Signaling Effectors Required for G Protein-Coupled Estrogen Receptor-, GPER, Induced Events Associated with Breast Cancer Progression

Total Page:16

File Type:pdf, Size:1020Kb

Signaling Effectors Required for G Protein-Coupled Estrogen Receptor-, GPER, Induced Events Associated with Breast Cancer Progression Signaling Effectors Required for G Protein-Coupled Estrogen Receptor-, GPER, Induced Events Associated with Breast Cancer Progression by Hilary Thompson Magruder B.A. Wheaton College, 2009 A dissertation submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in the Division of Biology and Medicine at Brown University. May, 2014 © Copyright 2014 by Hilary Thompson Magruder This presentation by Hilary Thompson Magruder is accepted in its present form by the Division of Biology and Medicine as satisfying the dissertation requirements for the degree of Doctor of Philosophy Date__________ ________________________________ Edward J. Filardo, Ph.D., Director Recommended to the Graduate Council Date__________ ________________________________ Richard Freiman, Ph.D., Reader Date__________ ________________________________ Jonathan Reichner, Ph.D., Reader Date__________ ________________________________ Wentian Yang, Ph.D., Reader Date__________ ________________________________ Eric Prossnitz, Ph.D., Outside Reader Approved by the Graduate Council Date_________ ________________________________ Peter M. Weber, Ph.D. Dean of the Graduate School iii Hilary T. Magruder 29 High Hawk Road Portsmouth, RI 02871 (401) 662-9588 [email protected] Education Brown University (Providence, Rhode Island) Anticipated 2014 Ph.D. Candidate in Pathobiology under the Division of Biology and Medicine Thesis: “Signaling Effectors Required for G Protein-Coupled Estrogen Receptor-, GPER, Induced Events Associated with Breast Cancer Progression” in Dr. Edward Filardo’s laboratory Mentored Brown University undergraduate students in Dr. Jonathan Reichner’s laboratory Teaching Assistant for a virology course Nominated for the June Rockwell Levy Predoctoral Fellowship in the Fall of 2009 Brown University (Providence, Rhode Island) Anticipated 2014 M.A. in Pathobiology under the Division of Biology and Medicine Wheaton College (Norton, Massachusetts) 2005 – 2009 B.A. in Biochemistry & Psychology (Double Major) Cumulative GPA- 3.75; Biochemistry GPA- 3.77 Honors: The Villar’s Prize in Science, Julia R. Lange Fellowship, Phi Beta Kappa Honors Society, Psi Chi Honors Society, Tri Beta Biological Honors Society, Biochemistry Departmental Honors, Dean’s List, National Scholars Honors Society Biochemistry Honors Thesis on GPR30 in ovarian cancer under the supervision of Dr. Edward Filardo from Rhode Island Hospital/Brown University and Dr. Elita Pastra-Landis from Wheaton College Publications, Citations, and Abstracts Magruder H, Quinn JA, Schwartzbauer JE, Reichner J, Huang A, Filardo EJ. The G-protein- coupled estrogen receptor, GPER-1, promotes fibrillogenesis via a Shc-dependent pathway resulting in anchorage-independent growth. Hormones and Cancer (in preparation). iv Magruder H, Reichner J, Huang A, Filardo EJ. PTPN12 inhibits estrogen action via the G- protein-coupled receptor, GPR30/GPER-1. (in preparation). Magruder H, Filardo EJ. Epidermal growth factor receptor transactivation and fibronectin matrix assembly by the G-protein coupled receptor, GPER, requires a transmembrane signaling complex consisting of PTPN12, integrin α5β1, and MMP-3. Abstract presented at the Experimental Biology Annual Meeting; April 2012, San Diego, California. Dewan S, Magruder H. Re-treatment of vestibular schwannomas with gamma knife radiosurgery. Abstract Presented at The 14th International Meeting of the Leksell Gamma Knife Society; May 2008, Quebec, Canada. McCormack E, Magruder H, Steinhoff MM, Gass J, Legare ED, Wiggins DL, Tejada-Berges T, Sikov W, Strenger R, Dizon DS. Clinicopathic analysis of tubular carcinoma of the breast: the experience from Women & Infants’ Hospital of Rhode Island. American Journal of Clinical Oncology, 2007; 30: 454-455. Bonzagni A, Magruder H, Benoit JM. Mercury uptake from fish fertilizer by spinach plants. Eighth Annual Northeast Student Chemistry Research Conference (NSCRC) 2006; Cambridge, MA. Work Experience and Internships Wheaton College 2013 - Present Laboratory Instructor of a general chemistry course and an organic chemistry course 2008 – 2009 Instructed a general and inorganic chemistry weekly review and graded papers under the supervision of Professor Matthew Evans 2007 Attempted to create an environmentally friendly stereoisomer of an amino acid through hydrogenation reactions under the supervision of Professor Christopher Kalberg 2006 – 2007 Teaching fellow in general and inorganic chemistry under the supervision of Professor Jani Benoit that included tutoring students and grading examinations 2006 – 2007 Kollett Center tutor for general and inorganic chemistry students Memorial Hospital of Rhode Island 2008-2009 v Conducted a clinical research project on patient satisfaction in labor and delivery, and disparities in access to healthcare American Cancer Society Fuller Fellowship 2007 Studied GPER at Alpert Medical School of Brown University/Rhode Island Hospital under the supervision of Dr. Edward Filardo New England Gamma Knife Center 2007 Investigated vestibular schwannomas at Alpert Medical School of Brown University/Rhode Island Hospital under the supervision of Dr. Georg Noren Research published in the Journal of Neurosurgery NeuroHealth 2007 Explored the correlation between lack of smell and apathy in Parkinson’s patients under the supervision of Dr. Joseph Friedman and Dr. Megan Spencer Merck Scholar Internship 2006 Investigated mercury levels in human hair and in leaves around the Wheaton College Vernal Pool under the supervision of Professor Jani Benoit Women & Infants Hospital- Program in Women’s Oncology 2006 – 2007 Chaired and managed the Patient Advocate Fundraiser, which raised over $60,000 Structured and conducted a clinical research project on tubular carcinomas of the breast Published an abstract in the American Journal of Clinical Oncology Research Presentations Experimental Biology Annual Meeting 2012 in San Diego 2012 Presented Epidermal growth factor receptor transactivation and fibronectin matrix assembly by the G-protein coupled receptor, GPER, requires a transmembrane signaling complex consisting of PTPN12, integrin α5β1, and MMP-3 Pathobiology Program Retreat 2012 Presented Epidermal growth factor receptor transactivation and fibronectin matrix assembly by the G-protein coupled receptor, GPER, requires a transmembrane signaling complex consisting of PTPN12, integrin α5β1, and MMP-3 19th Annual Hospital Research Celebration at Rhode Island Hospital 2011 vi Presented Transmembrane signaling effectors that regulate GPER-mediated fibrillogeness and EGFR transactivation Department of Medicine’s 17th Annual Research Forum- Brown University 2011 Presented Transmembrane signaling effectors that regulate GPER-mediated EGFR transactivation Brown University Pathology II Course 2011 Presented Extracellular Matrix: Integrins and Matrix Metalloproteinases in Cancer Brown University Virology Course 2011 Presented Herpesviridae Pathobiology Program Retreat 2011 Presented Transmembrane signaling effectors that regulate GPER-mediated EGFR transactivation 18th Annual Hospital Research Celebration at Rhode Island Hospital 2010 Presented Role of GPR30 in breast tumor cell survival and its influence on mammary stromal fibroblast transformation Pathobiology Program Retreat 2010 Presented Role of GPR30 in breast tumor cell survival and its influence on mammary stromal fibroblast transformation Fuller and Stone Fellowship Reception 2007 Presented Expression of GPR30, a novel membrane estrogen receptor, in human breast and ovarian cancer Wheaton College Academic Festival XVI 2007 Nominated and accepted to present Mercury Deposition to the Wheaton College Vernal Pool via Leaf Litter Fall Wheaton College Research Symposium 2007 Presented Mercury Deposition to the Wheaton College Vernal Pool via Leaf Litter Fall Achievements and Honors June Rockwell Levy Predoctoral Fellowship Nominee 2009 The Villar’s Prize in Science 2009 vii Julia R. Lange Fellowship 2009 Academic Festival XVIII Nominee and Participant at Wheaton College 2009 Outstanding Service as a Partner in Philanthropy Awarded by the 2007 Association of Fundraising Professionals American Cancer Society Fuller Fellow 2007 Academic Festival XVI Nominee and Participant at Wheaton College 2007 Merck Scholar 2006 Wheaton Fellows Scholarship 2006 – 2007 Dean’s List Fall 2005 – 2009 Memberships American Society for Pharmacology and Experimental Therapeutics 2011 - Present Phi Beta Kappa Honors Society 2008 - Present Psi Chi Honors Society in Psychology 2008 - Present Pre-Health Society - President 2008 – 2009 Tri-Beta Biological Honors Society, Chi Nu – Vice President 2008 – 2009 American Cancer Society’s Fuller Fellow 2007 – 2008 National Scholars Honors Society 2007 - Present Wheaton Fellow 2006 – 2007 Patient Advocate Fundraising Committee - Chair, Project Manager 2006 – 2007 Public Vaccination Council 2006 Pre-Health Society - Secretary and Events Coordinator 2006 – 2008 Biomedical Science Careers Program at Harvard 2006 - Present viii Program in Women’s Oncology Chemotherapy Committee 2006 Society of Surgical Oncology Application Committee 2006 Breast Fellowship Committee 2006 Certifications NIH Clinical Research Training Course Certificate 2013 NIH Office of Clinical Research Training and Medical Education Sheridan Teaching Certificate I 2010 Sheridan Center at Brown University Training in Responsible Conduct in Research Certificate 2009 Brown University Initiative to Maximize Student Development Certificate
Recommended publications
  • To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
    Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.
    [Show full text]
  • Time Resolved Quantitative Phosphoproteomics Reveals Distinct Patterns of SHP2
    bioRxiv preprint doi: https://doi.org/10.1101/598664; this version posted April 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Time resolved quantitative phosphoproteomics reveals distinct patterns of SHP2 dependence in EGFR signaling Vidyasiri Vemulapalli1,2, Lily Chylek3, Alison Erickson4, Jonathan LaRochelle1,2, Kartik Subramanian3, Morvarid Mohseni5, Matthew LaMarche5, Michael G. Acker5, Peter K. Sorger3, Steven P. Gygi4, and Stephen C. Blacklow1,2* 1Department of Cancer Biology, Dana-Farber Cancer Institute Boston, MA 02115, USA 2Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA 3Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA 4Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA 5Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA *To whom correspondence should be addressed: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/598664; this version posted April 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines; it is frequently mutated in childhood leukemias and other cancers. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by the small molecule SHP099.
    [Show full text]
  • The Regulatory Roles of Phosphatases in Cancer
    Oncogene (2014) 33, 939–953 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc REVIEW The regulatory roles of phosphatases in cancer J Stebbing1, LC Lit1, H Zhang, RS Darrington, O Melaiu, B Rudraraju and G Giamas The relevance of potentially reversible post-translational modifications required for controlling cellular processes in cancer is one of the most thriving arenas of cellular and molecular biology. Any alteration in the balanced equilibrium between kinases and phosphatases may result in development and progression of various diseases, including different types of cancer, though phosphatases are relatively under-studied. Loss of phosphatases such as PTEN (phosphatase and tensin homologue deleted on chromosome 10), a known tumour suppressor, across tumour types lends credence to the development of phosphatidylinositol 3--kinase inhibitors alongside the use of phosphatase expression as a biomarker, though phase 3 trial data are lacking. In this review, we give an updated report on phosphatase dysregulation linked to organ-specific malignancies. Oncogene (2014) 33, 939–953; doi:10.1038/onc.2013.80; published online 18 March 2013 Keywords: cancer; phosphatases; solid tumours GASTROINTESTINAL MALIGNANCIES abs in sera were significantly associated with poor survival in Oesophageal cancer advanced ESCC, suggesting that they may have a clinical utility in Loss of PTEN (phosphatase and tensin homologue deleted on ESCC screening and diagnosis.5 chromosome 10) expression in oesophageal cancer is frequent, Cao et al.6 investigated the role of protein tyrosine phosphatase, among other gene alterations characterizing this disease. Zhou non-receptor type 12 (PTPN12) in ESCC and showed that PTPN12 et al.1 found that overexpression of PTEN suppresses growth and protein expression is higher in normal para-cancerous tissues than induces apoptosis in oesophageal cancer cell lines, through in 20 ESCC tissues.
    [Show full text]
  • PTPN11 Is the First Identified Proto-Oncogene That Encodes a Tyrosine Phosphatase
    From www.bloodjournal.org by guest on July 4, 2016. For personal use only. Review article PTPN11 is the first identified proto-oncogene that encodes a tyrosine phosphatase Rebecca J. Chan1 and Gen-Sheng Feng2,3 1Department of Pediatrics, the Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis; 2Programs in Signal Transduction and Stem Cells & Regeneration, Burnham Institute for Medical Research, La Jolla, CA; 3Institute for Biomedical Research, Xiamen University, Xiamen, China Elucidation of the molecular mechanisms 2 Src-homology 2 (SH2) domains (Shp2). vation of the Ras-Erk pathway. This underlying carcinogenesis has benefited This tyrosine phosphatase was previ- progress represents another milestone in tremendously from the identification and ously shown to play an essential role in the leukemia/cancer research field and characterization of oncogenes and tumor normal hematopoiesis. More recently, so- provides a fresh view on the molecular suppressor genes. One new advance in matic missense PTPN11 gain-of-function mechanisms underlying cell transforma- this field is the identification of PTPN11 mutations have been detected in leuke- tion. (Blood. 2007;109:862-867) as the first proto-oncogene that encodes mias and rarely in solid tumors, and have a cytoplasmic tyrosine phosphatase with been found to induce aberrant hyperacti- © 2007 by The American Society of Hematology Introduction Leukemia and other types of cancer continue to be a leading cause tumor suppressor activity when overexpressed in vitro, and Ptprj of death in the United States, and biomedical scientists sorely note maps to the mouse colon cancer susceptibility locus,3 implicating that victories against cancer remain unacceptably rare.
    [Show full text]
  • Mutational Landscape and Clinical Outcome of Patients with De Novo Acute Myeloid Leukemia and Rearrangements Involving 11Q23/KMT2A
    Mutational landscape and clinical outcome of patients with de novo acute myeloid leukemia and rearrangements involving 11q23/KMT2A Marius Billa,1,2, Krzysztof Mrózeka,1,2, Jessica Kohlschmidta,b, Ann-Kathrin Eisfelda,c, Christopher J. Walkera, Deedra Nicoleta,b, Dimitrios Papaioannoua, James S. Blachlya,c, Shelley Orwicka,c, Andrew J. Carrolld, Jonathan E. Kolitze, Bayard L. Powellf, Richard M. Stoneg, Albert de la Chapelleh,i,2, John C. Byrda,c, and Clara D. Bloomfielda,c aThe Ohio State University Comprehensive Cancer Center, Columbus, OH 43210; bAlliance for Clinical Trials in Oncology Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210; cDivision of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210; dDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294; eNorthwell Health Cancer Institute, Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY 11042; fDepartment of Internal Medicine, Section on Hematology & Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157; gDepartment of Medical Oncology, Dana-Farber/Partners Cancer Care, Boston, MA 02215; hHuman Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210; and iDepartment of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 Contributed by Albert de la Chapelle, August 28, 2020 (sent for review July 17, 2020; reviewed by Anne Hagemeijer and Stefan Klaus Bohlander) Balanced rearrangements involving the KMT2A gene, located at patterns that include high expression of HOXA genes and thereby 11q23, are among the most frequent chromosome aberrations in contribute to leukemogenesis (14–16).
    [Show full text]
  • Genetic Alterations of Protein Tyrosine Phosphatases in Human Cancers
    Oncogene (2015) 34, 3885–3894 © 2015 Macmillan Publishers Limited All rights reserved 0950-9232/15 www.nature.com/onc REVIEW Genetic alterations of protein tyrosine phosphatases in human cancers S Zhao1,2,3, D Sedwick3,4 and Z Wang2,3 Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, PTP receptor T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11, which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs. Oncogene (2015) 34, 3885–3894; doi:10.1038/onc.2014.326; published online 29 September 2014 INTRODUCTION tyrosine/threonine-specific phosphatases. (4) Class IV PTPs include Protein tyrosine phosphorylation has a critical role in virtually all four Drosophila Eya homologs (Eya1, Eya2, Eya3 and Eya4), which human cellular processes that are involved in oncogenesis.1 can dephosphorylate both tyrosine and serine residues. Protein tyrosine phosphorylation is coordinately regulated by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases 1 THE THREE-DIMENSIONAL STRUCTURE AND CATALYTIC (PTPs). Although PTKs add phosphate to tyrosine residues in MECHANISM OF PTPS proteins, PTPs remove it. Many PTKs are well-documented oncogenes.1 Recent cancer genomic studies provided compelling The three-dimensional structures of the catalytic domains of evidence that many PTPs function as tumor suppressor genes, classical PTPs (RPTPs and non-RPTPs) are extremely well because a majority of PTP mutations that have been identified in conserved.5 Even the catalytic domain structures of the dual- human cancers are loss-of-function mutations.
    [Show full text]
  • Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
    Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................
    [Show full text]
  • S41467-017-02329-Y.Pdf
    ARTICLE DOI: 10.1038/s41467-017-02329-y OPEN The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy Dan A. Landau1,2,3, Clare Sun 4, Daniel Rosebrock2, Sarah E.M. Herman4, Joshua Fein1,3,5, Mariela Sivina6, Chingiz Underbayev4, Delong Liu4, Julia Hoellenriegel6, Sarangan Ravichandran7, Mohammed Z.H. Farooqui4, Wandi Zhang8, Carrie Cibulskis2, Asaf Zviran1,3, Donna S. Neuberg 9, Dimitri Livitz 2, Ivana Bozic10, Ignaty Leshchiner 2, Gad Getz 2, Jan A. Burger6, Adrian Wiestner4 & Catherine J. Wu2,8,11 1234567890 Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by targeted therapy in CLL, we perform serial exome and transcriptome sequencing for 61 ibrutinib-treated CLLs. Here, we report clonal shifts (change >0.1 in clonal cancer cell fraction, Q < 0.1) in 31% of patients during the first year of therapy, associated with adverse outcome. We also observe tran- scriptional downregulation of pathways mediating energy metabolism, cell cycle, and B cell receptor signaling. Known and previously undescribed mutations in BTK and PLCG2,or uncommonly, other candidate alterations are present in seventeen subjects at the time of progression. Thus, the frequently observed clonal shifts during the early treatment period and its potential association with adverse outcome may reflect greater evolutionary capacity, heralding the emergence of drug-resistant clones. 1 New York Genome Center, New York, NY 10013, USA. 2 Broad Institute, Cambridge, MA 02142, USA. 3 Meyer Cancer Center & Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA. 4 Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
    [Show full text]
  • The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
    The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem.
    [Show full text]
  • NSCLC): Comparison of Glycoproteomics and Global Proteomics Shuang Yang* , Lijun Chen, Daniel W
    Yang et al. Clin Proteom (2017) 14:31 DOI 10.1186/s12014-017-9166-9 Clinical Proteomics RESEARCH Open Access Protein signatures of molecular pathways in non‑small cell lung carcinoma (NSCLC): comparison of glycoproteomics and global proteomics Shuang Yang* , Lijun Chen, Daniel W. Chan, Qing Kay Li and Hui Zhang Abstract Background: Non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are sub- stantially diferent between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in diferent subtypes of NSCLC using advanced proteomic approaches has not yet been conducted. Methods: We applied mass spectrometry (MS) technology featuring proteomics and glycoproteomics to analyze six primary lung SqCCs and eleven ADCs, and we compared the expression level of proteins and glycoproteins in tumors using quantitative proteomics. Glycoproteins were analyzed by enrichment using a chemoenzymatic method, solid- phase extraction of glycopeptides, and quantifed by iTRAQ-LC–MS/MS. Protein quantitation was further annotated via Ingenuity Pathway Analysis. Results: Over 6000 global proteins and 480 glycoproteins were quantitatively identifed in both SqCC and ADC. ADC proteins (8337) consisted of enzymes (22.11%), kinases (5.11%), transcription factors (6.85%), transporters (6.79%), and peptidases (3.30%). SqCC proteins (6967) had a very similar distribution. The identifed glycoproteins, in order of rela- tive abundance, included membrane (42%) and extracellular matrix (>33%) glycoproteins.
    [Show full text]
  • Skeletal Stem and Progenitor Cells Maintain Cranial Suture Patency and Prevent Craniosynostosis
    ARTICLE https://doi.org/10.1038/s41467-021-24801-6 OPEN Skeletal stem and progenitor cells maintain cranial suture patency and prevent craniosynostosis Siddharth Menon1,2,3,4, Ankit Salhotra 1,2,3, Siny Shailendra1,2,3, Ruth Tevlin1,2,3, Ryan C. Ransom1,2,3, Michael Januszyk1,2,3, Charles K. F. Chan 1,2,3,4, Björn Behr5, Derrick C. Wan1,2,3, ✉ ✉ Michael T. Longaker 1,2,3,4 & Natalina Quarto 1,2,3,6 Cranial sutures are major growth centers for the calvarial vault, and their premature fusion 1234567890():,; leads to a pathologic condition called craniosynostosis. This study investigates whether skeletal stem/progenitor cells are resident in the cranial sutures. Prospective isolation by FACS identifies this population with a significant difference in spatio-temporal representation between fusing versus patent sutures. Transcriptomic analysis highlights a distinct signature in cells derived from the physiological closing PF suture, and scRNA sequencing identifies transcriptional heterogeneity among sutures. Wnt-signaling activation increases skeletal stem/progenitor cells in sutures, whereas its inhibition decreases. Crossing Axin2LacZ/+ mouse, endowing enhanced Wnt activation, to a Twist1+/− mouse model of coronal cra- niosynostosis enriches skeletal stem/progenitor cells in sutures restoring patency. Co- transplantation of these cells with Wnt3a prevents resynostosis following suturectomy in Twist1+/− mice. Our study reveals that decrease and/or imbalance of skeletal stem/pro- genitor cells representation within sutures may underlie craniosynostosis. These findings have translational implications toward therapeutic approaches for craniosynostosis. 1 Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. 2 Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, USA.
    [Show full text]
  • Live-Cell Imaging Rnai Screen Identifies PP2A–B55α and Importin-Β1 As Key Mitotic Exit Regulators in Human Cells
    LETTERS Live-cell imaging RNAi screen identifies PP2A–B55α and importin-β1 as key mitotic exit regulators in human cells Michael H. A. Schmitz1,2,3, Michael Held1,2, Veerle Janssens4, James R. A. Hutchins5, Otto Hudecz6, Elitsa Ivanova4, Jozef Goris4, Laura Trinkle-Mulcahy7, Angus I. Lamond8, Ina Poser9, Anthony A. Hyman9, Karl Mechtler5,6, Jan-Michael Peters5 and Daniel W. Gerlich1,2,10 When vertebrate cells exit mitosis various cellular structures can contribute to Cdk1 substrate dephosphorylation during vertebrate are re-organized to build functional interphase cells1. This mitotic exit, whereas Ca2+-triggered mitotic exit in cytostatic-factor- depends on Cdk1 (cyclin dependent kinase 1) inactivation arrested egg extracts depends on calcineurin12,13. Early genetic studies in and subsequent dephosphorylation of its substrates2–4. Drosophila melanogaster 14,15 and Aspergillus nidulans16 reported defects Members of the protein phosphatase 1 and 2A (PP1 and in late mitosis of PP1 and PP2A mutants. However, the assays used in PP2A) families can dephosphorylate Cdk1 substrates in these studies were not specific for mitotic exit because they scored pro- biochemical extracts during mitotic exit5,6, but how this relates metaphase arrest or anaphase chromosome bridges, which can result to postmitotic reassembly of interphase structures in intact from defects in early mitosis. cells is not known. Here, we use a live-cell imaging assay and Intracellular targeting of Ser/Thr phosphatase complexes to specific RNAi knockdown to screen a genome-wide library of protein substrates is mediated by a diverse range of regulatory and targeting phosphatases for mitotic exit functions in human cells. We subunits that associate with a small group of catalytic subunits3,4,17.
    [Show full text]