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Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ. Shared and distinct biological circuits in effector, memory and exhausted CD8 + T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol 2022; 23:1600-1613. [PMID: 36271148 PMCID: PMC10408358 DOI: 10.1038/s41590-022-01338-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]
Abstract
Naïve CD8+ T cells can differentiate into effector (Teff), memory (Tmem) or exhausted (Tex) T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within Teff, Tmem and Tex populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acute-resolving and chronic infection to address these gaps by applying longitudinal single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses. These analyses uncovered new subsets, including a subpopulation of Tex cells expressing natural killer cell-associated genes that is dependent on the transcription factor Zeb2, as well as multiple distinct TCF-1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of Tex subsets following programmed death 1 (PD-1) pathway blockade and identified a key role for the cell stress regulator, Btg1, in establishing the Tex population. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8+ T cell subsets with highly divergent underlying chromatin landscapes generated during different infections.
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Affiliation(s)
- Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Omar Khan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ping Wang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Staupe
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Infectious Disease & Vaccines, MRL, Merck & Co. Inc., West Point, PA, USA
| | - Mohamed S Abdel-Hakeem
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark M Painter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Wu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yinghui Jane Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rishi R Goel
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick K Yan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | | | - Xiaowei Xu
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Tara C Mitchell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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52
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Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen YG, Cui W. Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage. Life Sci Alliance 2022; 5:5/10/e202201503. [PMID: 35667687 PMCID: PMC9170949 DOI: 10.26508/lsa.202201503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Paired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype. Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell–mediated destruction of pancreatic β cells. We have previously shown that diabetogenic CD8 T cells in the islets of non-obese diabetic mice are phenotypically heterogeneous, but clonal heterogeneity remains relatively unexplored. Here, we use paired single-cell RNA and T-cell receptor sequencing (scRNA-seq and scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of non-obese diabetic mice. scTCR-seq demonstrates that CD8 T cells targeting the immunodominant β-cell epitope IGRP206-214 exhibit restricted TCR gene usage. scRNA-seq identifies six clusters of autoreactive CD8 T cells in the islets and six in the spleen, including memory and exhausted cells. Clonal overlap between IGRP206-214–reactive CD8 T cells in the islets and spleen suggests these cells may circulate between the islets and periphery. Finally, we identify correlations between TCR genes and T-cell clonal expansion and effector fate. Collectively, our work demonstrates that IGRP206-214–specific CD8 T cells are phenotypically heterogeneous but clonally restricted, raising the possibility of selectively targeting these TCR structures for therapeutic benefit.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Ashley E Ciecko
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jack Gorski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
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53
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Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. Functional inference of gene regulation using single-cell multi-omics. CELL GENOMICS 2022; 2:100166. [PMID: 36204155 PMCID: PMC9534481 DOI: 10.1016/j.xgen.2022.100166] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/31/2022] [Accepted: 07/13/2022] [Indexed: 01/21/2023]
Abstract
Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
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Affiliation(s)
- Vinay K. Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fabiana M. Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sai Ma
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Caleb A. Lareau
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | | | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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54
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Todorov H, Prieux M, Laubreton D, Bouvier M, Wang S, de Bernard S, Arpin C, Cannoodt R, Saelens W, Bonnaffoux A, Gandrillon O, Crauste F, Saeys Y, Marvel J. CD8 memory precursor cell generation is a continuous process. iScience 2022; 25:104927. [PMID: 36065187 PMCID: PMC9440290 DOI: 10.1016/j.isci.2022.104927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that these memory precursors are generated continuously with increasing numbers arising over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence and differentiate into memory cells was confirmed by BrdU pulse-chase experiment in vivo. Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided. Trajectory inference tools reconstruct the timing of memory precursors generation The trajectory is defined by both cell cycle and effector functions encoding genes Memory precursors numbers in lymphoid organs increase with time after priming In vivo BrdU labeling validate the in silico data
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Affiliation(s)
- Helena Todorov
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Margaux Prieux
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Daphne Laubreton
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Matteo Bouvier
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
- Vidium, Lyon, France
| | - Shaoying Wang
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Christophe Arpin
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Robrecht Cannoodt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Data Intuitive, Lebbeke, Belgium
| | - Wouter Saelens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | | | - Olivier Gandrillon
- Laboratoire de Biologie et de Modélisation de la cellule, Université de Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Lyon, France
- Inria, Villeurbanne, France
| | - Fabien Crauste
- Laboratoire MAP5 (UMR CNRS 8145), Université de Paris, Paris, France
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Jacqueline Marvel
- Centre International de recherche en Infectiologie, Université de Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Superieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Corresponding author
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55
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Jiao A, Liu H, Ding R, Zheng H, Zhang C, Feng Z, Lei L, Wang X, Su Y, Yang X, Sun C, Zhang L, Bai L, Sun L, Zhang B. Med1 Controls Effector CD8+ T Cell Differentiation and Survival through C/EBPβ-Mediated Transcriptional Control of T-bet. THE JOURNAL OF IMMUNOLOGY 2022; 209:855-863. [DOI: 10.4049/jimmunol.2200037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/25/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Effector CD8+ T cells are crucial players in adaptive immunity for effective protection against invading pathogens. The regulatory mechanisms underlying CD8+ T cell effector differentiation are incompletely understood. In this study, we defined a critical role of mediator complex subunit 1 (Med1) in controlling effector CD8+ T cell differentiation and survival during acute bacterial infection. Mice with Med1-deficient CD8+ T cells exhibited significantly impaired expansion with evidently reduced killer cell lectin-like receptor G1+ terminally differentiated and Ly6c+ effector cell populations. Moreover, Med1 deficiency led to enhanced cell apoptosis and expression of multiple inhibitory receptors (programmed cell death 1, T cell Ig and mucin domain–containing-3, and T cell immunoreceptor with Ig and ITIM domains). RNA-sequencing analysis revealed that T-bet– and Zeb2-mediated transcriptional programs were impaired in Med1-deficient CD8+ T cells. Overexpression of T-bet could rescue the differentiation and survival of Med1-deficient CD8+ effector T cells. Mechanistically, the transcription factor C/EBPβ promoted T-bet expression through interacting with Med1 in effector T cells. Collectively, our findings revealed a novel role of Med1 in regulating effector CD8+ T cell differentiation and survival in response to bacterial infection.
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Affiliation(s)
- Anjun Jiao
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Haiyan Liu
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Renyi Ding
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Huiqiang Zheng
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Cangang Zhang
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Zhao Feng
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Lei Lei
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xin Wang
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yanhong Su
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xiaofeng Yang
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Chenming Sun
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Lianjun Zhang
- ¶Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- ‖Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China; and
| | - Liang Bai
- #Institute of Cardiovascular Science, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Lina Sun
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Baojun Zhang
- *Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- †Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- ‡Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University, Ministry of Education, Xi’an, Shaanxi, China
- §Xi’an Key Laboratory of Immune Related Diseases, Xi’an Jiaotong University, Xi’an, Shaanxi, China
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56
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Neitzke-Montinelli V, Calôba C, Melo G, Frade BB, Caramez E, Mazzoccoli L, Gonçalves ANA, Nakaya HI, Pereira RM, Werneck MBF, Viola JPB. Differentiation of Memory CD8 T Cells Unravel Gene Expression Pattern Common to Effector and Memory Precursors. Front Immunol 2022; 13:840203. [PMID: 35677061 PMCID: PMC9168330 DOI: 10.3389/fimmu.2022.840203] [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: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Long-term immunological protection relies on the differentiation and maintenance of memory lymphocytes. Since the knowledge of memory generation has been centered on in vivo models of infection, there are obstacles to deep molecular analysis of differentiating subsets. Here we defined a novel in vitro CD8 T cell activation and culture regimen using low TCR engagement and cytokines to generate differentiated cells consistent with central memory-like cells, as shown by surface phenotype, gene expression profile and lack of cytotoxic function after challenge. Our results showed an effector signature expressed by in vitro memory precursors and their plasticity under specific conditions. Moreover, memory CD8 T cells conferred long-term protection against bacterial infection and slowed in vivo tumor growth more efficiently than effector cells. This model may allow further understanding of CD8 T cell memory molecular differentiation subsets and be suited for generating cells to be used for immunotherapy.
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Affiliation(s)
- Vanessa Neitzke-Montinelli
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Carolina Calôba
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Guilherme Melo
- Institute of Microbiology and Immunology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bianca B Frade
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Enzo Caramez
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciano Mazzoccoli
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - André N A Gonçalves
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Renata M Pereira
- Institute of Microbiology and Immunology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Miriam B F Werneck
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - João P B Viola
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
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57
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Kanbar JN, Ma S, Kim ES, Kurd NS, Tsai MS, Tysl T, Widjaja CE, Limary AE, Yee B, He Z, Hao Y, Fu XD, Yeo GW, Huang WJ, Chang JT. The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. J Exp Med 2022; 219:e20211756. [PMID: 35593887 PMCID: PMC9127983 DOI: 10.1084/jem.20211756] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/21/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-TEM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8+ T cell differentiation and broaden the knowledge base of lncRNAs in CD8+ T cell biology.
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Affiliation(s)
- Jad N. Kanbar
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Eleanor S. Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Nadia S. Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Matthew S. Tsai
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Abigail E. Limary
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Brian Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | - Wendy J. Huang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - John T. Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA
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58
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Phalke S, Rivera-Correa J, Jenkins D, Flores Castro D, Giannopoulou E, Pernis AB. Molecular mechanisms controlling age-associated B cells in autoimmunity. Immunol Rev 2022; 307:79-100. [PMID: 35102602 DOI: 10.1111/imr.13068] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022]
Abstract
Age-associated B cells (ABCs) have emerged as critical components of immune responses. Their inappropriate expansion and differentiation have increasingly been linked to the pathogenesis of autoimmune disorders, aging-associated diseases, and infections. ABCs exhibit a distinctive phenotype and, in addition to classical B cell markers, often express the transcription factor T-bet and myeloid markers like CD11c; hence, these cells are also commonly known as CD11c+ T-bet+ B cells. Formation of ABCs is promoted by distinctive combinations of innate and adaptive signals. In addition to producing antibodies, these cells display antigen-presenting and proinflammatory capabilities. It is becoming increasingly appreciated that the ABC compartment exhibits a high degree of heterogeneity, plasticity, and sex-specific regulation and that ABCs can differentiate into effector progeny via several routes particularly in autoimmune settings. In this review, we will discuss the initial insights that have been obtained on the molecular machinery that controls ABCs and we will highlight some of the unique aspects of this control system that may enable ABCs to fulfill their distinctive role in immune responses. Given the expanding array of autoimmune disorders and pathophysiological settings in which ABCs are being implicated, a deeper understanding of this machinery could have important and broad therapeutic implications for the successful, albeit daunting, task of targeting these cells.
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Affiliation(s)
- Swati Phalke
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Juan Rivera-Correa
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Daniel Jenkins
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Danny Flores Castro
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Evgenia Giannopoulou
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, New York, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Alessandra B Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Immunology & Microbial Pathogenesis, Weill Cornell Medicine, New York, New York, USA
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59
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Li S, Zou D, Chen W, Cheng Y, Britz GW, Weng YL, Liu Z. Ablation of BATF Alleviates Transplant Rejection via Abrogating the Effector Differentiation and Memory Responses of CD8 + T Cells. Front Immunol 2022; 13:882721. [PMID: 35514970 PMCID: PMC9062028 DOI: 10.3389/fimmu.2022.882721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/25/2022] [Indexed: 02/02/2023] Open
Abstract
Allogeneic CD8+ T cells are prominently involved in allograft rejection, but how their effector differentiation and function are regulated at a transcriptional level is not fully understood. Herein, we identified the basic leucine zipper ATF-like transcription factor (BATF) as a key transcription factor that drives the effector program of allogeneic CD8+ T cells. We found that BATF is highly expressed in graft-infiltrating CD8+ T cells, and its ablation in CD8+ T cells significantly prolonged skin allograft survival in a fully MHC-mismatched transplantation model. To investigate how BATF dictates allogeneic CD8+ T cell response, BATF-/- and wild-type (WT) CD8+ T cells were mixed in a 1:1 ratio and adoptively transferred into B6.Rag1-/- mice 1 day prior to skin transplantation. Compared with WT CD8+ T cells at the peak of rejection response, BATF-/- CD8+ T cells displayed a dysfunctional phenotype, evident by their failure to differentiate into CD127-KLRG1+ terminal effectors, impaired proliferative capacity and production of pro-inflammatory cytokines/cytotoxic molecules, and diminished capacity to infiltrate allografts. In association with the failure of effector differentiation, BATF-/- CD8+ T cells largely retained TCF1 expression and expressed significantly low levels of T-bet, TOX, and Ki67. At the memory phase, BATF-deficient CD8+ T cells displayed impaired effector differentiation upon allogeneic antigen re-stimulation. Therefore, BATF is a critical transcriptional determinant that governs the terminal differentiation and memory responses of allogeneic CD8+ T cells in the transplantation setting. Targeting BATF in CD8+ T cells may be an attractive therapeutic approach to promote transplant acceptance.
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Affiliation(s)
- Shuang Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,Institute of Clinical Pharmacology, Central South University, Changsha, China,Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Dawei Zou
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Wenhao Chen
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute & Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Yating Cheng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Gavin W. Britz
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States,Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States,*Correspondence: Zhaoqian Liu, ;Yi-Lan Weng,
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,Institute of Clinical Pharmacology, Central South University, Changsha, China,*Correspondence: Zhaoqian Liu, ;Yi-Lan Weng,
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60
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Riggan L, Ma F, Li JH, Fernandez E, Nathanson DA, Pellegrini M, O’Sullivan TE. The transcription factor Fli1 restricts the formation of memory precursor NK cells during viral infection. Nat Immunol 2022; 23:556-567. [PMID: 35288713 PMCID: PMC8989647 DOI: 10.1038/s41590-022-01150-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/31/2022] [Indexed: 01/19/2023]
Abstract
Natural killer (NK) cells are innate lymphocytes that possess traits of adaptive immunity, such as memory formation. However, the molecular mechanisms by which NK cells persist to form memory cells are not well understood. Using single-cell RNA sequencing, we identified two distinct effector NK cell (NKeff) populations following mouse cytomegalovirus infection. Ly6C- memory precursor (MP) NK cells showed enhanced survival during the contraction phase in a Bcl2-dependent manner, and differentiated into Ly6C+ memory NK cells. MP NK cells exhibited distinct transcriptional and epigenetic signatures compared with Ly6C+ NKeff cells, with a core epigenetic signature shared with MP CD8+ T cells enriched in ETS1 and Fli1 DNA-binding motifs. Fli1 was induced by STAT5 signaling ex vivo, and increased levels of the pro-apoptotic factor Bim in early effector NK cells following viral infection. These results suggest that a NK cell-intrinsic checkpoint controlled by the transcription factor Fli1 limits MP NK formation by regulating early effector NK cell fitness during viral infection.
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Affiliation(s)
- Luke Riggan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA.,Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Joey H. Li
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elizabeth Fernandez
- Department of Molecular and Medical Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, California, USA
| | - David A. Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA.,Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Timothy E. O’Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA,Corresponding Author: Timothy E. O’Sullivan, PhD, David Geffen School of Medicine at UCLA, 615 Charles E. Young Drive South, BSRB 245F, Los Angeles, CA 90095, Phone: 310-825-4454,
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61
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Vardam-Kaur T, van Dijk S, Peng C, Wanhainen KM, Jameson SC, Borges da Silva H. The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1686-1699. [PMID: 35264459 PMCID: PMC8976739 DOI: 10.4049/jimmunol.2100555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Development of CD8+ central memory T (Tcm) and resident memory T (Trm) cells, which promote immunity in the circulation and in barrier tissues, respectively, is not completely understood. Tcm and Trm cells may arise from common precursors; however, their fate-inducing signals are elusive. We found that virus-specific effector CD8+ T cells display heterogeneous expression of the extracellular ATP sensor P2RX7. P2RX7-high expression is confined, at peak effector phase, to CD62L+ memory precursors, which preferentially form Tcm cells. Among early effector CD8+ T cells, asymmetrical P2RX7 distribution correlated with distinct transcriptional signatures, with P2RX7-high cells enriched for memory and tissue residency sets. P2RX7-high early effectors preferentially form both Tcm and Trm cells. Defective Tcm and Trm cell formation in P2RX7 deficiency is significantly reverted when the transcriptional repressor Zeb2 is ablated. Mechanistically, P2RX7 negatively regulates Zeb2 expression, at least partially through TGF-β sensing in early effector CD8+ T cells. Our study indicates that unequal P2RX7 upregulation in effector CD8+ T cells is a foundational element of the early Tcm/Trm fate.
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Affiliation(s)
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ; and
| | - Changwei Peng
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Kelsey M Wanhainen
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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62
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Zinc Finger E-Box Binding Homeobox 2 as a Prognostic Biomarker in Various Cancers and Its Correlation with Infiltrating Immune Cells in Ovarian Cancer. Curr Issues Mol Biol 2022; 44:1203-1214. [PMID: 35723302 PMCID: PMC8947672 DOI: 10.3390/cimb44030079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 11/17/2022] Open
Abstract
This study investigated the expression of zinc finger E-box binding homeobox 2 (ZEB2), its prognostic significance in various cancers, and the correlation between ZEB2 and infiltrating immune cells and ZEB2-related proteins in ovarian cancer (OV). The Gene Expression Profiling Interactive Analysis tool was used to analyze RNA sequencing data and cancer survival rates, based on normal and tumor tissue data available in The Cancer Genome Atlas (TCGA) database. The Kaplan–Meier plotter and PrognoScan databases were used to analyze the prognostic value of ZEB2 in OV (n = 1144). The Tumor Immune Estimation Resource was used to investigate the correlation between ZEB2 and infiltrating immune cells in various cancers, including OV. High ZEB2 expression was associated with a poorer prognosis in OV. In OV, ZEB2 is positively correlated with CD8+T cells, neutrophils, macrophages, and dendritic cell invasion; and ZEB2 is negatively correlated with tumor-infiltrating B cells. The STRING database was used to investigate the correlations with ZEB2-related proteins. The results reveal that ZEB2 was positively correlated with SMAD1 and SMAD2 in OV. Our findings may serve as a potential prognostic biomarker, and provide novel insights into the tumor immunology in OV. Thus, ZEB2 may be a potential diagnostic and therapeutic target in OV.
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63
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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64
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Tsuda S, Pipkin ME. Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells. Cold Spring Harb Perspect Biol 2022; 14:a037945. [PMID: 34127445 PMCID: PMC8805646 DOI: 10.1101/cshperspect.a037945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Robust immunity to intracellular infections is mediated by antigen-specific naive CD8 T cells that become activated and differentiate into phenotypically and functionally diverse subsets of effector cells, some of which terminally differentiate and others that give rise to memory cells that provide long-lived protection. This developmental system is an outstanding model with which to elucidate how regulation of chromatin structure and transcriptional control establish gene expression programs that govern cell fate determination, insights from which are likely to be useful for informing the design of immunotherapeutic approaches to engineer durable immunity to infections and tumors. A unifying framework that describes how naive CD8 T cells develop into memory cells is still outstanding. We propose a model that incorporates a common early linear path followed by divergent paths that slowly lose capacity to interconvert and discuss classical and contemporary observations that support these notions, focusing on insights from transcriptional control and chromatin regulation.
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Affiliation(s)
- Shanel Tsuda
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
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65
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Evrard M, Wynne-Jones E, Peng C, Kato Y, Christo SN, Fonseca R, Park SL, Burn TN, Osman M, Devi S, Chun J, Mueller SN, Kannourakis G, Berzins SP, Pellicci DG, Heath WR, Jameson SC, Mackay LK. Sphingosine 1-phosphate receptor 5 (S1PR5) regulates the peripheral retention of tissue-resident lymphocytes. J Exp Med 2022; 219:e20210116. [PMID: 34677611 PMCID: PMC8546662 DOI: 10.1084/jem.20210116] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/16/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
Tissue-resident memory T (TRM) cells provide long-lasting immune protection. One of the key events controlling TRM cell development is the local retention of TRM cell precursors coupled to downregulation of molecules necessary for tissue exit. Sphingosine-1-phosphate receptor 5 (S1PR5) is a migratory receptor with an uncharted function in T cells. Here, we show that S1PR5 plays a critical role in T cell infiltration and emigration from peripheral organs, as well as being specifically downregulated in TRM cells. Consequentially, TRM cell development was selectively impaired upon ectopic expression of S1pr5, whereas loss of S1pr5 enhanced skin TRM cell formation by promoting peripheral T cell sequestration. Importantly, we found that T-bet and ZEB2 were required for S1pr5 induction and that local TGF-β signaling was necessary to promote coordinated Tbx21, Zeb2, and S1pr5 downregulation. Moreover, S1PR5-mediated control of tissue residency was conserved across innate and adaptive immune compartments. Together, these results identify the T-bet-ZEB2-S1PR5 axis as a previously unappreciated mechanism modulating the generation of tissue-resident lymphocytes.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Erica Wynne-Jones
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Changwei Peng
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Yu Kato
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Susan N. Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Simone L. Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas N. Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maleika Osman
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sapna Devi
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Scott N. Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - George Kannourakis
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Stuart P. Berzins
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Federation University Australia and Fiona Elsey Cancer Research Institute, Ballarat, Victoria, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
- Cellular Immunology Group, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - William R. Heath
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Laura K. Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
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66
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Kane H, LaMarche NM, Ní Scannail Á, Garza AE, Koay HF, Azad AI, Kunkemoeller B, Stevens B, Brenner MB, Lynch L. Longitudinal analysis of invariant natural killer T cell activation reveals a cMAF-associated transcriptional state of NKT10 cells. eLife 2022; 11:76586. [PMID: 36458691 PMCID: PMC9831610 DOI: 10.7554/elife.76586] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Innate T cells, including CD1d-restricted invariant natural killer T (iNKT) cells, are characterized by their rapid activation in response to non-peptide antigens, such as lipids. While the transcriptional profiles of naive, effector, and memory adaptive T cells have been well studied, less is known about the transcriptional regulation of different iNKT cell activation states. Here, using single-cell RNA-sequencing, we performed longitudinal profiling of activated murine iNKT cells, generating a transcriptomic atlas of iNKT cell activation states. We found that transcriptional signatures of activation are highly conserved among heterogeneous iNKT cell populations, including NKT1, NKT2, and NKT17 subsets, and human iNKT cells. Strikingly, we found that regulatory iNKT cells, such as adipose iNKT cells, undergo blunted activation and display constitutive enrichment of memory-like cMAF+ and KLRG1+ populations. Moreover, we identify a conserved cMAF-associated transcriptional network among NKT10 cells, providing novel insights into the biology of regulatory and antigen-experienced iNKT cells.
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Affiliation(s)
- Harry Kane
- Trinity Biomedical Science Institute, Trinity College DublinDublinIreland
| | - Nelson M LaMarche
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Áine Ní Scannail
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Amanda E Garza
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Hui-Fern Koay
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
| | - Adiba I Azad
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Britta Kunkemoeller
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Brenneth Stevens
- Trinity Biomedical Science Institute, Trinity College DublinDublinIreland,Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Lydia Lynch
- Trinity Biomedical Science Institute, Trinity College DublinDublinIreland,Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
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Wang J, Farkas C, Benyoucef A, Carmichael C, Haigh K, Wong N, Huylebroeck D, Stemmler MP, Brabletz S, Brabletz T, Nefzger CM, Goossens S, Berx G, Polo JM, Haigh JJ. Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity. PLoS Biol 2021; 19:e3001394. [PMID: 34550965 PMCID: PMC8489726 DOI: 10.1371/journal.pbio.3001394] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 10/04/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023] Open
Abstract
The ZEB2 transcription factor has been demonstrated to play important roles in hematopoiesis and leukemic transformation. ZEB1 is a close family member of ZEB2 but has remained more enigmatic concerning its roles in hematopoiesis. Here, we show using conditional loss-of-function approaches and bone marrow (BM) reconstitution experiments that ZEB1 plays a cell-autonomous role in hematopoietic lineage differentiation, particularly as a positive regulator of monocyte development in addition to its previously reported important role in T-cell differentiation. Analysis of existing single-cell (sc) RNA sequencing (RNA-seq) data of early hematopoiesis has revealed distinctive expression differences between Zeb1 and Zeb2 in hematopoietic stem and progenitor cell (HSPC) differentiation, with Zeb2 being more highly and broadly expressed than Zeb1 except at a key transition point (short-term HSC [ST-HSC]➔MPP1), whereby Zeb1 appears to be the dominantly expressed family member. Inducible genetic inactivation of both Zeb1 and Zeb2 using a tamoxifen-inducible Cre-mediated approach leads to acute BM failure at this transition point with increased long-term and short-term hematopoietic stem cell numbers and an accompanying decrease in all hematopoietic lineage differentiation. Bioinformatics analysis of RNA-seq data has revealed that ZEB2 acts predominantly as a transcriptional repressor involved in restraining mature hematopoietic lineage gene expression programs from being expressed too early in HSPCs. ZEB1 appears to fine-tune this repressive role during hematopoiesis to ensure hematopoietic lineage fidelity. Analysis of Rosa26 locus–based transgenic models has revealed that Zeb1 as well as Zeb2 cDNA-based overexpression within the hematopoietic system can drive extramedullary hematopoiesis/splenomegaly and enhance monocyte development. Finally, inactivation of Zeb2 alone or Zeb1/2 together was found to enhance survival in secondary MLL-AF9 acute myeloid leukemia (AML) models attesting to the oncogenic role of ZEB1/2 in AML. This study shows that the closely related transcription factors ZEB1 and ZEB2 cooperate to restrain myeloid and lymphoid differentiation programs in hematopoietic stem and progenitor cells, ensuring fidelity of differentiation in multiple lineages.
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Affiliation(s)
- Jueqiong Wang
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
| | - Carlos Farkas
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Aissa Benyoucef
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | | | - Katharina Haigh
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Nick Wong
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Marc P. Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Centre for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Centre for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Centre for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Christian M. Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Australia
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University and University Hospital, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jose M. Polo
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Centre for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Australia
| | - Jody J. Haigh
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
- * E-mail:
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68
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Tan S, Guo X, Li M, Wang T, Wang Z, Li C, Wu Z, Li N, Gao L, Liang X, Ma C. Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity. J Exp Med 2021; 218:e20210009. [PMID: 34279541 PMCID: PMC8292132 DOI: 10.1084/jem.20210009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/05/2021] [Accepted: 06/17/2021] [Indexed: 02/03/2023] Open
Abstract
The maturation and functional competence of natural killer (NK) cells is a tightly controlled process that relies on transcription factors (TFs). Here, we identify transcriptional repressor zinc fingers and homeoboxes 2 (Zhx2) as a novel regulator that restricts NK cell maturation and function. Mice with Zhx2 conditional deletion in NK cells (Zhx2Δ/Δ) showed accumulation of matured NK cells. Loss of Zhx2 enhanced NK cell survival and NK cell response to IL-15. Transcriptomic analysis revealed Zeb2, a key TF in NK cell terminal maturation, as a direct downstream target of Zhx2. Therapeutically, transfer of Zhx2-deficient NK cells resulted in inhibition of tumor growth and metastasis in different murine models. Our findings collectively unmask a previously unrecognized role of Zhx2 as a novel negative regulator in NK cell maturation and highlight its therapeutic potential as a promising strategy to enhance NK cell-mediated tumor surveillance.
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Affiliation(s)
- Siyu Tan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Xiaowei Guo
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Mengzhen Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Tixiao Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Zehua Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Chunyang Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Nailin Li
- Clinical Pharmacology Group, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
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69
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Zhang J, Wencker M, Marliac Q, Berton A, Hasan U, Schneider R, Laubreton D, Cherrier DE, Mathieu AL, Rey A, Jiang W, Caramel J, Genestier L, Marçais A, Marvel J, Ghavi-Helm Y, Walzer T. Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1 + T cell development. Cell Mol Immunol 2021; 18:2140-2152. [PMID: 32398809 PMCID: PMC8429412 DOI: 10.1038/s41423-020-0459-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/15/2023] Open
Abstract
T cell development proceeds under the influence of a network of transcription factors (TFs). The precise role of Zeb1, a member of this network, remains unclear. Here, we report that Zeb1 expression is induced early during T cell development in CD4-CD8- double-negative (DN) stage 2 (DN2). Zeb1 expression was further increased in the CD4+CD8+ double-positive (DP) stage before decreasing in more mature T cell subsets. We performed an exhaustive characterization of T cells in Cellophane mice that bear Zeb1 hypomorphic mutations. The Zeb1 mutation profoundly affected all thymic subsets, especially DN2 and DP cells. Zeb1 promoted the survival and proliferation of both cell populations in a cell-intrinsic manner. In the periphery of Cellophane mice, the number of conventional T cells was near normal, but invariant NKT cells, NK1.1+ γδ T cells and Ly49+ CD8 T cells were virtually absent. This suggested that Zeb1 regulates the development of unconventional T cell types from DP progenitors. A transcriptomic analysis of WT and Cellophane DP cells revealed that Zeb1 regulated the expression of multiple genes involved in the cell cycle and TCR signaling, which possibly occurred in cooperation with Tcf1 and Heb. Indeed, Cellophane DP cells displayed stronger signaling than WT DP cells upon TCR engagement in terms of the calcium response, phosphorylation events, and expression of early genes. Thus, Zeb1 is a key regulator of the cell cycle and TCR signaling during thymic T cell development. We propose that thymocyte selection is perturbed in Zeb1-mutated mice in a way that does not allow the survival of unconventional T cell subsets.
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Affiliation(s)
- Jiang Zhang
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mélanie Wencker
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Quentin Marliac
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Aurore Berton
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Uzma Hasan
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Raphaël Schneider
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, F-69364, Lyon, France
| | - Daphné Laubreton
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Dylan E Cherrier
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Amaury Rey
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Wenzheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Julie Caramel
- CRCL, Centre de Recherche sur le Cancer de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Genestier
- CRCL, Centre de Recherche sur le Cancer de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Jacqueline Marvel
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, F-69364, Lyon, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
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70
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Yang J, Wu M, Fang H, Su Y, Zhang L, Zhou H. Puerarin Prevents Acute Liver Injury via Inhibiting Inflammatory Responses and ZEB2 Expression. Front Pharmacol 2021; 12:727916. [PMID: 34421621 PMCID: PMC8378253 DOI: 10.3389/fphar.2021.727916] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
Puerarin, an isoflavone component extracted from herb radix puerariae, is widely used in China in the treatment of immune diseases and inflammation. Previous studies have demonstrated that puerarin prevented acute lung injury by regulating inflammatory responses. However, the effect of puerarin on acute liver injury (ALI) was unclear. The purpose of this study was to explore the beneficial effects of puerarin when applied to ALI. We found that puerarin inhibited liver injury and inflammatory cell infiltration in lipopolysaccharide (LPS)/D-galactose (D-Gal)-induced acute liver failure and the liver pro-inflammatory cytokines interleukin (IL)-1β, IL-6, and tumor necrosis factor-alpha (TNF-α) in liver tissues with ALI and LPS-induced L-02 cells but upregulated the expression level of zinc finger E-box-binding homeobox 2 (ZEB2). Significantly, the results of this study showed that the inhibition of liver pro-inflammatory cytokine (IL-1β, IL-6, and TNF-α) production in LPS-induced L-02 cells was caused by ZEB2 overexpression. However, knocking down ZEB2 promoted LPS-mediated secretion of liver pro-inflammatory cytokines in L-02 cells. Additional experiments showed that puerarin inhibited the activation of the NF-κB signaling pathway by elevating ZEB2 expression in L-02 cells. In summary, puerarin most likely prevented activation of the pro-inflammatory factors and reduced LPS/D-Gal-induced liver injury by enhancing the ZEB2 expression level and, consequently, blocking activation of the NF-κB signaling pathway in the liver.
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Affiliation(s)
- Junfa Yang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China.,School of Pharmacy, Anhui Medical University, Hefei, China
| | - Maomao Wu
- Department of Pharmacy, Anhui Chest Hospital, Hefei, China
| | - Hui Fang
- Hangzhou Normal University Affiliated Hospital, Hangzhou, China
| | - Yue Su
- Institute of Clinical Trial, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Lingling Zhang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Huan Zhou
- School of Public Basic, Bengbu Medical College, Bengbu, China
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71
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Chen Y, Shen J, Kasmani MY, Topchyan P, Cui W. Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8 + T Cells. Cells 2021; 10:2143. [PMID: 34440912 PMCID: PMC8392357 DOI: 10.3390/cells10082143] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022] Open
Abstract
During acute infections, CD8+ T cells form various memory subpopulations to provide long-lasting protection against reinfection. T central memory (TCM), T effector memory (TEM), and long-lived effector (LLE) cells are circulating memory populations with distinct plasticity, migration patterns, and effector functions. Tissue-resident memory (TRM) cells permanently reside in the frontline sites of pathogen entry and provide tissue-specific protection upon reinfection. Here, using single-cell RNA-sequencing (scRNA-seq) and bulk RNA-seq, we examined the different and shared transcriptomes and regulators of TRM cells with other circulating memory populations. Furthermore, we identified heterogeneity within the TRM pool from small intestine and novel transcriptional regulators that may control the phenotypic and functional heterogeneity of TRM cells during acute infection. Our findings provide a resource for future studies to identify novel pathways for enhancing vaccination and immunotherapeutic approaches.
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Affiliation(s)
- Yao Chen
- Versiti Blood Research Institute, Milwaukee, WI 53213, USA; (Y.C.); (J.S.); (M.Y.K.); (P.T.)
| | - Jian Shen
- Versiti Blood Research Institute, Milwaukee, WI 53213, USA; (Y.C.); (J.S.); (M.Y.K.); (P.T.)
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Moujtaba Y. Kasmani
- Versiti Blood Research Institute, Milwaukee, WI 53213, USA; (Y.C.); (J.S.); (M.Y.K.); (P.T.)
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Paytsar Topchyan
- Versiti Blood Research Institute, Milwaukee, WI 53213, USA; (Y.C.); (J.S.); (M.Y.K.); (P.T.)
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Weiguo Cui
- Versiti Blood Research Institute, Milwaukee, WI 53213, USA; (Y.C.); (J.S.); (M.Y.K.); (P.T.)
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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72
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Farsakoglu Y, McDonald B, Kaech SM. Motility Matters: How CD8 + T-Cell Trafficking Influences Effector and Memory Cell Differentiation. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a038075. [PMID: 34001529 PMCID: PMC8327832 DOI: 10.1101/cshperspect.a038075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Immunological memory is a hallmark of adaptive immunity that confers long-lasting protection from reinfections. Memory CD8+ T cells provide protection by actively scanning for their cognate antigen and migrating into inflamed tissues. Trafficking patterns of CD8+ T cells are also a major determinant of cell fate outcomes during differentiation into effector and memory cell states. CD8+ T-cell trafficking must therefore be dynamically and tightly regulated to ensure that CD8+ T cells arrive at the correct locations and differentiate to acquire appropriate effector functions. This review aims to discuss the importance of CD8+ T-cell trafficking patterns in regulating effector and memory differentiation, maintenance, and reactivation.
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Affiliation(s)
- Yagmur Farsakoglu
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California 92093, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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73
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Milner JJ, Toma C, Quon S, Omilusik K, Scharping NE, Dey A, Reina-Campos M, Nguyen H, Getzler AJ, Diao H, Yu B, Delpoux A, Yoshida TM, Li D, Qi J, Vincek A, Hedrick SM, Egawa T, Zhou MM, Crotty S, Ozato K, Pipkin ME, Goldrath AW. Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection. J Exp Med 2021; 218:e20202512. [PMID: 34037670 PMCID: PMC8160575 DOI: 10.1084/jem.20202512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 12/26/2022] Open
Abstract
In response to infection, pathogen-specific CD8 T cells differentiate into functionally diverse effector and memory T cell populations critical for resolving disease and providing durable immunity. Through small-molecule inhibition, RNAi studies, and induced genetic deletion, we reveal an essential role for the chromatin modifier and BET family member BRD4 in supporting the differentiation and maintenance of terminally fated effector CD8 T cells during infection. BRD4 bound diverse regulatory regions critical to effector T cell differentiation and controlled transcriptional activity of terminal effector-specific super-enhancers in vivo. Consequentially, induced deletion of Brd4 or small molecule-mediated BET inhibition impaired maintenance of a terminal effector T cell phenotype. BRD4 was also required for terminal differentiation of CD8 T cells in the tumor microenvironment in murine models, which we show has implications for immunotherapies. Taken together, these data reveal an unappreciated requirement for BRD4 in coordinating activity of cis regulatory elements to control CD8 T cell fate and lineage stability.
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Affiliation(s)
- J. Justin Milner
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Sara Quon
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Nicole E. Scharping
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Anup Dey
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Miguel Reina-Campos
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Hongtuyet Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Adam J. Getzler
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Huitian Diao
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Bingfei Yu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Arnaud Delpoux
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Tomomi M. Yoshida
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Adam Vincek
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stephen M. Hedrick
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Matthew E. Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
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74
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BATF regulates progenitor to cytolytic effector CD8 + T cell transition during chronic viral infection. Nat Immunol 2021; 22:996-1007. [PMID: 34282329 PMCID: PMC9258987 DOI: 10.1038/s41590-021-00965-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
During chronic viral infection, CD8+ T cells develop into three major phenotypically and functionally distinct subsets: Ly108+TCF-1+ progenitors, Ly108-CX3CR1- terminally exhausted cells and the recently identified CX3CR1+ cytotoxic effector cells. Nevertheless, how CX3CR1+ effector cell differentiation is transcriptionally and epigenetically regulated remains elusive. Here, we identify distinct gene regulatory networks and epigenetic landscapes underpinning the formation of these subsets. Notably, our data demonstrate that CX3CR1+ effector cells bear a striking similarity to short-lived effector cells during acute infection. Genetic deletion of Tbx21 significantly diminished formation of the CX3CR1+ subset. Importantly, we further identify a previously unappreciated role for the transcription factor BATF in maintaining a permissive chromatin structure that allows the transition from TCF-1+ progenitors to CX3CR1+ effector cells. BATF directly bound to regulatory regions near Tbx21 and Klf2, modulating their enhancer accessibility to facilitate the transition. These mechanistic insights can potentially be harnessed to overcome T cell exhaustion during chronic infection and cancer.
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75
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Huang X, Ferris ST, Kim S, Choudhary MNK, Belk JA, Fan C, Qi Y, Sudan R, Xia Y, Desai P, Chen J, Ly N, Shi Q, Bagadia P, Liu T, Guilliams M, Egawa T, Colonna M, Diamond MS, Murphy TL, Satpathy AT, Wang T, Murphy KM. Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. Immunity 2021; 54:1417-1432.e7. [PMID: 34004142 PMCID: PMC8282756 DOI: 10.1016/j.immuni.2021.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022]
Abstract
The transcriptional repressor ZEB2 regulates development of many cell fates among somatic, neural, and hematopoietic lineages, but the basis for its requirement in these diverse lineages is unclear. Here, we identified a 400-basepair (bp) region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins at several E-box motifs and was active in hematopoietic lineages. Germline deletion of this 400-bp region (Zeb2Δ-165mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC)-derived lineages. Zeb2Δ-165 mice lacked development of plasmacytoid dendritic cells (pDCs), monocytes, and B cells. All macrophages in Zeb2Δ-165 mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164-kb that was selectively active in embryonically derived lineages, but not HSC-derived ones. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the -165-kb Zeb2 enhancer.
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Affiliation(s)
- Xiao Huang
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Stephen T Ferris
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Changxu Fan
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raki Sudan
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Yu Xia
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Pritesh Desai
- Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Jing Chen
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Quanming Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Prachi Bagadia
- Department of Oncology, Amgen, 1120 Veterans Boulevard, South San Francisco, CA 94080, USA
| | - Tiantian Liu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Martin Guilliams
- Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA.
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76
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Birkhoff JC, Huylebroeck D, Conidi A. ZEB2, the Mowat-Wilson Syndrome Transcription Factor: Confirmations, Novel Functions, and Continuing Surprises. Genes (Basel) 2021; 12:1037. [PMID: 34356053 PMCID: PMC8304685 DOI: 10.3390/genes12071037] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type specific Zeb2 knockout (cKO) in mice. In between, it was further identified as causal gene causing Mowat-Wilson Syndrome (MOWS) and novel regulator of epithelial-mesenchymal transition (EMT). ZEB2's functions and action mechanisms in mouse embryos were first addressed in its main sites of expression, with focus on those that helped to explain neurodevelopmental and neural crest defects seen in MOWS patients. By doing so, ZEB2 was identified in the forebrain as the first TF that determined timing of neuro-/gliogenesis, and thereby also the extent of different layers of the cortex, in a cell non-autonomous fashion, i.e., by its cell-intrinsic control within neurons of neuron-to-progenitor paracrine signaling. Transcriptomics-based phenotyping of Zeb2 mutant mouse cells have identified large sets of intact-ZEB2 dependent genes, and the cKO approaches also moved to post-natal brain development and diverse other systems in adult mice, including hematopoiesis and various cell types of the immune system. These new studies start to highlight the important adult roles of ZEB2 in cell-cell communication, including after challenge, e.g., in the infarcted heart and fibrotic liver. Such studies may further evolve towards those documenting the roles of ZEB2 in cell-based repair of injured tissue and organs, downstream of actions of diverse growth factors, which recapitulate developmental signaling principles in the injured sites. Evident questions are about ZEB2's direct target genes, its various partners, and ZEB2 as a candidate modifier gene, e.g., in other (neuro)developmental disorders, but also the accurate transcriptional and epigenetic regulation of its mRNA expression sites and levels. Other questions start to address ZEB2's function as a niche-controlling regulatory TF of also other cell types, in part by its modulation of growth factor responses (e.g., TGFβ/BMP, Wnt, Notch). Furthermore, growing numbers of mapped missense as well as protein non-coding mutations in MOWS patients are becoming available and inspire the design of new animal model and pluripotent stem cell-based systems. This review attempts to summarize in detail, albeit without discussing ZEB2's role in cancer, hematopoiesis, and its emerging roles in the immune system, how intense ZEB2 research has arrived at this exciting intersection.
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Affiliation(s)
- Judith C. Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (J.C.B.); (D.H.)
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (J.C.B.); (D.H.)
- Department of Development and Regeneration, Unit Stem Cell and Developmental Biology, Biomedical Sciences Group, KU Leuven, 3000 Leuven, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (J.C.B.); (D.H.)
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77
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Raju S, Xia Y, Daniel B, Yost KE, Bradshaw E, Tonc E, Verbaro DJ, Kometani K, Yokoyama WM, Kurosaki T, Satpathy AT, Egawa T. Identification of a T-bet hi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3 +CX3CR1 + Effectors and Memory-like Cells. THE JOURNAL OF IMMUNOLOGY 2021; 206:2924-2936. [PMID: 34088768 DOI: 10.4049/jimmunol.2001348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 11/19/2022]
Abstract
Persistent Ag induces a dysfunctional CD8 T cell state known as "exhaustion" characterized by PD-1 expression. Nevertheless, exhausted CD8 T cells retain functionality through continued differentiation of progenitor into effector cells. However, it remains ill-defined how CD8 T cell effector responses are sustained in situ. In this study, we show using the mouse chronic lymphocytic choriomeningitis virus infection model that CX3CR1+ CD8 T cells contain a T-bet-dependent TIM3-PD-1lo subpopulation that is distinct from the TIM3+CX3CR1+PD-1+ proliferative effector subset. The TIM3-CX3CR1+ cells are quiescent and express a low but significant level of the transcription factor TCF-1, demonstrating similarity to TCF-1hi progenitor CD8 T cells. Furthermore, following the resolution of lymphocytic choriomeningitis virus viremia, a substantial proportion of TCF-1+ memory-like CD8 T cells show evidence of CX3CR1 expression during the chronic phase of the infection. Our results suggest a subset of the CX3CR1+ exhausted population demonstrates progenitor-like features that support the generation of the CX3CR1+ effector pool from the TCF-1hi progenitors and contribute to the memory-like pool following the resolution of viremia.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Yu Xia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Kathryn E Yost
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Elliot Bradshaw
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Elena Tonc
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Daniel J Verbaro
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Kohei Kometani
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Wayne M Yokoyama
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Tomohiro Kurosaki
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; and
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO;
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78
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Lu H, Liu F, Li Y, Wang J, Ma M, Gao J, Wang X, Shen Z, Wu D. Chromatin accessibility of CD8 T cell differentiation and metabolic regulation. Cell Biol Toxicol 2021; 37:367-378. [PMID: 32656717 DOI: 10.1007/s10565-020-09546-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/18/2020] [Indexed: 01/12/2023]
Abstract
CD8+T cells play an important role in controlling infections and tumorigenesis in vivo. naïve CD8+T cells exponentially expand and exert effector functions in response to TCR ligation. After antigen clearance, most effector CD8+T cells (Teff) experience activation-induced cell death, only a small portion becomes long-lived memory T cells (Tmem). The cell-intrinsic mechanisms driving the differentiation need further understanding. Here we used combined transposase-accessible chromatin (ATAC-seq) technology and RNA-seq analysis to explore chromatin accessibility in CD8+T cell subsets (naïve T cells, Teff, and Tmem). The data demonstrates different chromatin openness of CD8+T cell states is associated with metabolic regulation and the high accessibility of upstream binding site SP1 emerged as critical transcription factor for both Teff and Tmem in fatty acid oxidation (FAO) and glycolysis. The different presence of accessible regions in CD8+T cell subsets provides a novel perspective for understanding epigenetic mechanisms underlying T cell differentiation and related immune response.
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Affiliation(s)
- Haiyang Lu
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, 200233, China
| | - Fangming Liu
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yao Li
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiahui Wang
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, 200233, China
| | - Mingyue Ma
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jie Gao
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiangdong Wang
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Zan Shen
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, 200233, China.
| | - Duojiao Wu
- Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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79
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Frith K, Munier CML, Hastings L, Mowat D, Wilson M, Seddiki N, Macintosh R, Kelleher AD, Gray P, Zaunders JJ. The Role of ZEB2 in Human CD8 T Lymphocytes: Clinical and Cellular Immune Profiling in Mowat-Wilson Syndrome. Int J Mol Sci 2021; 22:ijms22105324. [PMID: 34070208 PMCID: PMC8158478 DOI: 10.3390/ijms22105324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
The Zeb2 gene encodes a transcription factor (ZEB2) that acts as an important immune mediator in mice, where it is expressed in early-activated effector CD8 T cells, and limits effector differentiation. Zeb2 homozygous knockout mice have deficits in CD8 T cells and NK cells. Mowat–Wilson syndrome (MWS) is a rare genetic disease resulting from heterozygous mutations in ZEB2 causing disease by haploinsufficiency. Whether ZEB2 exhibits similar expression patterns in human CD8 T cells is unknown, and MWS patients have not been comprehensively studied to identify changes in CD8 lymphocytes and NK cells, or manifestations of immunodeficiency. By using transcriptomic assessment, we demonstrated that ZEB2 is expressed in early-activated effector CD8 T cells of healthy human volunteers following vaccinia inoculation and found evidence of a role for TGFß-1/SMAD signaling in these cells. A broad immunological assessment of six genetically diagnosed MWS patients identified two patients with a history of recurrent sinopulmonary infections, one of whom had recurrent oral candidiasis, one with lymphopenia, two with thrombocytopenia and three with detectable anti-nuclear antibodies. Immunoglobulin levels, including functional antibody responses to protein and polysaccharide vaccination, were normal. The MWS patients had a significantly lower CD8 T cell subset as % of lymphocytes, compared to healthy controls (median 16.4% vs. 25%, p = 0.0048), and resulting increased CD4:CD8 ratio (2.6 vs. 1.8; p = 0.038). CD8 T cells responded normally to mitogen stimulation in vitro and memory CD8 T cells exhibited normal proportions of subsets with important tissue-specific homing markers and cytotoxic effector molecules. There was a trend towards a decrease in the CD8 T effector memory subset (3.3% vs. 5.9%; p = 0.19). NK cell subsets were normal. This is the first evidence that ZEB2 is expressed in early-activated human effector CD8 T cells, and that haploinsufficiency of ZEB2 in MWS patients had a slight effect on immune function, skewing T cells away from CD8 differentiation. To date there is insufficient evidence to support an immunodeficiency occurring in MWS patients.
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Affiliation(s)
- Katie Frith
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
| | - C. Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
| | - Lucy Hastings
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - David Mowat
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - Meredith Wilson
- Department of Clinical Genetics, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia;
| | - Nabila Seddiki
- INSERM U955 Eq16, Vaccine Research Institute and Université Paris Est Créteil, F-94010 Créteil, France;
| | - Rebecca Macintosh
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
| | - Anthony D. Kelleher
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Centre for Applied Medical Research, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Paul Gray
- Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.H.); (D.M.); (R.M.); (P.G.)
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2052, Australia
| | - John James Zaunders
- The Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Sydney, NSW 2052, Australia;
- Centre for Applied Medical Research, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
- Correspondence: (K.F.); (C.M.L.M.); (J.J.Z.)
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80
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Mold JE, Modolo L, Hård J, Zamboni M, Larsson AJM, Stenudd M, Eriksson CJ, Durif G, Ståhl PL, Borgström E, Picelli S, Reinius B, Sandberg R, Réu P, Talavera-Lopez C, Andersson B, Blom K, Sandberg JK, Picard F, Michaëlsson J, Frisén J. Divergent clonal differentiation trajectories establish CD8 + memory T cell heterogeneity during acute viral infections in humans. Cell Rep 2021; 35:109174. [PMID: 34038736 DOI: 10.1016/j.celrep.2021.109174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 02/15/2021] [Accepted: 05/04/2021] [Indexed: 02/08/2023] Open
Abstract
The CD8+ T cell response to an antigen is composed of many T cell clones with unique T cell receptors, together forming a heterogeneous repertoire of effector and memory cells. How individual T cell clones contribute to this heterogeneity throughout immune responses remains largely unknown. In this study, we longitudinally track human CD8+ T cell clones expanding in response to yellow fever virus (YFV) vaccination at the single-cell level. We observed a drop in clonal diversity in blood from the acute to memory phase, suggesting that clonal selection shapes the circulating memory repertoire. Clones in the memory phase display biased differentiation trajectories along a gradient from stem cell to terminally differentiated effector memory fates. In secondary responses, YFV- and influenza-specific CD8+ T cell clones are poised to recapitulate skewed differentiation trajectories. Collectively, we show that the sum of distinct clonal phenotypes results in the multifaceted human T cell response to acute viral infections.
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Affiliation(s)
- Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Laurent Modolo
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Moa Stenudd
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ghislain Durif
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Erik Borgström
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Simone Picelli
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pedro Réu
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Carlos Talavera-Lopez
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Franck Picard
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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81
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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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82
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Zhang W, Morris AB, Peek EV, Karadkhele G, Robertson JM, Kissick HT, Larsen CP. CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation. Front Immunol 2021; 12:620386. [PMID: 33936035 PMCID: PMC8081907 DOI: 10.3389/fimmu.2021.620386] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Cytomegalovirus (CMV) is one of the most commonly recognized opportunistic pathogens and remains the most influential known parameter in shaping an individual's immune system. As such, T cells induced by CMV infection could have a long-term impact on subsequent immune responses. Accumulating evidence indicates that memory T cells developed during past bacterial and viral infection can cross-react with unrelated pathogens, including transplant antigens, and can alter responses to de novo infections, vaccines, cancers, or rejection. Therefore, careful examination of T cell responses elicited by CMV is warranted to understand their potentially beneficial or harmful roles in future major immune events. Our detailed exploration of the distribution, phenotype, TCR repertoire and transcriptome of CD4+ T cells within CMV seropositive healthy individuals using high-dimensional flow cytometry and single cell multi-omics sequencing reveals that CMV seropositivity has highly significant age-independent effects, leading to a reduction in CD4+ naïve T cells and an expansion of CD4+ effector memory T cells and CD45RA+ effector memory T cells. These induced CD4+ effector memory T cells undergo a specific differentiation trajectory resulting in a subpopulation of CD57+CD27-CD28-CD244+ CD4+ T cells with cytotoxic function and TCR oligoclonality for optimal controlled coexistence with cytomegalovirus. Through gene set enrichment analysis, we found that this subpopulation is similar to virus-specific CD8+ T cells and T cells that mediate acute rejection in patients using tacrolimus and belatacept, a selective costimulation blocker. Together, these data suggest that memory CD4+ T cells induced by cytomegalovirus are formed via a distinct differentiation program to acquire cytotoxic function and can be potentially detrimental to transplant patients adopting costimulation blockade immunosuppressive regimen.
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Affiliation(s)
- Weiwen Zhang
- Xiangya School of Medicine, Central South University, Changsha, China.,Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Anna B Morris
- Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Erica V Peek
- Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Geeta Karadkhele
- Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer M Robertson
- Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, United States
| | - Christian P Larsen
- Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
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83
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Krueger PD, Goldberg MF, Hong SW, Osum KC, Langlois RA, Kotov DI, Dileepan T, Jenkins MK. Two sequential activation modules control the differentiation of protective T helper-1 (Th1) cells. Immunity 2021; 54:687-701.e4. [PMID: 33773107 PMCID: PMC8495663 DOI: 10.1016/j.immuni.2021.03.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 12/31/2020] [Accepted: 03/08/2021] [Indexed: 12/24/2022]
Abstract
Interferon-γ (IFN-γ)-producing CD4+ T helper-1 (Th1) cells are critical for protection from microbes that infect the phagosomes of myeloid cells. Current understanding of Th1 cell differentiation is based largely on reductionist cell culture experiments. We assessed Th1 cell generation in vivo by studying antigen-specific CD4+ T cells during infection with the phagosomal pathogen Salmonella enterica (Se), or influenza A virus (IAV), for which CD4+ T cells are less important. Both microbes induced T follicular helper (Tfh) and interleukin-12 (IL-12)-independent Th1 cells. During Se infection, however, the Th1 cells subsequently outgrew the Tfh cells via an IL-12-dependent process and formed subsets with increased IFN-γ production, ZEB2-transcription factor-dependent cytotoxicity, and capacity to control Se infection. Our results indicate that many infections induce a module that generates Tfh and poorly differentiated Th1 cells, which is followed in phagosomal infections by an IL-12-dependent Th1 cell amplification module that is critical for pathogen control.
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Affiliation(s)
- Peter D Krueger
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Michael F Goldberg
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Sung-Wook Hong
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Kevin C Osum
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Ryan A Langlois
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Dmitri I Kotov
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Thamotharampillai Dileepan
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Marc K Jenkins
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455 USA.
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84
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Chen GM, Chen C, Das RK, Gao P, Chen CH, Bandyopadhyay S, Ding YY, Uzun Y, Yu W, Zhu Q, Myers RM, Grupp SA, Barrett DM, Tan K. Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy. Cancer Discov 2021; 11:2186-2199. [PMID: 33820778 DOI: 10.1158/2159-8290.cd-20-1677] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022]
Abstract
The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function. SIGNIFICANCE: To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Gregory M Chen
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Changya Chen
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rajat K Das
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Peng Gao
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chia-Hui Chen
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Shovik Bandyopadhyay
- Graduate Group in Cellular and Molecular Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yang-Yang Ding
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yasin Uzun
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Wenbao Yu
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Qin Zhu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Regina M Myers
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stephan A Grupp
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David M Barrett
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. .,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kai Tan
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. .,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
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85
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Chung HK, McDonald B, Kaech SM. The architectural design of CD8+ T cell responses in acute and chronic infection: Parallel structures with divergent fates. J Exp Med 2021; 218:e20201730. [PMID: 33755719 PMCID: PMC7992501 DOI: 10.1084/jem.20201730] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
In response to infection, T cells adopt a range of differentiation states, creating numerous heterogeneous subsets that exhibit different phenotypes, functions, and migration patterns. This T cell heterogeneity is a universal feature of T cell immunity, needed to effectively control pathogens in a context-dependent manner and generate long-lived immunity to those pathogens. Here, we review new insights into differentiation state dynamics and population heterogeneity of CD8+ T cells in acute and chronic viral infections and cancer and highlight the parallels and distinctions between acute and chronic antigen stimulation settings. We focus on transcriptional and epigenetic networks that modulate the plasticity and terminal differentiation of antigen-specific CD8+ T cells and generate functionally diverse T cell subsets with different roles to combat infection and cancer.
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Affiliation(s)
- H. Kay Chung
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
| | - Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
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86
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CD45RB Status of CD8 + T Cell Memory Defines T Cell Receptor Affinity and Persistence. Cell Rep 2021; 30:1282-1291.e5. [PMID: 32023448 DOI: 10.1016/j.celrep.2020.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 10/18/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
The identity of CD45 isoforms on the T cell surface changes following the activation of naive T cells and impacts intracellular signaling. In this study, we find that the anti-viral memory CD8+ T pool is unexpectedly comprised of both CD45RBhi and CD45RBlo populations. Relative to CD45RBlo memory T cells, CD45RBhi memory T cells have lower affinity and display greater clonal diversity, as well as a persistent CD27hi phenotype. The CD45RBhi memory population displays a homeostatic survival advantage in vivo relative to CD45RBlo memory, and long-lived high-affinity cells that persisted long term convert from CD45RBlo to CD45RBhi. Human CD45RO+ memory is comprised of both CD45RBhi and CD45RBlo populations with distinct phenotypes, and antigen-specific memory to two viruses is predominantly CD45RBhi. These data demonstrate that CD45RB status is distinct from the conventional central/effector T cell memory classification and has potential utility for monitoring and characterizing pathogen-specific CD8+ T cell responses.
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87
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Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev 2021; 300:100-124. [PMID: 33682165 DOI: 10.1111/imr.12954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. This review examines how alterations in chromatin structure, transcription factor binding, extracellular signals, and single-cell gene expression explain the differential development of distinct effector (TEFF ) and memory (TMEM ) CD8 T cell subsets. Special emphasis is placed on how Runx proteins function with additional transcription factors to pioneer changes in chromatin accessibility and drive transcriptional programs that establish the core attributes of cytotoxic T lymphocytes, subdivide circulating and non-circulating TMEM cell subsets, and govern terminal differentiation. The discussion integrates the roles of specific cytokine signals, transcriptional circuits and how regulation of individual nucleosomes and RNA polymerase II activity can contribute to the process of differentiation. A model that integrates many of these features is discussed to conceptualize how activated CD8 T cells arrive at their fates.
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Affiliation(s)
- Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA
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88
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Ding R, Liu S, Wang S, Chen H, Wang F, Xu Q, Zhu L, Dong X, Gu Y, Zhang X, Chao CC, Gao Q. Single-cell transcriptome analysis of the heterogeneous effects of differential expression of tumor PD-L1 on responding TCR-T cells. Theranostics 2021; 11:4957-4974. [PMID: 33754038 PMCID: PMC7978322 DOI: 10.7150/thno.55075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023] Open
Abstract
Rationale: TCR-T cell therapy plays a critical role in the treatment of malignant cancers. However, it is unclear how TCR-T cells are affected by PD-L1 molecule in the tumor environment. We performed an in-depth evaluation on how differential expressions of tumor PD-L1 can affect the functionality of T cells. Methods: We used MART-1-specific TCR-T cells (TCR-TMART-1), stimulated with MART-127-35 peptide-loaded MEL-526 tumor cells, expressing different proportions of PD-L1, to perform cellular assays and high-throughput single-cell RNA sequencing. Results: Different clusters of activated or cytotoxic TCR-TMART-1 responded divergently when stimulated with tumor cells expressing different percentages of PD-L1 expression. Compared to control T cells, TCR-TMART-1 were more sensitive to exhaustion, and secreted not only pro-inflammatory cytokines but also anti-inflammatory cytokines with increasing proportions of PD-L1+ tumor cells. The gene profiles of chemokines were modified by increased expression of tumor PD-L1, which concurrently downregulated pro-inflammatory and anti-inflammatory transcription factors. Furthermore, increased expression of tumor PD-L1 showed distinct effects on different inhibitory checkpoint molecules (ICMs). In addition, there was a limited correlation between the enrichment of cell death signaling in tumor cells and T cells and increased tumor PD-L1 expression. Conclusion: Overall, though the effector functionality of TCR-T cells was suppressed by increased expression percentages of tumor PD-L1 in vitro, scRNA-seq profiles revealed that both the anti-inflammatory and pro-inflammatory responses were triggered by a higher expression of tumor PD-L1. This suggests that the sole blockade of tumor PD-L1 might inhibit not only the anti-inflammatory response but also the pro-inflammatory response in the complicated tumor microenvironment. Thus, the outcome of PD-L1 intervention may depend on the final balance among the highly dynamic and heterogeneous immune regulatory circuits.
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Affiliation(s)
- Renpeng Ding
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Shang Liu
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Shanshan Wang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | | | - Fei Wang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Qumiao Xu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics
| | - Linnan Zhu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics
| | | | - Qianqian Gao
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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89
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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90
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Yao C, Lou G, Sun HW, Zhu Z, Sun Y, Chen Z, Chauss D, Moseman EA, Cheng J, D'Antonio MA, Shi W, Shi J, Kometani K, Kurosaki T, Wherry EJ, Afzali B, Gattinoni L, Zhu Y, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T. BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8 + T cells. Nat Immunol 2021; 22:370-380. [PMID: 33574619 PMCID: PMC7906956 DOI: 10.1038/s41590-021-00868-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/04/2021] [Indexed: 01/28/2023]
Abstract
During chronic infection and cancer, a self-renewing CD8+ T cell subset maintains long-term immunity and is critical to the effectiveness of immunotherapy. These stem-like CD8+ T cells diverge from other CD8+ subsets early after chronic viral infection. However, pathways guarding stem-like CD8+ T cells against terminal exhaustion remain unclear. Here, we show that the gene encoding transcriptional repressor BACH2 is transcriptionally and epigenetically active in stem-like CD8+ T cells but not terminally exhausted cells early after infection. BACH2 overexpression enforced stem-like cell fate, whereas BACH2 deficiency impaired stem-like CD8+ T cell differentiation. Single-cell transcriptomic and epigenomic approaches revealed that BACH2 established the transcriptional and epigenetic programs of stem-like CD8+ T cells. In addition, BACH2 suppressed the molecular program driving terminal exhaustion through transcriptional repression and epigenetic silencing. Thus, our study reveals a new pathway that enforces commitment to stem-like CD8+ lineage and prevents an alternative terminally exhausted cell fate.
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Affiliation(s)
- Chen Yao
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Guohua Lou
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hong-Wei Sun
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ziang Zhu
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yi Sun
- Department of Surgery, Division of Surgical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - E Ashley Moseman
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Jun Cheng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marc A D'Antonio
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Wangke Shi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Kohei Kometani
- Laboratory of Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School Medicine, Philadelphia, PA, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luca Gattinoni
- Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Yuwen Zhu
- Department of Surgery, Division of Surgical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pamela L Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tuoqi Wu
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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91
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Seumois G, Ramírez-Suástegui C, Schmiedel BJ, Liang S, Peters B, Sette A, Vijayanand P. Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma. Sci Immunol 2021; 5:5/48/eaba6087. [PMID: 32532832 DOI: 10.1126/sciimmunol.aba6087] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/22/2020] [Indexed: 12/19/2022]
Abstract
CD4+ T helper (TH) cells and regulatory T (Treg) cells that respond to common allergens play an important role in driving and dampening airway inflammation in patients with asthma. Until recently, direct, unbiased molecular analysis of allergen-reactive TH and Treg cells has not been possible. To better understand the diversity of these T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells and Treg cells from asthmatics with HDM allergy and from three control groups: asthmatics without HDM allergy and nonasthmatics with and without HDM allergy. Our analyses show that HDM allergen-reactive TH and Treg cells are highly heterogeneous and certain subsets are quantitatively and qualitatively different in individuals with HDM-reactive asthma. The number of interleukin-9 (IL-9)-expressing HDM-reactive TH cells is greater in asthmatics with HDM allergy compared with nonasthmatics with HDM allergy, and this IL-9-expressing TH subset displays enhanced pathogenic properties. More HDM-reactive TH and Treg cells expressing the interferon response signature (THIFNR and TregIFNR) are present in asthmatics without HDM allergy compared with those with HDM allergy. In cells from these subsets (THIFNR and TregIFNR), expression of TNFSF10 was enriched; its product, tumor necrosis factor-related apoptosis-inducing ligand, dampens activation of TH cells. These findings suggest that the THIFNR and TregIFNR subsets may dampen allergic responses, which may help explain why only some people develop TH2 responses to nearly ubiquitous allergens.
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Affiliation(s)
- Grégory Seumois
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
| | | | | | - Shu Liang
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.,Clinical and Experimental Sciences, National Institute for Health Research Southampton Respiratory Biomedical Research Unit, Faculty of Medicine, University of Southampton, Southampton SO166YD, UK
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92
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Beaulieu AM. Transcriptional and epigenetic regulation of memory NK cell responses. Immunol Rev 2021; 300:125-133. [PMID: 33491231 DOI: 10.1111/imr.12947] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes with key roles in host protection against viruses and malignancy. Notwithstanding their historical classification as innate immune cells, NK cells are now understood to have some capacity to mount memory or memory-like immune responses in which effector cells undergo antigen-driven expansion and give rise to long-lived memory cells with enhanced functionality. Understanding how antigen-specific effector and memory NK responses are regulated is an important and active area of research in the field. Here, we discuss key transcription factors and epigenetic processes involved in antigen-specific effector and memory NK cell differentiation.
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Affiliation(s)
- Aimee M Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA.,Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
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93
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FitzPatrick MEB, Provine NM, Garner LC, Powell K, Amini A, Irwin SL, Ferry H, Ambrose T, Friend P, Vrakas G, Reddy S, Soilleux E, Klenerman P, Allan PJ. Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets. Cell Rep 2021; 34:108661. [PMID: 33472060 PMCID: PMC7816164 DOI: 10.1016/j.celrep.2020.108661] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/14/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Tissue-resident memory T (TRM) cells provide key adaptive immune responses in infection, cancer, and autoimmunity. However, transcriptional heterogeneity of human intestinal TRM cells remains undefined. Here, we investigate transcriptional and functional heterogeneity of human TRM cells through study of donor-derived TRM cells from intestinal transplant recipients. Single-cell transcriptional profiling identifies two transcriptional states of CD8+ TRM cells, delineated by ITGAE and ITGB2 expression. We define a transcriptional signature discriminating these populations, including differential expression of cytotoxicity- and residency-associated genes. Flow cytometry of recipient-derived cells infiltrating the graft, and lymphocytes from healthy gut, confirm these CD8+ TRM phenotypes. CD8+ CD69+CD103+ TRM cells produce interleukin-2 (IL-2) and demonstrate greater polyfunctional cytokine production, whereas β2-integrin+CD69+CD103− TRM cells have higher granzyme expression. Analysis of intestinal CD4+ T cells identifies several parallels, including a β2-integrin+ population. Together, these results describe the transcriptional, phenotypic, and functional heterogeneity of human intestinal CD4+ and CD8+ TRM cells. Human intestinal transplants were used to identify bona fide TRM cells Single-cell RNA sequencing identifies two distinct CD8+ TRM subsets CD103+CD69+ and CD103−CD69+ TRM cell subsets show distinct localization and function β2-integrin is highly expressed on CD103− TRM cells
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Affiliation(s)
- Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Kate Powell
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Sophie L Irwin
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Helen Ferry
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Tim Ambrose
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Peter Friend
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Georgios Vrakas
- Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Srikanth Reddy
- Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Elizabeth Soilleux
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK.
| | - Philip J Allan
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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94
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Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, Eschweiler S, Grifoni A, Pelosi E, Weiskopf D, Sette A, Ay F, Seumois G, Ottensmeier CH, Vijayanand P. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4 + T Cells in COVID-19. Cell 2020; 183:1340-1353.e16. [PMID: 33096020 PMCID: PMC7534589 DOI: 10.1016/j.cell.2020.10.001] [Citation(s) in RCA: 367] [Impact Index Per Article: 91.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/13/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022]
Abstract
The contribution of CD4+ T cells to protective or pathogenic immune responses to SARS-CoV-2 infection remains unknown. Here, we present single-cell transcriptomic analysis of >100,000 viral antigen-reactive CD4+ T cells from 40 COVID-19 patients. In hospitalized patients compared to non-hospitalized patients, we found increased proportions of cytotoxic follicular helper cells and cytotoxic T helper (TH) cells (CD4-CTLs) responding to SARS-CoV-2 and reduced proportion of SARS-CoV-2-reactive regulatory T cells (TREG). Importantly, in hospitalized COVID-19 patients, a strong cytotoxic TFH response was observed early in the illness, which correlated negatively with antibody levels to SARS-CoV-2 spike protein. Polyfunctional TH1 and TH17 cell subsets were underrepresented in the repertoire of SARS-CoV-2-reactive CD4+ T cells compared to influenza-reactive CD4+ T cells. Together, our analyses provide insights into the gene expression patterns of SARS-CoV-2-reactive CD4+ T cells in distinct disease severities.
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Affiliation(s)
| | | | | | - Serena J Chee
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | | | - Hayley Simon
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Alba Grifoni
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Emanuela Pelosi
- Southampton Specialist Virology Center, University Hospitals NHS Foundation Trust, Southampton SO16 6YD, UK
| | | | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Christian H Ottensmeier
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; Institute of Translational Medicine, Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool L69 7ZX, UK.
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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95
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Sun Y, Preiss NK, Valenteros KB, Kamal Y, Usherwood YK, Frost HR, Usherwood EJ. Zbtb20 Restrains CD8 T Cell Immunometabolism and Restricts Memory Differentiation and Antitumor Immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:2649-2666. [PMID: 32998985 PMCID: PMC7931848 DOI: 10.4049/jimmunol.2000459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022]
Abstract
CD8 T cell differentiation is orchestrated by dynamic metabolic changes that direct activation, proliferation, cytotoxic function, and epigenetic changes. We report that the BTB-ZF family transcriptional repressor Zbtb20 negatively regulates CD8 T cell metabolism and memory differentiation in mice. Effector and memory CD8 T cells with conditional Zbtb20 deficiency displayed enhanced mitochondrial and glycolytic metabolism, and memory CD8 T cells had enhanced spare respiratory capacity. Furthermore, Zbtb20-deficient CD8 T cells displayed increased flexibility in the use of mitochondrial fuel sources. Phenotypic and transcriptional skewing toward the memory fate was observed during the CD8 T cell response to Listeria monocytogenes Memory cells mounted larger secondary responses and conferred better protection following tumor challenge. These data suggest that inactivation of Zbtb20 may offer an approach to enhance metabolic activity and flexibility and improve memory CD8 T cell differentiation, useful attributes for T cells used in adoptive immunotherapy.
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Affiliation(s)
- Yanbo Sun
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755; and
| | - Nicholas K Preiss
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755; and
| | - Kristine B Valenteros
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755; and
| | - Yasmin Kamal
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Young-Kwang Usherwood
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755; and
| | - H Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756
| | - Edward J Usherwood
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755; and
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96
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Prinzing B, Schreiner P, Bell M, Fan Y, Krenciute G, Gottschalk S. MyD88/CD40 signaling retains CAR T cells in a less differentiated state. JCI Insight 2020; 5:136093. [PMID: 33148882 PMCID: PMC7710311 DOI: 10.1172/jci.insight.136093] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy for solid tumors has shown limited efficacy in early-phase clinical studies. The majority of CARs encode CD28 and/or 41BB costimulatory endodomains, and we explored whether MyD88 and CD40 (MC) costimulatory endodomains in CARs could improve their antitumor activity. We generated CD28-, 41BB-, and MC-CAR T cells and demonstrated that MC-CAR T cells have greater proliferative capacity and antitumor activity in repeat stimulation assays and in tumor models in vivo. Transcriptomic analysis revealed that MC-CAR T cells expressed higher levels of MYB and FOXM1, key cell cycle regulators, and were activated at baseline. After stimulation, MC-CAR T cells remained in a less differentiated state than CD28- and 41BB-CAR T cells as judged by low levels of transcription factor TBET and B lymphocyte induced maturation protein 1 expression and lower cytolytic activity in comparison with CD28- and 41BB-CAR T cells. Thus, including MyD88 and CD40 signaling domains in CARs may improve current CAR T cell therapy approaches for solid tumors.
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Affiliation(s)
- Brooke Prinzing
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA
| | | | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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97
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Tittarelli A, Navarrete M, Lizana M, Hofmann-Vega F, Salazar-Onfray F. Hypoxic Melanoma Cells Deliver microRNAs to Dendritic Cells and Cytotoxic T Lymphocytes through Connexin-43 Channels. Int J Mol Sci 2020; 21:ijms21207567. [PMID: 33066331 PMCID: PMC7589225 DOI: 10.3390/ijms21207567] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Alterations in microRNA (miRNA) profiles, induced by tumor microenvironment stressors, like hypoxia, allow cancer cells to acquire immune-resistance phenotypes. Indeed, hypoxia-induced miRNAs have been implicated in cancer progression through numerous cancer cell non-autonomous mechanisms, including the direct transfer of hypoxia-responsive miRNA from cancer to immune cells via extracellular vesicles. Connexin-43 (Cx43)-constituted gap junctions (GJs) have also been involved in miRNA intercellular mobilization, in other biological processes. In this report, we aimed to evaluate the involvement of Cx43-GJs in the shift of miRNAs induced by hypoxia, from hypoxic melanoma cells to dendritic cells and melanoma-specific cytotoxic T lymphocytes (CTLs). Using qRT-PCR arrays, we identified that miR-192-5p was strongly induced in hypoxic melanoma cells. Immune cells acquired this miRNA after co-culture with hypoxic melanoma cells. The transfer of miR-192-5p was inhibited when hypoxic melanoma cells expressed a dominant negative Cx43 mutant or when Cx43 expression was silenced using specific short-hairpin RNAs. Interestingly, miR-192-5p levels on CTLs after co-culture with hypoxic melanoma cells were inversely correlated with the cytotoxic activity of T cells and with ZEB2 mRNA expression, a validated immune-related target of miR-192-5p, which is also observed in vivo. Altogether, our data suggest that hypoxic melanoma cells may suppress CTLs cytotoxic activity by transferring hypoxia-induced miR-192-5p through a Cx43-GJs driven mechanism, constituting a resistance strategy for immunological tumor escape.
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Affiliation(s)
- Andrés Tittarelli
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana (UTEM), Santiago 8940577, Chile
- Correspondence: ; Tel.: +56-2-2787-7903
| | - Mariela Navarrete
- Disciplinary Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (M.N.); (M.L.); (F.H.-V.); (F.S.-O.)
- Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Marcelo Lizana
- Disciplinary Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (M.N.); (M.L.); (F.H.-V.); (F.S.-O.)
| | - Francisca Hofmann-Vega
- Disciplinary Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (M.N.); (M.L.); (F.H.-V.); (F.S.-O.)
| | - Flavio Salazar-Onfray
- Disciplinary Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (M.N.); (M.L.); (F.H.-V.); (F.S.-O.)
- Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
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98
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Milner JJ, Nguyen H, Omilusik K, Reina-Campos M, Tsai M, Toma C, Delpoux A, Boland BS, Hedrick SM, Chang JT, Goldrath AW. Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population. Proc Natl Acad Sci U S A 2020; 117:25667-25678. [PMID: 32978300 PMCID: PMC7568335 DOI: 10.1073/pnas.2008571117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Memory CD8 T cells provide durable protection against diverse intracellular pathogens and can be broadly segregated into distinct circulating and tissue-resident populations. Paradigmatic studies have demonstrated that circulating memory cells can be further divided into effector memory (Tem) and central memory (Tcm) populations based on discrete functional characteristics. Following resolution of infection, we identified a persisting antigen-specific CD8 T cell population that was terminally fated with potent effector function but maintained memory T cell qualities and conferred robust protection against reinfection. Notably, this terminally differentiated effector memory CD8 T cell population (terminal-Tem) was conflated within the conventional Tem population, prompting redefinition of the classical characteristics of Tem cells. Murine terminal-Tem were transcriptionally, functionally, and developmentally unique compared to Tem cells. Through mass cytometry and single-cell RNA sequencing (RNA-seq) analyses of human peripheral blood from healthy individuals, we also identified an analogous terminal-Tem population of CD8 T cells that was transcriptionally distinct from Tem and Tcm Key findings from this study show that parsing of terminal-Tem from conventionally defined Tem challenge the reported characteristics of Tem biology, including enhanced presence in lymphoid tissues, robust IL-2 production, and recall potential, greater than expected homeostatic fitness, refined transcription factor dependencies, and a distinct molecular phenotype. Classification of terminal-Tem and clarification of Tem biology hold broad implications for understanding the molecular regulation of memory cell states and harnessing immunological memory to improve immunotherapies.
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Affiliation(s)
- J Justin Milner
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
| | - Hongtuyet Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Miguel Reina-Campos
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Matthew Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Arnaud Delpoux
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Stephen M Hedrick
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
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99
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Early programming of CD8 + T cell response by the orphan nuclear receptor NR4A3. Proc Natl Acad Sci U S A 2020; 117:24392-24402. [PMID: 32913051 DOI: 10.1073/pnas.2007224117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enhancing long-term persistence while simultaneously potentiating the effector response of CD8+ T cells has been a long-standing goal in immunology to produce better vaccines and adoptive cell therapy products. NR4A3 is a transcription factor of the orphan nuclear receptor family. While it is rapidly and transiently expressed following T cell activation, its role in the early stages of T cell response is unknown. We show that NR4A3-deficient murine CD8+ T cells differentiate preferentially into memory precursor and central memory cells, but also produce more cytokines. This is explained by an early influence of NR4A3 deficiency on the memory transcriptional program and on accessibility of chromatin regions with motifs for bZIP transcription factors, which impacts the transcription of Fos/Jun target genes. Our results reveal a unique and early role for NR4A3 in programming CD8+ T cell differentiation and function. Manipulating NR4A3 activity may represent a promising strategy to improve vaccination and T cell therapy.
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100
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Zou D, Fu J, Guo Z, Chen W. Interferon regulatory factor 4 deficiency in CD8 + T cells abrogates terminal effector differentiation and promotes transplant acceptance. Immunology 2020; 161:364-379. [PMID: 32892353 DOI: 10.1111/imm.13258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Allogeneic CD8+ cytotoxic T cells play an essential role in rejecting transplanted allografts, but how their effector function is regulated on a transcriptional level remains unclear. Herein, we investigate the role of interferon regulatory factor 4 (IRF4) in controlling CD8+ T-cell function in response to transplant. B6.Rag1-/- mice were adoptively transferred with CD8+ T cells isolated from either Irf4fl/fl Cd4-Cre (T-cell-specific Irf4-deficient) or Irf4fl/fl control mice, followed by BALB/c skin transplantation. Recipients that received Irf4-deficient CD8+ T cells permanently accepted the skin allografts, whereas recipients that received control CD8+ T cells acutely rejected the transplanted skins. Mechanistically, compared with the transferred control CD8+ T cells in B6.Rag1-/- recipients, the transferred Irf4-deficient CD8+ T cells lost the capacity to differentiate into CD127- KLRG1+ terminal effector cells, barely produced effector cytokines and cytotoxic molecules (e.g. IL-2, IFN-γ, TNF-α, granzyme A and granzyme B), and displayed defect in proliferative capacity, evident by their decreased Ki67 expression and lower frequencies. Moreover, the transferred Irf4-deficient CD8+ T cells displayed low expression of transcription factors ID2 and T-bet that govern the terminal effector T-cell programmes, and high expression of transcription factor TCF1 that maintains the naïve-memory T-cell programmes. Hence, IRF4 deficiency in CD8+ T cells abrogates their terminal effector differentiation and promotes transplant acceptance. These findings suggest that targeting IRF4 expression represents an attractive and promising therapeutic approach for inducing transplant acceptance.
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Affiliation(s)
- Dawei Zou
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Jinfei Fu
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Zhiyong Guo
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenhao Chen
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX, USA.,Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
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