Development, Maintenance and Functions of CD8+ T-Regulatory Cells
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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 -
GABPA Is a Master Regulator of Luminal Identity and Restrains Aggressive Diseases in Bladder Cancer
Cell Death & Differentiation (2020) 27:1862–1877 https://doi.org/10.1038/s41418-019-0466-7 ARTICLE GABPA is a master regulator of luminal identity and restrains aggressive diseases in bladder cancer 1,2,3 3,4 5 2,5 5 3 5 5 Yanxia Guo ● Xiaotian Yuan ● Kailin Li ● Mingkai Dai ● Lu Zhang ● Yujiao Wu ● Chao Sun ● Yuan Chen ● 5 6 3 1,2 1,2 3,7 Guanghui Cheng ● Cheng Liu ● Klas Strååt ● Feng Kong ● Shengtian Zhao ● Magnus Bjorkhölm ● Dawei Xu 3,7 Received: 3 June 2019 / Revised: 20 November 2019 / Accepted: 21 November 2019 / Published online: 4 December 2019 © The Author(s) 2019. This article is published with open access Abstract TERT promoter mutations occur in the majority of glioblastoma, bladder cancer (BC), and other malignancies while the ETS family transcription factors GABPA and its partner GABPB1 activate the mutant TERT promoter and telomerase in these tumors. GABPA depletion or the disruption of the GABPA/GABPB1 complex by knocking down GABPB1 was shown to inhibit telomerase, thereby eliminating the tumorigenic potential of glioblastoma cells. GABPA/B1 is thus suggested as a cancer therapeutic target. However, it is unclear about its role in BC. Here we unexpectedly observed that GABPA ablation 1234567890();,: 1234567890();,: inhibited TERT expression, but robustly increased proliferation, stem, and invasive phenotypes and cisplatin resistance in BC cells, while its overexpression exhibited opposite effects, and inhibited in vivo metastasizing in a xenograft transplant model. Mechanistically, GABPA directly activates the transcription of FoxA1 and GATA3, key transcription factors driving luminal differentiation of urothelial cells. Consistently, TCGA/GEO dataset analyses show that GABPA expression is correlated positively with luminal while negatively with basal signatures. -
Stem Cell Differentiation As a Many-Body Problem
Stem cell differentiation as a many-body problem Bin Zhanga,b and Peter G. Wolynesa,b,c,1 Departments of aChemistry and cPhysics and Astronomy, and bCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005 Contributed by Peter G. Wolynes, May 9, 2014 (sent for review March 25, 2014) Stem cell differentiation has been viewed as coming from transitions transcription factors function as pioneers that can directly bind between attractors on an epigenetic landscape that governs the with the chromatin sites occupied by the nucleosome, slow dynamics of a regulatory network involving many genes. Rigorous DNA binding (14, 15) is still a good approximation to describe definition of such a landscape is made possible by the realization the effect of the progressive change of the chromatin structure that gene regulation is stochastic, owing to the small copy number of and histone modification induced by the pioneer factors on gene the transcription factors that regulate gene expression and because regulation (16). As a result, DNA binding must be treated on of the single-molecule nature of the gene itself. We develop an ap- equal footing together with protein synthesis and degradation proximation that allows the quantitative construction of the epige- to fully understand eukaryotic gene regulation (14–18). netic landscape for large realistic model networks. Applying this By increasing the dimensionality of the problem, investigating approach to the network for embryonic stem cell development ex- the effects arising from slow DNA-binding -
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. -
Transcription Factor SPZ1 Promotes TWIST-Mediated Epithelial–Mesenchymal Transition and Oncogenesis in Human Liver Cancer
OPEN Oncogene (2017) 36, 4405–4414 www.nature.com/onc ORIGINAL ARTICLE Transcription factor SPZ1 promotes TWIST-mediated epithelial–mesenchymal transition and oncogenesis in human liver cancer L-T Wang1, S-S Chiou2,3, C-Y Chai4, E Hsi5, C-M Chiang6, S-K Huang7, S-N Wang8,9, KK Yokoyama1,10,11,12,13,14 and S-H Hsu1,12 The epithelial–mesenchymal transition (EMT) is an important process in the progression of cancer. However, its occurrence and mechanism of regulation are not fully understood. We propose a regulatory pathway in which spermatogenic leucine zipper 1 (SPZ1) promotes EMT through its transactivating ability in increasing TWIST1 expression. We compared the expression of SPZ1 and TWIST1 in specimens of hepatocarcinoma cells (HCCs) and non-HCCs. Expression of SPZ1 exhibited a tumor-specific expression pattern and a high correlation with patients’ survival time, tumor size, tumor number and progression stage. Moreover, forced expression and knockdown of SPZ1 in hepatoma cells showed that SPZ1 was able to regulate the cellular proliferation, invasion, and tumorigenic activity in a TWIST1-dependent manner in vitro and in vivo. These data demonstrate that SPZ1, a newly dscribed molecule, transactivates TWIST1 promoters, and that this SPZ1-TWIST axis mediates EMT signaling and exerts significant regulatory effects on tumor oncogenesis. Oncogene (2017) 36, 4405–4414; doi:10.1038/onc.2017.69; published online 3 April 2017 INTRODUCTION by phosphorylation, which results in SPZ1 translocation into the Despite the identification of potential oncogenic drivers and their nucleus and activation of downstream gene expression such as 16 roles as master regulators of cancer initiation, the underlying the proliferating cell nuclear antigen. -
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. -
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. -
Nanog-Like Regulates Endoderm Formation Through the Mxtx2-Nodal Pathway
Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Xu, Cong, Zi Peng Fan, Patrick Muller, Rachel Fogley, Anthony DiBiase, Eirini Trompouki, Juli Unternaehrer, et al. “Nanog-Like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway.” Developmental Cell 22, no. 3 (March 2012): 625–638. © 2012 Elsevier Inc. As Published http://dx.doi.org/10.1016/j.devcel.2012.01.003 Publisher Elsevier Version Final published version Citable link http://hdl.handle.net/1721.1/91520 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Developmental Cell Article Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway Cong Xu,1,2 Zi Peng Fan,3 Patrick Mu¨ller,4 Rachel Fogley,1 Anthony DiBiase,1,2 Eirini Trompouki,1,2 Juli Unternaehrer,1,2 Fengzhu Xiong,5 Ingrid Torregroza,6 Todd Evans,6 Sean G. Megason,5 George Q. Daley,1,2 Alexander F. Schier,4 Richard A. Young,3 and Leonard I. Zon1,2,* 1Howard Hughes Medical Institute 2Division of Hematology/Oncology Children’s Hospital Boston and Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA 3Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA 4Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA 5Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA 6Department of Surgery, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA *Correspondence: [email protected] DOI 10.1016/j.devcel.2012.01.003 SUMMARY required for acquisition of the pluripotent ground state in both embryonic development and somatic cell reprogramming (Silva In mammalian embryonic stem cells, the acquisition et al., 2009). -
Integrated Computational Approach to the Analysis of RNA-Seq Data Reveals New Transcriptional Regulators of Psoriasis
OPEN Experimental & Molecular Medicine (2016) 48, e268; doi:10.1038/emm.2016.97 & 2016 KSBMB. All rights reserved 2092-6413/16 www.nature.com/emm ORIGINAL ARTICLE Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis Alena Zolotarenko1, Evgeny Chekalin1, Alexandre Mesentsev1, Ludmila Kiseleva2, Elena Gribanova2, Rohini Mehta3, Ancha Baranova3,4,5,6, Tatiana V Tatarinova6,7,8, Eleonora S Piruzian1 and Sergey Bruskin1,5 Psoriasis is a common inflammatory skin disease with complex etiology and chronic progression. To provide novel insights into the regulatory molecular mechanisms of the disease, we performed RNA sequencing analysis of 14 pairs of skin samples collected from patients with psoriasis. Subsequent pathway analysis and extraction of the transcriptional regulators governing psoriasis-associated pathways was executed using a combination of the MetaCore Interactome enrichment tool and the cisExpress algorithm, followed by comparison to a set of previously described psoriasis response elements. A comparative approach allowed us to identify 42 core transcriptional regulators of the disease associated with inflammation (NFκB, IRF9, JUN, FOS, SRF), the activity of T cells in psoriatic lesions (STAT6, FOXP3, NFATC2, GATA3, TCF7, RUNX1), the hyper- proliferation and migration of keratinocytes (JUN, FOS, NFIB, TFAP2A, TFAP2C) and lipid metabolism (TFAP2, RARA, VDR). In addition to the core regulators, we identified 38 transcription factors previously not associated with the disease that can clarify the pathogenesis of psoriasis. To illustrate these findings, we analyzed the regulatory role of one of the identified transcription factors (TFs), FOXA1. Using ChIP-seq and RNA-seq data, we concluded that the atypical expression of the FOXA1 TF is an important player in the disease as it inhibits the maturation of naive T cells into the (CD4+FOXA1+CD47+CD69+PD-L1(hi) FOXP3 − ) regulatory T cell subpopulation, therefore contributing to the development of psoriatic skin lesions.