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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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Qin S, Xie B, Wang Q, Yang R, Sun J, Hu C, Liu S, Tao Y, Xiao D. New insights into immune cells in cancer immunotherapy: from epigenetic modification, metabolic modulation to cell communication. MedComm (Beijing) 2024; 5:e551. [PMID: 38783893 PMCID: PMC11112485 DOI: 10.1002/mco2.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Cancer is one of the leading causes of death worldwide, and more effective ways of attacking cancer are being sought. Cancer immunotherapy is a new and effective therapeutic method after surgery, radiotherapy, chemotherapy, and targeted therapy. Cancer immunotherapy aims to kill tumor cells by stimulating or rebuilding the body's immune system, with specific efficiency and high safety. However, only few tumor patients respond to immunotherapy and due to the complex and variable characters of cancer immune escape, the behavior and regulatory mechanisms of immune cells need to be deeply explored from more dimensions. Epigenetic modifications, metabolic modulation, and cell-to-cell communication are key factors in immune cell adaptation and response to the complex tumor microenvironment. They collectively determine the state and function of immune cells through modulating gene expression, changing in energy and nutrient demands. In addition, immune cells engage in complex communication networks with other immune components, which are mediated by exosomes, cytokines, and chemokines, and are pivotal in shaping the tumor progression and therapeutic response. Understanding the interactions and combined effects of such multidimensions mechanisms in immune cell modulation is important for revealing the mechanisms of immunotherapy failure and developing new therapeutic targets and strategies.
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Affiliation(s)
- Sha Qin
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Bin Xie
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Qingyi Wang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Rui Yang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Jingyue Sun
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Chaotao Hu
- Regenerative Medicine, Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Shuang Liu
- Department of OncologyInstitute of Medical SciencesNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangsha, Hunan, China. UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of CarcinogenesisCancer Research Institute and School of Basic MedicineCentral South universityChangshaHunanChina
| | - Desheng Xiao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Liu Z, Wong HM, Chen X, Lin J, Zhang S, Yan S, Wang F, Li X, Wong KC. MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. Comput Biol Med 2024; 168:107753. [PMID: 38039889 DOI: 10.1016/j.compbiomed.2023.107753] [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: 06/06/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Trans-acting factors are of special importance in transcription regulation, which is a group of proteins that can directly or indirectly recognize or bind to the 8-12 bp core sequence of cis-acting elements and regulate the transcription efficiency of target genes. The progressive development in high-throughput chromatin capture technology (e.g., Hi-C) enables the identification of chromatin-interacting sequence groups where trans-acting DNA motif groups can be discovered. The problem difficulty lies in the combinatorial nature of DNA sequence pattern matching and its underlying sequence pattern search space. METHOD Here, we propose to develop MotifHub for trans-acting DNA motif group discovery on grouped sequences. Specifically, the main approach is to develop probabilistic modeling for accommodating the stochastic nature of DNA motif patterns. RESULTS Based on the modeling, we develop global sampling techniques based on EM and Gibbs sampling to address the global optimization challenge for model fitting with latent variables. The results reflect that our proposed approaches demonstrate promising performance with linear time complexities. CONCLUSION MotifHub is a novel algorithm considering the identification of both DNA co-binding motif groups and trans-acting TFs. Our study paves the way for identifying hub TFs of stem cell development (OCT4 and SOX2) and determining potential therapeutic targets of prostate cancer (FOXA1 and MYC). To ensure scientific reproducibility and long-term impact, its matrix-algebra-optimized source code is released at http://bioinfo.cs.cityu.edu.hk/MotifHub.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Hiu-Man Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Shixiong Zhang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Shankai Yan
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China.
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5
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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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Klocke C, Moran A, Adey A, McWeeney S, Wu G. Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566384. [PMID: 38014233 PMCID: PMC10680664 DOI: 10.1101/2023.11.09.566384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
While immune checkpoint inhibitors show success in treating a subset of patients with certain late-stage cancers, these treatments fail in many other patients as a result of mechanisms that have yet to be fully characterized. The process of CD8 T cell exhaustion, by which T cells become dysfunctional in response to prolonged antigen exposure, has been implicated in immunotherapy resistance. Single-cell RNA sequencing (scRNA-seq) produces an abundance of data to analyze this process; however, due to the complexity of the process, contributions of other cell types to a process within a single cell type cannot be simply inferred. We constructed an analysis framework to first rank human skin tumor samples by degree of exhaustion in tumor-infiltrating CD8 T cells and then identify immune cell type-specific gene-regulatory network patterns significantly associated with T cell exhaustion. Using this framework, we further analyzed scRNA-seq data from human tumor and chronic viral infection samples to compare the T cell exhaustion process between these two contexts. In doing so, we identified transcription factor activity in the macrophages of both tissue types associated with this process. Our framework can be applied beyond the tumor immune microenvironment to any system involving cell-cell communication, facilitating insights into key biological processes that underpin the effective treatment of cancer and other complicated diseases.
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [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: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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Gilbertson SE, Weinmann AS. Discovering effector domains in human transcription factors. Trends Immunol 2023; 44:493-495. [PMID: 37270301 DOI: 10.1016/j.it.2023.05.006] [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: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/05/2023]
Abstract
Genomic studies are transforming knowledge about the epigenetic, transcription factor, and 3D landscapes of the genome. However, comprehensive information is lacking about the effector domains used by transcription factors to influence gene expression. Addressing this gap, DelRosso et al. developed a high-throughput screen to discover effector domains in human regulatory factors.
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Affiliation(s)
- Sarah E Gilbertson
- Department of Microbiology, University of Alabama at Birmingham, AL 35294, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, AL 35294, USA.
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