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Chen W, Ma C, Wang M, Huang X, Chen X, Xu Z, Huang W, Wang R, Zheng Z, Fang J, Shen Y, Zhao D, Zhang H. BaP/BPDE suppresses homologous recombination repair in human trophoblast cells to induce miscarriage: The roles of lnc-HZ08. ENVIRONMENT INTERNATIONAL 2024; 191:108975. [PMID: 39190976 DOI: 10.1016/j.envint.2024.108975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/17/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
Benzo(a)pyrene (BaP) or benzo (a) pyrene 7,8-dihydrodiol-9,10-epoxide (BPDE) exposure causes trophoblast cell dysfunctions and induces miscarriage, which is generally epigenetically regulated. Homologous recombination (HR) repair of DNA double strand break (DSB) plays a crucial role in maintenance of genetic stability and cell normal functions. However, whether BaP/BPDE might suppress HR repair in human trophoblast cells to induce miscarriage, as well as its epigenetic regulatory mechanism, is largely unclear. In this study, we find that BaP/BPDE suppresses HR repair of DSB in trophoblast cells and eventually induces miscarriage by up-regulating lnc-HZ08. In mechanism, lnc-HZ08 (1) down-regulates the expression levels of FOXA1 (forkhead box A1) and thus suppresses FOXA1-mediated mRNA transcription of BRCA1 (Breast cancer susceptibility gene 1) and CtIP (CtBP-interacting protein), (2) impairs BRCA1 and CtIP protein interactions by competitive binding with CtIP through lnc-HZ08-1 fragment, and also (3) suppresses BRCA1-mediated CtIP ubiquitination without affecting CtIP stability, three of which eventually suppress HR repair in human trophoblast cells. Supplement with murine Ctip could efficiently restore (i.e. increase) HR repair and alleviate miscarriage in BaP-exposed mouse model. Collectively, this study not only reveals the association and causality among BaP/BPDE exposure, the defective HR repair, and miscarriage, but also discovers novel mechanism in lnc-HZ08-regulated BRCA1/CtIP-mediated HR repair, bridging epigenetic regulation and genetic instability and also providing an efficient approach for treatment against BaP/BPDE-induced unexplained miscarriage.
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Affiliation(s)
- Weina Chen
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; Department of Endocrinology, Translational Research of Diabetes Key Laboratory of Chongqing Education Commission of China, the Second Affiliated Hospital of Army Medical University, Chongqing 400037, China
| | - Chenglong Ma
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Manli Wang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Xinying Huang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; Jimei District Center for Disease Control and Prevention, Xiamen, Fujian, 361022, China
| | - Xueyu Chen
- Department of Reproductive Medicine, Affiliated Shenzhen maternity and child healthcare hospital, Southern Medical University, Shenzhen 518033, China
| | - Zhongyan Xu
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Wenxin Huang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Rong Wang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Zhaodian Zheng
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Jing Fang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Yanqiu Shen
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen maternity and child healthcare hospital, Southern Medical University, Shenzhen 518033, China.
| | - Huidong Zhang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China.
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2
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Liu Y, Yu K, Kong X, Zhang K, Wang L, Zhang N, Chen Q, Niu M, Li W, Zhong X, Wu S, Zhang J, Liu Y. FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer. SCIENCE ADVANCES 2023; 9:eadg7112. [PMID: 37595040 PMCID: PMC10438466 DOI: 10.1126/sciadv.adg7112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]
Abstract
FOXA1, a transcription factor involved in epigenetic reprogramming, is crucial for breast cancer progression. However, the mechanisms by which FOXA1 achieves its oncogenic functions remain elusive. Here, we demonstrate that the O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) of FOXA1 promotes breast cancer metastasis by orchestrating the transcription of numerous metastasis regulators. O-GlcNAcylation at Thr432, Ser441, and Ser443 regulates the stability of FOXA1 and promotes its assembly with chromatin. O-GlcNAcylation shapes the FOXA1 interactome, especially triggering the recruitment of the transcriptional repressor methyl-CpG binding protein 2 and consequently stimulating FOXA1 chromatin-binding sites to switch to chromatin loci of adhesion-related genes, including EPB41L3 and COL9A2. Site-specific depletion of O-GlcNAcylation on FOXA1 affects the expression of various downstream genes and thus inhibits breast cancer proliferation and metastasis both in vitro and in vivo. Our data establish the importance of aberrant FOXA1 O-GlcNAcylation in breast cancer progression and indicate that targeting O-GlcNAcylation is a therapeutic strategy for metastatic breast cancer.
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Affiliation(s)
- Yajie Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Kairan Yu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xiaotian Kong
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
- Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing, China
| | - Keren Zhang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Lingyan Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Nana Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Qiushi Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Science Park West Avenue, Hong Kong, China
| | - Mingshan Niu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wenli Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xiaomin Zhong
- Department of Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Sijin Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jianing Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yubo Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
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Boumpas P, Merabet S, Carnesecchi J. Integrating transcription and splicing into cell fate: Transcription factors on the block. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1752. [PMID: 35899407 DOI: 10.1002/wrna.1752] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) are present in all life forms and conserved across great evolutionary distances in eukaryotes. From yeast to complex multicellular organisms, they are pivotal players of cell fate decision by orchestrating gene expression at diverse molecular layers. Notably, TFs fine-tune gene expression by coordinating RNA fate at both the expression and splicing levels. They regulate alternative splicing, an essential mechanism for cell plasticity, allowing the production of many mRNA and protein isoforms in precise cell and tissue contexts. Despite this apparent role in splicing, how TFs integrate transcription and splicing to ultimately orchestrate diverse cell functions and cell fate decisions remains puzzling. We depict substantial studies in various model organisms underlining the key role of TFs in alternative splicing for promoting tissue-specific functions and cell fate. Furthermore, we emphasize recent advances describing the molecular link between the transcriptional and splicing activities of TFs. As TFs can bind both DNA and/or RNA to regulate transcription and splicing, we further discuss their flexibility and compatibility for DNA and RNA substrates. Finally, we propose several models integrating transcription and splicing activities of TFs in the coordination and diversification of cell and tissue identities. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Mechanisms.
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Affiliation(s)
- Panagiotis Boumpas
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
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5
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Recent insights into the role of Akt in CD4 T-cell activation and differentiation: alternative splicing and beyond. IMMUNOMETABOLISM (COBHAM (SURREY, ENGLAND)) 2023; 5:e00015. [PMID: 36710922 PMCID: PMC9869951 DOI: 10.1097/in9.0000000000000015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 01/31/2023]
Abstract
The activation and differentiation of CD4+ T cells is a complex process that is controlled by many factors. A critical component of the signaling pathway triggered following T-cell receptor (TCR) engagement is the serine threonine kinase Akt. Akt is involved in the control of many cellular processes including proliferation, metabolism, and differentiation of specific TH-cell subsets. Recent work has shown that, depending on the nature or strength of the TCR activation, Akt may activate different sets of substrates which then lead to differential cellular outcomes. Akt plays an important role in controlling the strength of the TCR signal and several recent studies have identified novel mechanisms including control of the expression of negative regulators of TCR signaling, and the influence on regulatory T cells (Treg) and TH17 differentiation. Many of these functions are mediated via control of the FoxO family of transcription factors, that play an important role in metabolism and Th cell differentiation. A theme that is emerging is that Akt does not function in the same way in all T-cell types. We highlight differences between CD4 and CD8 T cells as well as between Treg, TH17, and TFH cells. While Akt activity has been implicated in the control of alternative splicing in tumor cells, recent studies are emerging that indicate that similar functions may exist in CD4 T cells. In this mini review, we highlight some of the recent advances in these areas of Akt function that demonstrate the varied role that Akt plays in the function of CD4 T cells.
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Yao X, Zhou H, Duan C, Wu X, Li B, Liu H, Zhang Y. Comprehensive characteristics of pathological subtypes in testicular germ cell tumor: Gene expression, mutation and alternative splicing. Front Immunol 2023; 13:1096494. [PMID: 36713456 PMCID: PMC9883017 DOI: 10.3389/fimmu.2022.1096494] [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: 11/12/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Background Testicular germ cell tumor (TGCT) is the most common tumor in young men, but molecular signatures, especially the alternative splicing (AS) between its subtypes have not yet been explored. Methods To investigate the differences between TGCT subtypes, we comprehensively analyzed the data of gene expression, alternative splicing (AS), and somatic mutation in TGCT patients from the TCGA database. The gene ontology (GO) enrichment analyses were used to explore the function of differentially expressed genes and spliced genes respectively, and Spearman correlation analysis was performed to explore the correlation between differential genes and AS events. In addition, the possible patterns in which AS regulates gene expression were elaborated by the ensemble database transcript atlas. And, we identified important transcription factors that regulate gene expression and AS and functionally validated them in TGCT cell lines. Results We found significant differences between expression and AS in embryonal carcinoma and seminoma, while mixed cell tumors were in between. GO enrichment analyses revealed that both differentially expressed and spliced genes were enriched in transcriptional regulatory pathways, and obvious correlation between expression and AS events was determined. By analyzing the transcript map and the sites where splicing occurs, we have demonstrated that AS regulates gene expression in a variety of ways. We further identified two pivot AS-related molecules (SOX2 and HDAC9) involved in AS regulation, which were validated in embryonal carcinoma and seminoma cell lines. Differences in somatic mutations between subtypes are also of concern, with our results suggesting that mutations in some genes (B3GNT8, CAPN7, FAT4, GRK1, TACC2, and TRAM1L1) occur only in embryonal carcinoma, while mutations in KIT, KARS, and NRAS are observed only in seminoma. Conclusions In conclusion, our analysis revealed the differences in gene expression, AS and somatic mutation among TGCT subtypes, providing a molecular basis for clinical diagnosis and precise therapy of TGCT patients.
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Affiliation(s)
- Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoran Liu
- Stanford Bio-X, Stanford University, Stanford, CA, United States
| | - Yangjun Zhang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yangjun Zhang,
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7
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Choi JO, Ham JH, Hwang SS. RNA Metabolism in T Lymphocytes. Immune Netw 2022; 22:e39. [PMID: 36381959 PMCID: PMC9634142 DOI: 10.4110/in.2022.22.e39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023] Open
Abstract
RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.
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Affiliation(s)
- Jin Ouk Choi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong Hyeon Ham
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Soo Seok Hwang
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea.,Chronic Intractable Disease Systems Medicine Research Center, Institute of Genetic Science, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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8
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Yánez DC, Lau CI, Papaioannou E, Chawda MM, Rowell J, Ross S, Furmanski A, Crompton T. The Pioneer Transcription Factor Foxa2 Modulates T Helper Differentiation to Reduce Mouse Allergic Airway Disease. Front Immunol 2022; 13:890781. [PMID: 36003391 PMCID: PMC9393229 DOI: 10.3389/fimmu.2022.890781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/18/2022] [Indexed: 12/17/2022] Open
Abstract
Foxa2, a member of the Forkhead box (Fox) family of transcription factors, plays an important role in the regulation of lung function and lung tissue homeostasis. FOXA2 expression is reduced in the lung and airways epithelium of asthmatic patients and in mice absence of Foxa2 from the lung epithelium contributes to airway inflammation and goblet cell hyperplasia. Here we demonstrate a novel role for Foxa2 in the regulation of T helper differentiation and investigate its impact on lung inflammation. Conditional deletion of Foxa2 from T-cells led to increased Th2 cytokine secretion and differentiation, but decreased Th1 differentiation and IFN-γ expression in vitro. Induction of mouse allergic airway inflammation resulted in more severe disease in the conditional Foxa2 knockout than in control mice, with increased cellular infiltration to the lung, characterized by the recruitment of eosinophils and basophils, increased mucus production and increased production of Th2 cytokines and serum IgE. Thus, these experiments suggest that Foxa2 expression in T-cells is required to protect against the Th2 inflammatory response in allergic airway inflammation and that Foxa2 is important in T-cells to maintain the balance of effector cell differentiation and function in the lung.
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Affiliation(s)
- Diana C Yánez
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ching-In Lau
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Mira M Chawda
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jasmine Rowell
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Susan Ross
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Anna Furmanski
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | - Tessa Crompton
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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9
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Krueger A, Łyszkiewicz M, Heissmeyer V. Post-transcriptional control of T-cell development in the thymus. Immunol Lett 2022; 247:1-12. [DOI: 10.1016/j.imlet.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
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10
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Wu H, Dong J, Yu H, Wang K, Dai W, Zhang X, Hu N, Yin L, Tang D, Liu F, Dai Y. Single-Cell RNA and ATAC Sequencing Reveal Hemodialysis-Related Immune Dysregulation of Circulating Immune Cell Subpopulations. Front Immunol 2022; 13:878226. [PMID: 35720370 PMCID: PMC9205630 DOI: 10.3389/fimmu.2022.878226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background An increased risk of infection, malignancy, and cardiovascular diseases in maintenance hemodialysis patients is associated with hemodialysis-related immunity disturbances. Although defects in T-lymphocyte-dependent immune responses and preactivation of antigen-presenting cells have been documented in hemodialysis patients, the effects of long-term hemodialysis on the transcriptional program and chromosomal accessibility of circulating immune cell subpopulations remain poorly defined. Methods We integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to characterize the transcriptome profiles of peripheral mononuclear cells (PBMCs) from healthy controls and maintenance hemodialysis patients. Validation of differentially expressed genes in CD4+ T cells and monocytes were performed by magnetic bead separation and quantitative real-time PCR. Results We identified 16 and 15 PBMC subgroups in scRNA-seq and scATAC-seq datasets, respectively. Hemodialysis significantly suppressed the expression levels of T cell receptor (TCR) genes in CD4+ T cell subsets (e.g., TRAV4, CD45, CD3G, CD3D, CD3E) and major histocompatibility complex II (MHC-II) pathway-related genes in monocytes (HLA-DRB1, HLA-DQA2, HLA-DQA1, HLA-DPB1). Downstream pathways of TCR signaling, including PI3K-Akt-mTOR, MAPK, TNF, and NF-κB pathways, were also inhibited in CD4+ T cell subpopulations during the hemodialysis procedure. Hemodialysis altered cellular communication patterns between PBMC subgroups, particularly TGF-TGFBR, HVEM-BTLA, and IL16-CD4 signalings between CD4+ T cells and monocytes. Additionally, we found that hemodialysis inhibited the expression of AP-1 family transcription factors (JUN, JUND, FOS, FOSB) by interfering with the chromatin accessibility profile. Conclusions Our study provides a valuable framework for future investigations of hemodialysis-related immune dysregulation and identifies potential therapeutic targets for reconstituting the circulating immune system in maintenance hemodialysis patients.
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Affiliation(s)
- Hongwei Wu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Jingjing Dong
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Haiyan Yu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Kang Wang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, United States
| | - Xinzhou Zhang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Nan Hu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Donge Tang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Fanna Liu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Yong Dai
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
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11
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Bao X, Qin Y, Lu L, Zheng M. Transcriptional Regulation of Early T-Lymphocyte Development in Thymus. Front Immunol 2022; 13:884569. [PMID: 35432347 PMCID: PMC9008359 DOI: 10.3389/fimmu.2022.884569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
T-lymphocytes play crucial roles for maintaining immune homeostasis by fighting against various pathogenic microorganisms and establishing self-antigen tolerance. They will go through several stages and checkpoints in the thymus from progenitors to mature T cells, from CD4-CD8- double negative (DN) cells to CD4+CD8+ double positive (DP) cells, finally become CD4+ or CD8+ single positive (SP) cells. The mature SP cells then emigrate out of the thymus and further differentiate into distinct subsets under different environment signals to perform specific functions. Each step is regulated by various transcriptional regulators downstream of T cell receptors (TCRs) that have been extensively studied both in vivo and vitro via multiple mouse models and advanced techniques, such as single cell RNA sequencing (scRNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). This review will summarize the transcriptional regulators participating in the early stage of T cell development reported in the past decade, trying to figure out cascade networks in each process and provide possible research directions in the future.
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Affiliation(s)
- Xueyang Bao
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Yingyu Qin
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Linrong Lu
- Shanghai Immune Therapy Institute, Renji Hospital, Jiao Tong University School of Medicine, Shanghai, China.,Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhu Zheng
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
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