1
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Xing Q, Chang D, Xie S, Zhao X, Zhang H, Wang X, Bai X, Dong C. BCL6 is required for the thymic development of TCRαβ +CD8αα + intraepithelial lymphocyte lineage. Sci Immunol 2024; 9:eadk4348. [PMID: 38335269 DOI: 10.1126/sciimmunol.adk4348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/13/2023] [Indexed: 02/12/2024]
Abstract
TCRαβ+CD8αα+ intraepithelial lymphocytes (CD8αα+ αβ IELs) are a specialized subset of T cells in the gut epithelium that develop from thymic agonist selected IEL precursors (IELps). The molecular mechanisms underlying the selection and differentiation of this T cell type in the thymus are largely unknown. Here, we found that Bcl6 deficiency in αβ T cells resulted in the near absence of CD8αα+ αβ IELs. BCL6 was expressed by approximately 50% of CD8αα+ αβ IELs and by the majority of thymic PD1+ IELps after agonist selection. Bcl6 deficiency blocked early IELp generation in the thymus, and its expression in IELps was induced by thymic TCR signaling in an ERK-dependent manner. As a result of Bcl6 deficiency, the precursors of IELps among CD4+CD8+ double-positive thymocytes exhibited increased apoptosis during agonist selection and impaired IELp differentiation and maturation. Together, our results elucidate BCL6 as a crucial transcription factor during the thymic development of CD8αα+ αβ IELs.
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Affiliation(s)
- Qi Xing
- Shanghai Immune Therapy Institute, New Cornerstone Science Laboratory, Shanghai Jiao Tong University School of Medicine-affiliated Renji Hospital, Shanghai 200127, China
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dehui Chang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shiyuan Xie
- Institute for Advanced Interdisciplinary Studies and Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing 100084, China
| | - Xiaohong Zhao
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hao Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Bai
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chen Dong
- Shanghai Immune Therapy Institute, New Cornerstone Science Laboratory, Shanghai Jiao Tong University School of Medicine-affiliated Renji Hospital, Shanghai 200127, China
- Research Unit of Immune Regulation and Immune Diseases of Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai 200127, China
- Westlake University School of Medicine-affiliated Hangzhou First Hospital, Hangzhou 310024, China
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2
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Perriman L, Tavakolinia N, Jalali S, Li S, Hickey PF, Amann-Zalcenstein D, Ho WWH, Baldwin TM, Piers AT, Konstantinov IE, Anderson J, Stanley EG, Licciardi PV, Kannourakis G, Naik SH, Koay HF, Mackay LK, Berzins SP, Pellicci DG. A three-stage developmental pathway for human Vγ9Vδ2 T cells within the postnatal thymus. Sci Immunol 2023; 8:eabo4365. [PMID: 37450574 DOI: 10.1126/sciimmunol.abo4365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Vγ9Vδ2 T cells are the largest population of γδ T cells in adults and can play important roles in providing effective immunity against cancer and infection. Many studies have suggested that peripheral Vγ9Vδ2 T cells are derived from the fetal liver and thymus and that the postnatal thymus plays little role in the development of these cells. More recent evidence suggested that these cells may also develop postnatally in the thymus. Here, we used high-dimensional flow cytometry, transcriptomic analysis, functional assays, and precursor-product experiments to define the development pathway of Vγ9Vδ2 T cells in the postnatal thymus. We identify three distinct stages of development for Vγ9Vδ2 T cells in the postnatal thymus that are defined by the progressive acquisition of functional potential and major changes in the expression of transcription factors, chemokines, and other surface markers. Furthermore, our analysis of donor-matched thymus and blood revealed that the molecular requirements for the development of functional Vγ9Vδ2 T cells are delivered predominantly by the postnatal thymus and not in the periphery. Tbet and Eomes, which are required for IFN-γ and TNFα expression, are up-regulated as Vγ9Vδ2 T cells mature in the thymus, and mature thymic Vγ9Vδ2 T cells rapidly express high levels of these cytokines after stimulation. Similarly, the postnatal thymus programs Vγ9Vδ2 T cells to express the cytolytic molecules, perforin, granzyme A, and granzyme K. This study provides a greater understanding of how Vγ9Vδ2 T cells develop in humans and may lead to opportunities to manipulate these cells to treat human diseases.
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Affiliation(s)
- Louis Perriman
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
| | - Naeimeh Tavakolinia
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sedigheh Jalali
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Shuo Li
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Peter F Hickey
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Daniela Amann-Zalcenstein
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - William Wing Ho Ho
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Tracey M Baldwin
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Adam T Piers
- Murdoch Children's Research Institute, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
| | - Igor E Konstantinov
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
- Cardiothoracic Surgery, Royal Children's Hospital, Melbourne, Australia
| | - Jeremy Anderson
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Edouard G Stanley
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Paul V Licciardi
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
| | - Shalin H Naik
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Stuart P Berzins
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
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3
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You M, Liu J, Li J, Ji C, Ni H, Guo W, Zhang J, Jia W, Wang Z, Zhang Y, Yao Y, Yu G, Ji H, Wang X, Han D, Du X, Xu MM, Yu S. Mettl3-m 6A-Creb1 forms an intrinsic regulatory axis in maintaining iNKT cell pool and functional differentiation. Cell Rep 2023; 42:112584. [PMID: 37267102 DOI: 10.1016/j.celrep.2023.112584] [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] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
N6-methyladenosine (m6A) methyltransferase Mettl3 is involved in conventional T cell immunity; however, its role in innate immune cells remains largely unknown. Here, we show that Mettl3 intrinsically regulates invariant natural killer T (iNKT) cell development and function in an m6A-dependent manner. Conditional ablation of Mettl3 in CD4+CD8+ double-positive (DP) thymocytes impairs iNKT cell proliferation, differentiation, and cytokine secretion, which synergistically causes defects in B16F10 melanoma resistance. Transcriptomic and epi-transcriptomic analyses reveal that Mettl3 deficiency disturbs the expression of iNKT cell-related genes with altered m6A modification. Strikingly, Mettl3 modulates the stability of the Creb1 transcript, which in turn controls the protein and phosphorylation levels of Creb1. Furthermore, conditional targeting of Creb1 in DP thymocytes results in similar phenotypes of iNKT cells lacking Mettl3. Importantly, ectopic expression of Creb1 largely rectifies such developmental defects in Mettl3-deficient iNKT cells. These findings reveal that the Mettl3-m6A-Creb1 axis plays critical roles in regulating iNKT cells at the post-transcriptional layer.
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Affiliation(s)
- Menghao You
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jingjing Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ce Ji
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haochen Ni
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenhui Guo
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiarui Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Weiwei Jia
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhao Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yajiao Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yingpeng Yao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Guotao Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Huanyu Ji
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dali Han
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Meng Michelle Xu
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Shuyang Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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4
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Pankhurst TE, Buick KH, Lange JL, Marshall AJ, Button KR, Palmer OR, Farrand KJ, Montgomerie I, Bird TW, Mason NC, Kuang J, Compton BJ, Comoletti D, Salio M, Cerundolo V, Quiñones-Mateu ME, Painter GF, Hermans IF, Connor LM. MAIT cells activate dendritic cells to promote T FH cell differentiation and induce humoral immunity. Cell Rep 2023; 42:112310. [PMID: 36989114 PMCID: PMC10045373 DOI: 10.1016/j.celrep.2023.112310] [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: 10/25/2022] [Revised: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Protective immune responses against respiratory pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus, are initiated by the mucosal immune system. However, most licensed vaccines are administered parenterally and are largely ineffective at inducing mucosal immunity. The development of safe and effective mucosal vaccines has been hampered by the lack of a suitable mucosal adjuvant. In this study we explore a class of adjuvant that harnesses mucosal-associated invariant T (MAIT) cells. We show evidence that intranasal immunization of MAIT cell agonists co-administered with protein, including the spike receptor binding domain from SARS-CoV-2 virus and hemagglutinin from influenza virus, induce protective humoral immunity and immunoglobulin A production. MAIT cell adjuvant activity is mediated by CD40L-dependent activation of dendritic cells and subsequent priming of T follicular helper cells. In summary, we show that MAIT cells are promising vaccine targets that can be utilized as cellular adjuvants in mucosal vaccines.
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Affiliation(s)
- Theresa E Pankhurst
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kaitlin H Buick
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Joshua L Lange
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Andrew J Marshall
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Kaileen R Button
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Olga R Palmer
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kathryn J Farrand
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Isabelle Montgomerie
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Thomas W Bird
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Ngarangi C Mason
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Joanna Kuang
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Benjamin J Compton
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Mariolina Salio
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Gavin F Painter
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Lisa M Connor
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Malaghan Institute of Medical Research, Wellington 6242, New Zealand.
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5
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Barber-Axthelm IM, Wragg KM, Esterbauer R, Amarasena TH, Barber-Axthelm VR, Wheatley AK, Gibbon AM, Kent SJ, Juno JA. Phenotypic and functional characterization of pharmacologically expanded Vγ9Vδ2 T cells in pigtail macaques. iScience 2023; 26:106269. [PMID: 36936791 PMCID: PMC10014287 DOI: 10.1016/j.isci.2023.106269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/22/2022] [Accepted: 02/19/2023] [Indexed: 03/12/2023] Open
Abstract
While gaining interest as treatment for cancer and infectious disease, the clinical efficacy of Vγ9Vδ2 T cell-based immunotherapeutics has to date been limited. An improved understanding of γδ T cell heterogeneity across lymphoid and non-lymphoid tissues, before and after pharmacological expansion, is required. Here, we describe the phenotype and tissue distribution of Vγ9Vδ2 T cells at steady state and following in vivo pharmacological expansion in pigtail macaques. Intravenous phosphoantigen administration with subcutaneous rhIL-2 drove robust expansion of Vγ9Vδ2 T cells in blood and pulmonary mucosa, while expansion was confined to the pulmonary mucosa following intratracheal antigen administration. Peripheral blood Vγ9Vδ2 T cell expansion was polyclonal, and associated with a significant loss of CCR6 expression due to IL-2-mediated receptor downregulation. Overall, we show the tissue distribution and phenotype of in vivo pharmacologically expanded Vγ9Vδ2 T cells can be altered based on the antigen administration route, with implications for tissue trafficking and the clinical efficacy of Vγ9Vδ2 T cell immunotherapeutics.
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Affiliation(s)
- Isaac M. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathleen M. Wragg
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila H. Amarasena
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Valerie R.B. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anne M. Gibbon
- Monash Animal Research Platform, Monash University, Clayton, VIC 3800, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jennifer A. Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Corresponding author
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6
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Zelenka T, Klonizakis A, Tsoukatou D, Papamatheakis DA, Franzenburg S, Tzerpos P, Tzonevrakis IR, Papadogkonas G, Kapsetaki M, Nikolaou C, Plewczynski D, Spilianakis C. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun 2022; 13:6954. [PMID: 36376298 PMCID: PMC9663569 DOI: 10.1038/s41467-022-34345-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Despina Tsoukatou
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, HU-4032, Hungary
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming", 16672, Vari, Greece
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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7
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Chromatin organizer SATB1 controls the cell identity of CD4 + CD8 + double-positive thymocytes by regulating the activity of super-enhancers. Nat Commun 2022; 13:5554. [PMID: 36138028 PMCID: PMC9500044 DOI: 10.1038/s41467-022-33333-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/14/2022] [Indexed: 11/19/2022] Open
Abstract
CD4+ and CD8+ double-positive (DP) thymocytes play a crucial role in T cell development in the thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCRβ. DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, regulatory T cells, or invariant nature kill T cells (iNKT) in response to TCR signaling. Chromatin organizer SATB1 is highly expressed in DP cells and is essential in regulating Tcra rearrangement and differentiation of DP cells. Here we explored the mechanism of SATB1 orchestrating gene expression in DP cells. Single-cell RNA sequencing shows that Satb1 deletion changes the cell identity of DP thymocytes and down-regulates genes specifically and highly expressed in DP cells. Super-enhancers regulate the expressions of DP-specific genes, and our Hi-C data show that SATB1 deficiency in thymocytes reduces super-enhancer activity by specifically decreasing interactions among super-enhancers and between super-enhancers and promoters. Our results reveal that SATB1 plays a critical role in thymocyte development to promote the establishment of DP cell identity by globally regulating super-enhancers of DP cells at the chromatin architectural level.
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8
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Morgan RC, Kee BL. Genomic and Transcriptional Mechanisms Governing Innate-like T Lymphocyte Development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:208-216. [PMID: 35821098 DOI: 10.4049/jimmunol.2200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
Innate-like lymphocytes are a subset of lymphoid cells that function as a first line of defense against microbial infection. These cells are activated by proinflammatory cytokines or broadly expressed receptors and are able to rapidly perform their effector functions owing to a uniquely primed chromatin state that is acquired as a part of their developmental program. These cells function in many organs to protect against disease, but they release cytokines and cytotoxic mediators that can also lead to severe tissue pathologies. Therefore, harnessing the capabilities of these cells for therapeutic interventions will require a deep understanding of how these cells develop and regulate their effector functions. In this review we discuss recent advances in the identification of the transcription factors and the genomic regions that guide the development and function of invariant NKT cells and we highlight related mechanisms in other innate-like lymphocytes.
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Affiliation(s)
- Roxroy C Morgan
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL; and
| | - Barbara L Kee
- Cancer Biology and Immunology, Department of Pathology, University of Chicago, Chicago, IL
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9
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Planeta Kepp K. Bioinorganic Chemistry of Zinc in Relation to the Immune System. Chembiochem 2021; 23:e202100554. [PMID: 34889510 DOI: 10.1002/cbic.202100554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/09/2021] [Indexed: 01/18/2023]
Abstract
Zinc is well-known to have a central role in human inflammation and immunity and is itself an anti-inflammatory and antiviral agent. Despite its massively documented role in such processes, the underlying chemistry of zinc in relation to specific proteins and pathways of the immune system has not received much focus. This short review provides an overview of this topic, with emphasis on the structures of key proteins, zinc coordination chemistry, and probable mechanisms involved in zinc-based immunity, with some focus points for future chemical and biological research.
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Affiliation(s)
- Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kongens Lyngby, Denmark
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10
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Stamos DB, Clubb LM, Mitra A, Chopp LB, Nie J, Ding Y, Das A, Venkataganesh H, Lee J, El-Khoury D, Li L, Bhandoola A, Bosselut R, Love PE. The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. J Exp Med 2021; 218:e20202012. [PMID: 34726730 PMCID: PMC8570297 DOI: 10.1084/jem.20202012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 08/27/2021] [Accepted: 09/30/2021] [Indexed: 11/27/2022] Open
Abstract
Analysis of the transcriptional profiles of developing thymocytes has shown that T lineage commitment is associated with loss of stem cell and early progenitor gene signatures and the acquisition of T cell gene signatures. Less well understood are the epigenetic alterations that accompany or enable these transcriptional changes. Here, we show that the histone demethylase Lsd1 (Kdm1a) performs a key role in extinguishing stem/progenitor transcriptional programs in addition to key repressive gene programs during thymocyte maturation. Deletion of Lsd1 caused a block in late T cell development and resulted in overexpression of interferon response genes as well as genes regulated by the Gfi1, Bcl6, and, most prominently, Bcl11b transcriptional repressors in CD4+CD8+ thymocytes. Transcriptional overexpression in Lsd1-deficient thymocytes was not always associated with increased H3K4 trimethylation at gene promoters, indicating that Lsd1 indirectly affects the expression of many genes. Together, these results identify a critical function for Lsd1 in the epigenetic regulation of multiple repressive gene signatures during T cell development.
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Affiliation(s)
- Daniel B. Stamos
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lauren M. Clubb
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Apratim Mitra
- Bioinformatics and Scientific Programing Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Laura B. Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jan Lee
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Dalal El-Khoury
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - LiQi Li
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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11
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Cheng ZY, He TT, Gao XM, Zhao Y, Wang J. ZBTB Transcription Factors: Key Regulators of the Development, Differentiation and Effector Function of T Cells. Front Immunol 2021; 12:713294. [PMID: 34349770 PMCID: PMC8326903 DOI: 10.3389/fimmu.2021.713294] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
The development and differentiation of T cells represents a long and highly coordinated, yet flexible at some points, pathway, along which the sequential and dynamic expressions of different transcriptional factors play prominent roles at multiple steps. The large ZBTB family comprises a diverse group of transcriptional factors, and many of them have emerged as critical factors that regulate the lineage commitment, differentiation and effector function of hematopoietic-derived cells as well as a variety of other developmental events. Within the T-cell lineage, several ZBTB proteins, including ZBTB1, ZBTB17, ZBTB7B (THPOK) and BCL6 (ZBTB27), mainly regulate the development and/or differentiation of conventional CD4/CD8 αβ+ T cells, whereas ZBTB16 (PLZF) is essential for the development and function of innate-like unconventional γδ+ T & invariant NKT cells. Given the critical role of T cells in host defenses against infections/tumors and in the pathogenesis of many inflammatory disorders, we herein summarize the roles of fourteen ZBTB family members in the development, differentiation and effector function of both conventional and unconventional T cells as well as the underlying molecular mechanisms.
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Affiliation(s)
- Zhong-Yan Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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12
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Won HY, Kim HK, Crossman A, Awasthi P, Gress RE, Park JH. The Timing and Abundance of IL-2Rβ (CD122) Expression Control Thymic iNKT Cell Generation and NKT1 Subset Differentiation. Front Immunol 2021; 12:642856. [PMID: 34054809 PMCID: PMC8161506 DOI: 10.3389/fimmu.2021.642856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/27/2021] [Indexed: 12/26/2022] Open
Abstract
Invariant NKT (iNKT) cells are thymus-generated innate-like T cells, comprised of three distinct subsets with divergent effector functions. The molecular mechanism that drives the lineage trifurcation of immature iNKT cells into the NKT1, NKT2, and NKT17 subsets remains a controversial issue that remains to be resolved. Because cytokine receptor signaling is necessary for iNKT cell generation, cytokines are proposed to contribute to iNKT subset differentiation also. However, the precise roles and requirements of cytokines in these processes are not fully understood. Here, we show that IL-2Rβ, a nonredundant component of the IL-15 receptor complex, plays a critical role in both the development and differentiation of thymic iNKT cells. While the induction of IL-2Rβ expression on postselection thymocytes is necessary to drive the generation of iNKT cells, surprisingly, premature IL-2Rβ expression on immature iNKT cells was detrimental to their development. Moreover, while IL-2Rβ is necessary for NKT1 generation, paradoxically, we found that the increased abundance of IL-2Rβ suppressed NKT1 generation without affecting NKT2 and NKT17 cell differentiation. Thus, the timing and abundance of IL-2Rβ expression control iNKT lineage fate and development, thereby establishing cytokine receptor expression as a critical regulator of thymic iNKT cell differentiation.
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Affiliation(s)
- Hee Yeun Won
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Hye Kyung Kim
- Experimental Transplantation and Immunotherapy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Assiatu Crossman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Ronald E Gress
- Experimental Transplantation and Immunotherapy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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13
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Drashansky TT, Helm EY, Curkovic N, Cooper J, Cheng P, Chen X, Gautam N, Meng L, Kwiatkowski AJ, Collins WO, Keselowsky BG, Sant'Angelo D, Huo Z, Zhang W, Zhou L, Avram D. BCL11B is positioned upstream of PLZF and RORγt to control thymic development of mucosal-associated invariant T cells and MAIT17 program. iScience 2021; 24:102307. [PMID: 33870128 PMCID: PMC8042176 DOI: 10.1016/j.isci.2021.102307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/02/2020] [Accepted: 03/10/2021] [Indexed: 12/25/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells recognize microbial riboflavin metabolites presented by MR1 and play role in immune responses to microbial infections and tumors. We report here that absence of the transcription factor (TF) Bcl11b in mice alters predominantly MAIT17 cells in the thymus and further in the lung, both at steady state and following Salmonella infection. Transcriptomics and ChIP-seq analyses show direct control of TCR signaling program and position BCL11B upstream of essential TFs of MAIT17 program, including RORγt, ZBTB16 (PLZF), and MAF. BCL11B binding at key MAIT17 and at TCR signaling program genes in human MAIT cells occurred mostly in regions enriched for H3K27Ac. Unexpectedly, in human MAIT cells, BCL11B also bound at MAIT1 program genes, at putative active enhancers, although this program was not affected in mouse MAIT cells in the absence of Bcl11b. These studies endorse BCL11B as an essential TF for MAIT cells both in mice and humans. BCL11B controls MAIT cell development in mice, predominantly MAIT17 lineage BCL11B sustains MAIT17 and TCR signaling programs at steady state and in infection BCL11B binds at MAIT17 and TCR program genes in human MAIT cells Many BCL11B binding sites at MAIT17 and TCR genes are at putative active enhancers
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Affiliation(s)
- Theodore T Drashansky
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Eric Y Helm
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nina Curkovic
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jaimee Cooper
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Pingyan Cheng
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Xianghong Chen
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Namrata Gautam
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Lingsong Meng
- Department of Biostatistics, College of Medicine, College of Public Health & Health Professions, University of Florida, Gainesville, FL 32611, USA
| | - Alexander J Kwiatkowski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - William O Collins
- Department of Otolaryngology, College of Medicine, University of Florida, Gainesville, FL 32605, USA
| | - Benjamin G Keselowsky
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Derek Sant'Angelo
- Department of Pediatrics, The Child Health Institute of NJ, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, College of Public Health & Health Professions, University of Florida, Gainesville, FL 32611, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, Gainesville, FL 32610, USA
| | - Liang Zhou
- UF Health Cancer Center, Gainesville, FL 32610, USA.,Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA.,UF Health Cancer Center, Gainesville, FL 32610, USA
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14
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Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure. Nat Commun 2021; 12:1446. [PMID: 33664261 PMCID: PMC7933435 DOI: 10.1038/s41467-021-21574-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Invariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. Here we use RNA-seq and ATAC-seq analyses and show iNKT subsets are similar, regardless of tissue location. Lung iNKT cell subsets possess the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. Following antigenic stimulation, iNKT cells undergo chromatin and transcriptional changes delineating two populations: one similar to follicular helper T cells and the other NK or effector like. Phenotypic analysis indicates these changes are observed long-term, suggesting that iNKT cells gene programs are not fixed, but they are capable of chromatin remodeling after antigen to give rise to additional subsets. Invariant natural killer T cells are known to be composed of a number of phenotypic and functionally distinct populations. Here the authors use transcriptomic and epigenomic analysis to further characterize the peripheral iNKT compartment before and after antigenic stimulation.
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15
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recoup: flexible and versatile signal visualization from next generation sequencing. BMC Bioinformatics 2021; 22:2. [PMID: 33407065 PMCID: PMC7789646 DOI: 10.1186/s12859-020-03902-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022] Open
Abstract
Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging.
Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations.
Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.
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