Impact on Immune the Multifaceted Roles of Bcl11b in Thymic
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The T-ALL Related Gene BCL11B Regulates the Initial Stages of Human T-Cell Differentiation
Leukemia (2017) 31, 2503–2514 © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 0887-6924/17 www.nature.com/leu ORIGINAL ARTICLE The T-ALL related gene BCL11B regulates the initial stages of human T-cell differentiation VL Ha1, A Luong1,FLi2, D Casero3, J Malvar1,YMKim1,4, R Bhatia5, GM Crooks3,6,7,8 and C Parekh1,4 The initial stages of T-cell differentiation are characterized by a progressive commitment to the T-cell lineage, a process that involves the loss of alternative (myelo-erythroid, NK, B) lineage potentials. Aberrant differentiation during these stages can result in T-cell acute lymphoblastic leukemia (T-ALL). However, the mechanisms regulating the initial stages of human T-cell differentiation are obscure. Through loss of function studies, we showed BCL11B, a transcription factor recurrently mutated T-ALL, is essential for T-lineage commitment, particularly the repression of NK and myeloid potentials, and the induction of T-lineage genes, during the initial stages of human T-cell differentiation. In gain of function studies, BCL11B inhibited growth of and induced a T-lineage transcriptional program in T-ALL cells. We found previously unknown differentiation stage-specific DNA binding of BCL11B at multiple T-lineage genes; target genes showed BCL11B-dependent expression, suggesting a transcriptional activator role for BCL11B at these genes. Transcriptional analyses revealed differences in the regulatory actions of BCL11B between human and murine thymopoiesis. Our studies show BCL11B is a key regulator of the initial stages of human T-cell differentiation and delineate the BCL11B transcriptional program, enabling the dissection of the underpinnings of normal T-cell differentiation and providing a resource for understanding dysregulations in T-ALL. -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
The Histone Methyltransferase DOT1L Prevents Antigen-Independent
bioRxiv preprint doi: https://doi.org/10.1101/826255; this version posted November 18, 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. The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8+ T cells Eliza Mari Kwesi-Maliepaard1*, Muhammad Assad Aslam2,3*, Mir Farshid Alemdehy2*, Teun van den Brand4, Chelsea McLean1, Hanneke Vlaming1, Tibor van Welsem1, Tessy Korthout1, Cesare Lancini1, Sjoerd Hendriks1, Tomasz Ahrends5, Dieke van Dinther6, Joke M.M. den Haan6, Jannie Borst5, Elzo de Wit4, Fred van Leeuwen1,7,#, and Heinz Jacobs2,# 1Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands 2Division of Tumor Biology & Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands 3Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan 4Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, and Oncode Institute, The Netherlands 5Division of Tumor Biology & Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, and Oncode Institute, The Netherlands 6Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUmc, 1081HV Amsterdam, The Netherlands 7Department of Medical Biology, Amsterdam UMC, location AMC, UvA, 1105 AZ Amsterdam, The Netherlands * These authors contributed equally to this work. # Equal contribution and corresponding authors [email protected]; [email protected] Lead contact: Fred van Leeuwen 1 bioRxiv preprint doi: https://doi.org/10.1101/826255; this version posted November 18, 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. -
The Effects of Estrogen in Atrazine-Mediated Foxp3 Induction and Inhibition of Cd4+ T Effector Cells
University of Montana ScholarWorks at University of Montana Graduate Student Theses, Dissertations, & Professional Papers Graduate School 2014 THE EFFECTS OF ESTROGEN IN ATRAZINE-MEDIATED FOXP3 INDUCTION AND INHIBITION OF CD4+ T EFFECTOR CELLS Tiffany Emmons The University of Montana Follow this and additional works at: https://scholarworks.umt.edu/etd Let us know how access to this document benefits ou.y Recommended Citation Emmons, Tiffany, "THE EFFECTS OF ESTROGEN IN ATRAZINE-MEDIATED FOXP3 INDUCTION AND INHIBITION OF CD4+ T EFFECTOR CELLS" (2014). Graduate Student Theses, Dissertations, & Professional Papers. 4350. https://scholarworks.umt.edu/etd/4350 This Thesis is brought to you for free and open access by the Graduate School at ScholarWorks at University of Montana. It has been accepted for inclusion in Graduate Student Theses, Dissertations, & Professional Papers by an authorized administrator of ScholarWorks at University of Montana. For more information, please contact [email protected]. THE EFFECTS OF ESTROGEN IN ATRAZINE-MEDIATED FOXP3 INDUCTION AND INHIBITION OF CD4+ T EFFECTOR CELLS By TIFFANY ROSE EMMONS B.S. Biology, University of California, Merced, Merced, California, 2012 Thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Cellular, Molecular and Microbial Biology Option: Immunology The University of Montana Missoula, MT Official Graduation Date: July 2014 Approved by: J. B. Alexander Ross, Dean of The Graduate School Graduate School Dr. Scott Wetzel, Chair Division of Biological Sciences Dr. Stephen Lodmell Division of Biological Sciences Dr. David Shepherd Department of Biomedical and Pharmaceutical Sciences Emmons, Tiffany, M.S. Summer 2014 Biology The Effects of Estrogen in Atrazine-mediated Foxp3 Induction and Inhibition of CD4+ T effector Cells Atrazine (ATR) is a chlorotriazine herbicide that is heavily used in agricultural areas. -
The Transcription Factors Blimp-1 and IRF4 Jointly Control the Differentiation and Function of Effector Regulatory T Cells
ARTICLES The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells Erika Cretney1,2,6, Annie Xin1,2,6, Wei Shi1,3, Martina Minnich4, Frederick Masson1,2, Maria Miasari1,2, Gabrielle T Belz1,2, Gordon K Smyth1,5, Meinrad Busslinger4, Stephen L Nutt1,2 & Axel Kallies1,2 Regulatory T cells (Treg cells) are required for peripheral tolerance. Evidence indicates that Treg cells can adopt specialized differentiation programs in the periphery that are controlled by transcription factors usually associated with helper T cell differentiation. Here we demonstrate that expression of the transcription factor Blimp-1 defined a population of Treg cells that localized mainly to mucosal sites and produced IL-10. Blimp-1 was required for IL-10 production by these cells and for their tissue homeostasis. We provide evidence that the transcription factor IRF4, but not the transcription factor T-bet, was essential for Blimp-1 expression and for the differentiation of all effector Treg cells. Thus, our study defines a differentiation pathway that leads to the acquisition of Treg cell effector functions and requires both IRF4 and Blimp-1. + + Naturally occurring CD4 Foxp3 regulatory T cells (Treg cells) are Foxp3. The transcription factor IRF4 acts downstream of Foxp3, which derived from the thymus and are essential for the preservation of suggests that Treg cells use the transcriptional machinery of T helper 1,2 immune homeostasis and suppression of autoimmune pathology . type 2 (TH2) effector cells to specifically control this subset of helper 17 Treg cells depend on interleukin 2 (IL-2) for their maintenance and T cells . -
Escape from X Chromosome Inactivation and the Female Predominance in Autoimmune Diseases
International Journal of Molecular Sciences Review Escape from X Chromosome Inactivation and the Female Predominance in Autoimmune Diseases Ali Youness 1,†, Charles-Henry Miquel 1,2,† and Jean-Charles Guéry 1,* 1 Infinity-Toulouse Institute for Infectious and Inflammatory Diseases, University of Toulouse, INSERM, CNRS, UPS, 31300 Toulouse, France; [email protected] (A.Y.); [email protected] (C.-H.M.) 2 Arthritis R&D, 92200 Neuilly-Sur-Seine, France * Correspondence: [email protected]; Tel.: +33-5-62-74-83-78; Fax: +33-5-62-74-45-58 † These authors contributed equally to this work. Abstract: Women represent 80% of people affected by autoimmune diseases. Although, many studies have demonstrated a role for sex hormone receptor signaling, particularly estrogens, in the direct regulation of innate and adaptive components of the immune system, recent data suggest that female sex hormones are not the only cause of the female predisposition to autoimmunity. Besides sex steroid hormones, growing evidence points towards the role of X-linked genetic factors. In female mammals, one of the two X chromosomes is randomly inactivated during embryonic development, resulting in a cellular mosaicism, where about one-half of the cells in a given tissue express either the maternal X chromosome or the paternal one. X chromosome inactivation (XCI) is however not complete and 15 to 23% of genes from the inactive X chromosome (Xi) escape XCI, thereby contributing to the emergence of a female-specific heterogeneous population of cells with bi-allelic expression of some X-linked genes. Although the direct contribution of this genetic mechanism in the female susceptibility to autoimmunity still remains to be established, the cellular mosaicism resulting from XCI escape is likely to create a unique functional plasticity within female immune cells. -
Figure S17 Figure S16
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3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk 2 Factors in Human T-Lineage Acute Lymphoblastic Leukemia
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.11.988279; this version posted March 12, 2020. 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. 1 3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk 2 Factors in Human T-Lineage Acute Lymphoblastic Leukemia 3 Lu Yang1,2,3^, Fengling Chen4^, Haichuan Zhu1,2,3^§, Yang Chen4, Bingjie Dong1,2,3, 4 Minglei Shi4, Weitao Wang1,2,3, Qian Jiang6, Leping Zhang7, Xiaojun Huang2,6*, 5 Michael Q. Zhang4,5,8* and Hong Wu1,2,3,6* 6 7 1The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life 8 Sciences, 2Peking-Tsinghua Center for Life Sciences and 3Beijing Advanced 9 Innovation Center for Genomics, Peking University, Beijing 100871, China; 4MOE Key 10 Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, 11 Bioinformatics Division, BNRist, Department of Automation, 5School of Medicine, 12 Tsinghua University, Beijing 100084, China; 6Peking University Institute of Hematology, 13 National Clinical Research Center for Hematologic Disease, 7Department of Pediatric 14 Hematology/Oncology, Peking University People’s Hospital, Beijing 100044, China; 15 8Department of Biological Sciences, Center for Systems Biology, The University of 16 Texas, Dallas 800 West Campbell Road, RL11, Richardson, TX 75080-3021, USA 17 18 ^ These authors contributed equally to this work. 19 §Current address: Institute of Biology and Medicine, College of Life and Health 20 Sciences, Wuhan University of Science and Technology, Hubei 430081, China. -
Sex Differences in Immune Responses
REVIEWS Sex differences in immune responses Sabra L. Klein1 and Katie L. Flanagan2 Abstract | Males and females differ in their immunological responses to foreign and self-antigens and show distinctions in innate and adaptive immune responses. Certain immunological sex differences are present throughout life, whereas others are only apparent after puberty and before reproductive senescence, suggesting that both genes and hormones are involved. Furthermore, early environmental exposures influence the microbiome and have sex-dependent effects on immune function. Importantly, these sex-based immunological differences contribute to variations in the incidence of autoimmune diseases and malignancies, susceptibility to infectious diseases and responses to vaccines in males and females. Here, we discuss these differences and emphasize that sex is a biological variable that should be considered in immunological studies. Sex is a biological variable that affects immune responses have 40% less viral RNA in their blood than men, men to both self and foreign antigens (for example, those show an almost twofold higher risk of death from from fungi, viruses, bacteria, parasites and allergens). malignant cancer than women and antibody responses The sex of an individual is defined by the differential to seasonal influenza vaccines are consistently at least organization of chromosomes, reproductive organs, twice as strong in women than men. Generally, adult and sex steroid levels; it is distinct from gender, which females mount stronger innate and adaptive immune includes behaviours and activities that are determined responses than males. This results in faster clearance of by society or culture in humans. Male and female differ pathogens and greater vaccine efficacy in females than ences in immunological responses may be influenced by in males but also contributes to their increased suscepti both sex and gender, with sex contributing to physiologi bility to inflammatory and autoimmune diseases. -
Role of Estrogen Receptor in Breast Cancer Cell Gene Expression
4046 MOLECULAR MEDICINE REPORTS 13: 4046-4050, 2016 Role of estrogen receptor in breast cancer cell gene expression YABING ZHENG1, XIYING SHAO1, YUAN HUANG1, LEI SHI1, BO CHEN2, XIAOJIA WANG1, HONGJIAN YANG3, ZHANHONG CHEN1 and XIPING ZHANG3 Departments of 1Medical Oncology (Breast), 2Pathology and 3Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China Received April 28, 2015; Accepted February 23, 2016 DOI: 10.3892/mmr.2016.5018 Abstract. The aim of the present study was to establish the Europe in 2012, and the number of breast cancer-associated underlying regulatory mechanism of estrogen receptor (ER) mortalities is 131,000 (6). Furthermore, breast cancer is in breast cancer cell gene expression. A gene expression the most common cause of cancer-associated mortality in profile accession( no. GSE11324) was downloaded from the females. Therefore, it is essential to understand its molecular Gene Expression Omnibus (GEO) database. Differentially mechanism and develop more effective therapeutic methods expressed genes (DEGs) from an estrogen treatment group and for breast cancer treatment. a control group were identified. Chromatin immunoprecipita- The estrogen receptor (ER) is critical in determining the tion with high-throughput sequencing data (series GSE25710) phenotype of human breast cancers and is one of the most was obtained from the GEO for the ER binding sites, and important therapeutic targets (7). Furthermore, certain studies binding and expression target analysis was performed. A total have suggested that activation of ER is responsible for various of 3,122 DEGs were obtained and ER was demonstrated to biological processes, including cell growth and differentia- exhibit inhibition and activation roles during the regulation tion, and programmed cell death (8,9). -
Promoter Through Interaction with the FOXP3 RORC2 Is Involved in T Cell Polarization
RORC2 Is Involved in T Cell Polarization through Interaction with the FOXP3 Promoter This information is current as Simone Burgler, Pierre-Yves Mantel, Claudio Bassin, Nadia of September 28, 2021. Ouaked, Cezmi A. Akdis and Carsten B. Schmidt-Weber J Immunol 2010; 184:6161-6169; Prepublished online 28 April 2010; doi: 10.4049/jimmunol.0903243 http://www.jimmunol.org/content/184/11/6161 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2010/04/28/jimmunol.090324 Material 3.DC1 http://www.jimmunol.org/ References This article cites 64 articles, 27 of which you can access for free at: http://www.jimmunol.org/content/184/11/6161.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 28, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology RORC2 Is Involved in T Cell Polarization through Interaction with the FOXP3 Promoter Simone Burgler,* Pierre-Yves Mantel,*,† Claudio Bassin,* Nadia Ouaked,* Cezmi A.