1
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Belhocine M, Simonin M, Abad Flores JD, Cieslak A, Manosalva I, Pradel L, Smith C, Mathieu EL, Charbonnier G, Martens JH, Stunnenberg HG, Maqbool MA, Mikulasova A, Russell LJ, Rico D, Puthier D, Ferrier P, Asnafi V, Spicuglia S. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes. Genome Res 2022; 32:1328-1342. [PMID: 34162697 PMCID: PMC9341507 DOI: 10.1101/gr.266924.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/05/2021] [Indexed: 01/03/2023]
Abstract
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain-associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain-associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain-associated genes in preleukemic cells. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extent and number of broad domains. Our results show that the regulation of broad H3K4me3 domains is associated with leukemogenesis, and suggest that the presence of these structures might be used for epigenetic prioritization of cancer-relevant genes, including long noncoding RNAs.
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Affiliation(s)
- Mohamed Belhocine
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France;,Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France;,Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - José David Abad Flores
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Iris Manosalva
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Lydie Pradel
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Joost H.A. Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Muhammad Ahmad Maqbool
- CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Aderley Park, Macclesfield SK104TG, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J. Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Denis Puthier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France;,Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
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2
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Shiozawa S, Tsumiyama K, Miyazaki Y, Uto K, Sakurai K, Nakashima T, Matsuyama H, Doi A, Tarui M, Izumikawa M, Kimura M, Fujita Y, Satonaka C, Horiuchi T, Matsubara T, Oribe M, Yamane T, Kagawa H, Li QZ, Mizuno K, Mukai Y, Murakami K, Enya T, Tsukimoto S, Hakata Y, Miyazawa M, Shiozawa K. DOCK8-expressing T follicular helper cells newly generated beyond self-organized criticality cause systemic lupus erythematosus. iScience 2022; 25:103537. [PMID: 34977502 PMCID: PMC8689056 DOI: 10.1016/j.isci.2021.103537] [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: 05/12/2021] [Revised: 10/01/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Pathogens including autoantigens all failed to induce systemic lupus erythematosus (SLE). We, instead, studied the integrity of host's immune response that recognized pathogen. By stimulating TCR with an antigen repeatedly to levels that surpass host's steady-state response, self-organized criticality, SLE was induced in mice normally not prone to autoimmunity, wherein T follicular helper (Tfh) cells expressing the guanine nucleotide exchange factor DOCK8 on the cell surface were newly generated. DOCK8+Tfh cells passed through TCR re-revision and induced varieties of autoantibody and lupus lesions. They existed in splenic red pulp and peripheral blood of active lupus patients, which subsequently declined after therapy. Autoantibodies and disease were healed by anti-DOCK8 antibody in the mice including SLE-model (NZBxNZW) F1 mice. Thus, DOCK8+Tfh cells generated after repeated TCR stimulation by immunogenic form of pathogen, either exogenous or endogenous, in combination with HLA to levels that surpass system's self-organized criticality, cause SLE. Autoimmunity seldom takes place under integrated steady-state immune response Repeated invasion by pathogen, such as measles virus, is not exceptional but routine in life DOCK8+Tfh is generated upon TCR overstimulation by pathogen beyond self-organized criticality Newly generated DOCK8+Tfh induces autoantibodies and SLE, i.e., autoimmunity
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Affiliation(s)
- Shunichi Shiozawa
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan.,Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Ken Tsumiyama
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan.,Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Yumi Miyazaki
- Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Kenichi Uto
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Keiichi Sakurai
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan
| | - Toshie Nakashima
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Hiroko Matsuyama
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Ai Doi
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Miho Tarui
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Manabu Izumikawa
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Mai Kimura
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Yuko Fujita
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Chisako Satonaka
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Takahiko Horiuchi
- Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan
| | - Tsukasa Matsubara
- Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Motohiro Oribe
- Oribe Clinic, 1-8-15 Higashi-Odori, Oita 870-0823, Japan
| | - Takashi Yamane
- Department of Rheumatology, Kakogawa City Hospital, 439 Honmachi, Kakogawa 675-8611, Japan
| | - Hidetoshi Kagawa
- Department of Medicine, Red Cross Society Himeji Hospital, 1-12-1 Shimoteno, Himeji 670-8540, Japan
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, 6001 Forest Park Road/ND 6.504, Dallas, TX 75390-8814, USA
| | - Keiko Mizuno
- Drug Discovery Platform, KAN Research Institute, Inc., 6-8-2 Minatojimaminamicho, Kobe 650-0047, Japan
| | - Yohei Mukai
- Drug Discovery Platform, KAN Research Institute, Inc., 6-8-2 Minatojimaminamicho, Kobe 650-0047, Japan
| | - Kazuhiro Murakami
- Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsujima, Aobaku 981-8558, Japan
| | - Takuji Enya
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Department of Pediatrics, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Shota Tsukimoto
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Department of Anesthesiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Yoshiyuki Hakata
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Masaaki Miyazawa
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Kindai University Anti-Aging Center, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuko Shiozawa
- Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan.,Rheumatology and Collagen Disease Center, Hyogo Prefectural Kakogawa Medical Center, 203 Kanno, Kakogawa 675-8555, Japan
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3
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Uddin F, Srivastava M. Characterization of transcripts emanating from enhancer Eβ of the murine TCRβ locus. FEBS Open Bio 2021; 11:1014-1028. [PMID: 33426767 PMCID: PMC8016127 DOI: 10.1002/2211-5463.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 11/08/2022] Open
Abstract
Enhancers are well established as critical regulators of gene expression, but the mechanisms underlying the molecular basis of their specificity and activity are only partly understood. One of the most exciting recent observations is the discovery of enhancer RNA (eRNA), a class of noncoding RNAs derived from enhancer regions. Transcription of developmentally regulated enhancers has been observed to be associated with their active state. The nature of transcripts (eRNA) and their functional attributes are diverse and context dependent. The majority of eRNA are nonpolyadenylated and present in low abundance owing to their low stability, and may represent transcriptional noise. However, some eRNAs have been reported to be reasonably long and stable, are enriched in nuclei, exhibit tissue-specific expression and may contribute to enhancer function. Transcription of enhancers has been postulated to mediate enhancer function through either the act of transcription or via the transcribed RNA per se and is a useful feature to be analysed to understand mechanisms underlying enhancer activity. Enhancer Eβ at the murine TCRβ locus has been reported to exhibit enhanced occupancy of RNA polymerase II in developing thymocytes. Here, we investigated the transcriptional potential of Eβ in developing thymocytes and detected overlapping bidirectional transcripts at Eβ ranging between 0.7 and 1.7 kb. These noncoding transcripts are capped, polyadenylated, nuclear and expressed specifically in thymocytes. Delineation of these characteristics is important to further investigate their functional roles in mediating enhancer activity.
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Affiliation(s)
- Faizan Uddin
- Epigenetics Research Laboratory, National Institute of Immunology, New Delhi, India
| | - Madhulika Srivastava
- Epigenetics Research Laboratory, National Institute of Immunology, New Delhi, India
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4
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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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5
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Rodgers W, Byrum JN, Simpson DA, Hoolehan W, Rodgers KK. RAG2 localization and dynamics in the pre-B cell nucleus. PLoS One 2019; 14:e0216137. [PMID: 31075127 PMCID: PMC6510410 DOI: 10.1371/journal.pone.0216137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
RAG2 of the V(D)J recombinase is essential for lymphocyte development. Within the RAG2 noncore region is a plant homeodomain (PHD) that interacts with the modified histone H3K4me3, and this interaction is important for relieving inhibition of the RAG recombinase for V(D)J recombination. However, the effect of the noncore region on RAG2 localization and dynamics in cell nuclei is poorly understood. Here, we used cell imaging to measure the effect of mutating the RAG2 noncore region on properties of the full length protein. We measured GFP-labeled full length RAG2 (FL), the RAG2 core region alone (Core), and a T490A mutant in the noncore region, which has unique regulatory properties. This showed that FL, T490A, and Core localized to nuclear domains that were adjacent to DAPI-rich heterochromatin, and that contained the active chromatin marker H3K4me3. Within the RAG2-enriched regions, T490A exhibited greater colocalization with H3K4me3 than either FL or Core. Furthermore, colocalization of H3K4me3 with FL and T490A, but not Core, increased in conditions that increased H3K4me3 levels. Superresolution imaging showed H3K4me3 was distributed as puncta that RAG2 abutted, and mobility measurements showed that T490A had a significantly lower rate of diffusion within the nucleus than either FL or Core proteins. Finally, mutating Trp453 of the T490A mutant (W453A,T490A), which blocks PHD-dependent interactions with H3K4me3, abolished the T490A-mediated increased colocalization with H3K4me3 and slower mobility compared to FL. Altogether, these data show that Thr490 in the noncore region modulates RAG2 localization and dynamics in the pre-B cell nucleus, such as by affecting RAG2 interactions with H3K4me3.
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Affiliation(s)
- William Rodgers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, United States of America
| | - Jennifer N. Byrum
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Destiny A. Simpson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Walker Hoolehan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Karla K. Rodgers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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6
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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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7
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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8
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Outters P, Jaeger S, Zaarour N, Ferrier P. Long-Range Control of V(D)J Recombination & Allelic Exclusion: Modeling Views. Adv Immunol 2015; 128:363-413. [PMID: 26477371 DOI: 10.1016/bs.ai.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Allelic exclusion of immunoglobulin (Ig) and T-cell receptor (TCR) genes ensures the development of B and T lymphocytes operating under the mode of clonal selection. This phenomenon associates asynchronous V(D)J recombination events at Ig or TCR alleles and inhibitory feedback control. Despite years of intense research, however, the mechanisms that sustain asymmetric choice in random Ig/TCR dual allele usage and the production of Ig/TCR monoallelic expressing B and T lymphocytes remain unclear and open for debate. In this chapter, we first recapitulate the biological evidence that almost from the start appeared to link V(D)J recombination and allelic exclusion. We review the theoretical models previously proposed to explain this connection. Finally, we introduce our own mathematical modeling views based on how the developmental dynamics of individual lymphoid cells combine to sustain allelic exclusion.
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Affiliation(s)
- Pernelle Outters
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Nancy Zaarour
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
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9
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Majumder K, Bassing CH, Oltz EM. Regulation of Tcrb Gene Assembly by Genetic, Epigenetic, and Topological Mechanisms. Adv Immunol 2015; 128:273-306. [PMID: 26477369 DOI: 10.1016/bs.ai.2015.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The adaptive immune system endows mammals with an ability to recognize nearly any foreign invader through antigen receptors that are expressed on the surface of all lymphocytes. This defense network is generated by V(D)J recombination, a set of sequentially controlled DNA cleavage and repair events that assemble antigen receptor genes from physically separated variable (V), joining (J), and sometimes diversity (D) gene segments. The recombination process itself must be stringently regulated to minimize oncogenic translocations involving chromosomes that harbor immunoglobulin and T cell receptor loci. Indeed, V(D)J recombination is controlled at several levels, including tissue-, developmental stage-, allele-, and gene segment-specificity. These levels of control are imposed by a collection of architectural and regulatory elements that are distributed throughout each antigen receptor locus. Together, the genetic elements regulate developmental changes in chromatin, transcription, and locus topology that promote or disfavor long-range recombination. This chapter focuses on the cross talk between these mechanisms at the T cell receptor beta (Tcrb) locus, and how they sculpt a diverse TCRβ repertoire while maintaining monospecificity of this antigen receptor on each mature T lymphocyte. We also discuss how insights obtained from studies of Tcrb are more generally relevant to our understanding of gene regulation strategies employed by mammals.
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Affiliation(s)
- Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA.
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