1
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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2
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Sun L, Jiao A, Liu H, Ding R, Yuan N, Yang B, Zhang C, Jia X, Wang G, Su Y, Zhang D, Shi L, Sun C, Zhang A, Zhang L, Zhang B. Targeting a disintegrin and metalloprotease (ADAM) 17-CD122 axis enhances CD8 + T cell effector differentiation and anti-tumor immunity. Signal Transduct Target Ther 2024; 9:152. [PMID: 38918390 PMCID: PMC11199508 DOI: 10.1038/s41392-024-01873-6] [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: 10/21/2023] [Revised: 04/29/2024] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
CD8+ T cell immune responses are regulated by multi-layer networks, while the post-translational regulation remains largely unknown. Transmembrane ectodomain shedding is an important post-translational process orchestrating receptor expression and signal transduction through proteolytic cleavage of membrane proteins. Here, by targeting the sheddase A Disintegrin and Metalloprotease (ADAM)17, we defined a post-translational regulatory mechanism mediated by the ectodomain shedding in CD8+ T cells. Transcriptomic and proteomic analysis revealed the involvement of post-translational regulation in CD8+ T cells. T cell-specific deletion of ADAM17 led to a dramatic increase in effector CD8+ T cell differentiation and enhanced cytolytic effects to eliminate pathogens and tumors. Mechanistically, ADAM17 regulated CD8+ T cells through cleavage of membrane CD122. ADAM17 inhibition led to elevated CD122 expression and enhanced response to IL-2 and IL-15 stimulation in both mouse and human CD8+ T cells. Intriguingly, inhibition of ADAM17 in CD8+ T cells improved the efficacy of chimeric antigen receptor (CAR) T cells in solid tumors. Our findings reveal a critical post-translational regulation in CD8+ T cells, providing a potential therapeutic strategy of targeting ADAM17 for effective anti-tumor immunity.
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Affiliation(s)
- Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Renyi Ding
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Ning Yuan
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Biao Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Xiaoxuan Jia
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Gang Wang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Dan Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Lin Shi
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Chenming Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China.
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China.
| | - Aijun Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China.
| | - Lianjun Zhang
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China.
- Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China.
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China.
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China.
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3
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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024; 16:681-700. [PMID: 38587919 PMCID: PMC11160454 DOI: 10.2217/epi-2023-0409] [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: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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4
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Zhu S, Liu J, Patel V, Zhao X, Peng W, Xue HH. Antigen exposure reshapes chromatin architecture in central memory CD8 + T cells and imprints enhanced recall capacity. Proc Natl Acad Sci U S A 2023; 120:e2313476120. [PMID: 38085779 PMCID: PMC10742382 DOI: 10.1073/pnas.2313476120] [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: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
CD62L+ central memory CD8+ T (TCM) cells provide enhanced protection than naive cells; however, the underlying mechanism, especially the contribution of higher-order genomic organization, remains unclear. Systematic Hi-C analyses reveal that antigen-experienced CD8+ T cells undergo extensive rewiring of chromatin interactions (ChrInt), with TCM cells harboring specific interaction hubs compared with naive CD8+ T cells, as observed at cytotoxic effector genes such as Ifng and Tbx21. TCM cells also acquire de novo CTCF (CCCTC-binding factor) binding sites, which are not only strongly associated with TCM-specific hubs but also linked to increased activities of local gene promoters and enhancers. Specific ablation of CTCF in TCM cells impairs rapid induction of genes in cytotoxic program, energy supplies, transcription, and translation by recall stimulation. Therefore, acquisition of CTCF binding and ChrInt hubs by TCM cells serves as a chromatin architectural basis for their transcriptomic dynamics in primary response and for imprinting the code of "recall readiness" against secondary challenge.
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Affiliation(s)
- Shaoqi Zhu
- Department of Physics, The George Washington University, Washington, DC20052
| | - Jia Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Vanita Patel
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Xiuyi Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
- Solon High School, Solon, OH44139
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ07018
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5
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Salataj E, Spilianakis CG, Chaumeil J. Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells. Front Immunol 2023; 14:1156077. [PMID: 37215121 PMCID: PMC10193148 DOI: 10.3389/fimmu.2023.1156077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.
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Affiliation(s)
- Eralda Salataj
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Charalampos G. Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Julie Chaumeil
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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6
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Liu J, Zhu S, Hu W, Zhao X, Shan Q, Peng W, Xue HH. CTCF mediates CD8+ effector differentiation through dynamic redistribution and genomic reorganization. J Exp Med 2023; 220:e20221288. [PMID: 36752796 PMCID: PMC9948760 DOI: 10.1084/jem.20221288] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/12/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Differentiation of effector CD8+ T cells is instructed by stably and dynamically expressed transcription regulators. Here we show that naive-to-effector differentiation was accompanied by dynamic CTCF redistribution and extensive chromatin architectural changes. Upon CD8+ T cell activation, CTCF acquired de novo binding sites and anchored novel chromatin interactions, and these changes were associated with increased chromatin accessibility and elevated expression of cytotoxic program genes including Tbx21, Ifng, and Klrg1. CTCF was also evicted from its ex-binding sites in naive state, with concomitantly reduced chromatin interactions in effector cells, as observed at memory precursor-associated genes including Il7r, Sell, and Tcf7. Genetic ablation of CTCF indeed diminished cytotoxic gene expression, but paradoxically elevated expression of memory precursor genes. Comparative Hi-C analysis revealed that key memory precursor genes were harbored within insulated neighborhoods demarcated by constitutive CTCF binding, and their induction was likely due to disrupted CTCF-dependent insulation. CTCF thus promotes cytotoxic effector differentiation by integrating local chromatin accessibility control and higher-order genomic reorganization.
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Affiliation(s)
- Jia Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Wei Hu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Qiang Shan
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA
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7
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Zhao X, Zhu S, Peng W, Xue HH. The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2269-2278. [PMID: 36469845 PMCID: PMC9731349 DOI: 10.4049/jimmunol.2200625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 01/04/2023]
Abstract
T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.
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Affiliation(s)
- Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ 07018
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Chromatin structure undergoes global and local reorganization during murine dendritic cell development and activation. Proc Natl Acad Sci U S A 2022; 119:e2207009119. [PMID: 35969760 PMCID: PMC9407307 DOI: 10.1073/pnas.2207009119] [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] [Indexed: 12/20/2022] Open
Abstract
Classical dendritic cells (cDCs) are essential for immune responses and differentiate from hematopoietic stem cells via intermediate progenitors, such as monocyte-DC progenitors (MDPs) and common DC progenitors (CDPs). Upon infection, cDCs are activated and rapidly express host defense-related genes, such as those encoding cytokines and chemokines. Chromatin structures, including nuclear compartments and topologically associating domains (TADs), have been implicated in gene regulation. However, the extent and dynamics of their reorganization during cDC development and activation remain unknown. In this study, we comprehensively determined higher-order chromatin structures by Hi-C in DC progenitors and cDC subpopulations. During cDC differentiation, chromatin activation was initially induced at the MDP stage. Subsequently, a shift from inactive to active nuclear compartments occurred at the cDC gene loci in CDPs, which was followed by increased intra-TAD interactions and loop formation. Mechanistically, the transcription factor IRF8, indispensable for cDC differentiation, mediated chromatin activation and changes into the active compartments in DC progenitors, thereby possibly leading to cDC-specific gene induction. Using an infection model, we found that the chromatin structures of host defense-related gene loci were preestablished in unstimulated cDCs, indicating that the formation of higher-order chromatin structures prior to infection may contribute to the rapid responses to pathogens. Overall, these results suggest that chromatin structure reorganization is closely related to the establishment of cDC-specific gene expression and immune functions. This study advances the fundamental understanding of chromatin reorganization in cDC differentiation and activation.
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Papapietro O, Nejentsev S. Topoisomerase 2β and DNA topology during B cell development. Front Immunol 2022; 13:982870. [PMID: 36045673 PMCID: PMC9423374 DOI: 10.3389/fimmu.2022.982870] [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: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Topoisomerase 2β (TOP2B) introduces transient double strand breaks in the DNA helix to remove supercoiling structures and unwind entangled DNA strains. Advances in genomic technologies have enabled the discovery of novel functions for TOP2B in processes such as releasing of the paused RNA polymerase II and maintaining the genome organization through DNA loop domains. Thus, TOP2B can regulate transcription directly by acting on transcription elongation and indirectly by controlling interactions between enhancer and promoter regions through genome folding. The identification of TOP2B mutations in humans unexpectedly revealed a unique role of TOP2B in B-cell progenitors. Here we discuss the functions of TOP2B and the mechanisms leading to the B-cell development defect in patients with TOP2B deficiency.
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Affiliation(s)
- Olivier Papapietro
- Molecular Cell Biology and Immunology, Amsterdam University Medical Centers (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- *Correspondence: Sergey Nejentsev, ; Olivier Papapietro,
| | - Sergey Nejentsev
- Molecular Cell Biology and Immunology, Amsterdam University Medical Centers (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Sergey Nejentsev, ; Olivier Papapietro,
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10
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Shan Q, Zhu S, Chen X, Liu J, Yuan S, Li X, Peng W, Xue HH. Tcf1-CTCF cooperativity shapes genomic architecture to promote CD8 + T cell homeostasis. Nat Immunol 2022; 23:1222-1235. [PMID: 35882936 PMCID: PMC9579964 DOI: 10.1038/s41590-022-01263-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/09/2022] [Indexed: 02/03/2023]
Abstract
CD8+ T cell homeostasis is maintained by the cytokines IL-7 and IL-15. Here we show that transcription factors Tcf1 and Lef1 were intrinsically required for homeostatic proliferation of CD8+ T cells. Multiomics analyses showed that Tcf1 recruited the genome organizer CTCF and that homeostatic cytokines induced Tcf1-dependent CTCF redistribution in the CD8+ T cell genome. Hi-C coupled with network analyses indicated that Tcf1 and CTCF acted cooperatively to promote chromatin interactions and form highly connected, dynamic interaction hubs in CD8+ T cells before and after cytokine stimulation. Ablating CTCF phenocopied the proliferative defects caused by Tcf1 and Lef1 deficiency. Tcf1 and CTCF controlled a similar set of genes that regulated cell cycle progression and promoted CD8+ T cell homeostatic proliferation in vivo. These findings identified CTCF as a Tcf1 cofactor and uncovered an intricate interplay between Tcf1 and CTCF that modulates the genomic architecture of CD8+ T cells to preserve homeostasis.
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Affiliation(s)
- Qiang Shan
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110,These authors contributed equally to this work
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington DC, 20052,These authors contributed equally to this work
| | - Xia Chen
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Jia Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Shuang Yuan
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Xiang Li
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington DC, 20052,Corresponding authors: Hai-Hui Xue, 111 Ideation Way, Bldg. 102, Rm. A417, Nutley, NJ 07110, Tel: 201-880-3550; ; Weiqun Peng, Science & Engineering Hall 4790, 800 22nd St NW, Washington, DC 20052, Tel: 202-994-0129;
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110,New Jersey Veterans Affairs Health Care System, East Orange, NJ 07018,Corresponding authors: Hai-Hui Xue, 111 Ideation Way, Bldg. 102, Rm. A417, Nutley, NJ 07110, Tel: 201-880-3550; ; Weiqun Peng, Science & Engineering Hall 4790, 800 22nd St NW, Washington, DC 20052, Tel: 202-994-0129;
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11
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Rozario AM, Morey A, Elliott C, Russ B, Whelan DR, Turner SJ, Bell TDM. 3D Single Molecule Super-Resolution Microscopy of Whole Nuclear Lamina. Front Chem 2022; 10:863610. [PMID: 35572104 PMCID: PMC9096160 DOI: 10.3389/fchem.2022.863610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Single molecule (SM) super-resolution microscopies bypass the diffraction limit of conventional optical techniques and provide excellent spatial resolutions in the tens of nanometers without overly complex microscope hardware. SM imaging using optical astigmatism is an efficient strategy for visualizing subcellular features in 3D with a z-range of up to ∼1 µm per acquisition. This approach however, places high demands on fluorophore brightness and photoswitching resilience meaning that imaging entire cell volumes in 3D using SM super-resolution remains challenging. Here we employ SM astigmatism together with multiplane acquisition to visualize the whole nuclear lamina of COS-7 and T cells in 3D. Nuclear lamina provides structural support to the nuclear envelope and participates in vital nuclear functions including internuclear transport, chromatin organization and gene regulation. Its position at the periphery of the nucleus provides a visible reference of the nuclear boundary and can be used to quantify the spatial distribution of intranuclear components such as histone modifications and transcription factors. We found Alexa Fluor 647, a popular photoswitchable fluorophore, remained viable for over an hour of continuous high laser power exposure, and provided sufficient brightness detectable up to 8 µm deep into a cell, allowing us to capture the entire nuclear lamina in 3D. Our approach provides sufficient super-resolution detail of nuclear lamina morphology to enable quantification of overall nuclear dimensions and local membrane features.
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Affiliation(s)
- Ashley M. Rozario
- School of Chemistry, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Alison Morey
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Cade Elliott
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Brendan Russ
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Donna R. Whelan
- La Trobe Institute for Molecular Science, Bendigo, VIC, Australia
| | - Stephen J. Turner
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
- *Correspondence: Stephen J. Turner, ; Toby D. M. Bell,
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
- *Correspondence: Stephen J. Turner, ; Toby D. M. Bell,
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Ginhoux F, Yalin A, Dutertre CA, Amit I. Single-cell immunology: Past, present, and future. Immunity 2022; 55:393-404. [PMID: 35263567 DOI: 10.1016/j.immuni.2022.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/30/2021] [Accepted: 02/09/2022] [Indexed: 02/08/2023]
Abstract
The immune system is a complex, dynamic, and plastic ecosystem composed of multiple cell types that constantly sense and interact with their local microenvironment to protect from infection and maintain homeostasis. For over a century, great efforts and ingenuity have been applied to the characterization of immune cells and their microenvironments, but traditional marker-based and bulk technologies left key questions unanswered. In the past decade, the advent of single-cell genomic approaches has revolutionized our knowledge of the cellular and molecular makeup of the immune system. In this perspective, we outline the past, present, and future applications of single-cell genomics in immunology and discuss how the integration of multiomics at the single-cell level will pave the way for future advances in immunology research and clinical translation.
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Affiliation(s)
- Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Gustave Roussy Cancer Campus, Villejuif 94800, France; Inserm U1015, Gustave Roussy, Villejuif 94800, France; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore.
| | - Adam Yalin
- Department of Immunology, Weizmann Institute, Rehovot 7610001, Israel.
| | - Charles Antoine Dutertre
- Gustave Roussy Cancer Campus, Villejuif 94800, France; Inserm U1015, Gustave Roussy, Villejuif 94800, France.
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 7610001, Israel.
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A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes. Proc Natl Acad Sci U S A 2021; 118:2104297118. [PMID: 34750254 DOI: 10.1073/pnas.2104297118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
The commitment of hematopoietic multipotent progenitors (MPPs) toward a particular lineage involves activation of cell type-specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early-B and early-T lymphocyte development are mutually exclusive, we show that these cell types exhibit significantly correlated microRNA (miRNA) profiles. However, their corresponding miRNA targetomes are distinct and predominated by transcripts associated with natural killer, dendritic cell, and myeloid lineages, suggesting that miRNAs function in a cell-autonomous manner. The combinatorial expression of miRNAs miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuates their myeloid differentiation potential due to repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early-B and early-T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicates that B as well as T lineage determinants drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously expressed lineage-inappropriate genes to suppress the alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.
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Li M, Wei H, Zhong S, Cheng Y, Wen S, Wang D, Shu Y. Association of Single Nucleotide Polymorphisms in LEP, LEPR, and PPARG With Humoral Immune Response to Influenza Vaccine. Front Genet 2021; 12:725538. [PMID: 34745208 PMCID: PMC8569447 DOI: 10.3389/fgene.2021.725538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Although previous studies have proposed leptin plays an important role in energy metabolism as well as in immune response, the effects of leptin-related genes on influenza vaccine-induced immune response remain unexplored. In this study, we aimed to investigate the potential association of leptin gene (LEP), leptin receptor gene (LEPR), and peroxisome proliferator activated receptor gamma gene (PPARG) polymorphisms with humoral immune response to influenza vaccine. Methods: Based on the seroconversion to influenza vaccine, 227 low-responders and 365 responders were selected in this study, and 11 candidate single nucleotide polymorphisms (SNPs) were genotyped using the MassARRAY technology platform. Univariate and multivariate logistic regression analyses were used to explore the association of SNPs in LEP, LEPR, and PPARG with humoral immune response to influenza vaccine. We also conducted a stratified analysis by gender to further clarify this association. The haplotypes analysis was performed using SNPStats. Results: Significant differences were observed in the genotypic distribution of PPARG rs17793951 between the two groups (p = 0.001), and the PPARG rs17793951 AG + GG genotype was associated with a higher risk of low responsiveness to influenza vaccine adjusted for gender and age (additive genetic model: OR = 2.94, 95% CI = 1.67-5.19, dominant genetic model: OR = 2.81, 95% CI = 1.61-4.92). No significant association of other SNPs in LEP and LEPR with immune response to influenza vaccine was found. The stratified analysis found the gender difference in the association of LEPR and PPARG variants with immune response to influenza vaccine. We found that LEPR rs6673591 GA + AA genotype was correlated with low responsiveness to influenza vaccine only in males (OR = 1.96, 95% CI = 1.05-3.67), and PPARG rs17793951 AG + GG genotype was associated with low responsiveness to influenza vaccine in females (OR = 3.28, 95% CI = 1.61-6.67). Compared with the CGGAGGC haplotype composed of LEPR rs1327118, rs7602, rs1137101, rs1938489, rs6673591, rs1137100, and rs13306523, the CAAAAAC haplotype was positively correlated with immune response of influenza vaccine (OR = 0.34, 95% CI = 0.15-0.77). Haplotype TG comprised of PPARG rs796313 and rs17793951 was associated with a 2.85-fold increased risk of low responsiveness to influenza vaccine. Conclusion: Our study identified that PPARG rs17793951 variants were significantly associated with the immune response to influenza vaccine.
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Affiliation(s)
- Mao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Guangzhou, China
| | - Hejiang Wei
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Shuyi Zhong
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Guangzhou, China
| | - Yanhui Cheng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Simin Wen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Guangzhou, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Guangzhou, China
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