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Zhao X, Hu W, Park SR, Zhu S, Hu SS, Zang C, Peng W, Shan Q, Xue HH. The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8 + T cell fates. Nat Immunol 2024; 25:294-306. [PMID: 38238608 PMCID: PMC10916363 DOI: 10.1038/s41590-023-01720-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/28/2023] [Indexed: 02/03/2024]
Abstract
Antigen-experienced CD8+ T cells form effector and central memory T cells (TEM and TCM cells, respectively); however, the mechanism(s) controlling their lineage plasticity remains incompletely understood. Here we show that the transcription cofactor Tle3 critically regulates TEM and TCM cell fates and lineage stability through dynamic redistribution in antigen-responding CD8+ T cell genome. Genetic ablation of Tle3 promoted CD8+ TCM cell formation at the expense of CD8+ TEM cells. Lineage tracing showed that Tle3-deficient CD8+ TEM cells underwent accelerated conversion into CD8+ TCM cells while retaining robust recall capacity. Tle3 acted as a coactivator for Tbet to increase chromatin opening at CD8+ TEM cell-characteristic sites and to activate CD8+ TEM cell signature gene transcription, while engaging Runx3 and Tcf1 to limit CD8+ TCM cell-characteristic molecular features. Thus, Tle3 integrated functions of multiple transcription factors to guard lineage fidelity of CD8+ TEM cells, and manipulation of Tle3 activity could favor CD8+ TCM cell production.
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Affiliation(s)
- Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Wei Hu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Sung Rye Park
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Qiang Shan
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA.
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA.
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2
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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3
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Jaccard A, Wyss T, Maldonado-Pérez N, Rath JA, Bevilacqua A, Peng JJ, Lepez A, Von Gunten C, Franco F, Kao KC, Camviel N, Martín F, Ghesquière B, Migliorini D, Arber C, Romero P, Ho PC, Wenes M. Reductive carboxylation epigenetically instructs T cell differentiation. Nature 2023; 621:849-856. [PMID: 37730993 DOI: 10.1038/s41586-023-06546-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 08/15/2023] [Indexed: 09/22/2023]
Abstract
Protective immunity against pathogens or cancer is mediated by the activation and clonal expansion of antigen-specific naive T cells into effector T cells. To sustain their rapid proliferation and effector functions, naive T cells switch their quiescent metabolism to an anabolic metabolism through increased levels of aerobic glycolysis, but also through mitochondrial metabolism and oxidative phosphorylation, generating energy and signalling molecules1-3. However, how that metabolic rewiring drives and defines the differentiation of T cells remains unclear. Here we show that proliferating effector CD8+ T cells reductively carboxylate glutamine through the mitochondrial enzyme isocitrate dehydrogenase 2 (IDH2). Notably, deletion of the gene encoding IDH2 does not impair the proliferation of T cells nor their effector function, but promotes the differentiation of memory CD8+ T cells. Accordingly, inhibiting IDH2 during ex vivo manufacturing of chimeric antigen receptor (CAR) T cells induces features of memory T cells and enhances antitumour activity in melanoma, leukaemia and multiple myeloma. Mechanistically, inhibition of IDH2 activates compensating metabolic pathways that cause a disequilibrium in metabolites regulating histone-modifying enzymes, and this maintains chromatin accessibility at genes that are required for the differentiation of memory T cells. These findings show that reductive carboxylation in CD8+ T cells is dispensable for their effector response and proliferation, but that it mainly produces a pattern of metabolites that epigenetically locks CD8+ T cells into a terminal effector differentiation program. Blocking this metabolic route allows the increased formation of memory T cells, which could be exploited to optimize the therapeutic efficacy of CAR T cells.
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Affiliation(s)
- Alison Jaccard
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
| | - Tania Wyss
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Translational Data Science (TDS) Group, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Noelia Maldonado-Pérez
- Department of Genomic Medicine, Pfizer-University of Granada-Junta de Andalucía, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Jan A Rath
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Alessio Bevilacqua
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
| | - Jhan-Jie Peng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Anouk Lepez
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
| | - Christine Von Gunten
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Fabien Franco
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
| | - Kung-Chi Kao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
| | - Nicolas Camviel
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Francisco Martín
- Department of Genomic Medicine, Pfizer-University of Granada-Junta de Andalucía, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Bart Ghesquière
- Metabolomics Expertise Center, Center for Cancer Biology, VIB, KU Leuven, Leuven, Belgium
- Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Denis Migliorini
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Department of Oncology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Caroline Arber
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Pedro Romero
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Épalinges, Switzerland.
| | - Mathias Wenes
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
- AGORA Cancer Research Center, Lausanne, Switzerland.
- Swiss Cancer Center Léman, Lausanne, Switzerland.
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland.
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5
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Xu W, Patel CH, Zhao L, Sun IH, Oh MH, Sun IM, Helms RS, Wen J, Powell JD. GOT1 regulates CD8 + effector and memory T cell generation. Cell Rep 2023; 42:111987. [PMID: 36640309 PMCID: PMC9943022 DOI: 10.1016/j.celrep.2022.111987] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/20/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
T cell activation, proliferation, function, and differentiation are tightly linked to proper metabolic reprogramming and regulation. By using [U-13C]glucose tracing, we reveal a critical role for GOT1 in promoting CD8+ T cell effector differentiation and function. Mechanistically, GOT1 enhances proliferation by maintaining intracellular redox balance and serine-mediated purine nucleotide biosynthesis. Further, GOT1 promotes the glycolytic programming and cytotoxic function of cytotoxic T lymphocytes via posttranslational regulation of HIF protein, potentially by regulating the levels of α-ketoglutarate. Conversely, genetic deletion of GOT1 promotes the generation of memory CD8+ T cells.
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Affiliation(s)
- Wei Xu
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chirag H Patel
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Calico LLC, South San Francisco, CA 94080, USA
| | - Liang Zhao
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Im-Hong Sun
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Min-Hee Oh
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Im-Meng Sun
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel S Helms
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiayu Wen
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan D Powell
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Calico LLC, South San Francisco, CA 94080, USA.
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6
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Patel CH, Heikamp EB, Xu W, Sun IH, Oh MH, Sun IM, Wen J, Tam AJ, Blosser RL, Powell JD. Cutting Edge: mTORC2 Regulates CD8+ Effector and Memory T Cell Differentiation through Serum and Glucocorticoid Kinase 1. J Immunol 2022; 209:2287-2291. [PMID: 36469844 PMCID: PMC10065985 DOI: 10.4049/jimmunol.2100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/11/2022] [Indexed: 01/04/2023]
Abstract
The mechanistic target of rapamycin is an essential regulator of T cell metabolism and differentiation. In this study, we demonstrate that serum- and glucocorticoid-regulated kinase 1 (SGK1), a downstream node of mechanistic target of rapamycin complex 2 signaling, represses memory CD8+ T cell differentiation. During acute infections, murine SGK1-deficient CD8+ T cells adopt an early memory precursor phenotype leading to more long-lived memory T cells. Thus, SGK1-deficient CD8+ T cells demonstrate an enhanced recall capacity in response to reinfection and can readily reject tumors. Mechanistically, activation of SGK1-deficient CD8+ T cells results in decreased Foxo1 phosphorylation and increased nuclear translocation of Foxo1 to promote early memory development. Overall, SGK1 might prove to be a powerful target for enhancing the efficacy of vaccines and tumor immunotherapy.
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Affiliation(s)
- Chirag H. Patel
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Current address: Calico LLC, South San Francisco, CA 94080
- Equal contribution
| | - Emily B. Heikamp
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA 02215, USA
- Equal contribution
| | - Wei Xu
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Im-Hong Sun
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Min-Hee Oh
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Im-Meng Sun
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiayu Wen
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ada J. Tam
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Richard L. Blosser
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan D. Powell
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney-Kimmel Comprehensive Cancer Research Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Current address: Calico LLC, South San Francisco, CA 94080
- Lead Contact
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Zhang Z, Butler R, Koestler DC, Bell-Glenn S, Warrier G, Molinaro AM, Christensen BC, Wiencke JK, Kelsey KT, Salas LA. Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages. Clin Epigenetics 2022; 14:173. [PMID: 36522672 PMCID: PMC9753273 DOI: 10.1186/s13148-022-01399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common epigenetic pathways among cell lineages. Further, it remains unclear if long-lived memory cell subtypes differentiate distinctly by cell lineages. RESULTS We used the Illumina EPIC array to investigate the consistency of DNA methylation in B cell, CD4 T, and CD8 T naïve and memory cells states. In the process of naïve to memory activation across the three lineages, we identify considerable shared epigenetic regulation at the DNA level for immune memory generation. Further, in central to effector memory differentiation, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T cells with DNA methylation changes. Finally, we identified unique DNA methylation patterns in terminally differentiated effector memory (TEMRA) CD8 T cells compared to other CD8 T memory cell subtypes. CONCLUSIONS Our data suggest that epigenetic alterations are widespread and essential in generating human lymphocyte memory. Unique profiles are involved in methylation changes that accompany memory genesis in the three subtypes of lymphocytes.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Rondi Butler
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Devin C Koestler
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Gayathri Warrier
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - John K Wiencke
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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8
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Fuse N, Okamori C, Okaji R, Tang C, Hirai K, Kurata S. Transcriptome features of innate immune memory in Drosophila. PLoS Genet 2022; 18:e1010005. [PMID: 36252180 PMCID: PMC9612818 DOI: 10.1371/journal.pgen.1010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/27/2022] [Accepted: 10/03/2022] [Indexed: 11/21/2022] Open
Abstract
Immune memory is the ability of organisms to elicit potentiated immune responses at secondary infection. Current studies have revealed that similar to adaptive immunity, innate immunity exhibits memory characteristics (called "innate immune memory"). Although epigenetic reprogramming plays an important role in innate immune memory, the underlying mechanisms have not been elucidated, especially at the individual level. Here, we established experimental systems for detecting innate immune memory in Drosophila melanogaster. Training infection with low-pathogenic bacteria enhanced the survival rate of the flies at subsequent challenge infection with high-pathogenic bacteria. Among low-pathogenic bacteria, Micrococcus luteus (Ml) and Salmonella typhimurium (St) exerted apparent training effects in the fly but exhibited different mechanisms of action. Ml exerted training effects even after its clearance from flies, while live St persisted in the flies for a prolonged duration. RNA sequencing (RNA-Seq) analysis revealed that Ml training enhanced the expression of the immune-related genes under the challenge condition but not under the non-challenge condition. In contrast, St training upregulated the expression of the immune-related genes independent of challenge. These results suggest that training effects with Ml and St are due to memory and persistence of immune responses, respectively. Furthermore, we searched for the gene involved in immune memory, and identified a candidate gene, Ada2b, which encodes a component of the histone modification complex. The Ada2b mutant suppressed Ml training effects on survival and disrupted the expression of some genes under the training + challenge condition. These results suggest that the gene expression regulated by Ada2b may contribute to innate immune memory in Drosophila.
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Affiliation(s)
- Naoyuki Fuse
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- * E-mail: (NF); (SK)
| | - Chisaki Okamori
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ryoma Okaji
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Chang Tang
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kikuko Hirai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- * E-mail: (NF); (SK)
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9
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Gupta PK, Allocco JB, Fraipont JM, McKeague ML, Wang P, Andrade MS, McIntosh C, Chen L, Wang Y, Li Y, Andrade J, Conejo-Garcia JR, Chong AS, Alegre ML. Reduced Satb1 expression predisposes CD4 + T conventional cells to Treg suppression and promotes transplant survival. Proc Natl Acad Sci U S A 2022; 119:e2205062119. [PMID: 36161903 PMCID: PMC9546564 DOI: 10.1073/pnas.2205062119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Limiting CD4+ T cell responses is important to prevent solid organ transplant rejection. In a mouse model of costimulation blockade-dependent cardiac allograft tolerance, we previously reported that alloreactive CD4+ conventional T cells (Tconvs) develop dysfunction, losing proliferative capacity. In parallel, induction of transplantation tolerance is dependent on the presence of regulatory T cells (Tregs). Whether susceptibility of CD4+ Tconvs to Treg suppression is modulated during tolerance induction is unknown. We found that alloreactive Tconvs from transplant tolerant mice had augmented sensitivity to Treg suppression when compared with memory T cells from rejector mice and expressed a transcriptional profile distinct from these memory T cells, including down-regulated expression of the transcription factor Special AT-rich sequence-binding protein 1 (Satb1). Mechanistically, Satb1 deficiency in CD4+ T cells limited their expression of CD25 and IL-2, and addition of Tregs, which express higher levels of CD25 than Satb1-deficient Tconvs and successfully competed for IL-2, resulted in greater suppression of Satb1-deficient than wild-type Tconvs in vitro. In vivo, Satb1-deficient Tconvs were more susceptible to Treg suppression, resulting in significantly prolonged skin allograft survival. Overall, our study reveals that transplantation tolerance is associated with Tconvs' susceptibility to Treg suppression, via modulated expression of Tconv-intrinsic Satb1. Targeting Satb1 in the context of Treg-sparing immunosuppressive therapies might be exploited to improve transplant outcomes.
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Affiliation(s)
- Pawan K. Gupta
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Jennifer B. Allocco
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Jane M. Fraipont
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Michelle L. McKeague
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Peter Wang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Michael S. Andrade
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637
| | - Christine McIntosh
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Luqiu Chen
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Ying Wang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Yan Li
- Center for Research Informatics, University of Chicago, Chicago, IL 60637
| | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL 60637
| | - José R. Conejo-Garcia
- Department of Immunology, Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, FL 33612
| | - Anita S. Chong
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637
| | - Maria-Luisa Alegre
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
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10
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Abstract
Current studies have demonstrated that innate immunity possesses memory characteristics. Although the molecular mechanisms underlying innate immune memory have been addressed by numerous studies, genetic variations in innate immune memory and the associated genes remain unclear. Here, we explored innate immune memory in 163 lines of Drosophila melanogaster from the Drosophila Synthetic Population Resource. In our assay system, prior training with low pathogenic bacteria (Micrococcus luteus) increased the survival rate of flies after subsequent challenge with highly pathogenic bacteria (Staphylococcus aureus). This positive training effect was observed in most lines, but some lines exhibited negative training effects. Survival rates under training and control conditions were poorly correlated, suggesting that distinct genetic factors regulate training effects and normal immune responses. Subsequent quantitative trait loci analysis suggested that four loci containing 80 genes may be involved in regulating innate immune memory. Among them, Adgf-A, which encodes an extracellular adenosine deaminase-related growth factor, was shown to be associated with training effects. Our study findings help to elucidate the genetic architecture of innate immune memory in Drosophila and may provide insight for new therapeutic treatments aimed at boosting immunity.
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Affiliation(s)
| | | | - Naoyuki Fuse
- *Correspondence: Shoichiro Kurata, ; Naoyuki Fuse,
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11
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Machado HE, Mitchell E, Øbro NF, Kübler K, Davies M, Leongamornlert D, Cull A, Maura F, Sanders MA, Cagan ATJ, McDonald C, Belmonte M, Shepherd MS, Vieira Braga FA, Osborne RJ, Mahbubani K, Martincorena I, Laurenti E, Green AR, Getz G, Polak P, Saeb-Parsy K, Hodson DJ, Kent DG, Campbell PJ. Diverse mutational landscapes in human lymphocytes. Nature 2022; 608:724-732. [PMID: 35948631 PMCID: PMC9402440 DOI: 10.1038/s41586-022-05072-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022]
Abstract
The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.
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Affiliation(s)
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nina F Øbro
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kirsten Kübler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Megan Davies
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Molecular Diagnostics, Milton Road, Cambridge, United Kingdom
| | | | - Alyssa Cull
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Craig McDonald
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | - Mairi S Shepherd
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Robert J Osborne
- Wellcome Sanger Institute, Hinxton, UK
- Biofidelity, 330 Cambridge Science Park, Milton Road, Cambridge, United Kingdom
| | - Krishnaa Mahbubani
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Elisa Laurenti
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paz Polak
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - David G Kent
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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12
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Zhou J, Wen T, Li Q, Chen Z, Peng X, Wei C, Wei Y, Peng J, Zhang W. Single-Cell Sequencing Revealed Pivotal Genes Related to Prognosis of Myocardial Infarction Patients. Comput Math Methods Med 2022; 2022:6534126. [PMID: 35317194 PMCID: PMC8934393 DOI: 10.1155/2022/6534126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/19/2022] [Indexed: 02/06/2023]
Abstract
Objectives Myocardial infarction (MI) is a common cardiovascular disease. Histopathology is a main molecular characteristic of MI, but often, differences between various cell subsets have been neglected. Under this premise, MI-related molecular biomarkers were screened using single-cell sequencing. Methods This work examined immune cell abundance in normal and MI samples from GSE109048 and determined differences in the activated mast cells and activated CD4 memory T cells, resting mast cells. Weighted gene coexpression network analysis (WGCNA) demonstrated that activated CD4 memory T cells were the most closely related to the turquoise module, and 10 hub genes were screened. Single-cell sequencing data (scRNA-seq) of MI were examined. We used t-distributed stochastic neighbor embedding (t-SNE) for cell clustering. Results We obtained 8 cell subpopulations, each of which had different marker genes. 7 out of the 10 hub genes were detected by single-cell sequencing analysis. The expression quantity and proportion of the 7 genes were different in 8 cell clusters. Conclusion In general, our study revealed the immune characteristics and determined 7 prognostic markers for MI at the single-cell level, providing a new understanding of the molecular characteristics and mechanism of MI.
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Affiliation(s)
- Jiamin Zhou
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Tong Wen
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Qing Li
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Zhixin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Xiaoping Peng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Chunying Wei
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Yunfeng Wei
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Jingtian Peng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province 330006, China
- Hypertension Research Institute, Hypertension Research Institute of Jiangxi Province, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
| | - Wei Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, 17 Yongwai Zhengjie, Donghu District, Nanchang City Jiangxi Province, China
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13
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Corinaldesi C, Holmes AB, Shen Q, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K. Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis. Front Immunol 2022; 12:818758. [PMID: 35095922 PMCID: PMC8789751 DOI: 10.3389/fimmu.2021.818758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
In response to T-cell-dependent antigens, mature B cells in the secondary lymphoid organs are stimulated to form germinal centers (GCs), which are histological structures deputed to antibody affinity maturation, a process associated with immunoglobulin gene editing by somatic hypermutation (SHM) and class switch recombination (CSR). GC B cells are heterogeneous and transition across multiple stages before being eliminated by apoptosis or committing to post-GC differentiation as memory B cells or plasma cells. In order to explore the dynamics of SHM and CSR during the GC reaction, we identified GC subpopulations by single-cell (sc) transcriptomics and analyzed the load of immunoglobulin variable (V) region mutations as well as the isotype class distribution in each subpopulation. The results showed that the large majority of GC B cells display a quantitatively similar mutational load in the V regions and analogous IGH isotype class distribution, except for the precursors of memory B cells (PreM) and plasma cells (PBL). PreM showed a bimodal pattern with about half of the cells displaying high V region germline identity and enrichment for unswitched IGH, while the rest of the cells carried a mutational load similar to the bulk of GC B cells and showed a switched isotype. PBL displayed a bias toward expression of IGHG and higher V region germline identity compared to the bulk of GC B cells. Genes implicated in SHM and CSR were significantly induced in specific GC subpopulations, consistent with the occurrence of SHM in dark zone cells and suggesting that CSR can occur within the GC.
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Affiliation(s)
| | - Antony B. Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Eli Grunstein
- Department of Otolaringology Head and Neck Surgery, Columbia University, New York, NY, United States
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
- Department of Microbiology and Immunology, Columbia University, New York, NY, United States
- Department of Genetics and Development, Columbia University, New York, NY, United States
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
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14
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Leleux JA, Albershardt TC, Reeves R, James R, Krull J, Parsons AJ, ter Meulen J, Berglund P. Intratumoral expression of IL-12 from lentiviral or RNA vectors acts synergistically with TLR4 agonist (GLA) to generate anti-tumor immunological memory. PLoS One 2021; 16:e0259301. [PMID: 34855754 PMCID: PMC8638928 DOI: 10.1371/journal.pone.0259301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
Systemic interleukin-12 (IL12) anti-tumor therapy is highly potent but has had limited utility in the clinic due to severe toxicity. Here, we present two IL12-expressing vector platforms, both of which can overcome the deficiencies of previous systemic IL12 therapies: 1) an integrating lentiviral vector, and 2) a self-replicating messenger RNA formulated with polyethyleneimine. Intratumoral administration of either IL12 vector platform resulted in recruitment of immune cells, including effector T cells and dendritic cells, and the complete remission of established tumors in multiple murine models. Furthermore, concurrent intratumoral administration of the synthetic TLR4 agonist glucopyranosyl lipid A formulated in a stable emulsion (GLA-SE) induced systemic memory T cell responses that mediated complete protection against tumor rechallenge in all survivor mice (8/8 rechallenged mice), whereas only 2/6 total rechallenged mice treated with intratrumoral IL12 monotherapy rejected the rechallenge. Taken together, expression of vectorized IL12 in combination with a TLR4 agonist represents a varied approach to broaden the applicability of intratumoral immune therapies of solid tumors.
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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/immunology
- Female
- Gene Expression Regulation
- Genetic Vectors/administration & dosage
- Genetic Vectors/pharmacology
- Glucosides/pharmacology
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Immunologic Memory/drug effects
- Immunologic Memory/genetics
- Immunotherapy/methods
- Interferon-gamma/blood
- Interleukin-12/blood
- Interleukin-12/genetics
- Interleukin-12/immunology
- Lentivirus/genetics
- Lipid A/pharmacology
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/therapy
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Transgenic
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/pathology
- Toll-Like Receptor 4/agonists
- Mice
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Affiliation(s)
- Jardin A. Leleux
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Tina C. Albershardt
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Rebecca Reeves
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Reice James
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Jordan Krull
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Andrea J. Parsons
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Jan ter Meulen
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
| | - Peter Berglund
- Immune Design Corp., Seattle, WA, A wholly owned subsidiary of Merck & Co., Inc., Kenilworth, NJ, United States of America
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15
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Acevedo OA, Berrios RV, Rodríguez-Guilarte L, Lillo-Dapremont B, Kalergis AM. Molecular and Cellular Mechanisms Modulating Trained Immunity by Various Cell Types in Response to Pathogen Encounter. Front Immunol 2021; 12:745332. [PMID: 34671359 PMCID: PMC8521023 DOI: 10.3389/fimmu.2021.745332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022] Open
Abstract
The induction of trained immunity represents an emerging concept defined as the ability of innate immune cells to acquire a memory phenotype, which is a typical hallmark of the adaptive response. Key points modulated during the establishment of trained immunity include epigenetic, metabolic and functional changes in different innate-immune and non-immune cells. Regarding to epigenetic changes, it has been described that long non-coding RNAs (LncRNAs) act as molecular scaffolds to allow the assembly of chromatin-remodeling complexes that catalyze epigenetic changes on chromatin. On the other hand, relevant metabolic changes that occur during this process include increased glycolytic rate and the accumulation of metabolites from the tricarboxylic acid (TCA) cycle, which subsequently regulate the activity of histone-modifying enzymes that ultimately drive epigenetic changes. Functional consequences of established trained immunity include enhanced cytokine production, increased antigen presentation and augmented antimicrobial responses. In this article, we will discuss the current knowledge regarding the ability of different cell subsets to acquire a trained immune phenotype and the molecular mechanisms involved in triggering such a response. This knowledge will be helpful for the development of broad-spectrum therapies against infectious diseases based on the modulation of epigenetic and metabolic cues regulating the development of trained immunity.
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Affiliation(s)
- Orlando A. Acevedo
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roslye V. Berrios
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Linmar Rodríguez-Guilarte
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bastián Lillo-Dapremont
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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16
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Jergović M, Coplen CP, Uhrlaub JL, Besselsen DG, Cheng S, Smithey MJ, Nikolich-Žugich J. Infection-induced type I interferons critically modulate the homeostasis and function of CD8 + naïve T cells. Nat Commun 2021; 12:5303. [PMID: 34489451 PMCID: PMC8421345 DOI: 10.1038/s41467-021-25645-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/21/2021] [Indexed: 11/14/2022] Open
Abstract
Naïve T (Tn) cells require two homeostatic signals for long-term survival: tonic T cell receptor:self-peptide-MHC contact and IL-7 stimulation. However, how microbial exposure impacts Tn homeostasis is still unclear. Here we show that infections can lead to the expansion of a subpopulation of long-lived, Ly6C+ CD8+ Tn cells with accelerated effector function. Mechanistically, mono-infection with West Nile virus transiently, and polymicrobial exposure persistently, enhances Ly6C expression selectively on CD5hiCD8+ cells, which in the case of polyinfection translates into a numerical CD8+ Tn cell increase in the lymph nodes. This conversion and expansion of Ly6C+ Tn cells depends on IFN-I, which upregulates MHC class I expression and enhances tonic TCR signaling in differentiating Tn cells. Moreover, for Ly6C+CD8+ Tn cells, IFN-I-mediated signals optimize their homing to secondary sites, extend their lifespan, and enhance their effector differentiation and antibacterial function, particularly for low-affinity clones. Our results thus uncover significant regulation of Tn homeostasis and function via infection-driven IFN-I, with potential implications for immunotherapy.
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Affiliation(s)
- Mladen Jergović
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Christopher P Coplen
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - Shu Cheng
- Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Megan J Smithey
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
- Vir, Inc., San Francisco, CA, USA
| | - Janko Nikolich-Žugich
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA.
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17
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Éliás S, Schmidt A, Gomez-Cabrero D, Tegnér J. Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells. J Immunol Res 2021; 2021:8880585. [PMID: 34285924 PMCID: PMC8275380 DOI: 10.1155/2021/8880585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 12/13/2022] Open
Abstract
GM-CSF produced by autoreactive CD4-positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as multiple sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF-positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF-producing CD4 T cells from human peripheral blood by using a cytokine capture assay. We compared these cells to the corresponding GM-CSF-negative fraction, and furthermore, we studied naïve CD4 T cells, memory CD4 T cells, and bulk CD4 T cells from the same individuals as additional control cell populations. As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets and we show that the identified signatures are associated with human autoimmune diseases, especially multiple sclerosis. By combining information about mRNA expression, DNA accessibility, and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF-positive CD4 T cells as well as memory CD4 T cells. Our results suggest potential therapeutic targets to be investigated in the future in human autoimmune disease.
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Affiliation(s)
- Szabolcs Éliás
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
| | - Angelika Schmidt
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London SE1 9RT, UK
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Saudi Arabia
| | - Jesper Tegnér
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Saudi Arabia
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18
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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Tissue resident memory T cells (TRM) are a critical component of the immune system, providing the body with an immediate and highly specific response against pathogens re-infecting peripheral tissues. More recently, however, it has been demonstrated that TRM cells also form during autoimmunity. TRM mediated autoimmune diseases are particularly destructive, because unlike foreign antigens, the self-antigens are never cleared, continuously activating self-reactive TRM T cells. In this article, we will focus on how TRMs mediate disease in autoimmune skin conditions, specifically vitiligo, psoriasis, cutaneous lupus erythematosus, alopecia areata and frontal fibrosing alopecia.
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Affiliation(s)
- Grace E. Ryan
- Department of Dermatology, University of Massachusetts Medical School, Worcester, MA, United States
| | | | - Jillian M. Richmond
- Department of Dermatology, University of Massachusetts Medical School, Worcester, MA, United States
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20
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Kushnareva Y, Mathews IT, Andreyev AY, Altay G, Lindestam Arlehamn CS, Pandurangan V, Nilsson R, Jain M, Sette A, Peters B, Sharma S. Functional Analysis of Immune Signature Genes in Th1* Memory Cells Links ISOC1 and Pyrimidine Metabolism to IFN-γ and IL-17 Production. J Immunol 2021; 206:1181-1193. [PMID: 33547171 PMCID: PMC7946769 DOI: 10.4049/jimmunol.2000672] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
CCR6+CXCR3+CCR4-CD4+ memory T cells, termed Th1*, are important for long-term immunity to Mycobacterium tuberculosis and the pathogenesis of autoimmune diseases. Th1* cells express a unique set of lineage-specific transcription factors characteristic of both Th1 and Th17 cells and display distinct gene expression profiles compared with other CD4+ T cell subsets. To examine molecules and signaling pathways important for the effector function of Th1* cells, we performed loss-of-function screening of genes selectively enriched in the Th1* subset. The genetic screen yielded candidates whose depletion significantly impaired TCR-induced IFN-γ production. These included genes previously linked to IFN-γ or M. tuberculosis susceptibility and novel candidates, such as ISOC1, encoding a metabolic enzyme of unknown function in mammalian cells. ISOC1-depleted T cells, which produced less IFN-γ and IL-17, displayed defects in oxidative phosphorylation and glycolysis and impairment of pyrimidine metabolic pathway. Supplementation with extracellular pyrimidines rescued both bioenergetics and IFN-γ production in ISOC1-deficient T cells, indicating that pyrimidine metabolism is a key driver of effector functions in CD4+ T cells and Th1* cells. Results provide new insights into the immune-stimulatory function of ISOC1 as well as the particular metabolic requirements of human memory T cells, providing a novel resource for understanding long-term T cell-driven responses.
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Affiliation(s)
| | - Ian T Mathews
- La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Alexander Y Andreyev
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
- The Scripps Research Institute, La Jolla, CA 92037; and
| | - Gokmen Altay
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | | | | | | | - Mohit Jain
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sonia Sharma
- La Jolla Institute for Immunology, La Jolla, CA 92037;
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21
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Delgobo M, Heinrichs M, Hapke N, Ashour D, Appel M, Srivastava M, Heckel T, Spyridopoulos I, Hofmann U, Frantz S, Ramos GC. Terminally Differentiated CD4 + T Cells Promote Myocardial Inflammaging. Front Immunol 2021; 12:584538. [PMID: 33679735 PMCID: PMC7935504 DOI: 10.3389/fimmu.2021.584538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/04/2021] [Indexed: 12/03/2022] Open
Abstract
The cardiovascular and immune systems undergo profound and intertwined alterations with aging. Recent studies have reported that an accumulation of memory and terminally differentiated T cells in elderly subjects can fuel myocardial aging and boost the progression of heart diseases. Nevertheless, it remains unclear whether the immunological senescence profile is sufficient to cause age-related cardiac deterioration or merely acts as an amplifier of previous tissue-intrinsic damage. Herein, we sought to decompose the causality in this cardio-immune crosstalk by studying young mice harboring a senescent-like expanded CD4+ T cell compartment. Thus, immunodeficient NSG-DR1 mice expressing HLA-DRB1*01:01 were transplanted with human CD4+ T cells purified from matching donors that rapidly engrafted and expanded in the recipients without causing xenograft reactions. In the donor subjects, the CD4+ T cell compartment was primarily composed of naïve cells defined as CCR7+CD45RO-. However, when transplanted into young lymphocyte-deficient mice, CD4+ T cells underwent homeostatic expansion, upregulated expression of PD-1 receptor and strongly shifted towards effector/memory (CCR7- CD45RO+) and terminally-differentiated phenotypes (CCR7-CD45RO-), as typically seen in elderly. Differentiated CD4+ T cells also infiltrated the myocardium of recipient mice at comparable levels to what is observed during physiological aging. In addition, young mice harboring an expanded CD4+ T cell compartment showed increased numbers of infiltrating monocytes, macrophages and dendritic cells in the heart. Bulk mRNA sequencing analyses further confirmed that expanding T-cells promote myocardial inflammaging, marked by a distinct age-related transcriptomic signature. Altogether, these data indicate that exaggerated CD4+ T-cell expansion and differentiation, a hallmark of the aging immune system, is sufficient to promote myocardial alterations compatible with inflammaging in juvenile healthy mice.
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Affiliation(s)
- Murilo Delgobo
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Margarete Heinrichs
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Nils Hapke
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - DiyaaElDin Ashour
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Marc Appel
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Core Unit Systems Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Tobias Heckel
- Core Unit Systems Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Ioakim Spyridopoulos
- Freeman Hospital, Department of Cardiology, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Cardiovascular Biology and Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ulrich Hofmann
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Stefan Frantz
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Gustavo Campos Ramos
- Comprehensive Heart Failure Centre, University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
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22
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Diggins KE, Serti E, Muir V, Rosasco M, Lu T, Balmas E, Nepom G, Long SA, Linsley PS. Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects. JCI Insight 2021; 6:142680. [PMID: 33351781 PMCID: PMC7934874 DOI: 10.1172/jci.insight.142680] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Clinical trials of biologic therapies in type 1 diabetes (T1D) aim to mitigate autoimmune destruction of pancreatic β cells through immune perturbation and serve as resources to elucidate immunological mechanisms in health and disease. In the T1DAL trial of alefacept (LFA3-Ig) in recent-onset T1D, endogenous insulin production was preserved in 30% of subjects for 2 years after therapy. Given our previous findings linking exhausted-like CD8+ T cells to beneficial response in T1D trials, we applied unbiased analyses to sorted CD8+ T cells to evaluate their potential role in T1DAL. Using RNA sequencing, we found that greater insulin C-peptide preservation was associated with a module of activation- and exhaustion-associated genes. This signature was dissected into 2 CD8 memory phenotypes through correlation with cytometry data. These cells were hypoproliferative, shared expanded rearranged TCR junctions, and expressed exhaustion-associated markers including TIGIT and KLRG1. The 2 phenotypes could be distinguished by reciprocal expression of CD8+ T and NK cell markers (GZMB, CD57, and inhibitory killer cell immunoglobulin-like receptor [iKIR] genes), versus T cell activation and differentiation markers (PD-1 and CD28). These findings support previous evidence linking exhausted-like CD8+ T cells to successful immune interventions for T1D, while suggesting that multiple inhibitory mechanisms can promote this beneficial cell state.
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Affiliation(s)
- Kirsten E. Diggins
- Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | | | - Virginia Muir
- Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Mario Rosasco
- Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - TingTing Lu
- Immune Tolerance Network (ITN), Bethesda, Maryland, USA
| | - Elisa Balmas
- Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Gerald Nepom
- Immune Tolerance Network (ITN), Bethesda, Maryland, USA
| | - S. Alice Long
- Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Peter S. Linsley
- Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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23
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Affiliation(s)
- Andrew R DiNardo
- From the Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital (A.R.D.), the Immigrant and Global Health Program, Department of Pediatrics (A.R.D.), and the Departments of Medicine and Molecular Virology and Microbiology (D.M.M.), Baylor College of Medicine, and the Medical Care Line, Infectious Disease Section, Michael E. DeBakey Veterans Affairs Medical Center (D.M.M.) - all in Houston; the Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands (M.G.N.); and the Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany (M.G.N.)
| | - Mihai G Netea
- From the Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital (A.R.D.), the Immigrant and Global Health Program, Department of Pediatrics (A.R.D.), and the Departments of Medicine and Molecular Virology and Microbiology (D.M.M.), Baylor College of Medicine, and the Medical Care Line, Infectious Disease Section, Michael E. DeBakey Veterans Affairs Medical Center (D.M.M.) - all in Houston; the Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands (M.G.N.); and the Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany (M.G.N.)
| | - Daniel M Musher
- From the Global Tuberculosis Program, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital (A.R.D.), the Immigrant and Global Health Program, Department of Pediatrics (A.R.D.), and the Departments of Medicine and Molecular Virology and Microbiology (D.M.M.), Baylor College of Medicine, and the Medical Care Line, Infectious Disease Section, Michael E. DeBakey Veterans Affairs Medical Center (D.M.M.) - all in Houston; the Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands (M.G.N.); and the Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany (M.G.N.)
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24
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Glinos DA, Soskic B, Williams C, Kennedy A, Jostins L, Sansom DM, Trynka G. Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation. Genes Immun 2020; 21:390-408. [PMID: 33223527 PMCID: PMC7785515 DOI: 10.1038/s41435-020-00118-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
T-cell activation is a critical driver of immune responses. The CD28 costimulation is an essential regulator of CD4 T-cell responses, however, its relative importance in naive and memory T cells is not fully understood. Using different model systems, we observe that human memory T cells are more sensitive to CD28 costimulation than naive T cells. To deconvolute how the T-cell receptor (TCR) and CD28 orchestrate activation of human T cells, we stimulate cells using varying intensities of TCR and CD28 and profiled gene expression. We show that genes involved in cell cycle progression and division are CD28-driven in memory cells, but under TCR control in naive cells. We further demonstrate that T-helper differentiation and cytokine expression are controlled by CD28. Using chromatin accessibility profiling, we observe that AP1 transcriptional regulation is enriched when both TCR and CD28 are engaged, whereas open chromatin near CD28-sensitive genes is enriched for NF-kB motifs. Lastly, we show that CD28-sensitive genes are enriched in GWAS regions associated with immune diseases, implicating a role for CD28 in disease development. Our study provides important insights into the differential role of costimulation in naive and memory T-cell responses and disease susceptibility.
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Affiliation(s)
- Dafni A Glinos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- New York Genome Center, New York, NY, 10013, USA
| | - Blagoje Soskic
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Cayman Williams
- UCL Institute of Immunity and Transplantation, Royal Free Hospital, London, NW3 2PF, UK
| | - Alan Kennedy
- UCL Institute of Immunity and Transplantation, Royal Free Hospital, London, NW3 2PF, UK
| | - Luke Jostins
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
- Big Data Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Christ Church, St. Aldates, Oxford, OX1 1DP, UK
| | - David M Sansom
- UCL Institute of Immunity and Transplantation, Royal Free Hospital, London, NW3 2PF, UK.
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
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25
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Stefano GB, Kream RM. Convalescent Memory T Cell Immunity in Individuals with Mild or Asymptomatic SARS-CoV-2 Infection May Result from an Evolutionarily Adapted Immune Response to Coronavirus and the 'Common Cold'. Med Sci Monit 2020; 26:e929789. [PMID: 33239605 PMCID: PMC7706138 DOI: 10.12659/msm.929789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Recent studies have shown a significant level of T cell immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in convalescent coronavirus disease 2019 (COVID-19) patients and unexposed healthy individuals. Also, SARS-CoV-2-reactive T memory cells occur in unexposed healthy individuals from endemic coronaviruses that cause the 'common cold.' The finding of the expression of adaptive SARS-CoV-2-reactive T memory cells in unexposed healthy individuals may be due to multiple cross-reactive viral protein targets following previous exposure to endemic human coronavirus infections. The opinion of the authors is that determination of protein sequence homologies across seemingly disparate viral protein libraries may provide epitope-matching data that link SARS-CoV-2-reactive T memory cell signatures to prior administration of cross-reacting vaccines to common viral pathogens. Exposure to SARS-CoV-2 initiates diverse cellular immune responses, including the associated 'cytokine storm'. Therefore, it is possible that the intact virus possesses a required degree of conformational matching, or stereoselectivity, to effectively target its receptor on multiple cell types. Therefore, conformational matching may be viewed as an evolving mechanism of viral infection and viral replication by an evolutionary modification of the angiotensin-converting enzyme 2 (ACE2) receptor required for SARS-CoV-2 binding and host cell entry. The authors propose that convalescent memory T cell immunity in individuals with mild or asymptomatic SARS-CoV-2 infection may result from an evolutionarily adapted immune response to coronavirus and the 'common cold'.
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Affiliation(s)
- George B. Stefano
- International Scientific Information, Inc., Melville, NY, U.S.A
- Center for Cognitive and Molecular Neuroscience, First Faculty of Medicine Charles University in Prague, Prague, Czech Republic
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26
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Barnes S, Schilizzi O, Audsley KM, Newnes HV, Foley B. Deciphering the Immunological Phenomenon of Adaptive Natural Killer (NK) Cells and Cytomegalovirus (CMV). Int J Mol Sci 2020; 21:ijms21228864. [PMID: 33238550 PMCID: PMC7700325 DOI: 10.3390/ijms21228864] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
Natural killer (NK) cells play a significant and vital role in the first line of defense against infection through their ability to target cells without prior sensitization. They also contribute significantly to the activation and recruitment of both innate and adaptive immune cells through the production of a range of cytokines and chemokines. In the context of cytomegalovirus (CMV) infection, NK cells and CMV have co-evolved side by side to employ several mechanisms to evade one another. However, during this co-evolution the discovery of a subset of long-lived NK cells with enhanced effector potential, increased antibody-dependent responses and the potential to mediate immune memory has revolutionized the field of NK cell biology. The ability of a virus to imprint on the NK cell receptor repertoire resulting in the expansion of diverse, highly functional NK cells to this day remains a significant immunological phenomenon that only occurs in the context of CMV. Here we review our current understanding of the development of these NK cells, commonly referred to as adaptive NK cells and their current role in transplantation, infection, vaccination and cancer immunotherapy to decipher the complex role of CMV in dictating NK cell functional fate.
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Affiliation(s)
- Samantha Barnes
- Telethon Kids Institute, University of Western Australia, Perth Children’s Hospital, Nedlands, WA 6009, Australia; (S.B.); (O.S.); (K.M.A.); (H.V.N.)
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ophelia Schilizzi
- Telethon Kids Institute, University of Western Australia, Perth Children’s Hospital, Nedlands, WA 6009, Australia; (S.B.); (O.S.); (K.M.A.); (H.V.N.)
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Katherine M. Audsley
- Telethon Kids Institute, University of Western Australia, Perth Children’s Hospital, Nedlands, WA 6009, Australia; (S.B.); (O.S.); (K.M.A.); (H.V.N.)
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Hannah V. Newnes
- Telethon Kids Institute, University of Western Australia, Perth Children’s Hospital, Nedlands, WA 6009, Australia; (S.B.); (O.S.); (K.M.A.); (H.V.N.)
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Bree Foley
- Telethon Kids Institute, University of Western Australia, Perth Children’s Hospital, Nedlands, WA 6009, Australia; (S.B.); (O.S.); (K.M.A.); (H.V.N.)
- Correspondence:
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27
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Huang D, Tran JT, Olson A, Vollbrecht T, Tenuta M, Guryleva MV, Fuller RP, Schiffner T, Abadejos JR, Couvrette L, Blane TR, Saye K, Li W, Landais E, Gonzalez-Martin A, Schief W, Murrell B, Burton DR, Nemazee D, Voss JE. Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells. Nat Commun 2020; 11:5850. [PMID: 33203876 PMCID: PMC7673113 DOI: 10.1038/s41467-020-19650-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/15/2020] [Indexed: 01/12/2023] Open
Abstract
HIV broadly neutralizing antibodies (bnAbs) can suppress viremia and protect against HIV infection. However, their elicitation is made difficult by low frequencies of appropriate precursor B cell receptors and the complex maturation pathways required to generate bnAbs from these precursors. Antibody genes can be engineered into B cells for expression as both a functional antigen receptor on cell surfaces and as secreted antibody. Here, we show that HIV bnAb-engineered primary mouse B cells can be adoptively transferred and vaccinated in immunocompetent mice resulting in the expansion of durable bnAb memory and long-lived plasma cells. Somatic hypermutation after immunization indicates that engineered cells have the capacity to respond to an evolving pathogen. These results encourage further exploration of engineered B cell vaccines as a strategy for durable elicitation of HIV bnAbs to protect against infection and as a contributor to a functional HIV cure.
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Affiliation(s)
- Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jenny Tuyet Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alex Olson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas Vollbrecht
- Department of Medicine, The University of California San Diego, La Jolla, CA, USA
| | - Mary Tenuta
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mariia V Guryleva
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Faculty of Bioengineering and Bioinformatics, Moscow Lomonosov State University, Moscow, Russia
| | - Roberta P Fuller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center (IAVI), The Scripps Research Institute, La Jolla, CA, USA
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center (IAVI), The Scripps Research Institute, La Jolla, CA, USA
| | - Justin R Abadejos
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lauren Couvrette
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Faculty of Science, University of Ottawa, Ottawa, Canada
| | - Tanya R Blane
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karen Saye
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center (IAVI), The Scripps Research Institute, La Jolla, CA, USA
| | - Wenjuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Alicia Gonzalez-Martin
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - William Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center (IAVI), The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center (IAVI), The Scripps Research Institute, La Jolla, CA, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA.
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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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. J Immunol 2020; 205:2649-2666. [PMID: 32998985 PMCID: PMC7931848 DOI: 10.4049/jimmunol.2000459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Wilkinson NG, Kopulos RT, Yates LM, Briles WE, Taylor RL. Major histocompatibility complex recombinant R13 antibody response against bovine red blood cells. Poult Sci 2020; 99:4804-4808. [PMID: 32988515 PMCID: PMC7598299 DOI: 10.1016/j.psj.2020.06.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/21/2020] [Accepted: 06/02/2020] [Indexed: 12/01/2022] Open
Abstract
Recombination within the chicken major histocompatibility complex (MHC) has enabled more precise identification of genes controlling immune responses. Chicken MHC genes include BF, MHC class I; BL, MHC class II; and BG, MHC class IV that are closely linked on chromosome 16. A new recombination occurred during the 10th backcross generation to develop congenic lines on the inbred Line UCD 003 (B17B17) background. Recombinant R13 (BF17-BG23) was found in a single male chick from the Line 003.R1 (BF24-BG23) backcross. An additional backcross of this male to Line UCD 003 females increased the number of R13 individuals. Two trials tested this new recombinant for antibody production against the T cell-dependent antigen, bovine red blood cells. Fifty-one progeny segregating for R13R13 (n = 10), R13B17 (n = 26), and B17B17 (n = 15) genotypes were produced by a single R13B17 male mated to 5 R13B17 dams. One milliliter of 2.5% bovine red blood cell was injected intravenously into all genotypes at 4 and 11 wk of age to stimulate primary and secondary immune responses, respectively. Blood samples were collected 7 d after injection. Serum total and mercaptoethanol-resistant antibodies against bovine red blood cell were measured by microtiter methods. The least squares ANOVA used to evaluate all antibody titers included trial and B genotype as main effects. Significant means were separated by Fisher's protected least significant difference at P < 0.05. R13R13 chickens had significantly lower primary total and mercaptoethanol-resistant antibodies than did the R13B17 and B17B17 genotypes. Secondary total and mercaptoethanol-resistant antibodies were significantly lower in R13R13 chickens than in R13B17 but not B17B17 chickens. Gene differences generated through recombination impacted the antibody response of R13 compared with B17. Secondary antibody titers were not substantially higher than the primary titers suggesting that the memory response had waned in the 7-wk interval between injections. Overall, the results suggest that the lower antibody response in R13R13 homozygotes may be caused by recombination affecting a region that contributes to higher antibody response.
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Affiliation(s)
- N G Wilkinson
- Department of Animal and Nutritional Sciences, University of New Hampshire, Durham, NH, USA
| | - R T Kopulos
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - L M Yates
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - W E Briles
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - R L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA.
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30
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Weisberg SP, Carpenter DJ, Chait M, Dogra P, Gartrell-Corrado RD, Chen AX, Campbell S, Liu W, Saraf P, Snyder ME, Kubota M, Danzl NM, Schrope BA, Rabadan R, Saenger Y, Chen X, Farber DL. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep 2020; 29:3916-3932.e5. [PMID: 31851923 PMCID: PMC6939378 DOI: 10.1016/j.celrep.2019.11.056] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
Non-recirculating tissue-resident memory T cells (TRMs) are the predominant T cell subset in diverse tissue sites, where they mediate protective immune responses in situ. Here, we reveal a role for TRM in maintaining immune homeostasis in the human pancreas through interactions with resident macrophages and the PD-1/PD-L1 inhibitory pathway. Using tissues obtained from organ donors, we identify that pancreas T cells comprise CD8+PD-1hi TRMs, which are phenotypically, functionally, and transcriptionally distinct compared to TRMs in neighboring jejunum and lymph node sites. Pancreas TRMs cluster with resident macrophages throughout the exocrine areas; TRM effector functions are enhanced by macrophage-derived co-stimulation and attenuated by the PD-1/PD-L1 pathways. Conversely, in samples from chronic pancreatitis, TRMs exhibit reduced PD-1 expression and reduced interactions with macrophages. These findings suggest important roles for PD-1 and TRM-macrophage interactions in controlling tissue homeostasis and immune dysfunctions underlying inflammatory disease, with important implications for PD-1-based immunotherapies.
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Affiliation(s)
- Stuart P Weisberg
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Dustin J Carpenter
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael Chait
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Pranay Dogra
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Andrew X Chen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sean Campbell
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Wei Liu
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Pooja Saraf
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark E Snyder
- Department of Medicine, Columbia University Medical Center, New York, NY 00132, USA
| | - Masaru Kubota
- Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Nichole M Danzl
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Beth A Schrope
- Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Yvonne Saenger
- Department of Medicine, Columbia University Medical Center, New York, NY 00132, USA
| | - Xiaojuan Chen
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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31
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Geigges M, Arekatla G, Paro R. Priming exposures to lipopolysaccharides do not affect the induction of Polycomb target genes upon re-exposure. PLoS One 2020; 15:e0231498. [PMID: 32287290 PMCID: PMC7156044 DOI: 10.1371/journal.pone.0231498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/24/2020] [Indexed: 11/18/2022] Open
Abstract
The Polycomb group (PcG) proteins are chromatin factors underlying the process of transcriptional memory to preserve developmental decisions and keep cellular identities. However, not only developmental signals need to be memorized and thus maintained during the life of an organism. For host protection against pathogens, also a memory of previous exposures to an immunogenic stimulus is crucial to mount a more protective immune response upon re-exposure. The antigen-specific adaptive immunity in vertebrates is an example of such a memory to previous immunogenic stimulation. Recently, adaptive characteristics were also attributed to innate immunity, which was classically seen to lack memory. However, the mechanistic details of an adaptive innate immune response are yet to be fully understood and chromatin-based epigenetic mechanisms seem to play an important role in this phenomenon. Possibly, PcG proteins can contribute to such an epigenetic innate immune memory. In this study, we analyzed whether the PcG system can mediate a transcriptional memory of exposure to lipopolysaccharides (LPS). To this end, various forms of LPS pre-treatment were applied to reporter cells and expression kinetics of PcG target genes were analyzed after a second LPS exposure. Neither single nor multiple LPS pre-treatment affected the induction of endogenous LPS-responsive transcripts upon re-exposure. Altogether, our extensive analyses did not provide any evidence for a PcG system-mediated memory of LPS stimulation.
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Affiliation(s)
- Marco Geigges
- Department of Biosystems Science and Engineering, Epigenomics Group, ETH Zurich, Basel, Switzerland
| | - Geethika Arekatla
- Department of Biosystems Science and Engineering, Epigenomics Group, ETH Zurich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, Epigenomics Group, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
- * E-mail:
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32
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Li KP, Ladle BH, Kurtulus S, Sholl A, Shanmuganad S, Hildeman DA. T-cell receptor signal strength and epigenetic control of Bim predict memory CD8 + T-cell fate. Cell Death Differ 2020; 27:1214-1224. [PMID: 31558776 PMCID: PMC7206134 DOI: 10.1038/s41418-019-0410-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022] Open
Abstract
Most effector CD8+ T cells die, while some persist and become either "effector" (TEM) or "central" (TCM) memory T cells. Paradoxically, effector CD8+ T cells with greater memory potential have higher levels of the pro-apoptotic molecule Bim. Here, we report, using a novel Bim-mCherry knock-in mouse, that cells with high levels of Bim preferentially develop into TCM cells. Bim levels remained stable and were regulated by DNA methylation at the Bim promoter. Notably, high levels of Bcl-2 were required for Bimhi cells to survive. Using Nur77-GFP mice as an indicator of TCR signal strength, Nur77 levels correlated with Bim expression and Nur77hi cells also selectively developed into TCM cells. Altogether, these data show that Bim levels and TCR signal strength are predictive of TEM- vs. TCM-cell fate. Further, given the many other biologic functions of Bim, these mice will have broad utility beyond CD8+ T-cell fate.
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Affiliation(s)
- Kun-Po Li
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Brian H Ladle
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Johns Hopkins Hospital, 1800 Orleans Street, The Charlotte R. Bloomberg Children's Center Building, 11th Floor, Baltimore, MD, 21287, USA
| | - Sema Kurtulus
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Allyson Sholl
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Sharmila Shanmuganad
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - David A Hildeman
- Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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33
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Hayward SL, Scharer CD, Cartwright EK, Takamura S, Li ZRT, Boss JM, Kohlmeier JE. Environmental cues regulate epigenetic reprogramming of airway-resident memory CD8 + T cells. Nat Immunol 2020; 21:309-320. [PMID: 31953534 PMCID: PMC7044042 DOI: 10.1038/s41590-019-0584-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/16/2019] [Indexed: 12/28/2022]
Abstract
Tissue-resident memory T cells (TRM cells) are critical for cellular immunity to respiratory pathogens and reside in both the airways and the interstitium. In the present study, we found that the airway environment drove transcriptional and epigenetic changes that specifically regulated the cytolytic functions of airway TRM cells and promoted apoptosis due to amino acid starvation and activation of the integrated stress response. Comparison of airway TRM cells and splenic effector-memory T cells transferred into the airways indicated that the environment was necessary to activate these pathways, but did not induce TRM cell lineage reprogramming. Importantly, activation of the integrated stress response was reversed in airway TRM cells placed in a nutrient-rich environment. Our data defined the genetic programs of distinct lung TRM cell populations and show that local environmental cues altered airway TRM cells to limit cytolytic function and promote cell death, which ultimately leads to fewer TRM cells in the lung.
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Affiliation(s)
- Sarah L Hayward
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily K Cartwright
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Shiki Takamura
- Department of Immunology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Zheng-Rong Tiger Li
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jacob E Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory-UGA Center of Excellence for Influenza Research and Surveillance, Atlanta, GA, USA.
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34
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Wang W, Wang L, Liu Z, Song X, Yi Q, Yang C, Song L. The involvement of TLR signaling and anti-bacterial effectors in enhanced immune protection of oysters after Vibrio splendidus pre-exposure. Dev Comp Immunol 2020; 103:103498. [PMID: 31525382 DOI: 10.1016/j.dci.2019.103498] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
The phenomena of enhanced protection of innate immunity responding to a pre-exposed pathogen have been reported in invertebrates. The underpinning molecular basis and mechanism for the enhanced immune protection are still missing. In order to explore the possible molecular basis for enhanced immune protection in molluscs, the transcriptomic analysis of oysters Crassostrea gigas hemocytes after twice stimulation of Vibrio splendidus were conducted, and a total of 403 M clean reads and 34254 differentially expressed genes (DEGs) were collected. There were 2964 common DEGs up-regulated in hemocytes after both the first and second immune stimulation, which were mostly enriched in metabolic processes and immune related pathways, such as endocytosis, MAPK signaling pathway and TLR signal pathway. Moreover, 187 and 55 DEGs were higher expressed at resting (0 h after stimulation) and activating state (12 h after stimulation) of the second immune response than that of the first response, respectively, mainly including immune recognition receptor scavenger receptor 2, signal molecule MAPK2, immune regulator IL17-d, apoptosis inhibitor IAP and effector cathepsin. More importantly, 13 DEGs were long-lastingly higher expressed at both the resting and activating state within the second immune response than that of the first, including TLR signal molecule MyD88, anti-virulent tissue inhibitor of metalloproteinase, anti-bacterial proline-rich transmembrane protein, which might play indispensable roles in enhanced immune protection against V. splendidus re-infection. The expression patterns of TLR signals (CgTLR6 and CgMyD88) and effector molecules (CgTIMP and CgPRTP) were further validated by RT-PCR, which were consistent to transcriptomic results. All the results provided an overall molecular basis of enhanced immune protection for hemocytes defensing against the second stimulation of V. splendidus in oyster, which would be valuable for understanding the protection mechanisms of pre-exposure in invertebrates.
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Affiliation(s)
- Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Xiaorui Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Qilin Yi
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Chuanyan Yang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
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35
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Guerra T, Schilling S, Hake K, Gorzolka K, Sylvester FP, Conrads B, Westermann B, Romeis T. Calcium-dependent protein kinase 5 links calcium signaling with N-hydroxy-l-pipecolic acid- and SARD1-dependent immune memory in systemic acquired resistance. New Phytol 2020; 225:310-325. [PMID: 31469917 DOI: 10.1111/nph.16147] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/14/2019] [Indexed: 05/20/2023]
Abstract
Systemic acquired resistance (SAR) prepares infected plants for faster and stronger defense activation upon subsequent attacks. SAR requires an information relay from primary infection to distal tissue and the initiation and maintenance of a self-maintaining phytohormone salicylic acid (SA)-defense loop. In spatial and temporal resolution, we show that calcium-dependent protein kinase CPK5 contributes to immunity and SAR. In local basal resistance, CPK5 functions upstream of SA synthesis, perception, and signaling. In systemic tissue, CPK5 signaling leads to accumulation of SAR-inducing metabolite N-hydroxy-L-pipecolic acid (NHP) and SAR marker genes, including Systemic Acquired Resistance Deficient 1 (SARD1) Plants of increased CPK5, but not CPK6, signaling display an 'enhanced SAR' phenotype towards a secondary bacterial infection. In the sard1-1 background, CPK5-mediated basal resistance is still mounted, but NHP concentration is reduced and enhanced SAR is lost. The biochemical analysis estimated CPK5 half maximal kinase activity for calcium, K50 [Ca2+ ], to be c. 100 nM, close to the cytoplasmic resting level. This low threshold uniquely qualifies CPK5 to decode subtle changes in calcium, a prerequisite to signal relay and onset and maintenance of priming at later time points in distal tissue. Our data explain why CPK5 functions as a hub in basal and systemic plant immunity.
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Affiliation(s)
- Tiziana Guerra
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
| | - Silke Schilling
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
| | - Katharina Hake
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
| | - Karin Gorzolka
- Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Fabian-Philipp Sylvester
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
| | - Benjamin Conrads
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
| | | | - Tina Romeis
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
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36
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Mavigner M, Zanoni M, Tharp GK, Habib J, Mattingly CR, Lichterfeld M, Nega MT, Vanderford TH, Bosinger SE, Chahroudi A. Pharmacological Modulation of the Wnt/β-Catenin Pathway Inhibits Proliferation and Promotes Differentiation of Long-Lived Memory CD4 + T Cells in Antiretroviral Therapy-Suppressed Simian Immunodeficiency Virus-Infected Macaques. J Virol 2019; 94:e01094-19. [PMID: 31619550 PMCID: PMC6912121 DOI: 10.1128/jvi.01094-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/01/2019] [Indexed: 12/21/2022] Open
Abstract
The major obstacle to human immunodeficiency type 1 virus (HIV-1) eradication is a reservoir of latently infected cells that persists despite long-term antiretroviral therapy (ART) and is maintained through cellular proliferation. Long-lived memory CD4+ T cells with high self-renewal capacity, such as central memory (CM) T cells and stem cell memory (SCM) T cells, are major contributors to the viral reservoir in HIV-infected individuals on ART. The Wnt/β-catenin signaling pathway regulates the balance between self-renewal and differentiation of SCM and CM T cells, and pharmacological manipulation of this pathway offers an opportunity to interfere with the proliferation of latently infected cells. Here, we evaluated in vivo a novel approach to inhibit self-renewal of SCM and CM CD4+ T cells in the rhesus macaque (RM) model of simian immunodeficiency (SIV) infection. We used an inhibitor of the Wnt/β-catenin pathway, PRI-724, that blocks the interaction between the coactivator CREB-binding protein (CBP) and β-catenin, resulting in the cell fate decision to differentiate rather than proliferate. Our study shows that PRI-724 treatment of ART-suppressed SIVmac251-infected RMs resulted in decreased proliferation of SCM and CM T cells and modified the SCM and CM CD4+ T cell transcriptome toward a profile of more differentiated memory T cells. However, short-term treatment with PRI-724 alone did not significantly reduce the size of the viral reservoir. This work demonstrates for the first time that stemness pathways of long-lived memory CD4+ T cells can be pharmacologically modulated in vivo, thus establishing a novel strategy to target HIV persistence.IMPORTANCE Long-lasting CD4+ T cell subsets, such as central memory and stem cell memory CD4+ T cells, represent critical reservoirs for human immunodeficiency virus (HIV) persistence despite suppressive antiretroviral therapy. These cells possess stem cell-like properties of enhanced self-renewal/proliferation, and proliferation of latently infected memory CD4+ T cells plays a key role in maintaining the reservoir over time. Here, we evaluated an innovative strategy targeting the proliferation of long-lived memory CD4+ T cells to reduce viral reservoir stability. Using the rhesus macaque model, we tested a pharmacological inhibitor of the Wnt/β-catenin signaling pathway that regulates T cell proliferation. Our study shows that administration of the inhibitor PRI-724 decreased the proliferation of SCM and CM CD4+ T cells and promoted a transcriptome enriched in differentiation genes. Although the viral reservoir size was not significantly reduced by PRI-724 treatment alone, we demonstrate the potential to pharmacologically modulate the proliferation of memory CD4+ T cells as a strategy to limit HIV persistence.
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Affiliation(s)
- M Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - M Zanoni
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - G K Tharp
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - J Habib
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - C R Mattingly
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - M Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - M T Nega
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - T H Vanderford
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - S E Bosinger
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Emory + Children's Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - A Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Emory + Children's Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
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Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, Wood O, Chee SJ, Eschweiler S, King EV, Awad AS, Hanley CJ, McCann KJ, Bhattacharyya S, Woo E, Alzetani A, Seumois G, Thomas GJ, Ganesan AP, Friedmann PS, Sanchez-Elsner T, Ay F, Ottensmeier CH, Vijayanand P. Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer. J Exp Med 2019; 216:2128-2149. [PMID: 31227543 PMCID: PMC6719422 DOI: 10.1084/jem.20190249] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/04/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022] Open
Abstract
High numbers of tissue-resident memory T (TRM) cells are associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, single-cell and bulk transcriptomic analysis of TRM and non-TRM cells present in tumor and normal lung tissue from patients with lung cancer revealed that PD-1-expressing TRM cells in tumors were clonally expanded and enriched for transcripts linked to cell proliferation and cytotoxicity when compared with PD-1-expressing non-TRM cells. This feature was more prominent in the TRM cell subset coexpressing PD-1 and TIM-3, and it was validated by functional assays ex vivo and also reflected in their chromatin accessibility profile. This PD-1+TIM-3+ TRM cell subset was enriched in responders to PD-1 inhibitors and in tumors with a greater magnitude of CTL responses. These data highlight that not all CTLs expressing PD-1 are dysfunctional; on the contrary, TRM cells with PD-1 expression were enriched for features suggestive of superior functionality.
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Affiliation(s)
- James Clarke
- La Jolla Institute for Immunology, La Jolla, CA
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | | | - Divya Singh
- La Jolla Institute for Immunology, La Jolla, CA
| | | | - Oliver Wood
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Serena J Chee
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | | | - Emma V King
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Otolaryngology, Poole Hospital National Health Service Foundation Trust, Poole, Dorset, UK
| | - Amiera S Awad
- Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
- Clinical and Experimental Sciences, National Institute for Health Research Southampton, Respiratory Biomedical Research Unit, University of Southampton, Faculty of Medicine, Southampton, UK
| | - Christopher J Hanley
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Katy J McCann
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Edwin Woo
- Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | - Aiman Alzetani
- Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | | | - Gareth J Thomas
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Peter S Friedmann
- Clinical and Experimental Sciences, National Institute for Health Research Southampton, Respiratory Biomedical Research Unit, University of Southampton, Faculty of Medicine, Southampton, UK
| | - Tilman Sanchez-Elsner
- Clinical and Experimental Sciences, National Institute for Health Research Southampton, Respiratory Biomedical Research Unit, University of Southampton, Faculty of Medicine, Southampton, UK
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA
| | - Christian H Ottensmeier
- National Institute for Health Research and Cancer Research UK Southampton Experimental Cancer Medicine Center, National Institute for Health Research Southampton Biomedical Research Center, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA
- Clinical and Experimental Sciences, National Institute for Health Research Southampton, Respiratory Biomedical Research Unit, University of Southampton, Faculty of Medicine, Southampton, UK
- Department of Medicine, University of California San Diego, La Jolla, CA
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38
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Dahmani A, Janelle V, Carli C, Richaud M, Lamarche C, Khalili M, Goupil M, Bezverbnaya K, Bramson JL, Delisle JS. TGFβ Programs Central Memory Differentiation in Ex Vivo-Stimulated Human T Cells. Cancer Immunol Res 2019; 7:1426-1439. [PMID: 31308016 DOI: 10.1158/2326-6066.cir-18-0691] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/27/2019] [Accepted: 07/09/2019] [Indexed: 11/16/2022]
Abstract
The adoptive transfer of ex vivo-expanded T cells is a promising approach to treat several malignancies. Several lines of evidence support that the infusion of T cells with early memory features, capable of expanding and persisting after transfer, are associated with better outcomes. We report herein that exposure to exogenous TGFβ during human T-cell stimulation ex vivo leads to the accumulation of early/central memory (Tcm) cells. Exposure to TGFβ suppressed the expression of BLIMP-1, a key orchestrator of effector T-cell differentiation, and led to the upregulation of the memory-associated transcription factor ID3. Accordingly, this was associated with an early memory transcriptional signature in both CD4+ and CD8+ T-cell subsets. The T cells stimulated in the presence of TGFβ expanded normally, and displayed polyfunctional features and no suppressive activity. The adoptive transfer of ex vivo-stimulated T cells into immunodeficient mice confirmed that TGFβ-conditioned cells had an enhanced capacity to persist and mediate xenogeneic graft-versus-host disease, as predicted by their early T-cell memory phenotype. Chimeric antigen receptor-expressing T cells generated in the presence of exogenous TGFβ were cytotoxic and more effective at controlling tumor growth in immunodeficient animals. This work unveils a new role for TGFβ in memory T-cell differentiation and indicates that TGFβ signaling may be harnessed to program Tcm differentiation in the context of ex vivo T-cell stimulation for adoptive immunotherapy in humans.
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Affiliation(s)
- Amina Dahmani
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Valérie Janelle
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Cédric Carli
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Manon Richaud
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Caroline Lamarche
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Myriam Khalili
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Mathieu Goupil
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada
| | - Ksenia Bezverbnaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan L Bramson
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Sébastien Delisle
- Centre de Recherche de l'Hôpital Maisonneuve-Rosemont (CRHMR), Montreal, Quebec, Canada.
- Département de Médecine, Université de Montréal, Montreal, Quebec, Canada
- Hematology-Oncology Division, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
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39
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Abstract
Upon activation, naive T cells give rise to a heterogeneous cell population of effector and memory T cells that mediate antigen clearance and provide long-lived protection from rechallenge. Many of the transcriptional regulators that direct the differentiation of naive T cells to acquire the range of phenotypic and functional characteristics of effector and memory T cells have been described. However, the active programs that maintain the specific subsets of memory T cells are less clear. Here, we discuss recent studies that suggest effector and memory CD8+ T cells exist in cellular 'states' with inherent plasticity. Further, we consider the newly identified role of active transcriptional and epigenetic programming in maintaining the identity of the distinct subsets within the memory population.
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Affiliation(s)
- Kyla D Omilusik
- University of California San Diego, Division of Biological Sciences, Section of Molecular Biology, 9500 Gilman Drive, La Jolla, CA 92093-0377, United States
| | - Ananda W Goldrath
- University of California San Diego, Division of Biological Sciences, Section of Molecular Biology, 9500 Gilman Drive, La Jolla, CA 92093-0377, United States.
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40
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Shimizu K, Sato Y, Kawamura M, Nakazato H, Watanabe T, Ohara O, Fujii SI. Eomes transcription factor is required for the development and differentiation of invariant NKT cells. Commun Biol 2019; 2:150. [PMID: 31044175 PMCID: PMC6488575 DOI: 10.1038/s42003-019-0389-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Eomes regulates the differentiation of CD8+ T cells into effector and memory phases. However, its role in invariant (i)NKT cells remains unknown. Here, we show the impact of Eomes on iNKT cells in the thymus and peripheral tissue using conditional knockout (Eomes-cKO) mice. In the thymus, CD1d-tetramer+CD24+CD44-NK1.1-CD69+stage 0 iNKT cells express higher levels of Eomes than the other iNKT stages. We also found that Eomes regulates NKT1 cell differentiation predominantly. Interestingly, the expression of Eomes in the steady state is low, but can be upregulated after TCR stimulation. We also showed epigenetic changes in the Eomes locus after activation. In addition, vaccination of C57BL/6, but not Eomes-cKO mice with iNKT ligand-loaded dendritic cells generated KLRG1+iNKT cells in lung, characterized as effector memory phenotype by transcriptome profiling. Thus, Eomes regulates not only the differentiation of NKT1 cells in the thymus, but also their differentiation into memory-like KLRG1+iNKT cells in the periphery.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/immunology
- CD8-Positive T-Lymphocytes/cytology
- CD8-Positive T-Lymphocytes/immunology
- Cell Differentiation
- Cell Lineage/genetics
- Cell Lineage/immunology
- Cell Proliferation
- Dendritic Cells/cytology
- Dendritic Cells/immunology
- Gene Expression Profiling
- Gene Expression Regulation/immunology
- Immunologic Memory/genetics
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Lung/cytology
- Lung/immunology
- Lymphocyte Activation
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Natural Killer T-Cells/cytology
- Natural Killer T-Cells/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Signal Transduction
- T-Box Domain Proteins/deficiency
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/immunology
- Thymus Gland/cytology
- Thymus Gland/immunology
- Transcriptome/immunology
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Affiliation(s)
- Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Yusuke Sato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Masami Kawamura
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Hiroshi Nakazato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Takashi Watanabe
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045 Japan
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41
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Gautam S, Fioravanti J, Zhu W, Le Gall JB, Brohawn P, Lacey NE, Hu J, Hocker JD, Hawk NV, Kapoor V, Telford WG, Gurusamy D, Yu Z, Bhandoola A, Xue HH, Roychoudhuri R, Higgs BW, Restifo NP, Bender TP, Ji Y, Gattinoni L. The transcription factor c-Myb regulates CD8 + T cell stemness and antitumor immunity. Nat Immunol 2019; 20:337-349. [PMID: 30778251 PMCID: PMC6489499 DOI: 10.1038/s41590-018-0311-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022]
Abstract
Stem cells are maintained by transcriptional programs that promote self-renewal and repress differentiation. Here, we found that the transcription factor c-Myb was essential for generating and maintaining stem cells in the CD8+ T cell memory compartment. Following viral infection, CD8+ T cells lacking Myb underwent terminal differentiation and generated fewer stem cell-like central memory cells than did Myb-sufficient T cells. c-Myb acted both as a transcriptional activator of Tcf7 (which encodes the transcription factor Tcf1) to enhance memory development and as a repressor of Zeb2 (which encodes the transcription factor Zeb2) to hinder effector differentiation. Domain-mutagenesis experiments revealed that the transactivation domain of c-Myb was necessary for restraining differentiation, whereas its negative regulatory domain was critical for cell survival. Myb overexpression enhanced CD8+ T cell memory formation, polyfunctionality and recall responses that promoted curative antitumor immunity after adoptive transfer. These findings identify c-Myb as a pivotal regulator of CD8+ T cell stemness and highlight its therapeutic potential.
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Affiliation(s)
- Sanjivan Gautam
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jessica Fioravanti
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhu
- Department of Bioinformatics, Inova Translational Medicine Institute, Fairfax, VA, USA
| | - John B Le Gall
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Neal E Lacey
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jinhui Hu
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - James D Hocker
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nga Voong Hawk
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Veena Kapoor
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - William G Telford
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Devikala Gurusamy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hai-Hui Xue
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signaling and Development, Babraham Institute, Cambridge, UK
| | | | - Nicholas P Restifo
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Timothy P Bender
- Department of Microbiology, University of Virginia, Charlottesville, VA, USA
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, USA
| | - Yun Ji
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Cellular Biomedicine Group, Gaithersburg, MD, USA
| | - Luca Gattinoni
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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42
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Miragaia RJ, Gomes T, Chomka A, Jardine L, Riedel A, Hegazy AN, Whibley N, Tucci A, Chen X, Lindeman I, Emerton G, Krausgruber T, Shields J, Haniffa M, Powrie F, Teichmann SA. Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation. Immunity 2019; 50:493-504.e7. [PMID: 30737144 PMCID: PMC6382439 DOI: 10.1016/j.immuni.2019.01.001] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 09/28/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023]
Abstract
Non-lymphoid tissues (NLTs) harbor a pool of adaptive immune cells with largely unexplored phenotype and development. We used single-cell RNA-seq to characterize 35,000 CD4+ regulatory (Treg) and memory (Tmem) T cells in mouse skin and colon, their respective draining lymph nodes (LNs) and spleen. In these tissues, we identified Treg cell subpopulations with distinct degrees of NLT phenotype. Subpopulation pseudotime ordering and gene kinetics were consistent in recruitment to skin and colon, yet the initial NLT-priming in LNs and the final stages of NLT functional adaptation reflected tissue-specific differences. Predicted kinetics were recapitulated using an in vivo melanoma-induction model, validating key regulators and receptors. Finally, we profiled human blood and NLT Treg and Tmem cells, and identified cross-mammalian conserved tissue signatures. In summary, we describe the relationship between Treg cell heterogeneity and recruitment to NLTs through the combined use of computational prediction and in vivo validation.
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Affiliation(s)
- Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Agnieszka Chomka
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Angela Riedel
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Ahmed N Hegazy
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Natasha Whibley
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Andrea Tucci
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ida Lindeman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Guy Emerton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Krausgruber
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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43
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Jørgensen LVG, Korbut R, Jeberg S, Kania PW, Buchmann K. Association between adaptive immunity and neutrophil dynamics in zebrafish (Danio rerio) infected by a parasitic ciliate. PLoS One 2018; 13:e0203297. [PMID: 30204772 PMCID: PMC6133357 DOI: 10.1371/journal.pone.0203297] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023] Open
Abstract
The protective immune response in zebrafish (Danio rerio) against the parasitic ciliate Ichthyophthirius multifiliis, targeting host skin, fins and gills, comprises an accelerated and manifold elevated immunoglobulin gene expression as well as a significantly elevated number of neutrophils at infected sites. Experimental fish were subjected to a primary I. multifiliis infection followed by a series of secondary exposures before they were challenged by a high dosage of infective theronts. Immunized fish responded immediately with a protective response suggesting existence of immunological memory whereas fish exposed to the parasite for the first time obtained a marked infection. The primary response to infection was dominated by expression of genes encoding acute phase reactants and inflammatory cytokines as well as recruitment of neutrophils at infected locations. Immunized fish showed a significantly upregulated immunoglobulin gene expression following challenge, which indicates existence of a secondary response effected by antibodies. Both responses induced a significantly elevated expression of the Th2 signature cytokine Il13. The increased presence of neutrophils in immunized fish suggests that innate cell mediated immunity supplements or influence the protective response against the parasite.
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Affiliation(s)
- Louise von Gersdorff Jørgensen
- Section of Parasitology and Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
| | - Rozalia Korbut
- Section of Parasitology and Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sandra Jeberg
- Section of Parasitology and Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Per Walter Kania
- Section of Parasitology and Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kurt Buchmann
- Section of Parasitology and Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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44
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Chiba H, Kakuta Y, Kinouchi Y, Kawai Y, Watanabe K, Nagao M, Naito T, Onodera M, Moroi R, Kuroha M, Kanazawa Y, Kimura T, Shiga H, Endo K, Negoro K, Nagasaki M, Unno M, Shimosegawa T. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLoS One 2018; 13:e0194036. [PMID: 29547621 PMCID: PMC5856270 DOI: 10.1371/journal.pone.0194036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 02/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. METHODS CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. RESULTS We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). CONCLUSIONS We confirmed the existence of cis-regulated ASM around IBD susceptibility genes and the association between ASM SNP (rs36221701) genotype and SMAD3 expression, a susceptibility gene for IBD. These results give us supporting evidence that DNA methylation mediates genetic effects on disease susceptibility.
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Affiliation(s)
- Hirofumi Chiba
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Kinouchi
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuhiro Watanabe
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Munenori Nagao
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Motoyuki Onodera
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitake Kanazawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoya Kimura
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kenichi Negoro
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masao Nagasaki
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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45
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Shan L, Deng K, Gao H, Xing S, Capoferri AA, Durand CM, Rabi SA, Laird GM, Kim M, Hosmane NN, Yang HC, Zhang H, Margolick JB, Li L, Cai W, Ke R, Flavell RA, Siliciano JD, Siliciano RF. Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4 + T Cells Permissive for Latent HIV-1 Infection. Immunity 2017; 47:766-775.e3. [PMID: 29045905 DOI: 10.1016/j.immuni.2017.09.014] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/26/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022]
Abstract
The latent reservoir for HIV-1 in resting memory CD4+ T cells is the major barrier to curing HIV-1 infection. Studies of HIV-1 latency have focused on regulation of viral gene expression in cells in which latent infection is established. However, it remains unclear how infection initially becomes latent. Here we described a unique set of properties of CD4+ T cells undergoing effector-to-memory transition including temporary upregulation of CCR5 expression and rapid downregulation of cellular gene transcription. These cells allowed completion of steps in the HIV-1 life cycle through integration but suppressed HIV-1 gene transcription, thus allowing the establishment of latency. CD4+ T cells in this stage were substantially more permissive for HIV-1 latent infection than other CD4+ T cells. Establishment of latent HIV-1 infection in CD4+ T could be inhibited by viral-specific CD8+ T cells, a result with implications for elimination of latent HIV-1 infection by T cell-based vaccines.
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Affiliation(s)
- Liang Shan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kai Deng
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Hongbo Gao
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Sifei Xing
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - S Alireza Rabi
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregory M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle Kim
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nina N Hosmane
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA.
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46
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Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science 2017; 355:1433-1436. [PMID: 28360329 PMCID: PMC5405862 DOI: 10.1126/science.aah4115] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/07/2016] [Accepted: 02/23/2017] [Indexed: 12/24/2022]
Abstract
Aging is characterized by progressive loss of physiological and cellular functions, but the molecular basis of this decline remains unclear. We explored how aging affects transcriptional dynamics using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4+ T cells from young and old mice from two divergent species. In young animals, immunological activation drives a conserved transcriptomic switch, resulting in tightly controlled gene expression characterized by a strong up-regulation of a core activation program, coupled with a decrease in cell-to-cell variability. Aging perturbed the activation of this core program and increased expression heterogeneity across populations of cells in both species. These discoveries suggest that increased cell-to-cell transcriptional variability will be a hallmark feature of aging across most, if not all, mammalian tissues.
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Affiliation(s)
- Celia Pilar Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nils Eling
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hung-Chang Chen
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Catalina A Vallejos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Aleksandra A Kolodziejczyk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Connor
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Lovorka Stojic
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Timothy F Rayner
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maike de la Roche
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - John C Marioni
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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47
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Wood WA, Krishnamurthy J, Mitin N, Torrice C, Parker JS, Snavely AC, Shea TC, Serody JS, Sharpless NE. Chemotherapy and Stem Cell Transplantation Increase p16 INK4a Expression, a Biomarker of T-cell Aging. EBioMedicine 2016; 11:227-238. [PMID: 27591832 PMCID: PMC5049997 DOI: 10.1016/j.ebiom.2016.08.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/13/2022] Open
Abstract
The expression of markers of cellular senescence increases exponentially in multiple tissues with aging. Age-related physiological changes may contribute to adverse outcomes in cancer survivors. To investigate the impact of high dose chemotherapy and stem cell transplantation on senescence markers in vivo, we collected blood and clinical data from a cohort of 63 patients undergoing hematopoietic cell transplantation. The expression of p16INK4a, a well-established senescence marker, was determined in T-cells before and 6 months after transplant. RNA sequencing was performed on paired samples from 8 patients pre- and post-cancer therapy. In patients undergoing allogeneic transplant, higher pre-transplant p16INK4a expression was associated with a greater number of prior cycles of chemotherapy received (p = 0.003), prior autologous transplantation (p = 0.01) and prior exposure to alkylating agents (p = 0.01). Transplantation was associated with a marked increase in p16INK4a expression 6 months following transplantation. Patients receiving autologous transplant experienced a larger increase in p16INK4a expression (3.1-fold increase, p = 0.002) than allogeneic transplant recipients (1.9-fold increase, p = 0.0004). RNA sequencing of T-cells pre- and post- autologous transplant or cytotoxic chemotherapy demonstrated increased expression of transcripts associated with cellular senescence and physiological aging. Cytotoxic chemotherapy, especially alkylating agents, and stem cell transplantation strongly accelerate expression of a biomarker of molecular aging in T-cells. Peripheral blood T-cell senescence, as measured by the marker p16INK4a, increases following autologous or allogeneic HSCT. RNAseq of T-cells post- auto HSCT or chemotherapy show increased expression of transcripts associated with senescence. Autologous HCT in particular induces a stronger effect on Tcell p16INK4a expression than any other environmental stimulus tested to date.
Human chronological aging is associated with increased expression of markers of cellular aging (senescence). Cancer chemotherapy can produce frailty syndromes – recipients of cancer treatment may experience physiological changes ordinarily seen in individuals of more advanced chronological age. In our study, we found that a well-known marker of cellular senescence, p16INK4a, increased in patients following autologous or allogeneic hematopoietic cell transplantation. Expression of p16INK4a was higher in patients exposed to greater amounts of chemotherapy before transplant and those exposed to specific types of chemotherapy. These findings may ultimately influence clinical decision-making for patients with diseases that are commonly treated with transplantation.
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Affiliation(s)
- William A Wood
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Janakiraman Krishnamurthy
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Natalia Mitin
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Chad Torrice
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Joel S Parker
- Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Anna C Snavely
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Thomas C Shea
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jonathan S Serody
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Norman E Sharpless
- Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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48
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Zhang L, Tschumi BO, Lopez-Mejia IC, Oberle SG, Meyer M, Samson G, Rüegg MA, Hall MN, Fajas L, Zehn D, Mach JP, Donda A, Romero P. Mammalian Target of Rapamycin Complex 2 Controls CD8 T Cell Memory Differentiation in a Foxo1-Dependent Manner. Cell Rep 2016; 14:1206-1217. [PMID: 26804903 DOI: 10.1016/j.celrep.2015.12.095] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/23/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
Upon infection, antigen-specific naive CD8 T cells are activated and differentiate into short-lived effector cells (SLECs) and memory precursor cells (MPECs). The underlying signaling pathways remain largely unresolved. We show that Rictor, the core component of mammalian target of rapamycin complex 2 (mTORC2), regulates SLEC and MPEC commitment. Rictor deficiency favors memory formation and increases IL-2 secretion capacity without dampening effector functions. Moreover, mTORC2-deficient memory T cells mount more potent recall responses. Enhanced memory formation in the absence of mTORC2 was associated with Eomes and Tcf-1 upregulation, repression of T-bet, enhanced mitochondrial spare respiratory capacity, and fatty acid oxidation. This transcriptional and metabolic reprogramming is mainly driven by nuclear stabilization of Foxo1. Silencing of Foxo1 reversed the increased MPEC differentiation and IL-2 production and led to an impaired recall response of Rictor KO memory T cells. Therefore, mTORC2 is a critical regulator of CD8 T cell differentiation and may be an important target for immunotherapy interventions.
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Affiliation(s)
- Lianjun Zhang
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
| | - Benjamin O Tschumi
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | | | | | - Marten Meyer
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Guerric Samson
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Markus A Rüegg
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lluis Fajas
- Department of Physiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - Dietmar Zehn
- Swiss Vaccine Research Institute, 1066 Epalinges, Switzerland
| | - Jean-Pierre Mach
- Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland
| | - Alena Donda
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Pedro Romero
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
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49
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Behnamfar N, Zibaeenezhad MJ, Golmoghaddam H, Doroudchi M. CD45RO+ memory T-cells produce IL-17 in patients with atherosclerosis. Cell Mol Biol (Noisy-le-grand) 2015; 61:17-23. [PMID: 26667768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/05/2015] [Indexed: 06/05/2023]
Abstract
Several CD4+ T helper (Th) cell subsets are shown to play a role in atherosclerotic lesion formation and progression. We investigated the frequencies of IL-17 and IFN-γ producing CD4+ T-cell subsets in the peripheral blood mononuclear cells (PBMCs) of 10 patients with atherosclerosis and 6 individuals with normal/insignificant coronary artery disease. Th1 and Th17 memory and effector T-cells were enumerated by flowcytometry and correlated with the clinical data and lipid profiles of the subjects. We found the ex-vivo (P=0.0001) and in-vitro production of IL-17 (P=0.001) but not IFN-γ by CD4+ memory T-cells of patients. CD45RO+ memory cells were the major producers of IL-17 and the CD4+CD45RO+PD-1- T-cells of the patients produced higher levels of IFN-γ than controls (P=0.02). Positive correlations between the frequency of CD4+CD45RO+IL-17+IFN-γ- T-cells and serum LDL-C (P=0.007), triglyceride (P=0.02), and systolic (P=0.001) and diastolic (P=0.009) blood pressures (BP) were found. The frequency of CD4+CD45RO+IL-17-IFN-γ- T-cells, which was higher in controls than patients, showed negative correlations with the serum LDL-C (P=0.01) and triglyceride (P=0.02) levels and systolic (P=0.003) and diastolic (P=0.01) BPs. The ex-vivo Th17 deviation of memory T-cells in atherosclerosis and high PD-1 expression are associated with the correlates of atherogenesis such as LDL, TG, and BP.
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Affiliation(s)
- N Behnamfar
- Shiraz University of Medical Sciences Department of Immunology, School of Medicine Shiraz Iran
| | - M J Zibaeenezhad
- Shiraz University of Medical Sciences Cardiovascular Research Center Shiraz Iran
| | - H Golmoghaddam
- Shiraz University of Medical Sciences Department of Immunology, School of Medicine Shiraz Iran
| | - M Doroudchi
- Shiraz University of Medical Sciences Department of Immunology, School of Medicine Shiraz Iran
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50
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Galson JD, Clutterbuck EA, Trück J, Ramasamy MN, Münz M, Fowler A, Cerundolo V, Pollard AJ, Lunter G, Kelly DF. BCR repertoire sequencing: different patterns of B-cell activation after two Meningococcal vaccines. Immunol Cell Biol 2015; 93:885-95. [PMID: 25976772 PMCID: PMC4551417 DOI: 10.1038/icb.2015.57] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 12/24/2022]
Abstract
Next-generation sequencing was used to investigate the B-cell receptor heavy chain transcript repertoire of different B-cell subsets (naive, marginal zone (MZ), immunoglobulin M (IgM) memory and IgG memory) at baseline, and of plasma cells (PCs) 7 days following administration of serogroup ACWY meningococcal polysaccharide and protein-polysaccharide conjugate vaccines. Baseline B-cell subsets could be distinguished from each other using a small number of repertoire properties (clonality, mutation from germline and complementarity-determining region 3 (CDR3) length) that were conserved between individuals. However, analyzing the CDR3 amino-acid sequence (which is particularly important for antigen binding) of the baseline subsets showed few sequences shared between individuals. In contrast, day 7 PCs demonstrated nearly 10-fold greater sequence sharing between individuals than the baseline subsets, consistent with the PCs being induced by the vaccine antigen and sharing specificity for a more limited range of epitopes. By annotating PC sequences based on IgG subclass usage and mutation, and also comparing them with the sequences of the baseline cell subsets, we were able to identify different signatures after the polysaccharide and conjugate vaccines. PCs produced after conjugate vaccination were predominantly IgG1, and most related to IgG memory cells. In contrast, after polysaccharide vaccination, the PCs were predominantly IgG2, less mutated and were equally likely to be related to MZ, IgM memory or IgG memory cells. High-throughput B-cell repertoire sequencing thus provides a unique insight into patterns of B-cell activation not possible from more conventional measures of immunogenicity.
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Affiliation(s)
- Jacob D. Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
| | - Elizabeth A. Clutterbuck
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
| | - Maheshi N. Ramasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, United Kingdom
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, OX3 7LE, United Kingdom
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