Mef2d Sustains Activation of Effector Foxp3+ Tregs During Transplant Survival and Anticancer Immunity
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
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 -
Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin
cells Review Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin Agnieszka Bochy ´nska,Juliane Lüscher-Firzlaff and Bernhard Lüscher * ID Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany; [email protected] (A.B.); jluescher-fi[email protected] (J.L.-F.) * Correspondence: [email protected]; Tel.: +49-241-8088850; Fax: +49-241-8082427 Received: 18 January 2018; Accepted: 27 February 2018; Published: 2 March 2018 Abstract: Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Dephosphorylation of HDAC4 by PP2A-Bδ Unravels a New Role For
Veloso et et al. al.CellCell Death Death and and Disease Disease (2019) 10:512 (2019) 10:512 Page 1 of 16 https://doi.org/10.1038/s41419-019-1743-6 Cell Death & Disease ARTICLE Open Access Dephosphorylation of HDAC4 by PP2A-Bδ unravels a new role for the HDAC4/MEF2 axis in myoblast fusion Alexandra Veloso1,2, Maud Martin1,2,3, Jonathan Bruyr1,2,TinaO’Grady1,2, Christophe Deroanne1,4, Denis Mottet1,2, Jean-Claude Twizere1,2, Thomas Cherrier1,2,5 and Franck Dequiedt1,2 Abstract Muscle formation is controlled by a number of key myogenic transcriptional regulators that govern stage-specific gene expression programs and act as terminal effectors of intracellular signaling pathways. To date, the role of phosphatases in the signaling cascades instructing muscle development remains poorly understood. Here, we show that a specific PP2A-B55δ holoenzyme is necessary for skeletal myogenesis. The primary role of PP2A-B55δ is to dephosphorylate histone deacetylase 4 (HDAC4) following myocyte differentiation and ensure repression of Myocyte enhancer factor 2D (MEF2D)-dependent gene expression programs during myogenic fusion. As a crucial HDAC4/MEF2D target gene that governs myocyte fusion, we identify ArgBP2, an upstream inhibitor of Abl, which itself is a repressor of CrkII signaling. Consequently, cells lacking PP2A-B55δ show upregulation of ArgBP2 and hyperactivation of CrkII downstream effectors, including Rac1 and FAK, precluding cytoskeletal and membrane rearrangements associated with myoblast fusion. Both in vitro and in zebrafish, loss-of-function of PP2A-B55δ severely impairs fusion of myocytes and formation of multinucleated muscle fibers, without affecting myoblast differentiation. Taken together, our results establish PP2A-B55δ as the first protein phosphatase to be involved in myoblast fusion and suggest that reversible phosphorylation of HDAC4 may coordinate differentiation and fusion events during myogenesis. -
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 . -
Tissue-Specific Splicing of a Ubiquitously Expressed Transcription Factor Is Essential for Muscle Differentiation
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation Soji Sebastian,1 Herve´ Faralli,1,4 Zizhen Yao,2,4 Patricia Rakopoulos,1,3 Carmen Palii,1 Yi Cao,2 Kulwant Singh,1 Qi-Cai Liu,1 Alphonse Chu,1 Arif Aziz,1 Marjorie Brand,1,3 Stephen J. Tapscott,2 and F. Jeffrey Dilworth1,3,5 1Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada,; 2Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 3Department of Cellular and Molecular Medicine, University of Ottawa, Ontario K1H 8L6, Canada Alternate splicing contributes extensively to cellular complexity by generating protein isoforms with divergent functions. However, the role of alternate isoforms in development remains poorly understood. Mef2 transcription factors are essential transducers of cell signaling that modulate differentiation of many cell types. Among Mef2 family members, Mef2D is unique, as it undergoes tissue-specific splicing to generate a muscle-specific isoform. Since the ubiquitously expressed (Mef2Da1) and muscle-specific (Mef2Da2) isoforms of Mef2D are both expressed in muscle, we examined the relative contribution of each Mef2D isoform to differentiation. Using both in vitro and in vivo models, we demonstrate that Mef2D isoforms act antagonistically to modulate differentiation. While chromatin immunoprecipitation (ChIP) sequencing analysis shows that the Mef2D isoforms bind an overlapping set of genes, only Mef2Da2 activates late muscle transcription. Mechanistically, the differential ability of Mef2D isoforms to activate transcription depends on their susceptibility to phosphorylation by protein kinase A (PKA). -
Supplementary Material and Methods
Supplementary material and methods Generation of cultured human epidermal sheets Normal human epidermal keratinocytes were isolated from human breast skin. Keratinocytes were grown on a feeder layer of irradiated human fibroblasts pre-seeded at 4000 cells /cm² in keratinocyte culture medium (KCM) containing a mix of 3:1 DMEM and HAM’s F12 (Invitrogen, Carlsbad, USA), supplemented with 10% FCS, 10ng/ml epidermal growth factor (EGF; R&D systems, Minneapolis, MN, USA), 0.12 IU/ml insulin (Lilly, Saint- Cloud, France), 0.4 mg/ml hydrocortisone (UpJohn, St Quentin en Yvelelines, France) , 5 mg/ml triiodo-L- thyronine (Sigma, St Quentin Fallavier, France), 24.3 mg/ml adenine (Sigma), isoproterenol (Isuprel, Hospira France, Meudon, France) and antibiotics (20 mg/ml gentamicin (Phanpharma, Fougères, France), 100 IU/ml penicillin (Phanpharma), and 1 mg/ml amphotericin B (Phanpharma)). The medium was changed every two days. NHEK were then cultured over a period of 13 days according to the protocol currently used at the Bank of Tissues and Cells for the generation of clinical grade epidermal sheets used for the treatment of severe extended burns (Ref). When needed, cells were harvested with trypsin-EDTA 0.05% (Thermo Fisher Scientific, Waltham, MA, USA) and collected for analysis. Clonogenic assay Keratinocytes were seeded on a feeder layer of irradiated fibroblasts, at a clonal density of 10-20 cells/cm² and cultivated for 10 to 14 days. Three flasks per tested condition were fixed and colored in a single 30 mns step using rhodamine B (Sigma) diluted at 0.01 g/ml in 4% paraformaldehyde. In each tested condition, cells from 3 other flasks were numerated after detachment by trypsin treatment. -
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. -
Precision Medicine in Pediatric Oncology: Translating Genomic Discoveries Into Optimized Therapies Thai Hoa Tran1,2, Avanthi Tayi Shah3,4, and Mignon L
Published OnlineFirst June 9, 2017; DOI: 10.1158/1078-0432.CCR-16-0115 Review Clinical Cancer Research Precision Medicine in Pediatric Oncology: Translating Genomic Discoveries into Optimized Therapies Thai Hoa Tran1,2, Avanthi Tayi Shah3,4, and Mignon L. Loh3,4 Abstract Survival of children with cancers has dramatically improved aberrant activation of signaling pathways, and epigenetic modi- over the past several decades. This success has been achieved fiers that can be targeted by novel agents. Thus, the recently through improvement of combined modalities in treatment described genomic and epigenetic landscapes of many child- approaches, intensification of cytotoxic chemotherapy for hood cancers have expanded the paradigm of precision med- those with high-risk disease, and refinement of risk stratifica- icine in the hopes of improving outcomes while minimizing tion incorporating novel biologic markers in addition to tra- toxicities. In this review, we will discuss the biologic rationale ditional clinical and histologic features. Advances in cancer for molecularly targeted therapies in genomically defined sub- genomics have shed important mechanistic insights on disease sets of pediatric leukemias, solid tumors, and brain tumors. biology and have identified "driver" genomic alterations, Clin Cancer Res; 23(18); 5329–38. Ó2017 AACR. Introduction which may represent actionable therapeutic targets. In this review, we will discuss how genomic discoveries are being translated from Survival rates for children diagnosed with cancer have the bench into the clinic, resulting in the development of precision improved substantially over the past five decades. Today, long- medicine trials for specific subtypes of pediatric hematologic term survival is expected for approximately 80% of children malignancies, solid tumors, and brain tumors. -
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.