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Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605698. [PMID: 39131377 PMCID: PMC11312543 DOI: 10.1101/2024.07.29.605698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Effective tools for exploration and analysis are needed to extract insights from large-scale single-cell measurement data. However, current techniques for handling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that the tensor decomposition method PARAFAC2 (Pf2) enables the dimensionality reduction of single-cell data across conditions. We demonstrate these benefits across two distinct contexts of single-cell RNA-sequencing (scRNA-seq) experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. By isolating relevant gene modules across cells and conditions, Pf2 enables straightforward associations of gene variation patterns across specific patients or perturbations while connecting each coordinated change to certain cells without pre-defining cell types. The theoretical grounding of Pf2 suggests a unified framework for many modeling tasks associated with single-cell data. Thus, Pf2 provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts.
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Affiliation(s)
- Andrew Ramirez
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | - Sean Pascoe
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Armaan Abraham
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | | | - Aaron S. Meyer
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, CA, USA
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2
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024; 5:101640. [PMID: 38959885 PMCID: PMC11293343 DOI: 10.1016/j.xcrm.2024.101640] [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: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Su C, Kent CL, Pierpoint M, Floyd W, Luo L, Wiliams NT, Ma Y, Peng B, Lazarides AL, Subramanian A, Himes JE, Perez VM, Hernansaiz-Ballesteros RD, Roche KE, Modliszewski JL, Selitsky SR, Mari Shinohara, Wisdom AJ, Moding EJ, Mowery YM, Kirsch DG. Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573968. [PMID: 38260522 PMCID: PMC10802286 DOI: 10.1101/2024.01.03.573968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Radiation therapy is frequently used to treat cancers including soft tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to radiation therapy (RT) in transplanted tumors, but the mechanism(s) remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft tissue sarcomas with high tumor mutation burden. Treatment with a single fraction of 20 Gy RT and two doses of CpG significantly enhanced tumor response, which was abrogated by genetic or immunodepletion of CD8+ T cells. To characterize the immune response to RT + CpG, we performed bulk RNA-seq, single-cell RNA-seq, and mass cytometry. Sarcomas treated with 20 Gy and CpG demonstrated increased CD8 T cells expressing markers associated with activation and proliferation, such as Granzyme B, Ki-67, and interferon-γ. CpG + RT also upregulated antigen presentation pathways on myeloid cells. Furthermore, in sarcomas treated with CpG + RT, TCR clonality analysis suggests an increase in clonal T-cell dominance. Collectively, these findings demonstrate that RT + CpG significantly delays tumor growth in a CD8 T cell-dependent manner. These results provide a strong rationale for clinical trials evaluating CpG or other TLR9 agonists with RT in patients with soft tissue sarcoma.
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Affiliation(s)
- Chang Su
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Collin L. Kent
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Matthew Pierpoint
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Nerissa T. Wiliams
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Brian Peng
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Jonathan E. Himes
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | | - Mari Shinohara
- Department of Immunology, Duke University, Durham, NC, USA
| | - Amy J. Wisdom
- Department of Radiation Oncology, Harvard University, Cambridge, MA, USA
| | - Everett J. Moding
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - David G. Kirsch
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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4
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Chopp LB, Zhu X, Gao Y, Nie J, Singh J, Kumar P, Young KZ, Patel S, Li C, Balmaceno-Criss M, Vacchio MS, Wang MM, Livak F, Merchant JL, Wang L, Kelly MC, Zhu J, Bosselut R. Zfp281 and Zfp148 control CD4 + T cell thymic development and T H2 functions. Sci Immunol 2023; 8:eadi9066. [PMID: 37948511 DOI: 10.1126/sciimmunol.adi9066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
How CD4+ lineage gene expression is initiated in differentiating thymocytes remains poorly understood. Here, we show that the paralog transcription factors Zfp281 and Zfp148 control both this process and cytokine expression by T helper cell type 2 (TH2) effector cells. Genetic, single-cell, and spatial transcriptomic analyses showed that these factors promote the intrathymic CD4+ T cell differentiation of class II major histocompatibility complex (MHC II)-restricted thymocytes, including expression of the CD4+ lineage-committing factor Thpok. In peripheral T cells, Zfp281 and Zfp148 promoted chromatin opening at and expression of TH2 cytokine genes but not of the TH2 lineage-determining transcription factor Gata3. We found that Zfp281 interacts with Gata3 and is recruited to Gata3 genomic binding sites at loci encoding Thpok and TH2 cytokines. Thus, Zfp148 and Zfp281 collaborate with Gata3 to promote CD4+ T cell development and TH2 cell responses.
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Affiliation(s)
- Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA 19104, USA
| | - Xiaoliang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jatinder Singh
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Parimal Kumar
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kelly Z Young
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shil Patel
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- University of Maryland Medical School, Baltimore, MD 21201, USA
| | - Caiyi Li
- Flow Cytometry Core, Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariah Balmaceno-Criss
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael M Wang
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Ferenc Livak
- Flow Cytometry Core, Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juanita L Merchant
- Department of Gastroenterology and Hepatology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | - Lie Wang
- Institute of Immunology, and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Michael C Kelly
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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5
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Chen D, Li K, Pan L, Wu Y, Chen M, Zhang X, Xu J, Lou T. TCF7 and LEF-1 downregulation in sepsis promotes immune suppression by inhibiting CD4 + T cell proliferation. Microb Pathog 2023; 184:106362. [PMID: 37741305 DOI: 10.1016/j.micpath.2023.106362] [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: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Previous studies have shown that sepsis is implicated in a reduction in the number and function of CD4+ T cells. TCF7 and LEF-1 facilitate early T cell development and lineage selection of CD4+ T cells. However, the function and mechanism of TCF7 and LEF-1 in sepsis are uncharacterized. This study intended to delineate effect of TCF7 and LEF-1 on sepsis and the impact on proliferation of CD4+ T cells in sepsis. METHODS A mouse sepsis model was constructed by cecal ligation and puncture (CLP) method. Expression of TCF7 and LEF-1 in sepsis was investigated using bioinformatics analysis and molecular experiments. We then constructed TCF7 and LEF-1 overexpression cell lines to investigate their effects on proliferation, apoptosis, effector activation, and immunosuppressive molecules of CD4+ T cells in sepsis. RESULTS TCF7 and LEF-1 were downregulated in sepsis. As the duration of sepsis induction increased, the levels of TCF7 and LEF-1 gradually decreased, as did the number of CD4+ T cells. Cell experiments showed that overexpression of TCF7 and LEF-1 enhanced proliferation and effector activation of CD4+ T cells, reduced apoptosis, decreased PD-1 and LAG3 expression, and promoted immune response in sepsis. CONCLUSION In conclusion, this study confirmed that downregulation of TCF7 and LEF-1 expression in sepsis inhibited proliferation of CD4+ T cells, leading to immune suppression. This finding suggested that TCF7 and LEF-1 were potential biological targets for sepsis and indicated that immunotherapy aimed at improving CD4+ T cell proliferation may be a new strategy for immune therapy in sepsis patients.
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Affiliation(s)
- Deyuan Chen
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Ke Li
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Liuhua Pan
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Yueming Wu
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Miaomiao Chen
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Xian Zhang
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China
| | - Junlong Xu
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China.
| | - Tianzheng Lou
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui City, Zhejiang Province, 23000, China.
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6
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Yakou MH, Ghilas S, Tran K, Liao Y, Afshar-Sterle S, Kumari A, Schmid K, Dijkstra C, Inguanti C, Ostrouska S, Wilcox J, Smith M, Parathan P, Allam A, Xue HH, Belz GT, Mariadason JM, Behren A, Drummond GR, Ruscher R, Williams DS, Pal B, Shi W, Ernst M, Raghu D, Mielke LA. TCF-1 limits intraepithelial lymphocyte antitumor immunity in colorectal carcinoma. Sci Immunol 2023; 8:eadf2163. [PMID: 37801516 DOI: 10.1126/sciimmunol.adf2163] [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: 10/06/2022] [Accepted: 08/07/2023] [Indexed: 10/08/2023]
Abstract
Intraepithelial lymphocytes (IELs), including αβ and γδ T cells (T-IELs), constantly survey and play a critical role in maintaining the gastrointestinal epithelium. We show that cytotoxic molecules important for defense against cancer were highly expressed by T-IELs in the small intestine. In contrast, abundance of colonic T-IELs was dependent on the microbiome and displayed higher expression of TCF-1/TCF7 and a reduced effector and cytotoxic profile, including low expression of granzymes. Targeted deletion of TCF-1 in γδ T-IELs induced a distinct effector profile and reduced colon tumor formation in mice. In addition, TCF-1 expression was significantly reduced in γδ T-IELs present in human colorectal cancers (CRCs) compared with normal healthy colon, which strongly correlated with an enhanced γδ T-IEL effector phenotype and improved patient survival. Our work identifies TCF-1 as a colon-specific T-IEL transcriptional regulator that could inform new immunotherapy strategies to treat CRC.
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Affiliation(s)
- Marina H Yakou
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Sonia Ghilas
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Kelly Tran
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Shoukat Afshar-Sterle
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Anita Kumari
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Kevin Schmid
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Christine Dijkstra
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Chantelle Inguanti
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Simone Ostrouska
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Jordan Wilcox
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Maxine Smith
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Pavitha Parathan
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Amr Allam
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - 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
| | - Gabrielle T Belz
- University of Queensland Frazer Institute, Faculty of Medicine, University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Grant R Drummond
- Centre for Cardiovascular Biology and Disease Research; Department of Microbiology, Anatomy, Physiology and Pharmacology; and School of Agriculture, Biomedicine, and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - David S Williams
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
- Department of Anatomical Pathology, Austin Health, Heidelberg, Victoria, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Dinesh Raghu
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
| | - Lisa A Mielke
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3084, Australia
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7
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Zhao P, Sun L, Zhao C, Malik S. PD1 is transcriptionally regulated by LEF1 in mature T cells. Immunobiology 2023; 228:152708. [PMID: 37523793 DOI: 10.1016/j.imbio.2023.152708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
The role of programmed cell death 1 (PD1) in cancer immune evasion is of considerable importance, prompting the development of monoclonal antibodies that specifically target PD-1 to enhance the immune system for cancer therapy. Nevertheless, the efficacy of PD1/programmed cell death-Ligand 1 (PD-L1) blocking antibodies is limited to certain patients or tumor types. Although researchers have demonstrated the influence of PD-1 on the positive selection of T cells, its effect on the T-cell repertoire remains uncertain. Lymphoid enhancer binding factor 1 (LEF1) has been known to play a critical role as a transcription factor in the development and maturation of T cells. Despite the greater focus on the study of its homologous protein, T cell factor 1 (TCF1), we discovered that LEF1 had a positive regulatory effect on the transcription of PD1 in mature T cells, including CD4+ T cells, CD8+ T cells, and Treg cells. This finding was observed in LEF1 knockout and LEF1-stimulated mice models. Additionally, we confirmed the direct regulation of PD1 by LEF1 in tumor-infiltrating lymphocytes through tumor-implantation experiments. The direct regulation of PD1 by LEF1 was further validated in the LEF1 knockout cell line. The results of our study provide novel perspectives on the regulation of PD1 in immune responses and investigate potential approaches for clinical anti-PD1 therapy.
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Affiliation(s)
- Pin Zhao
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China.
| | - Lanming Sun
- Department of Prevention, Health Care and Fertility, Xinfuli Community Hospital, Linhongnong Road, Dahongmen, Fengtai District, Beijing, China
| | - Cong Zhao
- Department of Prevention, Health Care and Fertility, Xinfuli Community Hospital, Linhongnong Road, Dahongmen, Fengtai District, Beijing, China
| | - Samiullah Malik
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen 518055, China
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8
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Ivanova DL, Thompson SB, Klarquist J, Harbell MG, Kilgore AM, Lasda EL, Hesselberth JR, Hunter CA, Kedl RM. Vaccine adjuvant-elicited CD8 + T cell immunity is co-dependent on T-bet and FOXO1. Cell Rep 2023; 42:112911. [PMID: 37516968 PMCID: PMC10577800 DOI: 10.1016/j.celrep.2023.112911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
T-bet and FOXO1 are transcription factors canonically associated with effector and memory T cell fates, respectively. During an infectious response, these factors direct the development of CD8+ T cell fates, where T-bet deficiency leads to ablation of only short-lived effector cells, while FOXO1 deficiency results in selective loss of memory. In contrast, following adjuvanted subunit vaccination in mice, both effector- and memory-fated T cells are compromised in the absence of either T-bet or FOXO1. Thus, unlike responses to challenge with Listeria monocytogenes, productive CD8+ T cell responses to adjuvanted vaccination require coordinated regulation of FOXO1 and T-bet transcriptional programs. Single-cell RNA sequencing analysis confirms simultaneous T-bet, FOXO1, and TCF1 transcriptional activity in vaccine-elicited, but not infection-elicited, T cells undergoing clonal expansion. Collectively, our data show that subunit vaccine adjuvants elicit T cell responses dependent on transcription factors associated with effector and memory cell fates.
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Affiliation(s)
- Daria L Ivanova
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Scott B Thompson
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jared Klarquist
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael G Harbell
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Augustus M Kilgore
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Erika L Lasda
- Department of Biochemistry & Molecular Genetics, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry & Molecular Genetics, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ross M Kedl
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA.
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9
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Zelenka T, Papamatheakis DA, Tzerpos P, Panagopoulos G, Tsolis KC, Papadakis VM, Mariatos Metaxas D, Papadogkonas G, Mores E, Kapsetaki M, Papamatheakis J, Stanek D, Spilianakis C. A novel SATB1 protein isoform with different biophysical properties. Front Cell Dev Biol 2023; 11:1242481. [PMID: 37635874 PMCID: PMC10457122 DOI: 10.3389/fcell.2023.1242481] [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: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1's mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | | | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Vassilis M. Papadakis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Eleftherios Mores
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Joseph Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - David Stanek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
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10
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Louis TL, Wong WH, Yao P, Kurd NS, Tysl T, Indralingam CS, Ma S, Huang WJM, Chang JT. Regulation of CD8 T Cell Differentiation by the RNA-Binding Protein DDX5. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:241-251. [PMID: 37265401 PMCID: PMC10373580 DOI: 10.4049/jimmunol.2200778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
The RNA-binding protein DEAD-box protein 5 (DDX5) is a polyfunctional regulator of gene expression, but its role in CD8+ T cell biology has not been extensively investigated. In this study, we demonstrate that deletion of DDX5 in murine CD8+ T cells reduced the differentiation of terminal effector, effector memory T, and terminal effector memory cells while increasing the generation of central memory T cells, whereas forced expression of DDX5 elicited the opposite phenotype. DDX5-deficient CD8+ T cells exhibited increased expression of genes that promote central memory T cell differentiation, including Tcf7 and Eomes. Taken together, these findings reveal a role for DDX5 in regulating the differentiation of effector and memory CD8+ T cell subsets in response to microbial infection.
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Affiliation(s)
- Tiani L. Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, USA
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11
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Harris R, Karimi M. Dissecting the regulatory network of transcription factors in T cell phenotype/functioning during GVHD and GVT. Front Immunol 2023; 14:1194984. [PMID: 37441063 PMCID: PMC10333690 DOI: 10.3389/fimmu.2023.1194984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Transcription factors play a major role in regulation and orchestration of immune responses. The immunological context of the response can alter the regulatory networks required for proper functioning. While these networks have been well-studied in canonical immune contexts like infection, the transcription factor landscape during alloactivation remains unclear. This review addresses how transcription factors contribute to the functioning of mature alloactivated T cells. This review will also examine how these factors form a regulatory network to control alloresponses, with a focus specifically on those factors expressed by and controlling activity of T cells of the various subsets involved in graft-versus-host disease (GVHD) and graft-versus-tumor (GVT) responses.
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Affiliation(s)
- Rebecca Harris
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Mobin Karimi
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
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12
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Hao Y, Miraghazadeh B, Chand R, Davies AR, Cardinez C, Kwong K, Downes MB, Sweet RA, Cañete PF, D'Orsogna LJ, Fulcher DA, Choo S, Yip D, Peters G, Yip S, Witney MJ, Nekrasov M, Feng ZP, Tscharke DC, Vinuesa CG, Cook MC. CTLA4 protects against maladaptive cytotoxicity during the differentiation of effector and follicular CD4 + T cells. Cell Mol Immunol 2023:10.1038/s41423-023-01027-8. [PMID: 37161048 PMCID: PMC10166697 DOI: 10.1038/s41423-023-01027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
As chronic antigenic stimulation from infection and autoimmunity is a feature of primary antibody deficiency (PAD), analysis of affected patients could yield insights into T-cell differentiation and explain how environmental exposures modify clinical phenotypes conferred by single-gene defects. CD57 marks dysfunctional T cells that have differentiated after antigenic stimulation. Indeed, while circulating CD57+ CD4+ T cells are normally rare, we found that they are increased in patients with PAD and markedly increased with CTLA4 haploinsufficiency or blockade. We performed single-cell RNA-seq analysis of matched CD57+ CD4+ T cells from blood and tonsil samples. Circulating CD57+ CD4+ T cells (CD4cyt) exhibited a cytotoxic transcriptome similar to that of CD8+ effector cells, could kill B cells, and inhibited B-cell responses. CTLA4 restrained the formation of CD4cyt. While CD57 also marked an abundant subset of follicular helper T cells, which is consistent with their antigen-driven differentiation, this subset had a pre-exhaustion transcriptomic signature marked by TCF7, TOX, and ID3 expression and constitutive expression of CTLA4 and did not become cytotoxic even after CTLA4 inhibition. Thus, CD57+ CD4+ T-cell cytotoxicity and exhaustion phenotypes are compartmentalised between blood and germinal centers. CTLA4 is a key modifier of CD4+ T-cell cytotoxicity, and the pathological CD4cyt phenotype is accentuated by infection.
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Affiliation(s)
- Yuwei Hao
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rochna Chand
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ainsley R Davies
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Chelisa Cardinez
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristy Kwong
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Morgan B Downes
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rebecca A Sweet
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Pablo F Cañete
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Lloyd J D'Orsogna
- Department of Immunology, Fiona Stanley Hospital, Perth, WA, Australia
| | - David A Fulcher
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sharon Choo
- Department of Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Desmond Yip
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Geoffrey Peters
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Unit, The University of Sydney, Sydney, NSW, Australia
| | - Matthew J Witney
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Maxim Nekrasov
- The ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Zhi-Ping Feng
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia.
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- ANU Medical School, The Australian National University, Canberra, ACT, Australia.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.
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13
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Jin J, Mu Y, Zhang H, Sturmlechner I, Wang C, Jadhav RR, Xia Q, Weyand CM, Goronzy JJ. CISH impairs lysosomal function in activated T cells resulting in mitochondrial DNA release and inflammaging. NATURE AGING 2023; 3:600-616. [PMID: 37118554 PMCID: PMC10388378 DOI: 10.1038/s43587-023-00399-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/15/2023] [Indexed: 04/30/2023]
Abstract
Chronic systemic inflammation is one of the hallmarks of the aging immune system. Here we show that activated T cells from older adults contribute to inflammaging by releasing mitochondrial DNA (mtDNA) into their environment due to an increased expression of the cytokine-inducible SH2-containing protein (CISH). CISH targets ATP6V1A, an essential component of the proton pump V-ATPase, for proteasomal degradation, thereby impairing lysosomal function. Impaired lysosomal activity caused intracellular accumulation of multivesicular bodies and amphisomes and the export of their cargos, including mtDNA. CISH silencing in T cells from older adults restored lysosomal activity and prevented amphisomal release. In antigen-specific responses in vivo, CISH-deficient CD4+ T cells released less mtDNA and induced fewer inflammatory cytokines. Attenuating CISH expression may present a promising strategy to reduce inflammation in an immune response of older individuals.
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Affiliation(s)
- Jun Jin
- Multiscale Research Institute for Complex Systems, Fudan University, Shanghai, China.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
- Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Yunmei Mu
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Huimin Zhang
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Chenyao Wang
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Rohit R Jadhav
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Qiong Xia
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Cornelia M Weyand
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jorg J Goronzy
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
- Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA.
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14
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Kumar V, Umair Z, Lee U, Kim J. Two Homeobox Transcription Factors, Goosecoid and Ventx1.1, Oppositely Regulate Chordin Transcription in Xenopus Gastrula Embryos. Cells 2023; 12:cells12060874. [PMID: 36980215 PMCID: PMC10047115 DOI: 10.3390/cells12060874] [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: 01/18/2023] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The reciprocal inhibition between two signaling centers, the Spemann organizer (dorsal mesoderm) and ventral region (mesoderm and ectoderm), collectively regulate the overall development of vertebrate embryos. Each center expresses key homeobox transcription factors (TFs) that directly control target gene transcription. Goosecoid (Gsc) is an organizer (dorsal mesoderm)-specific TF known to induce dorsal fate and inhibit ventral/ectodermal specification. Ventx1.1 (downstream of Bmp signaling) induces the epidermal lineage and inhibits dorsal organizer-specific genes from the ventral region. Chordin (Chrd) is an organizer-specific secreted Bmp antagonist whose expression is primarily activated by Gsc. Alternatively, chrd expression is repressed by Bmp/Ventx1.1 in the ventral/epidermal region. However, the regulatory mechanisms underlying the transcription mediated by Gsc and Ventx1.1 remain elusive. Here, we found that the chrd promoter contained two cis-acting response elements that responded negatively to Ventx1.1 and positively to Gsc. In the ventral/ectodermal region, Ventx1.1 was directly bound to the Ventx1.1 response element (VRE) and inhibited chrd transcription. In the organizer region, Gsc was bound to the Gsc response elements (GRE) to activate chrd transcription. The Gsc-mediated positive response on the chrd promoter completely depended on another adjacent Wnt response cis-acting element (WRE), which was the TCF7 (also known as Tcf1) binding element. Site-directed mutagenesis of VRE, GRE, or WRE completely abolished the repressive or activator activity of Ventx1.1 and Gsc, respectively. The ChIP-PCR results confirmed the direct binding of Ventx1.1 and Gsc/Tcf7 to VRE and GRE/WRE, respectively. These results demonstrated that chrd expression is oppositely modulated by homeobox TFs, Ventx1.1, and Gsc/Tcf7 during the embryonic patterning of Xenopus gastrula.
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Affiliation(s)
- Vijay Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Zobia Umair
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Unjoo Lee
- Department of Electrical Engineering, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (U.L.); (J.K.); Tel.: +82-33-248-2354 (U.L.); +82-33-248-2544 (J.K.)
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (U.L.); (J.K.); Tel.: +82-33-248-2354 (U.L.); +82-33-248-2544 (J.K.)
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15
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Mammadli M, Suo L, Sen JM, Karimi M. TCF-1 Is Required for CD4 T Cell Persistence Functions during AlloImmunity. Int J Mol Sci 2023; 24:ijms24054326. [PMID: 36901757 PMCID: PMC10002223 DOI: 10.3390/ijms24054326] [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: 11/21/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
The transcription factor T cell factor-1 (TCF-1) is encoded by Tcf7 and plays a significant role in regulating immune responses to cancer and pathogens. TCF-1 plays a central role in CD4 T cell development; however, the biological function of TCF-1 on mature peripheral CD4 T cell-mediated alloimmunity is currently unknown. This report reveals that TCF-1 is critical for mature CD4 T cell stemness and their persistence functions. Our data show that mature CD4 T cells from TCF-1 cKO mice did not cause graft versus host disease (GvHD) during allogeneic CD4 T cell transplantation, and donor CD4 T cells did not cause GvHD damage to target organs. For the first time, we showed that TCF-1 regulates CD4 T cell stemness by regulating CD28 expression, which is required for CD4 stemness. Our data showed that TCF-1 regulates CD4 effector and central memory formation. For the first time, we provide evidence that TCF-1 differentially regulates key chemokine and cytokine receptors critical for CD4 T cell migration and inflammation during alloimmunity. Our transcriptomic data uncovered that TCF-1 regulates critical pathways during normal state and alloimmunity. Knowledge acquired from these discoveries will enable us to develop a target-specific approach for treating CD4 T cell-mediated diseases.
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Affiliation(s)
- Mahinbanu Mammadli
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Liye Suo
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jyoti Misra Sen
- National Institute on Aging-National Institute of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
- Center of Aging and Immune Remodeling and Immunology Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Mobin Karimi
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Correspondence: ; Tel.: 315-464-2344
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16
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Woestemeier A, Scognamiglio P, Zhao Y, Wagner J, Muscate F, Casar C, Siracusa F, Cortesi F, Agalioti T, Müller S, Sagebiel A, Konczalla L, Wahib R, Karstens KF, Giannou AD, Duprée A, Wolter S, Wong MN, Mühlig AK, Bielecka AA, Bansal V, Zhang T, Mann O, Puelles VG, Huber TB, Lohse AW, Izbicki JR, Palm NW, Bonn S, Huber S, Gagliani N. Multicytokine-producing CD4+ T cells characterize the livers of patients with NASH. JCI Insight 2023; 8:153831. [PMID: 36625344 PMCID: PMC9870087 DOI: 10.1172/jci.insight.153831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/17/2022] [Indexed: 01/11/2023] Open
Abstract
A role of CD4+ T cells during the progression from nonalcoholic fatty liver disease (NAFLD) to nonalcoholic steatohepatitis (NASH) has been suggested, but which polarization state of these cells characterizes this progression and the development of fibrosis remain unclear. In addition, a gut-liver axis has been suggested to play a role in NASH, but the role of CD4+ T cells in this axis has just begun to be investigated. Combining single-cell RNA sequencing and multiple-parameter flow cytometry, we provide the first cell atlas to our knowledge focused on liver-infiltrating CD4+ T cells in patients with NAFLD and NASH, showing that NASH is characterized by a population of multicytokine-producing CD4+ T cells. Among these cells, only those with a Th17 polarization state were enriched in patients with advanced fibrosis. In parallel, we observed that Bacteroides appeared to be enriched in the intestine of NASH patients and to correlate with the frequency of multicytokine-producing CD4+ T cells. In short, we deliver a CD4+ T cell atlas of NAFLD and NASH, providing the rationale to target CD4+ T cells with a Th17 polarization state to block fibrosis development. Finally, our data offer an early indication to test whether multicytokine-producing CD4+ T cells are part of the gut-liver axis characterizing NASH.
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Affiliation(s)
| | | | - Yu Zhao
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Jonas Wagner
- Department for General, Visceral and Thoracic Surgery
| | | | - Christian Casar
- Department for General, Visceral and Thoracic Surgery
- Bioinformatics Core, and
| | | | | | | | - Simone Müller
- Department for General, Visceral and Thoracic Surgery
| | | | | | - Ramez Wahib
- Department for General, Visceral and Thoracic Surgery
| | | | | | - Anna Duprée
- Department for General, Visceral and Thoracic Surgery
| | - Stefan Wolter
- Department for General, Visceral and Thoracic Surgery
| | - Milagros N. Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Anne K. Mühlig
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- University’s Children Hospital, UKE Hamburg, Hamburg, Germany
| | - Agata A. Bielecka
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Vikas Bansal
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Tianran Zhang
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | - Oliver Mann
- Department for General, Visceral and Thoracic Surgery
| | - Victor G. Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Tobias B. Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Noah W. Palm
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Stefan Bonn
- Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology (ZMNH)
| | | | - Nicola Gagliani
- Department for General, Visceral and Thoracic Surgery
- I Department of Medicine
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
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17
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Wang Y, Yang H, Geerts C, Furtos A, Waters P, Cyr D, Wang S, Mitchell GA. The multiple facets of acetyl-CoA metabolism: Energetics, biosynthesis, regulation, acylation and inborn errors. Mol Genet Metab 2023; 138:106966. [PMID: 36528988 DOI: 10.1016/j.ymgme.2022.106966] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
Acetyl-coenzyme A (Ac-CoA) is a core metabolite with essential roles throughout cell physiology. These functions can be classified into energetics, biosynthesis, regulation and acetylation of large and small molecules. Ac-CoA is essential for oxidative metabolism of glucose, fatty acids, most amino acids, ethanol, and of free acetate generated by endogenous metabolism or by gut bacteria. Ac-CoA cannot cross lipid bilayers, but acetyl groups from Ac-CoA can shuttle across membranes as part of carrier molecules like citrate or acetylcarnitine, or as free acetate or ketone bodies. Ac-CoA is the basic unit of lipid biosynthesis, providing essentially all of the carbon for the synthesis of fatty acids and of isoprenoid-derived compounds including cholesterol, coenzyme Q and dolichols. High levels of Ac-CoA in hepatocytes stimulate lipid biosynthesis, ketone body production and the diversion of pyruvate metabolism towards gluconeogenesis and away from oxidation; low levels exert opposite effects. Acetylation changes the properties of molecules. Acetylation is necessary for the synthesis of acetylcholine, acetylglutamate, acetylaspartate and N-acetyl amino sugars, and to metabolize/eliminate some xenobiotics. Acetylation is a major post-translational modification of proteins. Different types of protein acetylation occur. The most-studied form occurs at the epsilon nitrogen of lysine residues. In histones, lysine acetylation can alter gene transcription. Acetylation of other proteins has diverse, often incompletely-documented effects. Inborn errors related to Ac-CoA feature a broad spectrum of metabolic, neurological and other features. To date, a small number of studies of animals with inborn errors of CoA thioesters has included direct measurement of acyl-CoAs. These studies have shown that low levels of tissue Ac-CoA correlate with the development of clinical signs, hinting that shortage of Ac-CoA may be a recurrent theme in these conditions. Low levels of Ac-CoA could potentially disrupt any of its roles.
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Affiliation(s)
- Youlin Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Hao Yang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Chloé Geerts
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Furtos
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Paula Waters
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Denis Cyr
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Shupei Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Grant A Mitchell
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada.
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18
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Harris R, Mammadli M, Hiner S, Suo L, Yang Q, Sen JM, Karimi M. TCF-1 regulates NKG2D expression on CD8 T cells during anti-tumor responses. Cancer Immunol Immunother 2022; 72:1581-1601. [PMID: 36562825 DOI: 10.1007/s00262-022-03323-0] [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: 07/29/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
Cancer immunotherapy relies on improving T cell effector functions against malignancies, but despite the identification of several key transcription factors (TFs), the biological functions of these TFs are not entirely understood. We developed and utilized a novel, clinically relevant murine model to dissect the functional properties of crucial T cell transcription factors during anti-tumor responses. Our data showed that the loss of TCF-1 in CD8 T cells also leads to loss of key stimulatory molecules such as CD28. Our data showed that TCF-1 suppresses surface NKG2D expression on naïve and activated CD8 T cells via key transcriptional factors Eomes and T-bet. Using both in vitro and in vivo models, we uncovered how TCF-1 regulates critical molecules responsible for peripheral CD8 T cell effector functions. Finally, our unique genetic and molecular approaches suggested that TCF-1 also differentially regulates essential kinases. These kinases, including LCK, LAT, ITK, PLC-γ1, P65, ERKI/II, and JAK/STATs, are required for peripheral CD8 T cell persistent function during alloimmunity. Overall, our molecular and bioinformatics data demonstrate the mechanism by which TCF-1 modulated several critical aspects of T cell function during CD8 T cell response to cancer. Summary Figure: TCF-1 is required for persistent function of CD8 T cells but dispensable for anti-tumor response. Here, we have utilized a novel mouse model that lacks TCF-1 specifically on CD8 T cells for an allogeneic transplant model. We uncovered a molecular mechanism of how TCF-1 regulates key signaling pathways at both transcriptomic and protein levels. These key molecules included LCK, LAT, ITK, PLC-γ1, p65, ERK I/II, and JAK/STAT signaling. Next, we showed that the lack of TCF-1 impacted phenotype, proinflammatory cytokine production, chemokine expression, and T cell activation. We provided clinical evidence for how these changes impact GVHD target organs (skin, small intestine, and liver). Finally, we provided evidence that TCF-1 regulates NKG2D expression on mouse naïve and activated CD8 T cells. We have shown that CD8 T cells from TCF-1 cKO mice mediate cytolytic functions via NKG2D.
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Affiliation(s)
- Rebecca Harris
- Department of Microbiology and Immunology, SUNY Upstate Medical University, 766 Irving Ave Weiskotten Hall Suite 2281, Syracuse, NY, 13210, USA
| | - Mahinbanu Mammadli
- Department of Microbiology and Immunology, SUNY Upstate Medical University, 766 Irving Ave Weiskotten Hall Suite 2281, Syracuse, NY, 13210, USA
| | - Shannon Hiner
- Department of Microbiology and Immunology, SUNY Upstate Medical University, 766 Irving Ave Weiskotten Hall Suite 2281, Syracuse, NY, 13210, USA
| | - Liye Suo
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Qi Yang
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School Rutgers Child Health Institute of New Jersey, New Brunswick, NJ, 08901, USA
| | - Jyoti Misra Sen
- National Institute On Aging-National Institutes of Health, BRC Building, 251 Bayview Boulevard, Suite 100, Baltimore, MD, 21224, USA.,Center On Aging and Immune Remodeling and Immunology Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21224, USA
| | - Mobin Karimi
- Department of Microbiology and Immunology, SUNY Upstate Medical University, 766 Irving Ave Weiskotten Hall Suite 2281, Syracuse, NY, 13210, USA.
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19
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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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20
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He Q, Lu Y, Tian W, Jiang R, Yu W, Liu Y, Sun M, Wang F, Zhang H, Wu N, Dong Z, Sun B. TOX deficiency facilitates the differentiation of IL-17A-producing γδ T cells to drive autoimmune hepatitis. Cell Mol Immunol 2022; 19:1102-1116. [PMID: 35986136 PMCID: PMC9508111 DOI: 10.1038/s41423-022-00912-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/28/2022] [Indexed: 11/08/2022] Open
Abstract
The specification of the αβ/γδ lineage and the maturation of medullary thymic epithelial cells (mTECs) coordinate central tolerance to self-antigens. However, the mechanisms underlying this biological process remain poorly clarified. Here, we report that dual-stage loss of TOX in thymocytes hierarchically impaired mTEC maturation, promoted thymic IL-17A-producing γδ T-cell (Tγδ17) lineage commitment, and led to the development of fatal autoimmune hepatitis (AIH) via different mechanisms. Transfer of γδ T cells from TOX-deficient mice reproduced AIH. TOX interacted with and stabilized the TCF1 protein to maintain the balance of γδ T-cell development in thymic progenitors, and overexpression of TCF1 normalized αβ/γδ lineage specification and activation. In addition, TOX expression was downregulated in γδ T cells from AIH patients and was inversely correlated with the AIH diagnostic score. Our findings suggest multifaceted roles of TOX in autoimmune control involving mTEC and Tγδ17 development and provide a potential diagnostic marker for AIH.
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Affiliation(s)
- Qifeng He
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yijun Lu
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenfang Tian
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Runqiu Jiang
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiwei Yu
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yong Liu
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Meiling Sun
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fei Wang
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Haitian Zhang
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ning Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhongjun Dong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China.
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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21
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Arnovitz S, Mathur P, Tracy M, Mohsin A, Mondal S, Quandt J, Hernandez KM, Khazaie K, Dose M, Emmanuel AO, Gounari F. Tcf-1 promotes genomic instability and T cell transformation in response to aberrant β-catenin activation. Proc Natl Acad Sci U S A 2022; 119:e2201493119. [PMID: 35921443 PMCID: PMC9371646 DOI: 10.1073/pnas.2201493119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/06/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms promoting chromosomal translocations of the rearranging receptor loci in leukemia and lymphoma remains incomplete. Here we show that leukemias induced by aberrant activation of β-catenin in thymocytes, which bear recurrent Tcra/Myc-Pvt1 translocations, depend on Tcf-1. The DNA double strand breaks (DSBs) in the Tcra site of the translocation are Rag-generated, whereas the Myc-Pvt1 DSBs are not. Aberrantly activated β-catenin redirects Tcf-1 binding to novel DNA sites to alter chromatin accessibility and down-regulate genome-stability pathways. Impaired homologous recombination (HR) DNA repair and replication checkpoints lead to retention of DSBs that promote translocations and transformation of double-positive (DP) thymocytes. The resulting lymphomas, which resemble human T cell acute lymphoblastic leukemia (T-ALL), are sensitive to PARP inhibitors (PARPis). Our findings indicate that aberrant β-catenin signaling contributes to translocations in thymocytes by guiding Tcf-1 to promote the generation and retention of replication-induced DSBs allowing their coexistence with Rag-generated DSBs. Thus, PARPis could offer therapeutic options in hematologic malignancies with active Wnt/β-catenin signaling.
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Affiliation(s)
- Stephen Arnovitz
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Priya Mathur
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Melissa Tracy
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Azam Mohsin
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Soumi Mondal
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Jasmin Quandt
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | | | | | - Marei Dose
- Department of Medicine, University of Chicago, Chicago, IL 60637
| | | | - Fotini Gounari
- Department of Medicine, University of Chicago, Chicago, IL 60637
- Department of Immunology, Mayo Clinic, Scottsdale, AZ 85259
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22
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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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23
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Qiu C, Du G. Loss of
LEF
‐1 expression as a diagnostic indicator for extranodal
NK
/T‐cell lymphoma: An immunohistochemical study of 88 cases. Eur J Haematol 2022; 109:513-518. [PMID: 35871391 DOI: 10.1111/ejh.13836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Cen Qiu
- Department of Pathology, the Ninth People's Hospital Shanghai Jiaotong University School of Medicine China
| | - Guangye Du
- Department of Pathology, the Ninth People's Hospital Shanghai Jiaotong University School of Medicine China
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24
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Zhao C, Xu G, Zhang X, Ye Y, Cai W, Shao Q. RNA m6A modification orchestrates the rhythm of immune cell development from hematopoietic stem cells to T and B cells. Front Immunol 2022; 13:839291. [PMID: 35935968 PMCID: PMC9354743 DOI: 10.3389/fimmu.2022.839291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/28/2022] [Indexed: 11/15/2022] Open
Abstract
RNA, one of the major building blocks of the cell, participates in many essential life processes. RNA stability is well-established to be closely related to various RNA modifications. To date, hundreds of different RNA modifications have been identified. N6-methyladenosine (m6A) is one of the most important RNA modifications in mammalian cells. An increasing body of evidence from recently published studies suggests that m6A modification is a novel immune system regulator of the generation and differentiation of hematopoietic stem cells (HSCs) and immune cells. In this review, we introduce the process and relevant regulatory mechanisms of m6A modification; summarize recent findings of m6A in controlling HSC generation and self-renewal, and the development and differentiation of T and B lymphocytes from HSCs; and discuss the potential mechanisms involved.
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Affiliation(s)
- Chuanxiang Zhao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Guoying Xu
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Xiaoxian Zhang
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Yunfeng Ye
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Qixiang Shao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
- Reproductive Sciences Institute, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
- *Correspondence: Qixiang Shao,
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25
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Xie Q, Xue W. IgE-Mediated food allergy: Current diagnostic modalities and novel biomarkers with robust potential. Crit Rev Food Sci Nutr 2022; 63:10148-10172. [PMID: 35587740 DOI: 10.1080/10408398.2022.2075312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Food allergy (FA) is a serious public health issue afflicting millions of people globally, with an estimated prevalence ranging from 1-10%. Management of FA is challenging due to overly restrictive diets and the lack of diagnostic approaches with high accuracy and prediction. Although measurement of serum-specific antibodies combined with patient medical history and skin prick test is a useful diagnostic tool, it is still an imprecise predictor of clinical reactivity with a high false-positive rate. The double-blind placebo-controlled food challenge represents the gold standard for FA diagnosis; however, it requires large healthcare and involves the risk of acute onset of allergic reactions. Improvement in our understanding of the molecular mechanism underlying allergic disease pathology, development of omics-based methods, and advances in bioinformatics have boosted the generation of a number of robust diagnostic biomarkers of FA. In this review, we discuss how traditional diagnostic modalities guide appropriate diagnosis and management of FA in clinical practice, as well as uncover the potential of the latest biomarkers for the diagnosis, monitoring, and prediction of FA. We also raise perspectives for precise and targeted medical intervention to fill the gap in the diagnosis of FA.
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Affiliation(s)
- Qiang Xie
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
| | - Wentong Xue
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
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26
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Liu Y, Ni M, Li L, Wang J, Tu Z, Zhou H, Zhang S. A novel four-gene signature predicts immunotherapy response of patients with different cancers. J Clin Lab Anal 2022; 36:e24494. [PMID: 35588138 PMCID: PMC9279975 DOI: 10.1002/jcla.24494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/10/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Background Immune checkpoint blockade (ICB) therapy has demonstrated favorable clinical efficacy, particularly for advanced or difficult‐to‐treat cancer types. However, this therapy is ineffective for many patients displaying lack of immune response or resistance to ICB. This study aimed to establish a novel four‐gene signature (CD8A, CD8B, TCF7, and LEF1) to provide a prognostic immunotherapy biomarker for different cancers. Methods Transcriptome profiles and clinical data were obtained from The Cancer Genome Atlas database. Multivariate Cox regression analysis was used to establish a four‐gene signature. The R package estimate was used to obtain the immune score for every patient. Results Risk scores of the novel four‐gene signature could effectively divided all patients into high‐ and low‐risk groups, with distinct outcomes. The immune score calculated via the estimate package demonstrated that the four‐gene signature was significantly associated with the immune infiltration level. Furthermore, the four‐gene signature could predict the response to atezolizumab immunotherapy in patients with metastatic urothelial cancer. Conclusions The novel four‐gene signature developed in this study is a good prognostic biomarker, as it could identify many kinds of patients with cancer who are likely to respond to and benefit from immunotherapy.
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Affiliation(s)
- Yuanli Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Mingyue Ni
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Lamei Li
- Department of Dermatology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Junyan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Clinical Medicine (5+3 Programme), Anhui Medical University, Hefei, China
| | - Zhenzhen Tu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Haisheng Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Siping Zhang
- Department of Dermatology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China
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27
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Jerby-Arnon L, Regev A. DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data. Nat Biotechnol 2022; 40:1467-1477. [PMID: 35513526 PMCID: PMC9547813 DOI: 10.1038/s41587-022-01288-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/15/2022] [Indexed: 12/22/2022]
Abstract
Deciphering the functional interactions of cells in tissues remains a major challenge. We describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs) — combinations of coordinated cellular programs in different cell types that form higher-order functional units at the tissue level — from either spatial data or single-cell data obtained without spatial information. Tested on spatial datasets from the mouse hypothalamus, cerebellum, visual cortex, and neocortex, DIALOGUE identified MCPs associated with animal behavior and recovered spatial properties when tested on unseen data, while outperforming other methods and metrics. In spatial data from human lung cancer, DIALOGUE identified MCPs marking immune activation and tissue remodeling. Applied to scRNA-seq data across individuals or regions, DIALOGUE uncovered MCPs in Alzheimer’s disease, ulcerative colitis, and treatment with cancer immunotherapy. These programs were predictive of disease outcome and predisposition in independent cohorts and included risk genes from genome-wide association studies (GWAS). DIALOGUE enables the analysis of multicellular regulation in health and disease. Coordinated gene programs spanning multiple different cell types are identified in healthy and diseased tissues.
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Affiliation(s)
- Livnat Jerby-Arnon
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
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28
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TCF-1: a maverick in T cell development and function. Nat Immunol 2022; 23:671-678. [PMID: 35487986 PMCID: PMC9202512 DOI: 10.1038/s41590-022-01194-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
The T cell-specific DNA-binding protein TCF-1 is a central regulator of T cell development and function along multiple stages and lineages. Because it interacts with β-catenin, TCF-1 has been classically viewed as a downstream effector of canonical Wnt signaling, although there is strong evidence for β-catenin-independent TCF-1 functions. TCF-1 co-binds accessible regulatory regions containing or lacking its conserved motif and cooperates with other nuclear factors to establish context-dependent epigenetic and transcription programs that are essential for T cell development and for regulating immune responses to infection, autoimmunity and cancer. Although it has mostly been associated with positive regulation of chromatin accessibility and gene expression, TCF-1 has the potential to reduce chromatin accessibility and thereby suppress gene expression. In addition, the binding of TCF-1 bends the DNA and affects the chromatin conformation genome wide. This Review discusses the current understanding of the multiple roles of TCF-1 in T cell development and function and their mechanistic underpinnings.
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Ji C, Bao L, Yuan S, Qi Z, Wang F, You M, Yu G, Liu J, Cui X, Wang Z, Liu J, Guo W, Feng M, Chen F, Kang Y, Yu S. SRSF1 Deficiency Impairs the Late Thymocyte Maturation and the CD8 Single-Positive Lineage Fate Decision. Front Immunol 2022; 13:838719. [PMID: 35154164 PMCID: PMC8825371 DOI: 10.3389/fimmu.2022.838719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
The underlying mechanisms of thymocyte development and lineage determination remain incompletely understood, and the emerging evidences demonstrated that RNA binding proteins (RBPs) are deeply involved in governing T cell fate in thymus. Serine/arginine-rich splicing factor 1 (SRSF1), as a classical splicing factor, is a pivotal RBP for gene expression in various biological processes. Our recent study demonstrated that SRSF1 plays essential roles in the development of late thymocytes by modulating the T cell regulatory gene networks post-transcriptionally, which are critical in response to type I interferon signaling for supporting thymocyte maturation. Here, we report SRSF1 also contributes to the determination of the CD8+ T cell fate. By specific ablation of SRSF1 in CD4+CD8+ double positive (DP) thymocytes, we found that SRSF1 deficiency impaired the maturation of late thymocytes and diminished the output of both CD4+ and CD8+ single positive T cells. Interestingly, the ratio of mature CD4+ to CD8+ cells was notably altered and more severe defects were exhibited in CD8+ lineage than those in CD4+ lineage, reflecting the specific function of SRSF1 in CD8+ T cell fate decision. Mechanistically, SRSF1-deficient cells downregulate their expression of Runx3, which is a crucial transcriptional regulator in sustaining CD8+ single positive (SP) thymocyte development and lineage choice. Moreover, forced expression of Runx3 partially rectified the defects in SRSF1-deficient CD8+ thymocyte maturation. Thus, our data uncovered the previous unknown role of SRSF1 in establishment of CD8+ cell identity.
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Affiliation(s)
- Ce Ji
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Li Bao
- Department of Hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Shunzong Yuan
- Department of Hematology, The Fifth Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhihong Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fang Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Menghao You
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guotao Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jingjing Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao Cui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Juanjuan Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenhui Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Mingxia Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Chen
- Central Laboratory, School of Stomatology, Peking University, Beijing, China
| | - Youmin Kang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Abstract
TCF1 and its homologue LEF1 are historically known as effector transcription factors downstream of the WNT signalling pathway and are essential for early T cell development. Recent advances bring TCF1 into the spotlight for its versatile, context-dependent functions in regulating mature T cell responses. In the cytotoxic T cell lineages, TCF1 is required for the self-renewal of stem-like CD8+ T cells generated in response to viral or tumour antigens, and for preserving heightened responses to checkpoint blockade immunotherapy. In the helper T cell lineages, TCF1 is indispensable for the differentiation of T follicular helper and T follicular regulatory cells, and crucially regulates immunosuppressive functions of regulatory T cells. Mechanistic investigations have also identified TCF1 as the first transcription factor that directly modifies histone acetylation, with the capacity to bridge transcriptional and epigenetic regulation. TCF1 also has the potential to become an important clinical biomarker for assessing the prognosis of tumour immunotherapy and the success of viral control in treating HIV and hepatitis C virus infection. Here, we summarize the key findings on TCF1 across the fields of T cell immunity and reflect on the possibility of exploring TCF1 and its downstream transcriptional programmes as therapeutic targets for improving antiviral and antitumour immunity.
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Tcf1 preprograms the mobilization of glycolysis in central memory CD8 + T cells during recall responses. Nat Immunol 2022; 23:386-398. [PMID: 35190717 PMCID: PMC8904300 DOI: 10.1038/s41590-022-01131-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
Abstract
The mechanisms underlying the heightened protection mediated by central memory CD8+ T (TCM) cells remain unclear. Here we show that the transcription factor Tcf1 was required in resting TCM cells to generate secondary effector CD8+ T cells and to clear pathogens during recall responses. Recall stimulation of CD8+ TCM cells caused extensive reprogramming of the transcriptome and chromatin accessibility, leading to rapid induction of glycolytic enzymes, cell cycle regulators and transcriptional regulators, including Id3. This cluster of genes did not require Tcf1 in resting CD8+ TCM cells, but depended on Tcf1 for optimal induction and chromatin opening in recall-stimulated CD8+ TCM cells. Tcf1 bound extensively to these recall-induced gene loci in resting CD8+ TCM cells and mediated chromatin interactions that positioned these genes in architectural proximity with poised enhancers. Thus, Tcf1 preprogramed a transcriptional program that supported the bioenergetic and proliferative needs of CD8+ TCM cells in case of a secondary challenge.
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Tcf1 and Lef1 provide constant supervision to mature CD8 + T cell identity and function by organizing genomic architecture. Nat Commun 2021; 12:5863. [PMID: 34615872 PMCID: PMC8494933 DOI: 10.1038/s41467-021-26159-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 09/17/2021] [Indexed: 02/01/2023] Open
Abstract
T cell identity is established during thymic development, but how it is maintained in the periphery remains unknown. Here we show that ablating Tcf1 and Lef1 transcription factors in mature CD8+ T cells aberrantly induces genes from non-T cell lineages. Using high-throughput chromosome-conformation-capture sequencing, we demonstrate that Tcf1/Lef1 are important for maintaining three-dimensional genome organization at multiple scales in CD8+ T cells. Comprehensive network analyses coupled with genome-wide profiling of chromatin accessibility and Tcf1 occupancy show the direct impact of Tcf1/Lef1 on the T cell genome is to promote formation of extensively interconnected hubs through enforcing chromatin interaction and accessibility. The integrative mechanisms utilized by Tcf1/Lef1 underlie activation of T cell identity genes and repression of non-T lineage genes, conferring fine control of various T cell functionalities. These findings suggest that Tcf1/Lef1 control global genome organization and help form intricate chromatin-interacting hubs to facilitate promoter-enhancer/silencer contact, hence providing constant supervision of CD8+ T cell identity and function. How CD8+ T cell identity is maintained after exit from the thymus is not fully established. Here the authors use multiomics approaches including Hi-C to show that Tcf1 and Lef1 prevent aberrant expression of lineage-inappropriate genes by organizing three-dimensional genomic architecture in CD8+ T cells.
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Saxena V, Lakhan R, Iyyathurai J, Bromberg JS. Mechanisms of exTreg induction. Eur J Immunol 2021; 51:1956-1967. [PMID: 33975379 PMCID: PMC8338747 DOI: 10.1002/eji.202049123] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/19/2021] [Accepted: 05/10/2021] [Indexed: 12/18/2022]
Abstract
CD4+ CD25+ Foxp3+ Tregs play an important role in the maintenance of the immune system by regulating immune responses and resolving inflammation. Tregs exert their function by suppressing other immune cells and mediating peripheral self-tolerance. Under homeostatic conditions, Tregs are stable T-cell populations. However, under inflammatory environments, Tregs are converted to CD4+ CD25low Foxp3low cells. These cells are termed "exTreg" or "exFoxp3" cells. The molecular mechanism of Treg transition to exTregs remains incompletely understood. Uncertainties might be explained by a lack of consensus of biological markers to define Treg subsets in general and exTregs in particular. In this review, we summarize known markers of Tregs and factors responsible for exTreg generation including cytokines, signaling pathways, transcription factors, and epigenetic mechanisms. We also identify studies demonstrating the presence of exTregs in various diseases and sources of exTregs. Understanding the biology of Treg transition to exTregs will help in designing Treg-based therapeutic approaches.
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Affiliation(s)
- Vikas Saxena
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ram Lakhan
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jegan Iyyathurai
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jonathan S. Bromberg
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Zhang J, Lyu T, Cao Y, Feng H. Role of TCF-1 in differentiation, exhaustion, and memory of CD8 + T cells: A review. FASEB J 2021; 35:e21549. [PMID: 33913198 DOI: 10.1096/fj.202002566r] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/14/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022]
Abstract
T cell factor-1 (TCF-1) (encoded by the TCF7 gene) is a transcription factor that plays important role during the T cell development and differentiation for T cell to exercise its functions including producing memory T cells. Not only TCF-1 can modulate the T cell development but also exerts various effects on the differentiation and function of mature CD8+ T cells. In addition, it drives the production and maintenance of the immune response of CD8+ T cells after PD-1 checkpoint blockade therapy. TCF-1 can serve as a potential target of immunotherapy and may provide promising novel treatment strategies for patients with cancer and infections. Moreover, TCF-1 is a potential biomarker of CD8+ T cell functionality to predict the efficacy of immunotherapy in fighting against cancer and infections. Herein, we summarize the role of TCF-1 in T cell development and its applications in the treatment of cancer and infectious diseases.
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Affiliation(s)
- Jiaxue Zhang
- The First Clinical Medicine Faculty, China Medical University, Shenyang, Liaoning Province, China
| | - Tong Lyu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Hui Feng
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
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Abstract
Cytotoxic CD4 T lymphocytes (CD4-CTL) are important in anti-viral immunity. For example, we have previously shown that in mice, CD4-CTL are important to control ectromelia virus (ECTV) infection. How viral infections induce CD4-CTL responses remains incompletely understood. Here we demonstrate that not only ECTV but also vaccinia virus and Lymphocytic Choriomeningitis virus induce CD4-CTL, but that the response to ECTV is stronger. Using ECTV, we also demonstrate that in contrast to CD8-CTL, CD4-CTL differentiation requires constant virus replication and ceases once the virus is controlled. We also show that Major Histocompatibility Complex Class II molecules on CD11c+ cells are required for CD4-CTL differentiation and for mousepox resistance. Transcriptional analysis indicated that anti-viral CD4-CTL and non-cytolytic T Helper 1 (Th1) CD4 T cells have similar transcriptional profiles, suggesting that CD4-CTL are terminally differentiated classical Th1 cells. Interestingly, CD4-CTL and classical Th1 cells expressed similar mRNA levels of the transcription factors ThPOK and GATA-3, necessary for CD4 T cell linage commitment; and Runx3, required for CD8 T cell development and effector function. However, at the protein level, CD4-CTL had higher levels of the three transcription factors suggesting that further post-transcriptional regulation is required for CD4-CTL differentiation. Finally, using CRISPR-Cas9 deletion of Runx3 in CD4 T cells, we demonstrate that the development of CD4-CTL but not of classical Th1 CD4 T cells requires Runx3 following ECTV infection. These results further our understanding of the mechanisms of CD4-CTL differentiation during viral infection and the role of post-transcriptionally regulated Runx3 in this process. IMPORTANCE While it is well established that cytotoxic CD4 T cells (CD4-CTL) directly contribute to viral clearance, it remains unclear how CD4-CTL are induced. We now show that CD4-CTL require sustained antigen presentation and are induced by CD11c-expressing antigen presenting cells. Moreover, we show that CD4-CTL are derived from the terminal differentiation of classical T helper 1 (Th1) subset of CD4 cells. Compared to Th1 cells, CD4-CTL upregulate protein levels of the transcription factors ThPOK, Runx3 and GATA-3 post-transcriptionally. Deletion of Runx3 in differentiated CD4 T cells prevents CD4-CTL but not of classical Th1 cells. These results advance our knowledge of how CD4-CTL are induced during viral infection.
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Wen S, Lu H, Wang D, Guo J, Dai W, Wang Z. TCF-1 maintains CD8 + T cell stemness in tumor microenvironment. J Leukoc Biol 2021; 110:585-590. [PMID: 34047386 DOI: 10.1002/jlb.5mr1120-778r] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/01/2021] [Accepted: 04/30/2021] [Indexed: 01/22/2023] Open
Abstract
T cell factor 1 (TCF-1) is a transcription factor (TF) of the canonical Wnt signaling pathway that encoded by the Tcf7. The crucial role of TCF-1 in T cell development and memory formation has been widely recognized. Recent studies have demonstrated that exhausted CD8+ T cell with the expression of TCF-1 may have inspiring function to amplify immunoreaction and improve the response to immunotherapy in chronic viral infection and cancer. In this short review, we summarized recent progress in intratumoral exhausted CD8+ T cells expressing TCF-1 that represent a fantastic subset with stem cell-like properties that associated with improved antitumor immunity and response to immune checkpoint blockade (ICB).
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Affiliation(s)
- Shuqiong Wen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Huanzi Lu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Dikan Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Junyi Guo
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Wenxiao Dai
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Zhi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
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T FH cells depend on Tcf1-intrinsic HDAC activity to suppress CTLA4 and guard B-cell help function. Proc Natl Acad Sci U S A 2021; 118:2014562118. [PMID: 33372138 DOI: 10.1073/pnas.2014562118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Precise regulation of coinhibitory receptors is essential for maintaining immune tolerance without interfering with protective immunity, yet the mechanism underlying such a balanced act remains poorly understood. In response to protein immunization, T follicular helper (TFH) cells lacking Tcf1 and Lef1 transcription factors were phenotypically normal but failed to promote germinal center formation and antibody production. Transcriptomic profiling revealed that Tcf1/Lef1-deficient TFH cells aberrantly up-regulated CTLA4 and LAG3 expression, and treatment with anti-CTLA4 alone or combined with anti-LAG3 substantially rectified B-cell help defects by Tcf1/Lef1-deficient TFH cells. Mechanistically, Tcf1 and Lef1 restrain chromatin accessibility at the Ctla4 and Lag3 loci. Groucho/Tle corepressors, which are known to cooperate with Tcf/Lef factors, were essential for TFH cell expansion but dispensable for repressing coinhibitory receptors. In contrast, mutating key amino acids in histone deacetylase (HDAC) domain in Tcf1 resulted in CTLA4 derepression in TFH cells. These findings demonstrate that Tcf1-instrinsic HDAC activity is necessary for preventing excessive CTLA4 induction in protein immunization-elicited TFH cells and hence guarding their B-cell help function.
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Li ZY, Morman RE, Hegermiller E, Sun M, Bartom ET, Maienschein-Cline M, Sigvardsson M, Kee BL. The transcriptional repressor ID2 supports natural killer cell maturation by controlling TCF1 amplitude. J Exp Med 2021; 218:211997. [PMID: 33857289 PMCID: PMC8056751 DOI: 10.1084/jem.20202032] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/07/2021] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
Gaining a mechanistic understanding of the expansion and maturation program of natural killer (NK) cells will provide opportunities for harnessing their inflammation-inducing and oncolytic capacity for therapeutic purposes. Here, we demonstrated that ID2, a transcriptional regulatory protein constitutively expressed in NK cells, supports NK cell effector maturation by controlling the amplitude and temporal dynamics of the transcription factor TCF1. TCF1 promotes immature NK cell expansion and restrains differentiation. The increased TCF1 expression in ID2-deficient NK cells arrests their maturation and alters cell surface receptor expression. Moreover, TCF1 limits NK cell functions, such as cytokine-induced IFN-γ production and the ability to clear metastatic melanoma in ID2-deficient NK cells. Our data demonstrate that ID2 sets a threshold for TCF1 during NK cell development, thus controlling the balance of immature and terminally differentiated cells that support future NK cell responses.
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Affiliation(s)
- Zhong-Yin Li
- Department of Pathology, Committees on Immunology and Cancer Biology, The University of Chicago, Chicago, IL
| | - Rosemary E Morman
- Department of Pathology, Committees on Immunology and Cancer Biology, The University of Chicago, Chicago, IL
| | - Emma Hegermiller
- Department of Pathology, Committees on Immunology and Cancer Biology, The University of Chicago, Chicago, IL
| | - Mengxi Sun
- Department of Pathology, Committees on Immunology and Cancer Biology, The University of Chicago, Chicago, IL
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Mark Maienschein-Cline
- Core for Research Informatics, Research Resources Center, University of Illinois at Chicago, Chicago, IL
| | - Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Faculty for Health Sciences, Linköping University, Linköping, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden
| | - Barbara L Kee
- Department of Pathology, Committees on Immunology and Cancer Biology, The University of Chicago, Chicago, IL.,University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
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E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. Proc Natl Acad Sci U S A 2021; 118:2013452118. [PMID: 33859041 DOI: 10.1073/pnas.2013452118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During an acute viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off individual T cells on their own differentiation trajectories. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection-death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the transcriptional changes during effector and memory CD8 T cell differentiation at the single-cell level. Using single-cell, transcriptome-derived gene regulatory network analysis, we identified two main groups of regulons that govern this differentiation process. These regulons function in concert with changes in the enhancer landscape to confer the establishment of the regulatory modules underlying the cell fate decision of CD8 T cells. Furthermore, we found that memory precursor effector cells maintain chromatin accessibility at enhancers for key memory-related genes and that these enhancers are highly enriched for E2A binding sites. Finally, we show that E2A directly regulates accessibility of enhancers of many memory-related genes and that its overexpression increases the frequency of memory precursor effector cells and accelerates memory cell formation while decreasing the frequency of short-lived effector cells. Overall, our results suggest that effector and memory CD8 T cell differentiation is largely regulated by two transcriptional circuits, with E2A serving as an important epigenetic regulator of the memory circuit.
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Qi Z, Wang F, Yu G, Wang D, Yao Y, You M, Liu J, Liu J, Sun Z, Ji C, Xue Y, Yu S. SRSF1 serves as a critical posttranscriptional regulator at the late stage of thymocyte development. SCIENCE ADVANCES 2021; 7:7/16/eabf0753. [PMID: 33863728 PMCID: PMC8051871 DOI: 10.1126/sciadv.abf0753] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/25/2021] [Indexed: 05/05/2023]
Abstract
The underlying mechanisms of thymocyte maturation remain largely unknown. Here, we report that serine/arginine-rich splicing factor 1 (SRSF1) intrinsically regulates the late stage of thymocyte development. Conditional deletion of SRSF1 resulted in severe defects in maintenance of late thymocyte survival and a blockade of the transition of TCRβhiCD24+CD69+ immature to TCRβhiCD24-CD69- mature thymocytes, corresponding to a notable reduction of recent thymic emigrants and diminished periphery T cell pool. Mechanistically, SRSF1 regulates the gene networks involved in thymocyte differentiation, proliferation, apoptosis, and type I interferon signaling pathway to safeguard T cell intrathymic maturation. In particular, SRSF1 directly binds and regulates Irf7 and Il27ra expression via alternative splicing in response to type I interferon signaling. Moreover, forced expression of interferon regulatory factor 7 rectifies the defects in SRSF1-deficient thymocyte maturation via restoring expression of type I interferon-related genes. Thus, our work provides new insight on SRSF1-mediated posttranscriptional regulatory mechanism of thymocyte development.
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Affiliation(s)
- Zhihong Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fang Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Guotao Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Di Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingpeng Yao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Menghao You
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jingjing Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Juanjuan Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ce Ji
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Kaur KD, Wong CK, Baggio LL, Beaudry JL, Fuchs S, Panaro BL, Matthews D, Cao X, Drucker DJ. TCF7 is not essential for glucose homeostasis in mice. Mol Metab 2021; 48:101213. [PMID: 33741532 PMCID: PMC8086146 DOI: 10.1016/j.molmet.2021.101213] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/15/2022] Open
Abstract
Objective Glucose-dependent insulinotropic polypeptide (GIP) and Glucagon-like peptide-1 (GLP-1) are incretin hormones that exert overlapping yet distinct actions on islet β-cells. We recently observed that GIP, but not GLP-1, upregulated islet expression of Transcription Factor 7 (TCF7), a gene expressed in immune cells and associated with the risk of developing type 1 diabetes. TCF7 has also been associated with glucose homeostasis control in the liver. Herein we studied the relative metabolic importance of TCF7 expression in hepatocytes vs. islet β-cells in mice. Methods Tcf7 expression was selectively inactivated in adult mouse hepatocytes using adenoviral Cre expression and targeted in β-cells using two different lines of insulin promoter-Cre mice. Glucose homeostasis, plasma insulin and triglyceride responses, islet histology, hepatic and islet gene expression, and body weight gain were evaluated in mice fed regular chow or high fat diets. Tcf7 expression within pancreatic islets and immune cells was evaluated using published single cell RNA-seq (scRNA-seq) data, and in islet RNA from immunodeficient Rag2−/−Il2rg−/− mice. Results Reduction of hepatocyte Tcf7 expression did not impair glucose homeostasis, lipid tolerance or hepatic gene expression profiles linked to control of metabolic or immune pathways. Similarly, oral and intraperitoneal glucose tolerance, plasma insulin responses, islet histology, body weight gain, and insulin tolerance were not different in mice with targeted recombination of Tcf7 in insulin-positive β-cells. Surprisingly, islet Tcf7 mRNA transcripts were not reduced in total islet RNA containing endocrine and associated non-endocrine cell types from Tcf7βcell−/− mice, despite Cre-mediated recombination of islet genomic DNA. Furthermore, glucose tolerance was normal in whole body Tcf7−/− mice. Analysis of scRNA-seq datasets localized pancreatic Tcf7 expression to islet progenitors during development, and immune cells, but not within differentiated islet β-cells or endocrine lineages within mature islets. Moreover, the expression of Tcf7 was extremely low in islet RNA from Rag2−/−Il2rg−/− mice and, consistent with expression within immune cells, Tcf7 was highly correlated with levels of Cd3g mRNA transcripts in RNA from wild type mouse islets. Conclusions These findings demonstrate that Tcf7 expression is not a critical determinant of glucose homeostasis in mice. Moreover, the detection of Tcf7 expression within islet mRNA is attributable to the expression of Tcf7 RNA in islet-associated murine immune cells, and not in islet β-cells. •Reduction of hepatocyte Tcf7 does not impair glucose homeostasis. •Targeting beta cell Tcf7 using insulin-promoter-Cre does not reduce islet Tcf7 expression. •RNA-seq localizes pancreatic Tcf7 to islet progenitors and lymphocytes. •Tcf7 expression is markedly reduced in islet RNA from Rag2−/−Il2rg−/− mice.
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Affiliation(s)
- Kiran Deep Kaur
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Chi Kin Wong
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Laurie L Baggio
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Jacqueline L Beaudry
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Shai Fuchs
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Brandon L Panaro
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Dianne Matthews
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Xiemin Cao
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada
| | - Daniel J Drucker
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, ON, M5G1X5, Canada.
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42
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Schroeder AR, Zhu F, Hu H. Stepwise Tfh cell differentiation revisited: new advances and long-standing questions. Fac Rev 2021; 10. [PMID: 33644779 PMCID: PMC7894273 DOI: 10.12703/r/10-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
T follicular helper (Tfh) cells play an essential role in germinal center formation and the generation of high-affinity antibodies. Studies have proposed that Tfh cell differentiation is a multi-step process. However, it is still not fully understood how a subset of activated CD4+ T cells begin to express CXCR5 during the early stage of the response and, shortly after, how some CXCR5+ precursor Tfh (pre-Tfh) cells enter B cell follicles and differentiate further into germinal center Tfh (GC-Tfh) cells while others have a different fate. In this mini-review, we summarize the recent advances surrounding these two aspects of Tfh cell differentiation and discuss related long-standing questions, including Tfh memory.
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Affiliation(s)
- Andrew R Schroeder
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Fangming Zhu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hui Hu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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43
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Wang F, Qi Z, Yao Y, Yu G, Feng T, Zhao T, Xue HH, Zhao Y, Jiang P, Bao L, Yu S. Exploring the stage-specific roles of Tcf-1 in T cell development and malignancy at single-cell resolution. Cell Mol Immunol 2021; 18:644-659. [PMID: 32868912 PMCID: PMC8027857 DOI: 10.1038/s41423-020-00527-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
Tcf-1 (encoded by Tcf7) not only plays critical roles in promoting T cell development and differentiation but also has been identified as a tumor suppressor involved in preventing T cell malignancy. However, the comprehensive mechanisms of Tcf-1 involved in T cell transformation remain poorly understood. In this study, Tcf7fl/fl mice were crossed with Vav-cre, Lck-cre, or Cd4-cre mice to delete Tcf-1 conditionally at the beginning of the HSC, DN2-DN3, or DP stage, respectively. The defective T cell development phenotypes became gradually less severe as the deletion stage became more advanced in distinct mouse models. Interestingly, consistent with Tcf7-/- mice, Tcf7fl/flVav-cre mice developed aggressive T cell lymphoma within 45 weeks, but no tumors were generated in Tcf7fl/flLck-cre or Tcf7fl/flCd4-cre mice. Single-cell RNA-seq (ScRNA-seq) indicated that ablation of Tcf-1 at distinct phases can subdivide DN1 cells into three clusters (C1, C2, and C3) and DN2-DN3 cells into three clusters (C4, C5, and C6). Moreover, Tcf-1 deficiency redirects bifurcation among divergent cell fates, and clusters C1 and C4 exhibit high potential for leukemic transformation. Mechanistically, we found that Tcf-1 directly binds and mediates chromatin accessibility for both typical T cell regulators and proto-oncogenes, including Myb, Mycn, Runx1, and Lyl1 in the DN1 phase and Lef1, Id2, Dtx1, Fyn, Bcl11b, and Zfp36l2 in the DN2-DN3 phase. The aberrant expression of these genes due to Tcf-1 deficiency in very early T cells contributes to subsequent tumorigenesis. Thus, we demonstrated that Tcf-1 plays stage-specific roles in regulating early thymocyte development and transformation, providing new insights and evidence for clinical trials on T-ALL leukemia.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Hepatocyte Nuclear Factor 1-alpha/physiology
- Lymphocyte Activation
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/physiology
- Lymphoma, T-Cell/etiology
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Single-Cell Analysis/methods
- T-Lymphocytes, Regulatory/immunology
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Zhihong Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Yingpeng Yao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Guotao Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Tianyan Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Hai-Hui Xue
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China
| | - Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI, 53707, USA
| | - Li Bao
- Department Hematology, Beijing Jishuitan Hospital, 100096, Beijing, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road 2, 100193, Beijing, China.
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Henry S, Trousdell MC, Cyrill SL, Zhao Y, Feigman MJ, Bouhuis JM, Aylard DA, Siepel A, Dos Santos CO. Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. J Mammary Gland Biol Neoplasia 2021; 26:43-66. [PMID: 33988830 PMCID: PMC8217035 DOI: 10.1007/s10911-021-09486-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
The developing mammary gland depends on several transcription-dependent networks to define cellular identities and differentiation trajectories. Recent technological advancements that allow for single-cell profiling of gene expression have provided an initial picture into the epithelial cellular heterogeneity across the diverse stages of gland maturation. Still, a deeper dive into expanded molecular signatures would improve our understanding of the diversity of mammary epithelial and non-epithelial cellular populations across different tissue developmental stages, mouse strains and mammalian species. Here, we combined differential mammary gland fractionation approaches and transcriptional profiles obtained from FACS-isolated mammary cells to improve our definitions of mammary-resident, cellular identities at the single-cell level. Our approach yielded a series of expression signatures that illustrate the heterogeneity of mammary epithelial cells, specifically those of the luminal fate, and uncovered transcriptional changes to their lineage-defined, cellular states that are induced during gland development. Our analysis also provided molecular signatures that identified non-epithelial mammary cells, including adipocytes, fibroblasts and rare immune cells. Lastly, we extended our study to elucidate expression signatures of human, breast-resident cells, a strategy that allowed for the cross-species comparison of mammary epithelial identities. Collectively, our approach improved the existing signatures of normal mammary epithelial cells, as well as elucidated the diversity of non-epithelial cells in murine and human breast tissue. Our study provides a useful resource for future studies that use single-cell molecular profiling strategies to understand normal and malignant breast development.
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Affiliation(s)
- Samantha Henry
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, US
- Graduate Program in Genetics, Stony Brook University, NY, 11794, US
| | | | | | - Yixin Zhao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, US
| | - Mary J Feigman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, US
| | | | - Dominik A Aylard
- College of Biological Sciences, University of California, Davis, CA, 95616, US
| | - Adam Siepel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, US
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45
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Dybska E, Adams AT, Duclaux-Loras R, Walkowiak J, Nowak JK. Waiting in the wings: RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scand J Immunol 2021; 93:e13025. [PMID: 33528856 DOI: 10.1111/sji.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Complex interactions between the environment and the mucosal immune system underlie inflammatory bowel disease (IBD). The involved cytokine signalling pathways are modulated by a number of transcription factors, one of which is runt-related transcription factor 3 (RUNX3). OBJECTIVE To systematically review the immune roles of RUNX3 in immune regulation, with a focus on the context of IBD. METHODS Relevant articles and reviews were identified through a Scopus search in April 2020. Information was categorized by immune cell types, analysed and synthesized. IBD transcriptome data sets and FANTOM5 regulatory networks were processed in order to complement the literature review. RESULTS The available evidence on the immune roles of RUNX3 allowed for its description in twelve cell types: intraepithelial lymphocyte, Th1, Th2, Th17, Treg, double-positive T, cytotoxic T, B, dendritic, innate lymphoid, natural killer and macrophages. In the gut, the activity of RUNX3 is multifaceted and context-dependent: it may promote homeostasis or exacerbated reactions via cytokine signalling and regulation of receptor expression. RUNX3 is mostly engaged in pathways involving ThPOK, T-bet, IFN-γ, TGF-β/IL-2Rβ, GATA/CBF-β, SMAD/p300 and a number of miRNAs. RUNX3 targets relevant to IBD may include RAG1, OSM and IL-17B. Moreover, in IBD RUNX3 expression correlates positively with GZMM, and negatively with IFNAR1, whereas in controls, it strongly associates with TGFBR3. CONCLUSIONS Dysregulation of RUNX3, mostly in the form of deficiency, likely contributes to IBD pathogenesis. More clinical research is needed to examine RUNX3 in IBD.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rémi Duclaux-Loras
- INSERM U1111, Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
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46
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The E protein-TCF1 axis controls γδ T cell development and effector fate. Cell Rep 2021; 34:108716. [PMID: 33535043 PMCID: PMC7919611 DOI: 10.1016/j.celrep.2021.108716] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 12/25/2022] Open
Abstract
TCF1 plays a critical role in T lineage commitment and the development of αβ lineage T cells, but its role in γδ T cell development remains poorly understood. Here, we reveal a regulatory axis where T cell receptor (TCR) signaling controls TCF1 expression through an E-protein-bound regulatory element in the Tcf7 locus, and this axis regulates both γδ T lineage commitment and effector fate. Indeed, the level of TCF1 expression plays an important role in setting the threshold for γδ T lineage commitment and modulates the ability of TCR signaling to influence effector fate adoption by γδ T lineage progenitors. This finding provides mechanistic insight into how TCR-mediated repression of E proteins promotes the development of γδ T cells and their adoption of the interleukin (IL)-17-producing effector fate. IL-17-producing γδ T cells have been implicated in cancer progression and in the pathogenesis of psoriasis and multiple sclerosis.
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47
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Wu C, Tan S, Liu L, Cheng S, Li P, Li W, Liu H, Zhang F, Wang S, Ning Y, Wen Y, Zhang F. Transcriptome-wide association study identifies susceptibility genes for rheumatoid arthritis. Arthritis Res Ther 2021; 23:38. [PMID: 33482886 PMCID: PMC7821659 DOI: 10.1186/s13075-021-02419-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
Objective To identify rheumatoid arthritis (RA)-associated susceptibility genes and pathways through integrating genome-wide association study (GWAS) and gene expression profile data. Methods A transcriptome-wide association study (TWAS) was conducted by the FUSION software for RA considering EBV-transformed lymphocytes (EL), transformed fibroblasts (TF), peripheral blood (NBL), and whole blood (YBL). GWAS summary data was driven from a large-scale GWAS, involving 5539 autoantibody-positive RA patients and 20,169 controls. The TWAS-identified genes were further validated using the mRNA expression profiles and made a functional exploration. Results TWAS identified 692 genes with PTWAS values < 0.05 for RA. CRIPAK (PEL = 0.01293, PTF = 0.00038, PNBL = 0.02839, PYBL = 0.0978), MUT (PEL = 0.00377, PTF = 0.00076, PNBL = 0.00778, PYBL = 0.00096), FOXRED1 (PEL = 0.03834, PTF = 0.01120, PNBL = 0.01280, PYBL = 0.00583), and EBPL (PEL = 0.00806, PTF = 0.03761, PNBL = 0.03540, PYBL = 0.04254) were collectively expressed in all the four tissues/cells. Eighteen genes, including ANXA5, AP4B1, ATIC (PTWAS = 0.0113, downregulated expression), C12orf65, CMAH, PDHB, RUNX3 (PTWAS = 0.0346, downregulated expression), SBF1, SH2B3, STK38, TMEM43, XPNPEP1, KIAA1530, NUFIP2, PPP2R3C, RAB24, STX6, and TLR5 (PTWAS = 0.04665, upregulated expression), were validated with integrative analysis of TWAS and mRNA expression profiles. TWAS-identified genes functionally involved in endoplasmic reticulum organization, regulation of cytokine production, TNF signaling pathway, immune response-regulating signaling pathway, regulation of autophagy, etc. Conclusion We identified multiple candidate genes and pathways, providing novel clues for the genetic mechanism of RA. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02419-9.
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Affiliation(s)
- Cuiyan Wu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China.
| | - Sijian Tan
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Li Liu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Shiqiang Cheng
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Peilin Li
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Wenyu Li
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Huan Liu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng'e Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Sen Wang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yujie Ning
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yan Wen
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China.
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Kiuchi M, Onodera A, Kokubo K, Ichikawa T, Morimoto Y, Kawakami E, Takayama N, Eto K, Koseki H, Hirahara K, Nakayama T. The Cxxc1 subunit of the Trithorax complex directs epigenetic licensing of CD4+ T cell differentiation. J Exp Med 2021; 218:211672. [PMID: 33433611 PMCID: PMC7808308 DOI: 10.1084/jem.20201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Different dynamics of gene expression are observed during cell differentiation. In T cells, genes that are turned on early or turned off and stay off have been thoroughly studied. However, genes that are initially turned off but then turned on again after stimulation has ceased have not been defined; they are obviously important, especially in the context of acute versus chronic inflammation. Using the Th1/Th2 differentiation paradigm, we found that the Cxxc1 subunit of the Trithorax complex directs transcription of genes initially down-regulated by TCR stimulation but up-regulated again in a later phase. The late up-regulation of these genes was impaired either by prolonged TCR stimulation or Cxxc1 deficiency, which led to decreased expression of Trib3 and Klf2 in Th1 and Th2 cells, respectively. Loss of Cxxc1 resulted in enhanced pathogenicity in allergic airway inflammation in vivo. Thus, Cxxc1 plays essential roles in the establishment of a proper CD4+ T cell immune system via epigenetic control of a specific set of genes.
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Affiliation(s)
- Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chuo-ku, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Tomomi Ichikawa
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Yuki Morimoto
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Eiryo Kawakami
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Sciences Innovation Hub Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Naoya Takayama
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koji Eto
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Haruhiko Koseki
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan.,AMED-PRIME, Japan Agency for Medical Research and Development, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan.,Japan Agency for Medical Research and Development-Core Research for Evolutional Medical Science and Technology (AMED-CREST), Chiba, Japan
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49
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Chen C, Liu Y, Cui B. Effect of radiotherapy on T cell and PD-1 / PD-L1 blocking therapy in tumor microenvironment. Hum Vaccin Immunother 2021; 17:1555-1567. [PMID: 33428533 DOI: 10.1080/21645515.2020.1840254] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer is a worldwide problem that threatens human health. Radiotherapy plays an important role in a variety of cancer treatment methods. The administration of radiotherapy can alter the differentiation pathways and functions of T cells, which in turn improves the immune response of T cells. Radiotherapy can also induce up-regulation of PD-L1 expression, which means that it has great potential for enhancing the therapeutic effect of anti-PD-1/PD-L1 inhibitors and reducing the risk of drug resistance toward them. At present, the combination of radiotherapy and anti-PD-1/PD-L1 inhibitors has shown significant therapeutic effects in clinical tumor research. This review focuses on the mechanism of radiotherapy on T cells reported in recent years, as well as related research progress in the application of PD-1/PD-L1 blockers. It will provide a theoretical basis for the rational clinical application of radiotherapy combined with PD-1/PD-L1 inhibitors.
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Affiliation(s)
- Chen Chen
- Department of Colorectal Surgery, The Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Yanlong Liu
- Department of Colorectal Surgery, The Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Binbin Cui
- Department of Colorectal Surgery, The Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
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50
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Frkatovic A, Zaytseva OO, Klaric L. Genetic Regulation of Immunoglobulin G Glycosylation. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:259-287. [PMID: 34687013 DOI: 10.1007/978-3-030-76912-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Defining the genetic components that control glycosylation of the human immunoglobulin G (IgG) is an ongoing effort, which has so far been addressed by means of heritability, linkage and genome-wide association studies (GWAS). Unlike the synthesis of proteins, N-glycosylation biosynthesis is not a template-driven process, but rather a complex process regulated by both genetic and environmental factors. Current heritability studies have shown that while up to 75% of the variation in levels of some IgG glycan traits can be explained by genetics, some glycan traits are completely defined by environmental influences. Advances in both high-throughput genotyping and glycan quantification methods have enabled genome-wide association studies that are increasingly used to estimate associations of millions of single-nucleotide polymorphisms and glycosylation traits. Using this method, 18 genomic regions have so far been robustly associated with IgG N-glycosylation, discovering associations with genes encoding glycosyltransferases, but also transcription factors, co-factors, membrane transporters and other genes with no apparent role in IgG glycosylation. Further computational analyses have shown that IgG glycosylation is likely to be regulated through the expression of glycosyltransferases, but have also for the first time suggested which transcription factors are involved in the process. Moreover, it was also shown that IgG glycosylation and inflammatory diseases share common underlying causal genetic variants, suggesting that studying genetic regulation of IgG glycosylation helps not only to better understand this complex process but can also contribute to understanding why glycans are changed in disease. However, further studies are needed to unravel whether changes in IgG glycosylation are causing these diseases or the changes in the glycome are caused by the disease.
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Affiliation(s)
- Azra Frkatovic
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Olga O Zaytseva
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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