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Liu S, Cao Y, Cui K, Ren G, Zhao T, Wang X, Wei D, Chen Z, Gurram RK, Liu C, Wu C, Zhu J, Zhao K. Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction. Immunity 2024; 57:987-1004.e5. [PMID: 38614090 PMCID: PMC11096031 DOI: 10.1016/j.immuni.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/30/2023] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
The development and function of the immune system are controlled by temporospatial gene expression programs, which are regulated by cis-regulatory elements, chromatin structure, and trans-acting factors. In this study, we cataloged the dynamic histone modifications and chromatin interactions at regulatory regions during T helper (Th) cell differentiation. Our data revealed that the H3K4me1 landscape established by MLL4 in naive CD4+ T cells is critical for restructuring the regulatory interaction network and orchestrating gene expression during the early phase of Th differentiation. GATA3 plays a crucial role in further configuring H3K4me1 modification and the chromatin interaction network during Th2 differentiation. Furthermore, we demonstrated that HSS3-anchored chromatin loops function to restrict the activity of the Th2 locus control region (LCR), thus coordinating the expression of Th2 cytokines. Our results provide insights into the mechanisms of how the interplay between histone modifications, chromatin looping, and trans-acting factors contributes to the differentiation of Th cells.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gang Ren
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tingting Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuezheng Wang
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danping Wei
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rama Krishna Gurram
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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3
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Silva MH. Investigating open access new approach methods (NAM) to assess biological points of departure: A case study with 4 neurotoxic pesticides. Curr Res Toxicol 2024; 6:100156. [PMID: 38404712 PMCID: PMC10891343 DOI: 10.1016/j.crtox.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/28/2023] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Open access new approach methods (NAM) in the US EPA ToxCast program and NTP Integrated Chemical Environment (ICE) were used to investigate activities of four neurotoxic pesticides: endosulfan, fipronil, propyzamide and carbaryl. Concordance of in vivo regulatory points of departure (POD) adjusted for interspecies extrapolation (AdjPOD) to modelled human Administered Equivalent Dose (AEDHuman) was assessed using 3-compartment or Adult/Fetal PBTK in vitro to in vivo extrapolation. Model inputs were from Tier 1 (High throughput transcriptomics: HTTr, high throughput phenotypic profiling: HTPP) and Tier 2 (single target: ToxCast) assays. HTTr identified gene expression signatures associated with potential neurotoxicity for endosulfan, propyzamide and carbaryl in non-neuronal MCF-7 and HepaRG cells. The HTPP assay in U-2 OS cells detected potent effects on DNA endpoints for endosulfan and carbaryl, and mitochondria with fipronil (propyzamide was inactive). The most potent ToxCast assays were concordant with specific components of each chemical mode of action (MOA). Predictive adult IVIVE models produced fold differences (FD) < 10 between the AEDHuman and the measured in vivo AdjPOD. The 3-compartment model was concordant (i.e., smallest FD) for endosulfan, fipronil and carbaryl, and PBTK was concordant for propyzamide. The most potent AEDHuman predictions for each chemical showed HTTr, HTPP and ToxCast were mainly concordant with in vivo AdjPODs but assays were less concordant with MOAs. This was likely due to the cell types used for testing and/or lack of metabolic capabilities and pathways available in vivo. The Fetal PBTK model had larger FDs than adult models and was less predictive overall.
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4
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Schleussner N, Cauchy P, Franke V, Giefing M, Fornes O, Vankadari N, Assi SA, Costanza M, Weniger MA, Akalin A, Anagnostopoulos I, Bukur T, Casarotto MG, Damm F, Daumke O, Edginton-White B, Gebhardt JCM, Grau M, Grunwald S, Hansmann ML, Hartmann S, Huber L, Kärgel E, Lusatis S, Noerenberg D, Obier N, Pannicke U, Fischer A, Reisser A, Rosenwald A, Schwarz K, Sundararaj S, Weilemann A, Winkler W, Xu W, Lenz G, Rajewsky K, Wasserman WW, Cockerill PN, Scheidereit C, Siebert R, Küppers R, Grosschedl R, Janz M, Bonifer C, Mathas S. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun 2023; 14:6947. [PMID: 37935654 PMCID: PMC10630337 DOI: 10.1038/s41467-023-41954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/20/2023] [Indexed: 11/09/2023] Open
Abstract
Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University Medical Center Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, 60-479, Poland
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Thomas Bukur
- TRON gGmbH - Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Marco G Casarotto
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Frederik Damm
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Michael Grau
- Department of Physics, University of Marburg, 35052, Marburg, Germany
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Grunwald
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Martin-Leo Hansmann
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- Institute for Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lionel Huber
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Eva Kärgel
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Simone Lusatis
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Daniel Noerenberg
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Reisser
- Department of Physics, Institute of Biophysics, Ulm University, Ulm, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, Ulm, Germany
| | - Srinivasan Sundararaj
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andre Weilemann
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Wiebke Winkler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, 13125, Berlin, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Ralf Küppers
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany.
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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5
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Zhang D, Zhang C, Zhu Y, Xie H, Yue C, Li M, Wei W, Peng Y, Yin G, Guo Y, Guan Y. Recruitment of transcription factor ETS1 to activated accessible regions promotes the transcriptional program of cilia genes. Nucleic Acids Res 2023:gkad506. [PMID: 37326025 PMCID: PMC10359609 DOI: 10.1093/nar/gkad506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Defects in cilia genes, which are critical for cilia formation and function, can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of the networks of cilia genes in ciliopathies remain enigmatic. Herein, we have uncovered the genome-wide redistribution of accessible chromatin regions and extensive alterations of expression of cilia genes during Ellis-van Creveld syndrome (EVC) ciliopathy pathogenesis. Mechanistically, the distinct EVC ciliopathy-activated accessible regions (CAAs) are shown to positively regulate robust changes in flanking cilia genes, which are a key requirement for cilia transcription in response to developmental signals. Moreover, a single transcription factor, ETS1, can be recruited to CAAs, leading to prominent chromatin accessibility reconstruction in EVC ciliopathy patients. In zebrafish, the collapse of CAAs driven by ets1 suppression subsequently causes defective cilia proteins, resulting in body curvature and pericardial oedema. Our results depict a dynamic landscape of chromatin accessibility in EVC ciliopathy patients, and uncover an insightful role for ETS1 in controlling the global transcriptional program of cilia genes by reprogramming the widespread chromatin state.
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Affiliation(s)
- Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Chong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yanmei Zhu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Haixia Xie
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Caifeng Yue
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
- Department of Laboratory Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Mingfeng Li
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Wenlu Wei
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yu Peng
- Pediatric Intensive Care Unit Central, People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Guibin Yin
- Department of Orthopedics, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yunmiao Guo
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yiting Guan
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
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6
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Pham D, Silberger DJ, Nguyen KN, Gao M, Weaver CT, Hatton RD. Batf stabilizes Th17 cell development via impaired Stat5 recruitment of Ets1-Runx1 complexes. EMBO J 2023; 42:e109803. [PMID: 36917143 PMCID: PMC10106990 DOI: 10.15252/embj.2021109803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
Although the activator protein-1 (AP-1) factor Batf is required for Th17 cell development, its mechanisms of action to underpin the Th17 program are incompletely understood. Here, we find that Batf ensures Th17 cell identity in part by restricting alternative gene programs through its actions to restrain IL-2 expression and IL-2-induced Stat5 activation. This, in turn, limits Stat5-dependent recruitment of Ets1-Runx1 factors to Th1- and Treg-cell-specific gene loci. Thus, in addition to pioneering regulatory elements in Th17-specific loci, Batf acts indirectly to inhibit the assembly of a Stat5-Ets1-Runx1 complex that enhances the transcription of Th1- and Treg-cell-specific genes. These findings unveil an important role for Stat5-Ets1-Runx1 interactions in transcriptional networks that define alternate T cell fates and indicate that Batf plays an indispensable role in both inducing and maintaining the Th17 program through its actions to regulate the competing actions of Stat5-assembled enhanceosomes that promote Th1- and Treg-cell developmental programs.
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Affiliation(s)
- Duy Pham
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Daniel J Silberger
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Kim N Nguyen
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Min Gao
- Informatics InstituteUniversity of Alabama at BirminghamBirminghamALUSA
| | - Casey T Weaver
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Robin D Hatton
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
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7
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Zhao CQ, Liu JZ, Liu MM, Ren XT, Kong DQ, Peng J, Cao M, Liu R, Hai CX, Zhang XD. Heterogeneity of T cells and macrophages in chlorine-induced acute lung injury in mice using single-cell RNA sequencing. Inhal Toxicol 2022; 34:399-411. [PMID: 36260290 DOI: 10.1080/08958378.2022.2134526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Chlorine (Cl2), as an asphyxiant toxicant, induced poisoning incidents and acute lung injury (ALI) occur frequently. The specific pathogenesis of Cl2-induced ALI remains unclear. Immune cells play an important role in the process of lung damage. We used single-cell RNA sequencing (scRNA-seq) technology to explore T cells and macrophages molecular mechanism. METHODS Female BALB/c mice were exposed to 400 ppm Cl2 for 15 min. scRNA-seq technology was used to observe the heterogeneity of T cells and macrophages. Hematoxylin-eosin (H&E) staining was used to evaluate the degree of lung injury. Immunofluorescence was used to verify the highly expressed genes of our interest. RESULTS A total of 5316 to 7742 cells were classified into eight different cell types. Several new highly expressed anti-inflammatory and pro-inflammatory genes were found in T cells and macrophages, which were further verified in vitro. Through the pseudotime analysis of macrophages, it was found that the expression of pro-inflammatory and anti-inflammatory genes showed opposite trends in the development of Cl2-induced ALI. This study also mapped T cells-macrophage communication and identified the development of several important receptor-ligand complexes in Cl2-induced ALI. CONCLUSIONS These findings are worthy of further exploration and provide new resources and directions for the study of Cl2-induced ALI in mice, especially in immune and inflammation mechanisms.
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Affiliation(s)
- Chen-Qian Zhao
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Jiang-Zheng Liu
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Meng-Meng Liu
- Department of Health Service, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Xiao-Ting Ren
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - De-Qin Kong
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Jie Peng
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Meng Cao
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Rui Liu
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Chun-Xu Hai
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Xiao-di Zhang
- Department of Toxicology, Shaanxi Key Lab of Free Radical Biology and Medicine, the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
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8
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ETS-1 facilitates Th1 cell-mediated mucosal inflammation in inflammatory bowel diseases through upregulating CIRBP. J Autoimmun 2022; 132:102872. [DOI: 10.1016/j.jaut.2022.102872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
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9
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Bao X, Qin Y, Lu L, Zheng M. Transcriptional Regulation of Early T-Lymphocyte Development in Thymus. Front Immunol 2022; 13:884569. [PMID: 35432347 PMCID: PMC9008359 DOI: 10.3389/fimmu.2022.884569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
T-lymphocytes play crucial roles for maintaining immune homeostasis by fighting against various pathogenic microorganisms and establishing self-antigen tolerance. They will go through several stages and checkpoints in the thymus from progenitors to mature T cells, from CD4-CD8- double negative (DN) cells to CD4+CD8+ double positive (DP) cells, finally become CD4+ or CD8+ single positive (SP) cells. The mature SP cells then emigrate out of the thymus and further differentiate into distinct subsets under different environment signals to perform specific functions. Each step is regulated by various transcriptional regulators downstream of T cell receptors (TCRs) that have been extensively studied both in vivo and vitro via multiple mouse models and advanced techniques, such as single cell RNA sequencing (scRNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). This review will summarize the transcriptional regulators participating in the early stage of T cell development reported in the past decade, trying to figure out cascade networks in each process and provide possible research directions in the future.
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Affiliation(s)
- Xueyang Bao
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Yingyu Qin
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Linrong Lu
- Shanghai Immune Therapy Institute, Renji Hospital, Jiao Tong University School of Medicine, Shanghai, China.,Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhu Zheng
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
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10
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Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
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Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
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11
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Wen T, Barham W, Li Y, Zhang H, Gicobi JK, Hirdler JB, Liu X, Ham H, Peterson Martinez KE, Lucien F, Lavoie RR, Li H, Correia C, Monie DD, An Z, Harrington SM, Wu X, Guo R, Dronca RS, Mansfield AS, Yan Y, Markovic SN, Park SS, Sun J, Qin H, Liu MC, Vasmatzis G, Billadeau DD, Dong H. NKG7 Is a T-cell-Intrinsic Therapeutic Target for Improving Antitumor Cytotoxicity and Cancer Immunotherapy. Cancer Immunol Res 2022; 10:162-181. [PMID: 34911739 PMCID: PMC8816890 DOI: 10.1158/2326-6066.cir-21-0539] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/19/2021] [Accepted: 12/09/2021] [Indexed: 01/22/2023]
Abstract
Cytotoxic CD8+ T cells (CTL) are a crucial component of the immune system notable for their ability to eliminate rapidly proliferating malignant cells. However, the T-cell intrinsic factors required for human CTLs to accomplish highly efficient antitumor cytotoxicity are not well defined. By evaluating human CD8+ T cells from responders versus nonresponders to treatment with immune checkpoint inhibitors, we sought to identify key factors associated with effective CTL function. Single-cell RNA-sequencing analysis of peripheral CD8+ T cells from patients treated with anti-PD-1 therapy showed that cells from nonresponders exhibited decreased expression of the cytolytic granule-associated molecule natural killer cell granule protein-7 (NKG7). Functional assays revealed that reduced NKG7 expression altered cytolytic granule number, trafficking, and calcium release, resulting in decreased CD8+ T-cell-mediated killing of tumor cells. Transfection of T cells with NKG7 mRNA was sufficient to improve the tumor-cell killing ability of human T cells isolated from nonresponders and increase their response to anti-PD-1 or anti-PD-L1 therapy in vitro. NKG7 mRNA therapy also improved the antitumor activity of murine tumor antigen-specific CD8+ T cells in an in vivo model of adoptive cell therapy. Finally, we showed that the transcription factor ETS1 played a role in regulating NKG7 expression. Together, our results identify NKG7 as a necessary component for the cytotoxic function of CD8+ T cells and establish NKG7 as a T-cell-intrinsic therapeutic target for enhancing cancer immunotherapy.See related article by Li et al., p. 154.
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Affiliation(s)
- Ti Wen
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Whitney Barham
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Ying Li
- Division of Computational Biology, Mayo Clinic, Rochester, MN
| | - Henan Zhang
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Joanina K. Gicobi
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | | | - Xin Liu
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Hyoungjun Ham
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | | | | | | | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Cristina Correia
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Dileep D. Monie
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Zesheng An
- Department of Urology, Mayo Clinic, Rochester, MN
| | | | - Xiaosheng Wu
- Division of Hematology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Yiyi Yan
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Sean S. Park
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Jie Sun
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN.,Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Hong Qin
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Minetta C. Liu
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Daniel D. Billadeau
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Haidong Dong
- Department of Urology, Mayo Clinic, Rochester, MN.,Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN.,Corresponding Author: Haidong Dong, M.D., Ph.D., 200 First Street SW, Rochester, MN 55905; Phone: 507-284-5482;
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12
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Schönberger K, Obier N, Romero-Mulero MC, Cauchy P, Mess J, Pavlovich PV, Zhang YW, Mitterer M, Rettkowski J, Lalioti ME, Jäcklein K, Curtis JD, Féret B, Sommerkamp P, Morganti C, Ito K, Ghyselinck NB, Trompouki E, Buescher JM, Pearce EL, Cabezas-Wallscheid N. Multilayer omics analysis reveals a non-classical retinoic acid signaling axis that regulates hematopoietic stem cell identity. Cell Stem Cell 2022; 29:131-148.e10. [PMID: 34706256 PMCID: PMC9093043 DOI: 10.1016/j.stem.2021.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/05/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
Hematopoietic stem cells (HSCs) rely on complex regulatory networks to preserve stemness. Due to the scarcity of HSCs, technical challenges have limited our insights into the interplay between metabolites, transcription, and the epigenome. In this study, we generated low-input metabolomics, transcriptomics, chromatin accessibility, and chromatin immunoprecipitation data, revealing distinct metabolic hubs that are enriched in HSCs and their downstream multipotent progenitors. Mechanistically, we uncover a non-classical retinoic acid (RA) signaling axis that regulates HSC function. We show that HSCs rely on Cyp26b1, an enzyme conventionally considered to limit RA effects in the cell. In contrast to the traditional view, we demonstrate that Cyp26b1 is indispensable for production of the active metabolite 4-oxo-RA. Further, RA receptor beta (Rarb) is required for complete transmission of 4-oxo-RA-mediated signaling to maintain stem cells. Our findings emphasize that a single metabolite controls stem cell fate by instructing epigenetic and transcriptional attributes.
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Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Julian Mess
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany
| | - Polina V Pavlovich
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Yu Wei Zhang
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jasmin Rettkowski
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria-Eleni Lalioti
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Karin Jäcklein
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Betty Féret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Pia Sommerkamp
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Norbert B Ghyselinck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany.
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13
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Pavlovich PV, Cauchy P. Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data. Methods Mol Biol 2022; 2508:279-318. [PMID: 35737247 DOI: 10.1007/978-1-0716-2376-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA-Seq is now a routinely employed assay to measure gene expression. As the technique matured over the last decade, so have dedicated analytic tools. In this chapter, we first describe the mainstream as well as the most up-to-date protocols and their implications on downstream analysis. We then detail the steps entailing RNA-Seq analysis in three main stages: (i) preprocessing and data preparation, (ii) upstream processing, and (iii) high-level analyses. We review the most recent and relevant tools as one workflow following a stepwise order. The chapter further encompasses in-depth features of these tools. Details of the required code are made available throughout the chapter, as well as of the underlying statistics. We illustrate these steps with analysis of publicly available RNA-Seq data.
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Affiliation(s)
| | - Pierre Cauchy
- Universitätskilinkum Freiburg, Freiburg, Germany.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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14
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Yang X, Wang X, Lei L, Su Y, Zou Y, Liu H, Jiao A, Zhang C, Liu J, Li W, Ding R, Zhou X, Shi L, Zhang D, Sun C, Zhang B. Arid1a promotes thymocyte development through β-selection-dependent and β-selection-independent mechanisms. Immunology 2021; 165:402-413. [PMID: 34921692 DOI: 10.1111/imm.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 01/16/2023] Open
Abstract
Early T-cell development from CD4- CD8- double-negative (DN) stage to CD4+ CD8+ double-positive (DP) stage in the thymus is regulated through multiple steps involving a batch of sequentially expressed factors. Our preliminary data and a recent report showed that AT-rich interaction domain 1A (Arid1a) is required for the transition from DN to DP stages, but the mechanism is not fully understood. In this study, we consolidated that conditional deletion of Arid1a in T-cell lineage intrinsically caused developmental blocks from DN3 to DN4 stages, as well as from DN4 to DP stages using both in vivo adoptive T-cell transfer model and in vitro culture system. The expression of intracellular TCRβ is significantly decreased in Arid1a-deficient DN4 cells compared with WT cells. OT1 transgenic TCR can rescue the defect in the transition from DN3 to DN4 stages, but not from DN to DP stages. Furthermore, we observed a comparable or stronger proliferation capacity accompanied by a significant increase in cell death in Arid1a-/- DP cells compared with that in WT controls. RNA-Seq analysis shows a significant enrichment of apoptotic pathway within differentially expressed genes between Arid1a-/- and WT DP cells, including the upregulation of Bim, Casp3 and Trp53 and the downregulation of Rorc, Bcl-XL and Mcl1. Therefore, our study reveals a novel mechanism that Arid1a controls early T-cell development by maintaining intracellular TCRβ expression-mediated β-selection and activating parallel cell survival pathways.
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Affiliation(s)
- Xiaofeng Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lei Lei
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yujing Zou
- Duke University Medical Center, Durham, North Carolina, USA
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jun Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenhua Li
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Renyi Ding
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaobo Zhou
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lin Shi
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Dan Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chenming Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China.,Xi'an Key Laboratory of Immune Related Diseases, Xi'an, China
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15
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Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Genome Res 2021; 31:1680-1692. [PMID: 34330790 PMCID: PMC8415375 DOI: 10.1101/gr.275684.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.
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16
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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17
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Cieslak A, Charbonnier G, Tesio M, Mathieu EL, Belhocine M, Touzart A, Smith C, Hypolite G, Andrieu GP, Martens JHA, Janssen-Megens E, Gut M, Gut I, Boissel N, Petit A, Puthier D, Macintyre E, Stunnenberg HG, Spicuglia S, Asnafi V. Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation. J Exp Med 2021; 217:151947. [PMID: 32667968 PMCID: PMC7478722 DOI: 10.1084/jem.20192360] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 05/15/2020] [Indexed: 01/30/2023] Open
Abstract
Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints.
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Affiliation(s)
- Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Melania Tesio
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Mohamed Belhocine
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Aurore Touzart
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France.,Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Hypolite
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume P Andrieu
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Marta Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Denis Puthier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Salvatore Spicuglia
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
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18
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Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function. Int J Mol Sci 2020; 21:ijms21228478. [PMID: 33187197 PMCID: PMC7696796 DOI: 10.3390/ijms21228478] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The adaptive immune response in vertebrates depends on the expression of antigen-specific receptors in lymphocytes. T-cell receptor (TCR) gene expression is exquisitely regulated during thymocyte development to drive the generation of αβ and γδ T lymphocytes. The TCRα, TCRβ, TCRγ, and TCRδ genes exist in two different configurations, unrearranged and rearranged. A correctly rearranged configuration is required for expression of a functional TCR chain. TCRs can take the form of one of three possible heterodimers, pre-TCR, TCRαβ, or TCRγδ which drive thymocyte maturation into αβ or γδ T lymphocytes. To pass from an unrearranged to a rearranged configuration, global and local three dimensional (3D) chromatin changes must occur during thymocyte development to regulate gene segment accessibility for V(D)J recombination. During this process, enhancers play a critical role by modifying the chromatin conformation and triggering noncoding germline transcription that promotes the recruitment of the recombination machinery. The different signaling that thymocytes receive during their development controls enhancer activity. Here, we summarize the dynamics of long-distance interactions established through chromatin regulatory elements that drive transcription and V(D)J recombination and how different signaling pathways are orchestrated to regulate the activity of enhancers to precisely control TCR gene expression during T-cell maturation.
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19
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Depuydt MA, Prange KH, Slenders L, Örd T, Elbersen D, Boltjes A, de Jager SC, Asselbergs FW, de Borst GJ, Aavik E, Lönnberg T, Lutgens E, Glass CK, den Ruijter HM, Kaikkonen MU, Bot I, Slütter B, van der Laan SW, Yla-Herttuala S, Mokry M, Kuiper J, de Winther MP, Pasterkamp G. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics. Circ Res 2020; 127:1437-1455. [PMID: 32981416 PMCID: PMC7641189 DOI: 10.1161/circresaha.120.316770] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 09/23/2020] [Accepted: 02/25/2020] [Indexed: 02/01/2023]
Abstract
RATIONALE Atherosclerotic lesions are known for their cellular heterogeneity, yet the molecular complexity within the cells of human plaques has not been fully assessed. OBJECTIVE Using single-cell transcriptomics and chromatin accessibility, we gained a better understanding of the pathophysiology underlying human atherosclerosis. METHODS AND RESULTS We performed single-cell RNA and single-cell ATAC sequencing on human carotid atherosclerotic plaques to define the cells at play and determine their transcriptomic and epigenomic characteristics. We identified 14 distinct cell populations including endothelial cells, smooth muscle cells, mast cells, B cells, myeloid cells, and T cells and identified multiple cellular activation states and suggested cellular interconversions. Within the endothelial cell population, we defined subsets with angiogenic capacity plus clear signs of endothelial to mesenchymal transition. CD4+ and CD8+ T cells showed activation-based subclasses, each with a gradual decline from a cytotoxic to a more quiescent phenotype. Myeloid cells included 2 populations of proinflammatory macrophages showing IL (interleukin) 1B or TNF (tumor necrosis factor) expression as well as a foam cell-like population expressing TREM2 (triggering receptor expressed on myeloid cells 2) and displaying a fibrosis-promoting phenotype. ATACseq data identified specific transcription factors associated with the myeloid subpopulation and T cell cytokine profiles underlying mutual activation between both cell types. Finally, cardiovascular disease susceptibility genes identified using public genome-wide association studies data were particularly enriched in lesional macrophages, endothelial, and smooth muscle cells. CONCLUSIONS This study provides a transcriptome-based cellular landscape of human atherosclerotic plaques and highlights cellular plasticity and intercellular communication at the site of disease. This detailed definition of cell communities at play in atherosclerosis will facilitate cell-based mapping of novel interventional targets with direct functional relevance for the treatment of human disease.
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Affiliation(s)
- Marie A.C. Depuydt
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Einsteinweg 55, Leiden, the Netherlands (M.A.C.D., I.B., B.S., J.K.)
| | - Koen H.M. Prange
- Amsterdam University Medical Centers–Location AMC, University of Amsterdam, Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Meibergdreef 9, the Netherlands (K.H.M.P., M.P.J.d.W.)
| | - Lotte Slenders
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
| | - Tiit Örd
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.O., E.A., M.U.K., S.Y.-H.)
| | - Danny Elbersen
- Laboratory for Experimental Cardiology (D.E., S.C.A.d.J), University Medical Center Utrecht, Heidelberglaan 100, the Netherlands
| | - Arjan Boltjes
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
| | - Saskia C.A. de Jager
- Laboratory for Experimental Cardiology (D.E., S.C.A.d.J), University Medical Center Utrecht, Heidelberglaan 100, the Netherlands
| | - Folkert W. Asselbergs
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
| | - Gert J. de Borst
- Vascular Surgery (G.J.d.B.), University Medical Center Utrecht, Heidelberglaan 100, the Netherlands
| | - Einari Aavik
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.O., E.A., M.U.K., S.Y.-H.)
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland (T.L.)
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Munich, Germany (E.L., M.P.J.d.W.)
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany (E.L., M.P.J.d.W.)
| | - Christopher K. Glass
- Cell and Molecular Medicine (C.K.G.), University of California San Diego, CA
- School of Medicine (C.K.G.), University of California San Diego, CA
| | - Hester M. den Ruijter
- Cardiology (H.M.d.R., M.M.), University Medical Center Utrecht, Heidelberglaan 100, the Netherlands
| | - Minna U. Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.O., E.A., M.U.K., S.Y.-H.)
| | - Ilze Bot
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Einsteinweg 55, Leiden, the Netherlands (M.A.C.D., I.B., B.S., J.K.)
| | - Bram Slütter
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Einsteinweg 55, Leiden, the Netherlands (M.A.C.D., I.B., B.S., J.K.)
| | - Sander W. van der Laan
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
| | - Seppo Yla-Herttuala
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.O., E.A., M.U.K., S.Y.-H.)
| | - Michal Mokry
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
- Cardiology (H.M.d.R., M.M.), University Medical Center Utrecht, Heidelberglaan 100, the Netherlands
| | - Johan Kuiper
- Leiden Academic Centre for Drug Research, Division of Biotherapeutics, Leiden University, Einsteinweg 55, Leiden, the Netherlands (M.A.C.D., I.B., B.S., J.K.)
| | - Menno P.J. de Winther
- Amsterdam University Medical Centers–Location AMC, University of Amsterdam, Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Meibergdreef 9, the Netherlands (K.H.M.P., M.P.J.d.W.)
- Institute for Cardiovascular Prevention (IPEK), Munich, Germany (E.L., M.P.J.d.W.)
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany (E.L., M.P.J.d.W.)
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands (L.S., A.B., F.W.A., S.W.v.d.L., M.M., G.P.)
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20
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Lefkopoulos S, Polyzou A, Derecka M, Bergo V, Clapes T, Cauchy P, Jerez-Longres C, Onishi-Seebacher M, Yin N, Martagon-Calderón NA, Potts KS, Klaeylé L, Liu F, Bowman TV, Jenuwein T, Mione MC, Trompouki E. Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells. Immunity 2020; 53:934-951.e9. [DOI: 10.1016/j.immuni.2020.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
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21
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Iwasaki Y, Ikemura T, Kurokawa K, Okada N. Implication of a new function of human tDNAs in chromatin organization. Sci Rep 2020; 10:17440. [PMID: 33060757 PMCID: PMC7567086 DOI: 10.1038/s41598-020-74499-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/14/2020] [Indexed: 02/03/2023] Open
Abstract
Transfer RNA genes (tDNAs) are essential genes that encode tRNAs in all species. To understand new functions of tDNAs, other than that of encoding tRNAs, we used ENCODE data to examine binding characteristics of transcription factors (TFs) for all tDNA regions (489 loci) in the human genome. We divided the tDNAs into three groups based on the number of TFs that bound to them. At the two extremes were tDNAs to which many TFs bound (Group 1) and those to which no TFs bound (Group 3). Several TFs involved in chromatin remodeling such as ATF3, EP300 and TBL1XR1 bound to almost all Group 1 tDNAs. Furthermore, almost all Group 1 tDNAs included DNase I hypersensitivity sites and may thus interact with other chromatin regions through their bound TFs, and they showed highly conserved synteny across tetrapods. In contrast, Group 3 tDNAs did not possess these characteristics. These data suggest the presence of a previously uncharacterized function of these tDNAs. We also examined binding of CTCF to tDNAs and their involvement in topologically associating domains (TADs) and lamina-associated domains (LADs), which suggest a new perspective on the evolution and function of tDNAs.
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Affiliation(s)
- Yuki Iwasaki
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Norihiro Okada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan.
- School of Pharmacy, Kitasato University, Sagamihara, Kanagawa, Japan.
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22
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Pham D, Moseley CE, Gao M, Savic D, Winstead CJ, Sun M, Kee BL, Myers RM, Weaver CT, Hatton RD. Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf. Cell Rep 2020; 29:1203-1220.e7. [PMID: 31665634 PMCID: PMC7182170 DOI: 10.1016/j.celrep.2019.09.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/28/2019] [Accepted: 09/20/2019] [Indexed: 11/28/2022] Open
Abstract
The basic leucine zipper transcription factor activating transcription factor-like (Batf) contributes to transcriptional programming of multiple effector T cells and is required for T helper 17 (Th17) and T follicular helper (Tfh) cell development. Here, we examine mechanisms by which Batf initiates gene transcription in developing effector CD4 T cells. We find that, in addition to its pioneering function, Batf controls developmentally regulated recruitment of the architectural factor Ctcf to promote chromatin looping that is associated with lineage-specific gene transcription. The chromatin-organizing actions of Batf are largely dependent on Ets1, which appears to be indispensable for the Batf-dependent recruitment of Ctcf. Moreover, most of the Batf-dependent sites to which Ctcf is recruited lie outside of activating protein-1-interferon regulatory factor (Ap-1-Irf) composite elements (AICEs), indicating that direct involvement of Batf-Irf complexes is not required. These results identify a cooperative role for Batf, Ets1, and Ctcf in chromatin reorganization that underpins the transcriptional programming of effector T cells.
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Affiliation(s)
- Duy Pham
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Carson E Moseley
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Min Gao
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel Savic
- Human Genomics and Genetics, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Colleen J Winstead
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mengxi Sun
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Barbara L Kee
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Richard M Myers
- Human Genomics and Genetics, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Casey T Weaver
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Robin D Hatton
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
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23
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Maqbool MA, Pioger L, El Aabidine AZ, Karasu N, Molitor AM, Dao LTM, Charbonnier G, van Laethem F, Fenouil R, Koch F, Lacaud G, Gut I, Gut M, Amigorena S, Joffre O, Sexton T, Spicuglia S, Andrau JC. Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation. Cell Rep 2020; 32:108048. [PMID: 32814051 DOI: 10.1016/j.celrep.2020.108048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/13/2020] [Accepted: 07/28/2020] [Indexed: 01/08/2023] Open
Abstract
During thymic development and upon peripheral activation, T cells undergo extensive phenotypic and functional changes coordinated by lineage-specific developmental programs. To characterize the regulatory landscape controlling T cell identity, we perform a wide epigenomic and transcriptional analysis of mouse thymocytes and naive CD4 differentiated T helper cells. Our investigations reveal a dynamic putative enhancer landscape, and we could validate many of the enhancers using the high-throughput CapStarr sequencing (CapStarr-seq) approach. We find that genes using multiple promoters display increased enhancer usage, suggesting that apparent "enhancer redundancy" might relate to isoform selection. Furthermore, we can show that two Runx3 promoters display long-range interactions with specific enhancers. Finally, our analyses suggest a novel function for the PRC2 complex in the control of alternative promoter usage. Altogether, our study has allowed for the mapping of an exhaustive set of active enhancers and provides new insights into their function and that of PRC2 in controlling promoter choice during T cell differentiation.
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Affiliation(s)
- Muhammad Ahmad Maqbool
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France.
| | - Léo Pioger
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France
| | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France
| | - Nezih Karasu
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France; CNRS UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France; INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch, France; University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Anne Marie Molitor
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France; CNRS UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France; INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch, France; University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Lan T M Dao
- Aix-Marseille University, UMR-S 1090, TAGC, Marseille 13009, France
| | | | - Francois van Laethem
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France
| | - Romain Fenouil
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France
| | - Frederic Koch
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France
| | - Georges Lacaud
- CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Aderley Park, Macclesfield SK104TG, UK
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastian Amigorena
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Olivier Joffre
- Centre de Physiopathologie de Toulouse Purpan, INSERM UMR1043 CHU Purpan - BP 3028, 31024 Toulouse Cedex 3, France
| | - Thomas Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France; CNRS UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France; INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch, France; University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | | | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, CNRS, 1919 Route de Mende, Montpellier 34293, France.
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24
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Arnold PR, Wells AD, Li XC. Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate. Front Cell Dev Biol 2020; 7:377. [PMID: 31993419 PMCID: PMC6971116 DOI: 10.3389/fcell.2019.00377] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
Enhancers are cis-regulatory elements in the genome that cooperate with promoters to control target gene transcription. Unlike promoters, enhancers are not necessarily adjacent to target genes and can exert their functions regardless of enhancer orientations, positions and spatial segregations from target genes. Thus, for a long time, the question as to how enhancers act in a temporal and spatial manner attracted considerable attention. The recent discovery that enhancers are also abundantly transcribed raises interesting questions about the exact roles of enhancer RNA (eRNA) in gene regulation. In this review, we highlight the process of enhancer transcription and the diverse features of eRNA. We review eRNA functions, which include enhancer-promoter looping, chromatin modifying, and transcription regulating. As eRNA are transcribed from active enhancers, they exhibit tissue and lineage specificity, and serve as markers of cell state and function. Finally, we discuss the unique relationship between eRNA and super enhancers in phase separation wherein eRNA may contribute significantly to cell fate decisions.
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Affiliation(s)
- Preston R Arnold
- Texas A&M Health Science Center, College of Medicine, Bryan, TX, United States.,Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xian C Li
- Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
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25
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Abstract
In this review, Rothenburg discusses the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors in the primary establishment of T-cell identity. T-cell development in mammals is a model for lineage choice and differentiation from multipotent stem cells. Although T-cell fate choice is promoted by signaling in the thymus through one dominant pathway, the Notch pathway, it entails a complex set of gene regulatory network and chromatin state changes even before the cells begin to express their signature feature, the clonal-specific T-cell receptors (TCRs) for antigen. This review distinguishes three developmental modules for T-cell development, which correspond to cell type specification, TCR expression and selection, and the assignment of cells to different effector types. The first is based on transcriptional regulatory network events, the second is dominated by somatic gene rearrangement and mutation and cell selection, and the third corresponds to establishing a poised state of latent regulator priming through an unknown mechanism. Interestingly, in different lineages, the third module can be deployed at variable times relative to the completion of the first two modules. This review focuses on the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors TCF1, GATA3, PU.1, Bcl11b, Runx1, and E proteins in the primary establishment of T-cell identity.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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26
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An integrated transcriptional switch at the β-selection checkpoint determines T cell survival, development and leukaemogenesis. Biochem Soc Trans 2019; 47:1077-1089. [DOI: 10.1042/bst20180414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023]
Abstract
Abstract
In T cell development, a pivotal decision-making stage, termed β-selection, integrates a TCRβ checkpoint to coordinate survival, proliferation and differentiation to an αβ T cell. Here, we review how transcriptional regulation coordinates fate determination in early T cell development to enable β-selection. Errors in this transcription control can trigger T cell acute lymphoblastic leukaemia. We describe how the β-selection checkpoint goes awry in leukaemic transformation.
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27
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Rodríguez-Caparrós A, García V, Casal Á, López-Ros J, García-Mariscal A, Tani-ichi S, Ikuta K, Hernández-Munain C. Notch Signaling Controls Transcription via the Recruitment of RUNX1 and MYB to Enhancers during T Cell Development. THE JOURNAL OF IMMUNOLOGY 2019; 202:2460-2472. [DOI: 10.4049/jimmunol.1801650] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
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28
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Marcher AB, Bendixen SM, Terkelsen MK, Hohmann SS, Hansen MH, Larsen BD, Mandrup S, Dimke H, Detlefsen S, Ravnskjaer K. Transcriptional regulation of Hepatic Stellate Cell activation in NASH. Sci Rep 2019; 9:2324. [PMID: 30787418 PMCID: PMC6382845 DOI: 10.1038/s41598-019-39112-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022] Open
Abstract
Non-alcoholic steatohepatitis (NASH) signified by hepatic steatosis, inflammation, hepatocellular injury, and fibrosis is a growing cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma. Hepatic fibrosis resulting from accumulation of extracellular matrix proteins secreted by hepatic myofibroblasts plays an important role in disease progression. Activated hepatic stellate cells (HSCs) have been identified as the primary source of myofibroblasts in animal models of hepatotoxic liver injury; however, so far HSC activation and plasticity have not been thoroughly investigated in the context of NASH-related fibrogenesis. Here we have determined the time-resolved changes in the HSC transcriptome during development of Western diet- and fructose-induced NASH in mice, a NASH model recapitulating human disease. Intriguingly, HSC transcriptional dynamics are highly similar across disease models pointing to HSC activation as a point of convergence in the development of fibrotic liver disease. Bioinformatic interrogation of the promoter sequences of activated genes combined with loss-of-function experiments indicates that the transcriptional regulators ETS1 and RUNX1 act as drivers of NASH-associated HSC plasticity. Taken together, our results implicate HSC activation and transcriptional plasticity as key aspects of NASH pathophysiology.
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Affiliation(s)
- Ann-Britt Marcher
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Sofie M Bendixen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Mike K Terkelsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Sonja S Hohmann
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Maria H Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Bjørk D Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Henrik Dimke
- Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, 5000, Odense C, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, 5000, Odense C, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark.
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29
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Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat Genet 2018; 50:1140-1150. [PMID: 29988122 PMCID: PMC6097927 DOI: 10.1038/s41588-018-0156-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/22/2018] [Indexed: 12/15/2022]
Abstract
Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.
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30
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Hosokawa H, Rothenberg EV. Cytokines, Transcription Factors, and the Initiation of T-Cell Development. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028621. [PMID: 28716889 DOI: 10.1101/cshperspect.a028621] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multipotent blood progenitor cells migrate into the thymus and initiate the T-cell differentiation program. T-cell progenitor cells gradually acquire T-cell characteristics while shedding their multipotentiality for alternative fates. This process is supported by extracellular signaling molecules, including Notch ligands and cytokines, provided by the thymic microenvironment. T-cell development is associated with dynamic change of gene regulatory networks of transcription factors, which interact with these environmental signals. Together with Notch or pre-T-cell-receptor (TCR) signaling, cytokines always control proliferation, survival, and differentiation of early T cells, but little is known regarding their cross talk with transcription factors. However, recent results suggest ways that cytokines expressed in distinct intrathymic niches can specifically modulate key transcription factors. This review discusses how stage-specific roles of cytokines and transcription factors can jointly guide development of early T cells.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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31
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Bhat J, Helmuth J, Chitadze G, Kouakanou L, Peters C, Vingron M, Ammerpohl O, Kabelitz D. Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity. Scand J Immunol 2017; 86:184-195. [PMID: 28799233 DOI: 10.1111/sji.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/06/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic marks including histone modifications and DNA methylation are associated with the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning. Thus, it provides information on two levels of epigenetic regulation. Development and differentiation of T cells into functional subset cells including memory T cells are dynamic processes driven by environmental signals. Here, we briefly review the current knowledge of how epigenetic regulation contributes to subset specification, differentiation and memory development in T cells. Specifically, we focus on epigenetic mechanisms differentially active in the two distinct T cell populations expressing αβ or γδ T cell receptors. We also discuss examples of epigenetic alterations of T cells in autoimmune diseases. DNA methylation and histone acetylation are subject to modification by several classes of 'epigenetic modifiers', some of which are in clinical use or in preclinical development. Therefore, we address the impact of some epigenetic modifiers on T-cell activation and differentiation, and discuss possible synergies with T cell-based immunotherapeutic strategies.
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Affiliation(s)
- J Bhat
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - J Helmuth
- Otto-Warburg-Laboratories: Epigenomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - G Chitadze
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - L Kouakanou
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - C Peters
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - O Ammerpohl
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - D Kabelitz
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
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32
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Zhao JY, Osipovich O, Koues OI, Majumder K, Oltz EM. Activation of Mouse Tcrb: Uncoupling RUNX1 Function from Its Cooperative Binding with ETS1. THE JOURNAL OF IMMUNOLOGY 2017. [PMID: 28637900 DOI: 10.4049/jimmunol.1700146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T lineage commitment requires the coordination of key transcription factors (TFs) in multipotent progenitors that transition them away from other lineages and cement T cell identity. Two important TFs for the multipotent progenitors to T lineage transition are RUNX1 and ETS1, which bind cooperatively to composite sites throughout the genome, especially in regulatory elements for genes involved in T lymphopoiesis. Activation of the TCR β (Tcrb) locus in committed thymocytes is a critical process for continued development of these cells, and is mediated by an enhancer, Eβ, which harbors two RUNX-ETS composite sites. An outstanding issue in understanding T cell gene expression programs is whether RUNX1 and ETS1 have independent functions in enhancer activation that can be dissected from cooperative binding. We now show that RUNX1 is sufficient to activate the endogenous mouse Eβ element and its neighboring 25 kb region by independently tethering this TF without coincidental ETS1 binding. Moreover, RUNX1 is sufficient for long-range promoter-Eβ looping, nucleosome clearance, and robust transcription throughout the Tcrb recombination center, spanning both DβJβ clusters. We also find that a RUNX1 domain, termed the negative regulatory domain for DNA binding, can compensate for the loss of ETS1 binding at adjacent sites. Thus, we have defined independent roles for RUNX1 in the activation of a T cell developmental enhancer, as well as its ability to mediate specific changes in chromatin landscapes that accompany long-range induction of recombination center promoters.
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Affiliation(s)
- Jiang-Yang Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Oleg Osipovich
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Olivia I Koues
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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33
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Abstract
Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational modifications (PTMs) of histone tails, the exchange of canonical histones with histone variants, and nucleosome eviction. Such regulation requires the binding of signal-sensitive transcription factors (TFs) that recruit chromatin-modifying enzymes at regulatory elements defined as enhancers. Understanding how signaling cascades regulate enhancer activity requires a comprehensive analysis of the binding of TFs, chromatin modifying enzymes, and the occupancy of specific histone marks and histone variants. Chromatin immunoprecipitation (ChIP) assays utilize highly specific antibodies to immunoprecipitate specific protein/DNA complexes. The subsequent analysis of the purified DNA allows for the identification the region occupied by the protein recognized by the antibody. This work describes a protocol to efficiently perform ChIP of histone proteins in a mature mouse T-cell line. The presented protocol allows for the performance of ChIP assays in a reasonable timeframe and with high reproducibility.
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34
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Abstract
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.
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Affiliation(s)
- Gregory M K Poon
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA.,b Center for Diagnostics and Therapeutics, Georgia State University , Atlanta , GA , USA
| | - Hye Mi Kim
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA
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35
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Cauchy P, Koch F, Andrau JC. Two possible modes of pioneering associated with combinations of H2A.Z and p300/CBP at nucleosome-occupied enhancers. Transcription 2017; 8:179-184. [PMID: 28301306 DOI: 10.1080/21541264.2017.1291395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.
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Affiliation(s)
- Pierre Cauchy
- a Max Planck Institute of Immunobiology and Epigenetics , Department of Cellular and Molecular Immunology , Freiburg im Breisgau , Germany
| | - Frederic Koch
- b Max Planck Institute for Molecular Genetics , Department of Developmental Genetics , Berlin , Germany
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36
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Rothenberg EV, Kueh HY, Yui MA, Zhang JA. Hematopoiesis and T-cell specification as a model developmental system. Immunol Rev 2016; 271:72-97. [PMID: 27088908 DOI: 10.1111/imr.12417] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathway to generate T cells from hematopoietic stem cells guides progenitors through a succession of fate choices while balancing differentiation progression against proliferation, stage to stage. Many elements of the regulatory system that controls this process are known, but the requirement for multiple, functionally distinct transcription factors needs clarification in terms of gene network architecture. Here, we compare the features of the T-cell specification system with the rule sets underlying two other influential types of gene network models: first, the combinatorial, hierarchical regulatory systems that generate the orderly, synchronized increases in complexity in most invertebrate embryos; second, the dueling 'master regulator' systems that are commonly used to explain bistability in microbial systems and in many fate choices in terminal differentiation. The T-cell specification process shares certain features with each of these prevalent models but differs from both of them in central respects. The T-cell system is highly combinatorial but also highly dose-sensitive in its use of crucial regulatory factors. The roles of these factors are not always T-lineage-specific, but they balance and modulate each other's activities long before any mutually exclusive silencing occurs. T-cell specification may provide a new hybrid model for gene networks in vertebrate developmental systems.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Yuan Kueh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jingli A Zhang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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37
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Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. Proc Natl Acad Sci U S A 2016; 113:14805-14810. [PMID: 27911843 DOI: 10.1073/pnas.1617793113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ+ and γδ+ intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling-weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.
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