identified the detailed cellular neuropathology that develops
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 99 Dustin E. Schones, Ph.D. Associate Professor, Department of Diabetes Complications and Metabolism
EPIGENETICS AND GENOMICS
Our lab is interested in the interaction of genetic and SELECTED PUBLICATIONS epigenetic variation in complex diseases such as cancer, • Das, S., Senapati, P., Chen, Z., Reddy, M.A., Ganguly, R., diabetes and obesity. We utilize an integrative approach Lanting, L., Mandi, V., Bansal, A., Leung, A., Zhang, S., Jia, combining computational and experimental approaches to Y., Wu, X., Schones, D.E., and Natarajan, R. Regulation of study these problems. angiotensin II actions by enhancers and super-enhancers in A primary area of interest in the lab is in gene-by-environment vascular smooth muscle cells. Nat Commun. Nov 13, 2017 interactions mediated through chromatin modifications. • Du, J., Tian, J., Ding, L., Trac, C., Xia, B., Sun, S., Schones, We previously reported that one manner by which external D.E.†, and Huang, W.† Vertical sleeve gastrectomy reverses environmental factors can influence molecular pathways is diet-induced gene-regulatory changes impacting lipid through modification to chromatin, with a “western” high fat/ metabolism. Sci Rep. Jul 1, 2017 †Corresponding authors high sucrose (HF/HS) diet leading to chromatin remodeling in the livers of mice. We are currently exploring environmental • Du, J., Leung, A., Trac, C., Lee, M., Parks, B.W., Lusis, A.J., perturbations to chromatin modifications in a number of systems. Natarajan, R., and Schones, D.E. Chromatin variation Another area of interest is in the epigenetic dysregulation associated with liver metabolism is mediated by of repetitive elements. We have previously demonstrated transposable elements. Epigenetics Chromatin, Jul 8, 2016 that obesity leads to epigenetic modifications at particular • Leung, A., Trac., C., Du, J., Natarajan, R., and Schones, D.E. repetitive regions of the genome. We are investigating the Persistent chromatin modifications induced by high fat diet. mechanisms through which obesity leads to epigenetic J. Biol. Chem , Mar 22, 2016 modifications at these repetitive regions and the potential to prevent or reverse this through therapeutic intervention. • Chimge, N.O., Little, G.H., Baniwal, S.K., Adisetiyo, H., Xie, Y., Zhang, T., O’Laughlin, A., Liu, Z.Y., Ulrich, P., Martin, A., We have furthermore demonstrated that additional exogenous Mhawech-Fauceglia, P., Ellis, M.J., Tripathy, D., Groshen, stimuli can promote the epigenetic dysregulation of repetitive S., Liang, C., Li, Z., Schones, D.E., and Frenkel, B. RUNX1 elements in the genome. we have demonstrated that prevents oestrogen-mediated AXIN1 suppression and Epstein-Barr virus, a tumor virus associated with lymphoma β-catenin activation in ER positive breast cancer. Nat development, dramatically alters the epigenome leading to Commun. Feb 26;7 2016 dysregulation of certain classes of repetitive elements. We are currently characterizing the extent of repetitive element • Li, Z., Dai, H., Martos, S.N., Xu, B., Gao, Y., Li, T., Zhu, G., dysregulation in several types of lymphomas, as well as other Schones, D.E., and Wang, Z. Distinct roles of DNMT1- cancer types. dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biol. We are also interested in the molecular links between Jun 2 2015 diabetes and breast cancer. We have demonstrated that hyperinsulinemia promotes epigenetic alterations in vitro and • Jose, C.C., Xu, B., Jagannathan, L., Trac, C., Mallela, R.K., are currently pursuing similar studies in mice. Hattori, T., Lai, D., Koide, S., Schones, D.E.†, and Cuddapah, S.†. Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proc. Natl. Acad. Sci. USA. 111:14631-14636, 2014 †Corresponding authors
100 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Victoria Seewaldt, M.D. Ruth Ziegler Chair in Population Sciences Professor and Chair, Department of Population Sciences Associate Director, Comprehensive Cancer Center
EARLY DETECTION OF BIOLOGICALLY AGGRESSIVE CANCERS
Victoria Seewaldt, M.D., is an internationally recognized SELECTED PUBLICATIONS expert in early detection and translational research. She • Pilie, P., Ibarra-Drendall, C., Broadwater, G., Petricoin, leads a bench-to-community research program focusing on E., Liotta, L.A., Zalles, C., Geradts, J., Ford, A. Yu, D., and identifying molecular targets and multidisciplinary targets for Seewaldt, V.L. Protein Microarray Analysis of Mammary early detection of biologically aggressive cancers. Seewaldt has Epithelial Cells from Obese and Non-Obese Women at High- extensive basic/translational research expertise in identifying Risk for Breast Cancer. Cancer Epi Biomarkers Prev. 20:476- signaling networks that promote breast cancer initiation with 482, 2011 PMCID: PMC21647677. the goal of integrating novel functional imaging strategies • Henderson, B.*, Lee, N.*, Seewaldt, V.L.*, and Shen, H.*. The with risk-marker to provide early detection of interval influence of race and ethnicity on the biology of cancer. cancers. The proposed study will draw heavily on Seewaldt’s Nature Reviews Cancer, 12, 648-653, 2012. (*all authors ability to span from lab to the clinic to the community. She contributed equally). PMCID: PMC22854838. established a cohort of over 650 women who are at high-risk for breast cancer. Her outreach project works with community • Seewaldt, V.L. Destiny from density. Nature, 490, 490–491, members to target signaling networks that activated during 2012. PMCID: PMC3640457. the initiation of triple-negative breast cancer. The unique • Arendt, L.M., McCready, J., Seewaldt, V.L.*, and feature of Seewaldt’s program is that biomarkers identified Kuperwasser, C.*. Obesity promotes breast cancer by CCL2- in the laboratory can be immediately tested in the high-risk mediated macrophage recruitment and angiogenesis. Cancer women in her cohort as predictors of short-term breast Res. 73:6080-93, 2013. PMID: PMC23959857. *Joint senior cancer risk and targeted with novel pharmacologic agents and authors. imaging strategies. • Tung, J., Barnes, J., Desai, S.R., Sistrunk, C., Conklin, M., Currently, clinical decision-making is heavily dependent on Schedin, P., Keely, P.J., Seewaldt, V.L.*, and Weaver, V.*. morphology. My group’s studies provide evidence that some Tumor Mechanics and Metabolic Dysfunction. Free Radical morphologically normal breast biopsies are not biochemically Biology and Medicine. In press, e-pub S0891-5849:14 01392- normal. We are in the processing of identifying signaling 6. *Joint senior authors. networks that are activated in my high-risk cohorts (over 1,200 • Dietze, E., Sistrunk, C., Miranda, G., and Seewaldt, V.L. women) prior to the development of interval cancers. My Origins of the aggressive biology of triple-negative breast collaborators and I have worked to develop novel strategies cancer in African American women. Nature Medicine, 15(4): to prospectively identify biophysical properties and protein- 248-54, 2015 signaling networks activated during breast cancer initiation. We have identified signaling pathways that predict aggressive biology in noncancerous cells and validated these signaling strategies in live patient cells, to predict risk and identify sensitivity to targeted agents. Currently we have no means to identify women who will develop interval cancers. As a result, we overscreen the majority of women with benign biology in order to find the minority of women who will develop aggressive interval cancers. Currently we are using the technology we develop to identify aggressive biology before women develop interval cancers and stop overscreening women with benign biology.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 101 Binghui Shen, Ph.D. Professor and Chair, Department of Cancer Genetics and Epigenetics Co-leader, Molecular and Cellular Biology of Cancer
DNA REPLICATION, REPAIR, AND APOPTOSIS NUCLEASES IN GENOME STABILITY AND CANCER
DNA replication and repair are critical for maintaining genome SELECTED PUBLICATIONS stability. These processes are in part dependent on the activities • Li, S., Ali, S., Duan, X., Liu, S., Du,J., Liu, C., Dai, H., Zhou, M., of an emerging family of structure-specific nucleases. Flap Zhou, L., Yang, L., Chu, P., Li, L., Bhatia, R., Schones, D. E., Wu, endonuclease 1 (FEN1) is a metallo- and substrate-structure- X., Xu, H., Hua, Y., Guo, Z., Yang, Y., Zheng, L., and Shen, B. specific nuclease. It possesses three distinct biochemical Cell Reports 23, 389–403, 2018 activities, functioning as a flap endonuclease (FEN), a nick- specific exonuclease (EXO) and a gap dependent endonuclease • Zhou, L., Dai, H., Wu, J., Zhou, M., Yuan, H., Du, J., Yang, L., (GEN). FEN1 plays a critical role in maintaining human genome Wu, X., Xu, H., Hua, Y., Xu, J., Zheng, L., and Shen, B. (2017) stability via different pathways. It serves as a major nuclease Role of FEN1S187 phosphorylation in counteracting oxygen- for RNA primer removal during Okazaki fragment maturation induced stress and regulating postnatal heart development. FASEB J., 31:132-147, 2017 and for long patch base excision repair using its FEN activity. The multiple functions of FEN1 are regulated via three major • Ray-Chaudhuri, A.*, Callen, E.*, Ding, X., Gogola, E., Duarte, mechanisms: formation of complexes with different protein A.A., Lee, J.E., Wong, N., Lafarga, V., Calvo, J.A., Panzarino, partners, cellular compartmentalization and post-translational N.J., John, S., Day, A., Crespo, A.V., Shen, B., Starnes, modifications (PTMs). Sequential PTMs determine the timely L.M., de Ruiter, J.R., Daniel, J.A., Konstantinopoulos, P.A., actions of FEN1 in the DNA replication fork. Recently, we have Cortez, D., Cantor, S.B., Fernandez-Capetillo, O., Ge, K., identified the first arginine demethylase that demethylates FEN1. Jonkers, J., Rottenberg, S.,Sharan, S.K., and Nussenzweig, Three groups of FEN1 mutations with different functional defects A. (2016) HYPERLINK “http://www.ncbi.nlm.nih.gov/ have been identified in human cancer cells and knocked into the pubmed/27443740” Replication fork stability confers corresponding mouse genome to mimic their impact on cancer chemoresistance in BRCA-deficient cells. Nature, 535:382- initiation and progression. 387, 2016 Efficient and faithful replication of telomeric DNA is critical for • Liu, S., Lu, G., Ali, S., Liu, W., Zheng, L., Dai, H., Li, H., Xu, H., maintaining genome integrity. The G-quadruplex (G4) structure Hua, Y., Zhou, Y., Ortega, J., Li, G.-M., Kunkel, T.A., and Shen, arising in the repetitive TTAGGG sequence is thought to stall B. Okazaki fragment maturation involves α-segment error replication forks, impairing efficient telomere replication and editing by the mammalian FEN1/MutSα functional complex. leading to telomere instabilities. However, pathways modulating EMBO J., 2015. telomeric G4 are poorly understood, and it is unclear whether • Wang, H., Li, Y., Truong, L.N., Shi, L.Z., Hwang, P.Y., He, defects in these pathways contribute to genome instabilities in J., Do, J., Cho, M.J., Li, H., Negrete, A., Shiloach, J., Berns, vivo. Recently, we reported that mammalian DNA2 helicase/ M.W., Shen, B., Chen, L., and Wu, X. CtIP maintains stability nuclease recognizes and cleaves telomeric G4 in vitro. at common fragile sites and inverted repeats by an end Consistent with DNA2’s role in removing G4, DNA2 deficiency resection-independent endonuclease activity. Mol. Cell 54: in mouse cells leads to telomere replication defects, elevating 1012-1021, 2014. the levels of fragile telomeres and sister telomere associations. • Lin, W., Sampathi, S., Dai, H., Liu, C., Zhou, M., Hu, J., Such telomere defects are enhanced by stabilizers of G4. Huang, Q., Campbell, J., Zheng, L., Chai, W., and Shen, B. Moreover, DNA2 deficiency induces telomere DNA damage Mammalian DNA2 helicase/nuclease cleaves G-quadruplex and chromosome segregation errors, resulting in tetraploidy and is required for telomere integrity. EMBO J. 32, 1425-1439, and aneuploidy. Consequently, DNA2 deficient mice develop 2013. aneuploidy-associated cancers containing dysfunctional telomeres. Collectively, our genetic, cytological and biochemical • Guo, Z., Kanjanapangka, J., Liu, N., Liu, S., Liu, C., Wu, results suggest that mammalian DNA2 reduces replication Z., Wang, Y., Loh., T., Kowolik, C., Jamsen, J., Zhou, M., stress at telomeres, thereby preserving genome stability and Truong, K., Chen, Y., L. Zheng, and Shen, B. Sequential post- suppressing cancer development. translational modifications program FEN1 degradation during cell-cycle progression, Mol. Cell 47 444-456, 2012.
102 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Yanhong Shi, Ph.D. Professor and Director, Division of Stem Cell Biology Research, Department Developmental and Stem Cell Biology
STEM CELL-BASED DISEASE MODELING AND THERAPEUTIC DEVELOPMENT
Stem cell technology holds great promise for the treatment SELECTED PUBLICATIONS of many diseases that currently lack effective therapies. • Murai, K., Sun, G., Ye, P., Tian, E., Yang, S., Sun, G., Hong, Identifying factors that control stem cell maintenance and T., Kalkum, M., Riggs, A.D., Song, H., Ming, G-L., and Shi, Y. self-renewal could move stem cell technology from bench to 2016. Nuclear receptor TLX regulates miR-219 processing bedside. My laboratory has been characterizing the role of the in neural stem cells by interacting with the p68/Drosha/ nuclear receptor TLX signaling in neural stem cell self-renewal DGCR8 complex. Nature Communications 7:10965. doi: and differentiation, which has uncovered novel molecular 10.1038/ncomms10965. mechanisms governing neural stem cell self-renewal, • Cui, Q., Yang, S., Ye, P., Tian, E., Sun, G., Zhou, J., Sun, Gu., neurogenesis and cognition. Our future research effort will Liu, X., Chen, C., Murai, K., Zhao, C., Azizian, K.T., Warden, continue to define molecular mechanisms regulating neural C., Yang, L., Wu, X., D’Apuzzo, M., Brown, C., Badie, B., Peng, stem cell self-renewal and neurogenesis, which will allow us L., Riggs, A.D., Rossi, J.J., and Shi. Y. 2016. Downregulation of to develop new, targeted therapies for a host of neurological TLX induces TET3 expression and inhibits glioblastoma stem disorders, including brain tumors and neurodegenerative cell self-renewal and tumorigenesis. Nature Communications diseases such as Alzheimer and Parkinson disease. 7:10637. doi: 10.1038/ncomms10637. The establishment of induced pluripotent stem cell (iPSC) • Islam, M.M., Smith, D.K., Niu, W., Fang, S., Iqbal, N., Sun, technology pioneered by 2012 Nobel Prize winner Shinya G., Shi, Y., and Zhang, C-L. 2015. Enhancer analysis unveils Yamanaka M.D., Ph.D., opened a new era in biomedical genetic interactions between TLX and SOX2 in neural stem research. My laboratory aims to study pathological cells and in vivo reprogramming. Stem Cell Reports. 5: 805- mechanisms and develop therapeutic candidates for 815. neurological diseases using patient iPSCs. We are studying • Fong, M.Y., Zhou, W., Liu, L., Alontaga, A.Y., Chandra, M., leukodystrophy diseases that currently lack effective Ashby, J., Chow, A., O’Connor, S.T.F., Li, S., Chin, A.R., Somlo, therapy, and the most common neurodegenerative diseases, G., Palomares, M., Li, Z., Tremblay, J.R., Tsuyada, A., Sun, G., including Alzheimer and schizophrenia. We will study disease Reid, M.A., Wu, X., Swiderski, P., Ren, X., Shi, Y., Kong, M., mechanisms using these patient iPSC-derived cells as cellular Zhong, W., Chen, Y., and Wang, S.W. 2015. Breast cancer- models and perform drug screening using the iPSC platform. secreted miR-122 reprograms glucose metabolism in pre- After genetic correction, some of these cells will also be metastatic niche to promote metastasis. Nature Cell Biology. tested for their ability to recover disease phenotypes as 17: 183-194. therapeutic candidates. • Murai, K., Qu, Q., Sun, G., Ye, P., Li, W., Asuelime, G., Sun, E., Glioblastoma is one of the most lethal cancers in the United Tsai, G.E., and Shi, Y. 2014. Nuclear receptor TLX stimulates hippocampal neurogenesis and enhances learning and States. New therapies are desperately needed to treat this memory in a transgenic mouse model. PNAS 111: 9115-9120 disease. My laboratory will characterize the regulatory (Featured highlight in Nature Review Neurosciences). cascades that regulate glioblastoma stem cell self-renewal, invasiveness and tumorigenecity, in order to develop novel • Zhang, R-R., Cui, Q-Y., Murai, K., Lim, Y.C., Smith, Z.D., Jin, S., biomarkers and molecular targets for brain tumor treatment. Ye, P., Rosa, L., Lee, Y.K., Wu, H-P., Liu, W., Xu, Z-M., Yang, L., This study will yield new insights into glioblastoma biology, and Ding, Y-Q., Tang, F., Meissner, A., Ding, C.*, Shi, Y.*, and Xu, lead to development of therapies that target tumor initiating G-L.*. 2013. Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell 13: 237-245. (*co-corresponding cells for glioblastoma patients. authors).
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 103 Ben Hung-Ping Shih, Ph.D. Assistant Professor, Department of Translational Research and Cellular Therapeutics
STEM CELL BIOLOGY AND ORGANOGENESIS
Pancreas morphogenesis and disease SELECTED PUBLICATIONS The biology of the pancreas has been studied intensely, in the • Shih, H.P., Panlasiqui, D., Cirulli, and V. Sander, M. ECM hope of finding better treatments for pancreatic diseases such Signaling Regulates Collective Cellular Dynamics to Control as diabetes mellitus, pancreatitis and pancreatic cancer. We Pancreas Branching Morphogenesis. Cell Reports, 14: 169-79. have learned much about the molecular details underlying 2016 the ability of pancreatic progenitor cells to differentiate • Shih, H.P., Seymour, P.A., Patel, N.A., Xie, R., Wang, A., Liu, into distinct cell types; however, we are still limited in our P.P., Yeo, G.W., Magnuson, M.A., and Sander, M. A gene understanding of how individual progenitor cells create the regulatory network cooperatively controlled by Pdx1 and coherent communities with the organ architecture. The Sox9 governs lineage allocation of foregut progenitor cells. Cell Reports, 13: 1-11. 2015 primary goal of my laboratory is to gain a better understanding of two fundamentally important processes in developmental • Shih, H.P., and Sander, M. Embryonic pancreas explant biology, namely the molecular control of organ morphogenesis culture systems. Methods in Stem Cell and Tissue Repair, 1210:229-237, 2014. and the interplay between morphogenesis and cell-fate decisions during pancreas development. • Shih, H.P., Wang, A., and Sander, M. Pancreas organogenesis: From lineage determination to morphogenesis. Ann. Rev. Cell The molecular control of pancreas morphogenesis and Develop. Biol. 29: 19.1-25, 2013. We have established a live-imaging platform for mouse embryonic pancreas explants, allowing us to monitor pancreas • Rockich, B.E., Hrycaj, S.M., Shih, H.P., Nagy, M.S., Ferguson, M.A.H., Kopp, J.L., Sander, M., Wellik, D.M., and Spence, morphogenesis at single-cell resolution in real time. By using J.R. Sox9 plays multiple roles in the lung epithelium during this tool, my laboratory is investigating the interplay between branching morphogenesis. Proc. Natl. Acad. Sci. 110:4456-64. morphogenesis and cell fate decisions during organogenesis. 2013 Results from these studies will not only uncover the signaling • Jin, L., Feng, T., Shih, H.P., Zerda, R., Luo, A., Hsu, J., Mahdavi, crosstalk between morphogenesis and cell fate determination, A., Sander, M., Tirrell, D.A., Riggs, A.D., and Ku, H.T. Colony but may also identify novel mechanisms by which cell forming cells in the adult mouse pancreas are expandable differentiation programs orchestrate the cellular behaviors of in matrigel and form endocrine/acinar colonies in laminin progenitors to coordinate pancreas morphogenesis. hydrogel. Proc. Natl. Acad. Sci. 110:3907-3912, 2013. Generation of a human pancreas organoid culture system • Shih, H.P., Kopp, J.L., Sandhu, M., Dubois, C.L., Seymour, Organoids are derived from pluripotent stem cells or isolated P.A., Grapin-Botton, A., and Sander, M. A Notch-dependent molecular circuitry initiates pancreatic endocrine and ductal organ progenitors that differentiate to form a 3-D organ- cell differentiation. Development 139:2488-99, 2012. like tissue. Organoids have been generated for a number of organs from both mouse and human stem cells. An exciting • Seymour, P.A., Shih, H.P., Patel, N.A., Freude, K.K., Xie, R., Lim, C.J., and Sander, M. A Sox9/Fgf feed-forward loop perspective is the production of 3-D model systems of human maintains pancreatic organ identity. Development, 139, 3363- pancreas development for use as a model to study function 3372. 2012 and disease. We have used hPSC technology with 3-D culture conditions to generate pancreatic progenitor cells in vitro. My laboratory is developing this unique culture system and aiming to produce 3-D pancreas organoids that resemble the cellular organization of the organ itself. In the future, we will use organoids to model pancreatic diseases by introducing disease mutations using genome editing tools or patient-derived hPSCs, so as to better understand the disease itself and to screen for compounds and/or metabolites.
104 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES John E. Shively, Ph.D. Professor and Chair, Department of Molecular Imaging and Therapy Associate Dean, Irell & Manella Graduate School of Biological Sciences
STRUCTURE, FUNCTION AND REGULATION OF CARCINOEMBRYONIC ANTIGEN GENES
Carcinoembryonic antigen related antigen-1 for PET imaging. The advantage of 18F over 64Cu in this case CEACAM1, a member of the CEA gene family, is a cell surface, is that peptides are rapidly cleared from the body due to their cell adhesion molecule expressed on most epithelial cells, and, small size and it is important to match the isotope half-life like most epithelial cancers, is downregulated early on during with the biological half-life. The half-life of 18F is 110 minutes. tumorigenesis. For example, it is highly expressed in normal breast For this project we chose and absent in breast cancer. When breast cancer cells which do neurotensin as an excellent not express CEACAM1 are transfected with CEACAM1, they re- marker for colon cancer. establish a lumen forming phenotype in 3-D culture. CEACAM1 The image shows the tumor mRNA is alternatively spliced to give multiple isoforms, including on the right and bladder at 1-4 ecto-domains and a short or long cytoplasmic domains. the bottom. An epithelial specific short isoform has 12 amino acids in the cytoplasmic domain, and a lymphocyte specific long isoform has SELECTED PUBLICATIONS 72 amino acids that include two inhibitory motifs called ITIMs. • Dery, K.J., Kujawski, M., Grunert, D., Wu, X., Ngyuen, T., Cheung, C., Yim, J.H., and Shively, J.E. IRF-1 regulates The long isoform has ITIMs that when alternative mRNA splicing of carcinoembryonic antigen- phosphorylated recruit the inhibitory related cell adhesion molecule 1 (CEACAM1) in breast phosphatases, SHP-1 or SHP-2. A breast epithelial ells generating an immunoreceptor tyrosine-based inhibition motif (ITIM) containing isoform. Mol. Cancer 13: cancer xenograft that was stained for 64, 2014. CEACAM1 by immunofluorescence shows high expression only at the • Nguyen, T., Chen, C.J., and Shively, J.E. Phosphorylation of CEACAM1 molecule by calmodulin kinase IID in a three- leading edge of the tumor. When the isoform phenotype was dimensional model of mammary gland lumen formation. J. determined, it was predominantly the long isoform. Biol. Chem. 289: 2934-2945, 2014. Novel bone repair cells: monoosteophils • Selvaraju, R.K., Velikyan, I., Johansson, L., Wu, Z., Todorov, Monoosteophils are novel bone repair cells. While studying the I., Shively, J., Kandeel, F., Korsgren, O., and Eriksson, O. Pre-clinical evaluation of [(68)Ga]Ga-DO3A-VS-cys(40)- effects of natural peptide LL-37 on neutrophils and monocytes, Exendin-4 for imaging of insulinoma. Nucl. Med. Biol. 41: we found that monocytes began to make small clumps of 471-476, 2014. hydroxyapatite in tissue culture. Their morphology resembled • Li, Y., and Shively, J.E. CEACAM1 regulates Fas-mediated a mixture of osteoblasts and osteoclasts, classic bone making apoptosis in Jurkat T-cells via its interaction with β-catenin. and bone dissolving cells, but had distinct cell surface markers Exp. Cell Res. 319: 1061-1072, 2013. and gene expression patterns. We have shown that these cells • Zhang, H., Eisenried, A., Zimmermann, W., and Shively, J.E. can be prepared from fresh blood mono-nuclear cells with a Role of CEACAM1 and CEACAM20 in an in vitro model of single day treatment of LL-37 and accelerate the repair of both prostate morphogenesis. PLoS One, e53359, 2013. femur (published) nonunion (unpublished) defects. • Samineni, S., Zhang, Z., and Shively, J.E. Carcinoembryonic F-18 PET imaging antigen-related cell adhesion molecule 1 negatively regulates granulocyte colony-stimulating factor production by with neuroactive breast tumor-associated macrophages that mediate tumor peptides angiogenesis. Int. J. Cancer 133: 394-407, 2013. We have synthesized a novel 18F reagent for labeling peptides
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 105 Christopher Sistrunk, Ph.D. Assistant Professor, Department of Population Sciences Division of Biomarkers of Early Detection and Prevention
BIOMARKER DEVELOPMENT FOR CANCER INITIATION
The process of carcinogenesis relies heavily on genetic and utilized molecular pathology strategies to develop a biochemical epigenetic alterations to specific networks that impact the profile in patients at high-risk for developing aggressive cancers. hallmarks of cancer, including sustained mitogenic signal, immortality, induction of angiogenesis, evading growth suppression, and induction of invasion and metastasis. Each alteration provides a specific biochemical profile that has the potential to serve as a marker for cancer initiation. Our research focuses on eliciting specific biochemical profiles that can identify tumorigenesis at an earlier time point than our current standard of care diagnostic tools. Specifically, we utilize molecular pathology Biomarker discovery for breast tissue techniques to uncover potential genetic alterations linked to regulatory pathways. A secondary focus of our lab is to stratify SELECTED PUBLICATIONS these biochemical profiles by eliciting additional epigenetic • D’Amato, N.C., Ostrander, J.H., Bowie, M.L., Sistrunk, C., changes due to environmental stressors. Current studies in our Borowsky, A., Cardiff, R.D., Bell, K., Young, L.J., Simin, K., lab will investigate the links between environmental factors Bachelder, R.E., Delrow, J., Dawson, A., Yee, L.D., Mrózek, and changes in epigenetics. In particular, our lab investigates K., Clay, T.M., Osada, T., and Seewaldt, V.L. 2012. Evidence epigenetic alterations linked to the chronic exposure of standard for phenotypic plasticity in aggressive triple-negative breast drinking water. cancer: human biology is recapitulated by a novel model Biomarker development in breast cancer system. PLos One 7(9):e45684. Triple-Negative Breast Cancer (TNBC) is diagnosed when breast • Tung, J.C., Barnes, J.M., Desai, S.R., Sistrunk, C., Conklin, M., cancer cells have tested negative for estrogen receptors (-ER), Schedin, P., Keely, P.J., Seewaldt, V.L., and Weaver, V.M. 2015. hormonal epidermal growth factor 2 (-HER 2) and progesterone Tumor mechanics and metabolic dysfunction. Free Radical receptors (-PR). TNBC frequently carries a poor prognosis, Biology and Medicine particularly in young women of color. The five-year mortality • Dietze, E.C., Sistrunk, C., Miranda-Carboni, G., O’Regan, R., rate for pre-menopausal African-American women diagnosed and Seewaldt, V.L. 2015. Triple-negative breast cancer in with TNBC is over 56 percent. Since many triple-negative breast African-American women: disparities verses biology. Nature cancers are chemoresistant at diagnosis, there is a great need for Reviews Cancer developing early detection and chemoprevention strategies for • Jain, S., Wang, X., Chang, C.-C., Ibarra-Drendall, C., Wang, this disease. H., Zhang, Q., Brady, S.W., Li, P., Zhao, H., Dobbs, J., Kyrish, Conventional methods for determining breast and other M., Tkaczyk, T.S., Ambrose, A., Sistrunk, C., Arun, B.K., solid cancer diagnoses and their prognoses rely heavily on Richards-Kortum, R., Jia, W., Seewaldt, V., and Yu, D. 2015. morphological changes to normal tissues. In fact, receptor status SSrc Inhibition Blocks c-Myc Translation and Glucose for breast tissues are not tested until a patient is presented with Metabolism to Prevent the Development of Breast Cancer. breast cancer. While biochemical and molecular profiles are used Cancer Research readily to predict cancer outcomes, very few of these profiles have been used to predict the early onset of breast and other cancers. Recent studies from our lab have demonstrated the ability of molecular and metabolic markers to predict the onset of breast cancers, and more specifically TNBCs, at an earlier time point. We
106 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Steven S. Smith, Ph.D. Professor Emeritus, Division of Urology and Urologic Oncology
CANCER EPIGENETICS NON-B DNA STRUCTURE
The geological time point at the divergence node associated We are currently studying the breakdown of this control in with a given species best scales the developmental and prostate cancer cell lines by characterizing persistent regions therefore epigenetic complexity of a given organism. By of non-B structure that appear to be tumor specific and also adopting this convention one easily sees that the emergence appear to be prone to the formation of DNA breaks. Like of systems capable of suppressing non-B DNA conformations the Fragile X gene and the H-Ras VNTR region in breast during normal replication and repair has enabled the cancer the region is characterized by GC Skew. In this case, proliferation of sequences possessing this potential. In fact, in collaboration with Dr. Waller we have found an i-motif the observed number per base pair of genomic DNA (i.e., structure that is stable at neutral pH. the frequency) of G3+N1-7G3+N1-7G3+N1-7G3+ motifs has increased rapidly during eukaryotic evolution. SELECTED PUBLICATIONS This implied positive selection for sequences capable of • Wright, E.P. Lamparska, K. Smith S.S., and Waller Z.A.E. adopting non-B conformations requires that they are not (2017) Substitution of Cytosine with Guanylurea Decreases merely associated with their known harmful effects linked to the Stability of i-Motif DNA. Biochemistry 56:4879-4883. chromosome damage, but are also useful in increasing the • Lamparska, K., and Smith S.S. The Genetic and Epigenetic number of epigenetic states available to the cell. Effects of 5-Azacytidine and Its Major Breakdown Product In normal cells these non-B conformations are kept under Guanylurea (2015) Epigenetic Diagnosis and Therapy 1:28-36. strict control, but in cancer cells the control systems break • Smith, S.S. (2013) Maintaining the Unmethylated State down. This is most clearly seen resulting in de novo DNA Clinical Epigenetics 5:17. methylation that occurs during retroviral integration and triplet repeat expansion at FMR1, the gene for fragile X Syndrome. • Munson, K. Clark, J. Babilonia, G., Bedell, V. Yip, W., and Strict control in normal cells appears to involve suppression Smith, S.S. 2´- Deoxyriboguanylurea, the primary breakdown of non-B structure and may involve active induction of non-B product of 5-Aza-2´-deoxyribocytidine, is a mutagen, conformations in certain epigenetic contexts. Our recent work epimutagen, and inhibitor of DNA methyltransferases, and on the mechanism of action of 2´-deoxyguanylurea (GuaUre- inducer of 5-Azacytidine type fragile sites. Nucleic Acids Res. dR), the primary breakdown product of 5-azaC-dR, coupled 40:9788-9801, 2012. with work from multiple labs, as well as our own, on the action of DNA methyltransferase 1, the mechanism of action and • Smith, S.S. Evolutionary expansion of structurally complex biological effects of helicases like the XPD, ATRX, HELLS, WRN DNA sequences. Cancer Proteomics and Genomics 10: 207- and RecQ helicases and the TET dioxygenases, suggest that 215, 2010. the mechanism responsible for most of the hypermethylation observed during carcinogenesis involves the breakdown of an epigenetic repair cycle that maintains the unmethylated state in fully differentiated cells. Although a role for non-B structures in epigenetic control is controversial, several reports suggest that the i-motif formed on the C-Rich strand in regions of GC skew can play a role in the control of transcription. Recent data from our lab in collaboration with Dr. Waller at the University of East Anglia, demonstrates that the GuaUre-dR destabilizes the i-motif, suggesting a new mode of action for 5azadeoxycytidine.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 107 Jeremy M. Stark, Ph.D. Professor, Department of Cancer Genetics and Epigenetics Associate Dean of Assessment, Irell & Manella Graduate School of Biological Sciences FACTORS AND PATHWAYS THAT INFLUENCE MAMMALIAN CHROMOSOMAL STABILITY
The long-term goal of our laboratory research program SELECTED PUBLICATIONS is to understand the factors and pathways that influence • Bhargava, R., Carson, C.R., Lee, G., and Stark, J.M. (2017). mammalian genome stability. Such studies provide important Contribution of canonical nonhomologous end joining to insights into the etiology of cancer, as well as the mechanisms chromosomal rearrangements is enhanced by ATM kinase of cancer cell resistance to clastogenic therapeutics, such as deficiency. Proc Natl Acad Sci. 114(4):728-733. PMC5278456. radiotherapy. In one of our central projects, we are seeking • Bhargava, R., Onyango, D.O., and Stark, J.M. (2016). to define the factors that limit chromosomal rearrangements Regulation of Single Strand Annealing and its role in during the double strand break repair pathway end genome maintenance. Trends in Genetics. 32(9):566-75. joining, and thereby develop therapeutic targets for tumor PMC4992407. radiosensitization. To advance this goal, we developed unique assays to quantify the chromosomal rearrangements formed • Onyango, D.O., Howard, S.M., Neherin, K., Yanez, D.A., by end joining of multiple double strand breaks, as well as the and Stark, J.M. (2016). Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous mechanism of a mutagenic subpathway called alternative-EJ. recombination. Nucleic Acids Res. 44(12):5702-16. Using this approach, we are currently focused on defining the PMC4937314. role of several DNA repair factors whose aspects of end joining that are poorly understood, yet are critical to limit genome • Howard, S.M., Yanez, D.A., and Stark, J.M. (2015). DNA rearrangements, and furthermore are likely important damage response factors from diverse pathways, including for radioresistance. DNA crosslink repair, mediate alternative end joining. PLoS Genet. 11(1) e1004943. PMC4309583. Other projects in the lab are focused on characterizing the homologous recombination DNA repair pathway, particularly • Muñoz, M.C., Yanez, D.A., and Stark, J.M. (2014). An RNF168 a mutagenic sub-pathway called single stranded annealing. fragment defective for focal accumulation at DNA damage is proficient for inhibition of homologous recombination in For example, we are seeking to define genes that affect BRCA1 deficient cells. Nucleic Acids Res. 42(12):7720-33. the requirement for the tumor suppressor BRCA1 during PMC4081061. homologous recombination. Inherited mutations in BRCA1 result in defects in the homologous recombination pathway of DNA repair, which likely causes an accumulative loss of genetic information that contributes to increased risk of breast and ovarian cancer. We seek to identify genes that influence the BRCA1 pathway during homologous recombination, with a focus on the factors RNF168 and XAB2. In summary, by examining the mechanisms of several double strand break repair pathways (e.g., end joining and the SSA subpathway of homologous recombination), we aim to understand the factors and conditions that lead to chromosomal rearrangements, and develop new targets to sensitize cancer cells to clastogenic therapeutics.
108 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Cy A. Stein, M.D., Ph.D Professor, Department of Medical Oncology & Therapeutics Research
CELLULAR DELIVERY OF THERAPEUTIC OLIGONUCLEOTIDES
While gene silencing small molecules (antisense oligos, proteins (and there is evidence they are integrins) are then siRNAs) have been available for some time, to date we do recycled out of the endosomes, dragging the oligos with them. not have a single Food and Drug Administration approved As the oligo concentration decreases outside the endosome, anti-cancer oligonucleotide therapeutic drug. Why is this? the oligo dissociates from its bound protein (which is then One of the reasons is because oligo delivery is poorly recycled to the cell surface). The “free” antisense molecule understood and is often ineffective. Certainly, siRNAs cannot then translocates to the cell nucleus. This mechanism is be delivered to cells in the absence of carrier molecules, not very efficient for oligos which have high protein-binding usually lipid nanoparticles, although many other approaches capacity (e.g., phosphorothioates), but is even less so for have been tried. Unfortunately, all approaches, with respect molecules such as siRNAs that have low protein binding to clinical requirements, have ultimately failed due to cost, capacity. Determining how to improve this efficiency, both for toxicity or low efficacy, or a combination of all three. For siRNA and antisense oligo delivery and silencing, is one of the the delivery of antisense oligos, a somewhat different set of major goals of scientific research in our laboratory. circumstances prevails. 3’, 5’ end-LNA or 2’F-ANA-modified phosphorothioate oligos have high protein binding capacity, SELECTED PUBLICATIONS enter endosomes via adsorptive endocytosis and, as we have • Soifer, H., Souleimanian, N., Wang, S., Voskresenskiy, determined (and which has been verified by numerous other A., Collak, F., Cinar, B., and Stein, C.A. Direct regulation investigators), somehow manage to transit the endosomal of androgen receptor activity in prostate cancer cells by membrane and produce exquisite gene silencing without potent CYP17 inhibitors. J. Biol. Chem. 287: 3777-3787, any carriers or conjugations whatsoever. In this context it is 2012. (addresses another research subject of interest — the difficult to understand why the “leaky endosome” mechanism development of novel anti-prostate cancer drugs) of oligonucleotide release would apply to phosphorothioate • Stein, C.A., and Goel, S. Therapeutic oligonucleotides—the antisense oligos but not to siRNAs, even when the siRNAs are road not taken. Clin. Cancer Res. 17: 6369-6372, 2011. targeted to cell surface receptors, and thus presumably reach • Stein, C.A., Hansen, B., Lai, J., Soifer, H., Wu, S., high intra-endosomal concentrations. Therefore, we have Voskresenskiy, A., Hoeg, A., Worm, J., Hedtjarn, M., hypothesized that the leaky endosome hypothesis may be Soulemanian, N., Miller, P., Castanotto, D., Benimetskaya, L., only a partial explanation of endosomal permeability, and that Oerum, H., and Koch, T. Efficient gene silencing by delivery another way oligos transit endosomes is by “piggy-backing” of locked nucleic acid antisense oligonucleotides, unassisted onto the proteins that they were originally bound to in the by transfecton reagents. Nucleic Acids Res. DOI:10.1093/nar/ plasma membrane, and that are now found in the endosomal gkp841, 2009. membrane (topologically, the inside of the endosome is identical to the outside of the cell). These membrane-bound
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 109 Zijie (ZJ) Sun, M.D., Ph.D. Professor, Department of Cancer Biology Director, Prostate Cancer Research Program
TRANSCRIPTIONAL REGULATION, CELL SIGNALING, AND HORMONE ACTION IN ONCOGENESIS AND DEVELOPMENT
Transcriptional control is a key step in the regulation of Androgen signaling induced transcription is facilitated eukaryotic gene expression. Our lab focuses on understanding through direct or indirect interactions with different signaling the molecular mechanism of transcription factors that pathways and co-regulators. Emerging evidence suggests a govern the transformation of normal mammalian cells promotional role of the Wnt/β-catenin signaling pathway in to a neoplastic state. We are especially interested in the prostate tumorigenesis. We have demonstrated the interaction biological roles of steroid hormone receptors and their co- between the AR and β-catenin in prostate cancer cells. regulators in development and oncogenesis. We use targeted Because mutations in adenomatous polyposis coli (APC), beta- conditional and inducible mouse models, and other cellular catenin, and other components of the destruction-complex and molecular approaches to uncover gene-expression and are generally rare in prostate cancers, other mechanisms of genomic and epigenetic alteration during tumor development aberrant Wnt signaling activation have been speculated. To and progression, and to functionally analyze the biological address these critical questions, we developed several novel significance of these changes in oncogenic transformation. mouse models to evaluate the promotional role of androgen Ongoing projects in the lab are specifically addressing several signaling in β-catenin initiated oncogenic transformation important and unknown questions regarding the pathogenesis in prostate cells. The ongoing project will gain innovative of prostate cancer in order to develop novel therapeutics to information on prostatic stem/progenitor cells, and may lead target these tumor cells. to new directions to current paradigms in the field. Androgen signaling has been implicated as a critical pathway SELECTED PUBLICATIONS in prostate tumorigenesis. However, there is no appropriate animal model that can be used to evaluate ligand-dependent • Lee, S.H., Luong, R., Johnson, D.T., Cunha, G.R., Rivina, and independent androgen receptor (AR) action during the L., Gonzalgo, M.L., and Sun, Z. Androgen signaling is course of prostate cancer initiation and progression. We a confounding factor for β-catenin mediated prostate developed a unique AR transgenic mouse model, in which the tumorigenesis. Oncogene. 2016 Feb 11;35(6):702-14. PMID: AR expression can be “conditionally” activated in a constitutive 25893287 and tissue specific manner. We demonstrated that activation • He, Y., Hooker, E., Yu, E.J., Wu, H., Cunha, G.R., and Sun, of AR transgene expression induces prostatic adenocarcinoma Z. An Indispensable Role of Androgen Receptor in Wnt formation in mice, demonstrating an oncogenic role for AR Responsive Cells During Prostate Development, Maturation, in prostate tumorigenesis. This mouse model can also be and Regeneration. Stem Cells. 2018 Feb 16. used to characterize AR action in the absence of androgens, recapitulating ligand-independent AR effect during prostate • Lee, S.H., Johnson, D.T., Luong, R., Yu, E.J., Cunha, G.R., cancer progression and castration resistant prostate cancer Nusse, R., and Sun, Z. Wnt/β-catenin-responsive cells in (CRPC) development. prostatic development and regeneration. Stem Cells. 2015 Although nuclear hormone receptors in general are ligand- Nov;33(11):3356-67. PMID: 26220362 dependent transcriptional activators, our bench work • Lee, S.H., Johnson, D., Luong, R., and Sun, Z. Crosstalking has demonstrated a novel role of AR as a transcriptional between androgen and PI3K/AKT signaling pathways in repressor in c-Met expression, the receptor for HGF/SF. Our prostate cancer cells. J Biol Chem. 2015 Jan 30;290(5):2759- finding not only elucidates an aberrant regulation of c-Met 68. PMID: 25527506 expression in prostate cancer cells, but also implicates a novel mechanism by which current androgen ablation therapy induces CRPC development. Using several preclinical models, we demonstrated that combined inhibition of AR and c-Met oncogenic pathways can prevent or delay CRPC development. Our bench work has translated to several ongoing clinical trials to test whether adding c-Met inhibitors to current androgen ablation mono-therapy can improve clinical outcomes, which may delay and prevent CRPC development.
110 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Zuoming Sun, Ph.D. Professor, Department of Molecular Imaging and Therapy
MECHANISMS REGULATING T CELL-MEDIATED IMMUNITY
Activation and differentiation of T cells is the first step in the SELECTED PUBLICATIONS stimulation of our adaptive immune responses. Inappropriate • He, Z. H., Ma, J., Wang, R. Q., Zhang, J., Huang, Z. F., Want, activation of T cells leads to transplantation rejection and F., Sen, S., Rothenberg, E. V., and Sun, Z. (2017). A two amino autoimmune disorders such as diabetes, arthritis and acid substitution in the transcription factor RORgammat multiple sclerosis. Prevention of T cell activation leads to disrupts its Th17 differentiation but not in thymocyte development. Nature Immunology. 18:1128-1138. doi:10.1038/ immunodeficiency, resulting in the invasion of pathogens such ni.3832. as bacteria and virus infection. The goal of our research is to understand the mechanisms responsible for the regulation of T • Sen, S., Wang, F., Zhang, J., He, Z. H., Ma, J., Gwack, Y., Xu, J. M., and Sun, Z. (2017). SRC1 promotes Th17 differentiation cell activation so as to develop effective and safe treatments for by overriding Foxp3 suppression to stimulate RORgammat these immune disorders. activity in a PKC-theta-dependent manner. Proc. Natl. Acad. Sci. USA. 115: E258-E467. doi: 10.1073/pnas. Activation and differentiation of naïve T cells to effector T cells that mediate actual immune responses depend on engagement • He, Z. H., Wang, F., Zhang, J., Sen, S., Pang, Q. H., Luo, of T cell receptors (TCR) with antigens. Such engagement of S. W., Gwack, Y., and Sun, Z. (2017). Regulation of Th17 differentiation by IKKa-dependent and -independent TCR triggers a series of signaling pathways that eventually lead phosphorylation of RORgammat. J. Immunol. 199: 955-964. to turn on the program for T cell activation. Manipulation of these critical signaling pathways required for T cell activation • Zhang, J., He, Z., Sen, S., Wang, F., Zhang, Q., and Sun, Z. (2018). TCF-1 inhibits IL-17 gene expression to restrain Th17 and differentiation allows control of T cell-mediated immunity. immunity in a stage specific manner. J. Immunol. In press. Our research has focused on three such signaling pathways, PKC-theta ROR-gammat and beta-catenin/TCF-1. Inhibition • He, Z. H., Wang, F., Ma, J., Sen, S., Zhang, J., Gwack, Y., of the PKC-theta pathway prevents rejection of transplanted Zhou, Y., and Sun, Z. (2016). Ubiquitination of RORgammat at lysine 446 limits Th17 differentiation by controlling co- organs as well as autoimmune disorders. Inhibition of the ROR- activator recruitment. J. Immunol. 197, 1148-1158. gamma pathway prevents Th17-dependent autoimmunity such as experimental autoimmune encephalomyelitis and collagen- • Ma, J., Ding, Y. Fang, X., Wang, and R. Sun, Z. (2012). PKC-theta inhibits iTregs differentiation via an AKT- induced arthritis. Whereas the beta-catenin/TCF-1 pathway FoxO1/3a-dependent pathway. J. Immunol. 188, 5337-47 regulates T cell function via both affecting T cell development (PMID:22539794). and T cell differentiation. However, the precise mechanisms for • Kwon, M. J*., Ma, J*., Ding, Y., Wang, R., and Sun, Z. (2012). how these signaling pathways regulate immune responses still PKC-theta promotes Th17 differentiation via up-regulation remain unknown. We are actively studying these mechanisms of Stat3. J. Immunol. (*equal contribution). 188, 5887-97 and developing PKC-theta and ROR-gamma-based treatments (PMID: 22586032). to prevent autoimmune disorders and transplantation rejection. • Wang, R., Xie, H., Fang, X. Ding, Y., and Sun, Z. (2011). T cell factor 1 regulates thymocyte survival via a RORt-dependent pathway. J. Immunol. 187, 5964-5973 (PMID:22039299). • Sun, Z,, Unutmaz, D., Zou, Y., Sunshine, M.J., Pierani, A., Brenner-Morton, S., Mebius, R.E., and Littman, D.R. (2000). Requirement for RORgammat in thymocyte survival and lymphoid organ development. Science, 288, 2369-2373. • Sun, Z., Arendt, C.W., Ellmeier, W., Schaeffer, E.M., Sunshine, M.J., Gandhi, L., Annes, J., Petrzilka, D., Kupfer, A., Schwartzberg, P.L., and Littman, D.R. (2000). PKC-theta is required for TCR-induced NF-kappaB activation in mature but not in immature T lymphocytes. Nature, 404, 402-407.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 111 Timothy W. Synold, Pharm.D. Director, Analytical Pharmacology Core Facility Professor and Director, Division of Molecular Pharmacology, Department of Medical Oncology & Therapeutics Research
PHARMACOKINETICS AND PHARMACODYNAMICS OF ANTI-CANCER DRUGS
Understanding how a drug behaves once it is inside the of the literature has revealed conflicting reports regarding body is fundamental to the successful clinical development the relationship between age and either pharmacokinetics of new agents designed to treat cancer. For the past 20 or clinical toxicity, primarily because chronologic age is years, my laboratory has been dedicated to studying the only a crude measure of true physiologic age. Dr. Hurria pharmacokinetics and pharmacodynamics of anti-cancer has developed a comprehensive geriatric assessment tool agents. As scientific director of the City of Hope Solid that she is applying in her clinical program as a measure of Tumor Phase 1 clinical trial program and director of clinical physiologic age. In a recently completed study of the safety and pharmacology for National Cancer Institute-funded California pharmacokinetics of nanoparticle albumin bound paclitaxel Cancer Consortium (CCC), my laboratory is responsible for in the elderly, Dr. Hurria and I found that the rate of drug the design and conduct of preclinical, phase 1 and phase 2 clearance was significantly associated with the geriatric risk pharmacokinetic investigations. I have personally designed, score determined using the assessment tool, but not with conducted and reported several dozen cancer-related clinical chronologic age. The results of this initial trial have opened the trials over the course of my career, including 16 studies within door to many future pharmacokinetic studies of anti-cancer the past year alone. A particularly exciting recent highlight drugs in the elderly. has been the growth in the use of intracranial microdialysis as a clinical research tool to determine the penetration of drugs SELECTED PUBLICATIONS across the blood-brain barrier within the City of Hope Brain • Portnow, J., Synold, T.W., Badie, B., Tirughana, R., Lacey, S,F., Tumor Program. In collaboration with Jana Portnow, M.D., D’Apuzzo, M., Metz, M.Z., Najbauer, J., Bedell, V., Vo, T., and Behnam Badie, M.D., I have developed the Gutova, M., Frankel, P., Chen, M., and Aboody, K.S. Neural City of Hope clinical intracranial microdialysis program into Stem Cell-Based Anticancer Gene Therapy: A First-in- the largest of its kind in the U.S., with more than 50 patients Human Study in Recurrent High-Grade Glioma Patients. Clin. enrolled on four completed studies and three ongoing clinical Cancer Res. [Epub ahead of print] Dec 2016. trials. Based on the rapid success of this program, several additional studies are currently in development. In another • Gutova, M., Goldstein, L., Metz, M., Hovsepyan, A., Tsurkan, exciting collaboration with Karen Aboody, M.D., I have used L.G., Tirughana, R., Tsaturyan, L., Annala, A.J., Synold, T.W., a preclinical intracranial microdialysis nude rat model to Wan, Z., Seeger, R., Anderson, C., Moats, R.A., Potter, P.M., investigate the ability of neural stem cells to deliver a prodrug and Aboody KS. Optimization of a Neural Stem-Cell-Mediated activating transgene directly to the site of brain tumors in Carboxylesterase/Irinotecan Gene Therapy for Metastatic vivo. As the project leader of Team 4 (Pharmacology) for Neuroblastoma. Mol. Ther. Oncolytics 4:67-76, 2016. Aboody’s California Institute of Regenerative Medicine funded • Hurria, A., Blanchard, M.S., Synold, T.W., Mortimer, J., Chung, Disease Team Concept Proposal, I am applying my preclinical C.T., Luu, T., Katheria, V., Rotter, A.J., Wong, C., and Choi, A., model to the selection of the optimal enzyme variant and the Feng, T., Ramani, R., Doan, C.M., Brown, J., and Somlo, G. best route of neural stem cell administration for the first-in- Age-related changes in nanoparticle albumin-bound paclitaxel human clinical trial. In addition, I also provide many other pharmacokinetics and pharmacodynamics: influence of City of Hope investigators with preclinical pharmacokinetic chronological versus functional age. Oncologist 20:27-44, 2015. expertise in support of novel therapeutics under development within the City of Hope Developmental Cancer Therapeutics Program pipeline. For example, I am currently collaborating with Arti Hurria, M.D., of the Cancer and Aging Research Program to develop a robust clinical research program in geriatric oncology. Dr. Hurria and I have joined forces to initiate several clinical trials designed to assess the safety and pharmacokinetics of anti-cancer drugs in the elderly. Review
112 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES John Termini, Ph.D. Professor, Department of Molecular Medicine
MUTAGENESIS AND CARCINOGENESIS
DNA damage to the nucleoside bases can impact cellular SELECTED PUBLICATIONS metabolism by inducing copying errors during replication and • Jaramillo, R., Shuck, S.C., Chan, Y.S., Liu, X., Bates, S.E., Lim, by increasing genomic instability. These events play a critical P.P., Tamae, D., Lacoste, S., O’Connor, T.R., and Termini, role in driving the initiation, progression and metastasis of J. (2017) DNA Advanced Glycation End Products (DNA- human cancers. Our laboratory is interested in understanding AGEs) Are Elevated in Urine and Tissue in an Animal Model how specific DNA base damage accumulates under of Type 2 Diabetes. Chemical Research in Toxicology, 30(2): physiological conditions and how it promotes mutagenesis 689-698. PMID: 28107623, NIHMS851666 and cancer. These studies typically involve measuring DNA • Tamae, D., Lim, P., Wuenschell, G.E., and Termini, J. damage levels in vivo, determining the mutagenic profile of (2011) Mutagenesis and Repair Induced by the DNA specific damage products and examining the ability of cells Advanced Glycation End Product N2-1-(Carboxyethyl)-2’- to repair them. This effort is highly multidisciplinary and deoxyguanosine in Human Cells. Biochemistry, 50(12):2321- involves the application of synthetic DNA chemistry, analytical 2329. PMCID: PMC3384727 methodologies such as LC-ESI-MS/MS, protein purification, • Clin Exp Metastasis (2017) 34:401–410 DOI 10.1007/ enzyme kinetics, molecular biology and mammalian tissue s10585-017-9864-8 culture techniques. An important goal of these studies is to determine the suitability of these biologically relevant DNA • Neman, J., Termini, J., Wilczynski, S., Vaidehi, N., Choy, damage products as small molecule biomarkers of potential C., Kowolik, C.M., Li, H., Hambrecht, A.C., Roberts, E., and utility in disease diagnostics and treatment monitoring. In an Jandial, R. (2014) Human breast cancer metastases to the international collaboration involving research groups from brain display GABAergic properties in the neural niche. Caltech and Technion, we are also exploring the imaging and Proceedings of the National Academy of Sciences, 111(3):984- 9. PMCID: PMC3903266 therapeutic applications of metallocorroles in cancer diagnosis and treatment. Our program offers an excellent training • Int. J. Mol. Sci. 2018, 19, 406; doi:10.3390/ijms19020406 environment for chemistry and biochemistry students seeking • Pribisko, M., Palmer, J., Grubbs, R.H., Gray, H.B., Termini, to acquire the additional skills required for participating in J., and Lim, P. (2016) Cellular uptake and anticancer translational and biomedical research. activity of carboxylated gallium corroles. Proceedings of the National Academy of Sciences, 113(16): E2258-66. PMCID: PMC4843456
• Teo, R.D., Termini, J., and Gray, H.B., (2016) Lanthanides: Applications in Cancer Diagnosis and Therapy. Journal of Medicinal Chemistry, 59(13):6012-6024. PMCID: PMC4945403
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 113 Debbie C. Thurmond, Ph.D. Ruth B. & Robert K. Lanman Chair in Gene Regulation and Drug Discovery Research Professor and Chair, Department of Molecular and Cellular Endocrinology
INSULIN ACTION AND INSULIN SECRETION DYSFUNCTION IN DIABETES
Type 1 diabetes: Evidence suggests that β cells become state-of-the-art imaging, using a variety of biosensors to less efficient and exhibit dysfunction early in the disease collect live-cell time-lapse images of islet and skeletal muscle progression of type 1 diabetes (T1D). As such, there is cell actin remodeling, concurrent with cell signaling and SNARE great interest in developing strategies to enhance insulin exocytosis changes, in combination with islet perifusion and secretory function from the patient’s residual β cells, and muscle GLUT4 translocation/glucose uptake assays, which for transplantation success to ‘build a more efficientβ cell,’ allows investigations of protein-protein interactions and post- so that fewer islets would be required per patient. Toward translational modifications using primary human/rodent islets, these goals for a restorative/cure, we are investigating the as well as primary rodent and human skeletal muscle. translational potential of targeting specific exocytosis proteins crucial for the regulated release of insulin from the β cell. The SELECTED PUBLICATIONS team also is pursuing identification of novel biomarkers of T1D • Aslamy, A., Oh, E., Olson, E.M., Zhang, J., Ahn, M., Md susceptibility, useful in screening patients for preclinical T1D. Moin, A.S., Tunduguru, R., Salunkhe, V.A., Veluthakal, R., and Thurmond, D.C. (2018). Doc2b Protects β-Cells Against Type 2 diabetes (T2D): T2D is often described as a ‘two- Inflammatory Damage and Enhances Function. Diabetes. hit’ disease; one ‘hit’ is dysfunction of glucose clearance 2018 Apr 16. pii: db171352. doi: 10.2337/db17-1352. [Epub by the skeletal muscle and adipose tissues (GLUT4 vesicle ahead of print]. PMID: 29661782 translocation), and another ‘hit’ is dysfunction of insulin • Aslamy, A., Oh, E., Ahn, M., Moin, A.S.M., Chang, M., secretion by the pancreatic islet beta cells (insulin granule Duncan, M., Hacker-Stratton, J., El-Shahawy, M., Kandeel, exocytosis). Remarkably, these seemingly divergent processes F., DiMeglio, L.A., and Thurmond, D.C. (2018). Exocytosis require similar molecular machinery termed “SNARE” Protein DOC2B as a Biomarker of Type 1 Diabetes. J Clin Endocrinol Metab. 2018 Mar 1. doi: 10.1210/jc.2017-02492. exocytosis proteins, and aberrant quantities and functions [Epub ahead of print].PMID: 29506054 of particular SNARE and SNARE-associated proteins are implicated in each ‘hit’ of diabetes. Human type 2 diabetic • Tunduguru, R., Zhang, J., Aslamy, A., Salunkhe, V.A., Brozinick, J.T., Elmendorf, J.S., and Thurmond, D.C. (2017). islets and skeletal muscle are reported by numerous groups The actin-related p41ARC subunit contributes to p21- to lack normal abundances of particular SNARE proteins. activated kinase-1 (PAK1)-mediated glucose uptake into SNARE-mediated vesicle exocytosis is key to insulin secretion skeletal muscle cells. and to skeletal muscle/fat glucose clearance, both vital J Biol Chem. 2017 Nov 17;292(46):19034-19043. processes for controlling whole-body glucose homeostasis. • Ahn, M.*, Yoder, S.M.*, Wang, Z., Oh, E., Ramalingam, Defects in either or both processes concurrently engenders L, Tunduguru, R. and Thurmond, D.C. (2016). The p21- heightened susceptibility to pre- and T2D, particularly when Activated Kinase (PAK1) is Involved in Diet-Induced beta compounded with diabetogenic insults (e.g., high fat diet). Cell Mass Expansion and Survival. (*equal authorship). Our laboratory is currently focused upon 1) discovering new Diabetologia 59(10):2145-55. SNARE accessory proteins which regulate SNARE interactions • Oh, E., Miller, R. A., and Thurmond, D.C. (2015) Syntaxin and function, 2) of SNARE protein interactions with F-actin, 3) 4 overexpression ameliorates effects of aging and high discovering novel tissue-specific signaling cascades involving fat diet on glucose control, and may increase lifespan Cell Metabolism 22:499-507. actin remodeling and vesicle trafficking, and 4) how peptides derived from particular exocytosis-related proteins can be used • Oh, E., Stull, Natalie, Mirmira, R., and Thurmond, D.C. for therapeutic benefit to remediate diabetes. Increased syntaxin 4 abundance rescues insulin secretory function human and mouse diabetic islets. J. Clin. Endo. Our approaches: Our studies involve a variety of customized Metab. 99: E866-870, 2014. genetic and environmental model systems; the Thurmond • Jewell, J.L., Oh, Eunjin, Ramalingam, L., Kalwat, M.A., lab teams perform studies in β cells, skeletal muscle and Tagliabracci, V., Tackett, L., Elmendorf, J.S., and Thurmond, adipose tissues, entailing the physiological/biochemical D.C. Munc18c phosphorylation by the insulin receptor links studies of these tissues/cell types therefrom. We utilize cell signaling directly to SNARE exocytosis. J. Cell. Biol. 193:185-199, 2011.
114 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Nagarajan Vaidehi, Ph.D. Professor, Department of Molecular Imaging and Therapy
PREDICTING PROTEIN STRUCTURE AND DYNAMICS FOR DRUG DISCOVERY
The primary research goal of our laboratory is to allow us to identify druggable pockets on the protein- develop and apply computational methods to study the protein interface. structure and dynamics of membrane proteins and protein- protein complexes. Further, we design small molecules to SELECTED PUBLICATIONS inhibit or enhance the function of the membrane proteins • Bhattacharya, S., and Vaidehi, N. Differences in allosteric G-protein coupled receptors (GPCRs) and other protein- communication pipelines in the inactive and active states of a GPCR. Biophys. J. 107: 422-434, 2014. protein complexes. • Li, H., Kasam, V., Tautermann, C.S., Seeliger, D., and Vaidehi, GPCRs form one of the largest gene families of membrane N. Computational method to identify druggable binding sites bound proteins and also the largest superfamily of drug that target protein-protein interactions. J. Chem. Inf. Model targets. They play a critical physiological role in cell-to-cell 27: 1391-1400, 2014. communication and also in the pathology of many diseases. • Lee, S., Bhattacharya, S., Grisshammer, R., Tate, C., and We study the structure, function and design of small molecule Vaidehi, N. Dynamic behavior of the active and inactive inhibitors or activators to selectively block or activate states of the adenosine A(2A) receptor. J. Phys. Chem. B. 27: 3355-3365, 2014. GPCR mediated signaling pathways implicated in several types of cancer and diabetes. In my laboratory, we develop • Larsen, A.B., Wagner, J.R., Jain, A., and Vaidehi, N. Protein structure refinement of CASP target proteins using GNEIMO computational methods to predict the structural models of torsional dynamics method. J. Chem. Inf. Model 54: 508-517, GPCRs and to further understand the conformational dynamics 2014. that are critical for designing drugs with functional specificity. • Bhattacharya S., and Vaidehi, N., LITICon: A discrete Of particular interest to us are chemokine receptors (which conformational sampling computational method for mapping are GPCRs) since they play a fundamental role in carrying various functionally selective conformational states of diverse messages that are critical in mediating both innate transmembrane helical proteins. Methods. Mol. Biol. (in press), 2012. and adaptive immunity. Activation of chemokine receptors by chemokines can elicit different responses depending on the cell • Kim, J., Li, H, Hsin, C., Yip, R.L., and Vaidehi, N. Identification of antimalarial compounds as novel antagonists to CXCR4 in type including chemotaxis, adhesion, proliferation, maturation, pancreatic cancer cells. PLoS One, 7, e31004, 2012. differentiation, apoptosis, malignant transformation and dissemination. Inadvertent or overexpression of chemokines is • Park, I.H., Wagner, J., Jain A., and Vaidehi, N. 2012, Structure refinement of protein low resolution models using the an underlying cause of many clinically important diseases with GNEIMO constrained dynamics method folding of small an inflammatory component such as cancer and, consequently, proteins using constrained molecular dynamics. J. Phys. chemokine receptors have attracted much interest as targets Chem. B,116: 2365-2375, 2012. for therapeutic intervention. My laboratory is focused on using • Nedjai, B., Stroke, I.L., Wise, E.L., Webb, M.L., Merritt, J.R., computational methods to derive the structures of chemokine Henderson, I., Klon, A.E., Cole, A.G., Horuk, R., Vaidehi, N., receptors (CCR1, CCR2, CCR3, CCR5, CXCR2, CXCR3 and and Pease, J.E. Small molecule chemokine mimetics suggest a molecular basis for the observation that CXCL10 and CXCR4) and to understand the interaction of chemokines and CXCL11 are allosteric ligands of CXCR3. Br. J. Pharmacol. 166: small molecule antagonists to these receptors. 912-923, 2012. We are developing computational methods to study the • Vaidehi, N., and Bhattacharya, S. Multiscale computational dynamics of protein-protein complexes and understand methods for mapping conformational ensembles of G-protein coupled receptors. Adv. Protein Chem. Struct. Biol. their interactions on a fundamental level. We also apply these 85, 253-280, 2011. methods to predict the hotspot residues that dominate the stability of the protein-protein complexes. This would
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 115 Qiong (Annabel) Wang, Ph.D. Assistant Professor, Department of Molecular and Cellular Endocrinology
ADIPOSE TISSUE REMODELING IN HEALTH AND DISEASE
Adipocytes from anatomically distinct adipose tissues have The AdipoChaser mouse model unique functions. These adipocytes also contribute differently to whole body insulin resistance, dyslipidemia, chronic inflammation and numerous other metabolic disorders. We use inducible tissue-specific lineage tracing, overexpression or knockout mouse models to study adipogenesis, the process of cell differentiation by which preadipocytes become adipocytes. Our research efforts are devoted to the pathogenesis and treatment of obesity, type 2 diabetes and related metabolic syndromes. Utilizing the mature adipocyte-specific lineage tracing model SELECTED PUBLICATIONS AdipoChaser mice, we have shown that while facing the • Wang, Q.A., Tao, C., Jiang, L., Shao, M., Ye, Risheng, Zhu, same physiological challenges, different fat depots response Yi, Gordillo, R., Ali, A., Lian, Y., Holland, W.L., Gupta, R.K., in distinct patterns. For instance, during high fat diet feeding, and Scherer., P.E. Distinct Regulatory Mechanisms Govern visceral fat initiates adipogenesis, whereas subcutaneous fat Embryonic versus Adult Adipocyte Maturation. Nature Cell only undergoes hypertrophy. Using similar mature adipocyte- Biology (2015) 17(9):1099–111 PMID: 26280538 PMCID: PMC4553131. specific knockout mouse models, we also unraveled for the first time a surprising diversity of transcriptional signals • Ye*, R., Wang*, Q.A., Tao, C., Vishvanath, L., Shao, M., required at different stages of adipogenesis in vivo, opening up McDonald, J.G., Gupta, R.K., and Scherer, P.E. Impact new possibilities for the selective stage- and location-specific of Tamoxifen on Adipocyte Lineage Tracing: Inducer of Adipogenesis and Prolonged Nuclear Translocation of Cre interventions in the adipogenic process. Recombinase. Molecular Metabolism (2015) 4(17):771- We are currently working on two projects: 778 (*equal contribution) PMID: 26629402 PMCID: PMC4632120 1. The molecular mechanisms that regulate the dramatic white adipose tissue remodeling in the mammary gland, and how • Wang, Q.A., Tao, C., Gupta, R.K., and Scherer, P.E. Tracing dysregulation of this remodeling contributes to whole body adipogenesis during white adipose tissue development, expansion and regeneration. Nature Medicine (2013) metabolic disorders. 19(10):1338-1344 PMID: 23995282 PMCID: PMC4075943 2. Brown adipocyte heterogeneity, and how this heterogeneity • Wang, Q., Jiang, L., Shao, M., Li, W., and Liu, Y. Deficiency remodels the energy-burning capacity of brown in hepatic ATP-citrate lyase affects VLDL-triglyceride adipose tissue. mobilization and liver fatty acid composition in mice. Journal of Lipid Research (2010) 51(9): 2516-2526 PMID: 20488800 PMCID: PMC2918436.
The AdipoChaser mouse model • Wang, Q., Jiang, L., Wang, J., Li, S., Yu, Y., You, J., Zeng, R., Gao, X., Rui, L., Li, W., and Liu, Y. Abrogation of hepatic ATP-citrate lyase protects against fatty liver and ameliorates hyperglycemia in leptin receptor-deficient mice. Hepatology (2009) 49: 1166-1175 PMID: 19177596.
116 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Leo Wang, M.D., Ph.D. Assistant Professor, Department of Pediatrics and Department of Immuno-Oncology
FUNCTIONAL PROTEOMICS OF BLOOD AND IMMUNE CELLS
www.leowanglab.org Our work focuses on understanding blood development at a protein-focused level, using mass spectrometry to identify nongenetic determinants underlying functional differences in stem and progenitor cell states and fates. We couple this discovery platform with faithful disease model systems to answer fundamental biological questions about how cancer develops and how to treat it. Our research encompasses Proteomic interrogation of human leukemia stem cells four main areas: 1) small-scale mass spectrometry platform In collaboration with Dr. Guido Marcucci, we are defining development; 2) chimeric antigen receptor (CAR) T cell therapy the phosphoproteomic features of adult and pediatric for brain tumors; 3) the role of ARHGAP25 in hematopoiesis; leukemia stem cells (below). This will make possible the and 4) acute myeloid leukemia (AML) stem cells. proteomic profiling of individual patient samples, permitting the generation of unique patient-specific phosphoproteomic fingerprints and realizing the potential of precision medicine on a proteomic level. Proteomics of ARHGAP25 We identified the novel Rac-GAP ARHGAP25 as an important mediator of HSPC mobilization, development, and malignancy, and are studying the mechanisms through which ARHGAP25 phosphorylation affects its function in hematopoiesis and leukemogenesis. Additionally, we have uncovered a novel role for Arhgap25 in B lymphopoiesis and are actively investigating the contribution of this protein in B cell development and function.
Small scale proteomic discovery of activated pathways in blood cells. We develop high-resolution proteomic and phosphoproteomic discovery platforms capable of identifying thousands of proteins from hundreds of thousands of cells. We use these to identify protein pathways important for survival, function, and persistence of leukemia stem cells (LSCs) and CAR T cells. Our proteomics efforts are a collaboration with Dr. Markus Kalkum’s group at City of Hope. Mass spectrometry-based profiling of tumor-responsive immune cells In collaboration with Dr. Christine Brown’s group and other leading CAR T cell laboratories across the country, we are working to identify a proteomic signature of CAR T cell persistence in xenotransplantation models of pediatric brain tumors. This will permit improved engineering of these cells for solid tumor immunotherapy.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 117 Jeffrey N. Weitzel, M.D. Chief, Division of Clinical Cancer Genomics Professor, Department of Medical Oncology & Therapeutics Research and Department of Molecular Medicine
GENETIC PREDISPOSITION TO CANCER
The major themes of my multidisciplinary clinical and variants (most associated with clonal hematopoiesis) were laboratory research programs are translational research detected in germline multigene panel testing. Preclinical in cancer predisposition, genomic cancer risk assessment, research in collaboration with Tim O’Connor established that genetic epidemiology, chemoprevention, precision therapy carboplatin and a poly (ADP-ribose) polymerase (PARP) for hereditary cancers and clinical outcomes, with a focus on inhibitor (Velaparib) could act in a synergistic manner in a women’s cancers and addressing disparities in underserved BRCA-null setting, and lead to development of a therapeutic populations. We have investigated the genomic features protocol with George Somlo with promising results and some associated with women’s cancers, both inherited and metastatic breast cancer patients with extraordinary and acquired. A substantial body of work revolves around our durable responses. We reported for the first time that PBMC efforts to obtain a comprehensive dataset on the prevalence PAR levels could predict clinical outcome. I also developed and nature of BRCA mutations and other cancer risk and successfully completed chemoprevention protocols, variants among Hispanics. We documented that the BRCA1 including a phase II biomarker trial of deslorelin (GnRH 185delAG, is prevalent in Hispanic populations, and shares agonist), estradiol and testosterone in women at high risk of the Jewish founder haplotype. We discovered a novel BRCA1 breast cancer. My laboratory was the first to establish proof rearrangement (ex9-12del), the result of an Alu repeat- of principle that a hormonal chemoprevention regimen could mediated recombination event, that is prevalent among high- be used to reduce breast density in BRCA1 carriers without risk Hispanic families. We established that BRCA1 ex9-12del negatively affecting quality of life. is a Mexican founder mutation, estimated to have arisen ~1,500 years ago in an Amerindian population. We developed SELECTED PUBLICATIONS a panel of recurrent BRCA mutations on the Sequenom • Weitzel, J.N., Clague, J., Martir-Negron, A., Ogaz, R., platform for prospective screening of high-risk clinic cohorts, Herzog, J., Ricker, C., Jungbluth, C., Cina, C., and Duncan, and demonstrated ~75% sensitivity for 5% of the cost of P., et al. Prevalence and type of BRCA mutations in commercial sequencing. We have >22,000 high risk patients Hispanics undergoing genetic cancer risk assessment in enrolled in an IRB-approved prospective hereditary cancer the Southwestern United States: A report from the Clinical research registry, with contributions from 39 collaborating Cancer Genetics Community Research Network. J. Clin. sites across the U.S. and seven in Latin America, that enables Oncol. 31:210-16, 2013. participation in the multi-institutional consortia required • Villarreal-Garza, C., Alvarez-Gómez, R.M., Pérez-Plasencia, to assemble enough hereditary cases for epidemiological C., and Weitzel, J.N. (2015). Significant clinical impact of studies. My team has used this cohort to establish recurrent BRCA1 and BRCA2 mutations in Mexico. Cancer. collaborations with numerous international consortia (e.g., Feb 1;121(3):372-8 PMCID: PMC4304938 CIMBA, ENIGMA, PROSE, SIMPLEXO, LiFE, COMPLEXO), • Rebbeck, T.R., Mitra, N., Wan, F., Goldgar, D.E., Weitzel, J.N., and produced more than 124 peer reviewed manuscripts. This Garber, J.E., et al. (2015). Association of type and location of collaborative approach has yielded important observations BRCA1 and BRCA2 mutations with risk of breast and ovarian on the effect of oral contraceptive use and of pregnancy on cancer. JAMA. Apr 7;313(13):1347-61. PMCID: PMC4537700 penetrance of breast cancer in BRCA mutation carriers, as • Somlo, G., Frankel, P.H., Arun, B.K., Ma, C.X., Garcia, A.A., well the identification of genetic modifiers such as a RAD51 Cigler, T., Cream, L.V., Harvey, H.A., Sparano, J.A., Nanda, R., variant, the first known genetic modifier of breast cancer Chew, H.K., Moynihan, T.J., Vahdat, L.T., Goetz, M.P., Beumer, penetrance in BRCA2 carriers. Genome wide association J.H., Hurria, A., Mortimer, J., Piekarz, R., Sand, S., Herzog, studies identified breast cancer risk snps, and current clinical J., Van Tongeren, L.R., Ferry-Galow, K.V., Chen, A.P., Ruel, studies are assessing the clinical impact of polygenic risk C., Newman, E.M., Gandara, D.R., and Weitzel, J.N. (2017). scores. Along with Judy Garber and the LiFE consortium we Efficacy of the PARP Inhibitor Veliparib with Carboplatin helped characterize the phenotype (typically Her2/neu +) of or as a Single Agent in Patients with Germline BRCA1- or TP53-associated breast cancers. We recently documented BRCA2-Associated Metastatic Breast Cancer: California Cancer Consortium Trial NCT01149083. Clinical Cancer a significant clinical conundrum, wherein somatic TP53 Research. 23(15):4066-4076. PMCID: PMC5540749
118 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES John C. Williams, Ph.D. Professor, Department of Molecular Medicine
STRUCTURAL BIOLOGY AND BIOPHYSICS
Our group applies biophysical methods to design, characterize pancreatic neuroendocrine tumors. With Dr. Dellinger, we are and optimize novel therapeutics for cancer treatment. We also developing a series of antibody-drug conjugates and BiTes to use these methods to understand the mechanisms of signaling treat endometrial and ovarian cancer. With Drs. Brown and pathways, intracellular transport and cytoskeletal structure. Forman, we are developing meditope-enabled CAR-T therapies Currently, the majority of our projects focus on antibody and and novel approaches to address antigen escape. With Drs. protein engineering. Zeng and Riggs, we are developing novel reagents to mitigate 1) Using X-ray diffraction methods, biophysics and molecular graft versus host disease. With Drs. Casimiro and Roep, we are biology, our group discovered and developed the meditope developing novel, immune modulatory mAbs to treat diabetes. technology. Specifically, we identified a cyclic, twelve amino In addition to these collaborations, we continue to employ new acid peptide that binds to a hole formed at the interface of the engineering strategies to address unmet needs. light and heavy chains of the cetuximab Fab. We demonstrated 2) We also use X-ray diffraction and protein engineering to the binding of this peptide to the Fab is specific and does produce tumor-activated biologics. We are currently focusing not alter antigen binding (e.g., EGFR) and the residues from on immune checkpoint therapeutics. This class of therapeutics the Fab that define the binding site can be grafted onto any modulates the activity of the immune system. While this class antibody. Because the peptide binds in the middle of the Fab, of therapeutics has lead to a fundament change in cancer we have termed it a meditope (middle + place). Together with treatment, these therapeutics can also cause severe adverse the Horne group, we conducted extensive structure-activity side effects including sepsis, diabetes, and in some cases studies with multiple meditopes and Fabs and ultimately death. It has been demonstrated many of these side effects improved the meditope affinity to the Fab by over 1 million fold. are associated with activating the immune system at the We have added different functionalities to the meditope and wrong site. To prevent these side effects, we have effectively used the interaction to image specific cells in diseases and created a Trojan horse or pro-biologic. We hide the antigen- delivery drugs. To further improve the affinity, we developed an binding site or the therapeutic with a small peptide called interlocking mechanical bond where a meditope with an azide a ‘mask’ and exploit the natural biochemistry of the tumor group was threaded through the Fab hole and ‘bolted’ to a large microenvironment to activate the therapeutic potential of the protein using click chemistry. In addition, using structural data molecule. We have demonstrated that the masked α-mCTLA4 from diffraction studies, we identified adjacent residues on molecule was effective at eliminating tumors where as a nearly the Fab and the meditope peptide that could accommodate identical, catalytically inert masked α-mCTLA4 mAb failed cysteines and, upon mutagenesis, yielded a disulfide bond. to eradicate the tumor. We further showed that the parental The high affinity interaction of the meditope and Fab provided α-mCTLA4 molecule affected Tregs in the spleen whereas the a templated site for the disulfide reaction, leading to the tumor-activated molecule did not (similar levels of Treg using rapid formation of a kinetically and thermodynamically stable an isotype control). Similar observations were made using disulfide bond. More importantly, this templated reaction a rationally designed, α-mPD1 mAb. The lab is now turning was performed using natural amino acids, allowing us to to other mAbs and biologics where local activation could encode a ‘cys-meditope’ tag on any protein or biologic without dramatically improve the therapeutic index. introducing unnatural amino acids or other post-translational modification tags. To demonstrate the templated disulfides SELECTED PUBLICATIONS facile and broad application, we added the cys-meditope tag • King, J.D., Ma, Y., Kuo, Y.C., Bzymek, K.P., Goodstein, L.H., to the N-, C- or both termini of GFP, to the N- or C- termini of Meyer, K., Moore, R.E., Crow, D., Colcher, D., Singh, G., an αCD16 nanobody, and to the C terminus of a Her2 targeting Horne, D.A., and Williams, J.C. Template-catalyzed, disulfide affibody. Each readily and successfully formed a complex with conjugation of monoclonal antibodies using a natural amino a panel of unique, cys-modified, meditope-enabled mAbs. acid tag. Bioconjugate Chemistry 2018 (in press) PMID: These studies produced several potent, immune engaging, 29763554 bispecific mAbs with EC50s as low as 3.2 pM. • Bzymek, K.P., Puckett, J.W., Zer, C., Xie, J., Ma, Y., King, With these studies completed, we are now working with J.D., Goodstein, L.H., Avery, K.N., Colcher, D., Sing, G., Horne, D.A., and Williams, J.C. Mechanically interlocked multiple investigators to apply the meditope conjugation functionalization of monoclonal antibodies. Nat Commun. technology to produce novel therapeutics. With Dr. Singh, 2018 9(1):1580. doi: 10.1038/s41467-018-03976-5. we are developing chemical bispecific T cell engagers for PMID:29679060
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 119 Yanzhong (Frankie) Yang, M.D., Ph.D. Assistant Professor, Department of Cancer Genetics and Epigenetics
EPIGENETIC REGULATION OF GENE EXPRESSION AND GENOME STABILITY
Chromatin harbors two of the most important molecular SELECTED PUBLICATIONS directors of life, genetics and epigenetics, both of which have • Yang, Y.*, Hadjikyriacou, A., Xia, Z., Gayatri, S., Kim, D., a profound influence on human health. My long-term research Zurita-Lopez, C., Kelly, R., Guo, A., Li, W., Clarke, S.G., and goal is to understand chromatin dynamics in human diseases, Bedford, M.T*. PRMT9 is a Type II methyltransferase that especially cancer. Our research efforts focus on elucidating methylates the splicing factor SAP145. Nat. Commun. 6:6428 the epigenetic pathways that regulate gene expression and DOI: 10.1038/ncomms7428, 2015. *Co-corresponding genome stability. There are two major research directions in authors. my lab addressing the above questions: • Yang, Y., McBride, K., Hensley, S., Lu, Y., Chedin, F., 1. Understanding the biological role of protein arginine and Bedford, M.T. Arginine methylation facilitates the methyltransferases recruitment of TOP3B to chromatin to prevent R-loop Protein arginine methylation is catalyzed by a group of accumulation. Mol. Cell 53, 484-497, 2014. enzymes named protein arginine methyltransferases (PRMTs). • Yang, Y., and Bedford, M.T. Protein arginine There are nine PRMTs encoded in mammalian genomes, the methyltransferases and cancer. Nat. Rev. Cancer protein products of which catalyze three types of arginine 13: 37-50, 2013. methylation, namely monomethylation, asymmetrical dimethylation and symmetrical dimethylation. PRMTs are • Yang, Y., Lu, Y., Espejo, A., Wu, J., Xu, W., Liang, S., and involved in every aspect of cellular processes including Bedford, M.T. TDRD3 is an effector molecule for arginine- methylated histone marks. Mol. Cell 40: 1016-1023, 2010. transcription, pre-RNA splicing, DNA damage repair, etc. Overexpression of these enzymes is often associated with various cancers, which might make some of them viable targets for therapeutic strategies. Among all the nine PRMTs, PRMT9 is the last member whose biological function has not been characterized. We recently identified two spliceosome-associated proteins —SAP145 and SAP49 — as PRMT9-binding partners, linking PRMT9 to U2 snRNP maturation. We are currently in the process of generating PRMT9 gene knockout mice to unmask the biological roles of this new enzyme. 2. Investigating the biological role as well as regulatory network of R loops Transcription-mediated R loop formation occurs when the nascent RNA transcript anneals back to the template DNA strand in the wake of RNAP II. R loops form there owing to the presence of a negatively supercoiled region behind RNAP II and to the fact that RNA/DNA hybrids, particularly those formed by G-rich RNAs base-paired to C-rich DNA templates, are more stable than double stranded DNA. Although R loop formation has both beneficial and deleterious effects to the cells, its biological roles, as well as its regulatory network, are largely unknown. We are currently taking advantage of both biochemical and genetic approaches to address what are the biological roles of R loop formation in the cells and how R loop formation is regulated.
120 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Jiing-Kuan Yee, Ph.D. Professor, Department of Diabetes Complications and Metabolism
PROMOTE CELL DIFFERENTIATION FROM HUMAN PLURIPOTENT STEM CELLS
Diabetes affects over 300 million people worldwide. Diabetic SELECTED PUBLICATIONS patients, particularly those suffering from type 1 diabetes • Wang, X., Wang, Y., Wu, X., Wang, J., Wang, Y., Qiu, Z., Chang, (T1D), can potentially be cured through transplantation of T., Huang, H., Lin, R.J., and Yee, J.K. “An unbiased approach new islet cells. However, this procedure remains challenging to study the off-target effect of CRISPR/Cas9 reveals its due to the limited availability of healthy islet donors. Human tolerance of bulge formation in the genomic target” Nat. pluripotent stem cells (hPSCs) with their ability to expand Biotech. 33:175-178 (2015). indefinitely and differentiate into almost all tissue types provide a huge opportunity to produce functional islet cells in • Boza-Moran, M.G., Martinez-Hernandez, R., Bernal, S., clinically relevant quality and quantity. Using an established Wanisch, K., Also-Rallo, E., Le Heron, A., Alias, L., Denis, C., seven-step differentiation protocol, we efficiently differentiated Girard, M., Yee, J.K., Tizzano, E.F., and Yanez-Munoz, R.J. hPSCs into islet beta cells in vitro. The protocol involves “Decay in survival motor neuron and plastin 3 levels during adherent cell culture and is not suitable for scale-up beta differentiation of iPSC-derived human motor neurons” cell production. To address this issue, we have adapted the Scientific Reports 5: 11696 (2015). existing differentiation protocol into a suspension culture • Yee, J.K. “Off-target effects of engineered nucleases.” FEBS system that generates 3D spheroids from hPSCs. Beta cell Journal 283:3239 (2016). production from this platform is reproducible and the beta cells are glucose-responsive. This platform therefore provides • Xu, Y., Shan, W., Li, X., Wang, B., Liu, S., Wang, Y., Long, Y., Tie, a foundation for systematically evaluating media components R., Wang, L., Cai, S., Zhang, H., Lin, Y., Zhang, M., Zheng, W., and culture conditions to improve scale-up beta cell production Luo, Y., Yu, X., Yee, J.K, Ji, J, and Huang, H. “A synthetic three- from hPSCs. As beta cells generated from this protocol are dimensional niche system facilitates generation of functional not completely mature, we are evaluating different strategies hematopoietic cells from human-induced pluripotent stem to enhance the functionality of hPSC-derived beta cells. One cells.” J. Hematol. Oncol. 9: 102 (2016) strategy involves the use of the CRISPR/Cas9 gene editing technology to genetically manipulate the genome of hPSCs • Wang, Y., Wang Y.J., Chang, T., Huang, H., and Yee, J.-K. for ectopic expression of beta cell-specific factors. The goal “Integration-defective lentiviral vector mediates efficient gene is to enhance the expression of these factors during hPSC editing through homology-directed repair in human embryonic differentiation to increase the yield and maturation of hPSC- stem cells.” Nucleic Acids Res. pii: gkw1057 (2016). derived beta cells for transplant. We are also evaluating • Wu, Y., and Yee, J.-K. “Unbiased Detection of Off-target different strategies to genetically manipulate hPSCs for the Cleavage by CRISPR/Cas9 and TALENs Using Integrase- production of beta cells capable of escaping host immune defective Lentiviral Vectors” in “Genome Editing and rejection. Our ultimate goal is to produce safe and robust beta Engineering: From Talens, ZFNs and CRISPRs to Molecular cells in vitro suitable for the transplantation to treat T1D. Surgery”. Appasani K. ed., Cambridge University Press, New York, Chapter 2, (2018).
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 121 Hua Yu, Ph.D. Billy and Audrey L. Wilder Professor in Tumor Immunotherapy Professor and Associate Chair, Department of Immuno-Oncology Co-director, Cancer Immunotherapeutics Program
STAT3: FROM BASIC DISCOVERIES TO THE CLINIC
A tumor’s ability to proliferate, resist apoptosis, invade and • Priceman, S.J., Shen, S., Wang, L., Deng, J., Yue, C., Kujawki, thwart the immune system is the essence of cancer. Although M., and Yu, H. S1PR1 is crucial for accumulation of regulatory many anti-cancer therapies show promise, most are aimed T cells in tumors via STAT3. Cell Reports. March 2014 PMID: at the tumor cell as an independent entity and ignore the 24630990 importance of the many cell types that constitute the tumor • Yu, H.*, Lee, H.Y., Herrmann, A., Buettner, R., and Jove, R. microenvironment. An emerging picture of the tumor as an Revisiting STAT3 signaling in cancer, new and unexpected organ highlights the role of multiple tumor associated cells, biological functions. Nature Reviews Cancer 14:736-746, 2014. including fibroblasts, endothelial cells, hematopoietic cells/ *Co-corresponding author immune cells and stem cells, that interact intimately with • Priceman, S.J., Kujawski, M., Shen, S., Cherryholmes, G.A., the transformed cells in modulating the oncogenic process. Lee, H., Zhang, C., Kruper, L., Mortimer, J., Jove, R., Riggs, My group has shown that STAT3, which is constitutively- A.D., and Yu, H. Regulation of adipose tissue T cell subsets activated in tumor cells, is also persistently activated in by Stat3 is crucial for diet-induced obesity and insulin normal cells associated with the tumor. We have further resistance. Proc. Natl. Acad. Sci. USA 110: 13079-13084, 2013. demonstrated that STAT3 signaling coordinates multiple levels of crosstalk between tumor cells and their microenvironment, • Lee, H.Y., Zhang, P., Herrmann, H., Yang, C.Y., Xin, H., Wang, C.H., Hoon, D., Forman, S., Jove, R., Riggs, R.D., and Yu, affecting tumor growth, apoptosis, angiogenesis and H. Acetylated STAT3 is crucial for methylation of tumor immune surveillance. Our work, along with other studies, has suppressor gene promoters and inhibition by resveratrol established that STAT3 in tumor cells regulates a large array results in demethylation. Proc. Natl. Acad. Sci.USA 109: 7765- of genes important for proliferation, survival, angiogenesis, 7769, 2012. invasion/metastasis and immune suppression. Its central role in organizing the tumor microenvironment makes STAT3 a • Deng J., Liu, Y., Lee, H., Herrmann, A., Zhang, W., Zhang, promising target both in tumor cells and in the normal cells that C., Shen, S., Priceman, S., Kujawski, M., Pal, S., Raubitschek, A., Hoon, D., Forman, S., Figlin, R., Liu, J., Jove, R., and Yu, constitute the tumor organ. We have developed several novel H. 2012. S1PR1-STAT3 signaling is crucial for myeloid cell technologies to block challenging targets such as STAT3, some colonization at future metastatic sites. Cancer Cell 21: of which are poised and/or ready to be in first-human studies. 642–654, 2012.
SELECTED PUBLICATIONS • Lee, H., Deng, J., Kujawski, M., Liu, Y., Herrmann, A., Kortylewski, M., Horne, D., Forman, S., Jove, R., and Yu, • Wang, T., Fahrmann, J. F., Lee, H., Li, Y.-J., Tripathi, S.C., Yue, H. STAT3-induced expression of S1P1 receptor for the C., Zhang, C., Lifshitz, V., Song, J., Jandial, R., Yuan, Y., Soml, sphingolipid metabolite S1P is critical for persistent Stat3 G., Ann, D., Hanash, S., Jove, R., and Yu, H. (2018) JAK/ activation in tumors. Nat. Med. 16: 1421-1428, 2010. STAT3-Regulated Fatty Acid β-Oxidation Is Critical for Breast Cancer Stem Cell Self-Renewal and Chemoresistance. • Wang, L., Yi, T.S., Zhang, W., Pardoll, D., and Yu, H. IL-17 Cell Metabolism 27, 136-150. enhances tumor development in carcinogeninduced skin cancer. Cancer Res. 70: 10112-10120, 2010. • Zhang, C., Xin, H., Zhang, W., Yazaki, P.J., Zhang, Z.F., Le, K., Li, W.Z. , Lee, H.Y., Kwak, L., Forman, S.J., Jove, R., and Yu, H. • Kortylewski, M., Xin, H., Kujawski, M., Lee, H.-Y., Liu, Y., CD5 responds and binds to IL-6 forming a feed-forward loop Harris, T., Drake, C., Pardoll, D., and Yu, H. Regulation of with STAT3 in B cells to promote cancer. 2016. Immunity, 44, the IL-23/IL-12 balance by STAT3 signaling in the tumor 913-923. microenvironment. Cancer Cell 15: 114-123, 2009. Featured article. • Herrmann, A., Priceman, S.J., Kujawski, M., Xin, H., Cherryholmes, G., Zhang, W., Zhang, C., Lahtz, C., Kowolik, • Lee, H.Y., Deng, J.H., Herrmann, A., Niu, G.L., Xin, H., Li, Z.- C., Forman, S., Kortylewski, M., and Yu, H. CTLA4-aptamer- W., Kujawski, M., Forman, S., Jove, R., Pardoll, D., and Yu, H. siRNA targeting STAT3 in both tumorassociated and Persistently-activated STAT3 maintains NF-β constitutive malignant T cells. J. Clin. Invest. 124:2977-2987, 2014. activity in tumors. Cancer Cell 15: 283-293, 2009.
122 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Xiaochun Yu, M.D., Ph.D. Professor, Department of Cancer Genetics and Epigenetics
DNA DAMAGE RESPONSE, EPIGENETIC MODIFICATIONS AND THEIR ROLES IN TUMORIGENESIS
Genomic DNA that stores genetic information can be SELECTED PUBLICATIONS easily damaged by environmental and internal hazards. • Chen, Q., Chen, Y., Bian, C., Fujiki, R., and Yu, X. (2013) If not repaired, the lesions will induce genomic instability TET2 promotes histone O-GlcNacylation during gene and tumorigenesis. Fortunately, during evolution, cells transcription. Nature 493:561-564. develop a DNA damage response system that recognizes and repairs DNA lesions. Using genetic and biochemical • Ma, T., Chen, Y., Zhang, F., Yang, C-Y., Wang, S., and Yu, X. (2013) RNF111-dependent neddylation activates DNA tools, we have identified novel signal transduction pathways damage-induced ubiquitination. Molecular Cell. 49: 897-907. mediated by different posttranslational modifications, such as phosphorylation, ubiquitination and poly(ADP-ribosyl)ation • Li, M., and Yu, X. (2013) Function of BRCA1 in the DNA in response to DNA damage. In particular, it has been widely damage response is mediated by ADP-ribosylation. Cancer known that ubiquitination mediates protein degradation. Cell. 23: 693-704. However, we and others show that like phosphorylation • Lu, L, Korakavi, G., Kuang, H., and Yu, X. (2013) Distinct events, protein ubiquitination events serve as signals to DNA damage responses on male meiotic sex chromosomes. mediate protein-protein interaction, which regulates DNA Nature Communications. 3015. damage repair. More recently, we examined poly(ADP-ribosyl) ation and revealed novel “readers” of DNA damage-induced • Li, M., Lu, L., Yang, C., Wang, S., and Yu, X. (2013) The FHA and BRCT domains recognize ADP-ribosylation during DNA poly(ADP-ribosyl)ation. The results provide an explanation by damage response. Genes&Development. 27: 1752-1768. which PARP inhibitors selectively kill tumor cells with BRCA mutations. It may generate significant impact for clinical • Chen, Y., Chen, Q., McEachin, R.C., Cavalcoli J.D., and Yu, treatment of breast cancer patients with PARP inhibitors. We X. (2014) H2A.B facilitates transcription elongation at also pioneered research on the role of DNA damage response methylated CpG loci. Genome Research.24:570-579. in spermatogenesis, and utilized the unexpected findings from • Zhang, F., Chen, Y., Li, M., and Yu, X. (2014) The OB-fold spermatogenesis research to address fundamental questions motif is a poly(ADP-ribose)-binding domain that mediates in DNA damage repair. Besides DNA damage response, we DNA damage response. Proceedings of the National Academy have explored the molecular mechanism of post-translational of Sciences. 111:7278-7283. modifications on histones and DNA. We are particularly • Bian, C., Chen, Q., and Yu, X. (2015) ZNF644 and WIZ interested in the molecular mechanism of DNA methylation regulate the G9a/GLP complex for gene repression. eLife. and heterochromatin formation, which are often deregulated 08168. during tumorigenesis. Thus, novel findings from chromatin remodeling and epigenetic modifications contribute to the understanding of genomic instability and tumorigenesis.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 123 John A. Zaia, M.D. Aaron D. Miller and Edith Miller Chair in Gene Therapy Director, Center for Gene Therapy Deputy Director for Clinical Research
ANTI-HIV/AIDS GENE THERAPY
Treatment of AIDS with genetically modified blood stem cells CAR T cell therapy for HIV/AIDS hypothesizes that genetic modification of cells can limit HIV-1 Immunotherapy of HIV/AIDS is an attractive goal, given the (HIV) replication and prevent the progression to AIDS. Of the basic pathogenetic problem is the development of T cell various ways that this could be tested, one approach currently immunodeficiency. CAR T cell therapy for HIV/AIDS is a tests whether genetically transduced blood stem cells could collaborative project among scientists and clinicians in the repopulate in the host after autologous transplantation. Center for Gene Therapy (Morris, Burnett, Angelo Cardoso, City of Hope investigators originally developed a platform for M.D., Ph.D., and Zaia), working with both the Department testing new vectors in the setting of autologous blood stem/ of Hematology & Hematopoietic Cell Transplantation (Xiuli progenitor cell transplantation (HCT) for high-risk AIDS Wang, Ph.D., Elizabeth Budde, M.D., Ph.D., Ryotaro Nakamura, lymphoma, and have published results. M.D., and Forman), and the Department of Experimental Using a lentivirus vector (LV) developed at City of Hope, four Therapeutics (Don J. Diamond, Ph.D., and Corinna La Rosa, AIDS lymphoma patients, treated with LV-modified HCT Ph.D.). The project combines expertise in HIV, in CAR T cell progenitor cells, showed continued expression of anti-HIV development, and in CMV vaccine development to develop RNA, including siRNA and anti-CCR5 ribozyme, occurred a bispecific CAR T-cell that would be responsive both to for at least three years post-transplant. A second approach endogenous or exogenous CMV signals that maintain levels addresses whether genome editing of the CCR5 gene, of circulating cells and to HIV antigens that allow killing of which encodes for a protein important for HIV infection, infected cells. in autologous blood stem cells could result in outgrowth SELECTED PUBLICATIONS of progeny blood cells with resistance to HIV. For this, zinc • Nakamura, R., Rosa, C.L., Longmate, J., Drake, J., Slape, C., finger nuclease is used, and the first AIDS patients have Zhou, Q., Lampa, M.G., O’Donnell, M., Cai, J.L., Farol, L., undergone ZFN-based autologous HCT. This and other genetic Salhotra, A., Snyder, D.S., Aldoss, I., Forman, S.J., Miller, J.S., approaches to HIV treatment are being studied in collaboration Zaia, J.A., and Diamond, D.J. Viraemia, immunogenicity, with Amrita Krishnan, M.D., John Rossi, Ph.D., Kevin Morris, and survival outcomes of cytomegalovirus chimeric epitope Ph.D., John Burnett, Ph.D., and Stephen Forman, M.D. vaccine supplemented with PF03512676 (CMVPepVax) Laboratory for Cellular Medicine (LCM) in allogeneic haemopoietic stem-cell transplantation: Angelo Cardoso, M.D., Ph.D., is director of the LCM within the randomised phase 1b trial. Lancet Haematol. 2016 Feb;. Epub Center for Gene Therapy, and it is the LCM which develops 2015 Dec 24 PMC: 4926626 processes necessary for bringing these new approaches to the • DiGiusto, D., Cannon, P.M., Holmes, M.D., Li, L., Rao, A., Wang, clinic. Dr. Cardoso collaborates with bone marrow transplant J., Lee, G., Gregory, P.D., Kim, K.A., Hayward, S.B., Meyer, K., clinicians in both the departments of Pediatrics and the Exline, C., Lopez, E., Henley, J., Gonzalez, N., Bedell, V., Stan, Hematology & Hematopoietic Cell Transplantation regarding R., and Zaia, J.A. Preclinical development and qualification new graft engineering trials aimed at limiting graft-versus-host of ZFN-mediated CCR5 disruption in human hematopoietic disease in the treatment of leukemia and sickle cell disease. His stem/progenitor cells. Mol Ther Methods Clin Dev 2016, major interest is the preservation of “stemness” in genetically 3:16067. PMCID: 5102145 modified cell products. • La Rosa, C., Longmate, J., Martinez, J., Zhou, Q., Kaltcheva, T.I., Alpha Stem Cell Clinic (ASCC) Tsai, W., Drake, J., Carroll, M., Wussow, F., Chiuppesi, F., The Center for Gene Therapy administers an experimental • Hardwick, N., Dadwal, S., Aldoss, I., Nakamura, N., Zaia, J.A., clinic for novel stem cell-based therapies under the auspices and Diamond, D.J. MVA vaccine encoding CMV antigens of the California Institute for Regenerative Medicine. The goal safely induces durable expansion of CMV-specific T-cells in of the ASCC is to accelerate the successful completion of new healthy adults. Blood. 2017; 125:114-125. PMCID: PMC5216266 stem cell therapies and provide assistance in terms of patient care coordination, regulatory affairs, data management and biospecimen processing.
124 IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES Defu Zeng, M.D. Professor, Departments of Diabetes Immunology and Hematopoietic Cell Transplantation
TRANSPLANTATION IMMUNE TOLERANCE
SELECTED PUBLICATIONS Allogeneic hematopoietic cell transplantation (HCT) is a curative therapy for hematological malignancies and hereditary • Zhang, M., Racine, J., Liu, Y., Lin, Q., Qi, T., Wang, T., Riggs, disorders as well as refractory autoimmune diseases. Induction A.D., and Zeng, D. MHC-mismatched mixed chimerism of mixed chimerism via allogeneic HCT is also one of the most tolerize peripheral non-cross-reactive autoreactive T cells reliable approaches for induction of organ transplantation in mice (PNAS 2018: www.pnas.org/cgi/doi/10.1073/ pnas.1720169115). tolerance. However, graft-versus-host disease (GVHD) remains a major obstacle in classical HCT, in which recipients are • Deng, R., Hurtz, C., Song, Q., Yue, C., Xiao, G., Yu, H., Wu, X., required to be conditioned with total body irradiation (TBI) Muschen, M., FOrman, S., Martin, P.J., and Zeng, D. Extra- or high dose chemotherapy in order to allow donor stem cell follicular CD4+ T-B Interactions are sufficient for induction engraftment. Recent studies have shown that tissue damage of Autoimmune-like Chronic Graft-Versus-Host Disease. and activation of tissue dendritic cells caused by conditioning Nature Communications, 2017; 8: 978. TBI or chemotherapy plays a critical role in induction of GVHD. • Ni, X., Song, Q., Cassady, K., Deng, R., Jin, H., Zhang, M., Dong, H., Forman, S., Martin, P.J., Chen, .Z., Wang, J., and One of the research projects in the lab of Professor Defu Zeng Zeng, D. PD-L1 interact with CD80 to regulate graft versus is to understand the pathogenesis of GVHD, in which donor T leukemia activity of donor CD8+ T cells. JCI 127: 1960-1977, cells infiltrate the target tissues and mediate damage. Based 2017, featured article. on the clinical features, GVHD can be divided into acute and chronic GVHD. The same alloreactive T cells that mediate • Jin, H., Ni, X., Deng, R., Song, Q., Young, J., Cassady, K., GVHD also mediate the most beneficial effect of graft versus Zhang, M., Forman, S., Martin, P., Liu, Q., and Zeng, D. leukemia (GVL). Thus, prevention of GVHD while preserving Antibodies from donor B cells perpetuate scleroderma in chronic GVHD. Blood, 2016, 127: 2249-2260, feathered GVL effect remains the long-sought goal of allogeneic HCT. article. Immune check points (PD-L1/CD80 and PD-L1/PD-1 • Zhang, M., Lin, Q., Riggs, A., and Zeng, D. Growth factors interactions) play critical roles in regulating immune response and medium hyperglycemia induce Sox9+ ductal cell in both animal models and humans. We are studying how differentiation into β cells in mice with reversal of diabetes. immune check points regulate alloreactive T cell metabolism (PNAS 2016; 113:650-5) and mitochondria dynamics as well as regulate GVHD and GVL effect in murine models and humanized murine models. • Wu, L., Li, N., Zhang, M., Riggs, A., and Zeng, D. Induction of We are also dissecting the role of allo- and auto-reactive CD4+ MHC-mismatched mixed chimerism augments thymic Treg production and cures EAE (PNAS 2015; 112:15994-9. T (Th1, Th2 and Th17) cells, Treg cells, APCs (dendritic and B cells), as well as autoantibodies in the pathogenesis of acute • Racine, J.J., Zhang, M., Wang M, Morales, W., Shen, C., and chronic GVHD. and Zeng, D. MHC-mismatched mixed chimerism depletes cross-reactive autoreactive thymocytes. J. Immunol. 194:407- Another project is to develop a radiation-free GVHD 417, 2015. preventative conditioning regimen for induction of mixed chimerism for the therapy of autoimmune diseases (e.g., • Deng, R., Cassady, K., Li, X., Yao, S., Zhang, M., Racine, J., Lin, type 1 diabetes, multiple sclerosis and lupus) and organ L., Chen, L., and Zeng, D. B7H1/B7.1 interaction augments PD-1-dependent T cell apoptosis and ameliorates graft transplantation tolerance. We have observed that induction versus host disease. J. Immunol. 194:560-574, 2015. of mixed chimerism results in reversal of autoimmunity, elimination of insulitis, and beta cell regeneration, as well as • Wang, M., Racine, J., Zhang, M., Wu, T., Deng, R., Johnston, organ transplantation tolerance in overt diabetic NOD mice. H., Shen, C., Siswanto, K., and Zeng, D. MHC-mismatched We are dissecting the mechanisms whereby mixed chimerism chimerism is required for induction of transplantation reverses autoimmunity and alloimmunity. We are also tracing tolerance in autoimmune diabetic NOD recipients. J. the origin of beta cell neogenesis in type 1 diabetes and Immunol. 193: 2005-2015, 2014. characterizing cell progenitors in the mixed chimeric NOD mice.
IRELL & MANELLA GRADUATE SCHOOL OF BIOLOGICAL SCIENCES 125 NOTES NOTES NOTES
1500 East Duarte Road Duarte, CA 91010-3000 877-715-GRAD (4723) CityofHope.org/grad-school [email protected] 30000-NEW-20180