Scientific Report 2019 Report Scientific

Scientific Report 2019 stjude.org/scientificreport

262 Danny Thomas Place Memphis, TN 38105 Physician Referral Service 866.278.5833 General Information 901.595.3300 Translating Science into Survival Behind the Cover The cover depicts the 3-dimensional structures of proteins and drug molecules inside a cell. During a catastrophic disease, the functions of proteins and other biomolecules change. Structural biologists use various sophisticated techniques to study the structural basis of those deleterious changes and determine the best therapeutic strategy. The Faculty Editorial Board Department of Structural Biology is expanding to become the world’s Terrence L. Geiger, MD, PhD premier center for structural analyses and imaging of biomolecules in Michael A. Dyer, PhD health and disease. Department Chair Charalampos Babis Kalodimos, Charalampos Babis Kalodimos, PhD PhD, is recruiting leaders in the field to join our faculty and bringing Charles W. M. Roberts, MD, PhD innovative technologies to the St. Jude campus. Carlos Rodriguez-Galindo, MD David J. Solecki, PhD

Editoral Direction Angela J. McArthur, PhD, ELS

Creative Direction Jerry L. Harris

Photography Peter Barta Seth Dixon Ann-Margaret Hedges Jere Parobek

Prepared by Departments of Scientific Editing and Biomedical Communications

St. Jude Children’s Research Hospital and ALSAC are registered trademarks. ST. JUDE FREELY SHARES THE DISCOVERIES WE MAKE. EVERY CHILD SAVED AT ST. JUDE PROVIDES DOCTORS AND SCIENTISTS WORLDWIDE WITH THE KNOWLEDGE TO HELP SAVE THOUSANDS MORE CHILDREN.

Privileged communication. Copyright © 2019 St. Jude Children’s Research Hospital. No part of this communication may be cited, reproduced, stored in a retrieval system, or transmitted by electronic or other means without prior written permission of the President and CEO and the appropriate investigator. This report reflects the activities of St. Jude Children’s Research Hospital during 2018. 4 CEO STATEMENT 6 IN MEMORIAM 8 CANCER CENTER 34 STRUCTURAL BIOLOGY 54 ADVANCED MICROSCOPY 64 ST. JUDE GLOBAL 88 AFFILIATE PROGRAM 90 SHARED RESOURCES 94 SCIENTIFIC HIGHLIGHTS 114 ACADEMIC DEPARTMENTS 124 BOARDS & EXECUTIVE STAFF 127 OPERATIONS & STATISTICS

Mario Halic, PhD

2019 Scientific Report | 2 3 | 2019 Scientific Report In science and medicine, collaboration is the spark of knowledge, technology, and organizational that ignites progress. At St. Jude Children’s Research skills. Also, the World Health Organization (WHO) Hospital, talented faculty and staff work together— designated St. Jude as the first WHO Collaborating and with colleagues worldwide—to advance the Center for Childhood Cancer. Representatives from research and treatment of pediatric cancer and WHO and St. Jude announced this new effort—the other catastrophic diseases. In this Scientific Report, WHO Global Initiative for Childhood Cancer—at we showcase how the power of team science the United Nations General Assembly in New York enhances the discovery process. Collaborative City in September 2018. The goal of this initiative efforts in the laboratory, the clinic, and with partners is to increase the survival of children with the most around the globe are fueling discoveries and giving common pediatric cancers to 60% by 2030. new hope to families everywhere. Beyond the stories in this Report, St. Jude In the first feature, we highlight how the saw continued growth and progress last year. We St. Jude Comprehensive Cancer Center brings broke ground on a $412 million advanced research together scientists from various fields to focus on a center that will open in 2021 and launched 2 new shared problem and accelerate progress. In 2018, the online data-sharing portals for the global research Center received its second consecutive “Exceptional” community: St. Jude Cloud, which offers next- rating after its 5-year review by the National Cancer generation sequencing data and analysis tools for Institute. This is the highest-possible ranking, placing pediatric cancer and other life-threatening diseases, St. Jude among the nation’s elite Cancer Centers. and PROPEL, which freely shares patient-derived The second story outlines how the Structural xenograft samples of leukemias with researchers Biology department is recruiting and expanding around the world to accelerate leukemia biology to transform into one of the world’s most research. comprehensive structural biology research centers In 2018, St. Jude committed resources to tackling that houses imaging and analytical modalities that several faculty-proposed blue sky initiatives—ideas examine dynamic cellular processes at the atomic with the potential to have a game-changing impact level. Under the leadership of Charalampos Babis on health. Several projects are underway, including Kalodimos, PhD, the department has established 6 expanding our cloud-based genomic data–sharing centers to facilitate cutting-edge structural biology resources, initiating a gene therapy trial for research and transdisciplinary collaborations with hemophilia B in LMICs, and establishing a program St. Jude investigators in other departments. to explore the molecular pathology of pediatric In the third feature, we describe how neurological diseases. developmental neurobiologists at St. Jude are using St. Jude also gained recognition from several top James R. Downing, MD technologic innovations to propel neuroscience workplace resources, including Fortune’s “100 Best President and Chief Executive Officer and gain new insights into the nervous system Companies to Work For” list, Glassdoor’s “Best Places during health and disease. Michael A. Dyer, PhD, to Work” ranking, and “No. 1” on the National Society David Solecki, PhD, and Daniel Stabley, PhD, are of High School Scholars’ Annual Career Survey of part of an elite group of 4 laboratories working with places where high school and college students wish Nobel Laureate Eric Betzig (University of California, to work. Berkeley) to co-build the next-generation lattice The past year has been a time of great light-sheet microscope. This new instrument will productivity for our clinical, scientific, and “IMAGINE WHAT GREAT FEATS WE CAN enable scientists to visualize changes as they occur administrative operations. By building on this in living cells deep within the brain or other nervous foundation, working in transdisciplinary teams, and ACHIEVE TOGETHER, WORKING ACROSS system tissues. collaborating with colleagues around the world, The fourth story details a new St. Jude effort to St. Jude will advance cures for pediatric cancer and DISCIPLINES, ACROSS BORDERS, AND close the global gap in childhood cancer survival. other catastrophic childhood diseases worldwide. Today, one of the strongest predictors of whether AROUND THE WORLD.” a child is cured of cancer is where that child lives. More than 80% of all children live in low- or middle- income countries (LMICs) that often struggle to meet the healthcare needs of local populations. In 2018, St. Jude Global was launched, with the mission to improve the survival of children with cancer or blood disorders worldwide, through the sharing

2019 Scientific Report | 4 5 | 2019 Scientific Report In Memoriam The St. Jude family mourns the passing of Brian P. Sorrentino, MD, Wall Street Committee Endowed Chair in Bone Marrow Transplant Research, Director of the Division of Experimental Hematology, Member of the Department of Hematology, and a tremendous scientist who was also a fierce Corvette-racing, target-shooting, blues guitar–playing lover of life. Dr. Sorrentino was born and raised in Schenectady, NY. As a teenager, he battled Hodgkin lymphoma. Late effects of the high doses of radiation therapy and chemotherapy that cured him of that childhood disease caused health complications throughout his adult life and, ultimately, the lung cancer that took him from us too soon. Dedicating himself to becoming a physician–scientist, Dr. Sorrentino attended medical school at The State University of New York Upstate Medical Center (Syracuse, NY) and completed an internship in internal medicine at the University of North Carolina (Chapel Hill, NC). In 1988, he accepted a position as a hematology-oncology fellow at the National Heart, Lung, and Blood Institute and National Cancer Institute and joined the laboratory of Dr. Arthur Nienhuis to conduct gene therapy and hematology research, a decision that would set the course for the rest of his career. In 1993, Dr. Sorrentino followed Dr. Nienhuis to St. Jude and spent the next 25 years leading his own research laboratory, which pioneered new approaches to hematopoietic stem cell (HSC) gene therapy for various diseases. He became renowned in his field and served on the Advisory Council of the American Society of Cell and Gene Therapy and various committees for the American Society of Hematology. He also chaired numerous National Institutes of Health study sections to award grant funding. Dr. Sorrentino was elected to the American Society of Clinical Investigation, and in 2005, he received the McCulloch and Till Lectureship Award from the International Society of Experimental Hematology. He served on the editorial boards of major scientific journals and held several patents on his work. During his career at St. Jude, Dr. Sorrentino developed an interest in congenital immune disorders. In a 1998 article in Nature Medicine, his group was the first to report curing an animal model of human immunodeficiency by using HSC gene therapy. When early clinical trials of gene therapy were halted because the treatment vectors caused leukemia, Dr. Sorrentino refocused his laboratory to work on ensuring the safety of gene therapeutic approaches for monogenic disorders, while also increasing their efficacy and potency. His most recent project was gene therapy for X chromosome–linked severe combined immunodeficiency (X-SCID). He and his colleagues engineered a lentiviral vector that inserts a healthy copy of the IL2RG gene into the defective HSCs obtained from patients with X-SCID. The modified cells were produced in the Children’s GMP, LLC, on the St. Jude campus and then transplanted back into the patients. Nine infants born with X-SCID received this therapy and are now producing fully functional immune cells for the first time. It is uncertain whether this reconstitution of their immune systems will endure for their lifetime; however, as of now, all the patients appear to have been cured without any immediate adverse side effects. In addition, this therapy has the potential to help children with other disorders, such as Wiskott- Aldrich syndrome and sickle cell disease. This groundbreaking work was reported in the April 18, 2019, issue of The New England Journal of Medicine. Although the reward of Dr. Sorrentino’s labor is a posthumous one, it is a remarkable stamp on the life of the man who was a colleague, mentor, and friend to so many at St. Jude and around the world.

Brian P. Sorrentino, MD 1958–2018 2019 Scientific Report | 6 7 | 2019 Scientific Report UNITING RESEARCHERS TO IMPROVE CURES AND SURVIVAL FOR CHILDREN WITH CANCER: THE ST. JUDE COMPREHENSIVE CANCER CENTER RECEIVES AN “EXCEPTIONAL” RATING FROM THE NATIONAL CANCER INSTITUTE

As the only National Cancer Institute children with the most common cancer geneticists, surgeons, (NCI)–designated Comprehensive childhood cancer, acute lymphoblastic population scientists, and many Cancer Center focused exclusively on leukemia (ALL), to more than 90%. others—to identify the most promising children, St. Jude plays a crucial role Despite these achievements, much ways to pursue new treatments and in the nation’s portfolio of Cancer work remains to be done in all areas of cures for solid tumors, hematological Centers. During the 2 most recent pediatric oncology. malignancies, and brain tumors and NCI 5-year reviews, St. Jude received Cancer is still the leading cause to minimize the long-term effects of a score of “Exceptional,” the highest- of disease-related death in children cancer and its treatments. possible ranking, placing our Center aged 1 to 14 years in the U.S., and the The Center also leads the pursuit among the nation’s elite Cancer probability of cure for many pediatric of institutional strategic plan goals Centers. cancers continues to be dismal. that guide work in precision medicine; Children with cancer are a distinct Moreover, the growing population immunotherapy; proton therapy; population. The biological anomalies of adult survivors of childhood preclinical and clinical research that cause oncogenesis in children are cancer is at risk of severe long-term infrastructure; and basic, translational, often different than those in adults, sequelae associated with their disease, and clinical research collaborations. and the resulting diseases are distinct its treatment, or both. Therefore, Finally, Center leaders and members from their adult counterparts. Thus, childhood cancer survivors need collaborate with St. Jude Global most pediatric cancers cannot be lifelong medical surveillance and new investigators and international treated in the same manner as adult interventions to improve their quality partners to expand the reach of cancers and warrant independent of life. the Center and ensure that our research that specifically addresses To advance research, treatment, discoveries benefit countless patients the features of those diseases. Under and cures of childhood cancer, the and survivors of childhood cancer the direction of Charles W. M. Roberts, Center provides an overarching worldwide. MD, PhD, the St. Jude Comprehensive strategic vision and scientific direction, Cancer Center is leading the nation in a robust collaborative framework, these efforts. state-of-the-art shared resources, and Throughout its history, St. Jude an administrative hub that supports has directly contributed to seminal its members in making scientific advances in pediatric oncology. Work breakthroughs. The Center is designed from the Center has helped increase to bring together investigators the overall survival of children with with diverse expertise—oncologists, cancer to more than 80% and for pathologists, molecular biologists,

2019 Scientific Report | 8 9 | 2019 Scientific Report What is a Cancer Center? The NCI is the primary federal funding agency for cancer research in the U.S. Its Cancer Center Support Grant is awarded to institutions to recognize and support their scientific leadership, resources, and cancer-focused research in basic, clinical, and/or population science. Comprehensive Cancer Centers demonstrate an added depth and breadth of research, as well as substantial transdisciplinary research that bridges these scientific areas. Cancer Centers must also provide cancer-related professional training and community outreach activities. St. Jude plays a crucial role in the nation’s portfolio of 70 Cancer Centers, which includes 49 Comprehensive Cancer Centers, by advancing research and cures designed specifically for pediatric patients. St. Jude was designated an NCI Cancer Center in 1977 and was named a Comprehensive Cancer Center in 2008. Today, the Center includes laboratory-based and clinical faculty members working in 5 interactive research programs headed by program co-leaders; a dedicated administrative team; and directors, staff scientists, and technologists working in 9 NCI-funded shared resources that support research activities. (See p. 90 for details.) The Center also oversees strategic initiatives and the clinical trials enterprise for St. Jude. Dr. Roberts is assisted in leading the overarching direction of the Cancer Center by Deputy Director Charles G. Mullighan, MBBS, MD, and a senior leadership team of 8 Associate Directors who oversee Administration (Dana Wallace), Shared Resources (James I. Morgan, PhD), Basic Science (Suzanne J. Baker, PhD), Clinical Research (Victor M. Santana, MD), Population Sciences (Leslie Charles G. Mullighan, MBBS, MD; Charles W. M. Roberts, MD, PhD L. Robison, PhD), Outreach (Carlos Rodriguez-Galindo, MD), and Education & Training (Gerard P. Zambetti, PhD).

2019 Scientific Report | 10 11 | 2019 Scientific Report INCREASED PUBLICATIONS IN JOURNALS WITH THE HIGHEST IMPACT FACTORS In the recent vs. previous 5-Year Review Period CELL +360%

NATURE SCIENCE +23% +40%

Dana Wallace, Charles W. M. Roberts, MD, PhD THE NEW ENGLAND NATURE Scientific leadership, extensive The Center supports 5 multi- JOURNAL OF GENETICS Driving resources, and accomplished research disciplinary research programs. The MEDICINE in basic, clinical, and/or population Cancer Biology Program is engaged Transdisciplinary science distinguish the 70 NCI- primarily in laboratory-based research. Collaborations designated Cancer Centers from other Three disease-focused programs, +700% +163% research institutions in the U.S. The Developmental Biology & Solid primary function of the Center is to Tumor, Hematological Malignancies, drive transdisciplinary collaboration and Neurobiology & Brain Tumor, by bringing together diverse clinicians translate fundamental discoveries and scientists from across the into curative therapies. The Cancer NATURE institution, the country, and the globe. Control & Survivorship Program The Center also oversees the St. Jude assesses adverse effects of childhood MEDICINE clinical research enterprise, which cancer and treatment to improve the treats patients in clinical trials both at quality of life of long-term survivors of St. Jude and through the St. Jude childhood cancer. Brief descriptions of Affiliate Program comprising 8 clinics. the 5 Center programs and examples +200% (See p. 88 for details.) The Center of their recent achievements are additionally provides educational described in the following pages. opportunities about cancer and healthy living to the community CANCER CELL TOTAL and educates and trains the next generation of pediatric cancer PUBLICATIONS researchers. +55% 2290 Reprinted by permission from SNCSC GmbH:, Nature Immunology, 16, 2. © 2015 Nature Springer. Reprinted from Cell Stem Cell, vol 17/1. © 2015; Molecular Cell, vol. 62/4. © 2016; and Stem Cell Reports, vol. 10/8. © 2018, all with permission from Elsevier. 2019 Scientific Report | 12 13 | 2019 Scientific Report Establishing the Genomic and cancer study of pediatric cancers. The term Epigenomic Landscape of Pediatric “pan-cancer” indicates that multiple types of Cancer cancer, regardless of the cell of origin or tissue Cancer arises from DNA mutations, epigenetic in which they initiated, were included in the alterations, or a combination thereof. analysis. The team integrated whole-genome, To understand the fundamental driving -exome, and -transcriptome sequencing to mechanisms of pediatric cancers, Jinghui identify somatic alterations in 1699 pediatric Zhang, PhD (Computational Biology), led a leukemias and solid tumors. The findings, team of cancer biologists and computational published in Nature, demonstrated that most biologists in pioneering next-generation alterations were unique to pediatric cancer approaches to detailed analyses of pediatric and underscore the need to develop precision cancer genomes and epigenomes. This work therapies designed specifically for pediatric was initiated in 2010 through the St. Jude cancers. (See p. 97 for details.) Children’s Research Hospital—Washington Genomic discoveries and their integration University Pediatric Cancer Genome Project. into clinical care continue at a rapid pace; More recently, members of 3 programs every eligible St. Jude patient with cancer (Cancer Biology, Hematological Malignancies, is now offered clinical whole-genome and Neurobiology & Brain Tumor) identified sequencing. An innovative data-sharing germline mutations in cancer-predisposition platform, St. Jude Cloud (www.stjude.cloud), genes in 8.5% of children and adolescents was launched in April 2018 to provide genomic with pediatric cancers. Published in The datasets, analysis tools, and visualizations to New England Journal of Medicine, this work the global research community. The platform, demonstrates the importance of genetic a collaboration with Microsoft and DNAnexus, counseling in this population and has shaped currently offers more than 10,000 whole- the development of the St. Jude Cancer genome sequences from pediatric patients Douglas R. Green, PhD; Martine F. Roussel, PhD Predisposition Program, which is led by Kim with cancer and childhood cancer survivors. E. Nichols, MD (Oncology). To date, it has 800 registered users from 400 The primary goal of the Cancer Biology control, identify genetic mutations In 2018, Dr. Zhang’s team led a pan- institutions around the world. Cancer Program is to explore and understand and anomalies as new therapeutic the biology of cancer cells. The diverse targets for translation into clinical Biology nature of pediatric cancers and the trials, and advance our understanding Program complex molecular, genetic, and of the cancer microenvironment. To developmental contexts in which they address unmet needs and maximize form necessitate a broad spectrum opportunities for translation, research of basic research to build a strong in this Program spans 4 areas: signaling foundation. Basic science discoveries networks and therapeutics; cell stress, have driven numerous key advances in repair, metabolism, and death; tumor our understanding and treatment of microenvironment and immunology; pediatric cancers. and genome structure and function. The Program leads integrated, Here, we describe advances made in multidisciplinary efforts to define 2 of these key areas. pathways related to cancer and its

Kim E. Nichols, MD; James R. Downing, MD; Jinghui Zhang, PhD

2019 Scientific Report | 14 15 | 2019 Scientific Report Tumor Immunology and autophagy pathway, LC3-associated Immunotherapy phagocytosis (LAP), in the myeloid response to Although cancer cells evolve mechanisms to dying cells. A recent collaborative study led by escape immune surveillance, experimental Drs. Green and Opferman and Charles Gawad, manipulation of the immune system has MD, PhD (Oncology, Computational Biology), the potential to deliver substantial tumor- in Cell, showed that LAP influences anticancer killing benefits. Efforts in the Program have T-cell responses and inhibits anticancer provided fundamental insights into the immunity. Targeting LAP-specific proteins may, immune system’s ability to regulate cancer therefore, be a promising therapeutic strategy and effective approaches to exploit metabolic that will not interfere with the canonical events to generate an antitumor response. autophagy processes that are important for These studies represent ongoing collaborative tumor suppression. efforts among the laboratories of Hongbo The Program has also made strides Chi, PhD (Immunology), Thirumala-Devi toward understanding the molecular basis of Kanneganti, PhD (Immunology), Joseph T. inflammation, a key process in tumorigenesis. Opferman, PhD (Cell & Molecular Biology), and Dr. Kanneganti has led multiple studies Program Co-Leaders Douglas R. Green, PhD on the inflammasome, a protein complex (Immunology), and Martine F. Roussel, PhD involved in restricting the immune response (Tumor Cell Biology). to microbial challenges and tumorigenesis. In Science Immunology, Dr. Chi and In Gastroenterology, her team reported that colleagues recently reported that the the sensor protein pyrin, which initiates the integration of metabolic and signaling assembly of the inflammasome complex, pathways dictates lineage choices for T cells. protects against colon inflammation They found that metabolic processes guide and tumorigenesis in mice. Furthermore, the fate of immune cells. Signaling pathways work published in The Journal of Clinical affecting metabolism are essential to the Investigation identified tumor necrosis factor developmental fate of not only T lymphocytes as a critical modulator of pyrin expression and but also dendritic cells, which are crucial inflammasome activation. These studies point for stimulating T cells and guiding their to pyrin and its regulators as potential targets differentiation, as Dr. Chi’s team reported in for therapeutic intervention. Collectively, Nature. (See p. 103 for details.) these and other key mechanistic insights Collaborative studies on macrophage have contributed to the foundation for our activity in the tumor microenvironment have rapidly expanding translational efforts in revealed an important role for a noncanonical immunotherapy.

R. K. Subbarao Malireddi, PhD; Thirumala-Devi Kanneganti, PhD

Joseph T. Opferman, PhD; Douglas R. Green, PhD; Charles Gawad, MD, PhD

2019 Scientific Report | 16 17 | 2019 Scientific Report Developmental Origins and To hasten progress in pediatric solid tumor Therapeutic Approaches to research, all O-PDXs and their associated data Rhabdomyosarcoma are freely shared with researchers around the Rhabdomyosarcoma (RMS) is the most world through the CSTN, with no obligation to common soft-tissue cancer in children. collaborate. To date, 507 requests for O-PDXs Histologically, these tumors resemble have been received from 200 investigators embryonic skeletal muscle and have been working at 99 institutions in 16 countries. thought to arise from that tissue, but they The O-PDXs have enabled crucial insights can also arise in sites devoid of skeletal that are driving innovative clinical studies muscle. Mark E. Hatley, MD, PhD (Oncology), in RMS and other solid tumors. For example, recently found that cellular reprogramming work in these models identified an inhibitor of nonmyogenic cells can also lead to RMS, of the signaling kinase WEE1 as a promising demonstrating the disease’s diverse origins. therapeutic agent. In Cancer Cell, Elizabeth (See p. 105 for details.) A. Stewart, MD, Sara M. Federico, MD (both of A major barrier to developing new Oncology), and their colleagues reported the therapies for solid tumors has been the lack of most comprehensive analysis to date of RMS preclinical models that accurately recapitulate that integrated transcriptomic, epigenomic, human disease and predict clinical responses and proteomic/phosphoproteomic data to to novel therapeutics. The Program launched a elucidate the cellular origins and therapeutic large-scale effort to develop better preclinical vulnerabilities of the disease. RMS has 2 models, with a focus on orthotopic patient- major histologic subtypes: alveolar RMS and derived xenografts (O-PDXs). This led to the embryonic RMS. Dr. Stewart’s team found that development of the Childhood Solid Tumor alveolar RMS, which is the more aggressive Network (CSTN; www.stjude.org/CSTN). Since subtype, arises at a later stage in the the CSTN was established, 498 patients have developmental program than does embryonal donated surplus tumor tissue, resulting in the RMS. Their comprehensive preclinical testing successful generation of 201 independent also revealed that targeting WEE1 is the most

Alberto S. Pappo, MD; Michael A. Dyer, PhD xenografts that represent 27 tumor types. effective approach to treating high-risk RMS All models have undergone comprehensive in vivo. These results prompted the Children’s Some of the most devastating, poorly The Developmental Biology & Solid genomic and epigenomic analyses, including Oncology Group to expand their multicenter Developmental understood cancers that affect Tumor Program aims to improve the whole-genome and whole-exome sequencing, Phase I/II clinical trial of the WEE1 inhibitor children arise in the peripheral nervous survival and quality of life of children RNA-sequencing, and whole-genome AZD1775 and the chemotherapy agent Biology & Solid system, muscles, or bones. Despite with solid tumors by integrating basic, bisulfite sequencing; approximately half irinotecan to include pediatric patients with Tumor Program recent advances in genomics that translational, and clinical research. The of the models have undergone chromatin high-risk RMS. have enabled us to better understand Program has 4 working groups focused immunoprecipitation sequencing analysis. the etiology of pediatric solid tumors, on recurrent disease, immunotherapy, the overall survival of children and rare tumors, and precision medicine. adolescents with high-risk or recurrent Here, we present recent advances in disease has not improved in more than elucidating the developmental origins 20 years. This lag in improved cure of pediatric solid tumors, developing rates reflects the heterogeneity and unique preclinical resources and relative rarity of pediatric solid tumors. research pipelines, and identifying promising new therapeutic approaches.

Sara M. Federico, MD; Elizabeth A. Stewart, MD

2019 Scientific Report | 18 19 | 2019 Scientific Report Precision Therapy for Tumors this study were combined with those from a Bearing a TRK Fusion Oncogene Phase I study on adults and a Phase II study on Gene fusions involving NTRK1, NTRK2, or NTRK3 adolescents and adults and published in The (TRK fusions) are found in several childhood New England Journal of Medicine. The cohort and adult tumors. In 2018, a large multicenter included 55 patients (aged 4 months–76 trial testing the TRK inhibitor larotrectinib as a years) with 17 unique TRK fusion–positive new precision therapy for TRK-bearing tumors tumors, and 75% of the tumors responded to was completed. Collaborating with Theodore the drug. Larotrectinib was well tolerated, and Laestch (University of Texas Southwestern 30 (55%) patients remained progression-free Medical Center) and David Hyman (Memorial after 1 year. As a result of these studies, the Sloan Kettering), Program Co-Leader Alberto U.S. Food and Drug Administration approved S. Pappo, MD (Oncology), served as the larotrectinib as the first targeted, oral, tumor- St. Jude investigator on the landmark Phase agnostic therapy. Tumor-agnostic therapy I/II trial of larotrectinib. is defined as immunotherapy that attacks In The Lancet Oncology, the investigators any type of cancer that arises in any location, demonstrated that larotrectinib was well as long as the tumor cells have a specific tolerated by pediatric patients and showed molecular anomaly (e.g., TRK fusion) that is impressive antitumor activity in all patients targeted by the drug. with TRK fusion–positive tumors. Results from

Alberto S. Pappo, MD; Armita Bahrami, MD

2019 Scientific Report | 20 21 | 2019 Scientific Report A Genomic Portrait of Acute Mixed-phenotype acute leukemia (MPAL) Lymphoblastic Leukemia is a rare, difficult-to-treat subtype that ALL includes a spectrum of disease subtypes includes features of both ALL and acute with distinct mutations. Program Co-Leader myeloid leukemia. By integrating genome Charles G. Mullighan, MBBS, MD (Pathology), sequencing, experimental modeling, and and colleagues have conducted multiple tumor xenografting, Dr. Mullighan and in-depth genomic investigations of ALL and colleagues identified the genetic alterations defined numerous novel disease subtypes that define the most prevalent subtypes of and mechanisms of pathogenesis. Recently, MPAL. (See p. 101 for details.) Their findings, this work has contributed to the molecular published in Nature, are now being tested in reclassification of ALL in the revised World clinical trials of MPAL that are determining Health Organization guidelines. It has also whether disease subtype and treatment provided the basis for using targeted agents response can be correlated with the genetic in precision medicine trials, including the features of leukemic cells. ongoing St. Jude Total Therapy 17 clinical To promote research on leukemia biology trial for newly diagnosed ALL, which is led and help develop more effective cures, the by Hiroto Inaba, MD, PhD (Oncology). Program launched the Public Resource of Genomic discovery studies continue to Patient-derived and Expanded Leukemias accelerate. Earlier this year in Nature Genetics, (PROPEL; www.stjude.org/PROPEL) in 2018. Dr. Mullighan’s team reported their integrated PROPEL is a St. Jude–hosted resource for genomic analysis of 1988 pediatric and adult sharing unique patient-derived xenografts cases of B-progenitor ALL, thereby revising (PDXs) from patients with B- or T-lineage the classification of ALL to comprise at ALL, acute myeloid leukemia, or relapsed least 23 genetically distinct subtypes. This leukemia. In addition, PROPEL provides a tool comprehensive sequencing approach enabled with which to explore genomic data from the researchers to not only identify new both the PDXs and matched primary patient subtypes but also demonstrate the samples. This information is freely shared

Ching-Hon Pui, MD: Charles G. Mullighan, MBBS, MD power of transcriptome sequencing for with researchers around the world, with no guiding classification, risk stratification, and obligation to collaborate. Currently, PROPEL Hematological malignancies remain sparked innovative precision medicine tailored therapy. contains approximately 250 samples of adult Hematological a leading cause of cancer-related studies and therapeutic strategies. and pediatric leukemias and continues to grow death in children, despite therapeutic Program accomplishments have had with the addition of other subtypes of leukemia. Malignancies advances that have improved a global impact on the diagnosis, Program outcomes. The Hematological classification, and treatment of various Malignancies Program aims to improve hematological malignancies. the cure of childhood leukemias Research in the Program and lymphomas, while minimizing encompasses common and rare treatment-related adverse effects. childhood leukemias and lymphomas This highly interactive, and ranges from defining molecular transdisciplinary Program has a long taxonomy to experimental record of major discoveries in cancer modeling, preclinical studies, biology and treatment. The translation pharmacogenomics, and clinical trial of fundamental discoveries on the development. Here, we focus on recent genetic basis of leukemogenesis advances in our understanding of and treatment-related toxicities the molecular basis of ALL, the most into new diagnostic and treatment common childhood malignancy. approaches has changed the standard of care for children with hematological malignancies and

Hiroto Inaba, MD, PhD

2019 Scientific Report | 22 23 | 2019 Scientific Report Predisposition to Acute nonsilent TP53-coding variants, 22 of which Lymphoblastic Leukemia were predicted to be pathogenic. Children Growing evidence indicates that germline carrying TP53 pathogenic variants had poorer genetics influence the development of ALL, survival and a substantially higher risk of which was once regarded as a nonhereditary subsequent cancers. This study confirms the disease. For example, the IKZF1 gene, a known importance of TP53 in ALL development and somatic driver of high-risk ALL, is mutated in treatment response. Germline mutations families in which multiple members have ALL in TP53 also have implications for family and in patients with ALL with no known family members, who are now being screened for history. This work was published in Cancer this cancer-susceptibility gene through the Cell. After identifying 2 members of the same St. Jude Cancer Predisposition Program family with B-progenitor ALL and an IKZF1- to enable early diagnosis of cancer among truncating mutation, the team conducted siblings and parents. This work was published targeted sequencing of 4963 childhood ALL in the Journal of Clinical Oncology. samples. They found 28 unique predisposing Taking a more agnostic approach, Dr. Yang germline variants in 45 children, thereby and colleagues conducted genome-wide establishing IKZF1 as an ALL-predisposition association studies to seek novel ALL- gene and further emphasizing the importance susceptibility loci in Hispanic individuals who of heredity in ALL development. have a high proportion of Native American In another targeted sequencing study, Jun ancestry and an elevated risk of ALL and J. Yang, PhD (Pharmaceutical Sciences), and his poorer outcome. In the journal Blood, the team team followed up prior work from St. Jude that reported that the ERG gene is a novel ALL risk showed TP53 germline variants are common locus that correlates with Native American in childhood hypodiploid ALL. By conducting ancestry and is enriched in certain ALL targeted germline sequencing of TP53-coding subtypes. Thus, ERG has been added to the regions in DNA samples from 3801 children growing list of genetic factors that contribute with ALL, the researchers identified 49 unique, to racial/ethnic disparities in ALL.

WITHIN 30 DAYS OF A CANCER DIAGNOSIS, 90% OF PATIENTS ENROLL IN A CLINICAL TRIAL; 60% ENROLL IN A THERAPEUTIC TRIAL. In the recent vs. previous 5-Year Review Period NEW PATIENTS INTERNATIONAL PATIENTS ENROLLED WITH CANCER PATIENTS WITH ON THERAPEUTIC CANCER TRIALS +9% +30% +40%

Jun J. Yang, PhD

2019 Scientific Report | 24 25 | 2019 Scientific Report Modeling an Incurable Tumor: inducible H3 K27M mutation. In Cancer Cell, Diffuse Intrinsic Pontine Glioma they reported that the K27M-dependent, In 2012, Program Co-Leader Suzanne J. Baker, genome-wide decrease in H3K27me3 causes PhD (Developmental Neurobiology), and a selective increase in neurodevelopmental Cancer Biology Program member Dr. Zhang gene expression by releasing the epigenetic discovered recurrent histone H3 mutations regulation of poised promoters. The K27M in diffuse intrinsic pontine glioma (DIPG), mutation enhances the self-renewal of neural an incurable tumor of the brainstem, and in stem cells, which could expand the pool of pediatric high-grade gliomas. As a result, the cells susceptible to malignant transformation. histone H3 K27M mutation was defined as a Expression of the K27M mutation throughout molecular hallmark of DIPG, and an essential the central nervous system (CNS), combined connection between histone regulation and with DIPG-associated mutations in the Trp53 DIPG was revealed. and PDGFRaα genes, selectively accelerated To determine how the H3 K27M mutation tumorigenesis in the brainstem. Thus, these drives oncogenesis and why mutations in murine models revealed novel epigenetic this histone selectively drive gliomas in the contributions to DIPG pathogenesis developing brainstem, Dr. Baker and colleagues and will enable detailed studies of genetically engineered mice carrying an therapeutic response.

Suzanne J. Baker, PhD; Amar J. Gajjar, MD

Despite rapid advances in our Pediatric brain tumors arise during Neurobiology understanding of the biology of development; thus, the Program brain tumors, these diseases remain addresses regulatory mechanisms & Brain Tumor the leading cause of cancer-related that affect normal growth and Program death in children. Current treatment tumorigenic growth in the developing approaches are lacking for some brain. Program members continue to patients and lead to long-term investigate neural development, tumor debilitating side effects for others. cells of origin, key pathways that drive The Neurobiology & Brain Tumor tumorigenesis, and the epigenetic Program aims to improve survival landscape of brain tumors. Genome- and morbidity of children with brain wide studies of the major pediatric tumors by developing effective, brain tumor types have identified relatively nontoxic therapies through novel mutations, defined molecular a better understanding of disease subgroups, and opened new avenues pathogenesis. By integrating the latest of basic, translational, and clinical genomic and genetic technologies investigation. Furthermore, advances with studies of the developing nervous in the fields of molecular pathology, system, members of this Program are imaging, and radiation oncology hold translating laboratory findings into promise for advancing the treatment opportunities for new treatments. of these formidable diseases. Here we present recent advances made in 3 types of pediatric brain tumors.

Jon Larson, PhD; Lawryn Kasper, PhD; Suzanne J. Baker, PhD

2019 Scientific Report | 26 27 | 2019 Scientific Report Molecular Characterization of Brain Hopp Children’s Cancer Center (Heidelberg, Tumors Guides Treatment Germany) and The Hospital for Sick Children Medulloblastoma is the most common CNS (Toronto, Canada). Using whole-genome tumor of childhood. It includes 4 molecular and whole-exome sequencing, the teams subtypes (SHH, WNT, Group 3, and Group 4), assessed the prevalence of rare variants in 110 and each subtype has a distinct biology and cancer-predisposition genes in 1022 patients treatment outcome. Work by the Program has with medulloblastoma. This study, which been instrumental in further characterizing also appeared in The Lancet Oncology, is the medulloblastoma subtypes and identifying the largest to date on genetic predisposition to a contribution of germline predisposition to single pediatric brain tumor entity. The team the disease. discovered that genetic predisposition plays Children younger than 3 years at the a major role in causing medulloblastoma, time of diagnosis of medulloblastoma particularly in patients with the WNT or often have poorer overall survival, because SHH subtype. They also identified APC, radiation therapy must be delayed or the dose BRCA2, TP53, PALB2, PTCH1, and SUFU as key reduced to avoid debilitating side effects on medulloblastoma-predisposition genes. These the developing brain. A multicenter Phase II results indicate an urgent need to provide clinical trial (SJYC07) led by Giles W. Robinson, genetic counseling and testing for patients MD (Oncology), Program Co-Leader Amar with WNT or SHH medulloblastoma. J. Gajjar, MD (Pediatric Medicine, Oncology), Ependymomas are neuroepithelial tumors and Paul A. Northcott, PhD (Developmental of the CNS. They represent nearly 10% of all Neurobiology), used a risk-stratified treatment pediatric CNS tumors and about 30% of CNS strategy that omitted or minimized radiation tumors in children younger than 3 years. exposure in 81 patients younger than 3 years Comprehensive DNA-methylation profiling with medulloblastoma. The findings, published led by the Program has demonstrated distinct in The Lancet Oncology, support the pursuit of molecular groups of ependymoma and refined a molecularly driven, risk-adapted approach for approaches to disease classification, but these treating young children with medulloblastoma. developments have yet to be incorporated (See p. 96 for details.) into standard clinical practice. In Acta Historically, most medulloblastomas Neuropathologica, David W. Ellison, MD, PhD were thought to arise sporadically. A (Pathology), and colleagues characterized the team led by Drs. Gajjar, Northcott, and molecular heterogeneity in posterior fossa Robinson challenged this long-held belief type A ependymomas, revealing a role for a in collaboration with investigators at the previously uncharacterized gene, CXorf67. (See p. 112 for details.)

INCREASED FUNDING OF CANCER CENTER RESEARCH In the recent vs. previous 5-Year Review Period PEER-REVIEWED NCI FUNDING FUNDING

+13% +9% Giles W. Robinson, MD

2019 Scientific Report | 28 29 | 2019 Scientific Report Identifying Genetic Risk Factors for toxicity to cells and tissues. However, St. Jude Late Effects of Treatment is helping to pioneer a relatively nascent Some childhood cancer survivors fare better area of investigation—financial toxicity faced than others, even among those who had by childhood cancer survivors. The term similar diagnoses and completed comparable “financial toxicity” is used to describe problems therapeutic regimens. However, the way in experienced by cancer survivors resulting which survivors’ genetic makeup influences from the financial implications of receiving their long-term health outcomes has been a diagnosis and subsequent medical care poorly understood. In 2018, Dr. Zhang and for cancer. A team led by I-Chan Huang, PhD Program Co-Leader Leslie L. Robison, PhD (Epidemiology & Cancer Control), assessed 3 (Epidemiology & Cancer Control), led a study domains of financial hardship (i.e., material, of whole-genome sequencing of germline psychological, and coping/behavioral) in 2811 DNA from more than 3000 pediatric cancer long-term survivors in the SJLIFE cohort. survivors participating in the SJLIFE study. The majority (65%) of survivors reported This first-in-kind initiative was designed to hardship in at least 1 domain, with higher risks enable integrated analyses of genomic data found in middle-aged survivors (40 years or and comprehensive clinical data to identify older) versus younger survivors (18–39 years). new genetic risk factors for late effects of Depressive symptoms and suicidal ideation treatment, such as second neoplasms. This were associated with all 3 hardship domains. work was published in the Journal of Clinical This work was published in the Journal of Oncology. (See p. 110 for details.) the National Cancer Institute. The discovery that financial hardship is widespread among Understanding Financial Toxicity in childhood cancer survivors emphasizes the Childhood Cancer Survivors importance of systematically addressing the Minimizing the toxicity of anticancer therapy impact of health policies on survivors and is generally considered only in terms of developing strategies for early detection and intervention.

Melissa M. Hudson, MD; Leslie L. Robison, PhD

As treatments for childhood cancers This Program, which spans the Cancer Control improve, the number of long-term breadth of epidemiological, clinical, survivors in the U.S. is expected to and interventional research, has & Survivorship surpass 500,000 by the end of 2019. defined the landscape of childhood Program The Cancer Control & Survivorship cancer survivorship, influenced the Program conducts research to reduce design of contemporary pediatric treatment-related complications and cancer treatment strategies, and improve the long-term outcomes and provided crucial data to guide quality of life of individuals surviving surveillance and health-preserving childhood cancer. Two unique survivor interventions for survivors. Efforts to cohorts, the Childhood Cancer Survivor characterize the challenges faced by Study (CCSS) and the St. Jude Lifetime childhood cancer survivors and design Cohort Study (SJLIFE), include more effective interventions are a major than 40,000 participants who have ongoing focus. survived childhood cancer for at least 5 years after completion of therapy.

I-Chan Huang, PhD

2019 Scientific Report | 30 31 | 2019 Scientific Report AS THE ONLY NCI-DESIGNATED CANCER CENTER DEVOTED TO PEDIATRICS, WE HAVE AN OBLIGATION TO USE OUR TALENT AND RESOURCES TO ADVANCE CURES FOR PEDIATRIC CANCER WORLDWIDE.

Charles W. M. Roberts, MD, PhD

Every 5 years, the Center must reapply NCI review, the Center’s total peer- With the arrival of Dr. Roberts in Looking ahead, the Center will Measures of for funding and formal designation reviewed funding (i.e., federal and Looking 2015, the Center developed a new advance this vision through large- as a Comprehensive Cancer Center. private foundation awards) to support vision to bring about a new era of scale strategic initiatives, build on its Success of an For the recent renewal, Center cancer research increased by 13%. Ahead precision therapies and cures for strong foundation of transdisciplinary Exceptional administrative staff, shared resources The NCI awarded the Center its children with pediatric cancer via collaboration, and serve as a model directors, and leadership spent more second consecutive highest-possible pursuit of discoveries in epigenetics, for pediatric cancer research and Center than 18 months writing the 2300-page “Exceptional” ranking and the best genomics, and immunotherapy. To treatment across the globe. application. In May 2018, a panel of numerical score in the Center’s realize this vision, the Center is tapping 20 reviewers representing the NCI history. NCI reviewers referred to into the remarkable intellectual and conducted a site visit of the Center. St. Jude as a “national treasure,” philanthropic resources of St. Jude Dozens of examples of scientific invoking our remarkable success in to engage leading experts within the achievements across the Center translating science into advances Center and beyond in the fight against were presented. These included for the benefit of pediatric patients childhood cancer. an increase in the number of peer- with cancer everywhere. Exceptional reviewed publications, including a marks were also awarded to all 6 of the 27% increase in the number of articles essential characteristics of a Cancer published in scientific journals with Center: physical space, organizational an impact factor greater than 10 capabilities, transdisciplinary since the last NCI review. The Center collaboration and coordination, cancer also saw substantially more patients focus, institutional commitment, and with new diagnoses; accruals to the Center Director. The outcome of therapeutic clinical trials increased by the 2018 NCI review further reinforces 9%. Within 30 days of diagnosis, 90% the position of St. Jude, the only NCI- of new patients with cancer enrolled designated Cancer Center dedicated in a clinical trial; 60% enrolled in a solely to children, as one of the nation’s therapeutic trial. Finally, since the last elite Cancer Centers.

2019 Scientific Report | 32 33 | 2019 Scientific Report THE STRUCTURAL BIOLOGY DEPARTMENT EXPANDS TO BECOME THE WORLD’S PREMIER CENTER FOR STRUCTURAL ANALYSES AND IMAGING OF BIOMOLECULES

Biomolecules are dynamic; changes addition, complementary techniques discovery campaigns. Crystallographic in their 3-dimensional (3D) shape are used to probe specific details structure determination of targets endow them with an array of of biomolecular mechanisms. in complex with ligands is the gold activities. Proteins are the main class These include mass spectrometry, standard in drug discovery, facilitating of biomolecules in our bodies; they which reveals changes in the rational design and iterative chemical perform functions that make life composition and stoichiometry of synthesis and testing. Cryo-EM/TM possible. Proteins come in a range of protein complexes; single-molecule has great potential for enabling drug shapes and sizes and possess distinct imaging techniques, which monitor discovery for difficult targets, such as capabilities. Understanding how the structure and movement of membrane proteins that are difficult structural changes in proteins impart specific parts of biomolecules; and to visualize with other techniques. function is, therefore, fundamental computational simulations, which Some drug targets of interest to St. Jude to all biology, whether in health or use powerful computers to study investigators in structural biology disease. Providing this understanding the motions that occur when include kinases, E3 ligases, protein– is the task of structural biologists. biomolecules function. protein interactions, proteins involved Structural biologists use In catastrophic diseases, the in programmed cell death, essential sophisticated instruments to functions of biomolecules are altered. bacterial enzymes, ribosomes, and elucidate protein structures at the Structural biologists examine the various membrane proteins. highest (atomic) resolution to study structural basis for such functional their functions and understand alterations to gain insights into how abnormal proteins give rise to new therapeutic strategies. This diseases. Three frontline techniques can occur, for instance, through the are used to examine biomolecular generation of new drugs that are able structures: cryogenic electron to counteract disease by targeting microscopy and tomography deleterious alterations in the activities (cryo-EM/TM), nuclear magnetic of proteins and other biomolecules. resonance (NMR) spectroscopy, and The Department of Structural Biology X-ray crystallography. Each of these has built an infrastructure to not only techniques has unique strengths and elucidate biomolecular structures limitations, and structural biologists fundamental to health and disease often must integrate the results from but also enable the drug-discovery different techniques to fully visualize process at every step. For instance, and understand the structures of NMR-based binding screens can be complex biomolecular systems used to identify the ligands of any (e.g., multicomponent assemblies macromolecule assembly, irrespective and macromolecular machines). In of shape and size, to spearhead drug-

2019 Scientific Report | 34 35 | 2019 Scientific Report Structures are blueprints for developing nanometers; and large-scale domain motions hypotheses about biomolecular functions can take milliseconds to seconds and are that can be tested using genetic, biochemical, measured in tens of nanometers. The and cell biological approaches. However, techniques used to study these processes to fully understand function in detail, depend on the time scale and extent of the structural biologists need to examine the structural change. Cryo-EM/TM and X-ray movement of biomolecules, which is termed crystallography can distinguish biomolecular protein dynamics. Proteins are not static conformations but typically not the movement objects; they are rapidly changing molecules that gives rise to them. NMR spectroscopy is that move, bend, expand, and contract. particularly adept at determining the time Without such motions, many proteins and scale and amplitude of molecular movements. nucleic acids cannot function properly. The Single-molecule fluorescence imaging overarching goal of structural biology is captures individual molecules in different to elucidate all conformations needed for states, thereby enabling us to understand how a biomolecule to function and determine an interconversion occurs. how those conformations interconvert and No individual technique provides all the how this interconversion between structural information needed to understand structure conformations leads to biological functions. and activity, which is why structural biologists Structural changes in proteins and other must integrate results from comprehensive biomolecules span orders of magnitude analyses of protein structure and dynamics in time and space. For example, methyl acquired using multiple methods. By deploying sidechain rotations take picoseconds and and actively developing the wide range of lead to changes measured in angstroms; sophisticated techniques available, St. Jude different conformations of intrinsically has positioned itself at the forefront of disordered proteins occur in nanoseconds the emergent field of integrative to microseconds and are measured in structural biology.

The Department of Structural Biology has expanded to join premier Building research centers and aspires to become the top center for imaging and biophysical modalities, enabling St. Jude researchers to Cutting-Edge examine intricate cellular processes at the atomic level. Department Structural Chair Charalampos Babis Kalodimos, PhD, a world-renowned structural biologist, is directing this effort by recruiting world Biology leaders in structural biology to join the St. Jude faculty and bringing innovative technologies to the St. Jude campus. The department Technologies has created 6 centers: Cryo–EM/TM, NMR Spectroscopy, X-ray Crystallography, Single-Molecule Imaging, Mass Spectroscopy, at St. Jude and Protein Technologies. Researchers working in these centers will engage in cutting-edge structural biology research, and the Protein Technologies Center will facilitate collaborations between the department and St. Jude investigators working in other fields. Here we describe the technologic capabilities of those centers and STRUCTURES ARE BLUEPRINTS FOR introduce the scientists working in them. DEVELOPING HYPOTHESES ABOUT BIOMOLECULAR FUNCTIONS IN HEALTH AND DISEASE.

2019 Scientific Report | 36 37 | 2019 Scientific Report tomography (cryo-TM), also uses cryogenic houses all essential auxiliary equipment for methods for sample preparation and electron sample preparation, including a Vitrobot Mark microscopy methods for image acquisition, IV, a Solarus II plasma cleaner, and a carbon but cryo-TM includes added tomographic- coater. The Center plans to expand into cryo– reconstruction methods to reveal 3D correlative light and electron microscopy for structures of cells and tissues. This makes it high-resolution imaging of cells and tissues. possible to visualize structures of biological Cryo-EM experiments generate molecules in their native cellular environment. several terabytes of imaging data per day Thus, recent advances in cryo-EM/TM are per instrument. The images need to be transforming many life science and processed to generate a 3D map of the biomedical disciplines. biomolecule being studied, which requires Last year, St. Jude recruited Mario Halic, high-performance computing. The Center is PhD, a prominent leader in the field, to supported by state-of-the-art computational establish a preeminent research program in resources, including a dedicated cluster with cryo-EM. Dr. Halic’s research combines cryo- hundreds of computing central-processing EM, biochemistry, and genetics to determine units and a range of high-performance how enzymes and structural proteins modify computing facilities available at the St. Jude nucleosome and chromatin structure. Data Center. In so doing, he is defining the molecular The Center is committed to delivering mechanisms that recognize specific genetic the latest technology to the broader research elements and target them for epigenetic community at St. Jude. Its goal is to enable silencing by heterochromatin, a specialized researchers to visualize intricate biological silent chromatin structure. Furthermore, structures at atomic or near-atomic resolution Dr. Halic’s laboratory uses structural methods and cellular structures in their native context to understand how heterochromatic proteins with unprecedented detail and clarity. recognize and modify chromatin to establish The Center is opening avenues to various this silent state. His long-term goals are applications in basic and translational research

Mario Halic, PhD to understand the regulation of genome and is expected to have an immediate, expression by chromatin and discover why substantial impact on drug-discovery and In cryo-EM, biological samples are cameras. These detectors have mutations in chromatin proteins lead to the biomedical research at St. Jude. Cryo–Electron rapidly frozen to the solid state in a superior signal-to-noise performance, formation of cancer cells. manner that prevents dehydration making it possible to generate The Cryo-EM/TM Center at St. Jude has Microscopy and and ice crystallization. Biomolecules in images with unprecedented clarity capabilities to perform single-particle cryo-EM Tomography aqueous solutions are blotted to a thin and extract structural information and cryo-TM. Under the direction of Liang layer and plunged into liquid ethane of the finest detail. These advances Tang, PhD, the Center houses a 300-keV Center (−182 °C) cooled by liquid nitrogen. have led to a “resolution revolution” Titan Krios transmission electron microscope Rapid cooling traps the biomolecules in cryo-EM, which is now routinely that features a brilliant, highly coherent in their native hydrated state, used to generate 3D structures of X-FEG electron source, a cryo-autoloader for embedded in glass-like vitreous (or biomolecules. This development was automated and contamination-free sample amorphous) ice. The samples are then recognized with the Nobel Prize in loading, the latest K3 direct electron detector, transferred to an electron microscope Chemistry in 2017. and a BioQuantum energy filter, all of which and imaged by electrons near the Cryo-EM is particularly powerful are built onto an ultra-stable platform, temperature of liquid nitrogen (−196 °C). for studying large macromolecular ensuring maximal performance, throughput, The recorded images represent 2D complexes. Recently, it was used and resolution. The Krios is equipped with a projections of the sample and are used to solve the structures of several Volta phase plate, which extends its ability to reconstruct the 3D architecture of fundamental biomolecules, including to image smaller proteins and perform the biomolecule through intensive ribosomes and ion channels, and high-resolution cryo-TM. The Center also computational analyses. Single- human pathogens, such as Zika virus, has a 200-keV Talos Arctica transmission particle cryo-EM technology has influenza virus, and Ebola virus. These electron microscope equipped with a K3 made remarkable progress in recent discoveries have greatly influenced direct electron detector and a BioQuantum years due to the development of medicine and public health. A related energy filter and a 120-keV Talos transmission Liang Tang, PhD direct electron detector device technique, electron cryogenic electron microscope for sample screening and optimization. In addition, the Center

2019 Scientific Report | 38 39 | 2019 Scientific Report NMR spectroscopy uses very strong function in cells and how those in the world. In late 2019, the Center will outside the department collaborate with Nuclear superconducting magnets and high- functions are altered in diseases. receive the first of the world’s most powerful the Center’s staff. The staff are available to power radio-frequency pulses to study Furthermore, NMR spectroscopy is NMR spectrometer, operating at 1.1 GHz. This design and perform NMR experiments or train Magnetic the chemical structure of molecules, a powerful tool in the development device will enable more detailed studies of scientists working in other fields to perform Resonance ranging from small chemicals (e.g., of new therapeutics; the Center has biomolecular structure, motion, and function their own NMR experiments. This enables the drugs) to biological macromolecules 2 spectrometers dedicated to drug- and permit the study of more complex Center to influence research and discovery Spectroscopy (e.g., RNA, DNA, proteins). When discovery research in the Department biomolecular systems than is currently in many departments at St. Jude, including molecules are placed in a strong of Chemical Biology & Therapeutics. possible. Cell & Molecular Biology, Chemical Biology & Center magnetic field, the nuclei of certain The superconducting magnets in Although a specialized technique, NMR Therapeutics, Developmental Neurobiology, atoms (e.g., hydrogen, carbon, and the Center weigh as much as 10 tons spectroscopy is accessible to the entire Immunology, Infectious Diseases, Pathology, nitrogen) resonate. This is detected and are cooled with liquid helium St. Jude research community through and Pharmaceutical Sciences. The recent through powerful radio-frequency (–452 °F) to remain superconducting. the expert services of the NMR Center expansion of the Center and the acquisition of pulses. NMR signals can reveal the 3D The magnetic field strengths range Director Youlin Xia, PhD, and staff scientists. the 1.1-GHz NMR spectrometer will enhance structure and motions of biomolecules, from 94,000 to 258,500 Gauss— Several laboratories in the Department of our contributions to understanding the and NMR spectroscopy is used to more than 200,000 times stronger Structural Biology specialize in NMR studies molecular basis of pediatric catastrophic study the motions of biomolecules in than the Earth’s magnetic field. The of biomolecules, and scientists within and diseases and our ability to devise new cures. solution at ambient temperatures or Center houses 9 NMR spectrometers in solid form, conditions that reflect located in temperature-, humidity-, their environment within living cells. and vibration-controlled laboratories. By combining information about These instruments operate at Youlin Xia, PhD 3D structure with insight into how frequencies ranging from 400 to 850 MHz atoms move, we can comprehensively and represent one of the largest understand how biomolecules collections of NMR spectrometers

2019 Scientific Report | 40 41 | 2019 Scientific Report researchers at all levels of crystallographic St. Jude researchers measure the directions expertise. Like other techniques, crystallography and intensities of the resulting diffracted relies heavily on the purity and quality X-rays. The next steps are data processing and of the protein sample. Crystallographic semiautomated structure determination. If this analysis begins with obtaining a highly pure, process is successful, the result is an electron- monodispersed protein or protein complex. density map ready for interpretation and use Next, robotic instruments are deployed for in model building by the crystallographer. efficient screening of large numbers of Finally, during refinement, the atomic model crystallization conditions by using nanoliter is iteratively extended and revised to better fit dispensing and monitoring to identify the original diffraction data. conditions producing high-quality crystals. The X-ray crystallography continues to break latter task is greatly aided by a “plate hotel” new technologic ground. Recent advances in that automatically captures high-resolution X-ray source brilliance, beam focus, detector images of individual crystallization drops on a frame rate, and sample delivery have been customizable, user-defined schedule. combined in a new method, serial synchrotron The highest-resolution X-ray structures crystallography, that enables X-ray scientists are afforded by synchrotron light sources to collect data and solve structures from that produce brilliant, tunable X-rays. St. Jude smaller crystals than ever before possible. researchers working with the Center benefit Several national beamlines are pioneering this from regular access to the Advanced Photon method, which will enable us to determine Source at Argonne National Laboratory structures from micron-sized crystals. The (Lemont, IL), where remote data collection structural information gleaned will help us from a Center workstation is routine. A chosen better understand and develop therapeutic crystal is mounted by a robotic arm and approaches targeting cancer and other then rotated within the X-ray beam, while catastrophic pediatric diseases. Darcie Miller, PhD

X-ray crystallography is a powerful X-rays to produce distinctive patterns X-Ray tool that has served as a mainstay of diffraction intensities. These of drug-discovery programs. It is the diffraction patterns are determined by Crystallography most efficient method for obtaining the underlying atomic arrangement Center high-resolution structures of targets, of the molecules that form the crystal ranging from tiny proteins to protein and can be used to back-calculate the assemblies. In as little as 2 weeks, atomic structures of the molecules crystallographic techniques can within the crystal. X-rays allow for the reveal the overall architecture of resolution of interatomic distances, biomolecules, down to their atomic because the wavelengths of X-rays are details. Snapshots of enzymatic comparable to the distances between reactions and ligand interactions can atoms in molecules. The purpose of also be elucidated. Such exquisitely the crystals is to increase the signal- detailed structural information to-noise ratio. Molecules in solution do provides the framework for follow- not scatter X-rays to high resolution; up structure-to-function studies, however, in crystals, many identical therapeutic interventions, and molecules are arranged in a pattern understanding the molecular basis of that sharpens and reinforces the cancer-causing mutations. X-ray signal. X-ray crystallography is used to Under the direction of Darcie determine the arrangement of atoms Miller, PhD, the X-ray Crystallography within a crystal. Essentially, protein Center facilitates crystal structure crystals are grown and subjected to determination efforts by St. Jude

2019 Scientific Report | 42 43 | 2019 Scientific Report Scott Blanchard, PhD

fluorescent probes, molecular-engineering and a very low concentration to ensure that Alessandro Borgia, PhD tools, super high–speed cameras, and complex individual molecules are detected. It also takes data-analysis pipelines. Broadly speaking, advantage of flexible control of the confocal Like ordinary machines, molecular St. Jude is in the process of the Center uses 2 imaging approaches: illumination volume to visualize distal points in assemblies require dynamic processes building a world-class Single-Molecule Single-Molecule total internal reflection fluorescence (TIRF) space in which molecules are freely diffusing. to achieve their purpose and rapidly Imaging Center and has recruited microscopy and time-correlated single-photon Although a more time-intensive approach, Imaging Center change their shape and composition. Scott Blanchard, PhD, a preeminent counting. ultrafast diodes with single-photon sensitivity Single-molecule imaging technologies scientist in this field, to lead this effort. In TIRF microscopy, fluorescently labeled enable measurements at picosecond to directly monitor and image time- Dr. Blanchard’s research interests molecules of interest are sparsely tethered to nanosecond time scales. dependent changes in molecular are focused on understanding the the surface of microfluidic chambers made The integration of single-molecule systems. Such efforts are equivalent molecular basis of gene expression, of quartz glass. This tethering procedure imaging studies into more conventional to videos of biological molecules at signal transduction, solute transport enables individual molecules to be visualized studies has already increased our resolutions that enable visualization across cellular membranes, host–virus for seconds to minutes. Molecules are understanding of the regulation of protein of their molecular movements. By interactions, and the mechanism of illuminated by a focused laser that generates synthesis for the treatment of infectious recording the performances of tens protein synthesis during cancer. His a thin, evanescent (shimmering) field that diseases and cancer, the prevention of HIV of thousands of individual molecules laboratory seeks to determine how is hundreds of nanometers thick. This infection, the modulation of neurotransmission simultaneously, we can identify the full the protein synthesis machinery in approach enhances the signal needed to in psychiatric disorders and by drugs of abuse, diversity of behaviors that are normally metastatic cancer cells can be most see a single molecule. Despite the power of and the regulation of chromatin dynamics and masked when molecules are measured effectively targeted to treat the this approach to image tens of thousands gene expression through protein–protein and as a group. In so doing, single-molecule disease. of molecules simultaneously, it is limited protein–DNA interactions. Staff in the Center measurements advance scientific Under the direction of Alessandro by the fact that the plane of illumination will assist and train St. Jude researchers from understanding by establishing how Borgia, PhD, the Center aims to develop is fixed with respect to the quartz–solution other departments to plan and run single- individual members of a potentially and implement spectroscopic interface. To overcome this, the Center also molecule imaging experiments and initiate diverse group function and respond techniques that will enable us to uses time-correlated single-photon counting, transdisciplinary collaborations to better to a stimulus. Measurements of this visualize proteins and their complexes which focuses the laser illumination to an understand wide-ranging aspects of biology. kind are expected to facilitate the in real time. To make these efforts extremely small volume (about 1 µmm3) at The overarching goal of the Center is to bring development of precision medicines possible, the Center is developing any point of interest—or an array of points of the power of single-molecule spectroscopy for patient care. and using an array of cutting-edge interest—in solution. This method leverages the techniques to biomedical research at St. Jude technologies, including state-of-the-art combination of a small illumination volume for the betterment of human health.

2019 Scientific Report | 44 45 | 2019 Scientific Report posttranslational modifications of the protein, The third level of protein complexity is which are crucial regulators of biological whole-proteome profiling, which involves function, play a substantial role in cell and identifying and quantifying all protein tissue function, and have been linked to components within a cell type or tissue. We disease causation and progression. Abnormal have made great strides to improve this posttranslational modifications can serve technique via many technical advances. as potential drug targets. This technique of Cutting-edge technologies allow the analyzing an intact protein without digesting quantification of nearly all expressed it with specific enzymes is often referred to as proteins in a cell. This again involves the top-down MS. Bottom-up MS is also done to use of tandem mass tags coupled with 2D probe protein modifications that are present liquid chromatography and tandem MS. at low levels. It is now feasible to identify and quantify Identifying the interplay between proteins more than 12,000 proteins from mammalian and protein complexes, which are key cellular samples. By using these methods, combined components, is central to understanding with the enrichment for posttranslational how cells function. These complexes are modifications, it is also possible to identify interrogated using various approaches. Affinity and quantify protein modifications (i.e., purification and mass spectrometry (AP-MS) phosphorylation, ubiquitination, acetylation, is used to determine the components of a and methylation). The Center has the capacity complex. The system can then be perturbed to perform such large-scale experiments with a to see how the protein complex is affected. range of biomedical samples, from cancer cells Isotopic-labeling methods (e.g., tandem mass in culture to preclinical models and clinical tags and stable isotope labeling with amino specimens. Proteomic data are integrated with acids in cell culture) and AP-MS can also be genomic data and phenotypic information to used to measure complex protein dynamics offer a systems or holistic view. Together, these within a cell. Cross-linking MS is used to gain results provide an unbiased determination insight into the structure of protein complexes of disease networks and provide insights into and determine what proteins or regions of novel therapeutic strategies. Hong Wang, PhD; Junmin Peng, PhD proteins interact and how those interactions change within a biological system. Every cell within an organism has the Staff working in the laboratory Mass same genome, which is the blueprint of Junmin Peng, PhD, and the Center for making proteins. However, cells for Proteomics and Metabolomics Spectrometry– differ in terms of which genes are focus on using MS to explore protein Based Protein activated and which proteins are functions and structures. They deploy made. The proteome is defined as the several methods and instruments to and Proteome full set of proteins made by a single identify, characterize, and quantify cell type. Diseased cells often produce proteins in a way that gives insight to Studies proteins that either are not produced help discover the cause of disease, by healthy cells or have altered elucidate protein drivers as potential structures and/or functions. Mass drug targets, and validate proteins spectrometry (MS) is a fundamental recognized by drugs. Moreover, these approach to studying proteins and methods facilitate the identification proteomes. MS employs magnets or of clinical biomarkers that can be used electrical fields to resolve and measure to help diagnose disease or inform biomolecules according to the masses treatment. of their constituent atoms. Specialized MS and its use in proteomics can techniques provide the flexibility to be thought of in terms of 3 levels profile a single protein, small protein of increasing complexity: (1) the complexes, or tens of thousands of identification and characterization proteins and protein modifications of a single protein, (2) the study of simultaneously in a single experiment. protein complexes, and (3) whole- Our state-of-the-art MS platform proteome profiling. For single-protein can analyze samples with extremely analysis, we use MS to identify the high sensitivity, down to the level of protein by measuring its molecular attomoles (10-18 moles), and high mass mass. This approach also identifies accuracy (less than 1 ppm). 2019 Scientific Report | 46 47 | 2019 Scientific Report into several hosts (e.g., bacteria, insect, and in the sample via chromatographic systems. mammalian cells) to make the protein. The These systems in the PTC are equipped for PTC can process various cell culture volumes parallel processing and have a temperature- (1 mL-50 L) by using a parallel bubbling system controlled autosampler and ultraviolet and and temperature- and humidity-controlled fluorescence detectors, which are capable shakers. After the protein is made, the cells of screening and purifying 96 samples are opened via a specially designed robotic concurrently. The purified homogeneous sonicator, which is programmed for processing protein sample can be tested for stability small volumes. For large volumes, the CF1 cell using Tycho, a modified differential-scanning disruptor is used; this instrument processes as fluorimetry instrument. much as 6 L of cells per hour. After the cells are The PTC can also perform functional lysed, the samples are fractionated by high- assays by using Cytation 5, a microscope with speed ultracentrifuges to separate organelles a microplate reader. After the protein sample and macromolecules. is characterized, the labeled protein is used Every protein is different, and each one to solve its structure by NMR, crystallized for needs different conditions to be stable and X-ray crystallography, and/or flash-frozen to amenable to structural studies. For example, trap the protein particles in vitreous ice for membrane proteins are embedded in a lipid single-particle cryo-EM analysis. The PTC will bilayer on the cell membrane; thus, they must accelerate projects of investigators who are be handled using a mixture of detergents and keen to understand the structure of protein lipids. Once the protein of interest is isolated targets, and it is the “glue” that binds research from its constituents of cells, it is enriched, teams in departments across the institution. purified, and separated from the other proteins

Ravi Kalathur, PhD

Structural biology studies begin challenging problems in a single Protein with producing purified samples of center, thereby enabling investigators a biomolecule of interest. Molecular to make discoveries faster and tackle Technologies cloning and protein-engineering biological systems that have remained Center strategies and state-of-the-art, recalcitrant to structural studies. high-throughput instrumentation Under the direction of Ravi are used to optimize biomolecule Kalathur, PhD, a team of scientists production and purification. Proteins uses semiautomated, multipronged are often difficult to express outside approaches at each stage of the their host or overexpress within their pipeline: from construct design, host; even if expressed in necessary cloning, expression, and purification quantities, they are sometimes not to characterization of all protein stable enough to withstand the rigors targets, including membrane of experimentation. Furthermore, proteins, multiprotein complexes, and determining the best sample assemblies. The PTC can synthesize as conditions for protein production many as 32 different 2000-nucleotide using traditional techniques can DNA tiles in an overnight run by be a slow and arduous process. using the BioXp 3200 DNA printer. The Protein Technologies Center Synthesized DNA tiles can be inserted (PTC) was established to focus on into expression vectors by using advanced technologies needed for precise, sequence-independent, optimized protein production and scarless cloning methods. Once the expertise troubleshooting the most plasmid is generated, it is introduced

2019 Scientific Report | 48 49 | 2019 Scientific Report Structural biology studies provide be synthesized to fit in that pocket studies are providing new directions Structural in-depth characterization of key and inhibit the protein. Structural for developing therapeutics to target biomolecules and mutations or other biology techniques can be used to those diseases. The Structural Biology Biology disease-associated alterations that screen chemical compounds that bind department has a strong research Contributes disrupt cell function by causing protein in the pocket, quantify the binding program in this area spearheaded by misfolding, aggregation, and/or affinity of those compounds, guide Richard W. Kriwacki, PhD, and Tanja to Discovery altered protein dynamics. For example, their optimization, and determine Mittag, PhD. These are just a few NMR spectroscopic analysis revealed the 3D structure of the protein– examples of how structural biology and Cures how mutations in the BCR–ABL fusion compound complexes, thereby research forms a foundation for our protein associated with chronic allowing structure-based design molecular understanding of biology myelogenous leukemia (CML) cause of further-improved compounds. and disease and promotes the rational treatment resistance. The mutation Structural biology can further reveal development of novel therapeutics. changes the equilibrium between generalizable principles of drug design. the ground state of tyrosine kinase For example, the characterization and a high-energy conformation of numerous structures of enzyme– that enables kinase inhibitor binding, inhibitor complexes revealed that thereby diminishing the efficacy of inhibitors typically stabilize the tyrosine kinase inhibitors, a standard transition state of enzymes, thereby chemotherapy agent used to treat inhibiting their activity. This concept CML. This information on protein now guides the development of novel dynamics can be used to develop enzyme inhibitors. Structural biology improved, next-generation BCR–ABL thus plays a fundamental role in any inhibitors to treat drug-resistant effort to design and characterize new leukemias. therapeutics that target relevant Structural information has enabled biomolecules specifically and potently. rational engineering of more effective Although facilitating the discovery therapeutic antibodies, which have of new therapeutics is an important revolutionized immunotherapies role of structural biology research, against cancer. It has also enhanced its contributions to elucidating CRISPR/Cas9 genome-editing fundamental mechanisms of enzymes to improve their performance biomolecular function underpin and diminish nonspecific genome our understanding of molecular targeting. Structural information has and cell biology. Detailed insights improved fusion tags within technically into the structure, dynamics, and challenging membrane proteins, such function of specific biomolecules as G-protein–coupled receptors, to have revealed new information about determine the structures of their how biomolecules function. One various functional forms and enable example relates to how the interior of visualization of how these proteins are cells is organized. Structural biology altered by ligands that trigger cellular- investigations have recently shown signaling functions. that transient interactions between Atomic-resolution structures can intrinsically disordered proteins drive also be used to evaluate the suitability liquid–liquid phase separation within of biomolecules for therapeutic cells. This causes proteins and other targeting. For example, if X-ray biomolecules to co-associate and crystallography, cryo-EM, or NMR condense, forming membraneless data show that a disease-associated organelles. This process goes awry in protein has a deep pocket within its certain diseases, and the molecular 3D structure, new drug molecules can insights gained from structural biology

2019 Scientific Report | 50 51 | 2019 Scientific Report Most structural biology analyses study the structure and dynamics of In the are currently performed outside individual proteins within living cells, living cells. The next challenge in the and single-molecule fluorescence Future field is to develop and implement methods are used to monitor dynamic technologies that allow the study of biomolecular processes inside cells. the structure, dynamics, and function These and other methods yet to be of biomolecules in living cells. Cryo-TM developed will redirect the field from uses electron microscopy to examine studies of isolated biomolecules to frozen cell specimens at near-atomic those of biomolecular behavior in resolution, thereby simultaneously complex biological systems in living revealing the organization of all cells. This future holds the promise biomolecules in the cell. NMR of revolutionizing our molecular spectroscopy has been used to understanding of biology and disease.

Charalampos Babis Kalodimos, PhD

2019 Scientific Report | 52 53 | 2019 Scientific Report BUILDING A NEXT-GENERATION LATTICE LIGHT-SHEET MICROSCOPE TO VISUALIZE GENOMIC ACTIVITY IN LIVING NEURONS

The pursuit of mechanistic insights E. Moerner (Stanford University) and Lindsay A. Schwarz, PhD, uses into biological processes can drive for the development of super- light-sheet microscopy to understand technologic innovation. Likewise, resolution fluorescence microscopy. the neuronal circuits that control the advances in technology enable Conventional light microscopy is autonomic nervous system’s fight-or- biomedical researchers to answer limited by diffraction. Super-resolution flight response. questions that were previously fluorescence microscopy enhances Two St. Jude researchers, Michael intractable. Nowhere has this been resolution beyond these limits, making A. Dyer, PhD, and David J. Solecki, PhD, more evident than in the application it possible for researchers to visualize are engaged in the study of different of microscopy to neuroscience. single molecules within cells. areas of developmental neurobiology. Camillo Golgi published his classic The Department of Developmental They recently joined forces to tackle silver staining method that allowed Neurobiology at St. Jude uses the the development of new methods of for unprecedented definition of most advanced modern microscopy light and electron microscopy. Here we nervous tissue by light microscopy platforms available to gain a deeper retell the story of their entry into an in 1873. Ramón y Cajal then used understanding of the development, elite group of 4 laboratories working Golgi’s stain to show the remarkable function, and diseases of the nervous with Nobel Laureate Eric Betzig diversity of neurons in the brain. In system. Stanislav S. Zakharenko, MD, to help build his latest instrument, 1906, they shared the Nobel Prize PhD, uses in vivo 2-photon laser- the next-generation lattice light- in Physiology or Medicine. In 2014, scanning microscopy to understand sheet microscope. Thus, Drs. Dyer the Nobel Prize in Chemistry was the changes in neuronal function and Solecki are taking their place in awarded to Eric Betzig [University of associated with schizophrenia. James helping create technologic innovations California, Berkeley; Howard Hughes I. Morgan, PhD, uses 3-dimensional and neuroscience discoveries that will Medical Institute (HHMI)], Stefan Hell (3D) electron microscopy to study propel neuroscience in the future and (Max Planck Institute), and William synapse formation in the cerebellum, continue the legacy that began with Golgi and Cajal.

2019 Scientific Report | 54 55 | 2019 Scientific Report The researchers discovered that the for differential subnuclear localization of epigenetic signature of retinoblastoma cells inactive genes came from fluorescence in is the same as that of retinal progenitors situ hybridization studies combined with during the developmental stage when they immunofluorescence studies by Marcus produce the most retinal neurons. In addition, Valentine, the director of the St. Jude the team identified dozens of genes linked Cytogenetic Shared Resource. Those studies to retinal diseases that are epigenetically were performed on fixed tissue. To prove that silenced in a cell type–specific manner in facultative heterochromatin does contain the mature retina. The most unexpected silenced genes, Dr. Dyer and colleagues knew result from this study, which was published in they had to visualize individual genomic Neuron in 2017, was that those epigenetically loci moving across nuclear domains within silenced genes are sequestered in discrete living tissue. To do this, they needed to image domains within the nucleus called facultative developing viable retina at higher levels of heterochromatin. This finding contradicted a magnification than were possible at the time long-held dogma in the field at that time—that and directly correlate those images with 3D the facultative heterochromatin region of the electron microscopy images. nucleus does not contain genes. The evidence

Michael A. Dyer, PhD

Retinoblastoma is a childhood cancer The epigenome comprises the Epigenetic of the developing retina that begins in dynamic and heritable modifications utero and is diagnosed within the first in the structure and organization of Reprogramming few years of life. It is initiated when DNA as it is wrapped around histones, Mediates the RB1 gene is inactivated in retinal partitioned, and condensed in the progenitor cells. Dr. Dyer’s laboratory nucleus. Epigenetic changes can Retinoblastoma has been studying retinoblastoma profoundly influence gene expression. for the past 15 years to elucidate its The epigenome undergoes dramatic Formation cellular origins and develop more changes during brain development, effective, targeted therapy. Through and it is often disrupted in cancer. the St. Jude Children’s Research To gain a deeper understanding of Hospital–Washington University the dynamic changes that occur Pediatric Cancer Genome Project, in the epigenome during retinal Dr. Dyer and colleagues discovered development and retinoblastoma that inactivation of the RB1 gene formation, Dr. Dyer initiated a leads to epigenetic reprogramming 5-year effort to profile the covalent and activation of potent oncogenes modifications of the DNA and histones, that are not normally expressed in short- and long-range DNA-looping the developing retina. Their discovery interactions required for packing provided the first evidence suggesting of chromatin into discrete nuclear that retinal cells are vulnerable domains and gene regulation. to malignant transformation at a particular stage of development.

2019 Scientific Report | 56 57 | 2019 Scientific Report Most neurobiologists generate field of neuronal migration during Neuronal static snapshots of the brain regions brain development by using video they study; Dr. Solecki uses video microscopy. For example, their imaging Migration microscopy to capture young, living of the cellular machinery that drives During neurons in the act of building neuronal neuronal motility revealed for the first circuits in the developing cerebellum time that microtubules, the organelles Development of the mouse. The movies created by that support cell migration, are this powerful microscopy approach located far from where, for decades, of the have revealed previously unattainable investigators presumed them to be. insights into how a neuron matures, While studying cell migration during Cerebellum migrates, and interacts with the the development of the cerebellum, environment as it moves from its Dr. Solecki and colleagues, including germinal niche to a final functional Eric Betzig and Harald Hess (Janelia position in a developing brain. These Research Campus, HHMI), also studies are crucial to understanding discovered a dramatic change in the how brain development goes awry size and organization of the nuclei in children with cognitive deficits or of granule neuron precursors as David J. Solecki, PhD epilepsy, in whom neurons are either they migrate to their final location. misplaced in a circuit or the earliest Like Dr. Dyer, Dr. Solecki realized that stages of neuronal maturation his laboratory needed even better are delayed. imaging capabilities to study these Dr. Solecki’s team has made changes in nuclear size and structure several fundamental advances in the during cerebellar development.

2019 Scientific Report | 58 59 | 2019 Scientific Report to not only rapidly store but also analyze data is an expert in image and data analysis. captured on the instrument. Drs. Dyer, The NIML not only oversees the LLSM but Solecki, Stabley, and Kirby Campbell, PhD, a also provides training for other scientists in postdoctoral fellow working in Dr. Solecki’s using its advanced optics and developing laboratory, overcame the many challenges the computational image-analysis pipelines in developing culture conditions to keep required to interpret its data. neuronal samples alive throughout imaging Together, Drs. Dyer and Solecki and their experiments and to acquire optimized teams have now developed new probes images with this sophisticated and that enable developmental neurobiology sensitive instrument. researchers to track the location of After developing the necessary expertise individual genes within euchromatin and and formalizing processes for operating the heterochromatin domains during retinal and LLSM, the department incorporated the cerebellar development. Their studies bridge instrument into the advanced Neuroimaging the molecular and cellular underpinnings of Laboratory (NIML). This departmental core how cells of the nervous system reorganize facility brings together a team with expertise their nuclei to meet the dynamic control in advanced optics and computational data required for cellular gene expression during science. Dr. Stabley, the manager of the NIML, normal developmental maturation, stress is a specialist in microscopy and advanced responses, or malignant transformation into optics, and Abbas Shirinifard Pilehroud, PhD, pediatric cancers. a senior bioinformatics research scientist,

Daniel Stabley, PhD; Kirby Campbell, PhD

Although light microscopes are an implementation of a lattice light-sheet Convergence essential tool for neurobiologists, microscope (LLSM), an experimental 2 shortcomings limit their use in instrument developed by Eric Betzig of addressing many crucial questions. to overcome limitations in current Neurobiology First, the limited resolution of light microscopy. microscopy prevents the visualization The LLSM produces ultrathin Discoveries of the smallest, unexplored subcellular sheets of light that surpass the structures. Second, the high-energy resolution limit of conventional light and New laser light used by more modern microscopes and substantially reduce microscopes, such as 2-photon laser- the amount of laser light needed Technologies scanning microscopes, to produce for imaging live neurons. Operating images is toxic to delicate cells, such as an LLSM is technically challenging. developing neurons. The next-generation optics of the The Department of Developmental instrument necessitate a high degree Neurobiology has a long-standing of refined alignment to function initiative to continuously evaluate properly. This first-generation technologic advances in microscopy, advanced microscope was designed so that St. Jude research programs with only the barest-minimum forms are continuously driving forward of environmental control. Finally, the the leading edge of their field. As LLSM produces nearly 2 GB of imaging part of this initiative, Dr. Solecki, data per second of operation. This rate Daniel Stabley, PhD, and colleagues of image acquisition creates a high spearheaded the acquisition and demand for computational support

Marybeth Lupo, PhD; Abbas Shirinifard Pilehroud, PhD

2019 Scientific Report | 60 61 | 2019 Scientific Report Eric Betzig selected the NIML as one of only 4 laboratories worldwide to co-build his next-generation microscope. This new instrument will enable neurobiologists to significantly extend LLSM-like imaging deep within brain or other nervous system tissues. Through these efforts and collaborations, St. Jude developmental neurobiologists are perpetuating the centuries-old legacy in neuroscience, whereby technologic innovations and neuroscience discoveries David J. Solecki, PhD; Michael A. Dyer, PhD continuously propel one another, providing new insights into the nervous system during The efforts of the Department of microscopy data was used to create health and disease. From Developmental Neurobiology to the first correlated super-resolution/ procure and refine ground-breaking FIB-SEM CLEM (focused ion-beam Janelia to imaging technologies have recently combined with scanning electron St. Jude and attracted the attention of the imaging microscopy correlative light and field and provided opportunities electron microscopy) analysis Beyond for new collaborations that have pipelines. Unexpected discoveries positioned St. Jude at the forefront are already being made through of advanced microscopy. Luke Lavis this collaboration and as a result of (Janelia Research Campus, HHMI) has this technology. For instance, these provided St. Jude researchers with scientists have recently determined next-generation fluorescent dyes to that differentiating cerebellar neurons broaden the palette of image probes condense their nuclear volume and available to St. Jude investigators. compact heterochromatin 2 fold in as Furthermore, St. Jude’s LLSM expertise little as 2 hours. Drs. Dyer and Solecki has fostered a collaboration among 3 are working with Cam Robinson, external laboratories (Betzig, Hess, and PhD, the director of the Electron Lavis) and the laboratories of Microscopy division of the St. Jude Drs. Solecki and Dyer. For this Cell and Tissue Imaging Center, to collaboration, a 10K super-resolution develop an efficient LLSM/FIB-SEM cryostat that correlates super- CLEM pipeline that will enable St. resolution light microscopy images Jude researchers to routinely perform with ultra-high–resolution electron correlative studies on live neurons.

2019 Scientific Report | 62 63 | 2019 Scientific Report ST. JUDE GLOBAL IS IMPROVING QUALITY AND ACCESS TO CARE FOR CHILDREN WITH CATASTROPHIC DISEASES WORLDWIDE

An estimated 400,000 children (aged Medicine, and the expansion and methods for program building and 0–14 years) experience cancer each reimagining of St. Jude’s international impact assessment; (2) Population year. More than 90% of them live in activities to create St. Jude Global, a Sciences, which focuses on the low- or middle-income countries program that supports education and epidemiology and estimation of (LMICs), and nearly half of those training, innovation, and information burden of catastrophic childhood diseases are never diagnosed. sharing with international partners. diseases, cost-effective and simulation Medical institutions in LMICs often These efforts have been coupled with analyses, and health disparities and struggle to meet the needs of their the creation of new collaborative health systems research; and (3) local population. The probability of partnerships through the St. Jude Resource-Adapted Clinical Trials, which survival of children with cancer in Global Alliance, linking facilities around consolidates the implementation LMICs is 20% or less, contrasting with the world to advance clinical care of the department’s interventional an overall survival of cancer in high- delivery, education, and research on studies to advance care and improve income countries that now surpasses how to optimize the implementation outcomes. The department also works 80%. Where a child lives, therefore, of best-care practices everywhere. with the St. Jude Graduate School of plays a critical role in determining the The Department of Global Biomedical Sciences to develop and likelihood that he or she will survive. Pediatric Medicine seeks to advance deliver educational programs and with St. Jude has worked with health care and improve outcomes for the St. Jude Comprehensive Cancer care facilities in LMICs for more thean children with cancer or catastrophic Center to develop a clinical and 25 years to improve the care and hematological disorders worldwide translational research infrastructure survival of children with catastrophic through global health research and that facilitates and supports illnesses. Recently, those efforts have innovation. The department’s research international research programs been boosted by the establishment efforts are focused in 3 broad areas: and collaborations initiated by of a new academic department, (1) Quality and Implementation St. Jude researchers. the Department of Global Pediatric Sciences, which provides the core

2019 Scientific Report | 64 65 | 2019 Scientific Report Capacity-Building Initiatives of Research Network Model—St. Jude St. Jude Global Global Alliance Ensuring that all children have access to Advances in patient care are made by step- high-quality care requires a strengthening of wise improvements and occur within the the continuum of care necessary to carry a context of the local healthcare and financial child from diagnosis through completion of environments. By carefully integrating therapy. This includes engaging all aspects implementation science principles, St. Jude of care, from disease surveillance to patient- Global will advance the knowledge needed for centered care to health systems and national continuous, sustained growth. The goal is to policies. Capacity-building initiatives are facilitate research on a worldwide scale that integrated at the global, regional, and hospital enables institutions across the globe to better levels and include tools to assess, implement, implement innovative and context-adapted and monitor programs. Administrative and therapeutic protocols. These efforts will be organizational support is provided to help managed through the St. Jude Global Alliance, form regional networks of centers that may the functional structure that unites partner learn from one another, assist organizations institutions with the shared goal of improving in seeking the funding needed for care healthcare delivery and increasing survival delivery and improvement efforts, strengthen of children with cancer or nonmalignant existing health systems, and implement hematological disorders worldwide. The quality-control and safety programs. St. Jude Alliance will foster the growth of regional and support also helps regional networks develop global networks to adopt consortium-like evidence-based, resource-adjusted treatment functions that support research optimizing guidelines; nursing-care standards and resource-adapted care models. associated staffing models; infection control Led by St. Jude faculty members, the and supportive care programs; and regional Alliance integrates regional programs that centers for training and delivery of complex form an operational framework fostering medical procedures, advanced diagnostics, collaborative activities across institutions

Catherine G. Lam, MD, MPH and specialized treatment. and transversal programs that guide uniform interventions and discipline-specific standards In 2018, St. Jude Global was launched, Global has 3 key goals: (1) to train the Educational Initiatives of the across all regions. Together, the regional and Launching with the goal of improving the survival clinical workforce needed to meet St. Jude Global Academy transversal programs form a cohesive structure of children with cancer or other the treatment needs of children Caring for children with cancer requires a that facilitates advances in local care delivery St. Jude catastrophic diseases worldwide around the world; (2) to develop multidisciplinary team, and building those through research, sharing of knowledge Global through the sharing of knowledge, and strengthen health systems and teams is a major challenge to providing and experience, quality improvement, and technology, and organizational skills. patient-centered initiatives that quality care in LMICs. In response to this education and training. Alliance members The program extends beyond the encompass the continuum of care need, St. Jude Global has established the will have the opportunity to develop global Department of Global Pediatric required for children with cancer or St. Jude Global Academy, a comprehensive projects and studies, connect with committees Medicine, integrating expertise from nonmalignant hematological diseases; training program administered at St. Jude and working groups at the regional and global multiple departments and programs and (3) to advance knowledge in and at regional international sites. The level, and engage with St. Jude faculty and to realize its vision through capacity pediatric oncology-hematology educational opportunities provided by the staff for training and development. building, educational initiatives, and through research on how to improve Academy include a dedicated global health The Department of Global Pediatric the development of a global clinical the quality of care around the globe. track in the Pediatric Hematology-Oncology Medicine serves as the organizational core of research infrastructure. St. Jude Fellowship Program at St. Jude, fellowship the Alliance, providing vision, infrastructure, programs in pediatric hematology-oncology and governance structure. ALSAC (the at international locations to build regional fundraising arm of St. Jude) will support the capacity, a Masters of Science (MSc) in Global development of independent foundations in Child Health degree program through the Alliance members’ countries that will provide St. Jude Graduate School of Biomedical the financial support essential for sustained Sciences, specialized certificate-based training growth. In December 2018, the First Annual for healthcare providers, and advanced Meeting of the St. Jude Global Alliance was distance-learning curricula to support and held on campus. In attendance were 167 complement the educational initiatives participants from 52 countries, representing described here. 123 medical institutions and foundations.

2019 Scientific Report | 66 67 | 2019 Scientific Report REGIONAL PROGRAMS

Eurasia

Eastern Mediterranean China Mexico

Asia Pacific Central and South America Sub-Saharan Africa

St. Jude Global has established 7 regional programs in LMICs: Asia Pacific, Central and South America, China, Eastern Mediterranean, Eurasia, Mexico, and Sub-Saharan Africa. These programs facilitate collaboration, research, and transfer of knowledge, and their structure defines the framework for operations and implementation. Here we present the progress made by the Mexico, Asia Pacific, and China regional programs.

2019 Scientific Report | 68 69 | 2019 Scientific Report Mexico Educational efforts in Mexico include the Asia Pacific and China that include children and adolescents in In 2016, eight Mexican institutions, the Casa de Guadalajara Pediatric Hematology/Oncology The Asia Pacific regional program builds Myanmar and the Philippines. In Myanmar, la Amistad (a local foundation), representatives Fellowship Program and the Guadalajara on a foundation that began in 2006, when a national childhood cancer network was from the Mexican Ministry of Health, and Pediatric Hematology/Oncology Scholars St. Jude established partnerships in the launched; 17 sites were identified, mapped, those from St. Jude joined forces to create Program. The former is a 2-year program Philippines and Singapore. Collaborative and are now engaged in training. Sustainable Mexico in Alliance with St. Jude (MAS |│+). The that supports the training of 3 clinical fellows efforts have since expanded to include strategies have been developed to cultivate group’s mission is to improve the quality of per year. The latter is a 1-year program that national programs in Cambodia, Myanmar, a multidisciplinary workforce by providing care and survival for children with cancer in supports 3 scholars after completion of their and the Philippines, with extended regional local and cross-regional training programs, Mexico through multicenter collaboration and clinical training. St Jude provides funding and partnerships in Indonesia, Sri Lanka, Thailand, including new fellowships in pediatric oncology innovation in patient care delivery, education, mentorship for both programs. and Vietnam. Learning networks in the Asia and multisite training for the first pediatric and research. MAS |│+ membership now Pacific region have engaged more than 200 radiation oncologists in Cambodia and includes 23 institutions, various stakeholders, multidisciplinary providers from 55 institutions Myanmar. In Singapore, regional symposia on and a multidisciplinary team needed to +Modernization: +Quality: across 20 countries. The network’s clinical and retinoblastoma, pathology, and surgery, with achieve its mission. Technologies, techniques, Supportive care educational platforms facilitate the exchange ongoing working groups, have been organized and approach strategies toolkit From a research standpoint, the group’s of evidence-based resources and best-practice and funded. Regional nursing education and leadership applies a health-disparities teaching in oncology, surgery, pathology, and leadership development is being supported in perspective and relies on quality and radiology; the network’s smaller theme-based Cambodia, and the St. Jude VIVA Asia Pacific implementation science methods. In Spanish, groups facilitate problem solving and advance Nursing Institute will be launched this year “mas” means “more”; to improve quality of care regional projects. in Singapore, providing training for regional and survival for children with cancer, MAS |│+ The most recent achievement of nurse educators, followed by continuing has 4 strategies: more collaboration, St. Jude Global is the March 2019 formation education and mentored implementation more evidence, more modernization, and of an alliance between St. Jude and the projects. Finally, the Asia Pacific regional more quality. VIVA Foundation for Children with Cancer program is building multicenter research Project-based research efforts of the MAS |│+ (Singapore), VIVA China Children’s Cancer capacity, including quality and implementation alliance include the acute lymphoblastic Foundation (Hong Kong), KK Women’s & science research examining the local leukemia (ALL) trials MAS-ALL18 and Retro Children’s Hospital (Singapore), National causes of treatment failure (e.g., treatment MAS-ALL. MAS-ALL18 studies the feasibility University of Singapore, and Shanghai abandonment) and strategies to optimize of implementing a multicenter prospective Children’s Medical Center to improve the capacity development and context-adapted diagnostic and therapeutic strategy in centers +Collaboration +Evidence cure and treatment of childhood cancer in treatment implementation. Building leadership and Research protocols & with no prior experience in cooperative trials. a collaborative spirit clinical research Singapore, China, and other countries in Asia. Retro MAS-ALL is determining the outcomes infrastructure Extending across St. Jude Global’s Asia Pacific of cases of ALL diagnosed at MAS |│+ centers and China regional programs, this agreement during 2011–2015. These data serve as the will leverage local leadership and regional historic controls for the MAS-ALL18 protocol. strengths. Centers of Excellence in research and clinical care of children with cancer in Singapore and Shanghai will also serve as core training centers. An example of the progress made in the region and the potential to MAS | + Alliance Growth advance outcomes is the National Childhood ALL Study Group in China. Asia Pacific collaborations have China strengthened national health systems and increased the capacity for service delivery, workforce development, and research. Accomplishments across these areas include national strategic mapping and assessments initiated in Cambodia, Indonesia, Myanmar, Philippines, Sri Lanka, and Thailand. Regional case studies on critical gaps (e.g., shortages in essential medicines) have been completed to facilitate solutions. The region has also helped Asia Pacific develop national cancer control programs 2015—8 hospitals 2016—11 hospitals 2019—23 hospitals

2019 Scientific Report | 70 71 | 2019 Scientific Report Critical Care Transversal Program St. Jude. The conference was followed by the The Global Critical Care Program strives 2-day course “POCCS Basics,” which teaches to strengthen hospital care for critically the practical aspects of providing high-quality ill children with cancer to improve overall care to critically ill children. The Program plans survival. The Program identifies global to launch the St. Jude Global Academy in problems in pediatric onco-critical care Pediatric Onco-Critical Care in 2020. delivery and develops innovative solutions. The Global Critical Care Program also Its initiatives include using evidence-based collaborates on research to better understand interventions to improve hospital care; challenges in onco-critical care. Current work educational initiatives to improve provider focuses on developing an evidence-based knowledge of the care of critically ill children; tool to assess the capacity and quality of research on topics related to pediatric onco- pediatric onco-critical care in resource-limited critical care; and forming collaborative settings. In collaboration with Dr. Anita Arias networks for providers to share knowledge, (Le Bonheur Children’s Hospital, Memphis, experience, and best practices to improve the TN), Dylan E. Graetz, MD (Oncology), a St. Jude care and survival of critically ill children Pediatric Hematology-Oncology Fellow, is with cancer. evaluating how PEWS affects interdisciplinary One of the Program’s initiatives, the communication about patient deterioration in Pediatric Early Warning System (PEWS), hospitals with different resource levels. includes 48 pediatric cancer centers in 18 countries in Latin America. PEWS improves early identification of clinical deterioration in hospitalized patients to facilitate timely intervention and prevent complications and critical illness. PEWS has 2 components: a scoring tool calculated by the bedside nurse as part of routine care and an action

Asya Agulnik, MD, MPH algorithm that guides clinical teams responding to patients with deterioration. As St. Jude’s reach expands to more LMICs, interest in our transversal programs PEWS was first used in the Unidad Nacional Transversal continues to grow. Currently, 8 transversal programs instill uniform interventions de Oncologia Pediatrica (UNOP; Guatemala across regions and facilitate global research collaborations in Critical Care, City, Guatemala), where it was successfully Programs Disease Burden and Simulation, Health Systems, Infectious Diseases, Metrics implemented and validated as an accurate tool and Performance, Neuro-Oncology, Nursing, and Palliative Care. Here we briefly for identifying clinical deterioration in children describe work in 3 of these programs. with cancer who are hospitalized in a resource- limited setting. A cost–benefit analysis showed a substantial net annual cost savings resulting from fewer unplanned transfers to Dylan E. Graetz, MD the Pediatric Intensive Care Unit. Despite the PEWS Global Project impressive PEWS results at UNOP, whether this 48 centers in 18 countries MARACAIBO CALI QUITO experience is generalizable to other centers in TIJUANA GUAYAQUIL CHIHUAHUA CUENCA Latin America is unclear, because the centers vary in hospital organization, nursing staffing, HAITI SANTIAGO SANTA CRUZ LIMA SALVADOR LA PAZ COCHABAMBA BAHIA and pediatric intensive care unit availability. SANTO DOMINGO LA PAZ CULIACAN MONTERREY The Program also provides pediatric PARAGUAY SAN LUIS POTOSI CHILE onco-critical care education. This year, the CELAYA QUERETARO PACHUCA MERIDA BUENOS AIRES Program worked with the Division of Critical LEO GUADALAJANRA CDMX TOLUCA XALAPA CORDOBA Care at St. Jude to sponsor the first Pediatric CAMPECHE PUEBLA Onco-Critical Care Symposium (POCCS) CHIAPAS TEGUCIGALPA GUATEMALA in April 2019. St. Jude Global provided 30

SALVADOR scholarships to pediatric intensivists from all MANAGUA over the world to attend the conference at SAN JOSE

PANAMÁ CHIRIQUI

2019 Scientific Report | 72 73 | 2019 Scientific Report Infectious Diseases Transversal with the annual St. Jude/PIDS Pediatric Program Infectious Diseases Research Conference; Infections and their complications are major graduates of the course present their work contributors to treatment-related mortality and connect with leaders in the field. To date, in pediatric patients with cancer. The problem 103 participants from 77 institutions in 38 is exacerbated in low-resource settings, countries have completed the course. where most deaths during treatment are Pediatric oncology units operate mostly caused by infection. The Global Infectious in large public hospitals that have multiple Diseases Program was established to better competing needs and often limited resources. understand the reasons for the high incidence Optimizing the use of scarce resources of infections and poor treatment outcomes and effectively communicating the needs and to implement successful, sustainable of pediatric oncology units are essential solutions. Since its inception, the Program to delivering safe health care. To date, the has worked with local health professionals to Program has helped establish 15 care teams raise standards of care in infection control at pediatric oncology institutions, mostly and prevention, augment the quality of the in Latin America. The teams are composed local clinical workforce, and collaborate in of St. Jude–trained leaders and infection designing and conducting clinical and quality- preventionists who promote and deliver safe, improvement research to guide interventions high-quality infection care and prevention based on evidence. Sustained improvement in pediatric oncology units. The Program in the standards of infection care and collaborates with the local teams to improve prevention requires a robust local presence of standards for infection care and prevention, infectious diseases experts and the support of conduct on-site training, carry out surveillance hospital leaders. Therefore, the Program has of infections, implement quality improvement, established and manages 2 training tracks, one and establish processes to maximize the use of for infection preventionists and the other for local resources, incorporating such practices infectious diseases physicians and leaders. into routine institutional structures. The Intensive Infection Control Course Finally, the Program establishes regional for infection preventionists targets staff networks to enhance impact at the local responsible for institutional infection- level. The first network, PRINCIPAL, serves as control programs. The training covers all a model for collaboration among infectious areas relevant to the infection preventionist, disease specialists, supporting the continuous including the safety of patients and healthcare exchange of knowledge and expertise. workers. The Spanish-language version of this PRINCIPAL currently includes 29 institutions course was created in 2005. It uses distance in 13 countries in Latin America and the learning and in-person practicums on the Caribbean. Annual meetings at St. Jude essentials of infection control at selected strengthen the network and facilitate regional sites. In 2018, an English-language collaboration in research and quality- version of the course with a similar curriculum improvement projects. and method was launched. To date, more than 400 participants from 150 institutions in 30 countries have been trained through this course. The second training track targets physicians and leaders in pediatric infectious diseases. This track also combines distance learning and in-person learning. Participants learn the essentials of infections (especially those pertaining to immunocompromised children) leadership, team management, building and implementing research projects, and sharing results through scientific publications. This course is associated

Miguela A. Caniza, MD

2019 Scientific Report | 74 75 | 2019 Scientific Report Disease Burden and Simulation Transversal Program The Disease Burden and Simulation Program provides actionable data and toolkits to support clinicians, health administrators, and health policy stakeholders in better allocating resources to treat pediatric cancer and hematological diseases. The Program includes faculty, staff, and collaborators with expertise in statistics, decision sciences, cancer survivorship, health economics, and epidemiology. Due to the lack of cancer registration systems in LMICs, an accurate accounting of disease burden is impossible. Without knowing how many children need help, governments and nongovernment organizations cannot plan or advocate for increased resources to meet the affected children’s needs. Because statistical data are missing, many children who die of cancer are not accounted for. To address this, St. Jude and the Institute for Health Metrics and Evaluation (IHME) at the University of Washington (Seattle, WA) began a formal partnership to advance knowledge and understanding of childhood cancer around the world. The IHME is the coordinating center for the Global Burden of Disease (GBD) study, which aims to provide a comprehensive, comparable picture of what kills or disables people. The GBD study is quantifying total health loss from the hundreds of diseases, injuries, and risk factors for 195 countries from 1990 to the present. Until recently, childhood cancers were not a major focus of the GBD study. Recognizing that more work needed to be done, Nickhill Bhakta, MD, MPH (Global Pediatric Medicine, Epidemiology & Cancer Control, Oncology) and Lisa Force, MD (Oncology), a St. Jude Pediatric Hematology- Oncology Fellow, collaborated with Drs. Tina Fitzmaurice and Christopher Murray (both of IHME) to introduce methods to better quantify the global childhood cancer disease burden. Their goal is to generate the best-possible data needed to enable all stakeholders— policymakers, health advocates, and public and global health communities—to improve outcomes for pediatric patients with cancer around the world. Lisa Force, MD; Nickhill Bhakta, MD, MPH

2019 Scientific Report | 76 77 | 2019 Scientific Report Certificate-Based Seminars curriculum design, hosting fellows for clinical The St. Jude Global Academy provides short, rotations, and financial support. The programs competency-driven seminars in areas such span 2–3 years and follow competency-based as leadership, palliative and end-of-life care, training of physicians who have completed neuro-oncology, infectious diseases, and pediatrics residency programs. The Education infection prevention and control. These Program Assessment Tool objectively seminars deliver a structured curriculum assesses the quality of pediatric hematology- to improve the knowledge and skills of oncology fellowship programs. Twenty-three participants by using a “train the trainer” pediatric hematologists-oncologists from 8 model to maximize impact. The seminar countries have completed training at UNOP in format includes distance-learning modules Guatemala; they represent more than 90% of and a residential practicum; scholars and the new graduates trained in the region. The clinicians from all St. Jude Global regions number of new pediatric patients at facilities have participated. in the region has also increased more than 2 fold since the program was initiated in 2003. Masters of Science in Global Child Health The MSc in Global Child Health degree program is a collaboration between the St. Jude Graduate School of Biomedical Sciences and the Department of Global Pediatric Medicine. The Tennessee Higher Education Commission approved the program in January 2019. Shaloo Puri, MD (Global Pediatric Medicine), serves as the graduate school assistant dean and global pediatric medicine graduate studies director.

Shaloo Puri, MD In her position, Dr. Puri helped develop the interdisciplinary curriculum. The degree will be Key components of St. Jude Global are training a global workforce, building the offered as a 2-year program that incorporates Strategic clinical and research initiatives needed to advance programs, and training the online and onsite learning. The program offers next generation of leaders to improve care for all children with childhood cancers students around the world a transformative Educational or other catastrophic diseases. St. Jude Global builds human resources capacity educational experience that will enable them Initiatives through strategic educational programs. These include online seminars, guided to realize their potential to advance the courses, medical training programs, and a new MSc degree program in Global treatment and care of childhood cancers and Child Health. other catastrophic illnesses in global settings. It will provide training in basic and applied research, global health systems and innovation, and population sciences, all tailored to child health. The inaugural class will begin in July 2019.

Education Program Fellowship Support and Assessment Tool St. Jude currently collaborates with medical training programs in 6 countries (Brazil, Guatemala, Jordan, Lebanon, Mexico, and Uruguay) to increase the number of specialists who provide care around the world. Plans are being developed to replicate these models in all regions. The institution’s participation in these fellowship programs includes input in

2019 Scientific Report | 78 79 | 2019 Scientific Report by a simple, inexpensive measurement of Sciences), is working with the Department minimal residual disease at Day 19 of induction of Global Pediatric Medicine to develop therapy. Children whose residual leukemic cell research programs focused on the biology level is less than 0.01% at that time point are of racial/ethnic differences in ALL. Through candidates for therapy reduction. The 2 studies collaborations with colleagues in China, demonstrated that a simple, low-cost strategy Guatemala, Japan, and Singapore, Dr. Yang can be used to measure leukemia and identify has identified novel ALL genomic features children for whom therapy can be reduced unique to different ethnic groups and clinically without compromising cure. actionable biomarkers of drug toxicity with Jun J. Yang, MD, PhD (Pharmaceutical racial disparities.

Ching-Hon Pui, MD

St. Jude Global promotes the gradual September 2018. At 3 years after Building implementation of research activities completion of treatment, the at international sites through the probability of patient survival was Research St. Jude Global Alliance. Local 93.3%. This consortium now accrues Capacity—Acute and regional research expertise is approximately 1300 patients per year. developed through St. Jude Global Its progress has helped foster the Lymphoblastic Fellowships, St. Jude Global Scholars, Chinese government’s decision to and the St. Jude Global Academy. approve the development of National Leukemia Trials The regional networks are adopting Health Centers in Shanghai and Beijing consortium-like functions with a for research, education, and patient solid clinical research infrastructure care. Raul C. Ribeiro, MD (Oncology), to provide foundational support for and Gaston Rivera, MD (Global research activities. Pediatric Medicine), in collaboration For example, under the leadership with investigators at Children’s Cancer of Ching-Hon Pui, MD (Oncology, Hospital Egypt 57357 (Cairo, Egypt) Pathology), St. Jude has been and the Instituto Materno Infantil extensively involved in an advisory de Pernambuco (Recife, Brazil) and role in the development of a National former St. Jude faculty member Dr. Childhood ALL Study Group in China. Dario Campana, designed 2 studies Their ALL-2015 trial (a version of (RECIFE ALL-2005 and Egypt VLR ALL St. Jude Total Therapy XV tailored 2011) to reduce treatment intensity for to Chinese patients) accrued 5225 patients with very low–risk pediatric patients from November 2014 to B-lineage ALL. Disease risk is identified

2019 Scientific Report | 80 81 | 2019 Scientific Report based, secure tool specifically designed for St. Jude Global’s registry team has developed LMIC contexts, where trained personnel are a curriculum to train users in how to register limited and guidance on what data to collect children with cancer. As a requisite to having is lacking. We expect this electronic data- access to the registry, users will be required capture process to provide key information to complete training and be given access to physicians, hospital administrators, and to an SJCARES Registry Operations Manual government policy makers to enable them and SJCARES Data Dictionary to support and to design and track quality-improvement guide effective tool utilization. They will also initiatives and provide data for population- be asked to participate in regularly scheduled based cancer registries. The Disease Burden online conferences to discuss difficult cases or and Simulation team has worked closely common data-entry errors. with global partners to ensure that the Module 2 of SJCARES, PrOFILE, is a registry meets local needs and is easy to use. dynamic evaluation of health-services Importantly, all data in the registry will be delivery that helps define an improvement owned by the hospitals using it but sharable in strategy for increasing survival. It also acts as a a deidentified manner to help advance global diagnostic tool, identifying key issues requiring cancer-control efforts. attention and improvement. PrOFILE is not To ensure that patient information is safe a survey; it is a platform on which to build and the platform complies with data privacy local capacity in quality improvement and a laws around the world, the registry is built on community of quality-improvement experts. It top of the OmniComm TrialMaster application, emphasizes the development of metrics and the same program that St. Jude uses to the assessment of performance but recognizes conduct clinical trials. Data are protected by and embraces the expected differences across multiple features (e.g., data encryption and centers, promotes equity and integration segmentation, site- and role-based security, with general child health services, and aims and deidentification). All system users will be to reduce barriers to pediatric hematology- required to use industry-standard second- oncology care. Finally, PrOFILE’s data-

Paola Friedrich, MD, MPH; Miriam Gonzalez-Guzman factor authentication to ensure compliance driven approach facilitates decision making with regulatory requirements. within the limits of economic feasibility, Models and estimates alone are not is an integrated solution to support Because many hospitals lack a workforce and its repeated use will facilitate insightful Childhood sufficient to manage or resolve the evidence-based pediatric cancer care educated on how to enter these data, benchmarking and local tracking of progress. global health disparities attributable and decision making in LMICs. The Cancer to childhood cancer. Better data, system represents a new philosophy Analytics cancer registries, and measurements that aims to continuously identify, of the quality of care and the strength target, and monitor vital health Implementation of PrOFILE of health systems are essential. To metrics that affect patient outcomes. Resource and PHASE 1: PREPARATION 1+ years capture this information, new tools SJCARES is defined by 3 modules: Step 1: Engage pediatric hematology-oncology leadership Epidemiological specifically designed for childhood (1) a hospital-based pediatric cancer Step 2: Identify an assessment team 4 weeks cancer are required. In addition, registry, which ensures that descriptive Step 3: Confirm good fit of the site coordinator and MD Lead Surveillance Step 4: Enroll site coordinator to PrOFILE Train the Trainer healthcare workers will need to be epidemiology and outcomes are Step 5: Enroll participants to the PrOFILE Portal and educational website System educated to collect these data and reported in a standard format; (2) Phase 3 Phase 1 ensure they are of the highest quality. the PrOFILE tool, which provides 4 weeks PHASE 2: ASSESSMENT Finally, it is paramount that we create quantitative health facility data; and A PrOFILE module consists of a global repository and process (3) Systems Analysis, an integrated 1. Electronic forms Phase 2 for storing and integrating all the solution to support evidence-based 2. Educational training modules 3. Mentoring sessions

4. Exercises information, so that ultimately children pediatric cancer care decision making weeks 2 will benefit from it. in LMICs. To drive St. Jude Global growth, Module 1, the hospital-based PHASE 3: INTERPRETATION AND ACTION The PrOFILE team will assist with the St. Jude Global Childhood pediatric cancer registry network, is 1. Action plans based on the facility’s priorities Cancer Analytics Resource and being led by the Disease Burden and 2. Score-based analysis (internal, external, regional) 3. Ongoing monitoring and reporting of progress Epidemiological Surveillance System Simulation Transversal Program. The 6 weeks (SJCARES) was developed. SJCARES SJCARES registry is a free, cloud-

2019 Scientific Report | 82 83 | 2019 Scientific Report WHO Global Initiative for St. Jude as a WHO Implementing Childhood Cancer Partner In accordance with the recent World Health In addition to being a WHO Collaborating Assembly Resolution 70.12, Cancer Prevention Center, in July 2018, St. Jude executed a 5-year and Control in the Context of an Integrated agreement with the WHO to measurably and Approach, and the 2019–2023 WHO General sustainably improve outcomes for children Programme of Work, the WHO is committed with cancer worldwide. Per the agreement, to promoting health and equity for all, St. Jude is providing resources to create a including children with cancer. As mandated childhood cancer–focused WHO program, by the resolution, the WHO will work with with dedicated personnel to advance the nongovernment partners to establish and development of childhood cancer care and implement comprehensive cancer prevention control capacity through a novel global and control programs for managing cancers in initiative. This collaboration synergizes children and adolescents. the authority of the WHO (working with In September 2018, at an inaugural governments, nongovernment agencies, side event titled, “Ensuring a Right to Cure: and leaders across health systems) with Improving Childhood Cancer Care and the implementation expertise of St. Jude Decreasing Global Survival Disparities,” in Global (working with partners, including conjunction with the United Nations (UN) multidisciplinary providers and hospital General Assembly, the WHO announced a new administrators). effort—the WHO Global Initiative for Childhood St. Jude and the WHO have committed Cancer—with the aim of reaching at least a to an action plan inclusive of in-country 60% survival rate for children with the most assessments and implementation efforts common cancers by 2030, thereby saving that will be supported by St. Jude Global and an additional 1 million lives. This new target extend to linked global initiative deliverables. represents more than a doubling of the global During 2019, at least 6 focus countries with survival rate for children with cancer. The WHO regional and national offices will be

James R. Downing, MD Initiative will facilitate increased prioritization identified to receive tailored support from of childhood cancer through awareness raising the WHO and St. Jude. The countries will The World Health Organization (WHO) designates collaborating centers to carry at the global and national levels and expand demonstrate early measurable progress in The out specific activities to support WHO programs. These collaborations create the capacity of countries to deliver childhood childhood cancer care and serve to illustrate opportunities for sharing technology and exploiting the expertise and institutional cancer care. Cross-cutting efforts will engage advances in one or more pillars of the initiative First WHO capacity of designated centers and the visibility and leadership of the WHO. In global partners across 3 pillars: access, quality, (access, quality, policies), while providing Collaborating March 2018, St. Jude, through the Department of Global Pediatric Medicine, and policies. The UN event was hosted by the feedback for the refinement of tools to be became the first WHO Collaborating Center for Childhood Cancer. Permanent Missions to the United Nations of used in the broader global initiative. Center for the Republic of Uzbekistan and the Hashemite The WHO Global Initiative for Childhood Kingdom of Jordan, in partnership with Cancer creates an unprecedented opportunity Childhood St. Jude, the WHO, and the Permanent to address the disparities in global cancer Childhood Missions to the United Nations of El Salvador, outcomes. By transforming facility-based Cancer Cancer the Republic of Moldova, the Kingdom of efforts into national programs embedded 2030 Morocco, the Republic of the Philippines, the in the health systems and enforced in Target Russian Federation, and the United States. government policies, this initiative will The WHO will support governments accelerate improvements in patient outcomes in assessing current capacities in cancer across diagnostic, demographic, and country 3 Pillars Access Quality Policies diagnosis and treatment, including the borders, and it has the potential to have a availability of the workforce, medicines, and global impact not previously thought possible. 90%+ of children 90%+ of children technologies; setting and cost prioritizing with access to at 90%+ of children covered by a cancer diagnostic and treatment programs; least one fit-for- diagnosed and national policy purpose completing inclusive of and integrating childhood cancer into national 3 Subtargets treatment standardized social strategies, health benefits packages, and social center or therapy with protection network with a care to alleviate packages for insurance schemes. trained suffering childhood workforce cancer

By 2030, ensure at least 60% survival of children with cancer worldwide and alleviation of suffering for all. 2019 Scientific Report | 84 85 | 2019 Scientific Report St. Jude Global is seamlessly Reimagining integrating research, innovation, and advanced education. Using programs the Future of and capacity building, we are creating Pediatric Care a new paradigm in pediatric oncology in which global programs are Worldwide incorporated into academic medicine and disparities in access to modern treatments are narrowed. Through partnerships with governments and the WHO, we will develop sustainable, scalable models that ensure that all children with cancer or other catastrophic diseases can access quality care, wherever they are.

Carlos Rodriguez-Galindo, MD

2019 Scientific Report | 86 87 | 2019 Scientific Report THE AFFILIATE PROGRAM EXTENDS ST. JUDE CLINICAL RESEARCH

Baton Rouge, LA Peoria, IL

Our Lady of the Lake Children’s Hospital of Illinois Children’s Hospital – Our Lady OSF Healthcare System, of the Lake Regional Medical University of Illinois College of Center Medicine at Peoria

Charlotte, NC Shreveport, LA

Novant Health Hemby Feist-Weiller Cancer Center Children’s Hospital LSU Health Sciences Center

Huntsville, AL Springfield, MO The St. Jude Affiliate Program has 8 affiliate clinics. Under the leadership of Carolyn L. Russo, MD, this Huntsville Hospital for Women Mercy Children’s Hospital network of affiliated clinics works with the St. Jude Clinical & Children – Huntsville Hospital Springfield – Mercy Health Trials Administration to extend the institution’s mission. System Physicians and staff at each clinic participate in St. Jude treatment and research programs by enrolling and providing care to patients on St. Jude clinical protocols. The clinics also provide patients with the opportunity to receive part of their care at a facility near their home community. Johnson City, TN Tulsa, OK

Niswonger Children’s Hospital The Children’s Hospital at Saint Victor M. Santana, MD; Carolyn L. Russo, MD – Johnson City Medical Francis Center, East Tennessee State University

2019 Scientific Report | 88 89 | 2019 Scientific Report Center for Bioimage Informatics Director: Khaled Khairy, PhD SHARED RESOURCES CONTRIBUTE The Center offers state-of-the-art bioimage technologies to extract accurate, usable information from complex data sets EXPERTISE AND SUPPORT TO generated by advanced imaging technologies. The Center provides expertise in processing, registration, and segmentation ST. JUDE RESEARCH of biological images, as well as machine learning, computer vision, and image-based data quantitation and visualization.

These 19 Shared Resources, including 9 supported by the St. Jude Comprehensive Cancer Center (indicated by an *), provide expertise and cutting-edge technologies in support of all research at St. Jude. The nearly 400 Center for In Vivo Imaging and Therapeutics* scientists and technologists who staff the facilities described here not only process samples but also contribute Director: Walter Akers, DVM, PhD to the design, performance, and analysis of experiments. The Center provides cutting-edge imaging, surgery, and image-guided therapeutic services for preclinical studies. The technologies available include magnetic resonance imaging, Animal Resource Center positron emission tomography, high-frequency ultrasound, Director: Harshan Pisharath, DVM, PhD bioluminescence imaging, intravital multiphoton microscopy, and The Center provides a comprehensive animal care program that image-guided radiation therapy. The staff also assist investigators includes technical services (resource procurement, drug delivery, with planning and performing experiments to ensure that and biological sample collection), husbandry and specialized care, preclinical studies are conducted at the highest standard. cryopreservation and storage of biological specimens, and veterinary services to ensure the well-being and clinical care of laboratory animals. Center for Proteomics and Metabolomics Director: Junmin Peng, PhD Biorepository Research Coordinator: Anthony High, PhD Director: Charles G. Mullighan, MBBS, MD In support of basic and clinical research, Technical Director: Matthew Lear the proteomics and metabolomics staff Biorepository services include the processing and archiving of deliver a range of mass spectrometry–based normal human tissues and disease specimens for future research analyses, including protein identification studies. Cryopreserved specimens include cells, tissues, DNA, and and characterization, posttranslational- body fluids. The Biorepository staff processes more than 5000 modification analysis, affinity purification, specimens per month, and more than 370,000 specimens have * Cell and Tissue Imaging Center comprehensive profiling of the proteome been archived. Camenzind Director of Electron Microscopy: and phosphoproteome, and metabolite Robinson, PhD profiling. Director of Light Microscopy: Victoria C. * Biostatistics Frohlich, PhD Director: Deo Kumar Srivastava, PhD Staff in Cell and Tissue Imaging offer The Biostatistics Shared Resource within the Department consultation on the design and execution of Biostatistics provides innovative statistical support to all of optical-imaging experiments; assist with * research initiatives at St. Jude. This support includes designing image acquisition, analysis, quantification, Cytogenetics and analyzing studies and performing expert analyses of large presentation, and publication; and educate Director: Marcus Valentine datasets, such as those generated by genomic or imaging investigators about the theory and practice Cytogenetics performs studies. Biostatistics staff also provide biostatistical education, of imaging technologies. The Division of G-band karyotyping and a centralized randomization system, statistical software, and Light Microscopy houses laser-scanning spectral karyotyping technical support for hardware and software infrastructure. imaging systems, spinning-disk confocal of tumor or targeted imaging systems, super-resolution imaging, embryonic cell lines, sheet plane illumination microscopy, and patient-derived Center for Advanced Genome Engineering widefield imaging and automated scanning. orthotopic xenografts, Director: Shondra M. Miller, PhD The Division of Electron Microscopy and somatic cell hybrids The Center provides expertise in introducing investigator- houses transmission and scanning electron for preclinical studies. defined mutations into mammalian cells or human pluripotent microscopes, including a Helios NanoLab Various fluorescence in stem cells. The staff collaborate with our preclinical resources to DualBeam for 3-dimensional imaging. situ hybridization (FISH) produce knockout and knockin models and to generate validated Other technologies available include analyses, including tissue- genotyping protocols. The Center also has a strong focus on negative staining of single particles and section, protein, DNA, research and development, identifying, validating, and delivering immunoelectron microscopy. and RNA FISH, are also new genome-editing applications and technologies. available.

2019 Scientific Report | 90 91 | 2019 Scientific Report Diagnostic Biomarkers Pharmacokinetics* Preclinical Director: Ruth Tatevossian, MD, PhD Director: Mary V. Relling, PharmD Pharmacokinetics Technical Director: Paul Mead, PhD Co-Director: Kristine Crews, PharmD Director: Burgess Freeman III, Diagnostic Biomarkers provides expert advice and technical Pharmacokinetics staff provide PharmD and experimental support for conducting molecular assays (e.g., study design, modeling, and assay Staff in this Shared Resource nucleic acid extraction, PCR, RT-PCR) in prospective clinical implementation for investigator- support pharmacokinetic and trials. Staff members consult with researchers to design assays, initiated studies. They also pharmacodynamic studies optimize and validate methods, execute experiments, and perform clinical pharmacokinetic executed in the preclinical analyze data. and pharmacodynamic analyses setting, particularly in the and modeling. The goal of this context of disease modeling. Shared Resource is to develop Preclinical Pharmacokinetics new drugs and optimize drug enhances basic and Flow Cytometry and Cell Sorting* scheduling and dosing for clinical translational research through Director: Richard A. Ashmun, PhD studies. the development and This Shared Resource provides access to sophisticated flow validation of bioanalytical cytometry equipment, services, and expertise. The staff actively methods, preclinical study trains St. Jude investigators in flow cytometry theory and design, and pharmacometric applications, so that they can conduct flow cytometry analyses * Protein Production analyses. independently. Other technologies available include high-end Director: Richard Heath, PhD cell sorting, magnetic cell separation, and a repository of more Staff in Protein Production than 500 validated reagents. express and purify proteins from Transgenic and Gene bacterial, insect, or mammalian Knockout* producer cells. These proteins Director: Hartmut Berns, PhD Hartwell Center for are then used in biochemical This Shared Resource uses Bioinformatics and or structural analyses, high- cutting-edge transgenic and Biotechnology throughput screening, or as gene-targeting technologies Geoffrey Neale, PhD Director: reagents or antigens. This to generate genetically The Hartwell Center provides facility expresses and purifies engineered preclinical models services in a wide variety of approximately 110 proteins for investigators. It also offers high-throughput biotechnology per year. various additional services in platforms, including Sanger DNA support of model development, sequencing, DNA microarray including expertise in analysis, genome sequencing, Vector Development traditional embryonic stem cell Byoung Ryu, PhD genotype analysis, functional Director: targeting and culture. genomics, and macromolecular The Vector Development staff synthesis. Investigators working develop and provide research- with the Hartwell Center can grade viral vectors and maintain interface with the Bioinformatics an archive of well-characterized Veterinary Pathology and Biotechnology Core* to cellular and plasmid reagents. Core perform high-end analytics They also help investigators Director: Peter Vogel, DVM, PhD required for data interpretation. transition promising preclinical The Core’s services include vectors into clinical-grade viral diagnostic analysis of vectors that are then produced in biological fluids and necropsy Molecular Interaction Analysis the Children’s GMP, LLC, for gene (e.g., tissue collection and Director: Amanda Nourse, PhD therapy clinical trials. perfusion), histology (e.g., Staff in this Shared Resource assist investigators by using immunohistochemistry and biophysical approaches for molecular interaction–based research. antibody optimization), and The technologies available include analytical ultracentrifugation, pathology (e.g., laser-capture surface plasmon resonance, isothermal iteration calorimetry, microdissection and image multiangle light scattering, and microscale thermophoresis. analysis) of preclinical models.

2019 Scientific Report | 92 93 | 2019 Scientific Report SCIENTIFIC HIGHLIGHT

Dual-Energy Computed Tomography Holds Promise to SCIENTIFIC Improve the Accuracy of Radiation Therapy Planning

Radiation therapy planning based on computed the phantoms. With scan conditions of 120-kVp tube HIGHLIGHTS tomography (CT) images conventionally uses potential and 20-mGy CTDIvol, the accuracies of calibration curves to convert the value in Hounsfield the measured ED and Zeff were on the order of Units of each pixel in the images to the electron ± 1% and ± 2%, respectively, for both soft-tissue and density (ED), in the case of photon therapy, or the bone-equivalent materials, with somewhat larger proton stopping power, in the case of proton therapy, percentage deviations for lung-mimicking materials. of the tissue. However, concern over deviations For iodine quantification, the median absolute from the calibration conditions often prompts the deviations from the nominal values were 0.3 mg/mL restriction of patient scans to fixed parameters, or less for concentrations of 2-20 mg/mL, with potentially resulting in suboptimal image quality. an overall median deviation of –0.1 mg/mL. The For proton therapy, the conversion process also accuracies appeared to be unaffected by changes introduces range uncertainties that typically in the tube potential, radiation dose, gantry necessitate the use of an expanded target margin or rotation time, or spectral reconstruction level. The increased plan robustness. These strategies are not researchers thus demonstrated the high accuracy of

ideal and may result in more normal tissues being the ED, Zeff, and iodine concentration values derived irradiated. from DL-DECT.

Dual-energy CT (DECT) allows direct calculation Direct derivation of the ED and Zeff from DL- on a pixel-by-pixel basis of the ED, the effective DECT scans can potentially improve the accuracy

atomic number (Zeff), and subsequently the proton of radiation therapy planning, especially for proton stopping power. This approach holds promise to therapy. If the proton stopping power can be eliminate the need for calibration-curve mapping for calculated with greater confidence, the current photon therapy and to improve the range accuracy conservative safety margins and plan robustness for proton therapy. Another advantage of DECT is may no longer be required. Furthermore, because that it enables the iodine concentration in tissues DECT enhances iodine contrast, it should be possible to be estimated. Iodinated contrast agent is often to reduce the dose of iodinated contrast agent for administered to patients undergoing CT simulation pediatric patients. Work is ongoing at St. Jude to to better visualize tumors and blood vessels, but the bring these potentials to realization. Hua C et al, Med contrast agent may cause side effects; therefore, Phys 45:2486–97, 2018 reducing the dose required would be beneficial. St. Jude is pioneering the use of DECT in radiation therapy. Because DECT was originally developed for diagnostic radiology applications, early adopters in the radiation oncology community are working to define its roles in radiation therapy and provide guidelines for its use. As an initial contribution to this effort, Chia-ho Hua, PhD (Radiation Oncology), and colleagues studied the

accuracy of the ED, Zeff, and iodine concentration values determined with a new dual-layer DECT (DL- DECT) system (IQon Spectral CT, Philips Healthcare) and examined the dependence of the accuracy on the scan and reconstruction parameters used. Their findings were published in Medical Physics. The accuracy measurements were performed Chia-ho Hua, PhD on polymer test phantoms with various tissue- equivalent inserts and iodine inserts of different concentrations. The expected values of the ED and

Zeff were derived from the chemical composition of

2019 Scientific Report | 94 95 | 2019 Scientific Report SCIENTIFIC HIGHLIGHT SCIENTIFIC HIGHLIGHT

Risk-Stratified Therapy for Young Children with Pan-Cancer Study Reveals the Genomic Architecture of Medulloblastoma: Results of the Phase II Trial SJYC07 Pediatric Cancers

Medulloblastoma, the most common malignant and cyclophosphamide), for high-risk disease. The transformation of a normal cell into a cancer generated by ultraviolet light (UV) exposure and brain tumor in children, accounts for 18%-20% Maintenance consisted of cyclophosphamide, cell involves the dysregulation of key biological was present in 8 B-lineage acute lymphoblastic of childhood brain tumors. Young patients with topotecan, and erlotinib for all patients. To refine processes driven by specific genes and proteins. Pan- leukemia samples, suggesting that UV exposure or medulloblastoma have a lower overall survival than the stratification, a molecular cohort of 190 patient cancer analysis, which studies molecular aberrations other mutational processes could lead to pediatric do older children, mainly because radiation therapy samples with methylation and matched germline across multiple cancer types, yields vital information leukemogeneis. Enrichment of somatic alterations (RT) is reduced or omitted in young children due and tumor-sequencing data were analyzed. Primary on commonalities and differences across tumor in individual histotypes or the pan-cancer cohort to severe long-term sequelae. Medulloblastoma endpoints were event-free survival (EFS) and lineages. To date, pan-cancer studies have been revealed 142 mutated driver genes in pediatric is classified into 4 molecular subgroups—WNT, methylation-profiling patterns associated with performed for adult but not pediatric cancers. cancer. Strikingly, 78 (55%) of those genes were not sonic hedgehog (SHH), group 3, and group 4—that progression-free survival (PFS). To unravel the genetic repertoire of childhood found in adult pan-cancer studies. Furthermore, have distinct clinical, genetic, and prognostic At a median follow-up of 5.5 years, 5-year EFS cancers, with the goal of developing targeted, safe CNAs and structural variations, which are often characteristics. In infants and young children, was 31.3%, 55.3%, 24.6%, and 16.7% for the entire, low-, therapies for this population, Jinghui Zhang, PhD driving events in childhood cancers, made up 62% medulloblastoma has not been systematically intermediate-, and high-risk cohorts, respectively. (Computational Biology), and her team analyzed of events and were more efficiently detected by studied; molecular classification has not been The team identified 2 infant molecular subtypes paired tumor and normal samples from 1699 WGS than by WES. Dr. Zhang’s team identified uniformly applied; and outcomes have not been within the SHH subgroup: iSHH-I and iSHH-II. Infants patients (aged 21 years or younger) enrolled in 21 recurrently altered biological pathways in 682 assessed by subtype or subgroup. with iSHH-II had better 5-year PFS than did those clinical trials by the Children’s Oncology Group leukemia and 236 solid tumor samples. Point Giles W. Robinson, MD (Oncology), Amar J. Gajjar, with iSHH-I (75.4% vs. 27.8%). The 5-year PFS of (COG). This study, reported in Nature, analyzed mutations affecting signaling pathways were MD (Pediatric Medicine, Oncology), and Paul A. patients with low-risk iSHH-II was 90.9% versus 22.2% samples from 6 tumor histotypes. Patient mostly subclonal, indicative of subclonal mutations Northcott, PhD (Developmental Neurobiology), led for those with high-risk iSHH-I. Most progressions samples were obtained through the COG and the contributing to tumorigenesis. Analysis of 6959 the effort to analyze the therapeutic and molecular or relapses occurred during therapy; 55% occurred Therapeutically Applicable Research to Generate coding mutations with matching WGS and RNA- outcomes of early childhood medulloblastoma in during maintenance. Therapy was well tolerated, and Effective Treatments project of the National Cancer sequencing data showed that mutant alleles were the Phase II trial SJYC07, which was reported in there were no protocol-related deaths. Institute. The researchers used whole-genome expressed in 34% of the mutations, and 20% of the The Lancet Oncology. SJYC07 enrolled 81 children This study provides a comprehensive landscape sequencing (WGS), whole-exome sequencing (WES), mutations had allele-specific expression. younger than 3 years with newly diagnosed of medulloblastoma in infants and young children and transcriptome sequencing to analyze data on This landmark study provides a detailed overview medulloblastoma or aged 3–5 years with newly and advocates the use of molecular risk-adapted somatic mutation rates and signatures and process of the mutational landscape in childhood cancer. It diagnosed nonmetastatic medulloblastoma without models in future trials. Although treatment was well it under a uniform analytical pipeline. Somatic reveals that only 45% of driver genes are common in high-risk features at 6 centers in the U.S. and tolerated and primary outcomes differed by clinically mutations analyzed included single-nucleotide childhood and adult cancers. Thus, the genetic basis Australia. All patients received identical induction risk-stratified groups, EFS did not improve. However, variations, small insertions/deletions, copy number for childhood cancer is distinct from that of adult chemotherapy (methotrexate, vincristine, cisplatin, improved PFS in patients with the iSHH-II subtype alterations (CNAs), and structural variations. cancer, and gene panels used to detect genomic and cyclophosphamide; vinblastine was added without RT or ventricular/high-dose chemotherapy The median somatic mutation rate ranged from abnormalities in adults with cancer are not sufficient for high-risk disease). Risk was assigned based supports the notion that patients with this subtype 0.17 per million bases in acute myeloid leukemia and for genomic profiling of pediatric patients with on the clinical characteristics, and risk-adapted can receive radiation-sparing therapy, and molecular Wilms tumor to 0.19 per million in osteosarcomas, cancer. Datasets developed in this pan-cancer study consolidation (cyclophosphamide, etoposide, classification will improve risk stratification in future which was lower than that for many adult cancers. will provide a roadmap for functional validation and carboplatin) was given for low-risk; focal RT, for trials of childhood medulloblastoma. Robinson GW et Eleven genome-wide mutational signatures were implementation of genomics to facilitate precision intermediate-risk; and chemotherapy (topotecan al, Lancet Oncol 19:768–84, 2018 identified. Notably, 1 signature matched that medicine in children with cancer. Ma X, Nature 555:371–6, 2018 A B Figure. (A) The

6 303 Subtype 100 t-distributed stochastic iSHH−I (n = 38) neighbor embedding 200 B-ALL T-ALL AML NBL WT OS 4 iSHH−II (n = 49) 80 (t-SNE) plot showing the separation of 100 60 the iSHH-I and 2 iSHH-II subtypes of

40 medulloblastoma. KIT NF1 ALK RB1 WT1 IL7R MYB MYC FLT3 TAL1 JAK3 JAK2 TP53 LEF1 TLX3 PAX5 ABL1 TCF3 ETV6 ATRX PHF6 EZH2 TERT BTG1 USP7 CTCF CBFB PTEN KRAS IKZF1

(B) Progression- NRAS DNM2 MYCN CRLF2 SETD2

0 USP9X KMT2A RUNX1 KMT2D CCND3 KDM6A FBXW7 WHSC1 BCL11B 20 free survival (PFS) PTPN11 SHANK2 CDKN2A CDKN1B NOTCH1 analysis of iSHH-I CREBBP t-SNE 2 * * * * * * * * * * * * *

Progression-Free Survival (%) * * * * * −2 0 and iSHH-II subtypes. Reprinted from Lancet 30 0 1 2 3 4 5 6 7 8 9 10 Oncol, 19, Risk- 15 −4 Years From Start of Treatment adapted therapy for young children with iSHH-I 21(0) 10(0) 7(0) 6(1) 6(1) 5(1) 3(3) 3(3) 1(5) 0(6) 0(6) medulloblastoma

−6 CBL TOX (SJYC07): therapeutic EED ERG WAC MGA JAK1 TLX1 TET2 TCF7 EBF1 ZEB2 XBP1 UBA2 BRAF ADD3 RAG1 CHD4 LMO2 iSHH-II 21(0) 16(1) 15(1) 14(2) 13(3) 12(4) 12(4) 9(7) 3(13) 0(16) 0(16) NPM1 BCOR NIPBL ARID2 EP300 GATA2 RPL22 RPL10 SUZ12 ASXL1 ASXL2 STAG2 SH2B3 NUP98 PTPN2 ATF7IP and molecular CEBPA PTPRD PIK3R1 NCOR1 S TA T5B MLLT10 ZNF217 ZNF384 ARID1A NKX2−1 BCORL1 ZFP36L2 DROSHA Number at Risk (Number Censored) outcomes from a TBL1XR1 −6 −4 −2 0 2 4 6 multicenter, phase 2 * * * * * * * * * * * * * * * * * * SMARCA4 * * * * * * * * * * * t-SNE 1 trial. Robinson GW et * al, 768–84, © 2018, Figure. Top 100 recurrently mutated genes in childhood cancer. The case count for each histotype is shown in the same color as the legend. Asterisks indicate genes iSHH−I: 5-yr PFS = 27.8% (95% CI 9.0-46.6%) with permission from not reported in previous adult pan-cancer analyses. Abbreviations: B-ALL, B-lineage acute lymphoblastic leukemias; T-ALL, T-lineage acute lymphoblastic iSHH−II: 5-yr PFS = 75.4% (95% CI 55.0-95.8%) Elsevier. leukemias, AML, acute myeloid leukemias; NBL, neuroblastomas; WT, Wilms tumor; OS, osteosarcoma. Reprinted by permission from SNCSC GmbH: Nature, 555:371–6, Ma X et al, Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. © 2018 Springer Nature

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CIRCLE-Seq: a New Technique for Identifying the On-Target and Off-Target Effects of CRISPR–Cas9

Genome editing by CRISPR–Cas9 is now widely In comparison with previously reported methods (i - ii) Cell culture and gDNA Isolated used for specifically directing mutations in genomic for detecting the off-target effects of genome isolation (Steps 1-8) Cells gDNA DNA. However, CRISPR–Cas9 is limited by the editing, CIRCLE-seq provides numerous advantages. introduction of off-target mutations within the CIRCLE-seq requires a relatively small number of genome that may be deleterious to the organism. sequencing reads (3-5 × 106 reads) and reduces Identifying such off-target mutations is imperative the uniformly high background of random reads

for clinical applications of CRISPR–Cas9, because associated with other cell-free methods. In contrast T7 gRNA unknown off-target mutations may drive oncogenic with cell-based methods of off-target detection, (iii) sgRNA cloning and in sgRNA vitro transcription (IVT) IVT transformation of cells. CIRCLE-seq does not rely on DNA damage–repair (Step 9) Several methods are available for defining machinery for detection, is not affected by the the off-target effects of CRISPR–Cas9-mediated method of Cas9 delivery, and has greatly improved Cas9 + sgRNA (RNP) genome editing. However, these methods are sensitivity. Moreover, CIRCLE-seq does not require (iv) In vitro cleavage of PCR generally limited by low sensitivity, high background, alignment with a reference genome to identify amplicon with RNP PCR and a reliance on cellular DNA damage–repair potential Cas9-mediated DNA double-stranded (Steps 10-21) pathways for detection. To address these breaks, permitting detection of off-target mutations shortcomings, Shengdar Q. Tsai, PhD (Hematology), in the genomes of organisms lacking complete and colleagues developed a novel approach to sequencing or annotation or in genomes with high identify the on-target and off-target mutations genetic variability. CIRCLE-seq greatly reduces Random resulting from CRISPR–Cas9-based genome editing. the sequencing coverage requirements required shearing Sheared gDNA Circularization for in vitro reporting of cleavage by other methods. Therefore, CIRCLE-seq is easily ~300 bp effects by sequencing (CIRCLE-seq) is a cell-free adaptable and can be performed in any laboratory method that uses circularization of randomly with high-throughput sequencing capability. sheared genomic DNA fragments containing both Lazzarotto CR et al, Nat Protoc 13:2615–42, 2018 (v - vi) CIRCLE-seq library on- and off-target CRISPR–Cas9 sites, which are then preparation (gDNA shearing Circularization subjected to nuclease cleavage, adaptor ligation, and and intramolecular selective sequencing. circularization) Degrade residual linear DNA In Nature Protocols, Dr. Tsai’s team reported (Steps 22-57) the specific method by which CIRCLE-seq is performed to identify genome-wide on- and off- target mutations introduced by CRISPR–Cas9. The protocol consists of 97 steps that are performed over the course of 2 weeks. These CIRCLE-seq protocol steps are divided into 8 distinct stages: Cas9 + sgRNA (1) Cells or tissues are harvested. (2) Genomic DNA (RNP) is extracted. (3) Single-guide RNAs (sgRNAs) are (vii) In vitro cleavage of cloned and transcribed in vitro. (4) The Cas9–sgRNA circularized gDNA with RNP ribonuclear protein complexes are tested for their ability to cleave a PCR amplicon containing the (Steps 58-62) intended CRISPR–Cas9 target site. (5) The genomic Adapter ligation + PCR DNA is sheared into fragments. (6) A CIRCLE-seq Paired-end library is prepared by circularizing the genomic DNA high-throughput sequencing fragments and degrading any residual linear DNA. (viii) NGS library preparation, (7) The circularized DNA fragments containing the NGS and data analysis CRISPR–Cas9 on- and off-target sites are cleaved (Steps 63-97) with an optimized Cas9–sgRNA ribonuclear protein CIRCLE-seq complex. (8) Adapters are added to the cleaved reads ends of the genomic DNA fragments, which are then Figure. Overview of the CIRCLE-seq workflow. Reprinted by permission DSB PCR amplified and subjected to paired-end high- from SNCSC GmbH: Nat Protoc, 13:2615–42, Lazzarotto CR et al, Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq. throughput sequencing. © 2018 Springer Nature

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A Novel Druggable Target to Selectively Modulate Androgen Mixed Phenotype Acute Leukemia Study Motivates the Receptor Activity for the Treatment of Spinal Bulbar Expansion of the WHO Classification Scheme for Acute Muscular Atrophy Leukemias

Spinal bulbar muscular atrophy (SBMA) is a recapitulated the symptoms and pathology of Mixed phenotype acute leukemia (MPAL) represents the WT1 gene was frequently altered in T/myeloid debilitating motor neuron disease affecting 1 in the human disease. When TA and MEPB were 2%-3% of pediatric acute leukemias, and children MPAL. T/myeloid MPAL resembled early T-cell 40,000 men worldwide. It is caused by a CAG- administered to the SBMA mice, MEPB was more with this rare disease typically experience poor precursor ALL (ETP-ALL), in that it carried mutations repeat expansion in the androgen receptor (AR) effective than TA at diminishing SBMA phenotypic survival (i.e., 20%-40%). Clinicians have yet to that affected hematopoietic development and gene, which confers a toxic gain of function. This symptoms and pathology. Pharmacokinetic determine the optimal treatment for patients with signaling. Differences also existed among specific gain of function requires activation of the AR by its analysis of TA and MEPB in mice revealed that MPAL, which has features similar to those of both signaling pathways and epigenetic regulators in the cognate ligands testosterone or dihydrotestosterone MEPB exhibits superior bioavailability compared acute lymphoblastic leukemia (ALL) and acute different subtypes of MPAL. (DHT), in addition to binding of various activating or with TA, suggesting that MEPB is a more beneficial myeloid leukemia. Although some MPAL cases have During their search for the MPAL cell of origin, repressing cofactors. One domain within the AR in therapeutic because it has optimal duration a classic MLL rearrangement or BCR–ABL fusion, the the researchers discovered that the founding which such cofactors bind is termed the activation and penetration in the tissues affected by SBMA genetic basis of most cases has remained unknown. genetic lesions arose in early hematopoietic function 2 (AF2) domain. A previous study in a pathology. In a large, blinded preclinical trial in To improve the treatment and ultimately progenitors and that individual subpopulations Drosophila model of SBMA by J. Paul Taylor, MD, PhD SBMA mice, MEPB improved several phenotypic the survival of children with this rare leukemia, of cells could regenerate the immunophenotypic (Cell & Molecular Biology), and colleagues revealed outcomes and quality-of-life parameters, including Charles G. Mullighan, MBBS, MD (Pathology), and diversity. Thus, MPAL cells are primed for lineage that cofactor binding specifically to the AF2 domain body weight, motor control and coordination, and an international group of collaborators analyzed promiscuity by their cell of origin and founding is required for driving neurodegeneration in SBMA. muscle strength. Moreover, spinal cord, muscle, and data from 115 patients with MPAL and identified the lesions and not by secondarily acquired genomic Because cofactor binding to the AF2 domain can be testicular degeneration were reduced in a dose- disease’s genetic basis. In a recent Nature article, alterations. selectively modulated by small-molecule compounds dependent manner in the SBMA mice. the researchers reported the distinct genomic These findings prompted Dr. Mullighan and that bind a nearby motif termed binding function 3 To glean insight into the mechanism of action of profiles of the 3 most common subtypes of MPAL—T/ his collaborators to propose that the World Health (BF3), the BF3 motif is an ideal druggable target for MEPB on CAG repeat–expanded AR, the researchers myeloid, B/myeloid, and KMT2A (MLL)-rearranged Organization update the classification scheme for simultaneously mitigating the toxic gain of function conducted several in vitro assays of AR functional MPAL—as determined by sequencing of exomes, acute leukemias to include the 3 subtypes of MPAL. resulting from CAG-repeat expansion in activity. MEPB treatment did not affect DHT- transcriptomes, and whole genomes, among other This work has implications for risk stratification AR and preserving its native function as a dependent translocation of the AR to the nucleus analyses. and tailoring of treatments based on genomic data transcription factor. or its transcriptional activity, indicating that MEPB Dr. Mullighan’s team found that the ZNF384 gene and immunophenotyping of the acute leukemia. In a follow-up study published in Nature Medicine, does not inhibit AR-mediated transcription of was rearranged in 48% of B/myeloid MPAL cases and Alexander TB et al, Nature 562:373–9, 2018 Dr. Taylor’s group screened several potential SBMA target genes. Indeed, the transcription of 8 known therapeutic compounds that specifically bind to the motor neuron–specific target genes was unaffected BF3 motif of the AR and modulate cofactor binding by MEPB treatment. However, MEPB specifically to the AF2 domain in a Drosophila model of SBMA. increased the recruitment of nuclear receptor KMT2Ar Ph+ MPAL AUL This screen revealed 2 compounds, tolfenamic corepressor 1 to the AF2 domain, suggesting that the A T/M MPAL B/M MPAL MPAL NOS MPAL B ALAL presentation acid (TA) and 1-[2-(4-methylphenoxy)ethyl]-2-[(2- selective modulation of CAG repeat–expanded AR by Age HSC Initial therapy phenoxyethyl)sulfanyl]-1H-benzimidazole (MEPB), MEPB is mediated by recruiting corepressors, rather Outcome Gene Expression that restored several indicators of DHT-dependent than coactivators, to the AF2 domain. Together, WT1 (27) ETV6 (21) MPP neurodegeneration, including viability, motor these findings provide proof-of-principle evidence CEBPA (5) RUNX1 (14) control, and neuromuscular junction architecture. for the subtle modulation of cofactor binding to ZNF384 (16) PAX5 (13) VPREB1 (15)

To further characterize the efficacy of these 2 the AR AF2 domain by BF3-binding compounds for Regulation IKZF1 (13) MLP TCF3 (15) Transcriptional compounds for treating SBMA, the researchers SBMA therapy without complete androgen-signaling CUX1 (7) BCL11B (6) CMP generated a novel mouse model of SBMA that ablation. Badders NM et al, Nat Med 24:427-37, 2018

TA MEPB Clinical Gene expression Mutation Type A BF3 unbound B C ALAL presentation Age at presenation Hyperdiploid ZNF384r Missense Protein del >10 years old Diagnosis Ph-positive KMT2Ar Exon Protein ins 1-10 years old Myeloid blasts Lymphoid blasts AF2 Relapse Ph-like KMT2A-like Frameshift Fusion transcript <1 year old K720K720 K720K720 ETV6-like Other Nonsense Copy-number loss KK720720 M894M894 Initial therapy Outcome Splice Copy-number gain M894M894 ALL Alive

BF3 ITD Loss of heterozygosity L MM894894 F M734M734 AML Death M734M734 EE897897 Hybrid Unknown M734M734 F E897E897 E897E897 L L MEPB TA L L L L L L Figure. (A) Oncoprint of the main classifying genetic alterations in B/myeloid (B/M) and T/myeloid (T/M) MPAL. (B) Model of MPAL leukemogenesis in which F F acquisition of genetic changes in a subset of hematopoietic stem cells primes cells for lineage aberrancy. Abbreviations: ALAL, acute leukemia of ambiguous F F lineage; CMP, common myeloid progenitors; HSC, hematopoietic stem cells; ITD, internal tandem duplications; MLP, multilymphoid progenitors; MPP, multipotent S progenitors. Reprinted by permission from SNCSC GmbH: Nature, 562:373–9, Alexander TB et al, The genetic basis and cell of origin of mixed phenotype acute leukaemia. © 2018 Springer Nature Figure. Structural depiction of the AR ligand–binding domain unbound (A) or in complex with TA (B) or MEPB (C). The AF2 domain is shown in red; the BF3 domain, in green; and TA and MEPB, in purple. Reprinted by permission from SNCSC GmbH: Nature Med, 24:427-37, Badders NM et al, Selective modulation of the androgen receptor AF2 domain rescues degeneration in spinal bulbar muscular atrophy. © 2018 Springer Nature

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Pantazine PZ-2891 Is a Promising Therapeutic for Patients The NetBID Algorithm Reveals Coupling of the Metabolic with Pantothenate Kinase–Associated Neurodegeneration State and Immune Function of CD8a+ Dendritic Cells

Pantothenate kinase (PANK) is a key regulator of the concentration of CoA in neural tissues. PZ-2891 Dendritic cells (DCs) are antigen-presenting cells In summary, the researchers defined a coenzyme A (CoA), a cofactor required for many activates all 4 mouse and human PANK isoforms. whose primary function is to process antigens into noncanonical Hippo signaling pathway that enzymatic and metabolic processes. In humans, Kinetic and thermal stabilization studies revealed peptide fragments and present them to T cells to coordinates mitochondrial activity, noncanonical 3 PANK genes express 4 closely related isoforms, that PZ-2891 occupies the pantothenate pocket and activate them. DCs that express the glycoprotein NF-kB signaling, and cytokine signaling in CD8a+ and inactivating mutations in PANK2 lead to PANK– bound tightly to the PANK·ATP·Mg2+ complex. Crystal CD8aα chain on their surface (CD8a+ DCs) DCs, and they showed that Mst1/2 kinases are crucial associated neurodegeneration (PKAN), a rare structures of the PANK3·ATP·Mg2+·PZ-2891 complex preferentially present antigens to CD8+ T cells and and selective regulators of CD8a+ DC function. This disorder marked by iron deposition in the basal showed that PZ-2891 bound across the PANK-dimer elicit cytotoxic T-cell responses to viruses, bacteria, interplay between immune signaling and metabolic ganglia. Symptoms of PKAN include progressive interface to stabilize the active PANK conformation. and tumors. In contrast, DCs that do not express reprogramming underlies the unique functions of movement abnormalities, speech problems, vision PZ-2891 acts as an allosteric activator at the CD8aα chain (CD8a– DCs) are more efficient DC subsets. Accordingly, strategies that modulate loss, behavioral issues, and intellectual deterioration. subsaturating concentrations and as an orthosteric at priming CD4+ T cells (T helper cells). Although the activities of DC subset–specific Mst1/2 signaling PANK is the first and rate-limiting enzyme in inhibitor at very high concentrations. The activation some lineage-specific transcriptional regulators of and metabolic regulation are attractive candidates the CoA biosynthesis pathway, and CoA supports by PZ-2891 prevents the natural feedback regulation CD8a+ DC development have been identified, the for therapeutic interventions against cancers and oxidative metabolism, ketone utilization, and lipid inhibition of PANK3 and increases CoA levels. molecular pathways that orchestrate CD8a+ DC immune-mediated diseases. Furthermore, the and glucose metabolism. CoA deficiency in neurons A human liver–derived cell line treated with function remain elusive. Metabolic reprogramming NetBID algorithm has demonstrated its advantage most likely leads to the symptoms of PKAN. However, PZ-2891 had elevated CoA levels. Increasing is important for DC development and activation, but over conventional analysis methods by successfully no effective treatment has been developed to pantothenate in the cell culture medium without the metabolic regulation of specific DC subsets has identifying “hidden” kinase drivers. This approach combat the debilitating symptoms of the disease. adding PZ-2891 did not affect CoA content, been poorly defined. can now be extended to other drivers and biological Compounds that bypass a PANK genetic deficiency supporting the notion that PANK is the rate- Hongbo Chi, PhD (Immunology), and Jiyang Yu, questions. Du X et al, Nature 558:141–5, 2018 and increase CoA production have been tested, controlling factor in the CoA pathway. In mice, PZ- PhD (Computational Biology), led a team to develop but they fail to cross the blood–brain barrier (BBB) 2891 plus pantothenate increases the CoA content a data-driven systems biology tool called Network- Transcriptomics efficiently and do not affect brain CoA levels. in the brain and liver. Finally, a mouse model of brain based Bayesian Inference of Drivers (NetBID), which DC signaling interactome NetBID: data-driven To develop an optimal treatment for PKAN, CoA deficiency revealed that PZ-2891 treatment integrates transcriptomic, whole-proteomic, and Reverse- Network-based engineering Bayesian Inference of Suzanne Jackowski, PhD (Infectious Diseases), increases weight and longevity and improves phosphoproteomic data. They used this algorithm to Drivers and her team used a novel therapeutic strategy to locomotor activity. determine the role of kinases of the Hippo signaling develop a drug that allosterically activates PANK Although the pharmaceutical properties of PZ- pathway in the selective reprogramming of CD8a+ isoforms PANK1a,b,β and PANK3 to compensate for 2891 remain to be optimized, these studies provide DC function and metabolism, and they published Differential expression the loss of PANK2. In a study reported in Nature compelling proof that this PANK activator has their findings in Nature. CD8α+ vs. CD8α– DCs Communications, the group used hit-to-lead excellent oral bioavailability, target affinity, and BBB The NetBID analysis of DCs revealed that the optimization and studied the hit list by using an permeability. These studies validate the activations activities of Hippo-pathway kinases were enriched alternative approach to filter compounds, with of alternative PANK isoforms as a promising in CD8a+ DCs, as compared to CD8a− DCs. The lipophilic ligand efficiency as the primary metric. approach to treating PKAN, and PZ-2891 should be researchers then engineered mice with DC-specific This optimization approach identified the pantazine further explored as a therapeutic agent in the clinic. deletions of the Hippo-pathway kinases Mst1 and PZ-2891, which is about 800 times more potent than Sharma LK et al, Nat Commun 9:1–15, 2018 Mst2 (Mst1/2), Lats1 and Lats2 (Lats1/2), or Yap and Transcriptomics Whole proteomics Phosphoproteomics the initial hit, penetrates the BBB, and increases Taz (Yap/Taz). They found that DC-specific depletion ! of Mst1/2 disrupted the homeostasis and function of CD8+ T cells and, thus, antitumor immunity in the " Figure. Diagram showing that PZ-2891 (pink) mice, whereas DC-specific depletion of Lats1/2 or mRNA wProtein # 56 binds with AMPPNP Yap/Taz, which mediate canonical Hippo signaling, (136) (145) (green) across the PANK3 42 45 protomers (cyan and gold). had no effect. Mst1/2-deficient CD8a+ DCs were $ 36 Reprinted by permission + 2 8 from SNCSC GmbH: Nat impaired in their presentation of antigens to CD8 Top kinase drivers + Commun, 9:1–15, Sharma − of CD8α DCs LK et al, A therapeutic T cells, whereas CD8a DCs that lacked Mst1/2 8 approach to pantothenate had essentially normal function. Compared to kinase associated pProtein − + neurodengeration. © 2018 CD8a DCs, CD8a DCs exhibited much stronger (54) Springer Nature oxidative metabolism and depended on Mst1/2

signaling to maintain the bioenergetic activities and Figure. Overview of NetBID. Reprinted by permission from SNCSC GmbH: mitochondrial dynamics that are necessary to their Nature, 558:141–5, Du X et al, Hippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells. © 2018 Springer Nature function. In a subsequent experiment, the selective expression by CD8a+ DCs of the cytokine interleukin 12 (Il-12), which serves as a signal for CD8+ T-cell activation, depended on Mst1/2 and crosstalk with noncanonical NF-kB signaling. 2019 Scientific Report | 102 103 | 2019 Scientific Report SCIENTIFIC HIGHLIGHT SCIENTIFIC HIGHLIGHT

Apurinic Endonuclease 1 Suppresses Oxidative DNA Damage Nonmyogenic Progenitors Give Rise to Fusion-Negative in the Neural Genome Rhabdomyosarcoma

Genome stability is crucial for the development stability and sensitize cells to genotoxins. Ape1Nes-cre Rhabdomyosarcoma is the most common pediatric The group also examined the role of and functioning of organisms. DNA-repair enzymes mice exhibited shivering, and using heating pads soft-tissue sarcoma; however, the cell of origin of this the Sonic hedgehog pathway in the murine prevent the accumulation of DNA lesions, which extended their survival. The thermoregulatory defect common tumor has remained unknown. The tumor rhabdomyosarcoma model, because this pathway is can affect several organ systems and are linked to compromising survival in the shivering phenotype cells resemble skeletal muscle–derived cells, and vital to skeletal muscle formation outside the head disease pathologies. High oxygen consumption in was traced to the loss of thermoregulatory rhabdomyosarcoma occurs throughout the body, and neck. They found that the abnormal activation the nervous system makes it susceptible to oxidative serotonergic neurons in the rostral medullary Raphe including areas devoid of skeletal muscle. Because of the Sonic hedgehog pathway caused SmoM2 damage, caused mainly by reactive oxygen species nuclei. these tumors often express PAX3–FOXO1 or PAX7– expression in Cre-expressing endothelial progenitor (ROS). Given that neurons consume a large quotient Apart from its DNA-repair activity, APE1 FOXO1 fusion proteins, which are linked to poorer cells that were predestined to become blood vessel of oxygen, DNA repair of ROS damage is essential in controls the redox status and DNA-binding activity prognosis, rhabdomyosarcoma is classified as being cells, causing them to instead transdifferentiate into the nervous system. of transcription factors. This redox effector either fusion-negative or fusion-positive. muscle-like cells. Therefore, rhabdomyosarcoma can Oxidative damage–related DNA lesions are factor role was confirmed by kainic acid–induced Mark E. Hatley, MD, PhD (Oncology), and arise from nonmyogenic cells. repaired by the base excision repair (BER) pathway, hippocampal stimulation, which activated binding his colleagues performed in-depth analyses A better understanding of the cellular origins in which DNA glycosylases recognize and remove of the transcription factor AP-1. Notably, APE1 and of the cellular origins of fusion-negative and molecular drivers of this tumor might provide base damage to generate apurinic/apyramidinic p53 inactivation made mice susceptible to brain rhabdomyosarcoma by using their previously insight into the mechanisms of tumorigenesis (AP) sites. AP endonuclease 1 (APE1, also known tumors (e.g., glioblastoma and medulloblastoma), designed mouse model of the disease. The model and enable the use of more personalized therapy, as redox effector factor) recognizes AP sites and supporting the hypotheses that APE1 is a potent includes a conditional constitutively active thereby benefitting patients with fusion-negative nicks the phosphodiester backbone 5ʹ to the tumor suppressor, and oxidative DNA lesions initiate Smoothened mutant (SmoM2) that is activated by rhabdomyosarcoma. Drummond CJ et al, Cancer Cell lesion to generate a single-stranded break. Several events in tumorigenesis. aP2-Cre. In Cancer Cell, the researchers reported 33:108–24, 2018 components of the BER pathway play key roles in This study shows key roles for APE1 in their findings from a series of genetic fate-mapping the nervous system, but the role of APE1 remains maintaining postnatal neurodevelopment and experiments. Their model recapitulated fusion- unknown. genomic integrity in mature neurons. These results negative rhabdomyosarcoma in nonmuscle cells To characterize the physiological role of APE1 are clinically important for understanding the exclusively in the head and neck, which is the most in the nervous system, Peter J. McKinnon, PhD underlying pathology of diseases related to oxidative common site of rhabdomyosarcoma in patients. (Genetics), and his group generated a conditional- DNA damage in the nervous system and developing To their surprise, SmoM2 was activated in aP2- knockout Ape1 (Ape1Nes-cre) murine model to study effective therapeutics for them. Dumitrache LC et al, Cre–expressing endothelial cells within muscle neurogenesis during embryonic and postnatal Proc Natl Acad Sci U S A 115:E12285–94, 2018 interstitium. stages and in neural homeostasis. Their findings were reported in the Proceedings of the National Academy of Sciences U S A. Embryonic neural A B development occurred, despite the absence of APE1 during neurogenesis. However, after birth A B C [postnatal day (P) 5 onward], Ape1Nes-cre mice had a decline in vigor, stunted growth, low body weight, * and ataxia, and they died after 3 weeks. Brains of * P9 Ape1Nes-cre mice showed a conspicuous defect in cerebellar development, marked by widespread loss * MHC Tomato of granule neurons and decrease in interneurons. By * studying DNA damage with the marker γH2AX and apoptosis by TUNEL, the group concluded that DNA damage–induced apoptosis leads to cellular atrophy. * * Furthermore, cortex size was markedly reduced postnatally in Ape1Nes-cre mice, confirming that APE1 is Figure. Mice with inactivation of APE1 and p53 develop medulloblastoma within DAPI Tomato MHC DAPI Merge 1–3 months. (A) Hematoxylin and eosin (H&E) staining and proliferating cell nuclear required for cortical homeostasis. antigen (PCNA) immunostaining of medulloblastomas in the cerebellum indicate tumor cell proliferation in 2-month-old mice. (B) Math1 immunostaining of immature granule APE1 loss also resulted in other neural defects, cells (GC) in wild-type (WT) P5 cerebellum and medulloblastoma (MB) indicates that Figure. (A) Transverse section of an E17.5 murine model of rhabdomyosarcoma. (B) Magnification of boxed inset in A. Asterisks indicate regions of Tomato- such as loss of myelination in oligodendrocyte- the tumor is derived from granule cell precursors. Reprinted from Proc Natl Acad Sci U S A 115: E12285–94. © 2018 Dumitrache LC et al positive adipose tissue (red) between developing myosin heavy chain (MHC)–positive myofibers (green). Scale bar, 500 µm. (C) Magnification of boxed inset in B. Scale bar, 50 µm. Reprinted from Cancer Cell, 33, Drummond CJ et al, Hedgehog pathway drives fusion-negative rhabdomyosarcoma initiated from rich regions of the brain and disruption of upper non-myogenic endothelial progenitors, pp. 108–24, © 2018 with permission from Elsevier. cortical layers. In neural cells, APE1 was crucial for repairing oxidative DNA lesions to maintain genome

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Interferon Regulatory Factor 8 Is a Crucial Regulator of NLRC4 Inflammasome Activation

Inflammasomes are molecular platforms that with Pseudomonas aeruginosa or Burkholderia assemble in response to threat-associated thailandensis, which also engage the NLRC4 intracellular stimuli to process caspase-1 into its inflammasome. Thus, IRF8 is required for optimal Salmonella active form, enabling the production of interleukin activation of the NLRC4 inflammasome in murine LPS 1β (IL-1β) and interleukin 18 (IL-18) and ultimately BMDMs infected with various bacterial species but is inducing pyroptosis, a form of inflammatory cell dispensable for activation of the NLRP3, AIM2, and TLR4 death. Inflammasome activation is an essential pyrin inflammasomes. component of the host defense against many Dr. Kanneganti’s team then performed microbial infections. transcription-based analyses of the differential The NLRC4 inflammasome is crucial for regulation of innate immune sensors in WT and T3SS protection against flagellated bacterial pathogens Irf8−/− BMDMs infected with S. Typhimurium. In MyD88 such as Salmonella or Legionella species. This Irf8−/− cells, they found reduced expression of 4 Vacuole inflammasome is unusual, in that it requires another Naip genes (Naip1, Naip2, Naip5, and Naip6) and of sensor for ligand recognition and activation. the gene encoding NLRC4, whereas an analysis of Specifically, it requires NLR-family apoptosis- ChIP-seq data from WT cells showed IRF8 binding Needle Inner rod Flagellin inhibitory proteins (NAIPs) to detect bacterial to the promoters of the Naip2, Naip5, and Naip6 P I B flagellin or type-III secretion system (T3SS) genes and to the intronic region of the Nlcr4 gene. NAIP1 NAIP2 NAIP5/6 components in the cytosol. However, the mechanism Thus, IRF8 regulates the transcription of Naip genes p50 p65 by which this activation pathway is regulated and, consequently, the detection of flagellin or was unknown. Mutations in NLRC4 and NAIPs are T3SS proteins to mediate NLRC4 inflammasome associated with autoinflammatory diseases such as activation. −/− infantile enterocolitis and recurrent macrophage In a subsequent experiment, WT and Irf8 NLRC4 activation syndrome. mice were infected with S. Typhimurium or B. Thirumala-Devi Kanneganti, PhD (Immunology), thailandensis. Compared to WT mice, Irf8−/− mice Naips and her colleagues studied the regulation of the exhibited markedly accelerated weight loss and p50 p65 NLRC4 NLRC4 inflammasome in bone marrow–derived mortality after infection, indicating that IRF8 confers Inflammasome macrophages (BMDMs) from mice and published protection against bacterial infection in vivo. In their findings in Cell. Interferon regulatory factors summary, these findings suggest that IRF8 is a II1b 1 and 8 (IRF1 and IRF8) are both present in crucial regulator of NAIPs and NLRC4 inflammasome macrophages, and IRF1 is required for the activation activation for defense against infection by bacterial Gasdermin D of the AIM2 inflammasome in response to bacterial pathogens. Karki R et al, Cell 173:920–33, 2018 Active CASP1 infection. Thus, the researchers investigated whether C . IRF8 had a similar role in the inflammasome’s Pro-IL-1β activation. They first exposed BMDMs from wild- N type (WT) mice and from mice lacking the Irf8 gene (Irf8−/− mice) to ligands that prompt the activation Pro-IL-18 of specific inflammasomes in WT cells. When the cells were exposed to stimulators of activation of the AIM2, NLRP3, and pyrin inflammasomes, the levels of caspase-1 activation, cytokine production, −/− Pyroptosis and cell death in Irf8 BMDMs were comparable IL-1β IL-18 to those in WT cells. However, when WT and Irf8−/− BMDMs were infected with Salmonella Typhimurium, a stimulator of NLRC4 inflammasome activation, the levels of caspase-1 activation, cytokine production, and cell death were substantially lower in the Figure. Model showing that the optimal activation of the NLRC4 inflammasome in Irf8−/− cells than in the WT cells. Similar results were response to pathogenic bacteria depends on IRF8. Reprinted from Cell, 173, Karki R et al, IRF8 regulates transcription of Naips for NLRC4 inflammasome activation, 920–33, obtained when WT and Irf8−/− BMDMs were infected © 2018 with permission from Elsevier.

2019 Scientific Report | 106 107 | 2019 Scientific Report SCIENTIFIC HIGHLIGHT SCIENTIFIC HIGHLIGHT

MAGE-F1–NSE3 E3 Ubiquitin Ligase Controls Flux Through Social and Functional Independence Among Adult Survivors the Cytosolic Iron–Sulfur Cluster Assembly Pathway by of Childhood Central Nervous System Tumors Ubiquitinating and Degrading MMS19

The cytosolic iron–sulfur (Fe–S) cluster assembly The team also unexpectedly found that adaptive (CIA) pathway is an evolutionarily conserved pseudogenization (i.e., conversion of a gene to a process that is vital for many cellular functions. For pseudogene) of MAGE-F1 occurred multiple times in cytoplasmic and nuclear Fe–S proteins, Fe–S clusters specific mammalian lineages and most likely altered are generated by coordinated activity of the CIA MMS19 and CIA-pathway function. Furthermore, machinery. In humans, the CIA pathway has at least genomic analysis of tumors in The Cancer Genome 9 components and is the pipeline through which Atlas revealed that several cancer types, prominently iron- and sulfur-containing cofactors are generated lung squamous cell carcinomas, had amplification of from a precursor and processed for incorporation MAGE-F1. Overexpression of MAGE-F1 in a squamous into cytosolic or nuclear proteins that need the carcinoma cell line increased tumor xenograft Fe–S cluster as a structural, enzymatic, or electron- rates, suggesting that MAGE-F1 amplification or transfer component. MMS19 is a key component overexpression triggers tumorigenesis. and end-target binding factor for the CIA Fe–S This study provides strong evidence that complex, and its loss in human cells can increase the CIA pathway can be posttranslationally their susceptibility to DNA-damaging agents. regulated by ubiquitination and degradation of However, the mechanisms by which the CIA pathway the MMS19 protein. These results have potential Tara M. Brinkman, PhD is regulated in normal and disease states and those clinical implications for patients with cancer or by which MMS19 is targeted during this process have genomic instability and provide the basis for The survival of children with central nervous system independently, assistance with routine needs, not yet been elucidated. altering the CIA pathway in cancer, especially (CNS) tumors has increased dramatically since the assistance with personal care needs, obtaining In humans, the melanoma antigen gene (MAGE) smoking-induced cancers (e.g., lung squamous cell 1980s, when the 5-year survival was less than 60%; a driver’s license, and history of marriage or protein family is highly expressed in cancer and carcinoma, esophageal carcinoma, and head and today the survival is approximately 74%. However, partnership. Overall, 123 (40%) pediatric CNS plays a role in tumorigenesis. In a study reported neck squamous carcinoma), in which MAGE-F1 is long-term survivors of childhood cancer are at risk tumor survivors were independent as adults; 104 in Molecular Cell, Ryan Potts, PhD (Cell & Molecular amplified. Weon JL et al, Mol Cell 69:113–25, 2018 for neurocognitive impairment, physical limitations, (34%) were moderately independent, and 79 (26%) Biology), and his team pinpointed the mechanism and other devastating ill effects that may adversely were nonindependent. Craniospinal irradiation regulating the CIA pathway by studying MAGE-F1. affect their social participation and functional and younger age at diagnosis were associated MAGE-F1 is amplified in several types of cancer, independence. Previous results from the ongoing with increased risk of nonindependence, as were but its specific functions had remained unknown. Childhood Cancer Survivor Study, which includes limitations in key measures of physical performance Pull-down experiments and in vitro binding assays follow-up of 5-year survivors of childhood cancer (i.e., aerobic capacity, strength, flexibility, balance, for partners interacting with MAGE-F1 identified whose primary disease was initially diagnosed mobility, and adaptive physical function). Despite the E3 ubiquitin ligase NSE1, a member of the from 1970 through 1999, show that survivors of the need for more assistance, nonindependent MAGE–RING ligase family, bound to MAGE-F1. CNS tumors are much less likely to be employed survivors reported mental health–related quality of Unlike MAGE-G1, MAGE-F1 did not incorporate into than their siblings and are also far less likely to life comparable to that reported by independent the SMC5/6 complex, which plays a central role in live independently than other childhood cancer survivors. maintaining genomic stability. In a search for targets survivors. Tara M. Brinkman, PhD (Epidemiology & The prevalence of medulloblastoma (for which of MAGE-F1–NSE1, Dr. Potts’ team identified MMS19 Cancer Control, Psychology), and her colleagues treatment with craniospinal irradiation is essential and showed that an increase in its ubiquitination analyzed additional data from adult survivors for cure) among the participants may have increased and degradation controls flux through the CIA participating in the St. Jude Lifetime Cohort Study the prevalence of nonindependence. Nevertheless, pathway. They also found that MAGE-F1 decreases (SJLIFE) to assess the independence of survivors these findings indicate that a substantial percentage the incorporation of iron into MMS19 targets; thus, of CNS tumors and the impact of independence on of survivors need continued assistance in adulthood. the protein regulates iron homeostasis. The group survivors’ health-related quality of life. Vocational rehabilitation and physical performance then used homologous recombination assays to In a recent article in the Journal of Clinical interventions may be particularly useful in assisting determine whether this decreased incorporation Oncology, Dr. Brinkman and her colleagues report the moderately independent survivors toward of iron affects cellular DNA-repair mechanisms in results of analyses of 306 survivors of childhood increased social and functional independence. HeLa-Cas9 cells with overexpression or knockout Figure. Scheme showing how MAGE-F1 specifies the cytosolic iron–sulfur CNS tumor survivors who were older than 18 years Brinkman TM et al, J Clin Oncol 36:2762–9, 2018 assembly (CIA) pathway protein MMS19 for ubiquitination and degradation. and at least 10 years from diagnosis. The study of the MAGE-F1 gene. Indeed, downregulation of Reprinted from Molecular Cell, 69, Weon JL et al, Cytosolic iron–sulfur MMS19 by MAGE-F1–NSE1 inhibited homologous assembly is evolutionarily tuned by a cancer-amplified ubiquitin ligase, examined 6 validated indicators of functional and 113–25, © 2018, with permission from Elsevier. recombination, reduced the DNA-repair capacity, social independence: full-time employment, living and sensitized cells to DNA-damaging agents.

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Pathogenic Mutations in Cancer-Predisposition Genes Ethanol-Lock Therapy Is Not Recommended for Preventing Increase the Risk of Subsequent Neoplasms in Survivors of Central Line–Associated Bloodstream Infections in Children Childhood Cancer Children undergoing anticancer treatment or The discovery of new anticancer therapies and likely pathogenic mutations to the risk of a specific hematopoietic cell transplantation often require improvement of existing therapies has increased the SN after adjusting for initial cancer therapy. the long-term insertion of a central venous catheter number of long-term survivors of childhood cancer. Among 439 long-term survivors of childhood (CVC), known as a central line, to facilitate the As this population continues to expand and age, the cancer, 1120 SNs occurred, including nonmelanoma administration of chemotherapy drugs, blood incidence of long-term therapy- or disease-related skin cancer, meningioma, thyroid cancer, sarcoma, products, and fluids. Although CVCs are essential to sequelae is also increasing. Subsequent neoplasms and breast cancer. In these patients, 175 pathogenic/ cancer care, they can give rise to serious infections. (SNs) are a relatively common long-term outcome likely pathogenic mutations were present in Approximately 25% of pediatric patients with cancer for survivors of childhood cancers. Anticancer 32 cancer-predisposition genes. Although the in high-income countries experience at least 1 therapies, especially radiation therapy, increase the cumulative incidence of an SN was the same for episode of central line–associated bloodstream risk of SNs. However, the contribution of pathogenic survivors with or without germline mutations who infection (CLABSI), which often necessitates the mutations in cancer-predisposition genes to SNs in received radiation therapy, the incidence of SNs for removal of the CVC and can cause life-threatening these patients is unknown. To determine whether those who did not receive radiation therapy was sepsis. Even after apparently successful treatment germline mutations in cancer-predisposition higher in survivors with pathogenic/likely pathogenic with antibiotics, the infections often return. genes play a role in the development of SNs in mutations than in those without. Nevertheless, the CLABSI is attributed to microorganisms that survivors of childhood cancer, Jinghui Zhang, PhD statistically inferred relative rate of developing any form “biofilms” on the surface of the CVC lumen (Computational Biology), and Leslie L. Robison, PhD SN was higher when pathogenic/likely pathogenic and then spread to the bloodstream. These biofilms (Epidemiology & Cancer Control), led a collaborative mutations were present. Furthermore, the relative are resistant to systemic antibiotic therapies and Joshua Wolf, MBBS study of the prevalence of pathogenic/likely rate of breast cancer and sarcoma was highest immune clearance; to address this, adjunctive had very high adherence to the protocol therapy, pathogenic mutations in 60 cancer-predisposition among survivors who received radiation therapy, antimicrobial catheter-lock therapy has been with 85% receiving at least 75% of their scheduled genes in 3006 long-term survivors of childhood suggesting that these survivors are particularly used with the aim of eradicating or preventing doses. The incidence of treatment failure (defined cancer. vulnerable to radiation-induced neoplasms. biofilm-associated CLABSI. In this technique, an as CVC removal or patient death attributable to In the Journal of Clinical Oncology, the Genetic heterogeneity and pleiotropy were antimicrobial agent is allowed to dwell inside the infection, new or persistent infection, a need for researchers reported their findings from whole- also prevalent among the long-term survivors. CVC for a set period to kill the biofilm organisms. additional lock therapy during the treatment phase, genome and/or whole-exome sequencing of DNA Specifically, mutations within different genes At high concentrations, ethanol kills organisms or recurrent CLABSI during the prophylaxis phase) derived from blood samples from patients who had frequently resulted in the same SN type, and in biofilms. Ethanol-lock therapy (ELT) has been was similar in both groups, occurring in 21 (44%) survived at least 5 years after their cancer diagnoses. mutations within the same gene often resulted proposed as a likely effective preventative measure. of the ELT recipients and 20 (43%) of the placebo The initial cancer types that occurred in these in different SN types. Together, these findings However, no trials had been conducted to evaluate recipients. However, adverse events attributable to survivors included leukemias (35%), lymphomas indicate that referrals for genetic counseling for its efficacy as treatment and secondary prophylaxis lock therapy were more frequent in the ELT group. (19%), tumors with CNS involvement (11%), and all survivors and genetic testing, cancer screening for patients who already have CLABSI, though ELT is Notably, catheter occlusion requiring thrombolytic other solid tumors (35%). The team classified the recommendations, and risk-reduction strategies used for this purpose around the world. therapy occurred in 28 (58%) of the ELT recipients pathogenicity of single-nucleotide variants, copy- should be prioritized for a specific subset of patients Joshua Wolf, MBBS (Infectious Diseases), and but in only 15 (33%) of the placebo recipients. number variations, and small insertions and deletions with pathogenic/likely pathogenic mutations in colleagues designed and conducted the ETHEL Dr. Wolf and his colleagues thus showed that in the cancer-predisposition genes according to cancer-predisposition genes to reduce the long-term Study, a randomized, double-blinded, placebo- ELT was ineffective as treatment and secondary guidelines set forth by the American College of risks associated with survival of childhood cancers. controlled trial of the efficacy and tolerability of ELT prophylaxis for CLABSI in the pediatric populations Medical Genetics and Genomics. They also assessed Wang Z et al, J Clin Oncol 36:2078–87, 2018 as treatment and secondary prophylaxis for CLABSI studied; ELT demonstrated no advantage over the independent contribution of these pathogenic/ in children and adolescents receiving treatment for placebo. Furthermore, such therapy increased the cancer or hematologic disorders. The results of the risk of catheter occlusion requiring thrombolytic AA. Figure. Multivariable piecewise exponential regression Total no. of survivors Relative Rate trial were published in The Lancet Infectious Diseases. therapy. This is important because the treatment (No. of survivors with SN) (95% CI) was used to calculate the relative rate (RR) of ● subsequent neoplasms (SNs) and 95% confidence Any SN 1671 ( 384) 1.3 ( 0.8− 2.1) The trial was conducted at St. Jude and at the has been used in many centers without high-quality ● intervals (CI) for mutation status stratified by A( ) Breast 442 ( 38) 13.9 ( 6.0−32.2) exposure to radiation or (B) no exposure to radiation. 1671 ( 22) 10.6 ( 4.3−26.3) ● Royal Children’s Hospital Melbourne (Parkville VIC, evaluation of its safety or efficacy. The researchers Sarcoma RR and 95% CI are plotted along the X-axis in a log Thyroid 1328 ( 58) 2.0 ( 0.6− 6.6) ● 10 Australia). Of the 94 evaluable patients enrolled concluded that ELT should not be used routinely in Meningioma 952 ( 99) 1.0 ( 0.3− 3.6) ● scale. Abbreviations: NA, not applicable; NMSC, nonmelanoma skin cancer. Wang Z et al, Genetic risk NMSC 1671 ( 163) 1.0 ( 0.2− 4.0) ● in the trial, 48 received ELT with 70% ethanol and children with cancer or hematologic disorders. Wolf J 2+ SN 1671 ( 85) 2.1 ( 0.9− 5.1) ● for neoplasms among long-term survivors of childhood cancer. J Clin Oncol 36, 20, 2078–87. Reprinted with 0 0 46 received heparinized saline placebo locks. et al, Lancet Infect Dis 18:854–63, 2018 B. permission. © 2018 American Society of Clinical Oncology. All rights reserved. B Any SN 1335 ( 55) 4.7 ( 2.4− 9.3) Treatment was administered for 2–4 hours per Breast 2564 ( 15) 7.7 ( 2.4−24.4) ● lumen per day for 5 days (the treatment phase) and Sarcoma 1335 ( 4) N/A ● Thyroid 1678 ( 9) 3.0 ( 0.6−14.8) then up to 3 nonconsecutive days per week for 6 Meningioma 2054 ( 3) N/A ● NMSC 1335 ( 8) 11.0 ( 2.9−41.4) months (the prophylaxis phase). Most participants 2+ SN 1335 ( 6) 18.6 ( 3.5−99.3) ● 0 0 ●

0.1 1 10 100

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Molecular Diversity and Alterations in the Uncharacterized Improving Immunohistochemistry Capability in Central Gene CXorf67 in Posterior Fossa Group A Ependymomas America and the Caribbean

The Asociacíon de Hemato-Oncología Pediátrica de Centro América (AHOPCA) is a consortium of pediatric oncology centers in low- and middle- income countries (LMICs) in Central America and the Caribbean. St. Jude collaborates with AHOPCA in multidisciplinary educational activities to improve the quality of health care for children with cancer in those countries. One area requiring improvement is access to immunohistochemistry (IHC) resources, which are essential for the proper diagnosis and treatment of cancer. Whereas IHC is widely available in anatomic pathology laboratories in high-income countries, its availability in LMICs is limited or nonexistent. Even

when IHC is available in LMICs, the results may be Teresa Santiago, MD of suboptimal or inconsistent quality, leading to an overview of their laboratory operations and incorrect diagnoses. Accordingly, for many years, assets, the participants were asked to bring paraffin- St. Jude pathologists have provided second-opinion embedded tissue specimens from patients with Wilda Orisme, PhD; David W. Ellison, MD, PhD diagnoses to AHOPCA members. However, it would non-Hodgkin lymphoma, corresponding hematoxylin be preferable if pathologists in LMICs were able Ependymomas account for nearly 30% of central were associated with local recurrence and PFA- and eosin–stained slides, and previously stained IHC to provide high-quality IHC services at their nervous system tumors in infants, and targeted 2 ependymomas were associated with distant slides, where available. After intensive didactic and respective institutions. therapies could reduce morbidity and mortality relapse. Furthermore, PFA subtypes were associated practical training in IHC, the participants applied the In an article published in the Journal of Global in patients whose tumors are inoperable. Previous with distinct outcomes; in particular, OTX2- techniques to new slides prepared from the same Oncology, Teresa Santiago, MD (Pathology), and her DNA-methylation profiling studies undertaken, overexpressing PFA-2c tumors appeared to have specimens, and the results were compared to those colleagues reported on a 5-day training workshop on in part, to uncover such targets revealed that very favorable rates of progression-free and overall obtained before the workshop. IHC techniques that was organized by the AHOPCA ependymomas from the supratentorial, spinal, survival. Poor antigen retrieval, nonspecific staining, Pathology Working Group for pathologists and and posterior fossa regions of the central nervous In a reanalysis of published sequencing data and intense background staining were some of the histotechnologists from 7 Central American and system can be separated into molecular groups, of ependymomas, Dr. Ellison’s team found novel problems identified in the IHC slides prepared before Caribbean countries. with posterior fossa group A (PFA) being the most recurrent mutations in the uncharacterized gene the workshop; inadequate fixation and processing The workshop was held at the Hospital Nacional common form of the disease. CXorf67. This gene was mutated only in PFA tumors, of tissue were also noted in some cases. Strategies de Niños Benjamin Bloom (HNNBB) in San Salvador, Following up on their previous work, David W. at a frequency of 9.2%. They also noticed that to correct these deficiencies were addressed during El Salvador. This institution was chosen as the Ellison, MD, PhD (Pathology), and his collaborators CXorf67 is highly expressed in PFA ependymomas the training sessions, and the participants received training center because its pathologists perform at St. Jude, the German Cancer Research Center, but not in other ependymoma molecular groups. personalized recommendations on their IHC their IHC assays manually but obtain results of the Hospital for Sick Children (Toronto, Canada), and Using immunoprecipitation and mass spectrometry technique and laboratory practices. excellent overall quality. Therefore, their IHC the University of Nottingham, U.K., performed DNA- studies to show that CXorf67 binds to core Based on an assessment of the participants’ techniques were considered suitable for adoption methylation profiling on 675 PFA ependymomas components of the polycomb repressive complex performance during the workshop and comparisons by other pathology laboratories for which the cost to discover novel molecular subtypes with distinct 2 (PRC2) and by modulating levels of CXorf67 in of their original IHC slides with the slides they of acquiring and maintaining an automated IHC- clinical characteristics. cell lines to show that CXorf67 can inhibit PRC2, prepared during the practical sessions, the staining system is prohibitive. In Acta Neuropathologica, Dr. Ellison and his team they also discovered a mechanism for the depletion organizers concluded that intensive workshops of The workshop participants comprised a reported that PFA ependymomas are molecularly of H3 K27-trimethylation in PFA ependymoma this kind can train participants to perform manual pathologist and a histotechnologist from each of diverse and can be categorized into 2 subgroups tumor cells. These studies implicate CXorf67 as an IHC assays that yield high-quality, reproducible 8 centers in Costa Rica, the Dominican Republic, (PFA-1 and PFA-2) that are composed of 9 subtypes oncogenic driver in PFA ependymomas and suggest results comparable to those obtained with Guatemala, Haiti, Honduras, Nicaragua, and and may arise from separate anatomic locations. that targeting of CXorf67’s inhibition of PRC2 may automated IHC systems and that this is a useful Panama. The participants from 3 centers had never To determine whether this hierarchical molecular be a useful therapeutic strategy in children with PFA strategy for improving IHC capability and proficiency performed IHC staining in their daily practice. The classification is clinically relevant, the researchers ependymomas. Pajtler KW et al, Acta Neuropathol in regions with limited resources. Santiago T et al, J training team consisted of 2 histotechnologists and analyzed patient data and tumor profiles from 136:211–26, 2018 Global Oncol 4:1–9, 2018 569 cases. They found that PFA-1 ependymomas a pathologist from the HNNBB and a pathologist (Dr. Santiago) from St. Jude. In addition to providing

2019 Scientific Report | 112 113 | 2019 Scientific Report ACADEMIC DEPARTMENTS

BIOSTATISTICS CELL & MOLECULAR COMPUTATIONAL DIAGNOSTIC IMAGING BIOLOGY BIOLOGY Interim Chair Chair Deo Kumar S. Srivastava, PhD • Clinical Chair Zoltán Patay, MD, PhD; Endowed Chair trials, robust methods, survival 1 Chair in Diagnostic Imaging • Imaging J. Paul Taylor, MD, PhD ; Edward 1 analysis F. Barry Endowed Chair in Cell Jinghui Zhang, PhD ; Endowed Chair genomics & brain tumor & Molecular Biology • Molecular in Bioinformatics • Cancer genomic characterization by quantitative MRI genetics of neurological diseases variant analysis & visualization

Members Associate Members Associate Member 1,2 2 Cheng Cheng, PhD • Statistical methods in cancer biology, clinical & Mondira Kundu, MD, PhD • Autophagy-related proteins in health & human Zhaoming Wang, PhD • Genetic epidemiology of pediatric cancer & Members translational studies disease survivorship 1 1 Sue C. Kaste, DO • Skeletal toxicities in childhood cancer Arzu Onar-Thomas, PhD • Phase I/II designs, survival analysis, Bayesian Stacey K. Ogden, PhD • Mechanisms of Hedgehog signal transduction 4 1 Robert A. Kaufman, MD statistics Joseph T. Opferman, PhD • Regulation of cell death & mitochondrial Assistant Members 1 1 Mary E. (Beth) McCarville, MD • Solid tumor imaging & contrast-enhanced Stanley B. Pounds, PhD • Statistical methods for genomics studies function Xiang Chen, PhD • OMICS integration & tumor heterogeneity by machine ultrasonography Ryan Potts, PhD1 • Biochemical & molecular characterization of MAGE learning approaches 1,2 Wilburn E. Reddick, PhD • White matter injury in leukemia & CNS tumors Associate Members proteins Yong Cheng, PhD • Cis-regulatory modules in hematopoiesis & its Barry L. Shulkin, MD, MBA • PET imaging evaluation of pediatric tumors Guolian Kang, PhD • Statistical genetics/genomics, modeling of complex data disorders 2 Yimei Li, PhD • Statistical analysis of complex imaging data, survival data Assistant Members Charles Gawad, MD, PhD • Cellular & genetic origins of childhood cancers Associate Members analysis & clinical trial design Hans-Martin Herz, PhD1 • Regulation of transcription & enhancer activity Jiyang Yu, PhD • Systems biology, systems immunology, & translational 1 Asim K. Bag, MBBS, MD • Response assessment of immunotherapy & Li Tang, PhD • Prediction, validation, diagnostic testing, microbiome analysis Malia B. Potts, PhD • Higher-order regulation of autophagy oncology radiation therapy, assessment of cancer therapy–related brain damage Hui Zhang, PhD • Longitudinal missing discrete data & computational Shondra M. Miller, PhD • Genome-editing technologies Mikhail Doubrovin, MD, PhD3 neuroscience Adjunct Member Julie H. Harreld, MD1 • Magnetization transfer MR imaging & cerebral Neil Hayes, MD, MS, MPH • Translational biomarkers, genomics, & clinical perfusion Assistant Members trials Claudia M. Hillenbrand, PhD • Novel MR techniques in solid tumors & sickle Zhaohua Lu, PhD • Statistical analysis of neuroimaging & genetic data, cell disease longitudinal & functional data analysis Robert J. Ogg, PhD • Imaging assessments of brain function in CNS & ocular Sedigheh Mirzaei Salehabadi, PhD • Statistical methods for incomplete tumors survival data, epidemiologic study designs Noah D. Sabin, MD, JD • Imaging of brain tumors & side effects of therapy Haitao Pan, PhD • Bayesian adaptive designs for clinical trials, graphical Scott E. Snyder, PhD1 • Design of radioactive diagnostic agents for modeling, microbiome data modeling molecular imaging Natasha A. Sahr, PhD • Variable classification, screening, selection in high- dimensional data Assistant Member Scott N. Hwang, MD, PhD • Brain tumors, quantitative imaging, computational modeling

Instructor Cara E. Morin, MD, PhD • Novel MR body & cardiac imaging techniques

BONE MARROW CHEMICAL BIOLOGY & DEVELOPMENTAL EPIDEMIOLOGY & CANCER TRANSPLANTATION & THERAPEUTICS NEUROBIOLOGY CONTROL CELLULAR THERAPY Interim Chair Chair Chair 1 1 Chair Richard E. Lee, PhD ; Endowed Chair Michael A. Dyer, PhD ; Richard Leslie L. Robison, PhD; Endowed Chair Stephen M. Gottschalk, MD1; Endowed in Medicinal Chemistry • Discovery of C. Shadyac Endowed Chair in in Epidemiology & Cancer Control Chair in Bone Marrow Transplantation new antibiotic agents and structure- Pediatric Cancer Research • Retinal • Pediatric cancer epidemiology & & Cellular Therapy • Cancer based drug design development, retinoblastoma, & outcomes immunotherapy, cell therapy, stem pediatric solid tumor cell transplantation translational research

Member Member Members Members William E. Janssen, PhD • Therapeutic use of intact cell products Taosheng Chen, PhD, PMP1 • Xenobiotic receptors and therapeutic Suzanne J. Baker, PhD1; Endowed Chair in Brain Tumor Research • Genetic Gregory T. Armstrong, MD, MSCE1 • Cancer survivorship & long-term follow-up responses and epigenetic drivers of pediatric high-grade glioma Melissa M. Hudson, MD2; The Charles E. Williams Endowed Chair in Associate Members James I. Morgan, PhD; Scientific Director; Edna & Albert Abdo Shahdam Oncology–Cancer Survivorship • Health outcomes after childhood cancer Ashok Srinivasan, MD • Infections in the immune-compromised host Associate Members Endowed Chair in Basic Research • Control of neuronal death & Kevin R. Krull, PhD • Cognitive neuroscience approaches to outcomes and Brandon M. Triplett, MD1 • Hematopoietic cell transplantation Naoaki Fujii, PhD3 differentiation interventions in pediatric cancer survivors Philip M. Potter, PhD • Anticancer drug hydrolysis by carboxylesterases Junmin Peng, PhD1,2 • Proteomics & metabolomics in human disease Kirsten K. Ness, PT, PhD • Physical health and accelerated aging in Assistant Members Anang A. Shelat, PhD1 • Translational research & chemical biology Stanislav S. Zakharenko, MD, PhD1 • Learning & memory, synaptic childhood cancer survivors Christopher DeRenzo, MD, MBA • T-cell therapy for patients with solid Scott E. Snyder, PhD1,2 • Design of radioactive diagnostic agents for mechanisms of schizophrenia Yutaka Yasui, PhD • Genetics & risk of therapy-related outcomes tumors molecular imaging Jian Zuo, PhD3 Caitlin Hurley, MD2 • Onco-critical care, HSCT/immunotherapy patients, Associate Members 2 long-term care Assistant Members Associate Members Wassim Chemaitilly, MD • Endocrine sequelae in childhood cancer Ewelina K. Mamcarz, MD • Transplantation in patients with nonmalignant Marcus Fischer, PhD1 • Protein conformational landscapes for ligand Xinwei Cao, PhD1 • Growth control during neural tube development survivors diseases discovery Young-Goo Han, PhD1 • Regulatory mechanisms of neural progenitors in I-Chan Huang, PhD • Patient-reported outcomes measurement after Amr Qudeimat, MD • Transplant for bone marrow failure syndromes Tudor Moldoveanu, PhD1,2 • Programmed cell death in health & disease brain development, diseases, & evolution pediatric cancer Paulina Velasquez, MD1 • Immunotherapy of hematologic malignancies Fatima R. Rivas, PhD1 • Organic chemistry synthesis/natural product Khaled Khairy, PhD1 • Biomechanics-based computational models as priors Daniel A. Mulrooney, MD, MS1,2 • Cardiovascular outcomes of cancer therapy discovery for biological image analysis Zhaoming Wang, PhD • Genetic epidemiology of pediatric cancer & Instructors David J. Solecki, PhD1 • Cell polarity in neuron precursor differentiation survivorship Giedre Krenciute, PhD • CAR T-cell immunotherapy for pediatric brain tumors Assistant Members Assistant Members Akshay Sharma, MBBS • Gene therapy & transplantation for nonmalignant Jay B. Bikoff, PhD • Neural circuits controlling movement Nickhill Bhakta, MD, MPH1,2 • Global pediatric medicine hematological diseases Fabio Demontis, PhD1 • Protein homeostasis & stress sensing in skeletal Tara M. Brinkman, PhD • Psychosocial outcomes of pediatric cancer Aimee C. Talleur, MD • Cancer immunotherapy & cellular therapy muscle aging Matthew J. Ehrhardt, MD, MS2 • Late effects of childhood cancer therapy Myriam Labelle, PhD1 • The role of platelets in cancer metastasis Todd M. Gibson, PhD • Risk factors for late effects after pediatric cancer Paul A. Northcott, PhD1 • Genomics & developmental biology of childhood Carmen L. Wilson, PhD • Late effects of childhood cancer therapy brain tumors Jamy C. Peng, PhD1 • Epigenetic regulation of stem cell functions Lindsay A. Schwarz, PhD • Mechanisms of neuromodulatory circuit organization Elizabeth A. Stewart, MD1,2 • Translational research of pediatric solid tumors

1Graduate school faculty member; 2Secondary appointment; 3No longer at St. Jude; 4Emeritus; 5Deceased

2019 Scientific Report | 114 115 | 2019 Scientific Report ACADEMIC DEPARTMENTS

ONCOLOGY- cont GENETICS HEMATOLOGY INFECTIOUS DISEASES Associate Members Chair Chair Chair 1 1 1 Richard A. Ashmun, PhD • Applications of flow cytometry & cell separation Gerard C. Grosveld, PhD ; Albert & Mitchell J. Weiss, MD, PhD ; Arthur Elaine I. Tuomanen, MD ; Endowed Rachel C. Brennan, MD1 • Retinoblastoma, novel therapeutics, renal tumors Rosemary Joseph Endowed Chair in Nienhuis Endowed Chair in Chair in Infectious Diseases Sara M. Federico, MD1 • Drug development, pediatric soft-tissue sarcomas Genetic Research • Unraveling Hematology • Blood development & • Pathogenesis of pneumococcal Tanja A. Gruber, MD, PhD • Pathogenesis of infantile ALL & pediatric AMKL mTORC3’s role in development & associated diseases infection Mark E. Hatley, MD, PhD1 • Origins of pediatric sarcomas cancer Catherine G. Lam, MD, MPH1,2 • Global health, health systems, pediatric solid tumors Daniel A. Mulrooney, MD, MS1 • Cardiovascular outcomes of cancer therapy Ibrahim A. Qaddoumi, MD, MS1,2 • Global health, brain tumors, telemedicine, retinoblastoma Jun J. Yang, PhD1,2 • Pharmacogenomics of anticancer agents & drug resistance

Assistant Members Nickhill Bhakta, MD, MPH1,2 • Global health, survivorship, epidemiology, childhood leukemias Michael W. Bishop, MD • Osteosarcoma, Ewing sarcoma, soft-tissue sarcomas Members Members Members 1 Patrick K. Campbell, MD, PhD • Histiocytic disorders, clinical informatics, Alessandra d’Azzo, PhD ; Jeweler’s Charity Fund Endowed Chair in Genetics Ellis J. Neufeld, MD, PhD; Clinical Director; John & Lorine Thrasher Endowed Patricia M. Flynn, MD; Deputy Clinical Director; Arthur Ashe Endowed Chair patient safety and Gene Therapy • Lysosomal/proteasomal function in health & disease Chair in Pediatric Medicine • Patient-oriented studies in nonmalignant in Pediatric AIDS Research • HIV/AIDS in children & infections in children 1 Matthew J. Ehrhardt, MD, MS • Late effects of childhood cancer therapy Peter J. McKinnon, PhD • DNA damage responses in the nervous system hematology with cancer Jamie E. Flerlage, MD, MS • Reduction of the late effects for Hodgkin Arthur W. Nienhuis, MD4 Aditya H. Gaur, MD, MBBS1 • Clinical research in HIV prevention & treatment 5 4 lymphoma survivors Brian P. Sorrentino, MD Walter T. Hughes, MD 1,2 1 Paola Friedrich, MD, MPH • Global health, health disparities, health Clifford M. Takemoto, MD • Hemostasis & thrombosis, vascular Julia L. Hurwitz, PhD • Pathogen/vaccine-induced immunity, nuclear services, pediatric solid tumors malformations, bone marrow failure hormones 4 1 Charles Gawad, MD, PhD • Cellular & genetic origins of childhood cancers Winfred C. Wang, MD Suzanne Jackowski, PhD • Coenzyme A in health & disease, regulation of Kellie Haworth, MD • Immunotherapies for pediatric neurogenic tumors membrane phospholipids Sara Helmig, MD • Sarcoma, thyroid carcinoma, & quality improvement Associate Members Charles O. Rock, PhD • Membrane phospholipid metabolism Liza-Marie Johnson, MD, MPH, MSB • Ethical issues in pediatrics Wilson K. Clements, PhD1 • Hematopoietic development & leukemia Stacey L. Schultz-Cherry, PhD1 • Pathogenesis of influenza & enteric virus 1 Seth E. Karol, MD • Toxicity reduction during acute leukemia therapy Jane S. Hankins, MD, MS • Sickle cell disease, transition to adult care & infections Erica C. Kaye, MD • Prognostic communication, early integration of health outcomes during adolescence & young adulthood Richard J. Webby, PhD1 • Influenza virus pathogenicity 1 4 palliative care in oncology Shannon L. McKinney-Freeman, PhD • Mechanisms of hematopoietic stem Robert G. Webster, PhD Chimene Kesserwan, MD • Cancer predisposition cell development & transplantation 1 Deena R. Levine, MD • Pediatric palliative & end-of-life care Ulrike M. Reiss, MD • Bleeding disorders, gene therapy for hemophilia, bone Associate Members Esther A. Obeng, MD, PhD • Myeloid malignancies & bone marrow failure marrow failure Elisabeth E. Adderson, MD • Epidemiology & treatment of infections 1,2 syndromes Carolyn Russo, MD • Quality improvement in clinical networks Miguela A. Caniza, MD • Global health, infection care & control 1 1 Giles W. Robinson, MD • Origin & genomics of medulloblastoma, Byoung Ryu, PhD • Stem cell gene therapy for blood disorders Hans Haecker, MD, PhD • Signal transduction of Toll-like & TNF receptors translational studies Hana Hakim, MD • Infection prevention & control Jitsuda Sitthi-Amorn, MD • Quality improvement & patient safety Assistant Members Diego R. Hijano, MD • Host–pathogen interactions of respiratory virus Holly Spraker-Perlman, MD, MS • Pediatric palliative care, symptom- Yong Cheng, PhD1 • Cis-regulatory modules in normal & pathologic gene Katherine Knapp, MD • Perinatal HIV exposure/HIV clinical trials 1 management strategies expression Jason W. Rosch, PhD • Bacterial genomics & pathogenesis Elizabeth A. Stewart, MD1 • Translational research of pediatric solid tumors Jeremie H. Estepp, MD1 • Sickle cell disease, novel therapies, translational Charles J. Russell, PhD1 • Respiratory viruses: disease, cures, & prevention 2 Linda Stout, MD • Pediatric oncology studies Megan L. Wilkins, PhD • Clinical & research psychological services for youth Anna Vinitsky, MD, MS • Pediatric neuro-oncology & process improvement Latika Puri, MD • Sickle cell disease, thrombocytopenias, chronic transfusion with HIV/AIDS Liqin Zhu, PhD1,2 • Stem cells in normal & malignant development Shengdar Q. Tsai, PhD1 • Genome engineering technologies for therapeutics Marcin W. Wlodarski, MD, PhD • Inherited bone marrow failure & MDS Assistant Members Instructor predisposition syndromes Elisa Margolis, MD, PhD • Microbiome dynamics in immunocompromised Santhosh Upadhyaya, MD • Atypical teratoid rhabdoid tumor (ATRT) and patients ependymoma Instructors Gabriela M. Marón Alfaro, MD • Infectious complications in transplant Nidhi Bhatt, MD • Health communication & implementation science patients Parul Rai, MD • Cardiac injury in sickle cell disease Joshua Wolf, MBBS1 • Prediction, prevention, & treatment of infections in Jason R. Schwartz, MD, PhD • Pediatric MDS & bone marrow failure immunocompromised children

Instructor Sheena Mukkada, MD, MPH1,2 • Global health, infection care & control

Adjunct Member Jonathan A. McCullers, MD • Interactions between viruses & bacteria

GLOBAL PEDIATRIC IMMUNOLOGY ONCOLOGY PATHOLOGY MEDICINE Chair Chair Chair Douglas R. Green, PhD1; Peter Ching-Hon Pui, MD; Fahad Nassar David W. Ellison, MD, PhD; Joan & Roy Chair C. Doherty Endowed Chair in Al-Rashid Endowed Chair in Leukemia Gignac Endowed Chair in Pathology Carlos Rodriguez-Galindo, MD1; Four Immunology • Cell death, autophagy, & Research • Biology & treatment of & Laboratory Medicine • Pathologic/ Stars of Chicago Endowed Chair in immune function childhood leukemia molecular classification of CNS International Pediatric Outreach tumors • Global medicine, pediatric solid tumors

Members Co-Chair 1 Vice-Chair 2 Sima Jeha, MD • Global health, childhood leukemias, developmental 1 Amar J. Gajjar, MD ; Scott & Tracie Hamilton Endowed Chair in Brain Tumor Members Thirumala-Devi Kanneganti, PhD ; Rose Marie Thomas Endowed Chair in James R. Downing, MD; President and Chief Executive Officer; Dr. Donald therapeutics Immunology • Mechanisms of host defense & inflammation Research • Novel treatments for children with brain tumors Monika L. Metzger, MD1 • Global health, Hodgkin & non-Hodgkin lymphomas Pinkel Chair of Childhood Cancer Treatment • The molecular pathology Ching-Hon Pui, MD1,2; Fahad Nassar Al-Rashid Endowed Chair in Leukemia Members of acute leukemia Members 1,2 1 Research • Biology & treatment of childhood leukemia 1 Gregory T. Armstrong, MD, MSCE • Pediatric neuro-oncology & cancer Terrence L. Geiger, MD, PhD ; Deputy Director for Academic and 2 Hongbo Chi, PhD ; Robert G. Webster Endowed Chair in Immunology Biomedical Operations; Endowed Chair in Pediatrics • T-cell regulation, Victor M. Santana, MD ; Charles B. Pratt Chair in Solid Tumor Research • Immune signaling and metabolism survivorship • Global health, novel therapeutics, neuroblastoma, research ethics 4 Justin N. Baker, MD • Quality of life/palliative care & ethics adoptive immunotherapy Peter C. Doherty, PhD ; Nobel Laureate; Michael F. Tamer Endowed Chair in Randall T. Hayden, MD • Clinical microbiology of immunocompromised Immunology Wayne L. Furman, MD • New drug development, neuroblastoma, liver Associate Members 1 tumors hosts Paul G. Thomas, PhD • Mechanisms of antiviral and antitumor immunity 1 Miguela A. Caniza, MD1 • Global health, infection care & control Daniel M. Green, MD1 • Adverse hepatic, renal, & reproductive effects of Michael M. Meagher, PhD ; President, Children’s GMP, LLC • Cell culture, 1 fermentation, protein purification, process scale-up, & GMP Catherine G. Lam, MD, MPH • Global health, health systems, pediatric solid Associate Members therapy tumors 1 Melissa M. Hudson, MD; The Charles E. Williams Endowed Chair in manufacturing 1 Maureen A. McGargill, PhD • Regulation of the immune response Charles G. Mullighan, MBBS, MD1; William E. Evans Endowed Chair Ibrahim A. Qaddoumi, MD, MS • Global health, brain tumors, telemedicine, Benjamin A. Youngblood, PhD1 • T-cell memory differentiation, T-cell Oncology–Cancer Survivorship • Health outcomes after childhood retinoblastoma cancer • Genomic, experimental, & preclinical studies of acute leukemia exhaustion, and immunotherapy 2 Hiroto Inaba, MD, PhD1 • New therapeutic strategies for leukemia Ching-Hon Pui, MD ; Fahad Nassar Al-Rashid Endowed Chair in Leukemia 1,2 Research • Biology & treatment of childhood leukemia Assistant Members Assistant Members Sima Jeha, MD • Global health, childhood leukemias, developmental Asya Agulnik, MD, MPH1 • Global health, pediatric onco-critical care, quality therapeutics Susana C. Raimondi, PhD • Cytogenetics & FISH of leukemias, lymphomas, Yongqiang Feng, PhD • Epigenetic & transcriptional basis of T-cell immunity 2 & solid tumors improvement Rhea M. Sumpter Jr, MD, PhD • Selective autophagy, innate immunity, Sue C. Kaste, DO • Skeletal toxicities in childhood cancer Nickhill Bhakta, MD, MPH1 • Global health, survivorship, epidemiology, Monika L. Metzger, MD1,2 • Global health, Hodgkin & non-Hodgkin lymphomas Jerold E. Rehg, DVM • Preclinical models of infectious diseases & cancer inflammation 1 A. Peter Vogel, DVM, PhD • Pathology of animal models of human disease childhood leukemias Kim E. Nichols, MD • Heritable cancers & primary immunodeficiency 1 Paola Friedrich, MD, MPH1 • Global health, health disparities, health services, syndromes Gerard P. Zambetti, PhD • The function of p53 in tumor suppression & pediatric solid tumors Alberto S. Pappo, MD1; Alvin Mauer Endowed Chair • New therapies for tumorigenesis sarcomas & rare pediatric cancers Instructors Raul C. Ribeiro, MD1 • Hematological malignancies Associate Members 2 1 Armita Bahrami, MD1 • Molecular pathogenesis of sarcomas and melanoma Abdelhafeez Abdelhafeez, MD • Global health, fluorescence-guided Charles W. M. Roberts, MD, PhD ; Lillian R. Cannon Comprehensive Cancer 1 minimally invasive & subamputative pediatric surgical oncology Center Director Endowed Chair • SWI/SNF (BAF) chromatin remodeling/ John K. Choi, MD, PhD • Transcription factors in acute leukemias 1 Laura Janke, DVM, PhD • Pathology of mouse models of disease Sheena Mukkada, MD, MPH • Global health, infection care & control tumor suppressor 1 Carlos Rodriguez-Galindo, MD1,2; Four Stars of Chicago Endowed Chair Mondira Kundu, MD, PhD • Autophagy-related proteins in health & human in International Pediatric Outreach • Global medicine, pediatric solid disease tumors Brent A. Orr, MD, PhD • Molecular classification of tumors of the nervous system Jeffrey E. Rubnitz, MD, PhD • Treatment of acute myeloid leukemia 1 John T. Sandlund, MD1 • Clinical & biologic investigation of NHL & ALL Janet F. Partridge, PhD • Chromosome segregation, heterochromatin Victor M. Santana, MD; Charles B. Pratt Endowed Chair in Solid Tumor assembly Research • Novel therapeutics, neuroblastoma, research ethics Harshan Pisharath, DVM, PhD • Animal models of human diseases, preclinical safety Richard Rahija, DVM, PhD • Animal models of human disease

1Graduate school faculty member; 2Secondary appointment; 3No longer at St. Jude; 4Emeritus; 5Deceased

2019 Scientific Report | 116 117 | 2019 Scientific Report ACADEMIC DEPARTMENTS

PATHOLOGY- cont PHARMACEUTICAL RADIATION ONCOLOGY SURGERY SCIENCES András Sablauer, MD, PhD; Chief Medical Information Officer • Imaging Chair Chair 1 1 informatics & computerized tumor modeling Chair Thomas E. Merchant, DO, PhD ; Baddia Andrew M. Davidoff, MD ; Endowed Lu Wang, MD, PhD • Genomic profiling & functional analysis of genetic Mary V. Relling, PharmD1; Endowed J. Rashid Endowed Chair in Radiation Chair in Surgical Research • Surgical alterations in pediatric tumors Chair in Pharmaceutical Sciences Oncology • Proton radiotherapy for management of solid tumors, gene • Leukemia therapy & clinical CNS tumors & radiation-related CNS therapy, angiogenesis inhibition, Assistant Members pharmacogenetics effects neuroblastoma, Wilms tumor Elizabeth M. Azzato, MD, PhD3 Jason Cheng-Hsuan Chiang, MD, PhD • Diagnosis & classification of CNS tumors Michael R. Clay, MD • Molecular & histologic classification of pediatric solid tumors & sarcomas, DNA-methylation profiling of pediatric malignancies Jeffrey M. Klco, MD, PhD1 • Genomic & functional characterization of pediatric myeloid neoplasms Vasiliki Leventaki, MD3 Teresa C. Santiago, MD • Laboratory quality improvement & assessment Heather S. Tillman, DVM, PhD • Comparative pathology Yan Zheng, MD, PhD • Red blood cell genotyping & alloimmunization, cancer immunotherapy Members Member Members William E. Evans, PharmD1; Endowed Chair in Pharmacogenomics Matthew J. Krasin, MD • Developing radiation therapy strategies & toxicity Bhaskar N. Rao, MD4 • Pharmacogenomics of antileukemic agents in children profiles for pediatric sarcomas Stephen J. Shochat, MD4 William L. Greene, PharmD; Chief Pharmaceutical Officer • Optimizing pharmacotherapy Associate Member Assistant Members Erin G. Schuetz, PhD1 • Mechanisms of human variation in drug response Chia-ho Hua, PhD • Improving proton therapy accuracy, advanced imaging Kevin W. Freeman, PhD3 John D. Schuetz, PhD1 • Regulation & function of ABC transporters for radiation therapy, normal tissue complication modeling Andrew Jackson Murphy, MD • Renal tumors, neuroblastoma, Wilms Clinton F. Stewart, PharmD1 • Pharmacology of anticancer drugs in children tumorigenesis, cancer stem cells Assistant Members Jun Yang, MD, PhD • Cancer epigenetics & targeted therapy Associate Members Sahaja Acharya, MD • Brain tumors, proton therapy, image-guided radiation James M. Hoffman, PharmD; Chief Patient Safety Officer • Medication Austin M. Faught, PhD • Proton therapy, biological modeling, adaptive Instructors safety & outcomes therapy Abdelhafeez Abdelhafeez, MD • Fluorescence-guided minimally invasive Jun J. Yang, PhD1 • Pharmacogenomics of anticancer agents & drug John T. Lucas Jr, MS, MD • Brain tumors, neuroblastoma, proton therapy, & subamputative pediatric surgical oncology resistance clinical trial design Lindsay J. Talbot, MD • Sarcomas, immunotherapeutic strategies against Christopher L. Tinkle, MD, PhD1 • Preclinical evaluation of novel sarcoma & solid tumor metastases Assistant Members combination therapies and clinical trial development for high-risk brain Daniel D. Savic, PhD1 • Pharmacogenomics & cis-regulatory architecture of tumors and sarcomas Adjunct Members pediatric leukemia Weiguang Yao, PhD3 Frederick Boop, MD; St. Jude Chair in Neurosurgery • Pediatric neurosurgery Liqin Zhu, PhD1 • Stem cells in normal & malignant liver development Joseph M. Gleason, MD • Pediatric urology, Wilms tumor, pelvic RMS Mary Ellen Hoehn, MD • Pediatric ophthalmology Paul D. Klimo Jr, MD • Pediatric neurosurgery Michael Neel, MD • Pediatric orthopedic oncology Anthony Sheyn, MD • Pediatric otolaryngology Jerome Thompson, MD, MBA • Pediatric otolaryngology Robert D. Wallace, MD • Pediatric plastic surgery Matthew W. Wilson, MD; St. Jude Chair in Pediatric Ophthalmology • Pediatric ophthalmology

PEDIATRIC MEDICINE PSYCHOLOGY STRUCTURAL BIOLOGY TUMOR CELL BIOLOGY Chair Chair Chair Chair Amar J. Gajjar, MD; Scott & Tracie Sean Phipps, PhD1; Endowed Chair in Charalampos Babis Kalodimos, Charles J. Sherr, MD, PhD; Herrick Hamilton Endowed Chair in Brain Psychology • Coping & adjustment in PhD1; Joseph Simone Endowed Foundation Endowed Chair in Tumor Tumor Research • Novel treatments children with cancer Chair in Basic Research • Functional Cell Biology • Tumor suppressor– for children with brain tumors mechanisms of protein machineries dependent signaling networks

Anesthesiology Members Members Members Michael G. Rossi, DO; Division Director • Patient safety & cognitive effects Heather M. Conklin, PhD1 • Cognitive outcomes of childhood cancer Richard W. Kriwacki, PhD1 • Structural basis of tumor suppressor function Linda M. Hendershot, PhD1 • ER quality control in development & disease of anesthesia treatment Junmin Peng, PhD1 • Proteomics & metabolomics in human disease Martine F. Roussel, PhD1; Endowed Chair in Molecular Oncogenesis Doralina L. Anghelescu, MD1 • Pain management, anesthesia risks, palliative care Melissa M. Hudson, MD2; The Charles E. Williams Endowed Chair in Stephen White, DPhil1; Endowed Chair–Dean of St. Jude Children’s Research • Genomics & epigenomics in pediatric brain tumors Wasif H. Dweik, DO • Patient safety, regional anesthesia, acute pain management Oncology–Cancer Survivorship • Health outcomes after childhood cancer Hospital Graduate School of Biomedical Sciences • DNA repair, catalysis, Michael J. Frett, MD • Pediatric anesthesia Kevin R. Krull, PhD2 • Neurocognitive outcomes of pediatric cancer & structure-based drug discovery Assistant Member Kyle J. Morgan, MD • Pain management for pediatric cancer & sickle cell disease Chunliang Li, PhD1 • 3D genome and transcriptional regulation in cancer Kavitha C. Raghavan, MBBS, FRCA • Patient safety & quality of care in Associate Members Associate Members pediatric anesthesia Valerie M. Crabtree, PhD1 • Sleep disruptions and fatigue in pediatric Eric J. Enemark, PhD1 • Molecular mechanisms of DNA replication Adjunct Member Luis A. Trujillo Huaccho, MD • Regional anesthesia & anesthetic approach in oncology Mario Halic, PhD • Regulation of genome expression Brenda A. Schulman, PhD • Cellular regulation by ubiquitin-like proteins high-risk cases Niki Jurbergs, PhD • Psychological & cognitive impact of pediatric cancer Tanja Mittag, PhD1 • Molecular basis of liquid–liquid phase separation Becky B. Wright, MD • Pain management techniques, peripheral nerve blocks Megan L. Wilkins, PhD • Clinical & research psychological services for youth with HIV/AIDS Assistant Members Critical Care Medicine Marcus Fischer, PhD1,2 • Protein conformational ensembles R. Ray Morrison, MD1; Division Director • Pediatric critical care, myocardial Assistant Members Tudor Moldoveanu, PhD1 • Programmed cell death in health & disease protection Nicole M. Alberts, PhD • Pain, psycho-social outcomes, & eHealth/mHealth in Asya Agulnik, MD, MPH1, 2 • Global health, pediatric onco-critical care, psycho-oncology & sickle cell disease Adjunct Member quality improvement Tara M. Brinkman, PhD2 • Psychosocial outcomes of pediatric cancer Brenda A. Schulman, PhD • Cellular regulation by ubiquitin-like proteins Lama Elbahlawan, MD • Pediatric critical care, acute lung injury Kristin E. Canavera, PhD • Pediatric bioethics Melissa R. Hines, MD • Pediatric critical care, hemophagocytic Jennifer L. Harman, PhD • Psychosocial functioning of young children with lymphohistiocytosis cancer Caitlin Hurley, MD • Onco-critical care, HSCT/immunotherapy patients, Lisa M. Jacola, PhD • Neurobehavioral outcomes in children treated for long-term care cancer Jennifer A. McArthur, DO • Improving outcomes in critically ill pediatric patients Kendra R. Parris, PhD • Coping & adjustment in youth with cancer Jerlym S. Porter, PhD, MPH • Transition from pediatric to adult care in SCD Endocrinology Brian Potter, PhD • Neurocognitive outcomes in children with cancer Wassim Chemaitilly, MD1; Division Director • Endocrine sequelae in Darcy Raches, PhD • Acute neurological injury & cognitive outcomes childhood cancer survivors associated with childhood cancer treatment Victoria W. Willard, PhD • Social outcomes in children with cancer Neurology Raja B. Khan, MD; Division Director • Effect of cancer on central & peripheral Instructors nervous systems Jennifer Allen, PhD • Pain management, adolescent/young adults, health Zsila Sadighi, MD3 behavior Daniel Garrison, PhD3 Nursing Research Katianne Sharp, PhD • Cancer predisposition & adjustment in families of Belinda N. Mandrell, PhD, RN, CPNP1; Division Director • Biological children with cancer mechanism of symptoms associated with cancer & cancer therapy Rachel N. Tillery, PhD • Promotion of healthy lifestyle behaviors in children with cancer & survivors of childhood cancer 1Graduate school faculty member; 2Secondary appointment; 3No longer at St. Jude; 4Emeritus; 5Deceased

2019 Scientific Report | 118 119 | 2019 Scientific Report ENDOWED CHAIRS

Alessandra d’Azzo, PhD James I. Morgan, PhD Jewelers Charity Fund Endowed Chair in Genetics Edna & Albert Abdo Shahdam Endowed Chair in & Gene Therapy Basic Research

Suzanne J. Baker, PhD Charles G. Mullighan, MBBS, MD Endowed Chair in Brain Tumor Research William E. Evans Endowed Chair

Hongbo Chi, PhD Ellis J. Neufeld, MD, PhD Robert G. Webster Endowed Chair in Immunology John & Lorine Trasher Endowed Chair in Pediatric Medicine

Peter C. Doherty, PhD Alberto S. Pappo, MD Nobel Laureate Alvin Mauer Endowed Chair Michael F. Tamer Endowed Chair in Immunology

James R. Downing, MD Charles W. M. Roberts, MD, PhD Dr. Donald Pinkel Endowed Chair in Childhood Lillian R. Cannon Comprehensive Cancer Center Director Cancer Treatment Endowed Chair

William E. Evans, PharmD Martine F. Roussel, PhD Endowed Chair in Pharmacogenomics Endowed Chair in Molecular Oncogenesis

Patricia M. Flynn, MD Victor M. Santana, MD Arthur Ashe Endowed Chair in Pediatric AIDS Research Dr. Charles B. Pratt Endowed Chair in Solid Tumor Research

Terrence L. Geiger, MD, PhD Brian P. Sorrentino, MD1 Endowed Chair in Pediatrics Wall Street Committee Endowed Chair in Bone Marrow Transplant Research

Melissa M. Hudson, MD Stephen W. White, DPhil The Charles E. Williams Endowed Chair in Oncology– Endowed Chair — Dean, St. Jude Children’s Research Hospital Cancer Survivorship Graduate School of Biomedical Sciences

Thiramala-Devi Kanneganti, PhD Rose Marie Thomas Endowed Chair in Immunology

Emily Walker 1Deceased

2019 Scientific Report | 120 121 | 2019 Scientific Report FELLOWS & SCHOLARS

POSTDOCTORAL FELLOWS Clifford Gee, PhD, Chemical Biology & Therapeutics Cecile Mathieu, PhD, Cell & Molecular Biology Liqing Tian, PhD, Computational Biology Caitlin E. Hurley, MD2 Robert Autry, Pharmaceutical Sciences Hossam Abdelsamed, PhD, Immunology Jamie K. Genthe, PhD, Hematology1 Yurika Matsui, PhD, Developmental Neurobiology Michele Tolbert, PhD, Structural Biology Harry Lesmana, MD Jacob Basham, Pathology Aditi, PhD, Genetics Hazem Ghoneim, PhD, Immunology Jayadev Mavuluri, PhD, Pathology Rachana Tomar, PhD, Structural Biology1 Michael McNeil, MD Daniel Bastardo Blanco, Immunology Issam Al Diri, PhD, Developmental Neurobiology1 Subho Ghosh, PhD, Immunology Brian Maxwell, PhD, Cell & Molecular Biology Ingrid Tonning Olsson, PhD, Epidemiology & Cancer Jonathan J. Miller, MD, PhD Meredith Bernhard, Surgery Sabrin Albeituni, PhD, Oncology Eric Gibbs, PhD, Structural Biology Thiyagaraj Mayuranathan, PhD, Hematology Control Anand G. Patel, MD Thomas Beazley, Surgery1 Tyler Alexander, PhD, Epidemiology & Cancer Nicole Glenn, PhD, Hematology S. Stuart McAfee, PhD, Diagnostic Imaging Sania Trifkovic, PhD, Infectious Diseases Akshay Sharma, MD2 Christopher Trent Brewer, Chemical Biology & Control Yoshihiro Gocho, MD, PhD, Pharmaceutical Sciences Ezelle T. McDonald, PhD, Chemical Biology & Bart Tummers, PhD, Immunology Richa Sharma, MD Therapeutics Johanna Amunjela, PhD, Cell & Molecular Biology Yinan Gong, PhD, Immunology1 Therapeutics1 Jolieke Van Oosterwijk, PhD, Tumor Cell Biology1 Michael A. Terao, MD Mark Allen Brimble, Surgery Shariq Ansari, PhD, Cell & Molecular Biology Charnise Goodings Harris, PhD, Pharmaceutical Sciences Dan McNamara, PhD, Structural Biology BaoHan Vo, PhD, Tumor Cell Biology2 Jessica M. Valdez, MD1 Anthony Brown, Pharmaceutical Sciences David Arroyo, PhD, Developmental Neurobiology Tomoka Gose, PhD, Pharmaceutical Sciences Martin Meagher, PhD, Structural Biology2 Jessica Wagner, PhD, Bone Marrow Transplantation Caitlin C. Zebley, MD Winter Bruner, Pharmaceutical Sciences Jesse Bakke, PhD, Chemical Biology & Flávia Graça Zuanazzi, PhD, Developmental Neurobiology Christopher Meyer, PhD, Chemical Biology & & Cellular Therapy Michael Brunner, Diagnostic Imaging Therapeutics1 Elizabeth Griffith, PhD, PharmD, Chemical Biology & Therapeutics LaShanale Wallace, PhD, Oncology PEDIATRIC INFECTIOUS DISEASES FELLOWS Oravec Chesney, Surgery1 Arjun Balakrishnan, PhD, Immunology1 Therapeutics Nicole Milkovic, PhD, Structural Biology Bo Wang, PhD, Pathology Ruba Barbar, MD Brandi Clark, Immunology Stefanie Baril, PhD, Pharmaceutical Sciences Zhaohui Gu, PhD, Pathology Colton Miller, MD, Pathology Yuanyuan Wang, PhD, Structural Biology2 Timothy Flerlage, MD Kenneth Coca, Oncology1 Justin Batte, PhD, Infectious Diseases Brian Gudenas, PhD, Developmental Neurobiology Priya Mittal, PhD, Oncology Jun Wei, PhD, Immunology2 Patrick Gavigan, MD Jane Craig, Cell & Molecular Biology Jordan Beard, PhD, Pharmaceutical Sciences Jessica Gullett, PhD, Infectious Diseases R. Jackson Mobley, PhD, Oncology Jing Wen, PhD, Immunology1 Kathryn Goggin, MD Ashley Crumby, Pharmaceutical Sciences1 Swarna Beesetti, PhD, Immunology Ao Guo, PhD, Immunology Baisakhi Mondal, PhD, Cell & Molecular Biology Sarah Whaley, PharmD, PhD, Infectious Diseases Amanda Green, MD Tina Hong Dao, Infectious Diseases Anannya Bhattacharya, PhD, Immunology1 Chuansheng Guo, PhD, Immunology Antonio Morales-Hernandez, PhD, Hematology Michael White, PhD, Structural Biology Daniel Darnell, Infectious Diseases Anusarka Bhaumik, PhD, Structural Biology2 Youngdae Gwon, PhD, Cell & Molecular Biology Takaya Moriyama, MD, PhD, Pharmaceutical Juwina Wijaya, PhD, Pharmaceutical Sciences PEDIATRIC NEURO-ONCOLOGY FELLOWS Nisha Das, Chemical Biology & Therapeutics Wenjian Bi, PhD, Biostatistics1 Kohei Hagiwara, MD, Computational Biology Sciences Justin Williams, PhD, Computational Biology Anthony Liu, MD Kirsten Dickerson, Pathology Laure Bihannic, PhD, Developmental Neurobiology Priyanka Halder, PhD, Genetics Ardiana Moustaki, PhD, Immunology Laura Wilt, PhD, Chemical Biology & Therapeutics Daniel Moreira Ridsdale, MD Austin Dove, Radiation Oncology1 Randall Binder, PhD, Chemical Biology & Eric Hall, PhD, Cell & Molecular Biology Brett Mulvey, PhD, Developmental Neurobiology1 Nicholas Wohlgemuth, PhD, Infectious Diseases Ryuma Tanaka, MD1 Michael Edwards, Oncology1 Therapeutics Laura Hamel, PhD, Pharmaceutical Sciences2 Hilmarie Muniz-Talavera, PhD, Developmental Lara Megan Wood, PhD, Developmental Louisa Ekem, Global Pediatric Medicine Emilio Boada Romero, PhD, Immunology Lindsay Hammack, PhD, Structural Biology Neurobiology Neurobiology1 PEDIATRIC SURGICAL ONCOLOGY FELLOWS Leigh Fremuth, Genetics Jill Bouchard, PhD, Structural Biology Seung Baek Han, PhD, Developmental Neurobiology Sivaraman Natarajan, PhD, Oncology Boer Xie, PhD, Structural Biology Hafeez Abdelhafeez, MD2 Jesse Gammons, Developmental Neurobiology David Boyd, PhD, Immunology Jason A. Hanna, PhD, Oncology Christopher Nevitt, MD, Hematology Jia Xie, PhD, Radiation Oncology2 Yousef El-Gohary, MD Samit Ganguly, Pharmaceutical Sciences1 Nicolas Bravo Vasquez, DVM, PhD, Infectious Rhodri Harfoot, PhD, Infectious Diseases Rina Nishii, PhD, Pharmaceutical Sciences Tao Xie, PhD, Structural Biology2 Sara Mansfield, MD Elizabeth Garfinkle, Oncology Diseases Samah Hayek, DPH, Epidemiology & Cancer Control Mingming Niu, PhD, Structural Biology Qiong Xing, PhD, Structural Biology Xizhi Guo, Immunology Anne Bremer, PhD, Structural Biology Robert Hazlitt, PhD, Chemical Biology & Therapeutics Monicah Njogu, PhD, Chemical Biology & Peng Xu, PhD, Hematology PHARMACOGENETICS RESIDENTS Trent Hall, Hematology Benoit Briard, PhD, Immunology Yanghua He, PhD, Hematology Therapeutics Peiguo Yang, PhD, Cell & Molecular Biology2 Keito Hoshitsuki, PharmD Xian Han, Structural Biology John Brooke, PhD, Epidemiology & Cancer Control Nikhil Hebbar, PhD, Bone Marrow Transplantation & Jacqueline Norrie, PhD, Developmental Seung Wook Yang, PhD, Cell & Molecular Biology Cameron Thomas, PharmD1 Virginia Hargest, Infectious Diseases Victoria Bryant, PhD, Pathology1 Cellular Therapy2 Neurobiology Xiaoyang Yang, MD, PhD, Developmental Camden Hastings, Oncology1 Cameron Buchman, PhD, Chemical Biology & Bradlee Heckmann, PhD, Immunology Cameron Ogg, PhD, Developmental Neurobiology Neurobiology2 PHARMACY FELLOWS Rebekah Honce, Infectious Diseases Therapeutics Roketa Henry, PhD, Genetics Faten Okda, DVM, PhD, Infectious Diseases Xu Yang, PhD, Cell & Molecular Biology Amanda Gillispie, PharmD Jessica Hoyer, Chemical Biology & Therapeutics Amit Budhraja, PhD, Cell & Molecular Biology2 Laura Hover, PhD, Developmental Neurobiology Taren Ong, PhD, Developmental Neurobiology Daisuke Yoneoka, PhD, Epidemiology & Cancer Kelsey Hyman, PharmD1 Jianzhong Hu, Pharmaceutical Sciences Laura Buttrum, PhD, Infectious Diseases1 Meng Hu, PhD, Infectious Diseases Yi-Hung Ou, PhD, Immunology Control1 Arathi Lambrix, PharmD1 Viraj Ichhaporia, Tumor Cell Biology Kirby Campbell, PhD, Developmental Neurobiology Hongling Huang, PhD, Immunology Qingfei Pan, PhD, Computational Biology Hiroki Yoshihara, MD, PhD, Pathology Hannah Sauer, PharmD Chuang Jiang, Pharmaceutical Sciences Deviprasanna Chakka, PhD, Structural Biology Xin Huang, PhD, Cell & Molecular Biology Tanushree Pandit, PhD, Cell & Molecular Biology2 Kaiwen Yu, PhD, Structural Biology Olivia Kan, Oncology Bappaditya Chandra, PhD, Structural Biology Andrew Huber, PhD, Chemical Biology & Therapeutics Yakun Pang, PhD, Computational Biology Shanshan Yu, PhD, Chemical Biology & Cellular PHARMACY–MEDICATION SAFETY RESIDENTS Ayub Karwandyar, Surgery Nicole Chapman, PhD, Immunology Ryan Hughes, PhD, Structural Biology Jun Young Park, PhD, Developmental Neurobiology Therapeutics Philip Carpiniello, PharmD1 Nick Keeling, Pharmaceutical Sciences Phillip Chapman, PhD, Developmental Liam Hunt, PhD, Developmental Neurobiology Jung Mi Park, PhD, Cell & Molecular Biology Anthony Zamora, PhD, Immunology Kristen Hughes, PharmD Xin Lan, Hematology Neurobiology Carolyn Jablonowski, PhD, Surgery Philippe Pascua, PhD, Infectious Diseases Mark P. Zanin, PhD, Infectious Diseases1 Shelby Lane, Radiation Oncology Deepti Chaturvedi, PhD, Structural Biology Yoonjeong Jang, DVM, PhD, Hematology Mary Patton, PhD, Developmental Neurobiology Maged Helmy Abdalla Zeineldin, MD, PhD, PHYSICIAN-SCIENTIST TRAINING PROGRAM Anna Lee, Cell & Molecular Biology Meixia Che, PhD, Oncology Yajun Jiang, PhD, Structural Biology Rhiannon Penkert, PhD, Infectious Diseases Developmental Neurobiology FELLOWS Ein Lee, Immunology1 Helen Chen, PhD, Cell & Molecular Biology Yanbo Jiang, PhD, Developmental Neurobiology Ivan Peran, PhD, Structural Biology Jingliao Zhang, PhD, Pharmaceutical Sciences Kari Bjornard, MD, MPH Victoria Liddle, Oncology1 Ping Chung Chen, PhD, Structural Biology2 Jianqin Jiao, PhD, Developmental Neurobiology Christopher Petersen, PhD, Bone Marrow Peipei Zhang, PhD, Cell & Molecular Biology Jennifer L. Kamens, MD Jock Lillard, Surgery2 Li Cheng, MD, PhD, Hematology Kasey Jividen, PhD, Hematology Transplantation & Cell Therapy Fei Zheng, PhD, Developmental Neurobiology2 Spencer Mangum, MD1 Victoria Loudon-Hossler, Chemical Biology & Jude Chenge, PhD, Chemical Biology & Jenny Johnson, PhD, Immunology1 Nicholas Phillips, MD, PhD, Epidemiology & Cancer Janet Huimei Zheng, PhD, Structural Biology Hong Ha Rosa Nguyen, MD Therapeutics2 Therapeutics Barbara M. Jonchere, MD, PhD, Tumor Cell Biology Control Min Zheng, PhD, Immunology Jason Schwartz, MD, PhD2 Joseph Miller, Cell & Molecular Biology Peter Chockley, PhD, Bone Marrow Transplantation Zachary Jones, PhD, Pharmaceutical Sciences1 Jeanne Pierzynski, PhD, Epidemiology & Cancer Wenting Zheng, PhD, Pathology Christina Moore, Nursing Research2 & Cellular Therapy Halime Kalkavan, MD, Immunology Control Peipei Zhou, MD, PhD, Immunology PSYCHOLOGY FELLOWS Alex Mugengana, Chemical Biology & Therapeutics Shelbi Christgen, PhD, Immunology Maduka Kalaurachchi, PhD, Radiation Oncology1 David Place, PhD, Immunology Jiahua Zhu, PhD, Radiation Oncology Lauren Cox, PhD1 Richard Grant Muller, Surgery1 Elizabeth Cleverdon, PhD, Cell & Molecular Biology Nandish Khanra, PhD, Structural Biology1 Kristine Faye Pobre, PhD, Tumor Cell Biology Jing Zhu, PhD, Structural Biology2 Mallorie Gordon, PhD Christina Oikonomou, Tumor Cell Biology Christopher Coke, PhD, Pharmaceutical Sciences Hyunsuh Kim, PhD, Infectious Diseases Gregory Poet, PhD, Tumor Cell Biology Zhexin Zhu, PhD, Oncology Rebecca Elyse Heidelberg, PhD Majek Olaleye, Global Pediatric Medicine1 Evan Comeaux, PhD, Pathology1 Sajjan Koirala, PhD, Cell & Molecular Biology Amir Pourmoghaddas, PhD, Radiation Oncology1 Xinying Zong, PhD, Immunology Kayla LaRosa, PhD Aurora Peck, Infectious Diseases1 Valerie Cortez, PhD, Infectious Diseases David Krist, PhD, Structural Biology1 Maria Purice, PhD, Cell & Molecular Biology1 Vicky Lehman, PhD1 Gregory Phelps, Chemical Biology & Therapeutics Rebecca Crawford, PhD, Pharmaceutical Sciences1 Teneema Kuriakose, PhD, Immunology2 Maoxiang Qian, PhD, Pharmaceutical Sciences1 CLINICAL FELLOWS Megan Loew, PhD Ashlin Philip, Oncology1 Yixin Cui, PhD, Structural Biology Casey Langdon, PhD, Oncology Christopher Radka, PhD, Infectious Diseases Kristin Niel, PhD1 Mary Portera, Surgery Maxime Cuypers, PhD, Structural Biology2 Shannon Lange, PhD, Bone Marrow Transplantation & Mamta Rai, PhD, Developmental Neurobiology BONE MARROW TRANSPLANTATION & Sasja Schepers, PhD1 Lee Pribyl, Genetics Erich Damm, PhD, Hematology Cellular Therapy Pilar Ramos, PhD, Oncology1 CELLULAR THERAPY FELLOWS Justin Williams, PhD1 Brooke Prinzing, Bone Marrow Transplantation & Emily Darrow, PhD, Developmental Neurobiology Jon D. Larson, PhD, Developmental Neurobiology Shuquan Rao, PhD, Structural Biology1 Mansi Sachdev, MD1 Cellular Therapy Jitendra Das, PhD, Structural Biology Christophe Laumonnerie, PhD, Developmental Sanaz Rasouli, PhD, Structural Biology Ali Suliman, MD, MSc RADIATION ONCOLOGY FELLOW Spencer Richardson, Immunology Soumyasri Das Gupta, PhD, Cell & Molecular Neurobiology2 Anisha Rathi, PhD, Cell & Molecular Biology Yousef Ismael, MD Jordan Roach, Surgery Biology2 Cicera Lazzarotto, DVM, PhD, Hematology Jana Raynor, PhD, Immunology CANCER SURVIVORSHIP FELLOWS Sushree Sahoo, Hematology Prakash Devaraju, PhD, Developmental Ana Leal Cervantes, PhD, Oncology Kavya Reddy, PhD, Infectious Diseases Neel Bhatt, MBBS, MD SOLID TUMOR FELLOW Anjelica Saulsberry, Hematology Neurobiology Natalie Lee, PhD, Infectious Diseases Stephanie Reeve, PhD, Chemical Biology & Alia Zaidi, MD2 Hadeel Halalsheh, MD1 Hao Shi, Immunology Kaushik Dey, PhD, Structural Biology Shaohua Lei, PhD, Computational Biology Therapeutics Kenneth Shiao, Oncology Suresh Dharuman, PhD, Chemical Biology & William Letsou, PhD, Epidemiology & Cancer Control Ricardo Rodriguez-Enriquez, PhD, Cell & Molecular INFECTIOUS DISEASES IN ST. JUDE GRADUATE STUDENTS Geetika Singh, Structural Biology Therapeutics Jun Li, PhD, Immunology Biology IMMUNOCOMPROMISED CHILDREN AND Alexandra Beckett Kaitlyn Smith, Cell & Molecular Biology Larissa Dias da Cunha, PhD, Immunology1 Yizhen Li, PhD, Pharmaceutical Sciences Hannah Rowe, PhD, Infectious Diseases ADOLESCENTS FELLOWS Matthew Bell, Bone Marrow Transplantation & Cellular Aisha Souquette, Immunology Jonathan Diedrich, PhD, Pharmaceutical Sciences Yongtao Li, PhD, Chemical Biology & Therapeutics Vasilisa Rudneva, PhD, Developmental Sujittra Chaisavaneeyakorn, MD, PhD Therapy Wei Su, Immunology Phillip Doerfler, PhD, Hematology Swantje Liedmann, PhD, Immunology Neurobiology1 Maria Garcia-Fernandez, MD1 Brennan Bergeron, Pharmaceutical Sciences Parker Tumlin, Radiation Oncology Catherine Drummond, PhD, Oncology1 Seon Ah Lim, PhD, Immunology Sebastian Ruehl, PhD, Immunology Mackenzie Bloom, Oncology Patricia Umberger, Cell & Molecular Biology Xingrong Du, PhD, Immunology Beiyun Liu, PhD, Immunology Aaryani Sajja, PhD, Diagnostic Imaging1 INFECTIOUS DISEASES PEDIATRIC HIV FELLOW Kaitlyn Budd Mitra Varedi Kolaei, Epidemiology & Cancer Control2 Haley Echlin, PhD, Infectious Diseases Danting Liu, PhD, Structural Biology Farimah Salami, PhD, Diagnostic Imaging1 Dana Sanders, MD1 Madeline Bush, Oncology Elena Varotto, Oncology Anne Edwards, PhD, Chemical Biology & Fengming Liu, PhD, Developmental Neurobiology Muneeb Salie, PhD, Developmental Neurobiology Christina Daly Nicole Vita, Chemical Biology & Therapeutics Therapeutics Jingjing Liu, PhD, Computational Biology Parimal Samir, PhD, Immunology OCULAR ONCOLOGY FELLOW Rebecca Florke, Cell & Molecular Biology Anh Vo, Infectious Diseases1 Rabeh El Shesheny, PhD, Infectious Diseases Shaofeng Liu, PhD, Immunology Kesavardana Sannula, PhD, Immunology Benjamin King, MD1 Jessica Gaevert Xinyu von Buttlar, Oncology Tae-Yeon Eom, PhD, Developmental Neurobiology2 Xueyan Liu, PhD, Biostatistics1 Jordy Saravia, PhD, Immunology Liam Hallada Megan Walker, Hematology Leonardo Estrada, PhD, Infectious Diseases Yanling Liu, PhD, Computational Biology Mohona Sarkar, PhD, Cell & Molecular Biology2 NEUROPSYCHOLOGY FELLOWS Victoria Honnell, Developmental Neurobiology Kirby Wallace, Surgery1 Myron Evans, PhD, Developmental Neurobiology Yiwei Liu, PhD, Pharmaceutical Sciences Shobhit Saxena, PhD, Hematology1 Jeanelle Ali, PhD Alex Hughes, Developmental Neurobiology Miranda Wallace, Chemical Biology & Therapeutics Thomas Fabrizio, PhD, Infectious Diseases Yu Liu, PhD, Computational Biology1 Stefan Schattgen, PhD, Immunology Traci Olivier, PsyD1 Christina Kackos, Infectious Diseases Amber Ward, Pathology Li Fan, MD, PhD, Pharmaceutical Sciences Ogheneochukome Lolodi, PhD, Chemical Biology & Ming Shao, PhD, Chemical Biology & Therapeutics Marita Partanen, PhD Allison Kirk, Immunology Jason A. Weesner, Genetics Ruopeng Feng, PhD, Hematology Therapeutics Bhesh Raj Sharma, PhD, Immunology Rahul Kumar, Developmental Neurobiology Rachael Wood, Tumor Cell Biology Daniel Ferguson, PhD, Pharmaceutical Sciences Lingyun Long, PhD, Immunology Deepika Sharma, PhD, Immunology1 PEDIATRIC HEMATOLOGY-ONCOLOGY FELLOWS Andrea Lee Kaitly Woodard, Hematology Dinesh Fernando, PhD, Chemical Biology & Allister Loughran, PhD, Infectious Diseases1 Piyush Sharma, PhD, Immunology Maggie Besler, MD Sandi Radko William Charles Wright, Chemical Biology & Therapeutics Margaret Lubas, PhD, Epidemiology & Cancer Control Jeffrey Sifford, PhD, Structural Biology Senthil Bhoopalan, MBBS Isaiah Reeves Therapeutics Mylene H. Ferrolino, PhD, Structural Biology2 Marybeth Lupo, PhD, Developmental Neurobiology Andre Silveira, PhD, Developmental Neurobiology1 Lindsay Blazin, MD Maria Smith Tianhua Wu, Pathology1 Emily Finch, PhD, Pharmaceutical Sciences Brianna Lutz, PhD, Structural Biology Shivendra Singh, PhD, Surgery Kenneth Caldwell, MD Ana Vazquez-Pagan Zemin Yang, Cell & Molecular Biology Diane Flasch, PhD, Computational Biology Eda Rita Machado De Seixas, PhD, Genetics2 Emma K. Sliger, PhD, Immunology Steven Carey, MD, PhD2 Elizabeth Wickman David Yanishevski, Surgery Guotong Fu, PhD, Immunology Joelle Magne, PhD, Immunology Stephanie Smith, PhD, Tumor Cell Biology1 David Cervi, DO, PhD Benjamin Wilander Jay Yarbro, Structural Biology Katherine Gadek, PhD, Oncology Ousman Mahmud, PhD, Oncology1 Munia Sowaileh, PhD, Structural Biology David A. Claassen, MD1 McLean Williamson Sarah Youssef, Oncology1 Debolina Ganguly, PhD, Tumor Cell Biology Yujiao Mai, PhD, Biostatistics Katherine Stanford, PhD, Pathology Stephanie Berry Dixon, MD Caitlin C. Zebley, MD, Immunology Xujie Zhao, Pharmaceutical Sciences Ruchika Gangwar, PhD, Developmental Ankit Malik, PhD, Immunology1 Jennifer Stripay, PhD, Tumor Cell Biology Rebecca A. Epperly, MD Yumei Zheng, Structural Biology Neurobiology1 Luigi Mari, PhD, Immunology Xiaojun Sun, MD, PhD, Structural Biology Lisa Force, MD GRADUATE RESEARCH SCHOLARS Qifan Zhu, Immunology1 Miguel Ganuza Fernandez, PhD, Hematology Erik Martin, PhD, Structural Biology Benjamin Sunkel, PhD, Oncology1 Kayla Foster, MD Ahmed Abuzaid, Surgery Tony Zhuang, Oncology Jesús García López, PhD, Developmental Nancy Martinez, PhD, Chemical Biology & Therapeutics Sarang Tartey, PhD, Immunology Jessica A. Gartrell, MD Fabienne Adriaanse, Oncology Chan Zou, Pharmaceutical Sciences Neurobiology Joshua Mason, PhD, Bone Marrow Transplantation & Kristen Thomas, PhD, Developmental Neurobiology Dylan E. Graetz, MD Hannah Allen, Oncology Marcela Garza, MD, Global Pediatric Medicine Cellular Therapy Melvin Thomas III, PhD, Pathology Joshua A. Hess, MD Kavya Annu, Pharmaceutical Sciences 1No longer at St. Jude; 2Promoted to staff position

2019 Scientific Report | 122 123 | 2019 Scientific Report BOARD OF GOVERNORS EXECUTIVE COMMITTEE

These volunteers served on the Board of Governors of St. Jude Children’s Research Hospital during 2018. Officers are indicated by the titles under their names.

Joyce A. Aboussie Gabriel G. Haddad, MD Paul J. Simon James R. Downing, MD, Chair Pat Keel, MHA Mary V. Relling, PharmD President and Chief Executive Officer Senior Vice President Chair, Pharmaceutical Sciences Susan Mack Aguillard, MD Paul K. Hajar Tony Thomas Chief Financial Officer Secretary Justin N. Baker, MD Charles W. M. Roberts, MD, PhD Charles C. Hajjar Richard M. Unes Oncology Richard Lee, PhD Executive Vice President Sandy Alexander1,2 Fouad M. Hajjar, MD Paul H. Wein Interim Chair, Chemical Biology & Director, Comprehensive Cancer Center Epsilon Sigma Alpha Suzanne J. Baker, PhD Therapeutics representative Frederick R. Harris Jr, MD Thomas C. Wertz Developmental Neurobiology Leslie L. Robison, PhD Mahir R. Awdeh, MD Jonathan A. McCullers, MD Chair, Epidemiology & Cancer Control Bruce B. Hopkins Tama H. Zaydon Shari M. Capers, MBA, MHA Chair, Pediatrics, University of Joseph S. Ayoub Jr Vice President, Strategic Planning & Tennessee Health Science Center Carlos Rodriguez-Galindo, MD J. David Karam II Decision Support Pediatrician-in-Chief, Le Bonheur Executive Vice President

Paul J. Ayoub 1,4 Children’s Hospital Chair, Department of Global Pediatric Kim Kummer Andrew M. Davidoff, MD Infectious Diseases Medicine Frederick M. Azar, MD Epsilon Sigma Alpha representative Chair, Surgery Director, St. Jude Global Sharon L. McCollam Thomas E. Merchant, DO, PhD James B. Barkate Robyn Diaz, JD Chair, Radiation Oncology Martine F. Roussel, PhD Martha Perine Beard Michael D. McCoy Senior Vice President Tumor Cell Biology Chief Legal Officer James I. Morgan, PhD Sheryl A. Bourisk Robert T. Molinet Executive Vice President Victor M. Santana, MD Michael A. Dyer, PhD Scientific Director Vice President, Clinical Trials Administration Robert A. Breit, MD Ramzi N. Nuwayhid Chair, Developmental Neurobiology Oncology Charles G. Mullighan, MBBS, MD Terry L. Burman Thomas J. Penn III David W. Ellison, MD, PhD Pathology Charles J. Sherr, MD, PhD Christina M. Rashid Chair, Pathology Chair, Tumor Cell Biology Ann M. Danner Robin Mutz, RN, MHA Joseph M. DeVivo Camille F. Sarrouf Jr Patricia M. Flynn, MD Senior Vice President, Patient Care Ronald Smith, MHA Chair Senior Vice President Services Vice President, Scientific Operations James R. Downing, MD3 Deputy Clinical Director Chief Nursing Executive St. Jude President and CEO Richard C. Shadyac Jr3 Deo Kumar Srivastava, PhD Amar J. Gajjar, MD Ellis J. Neufeld, MD, PhD Interim Chair, Biostatistics Fred P. Gattas III, PharmD Joseph C. Shaker Chair, Pediatric Medicine Executive Vice President Co-Chair, Oncology Clinical Director J. Paul Taylor, MD, PhD Ruth C. Gaviria Joseph G. Shaker Physician-in-Chief Chair, Cell & Molecular Biology George A. Simon II Terrence L. Geiger, MD, PhD Christopher B. George, MD Senior Vice President Alberto S. Pappo, MD Elaine I. Tuomanen, MD Vice Chair Michael C. Simon Deputy Director for Academic and Oncology Chair, Infectious Diseases Judy A. Habib Biomedical Operations Zoltán Patay, MD, PhD Mitchell J. Weiss, MD, PhD Stephen M. Gottschalk, MD Chair, Diagnostic Imaging Chair, Hematology Chair, Bone Marrow Transplantation & EMERITUS MEMBERS Cellular Therapy Keith Perry, MBA Stephen W. White, DPhil Senior Vice President Dean, St. Jude Graduate School of Thomas G. Abraham Frederick R. Harris David B. Nimer Douglas R. Green, PhD Chief Information Officer Biomedical Sciences Jack A. Belz Theodore J. Hazer Talat M. Othman Chair, Immunology Stephen J. Camer, MD Joseph G. Hyder5 Manal B. Saab Sean Phipps, PhD Jinghui Zhang, PhD Joseph G. Cory, PhD Richard J. Karam Camille F. Sarrouf Sr5 Gerard C. Grosveld, PhD Chair, Psychology Chair, Computational Biology Leslie S. Dale James A. Kinney Frederick W. Smith Chair, Genetics 5 Ching-Hon Pui, MD Lewis R. Donelson III Salli E. LeVan Ronald A. Terry Melissa M. Hudson, MD Chair, Oncology George Elias Jr Donald G. Mack, MD Terre Thomas Oncology Hasan M. Elkhatib George M. Maloof Pat Kerr Tigrett Mary Anna Quinn Fred P. Gattas Jr Paul J. Marcus Robert P. Younes, MD Charalampos Babis Kalodimos, PhD Executive Vice President Sam F. Hamra James O. Naifeh Sr Ramzi T. Younis, MD Chair, Structural Biology Chief Administrative Officer

1Ex officio voting member; 2January 2017–June 2018; 3Nonelected member; 4July–December 2018; 5Deceased

2019 Scientific Report | 124 125 | 2019 Scientific Report SCIENTIFIC ADVISORY BOARD OPERATIONS & STATISTICS

This panel of physicians and scientists, serving during 2018, fostered the institution’s development through discussion with faculty members, reports to the Board of Governors, and advice to the President and CEO on scientific and clinical research directions.

Mignon L. Loh, MD, Chair Raphael E. Pollock, MD, PhD OPERATIONS UCSF Benioff Chair of Children’s Health Director, Comprehensive Cancer Center Deborah and Arthur Ablin Endowed Chair in Pediatric Kathleen Wellenreiter Klotz Chair in Cancer Research Operating expenses1 $937.2 million Molecular Oncology The Ohio State University Health System Division Chief, Hematology/Oncology Number of employees2 4682 University of California Benioff Children’s Hospital Aviv Regev, PhD University of California, San Francisco Investigator, Howard Hughes Medical Institute Professor, Department of Biology RESEARCH STATISTICS Joseph W. St. Geme III, MD, Vice Chair Massachusetts Institute of Technology Leonard and Madlyn Abramson Professor of Pediatrics and Core Member and Chair of the Faculty Grant funding1 $94.4 million Microbiology Director, Cell Circuits Program and Klarman Cell Observatory Perelman School of Medicine, University of Pennsylvania Broad Institute Physician-in-Chief and Chair, Department of Pediatrics Peer-reviewed publications 764 The Children’s Hospital of Philadelphia Michael K. Rosen, PhD Member, Institute of Medicine of the National Academies Investigator, Howard Hughes Medical Institute Faculty members 296 Mar Nell and F. Andrew Bell Distinguished Chair in Biochemistry Benjamin F. Cravatt III, PhD Postdoctoral fellows 313 Professor and Chair, Department of Chemical Physiology University of Texas Southwestern Medical Center The Skaggs Institute for Chemical Biology The Scripps Research Institute Michel W. Sadelain, MD, PhD Clinical residents and fellows3 359 Member, Institute of Medicine of the National Academies Stephen and Barbara Friedman Chair Director, Center for Cell Engineering Graduate research scholars 121 Patricia A. Ganz, MD Memorial Sloan-Kettering Cancer Center Distinguished Professor of Health Policy and Management UCLA Fielding School of Public Health Joshua R. Sanes, PhD CLINICAL STATISTICS UCLA David Geffen School of Medicine Jeff C. Tarr Professor of Molecular and Cellular Biology Director, Cancer Prevention & Control Research Paul J. Finnegan Family Director, Center for Brain Science Number of beds open4 73 Jonsson Comprehensive Cancer Center Harvard University University of California, Los Angeles Outpatient encounters5 294,798 Member, Institute of Medicine of the National Academies Akiko Shimamura, MD, PhD Associate Professor of Pediatrics, Harvard Medical School Mary K. Gospodarowicz, MD, FRCPC, FRCR (Hon) Samuel E. Lux IV Chair in Hematology/Oncology Inpatient admissions 3472 Professor of Radiation Oncology Director, Bone Marrow Failure and Myelodysplastic Medical Director, Princess Margaret Cancer Centre Syndrome Programs Total inpatient days 18,921 University Health Network, University of Toronto Dana-Farber Cancer Institute Boston Children’s Cancer & Blood Disorders Center Daphne A. Haas-Kogan, MD Total protocol enrollments in 2018 7265 Professor of Radiation Oncology Kimberly Stegmaier, MD Harvard Medical School Professor of Pediatrics, Harvard Medical School Patients enrolled in therapeutic trials 844 Chair, Department of Radiation Oncology Attending Physician, Pediatric Oncology, Boston Children’s Dana-Farber Cancer Institute Hospital Principal Investigator, Pediatric Oncology Patients enrolled in nontherapeutic trials 6421 David P. Harrington, PhD Dana-Farber Cancer Institute Professor of Biostatistics Co-Director, Pediatric Hematologic Malignancy Program 5020 in prospective trials Harvard TH Chan School of Public Health Boston Children’s Hospital and Dana-Farber Cancer Institute Professor, Department of Biostatistics and Computational Ted Williams Chair, Pediatric Oncology, Dana-Farber Cancer 1401 in tissue-banking protocols Biology Institute Dana-Farber Cancer Institute Dana-Farber/Boston Children’s Cancer & Blood Disorders Center Number of protocols open to accrual in 2018 338 John Kuriyan, PhD Investigator, Howard Hughes Medical Institute Number of active therapeutic trials 174 Chancellor’s Professor Professor of Molecular Biology and Professor of Chemistry Number of active nontherapeutic trials 164 University of California, Berkeley Member, Institute of Medicine of the National Academies 162 prospective trials

2 tissue-banking protocols

1Data represents the period July 1, 2017–June 30, 2018. 2Data is from July 1, 2018. 3Data includes 183 full-time St. Jude fellows and 176 rotating fellows from the University of Tennessee Health Science Center or other medical schools. 4Data represents the number of beds in use. St. Jude is licensed for 80 beds. 5Data represents the total number of ambulatory or ancillary encounters not daily visits.

2019 Scientific Report | 126 127 | 2019 Scientific Report To cure one child at St. Jude is to cure countless children worldwide.

2019 Scientific Report | 128