51
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Yang Y, Huh R, Culpepper HW, Lin Y, Love MI, Li Y. SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data. Bioinformatics 2020; 35:1269-1277. [PMID: 30202935 DOI: 10.1093/bioinformatics/bty793] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/03/2018] [Accepted: 09/06/2018] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION Accurately clustering cell types from a mass of heterogeneous cells is a crucial first step for the analysis of single-cell RNA-seq (scRNA-Seq) data. Although several methods have been recently developed, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments. RESULTS Here, we present SAFE-clustering, single-cell aggregated (From Ensemble) clustering, a flexible, accurate and robust method for clustering scRNA-Seq data. SAFE-clustering takes as input, results from multiple clustering methods, to build one consensus solution. SAFE-clustering currently embeds four state-of-the-art methods, SC3, CIDR, Seurat and t-SNE + k-means; and ensembles solutions from these four methods using three hypergraph-based partitioning algorithms. Extensive assessment across 12 datasets with the number of clusters ranging from 3 to 14, and the number of single cells ranging from 49 to 32, 695 showcases the advantages of SAFE-clustering in terms of both cluster number (18.2-58.1% reduction in absolute deviation to the truth) and cluster assignment (on average 36.0% improvement, and up to 18.5% over the best of the four methods, measured by adjusted rand index). Moreover, SAFE-clustering is computationally efficient to accommodate large datasets, taking <10 min to process 28 733 cells. AVAILABILITY AND IMPLEMENTATION SAFEclustering, including source codes and tutorial, is freely available at https://github.com/yycunc/SAFEclustering. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuchen Yang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruth Huh
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Houston W Culpepper
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yuan Lin
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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52
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Kretschmer L, Flossdorf M, Mir J, Cho YL, Plambeck M, Treise I, Toska A, Heinzel S, Schiemann M, Busch DH, Buchholz VR. Differential expansion of T central memory precursor and effector subsets is regulated by division speed. Nat Commun 2020; 11:113. [PMID: 31913278 PMCID: PMC6949285 DOI: 10.1038/s41467-019-13788-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
While antigen-primed T cells proliferate at speeds close to the physiologic maximum of mammalian cells, T cell memory is maintained in the absence of antigen by rare cell divisions. The transition between these distinct proliferative programs has been difficult to resolve via population-based analyses. Here, we computationally reconstruct the proliferative history of single CD8+ T cells upon vaccination and measure the division speed of emerging T cell subsets in vivo. We find that slower cycling central memory precursors, characterized by an elongated G1 phase, segregate early from the bulk of rapidly dividing effector subsets, and further slow-down their cell cycle upon premature removal of antigenic stimuli. In contrast, curtailed availability of inflammatory stimuli selectively restrains effector T cell proliferation due to reduced receptivity for interleukin-2. In line with these findings, persistence of antigenic but not inflammatory stimuli throughout clonal expansion critically determines the later size of the memory compartment.
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Affiliation(s)
- Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Michael Flossdorf
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Jonas Mir
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Yi-Li Cho
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Marten Plambeck
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Irina Treise
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany.,German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Albulena Toska
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Susanne Heinzel
- Division of Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany. .,German Center for Infection Research (DZIF), Partner site Munich, Munich, Germany.
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany.
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53
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Green DR. Dances with Cells. Crit Rev Immunol 2020; 40:355-366. [PMID: 33463948 PMCID: PMC11019855 DOI: 10.1615/critrevimmunol.2020035038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Like all of us, cells proceed through stages of life. In this whimsical review, aspects of several such stages, including birth, growth, aging, death, and "afterlife," are considered, with a special emphasis on cells of the immune system. Discussed along the way are asymmetric division of activated, naive cluster of differentiation 8+ T cells, c-Myc and polyamines in lymphocyte function and aging, cell survival after induction of cell death pathways, cell death consequences, and clearance of dead cells from surrounding tissues. This is offered in memory of the unique and wonderful Dr. Eli Sercarz.
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Affiliation(s)
- Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
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54
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Arsenio J. Single-cell analysis of CD8 T lymphocyte diversity during adaptive immunity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1475. [PMID: 31877242 DOI: 10.1002/wsbm.1475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/22/2019] [Accepted: 12/05/2019] [Indexed: 11/11/2022]
Abstract
An effective adaptive immune response to microbial infection relies on the generation of heterogeneous T lymphocyte fates and functions. CD8 T lymphocytes play a pivotal role in mediating immediate and long-term protective immune responses to intracellular pathogen infection. Systems-based analysis of the immune response to infection has begun to identify cell fate determinants and the molecular mechanisms underpinning CD8 T lymphocyte diversity at single-cell resolution. Resolving CD8 T lymphocyte heterogeneity during adaptive immunity highlights the advantages of single-cell technologies and computational approaches to better understand the ontogeny of CD8 T cellular diversity following infection. Future directions of integrating single-cell multiplex approaches capitalize on the importance of systems biology in the understanding of immune CD8 T cell differentiation and functional diversity. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Fates.
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Affiliation(s)
- Janilyn Arsenio
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.,Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada
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55
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Dropout imputation and batch effect correction for single-cell RNA sequencing data. JOURNAL OF BIO-X RESEARCH 2019. [DOI: 10.1097/jbr.0000000000000053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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56
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Kallionpää H, Somani J, Tuomela S, Ullah U, de Albuquerque R, Lönnberg T, Komsi E, Siljander H, Honkanen J, Härkönen T, Peet A, Tillmann V, Chandra V, Anagandula MK, Frisk G, Otonkoski T, Rasool O, Lund R, Lähdesmäki H, Knip M, Lahesmaa R. Early Detection of Peripheral Blood Cell Signature in Children Developing β-Cell Autoimmunity at a Young Age. Diabetes 2019; 68:2024-2034. [PMID: 31311800 DOI: 10.2337/db19-0287] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/10/2019] [Indexed: 11/13/2022]
Abstract
The appearance of type 1 diabetes (T1D)-associated autoantibodies is the first and only measurable parameter to predict progression toward T1D in genetically susceptible individuals. However, autoantibodies indicate an active autoimmune reaction, wherein the immune tolerance is already broken. Therefore, there is a clear and urgent need for new biomarkers that predict the onset of the autoimmune reaction preceding autoantibody positivity or reflect progressive β-cell destruction. Here we report the mRNA sequencing-based analysis of 306 samples including fractionated samples of CD4+ and CD8+ T cells as well as CD4-CD8- cell fractions and unfractionated peripheral blood mononuclear cell samples longitudinally collected from seven children who developed β-cell autoimmunity (case subjects) at a young age and matched control subjects. We identified transcripts, including interleukin 32 (IL32), that were upregulated before T1D-associated autoantibodies appeared. Single-cell RNA sequencing studies revealed that high IL32 in case samples was contributed mainly by activated T cells and NK cells. Further, we showed that IL32 expression can be induced by a virus and cytokines in pancreatic islets and β-cells, respectively. The results provide a basis for early detection of aberrations in the immune system function before T1D and suggest a potential role for IL32 in the pathogenesis of T1D.
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Affiliation(s)
- Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Juhi Somani
- Department of Computer Science, Aalto University School of Science, Espoo, Finland
| | - Soile Tuomela
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ubaid Ullah
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rafael de Albuquerque
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elina Komsi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Heli Siljander
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jarno Honkanen
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Taina Härkönen
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Aleksandr Peet
- Department of Pediatrics, University of Tartu, Tartu, Estonia
- Children's Clinic of Tartu, Tartu University Hospital, Tartu, Estonia
| | - Vallo Tillmann
- Department of Pediatrics, University of Tartu, Tartu, Estonia
- Children's Clinic of Tartu, Tartu University Hospital, Tartu, Estonia
| | - Vikash Chandra
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Gun Frisk
- Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Timo Otonkoski
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, Espoo, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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57
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Shin KS, Jeon I, Kim BS, Kim IK, Park YJ, Koh CH, Song B, Lee JM, Lim J, Bae EA, Seo H, Ban YH, Ha SJ, Kang CY. Monocyte-Derived Dendritic Cells Dictate the Memory Differentiation of CD8 + T Cells During Acute Infection. Front Immunol 2019; 10:1887. [PMID: 31474983 PMCID: PMC6706816 DOI: 10.3389/fimmu.2019.01887] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/25/2019] [Indexed: 11/13/2022] Open
Abstract
Monocyte-derived dendritic cells (moDCs) have been shown to robustly expand during infection; however, their roles in anti-infectious immunity remain unclear. Here, we found that moDCs were dramatically increased in the secondary lymphoid organs during acute LCMV infection in an interferon-γ (IFN-γ)-dependent manner. We also found that priming by moDCs enhanced the differentiation of memory CD8+ T cells compared to differentiation primed by conventional dendritic cells (cDCs) through upregulation of Eomesodermin (Eomes) and T cell factor-1 (TCF-1) expression in CD8+ T cells. Consequently, impaired memory formation of CD8+ T cells in mice that had reduced numbers of moDCs led to defective clearance of pathogens upon rechallenge. Mechanistically, attenuated interleukin-2 (IL-2) signaling in CD8+ T cells primed by moDCs was responsible for the enhanced memory programming of CD8+ T cells. Therefore, our findings unveil a specialization of the antigen-presenting cell subsets in the fate determination of CD8+ T cells during infection and pave the way for the development of a novel therapeutic intervention on infection.
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Affiliation(s)
- Kwang-Soo Shin
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Insu Jeon
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Byung-Seok Kim
- Laboratory of Immune Regulation, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Il-Kyu Kim
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Young-Jun Park
- Laboratory of Immune Regulation, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Choong-Hyun Koh
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Boyeong Song
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Jeong-Mi Lee
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jiyoung Lim
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Eun-Ah Bae
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Hyungseok Seo
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Young Ho Ban
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Chang-Yuil Kang
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, South Korea.,Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
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58
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Diao H, Pipkin M. Stability and flexibility in chromatin structure and transcription underlies memory CD8 T-cell differentiation. F1000Res 2019; 8. [PMID: 31448086 PMCID: PMC6676507 DOI: 10.12688/f1000research.18211.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 12/17/2022] Open
Abstract
The process by which naïve CD8 T cells become activated, accumulate, and terminally differentiate as well as develop into memory cytotoxic T lymphocytes (CTLs) is central to the development of potent and durable immunity to intracellular infections and tumors. In this review, we discuss recent studies that have elucidated ancestries of short-lived and memory CTLs during infection, others that have shed light on gene expression programs manifest in individual responding cells and chromatin remodeling events, remodeling factors, and conventional DNA-binding transcription factors that stabilize the differentiated states after activation of naïve CD8 T cells. Several models have been proposed to conceptualize how naïve cells become memory CD8 T cells. A parsimonious solution is that initial naïve cell activation induces metastable gene expression in nascent CTLs, which act as progenitor cells that stochastically diverge along pathways that are self-reinforcing and result in shorter- versus longer-lived CTL progeny. Deciphering how regulatory factors establish and reinforce these pathways in CD8 T cells could potentially guide their use in immunotherapeutic contexts.
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Affiliation(s)
- Huitian Diao
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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59
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Cassioli C, Baldari CT. A Ciliary View of the Immunological Synapse. Cells 2019; 8:E789. [PMID: 31362462 PMCID: PMC6721628 DOI: 10.3390/cells8080789] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/15/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
The primary cilium has gone from being a vestigial organelle to a crucial signaling hub of growing interest given the association between a group of human disorders, collectively known as ciliopathies, and defects in its structure or function. In recent years many ciliogenesis proteins have been observed at extraciliary sites in cells and likely perform cilium-independent functions ranging from regulation of the cytoskeleton to vesicular trafficking. Perhaps the most striking example is the non-ciliated T lymphocyte, in which components of the ciliary machinery are repurposed for the assembly and function of the immunological synapse even in the absence of a primary cilium. Furthermore, the specialization traits described at the immunological synapse are similar to those seen in the primary cilium. Here, we review common regulators and features shared by the immunological synapse and the primary cilium that document the remarkable homology between these structures.
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Affiliation(s)
- Chiara Cassioli
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Cosima T Baldari
- Department of Life Sciences, University of Siena, 53100 Siena, Italy.
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60
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Auladell M, Jia X, Hensen L, Chua B, Fox A, Nguyen THO, Doherty PC, Kedzierska K. Recalling the Future: Immunological Memory Toward Unpredictable Influenza Viruses. Front Immunol 2019; 10:1400. [PMID: 31312199 PMCID: PMC6614380 DOI: 10.3389/fimmu.2019.01400] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
Persistent and durable immunological memory forms the basis of any successful vaccination protocol. Generation of pre-existing memory B cell and T cell pools is thus the key for maintaining protective immunity to seasonal, pandemic and avian influenza viruses. Long-lived antibody secreting cells (ASCs) are responsible for maintaining antibody levels in peripheral blood. Generated with CD4+ T help after naïve B cell precursors encounter their cognate antigen, the linked processes of differentiation (including Ig class switching) and proliferation also give rise to memory B cells, which then can change rapidly to ASC status after subsequent influenza encounters. Given that influenza viruses evolve rapidly as a consequence of antibody-driven mutational change (antigenic drift), the current influenza vaccines need to be reformulated frequently and annual vaccination is recommended. Without that process of regular renewal, they provide little protection against “drifted” (particularly H3N2) variants and are mainly ineffective when a novel pandemic (2009 A/H1N1 “swine” flu) strain suddenly emerges. Such limitation of antibody-mediated protection might be circumvented, at least in part, by adding a novel vaccine component that promotes cross-reactive CD8+ T cells specific for conserved viral peptides, presented by widely distributed HLA types. Such “memory” cytotoxic T lymphocytes (CTLs) can rapidly be recalled to CTL effector status. Here, we review how B cells and follicular T cells are elicited following influenza vaccination and how they survive into a long-term memory. We describe how CD8+ CTL memory is established following influenza virus infection, and how a robust CTL recall response can lead to more rapid virus elimination by destroying virus-infected cells, and recovery. Exploiting long-term, cross-reactive CTL against the continuously evolving and unpredictable influenza viruses provides a possible mechanism for preventing a disastrous pandemic comparable to the 1918-1919 H1N1 “Spanish flu,” which killed more than 50 million people worldwide.
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Affiliation(s)
- Maria Auladell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Peter C Doherty
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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61
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Omilusik KD, Goldrath AW. Remembering to remember: T cell memory maintenance and plasticity. Curr Opin Immunol 2019; 58:89-97. [PMID: 31170601 PMCID: PMC6612439 DOI: 10.1016/j.coi.2019.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
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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62
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Pandit A, De Boer RJ. Stochastic Inheritance of Division and Death Times Determines the Size and Phenotype of CD8 + T Cell Families. Front Immunol 2019; 10:436. [PMID: 30923522 PMCID: PMC6426761 DOI: 10.3389/fimmu.2019.00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
After antigen stimulation cognate naïve CD8+ T cells undergo rapid proliferation and ultimately their progeny differentiates into short-lived effectors and longer-lived memory T cells. Although the expansion of individual cells is very heterogeneous, the kinetics are reproducible at the level of the total population of cognate cells. After the expansion phase, the population contracts, and if antigen is cleared, a population of memory T cells remains behind. Different markers like CD62L, CD27, and KLRG1 have been used to define several T cell subsets (or cell fates) developing from individual naïve CD8+ T cells during the expansion phase. Growing evidence from high-throughput experiments, like single cell RNA sequencing, epigenetic profiling, and lineage tracing, highlights the need to model this differentiation process at the level of single cells. We model CD8+ T cell proliferation and differentiation as a competitive process between the division and death probabilities of individual cells (like in the Cyton model). We use an extended form of the Cyton model in which daughter cells inherit the division and death times from their mother cell in a stochastic manner (using lognormal distributions). We show that this stochastic model reproduces the dynamics of CD8+ T cells both at the population and at the single cell level. Modeling the expression of the CD62L, CD27, and KLRG1 markers of each individual cell, we find agreement with the changing phenotypic distributions of these markers in single cell RNA sequencing data. Retrospectively re-defining conventional T-cell subsets by “gating” on these markers, we find agreement with published population data, without having to assume that these subsets have different properties, i.e., correspond to different fates.
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Affiliation(s)
- Aridaman Pandit
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Rob J De Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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63
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Ly CL, Cuzzone DA, Kataru RP, Mehrara BJ. Small Numbers of CD4+ T Cells Can Induce Development of Lymphedema. Plast Reconstr Surg 2019; 143:518e-526e. [PMID: 30601329 PMCID: PMC6395505 DOI: 10.1097/prs.0000000000005322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND CD4 T cells have been implicated in the pathology of lymphedema. Interestingly, however, there have been case reports of lymphedema development in patients with low levels of CD4 T cells because of immunosuppression. In this study, the authors sought to delineate the effect of relative CD4 T-cell deficiency on the development of lymphedema in a mouse model. METHODS A mouse model of relative CD4 T-cell deficiency was created through lethal total body irradiation of wild-type mice that then underwent bone marrow transplantation with progenitors harvested from CD4 knockout mice (wild-type/CD4 knockout). Irradiated CD4 knockout mice reconstituted with wild-type mouse-derived progenitors (CD4 knockout/wild-type), and unirradiated CD4 knockout and wild-type mice were used as controls. All mice underwent tail skin and lymphatic excision to induce lymphedema, and analysis was performed 6 weeks later. RESULTS Wild-type/CD4 knockout chimeras were not protected from developing lymphedema. Despite a global deficit in CD4 T cells, these mice had swelling, fibrosis, inflammation, and impaired lymphatic transport function indistinguishable from that in wild-type and CD4 knockout/wild-type mice. In contrast, unirradiated CD4 knockout mice had no features of lymphedema after lymphatic injury. CONCLUSIONS Relatively small numbers of bone marrow and peripheral CD4 T cells are sufficient to induce the development of lymphedema. These findings suggest that lymphatic injury results in expansion of CD4 T-cell populations in lymphedematous tissues.
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Affiliation(s)
- Catherine L. Ly
- Plastic and Reconstructive Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Daniel A. Cuzzone
- Plastic and Reconstructive Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Raghu P. Kataru
- Plastic and Reconstructive Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Babak J. Mehrara
- Plastic and Reconstructive Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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64
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Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8 + T cell response to viral infections. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1446. [PMID: 30811096 PMCID: PMC6614031 DOI: 10.1002/wsbm.1446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
Abstract
The CD8+ T cell response is critical to the control of viral infections. Yet, defining the CD8+ T cell response to viral infections quantitatively has been a challenge. Following antigen recognition, which triggers an intracellular signaling cascade, CD8+ T cells can differentiate into effector cells, which proliferate rapidly and destroy infected cells. When the infection is cleared, they leave behind memory cells for quick recall following a second challenge. If the infection persists, the cells may become exhausted, retaining minimal control of the infection while preventing severe immunopathology. These activation, proliferation and differentiation processes as well as the mounting of the effector response are intrinsically multiscale and collective phenomena. Remarkable experimental advances in the recent years, especially at the single cell level, have enabled a quantitative characterization of several underlying processes. Simultaneously, sophisticated mathematical models have begun to be constructed that describe these multiscale phenomena, bringing us closer to a comprehensive description of the CD8+ T cell response to viral infections. Here, we review the advances made and summarize the challenges and opportunities ahead. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Cell Fates Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models.
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Affiliation(s)
- Subhasish Baral
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pramita Sen
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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65
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Endo Y, Onodera A, Obata-Ninomiya K, Koyama-Nasu R, Asou HK, Ito T, Yamamoto T, Kanno T, Nakajima T, Ishiwata K, Kanuka H, Tumes DJ, Nakayama T. ACC1 determines memory potential of individual CD4 + T cells by regulating de novo fatty acid biosynthesis. Nat Metab 2019; 1:261-275. [PMID: 32694782 DOI: 10.1038/s42255-018-0025-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/07/2018] [Indexed: 01/14/2023]
Abstract
Immunological memory is central to adaptive immunity and protection from disease. Changing metabolic demands as antigen-specific T cells transition from effector to memory cells have been well documented, but the cell-specific pathways and molecules that govern this transition are poorly defined. Here we show that genetic deletion of ACC1, a rate-limiting enzyme in fatty acid biosynthesis, enhances the formation of CD4+ T memory cells. ACC1-deficient effector helper T (Th) cells have similar metabolic signatures to wild-type memory Th cells, and expression of the gene encoding ACC1, Acaca, was inversely correlated with a memory gene signature in individual cells. Inhibition of ACC1 function enhances memory T cell formation during parasite infection in mice. Using single-cell analyses we identify a memory precursor-enriched population (CCR7hiCD137lo) present during early differentiation of effector CD4+ T cells. Our data indicate that fatty acid metabolism directs cell fate determination during the generation of memory CD4+ T cells.
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Affiliation(s)
- Yusuke Endo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
- Laboratory of Medical Omics Research, KAZUSA DNA Research Institute, Kisarazu, Chiba, Japan
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Kazushige Obata-Ninomiya
- Department of Advanced Allergology of the Airway, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ryo Koyama-Nasu
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Hikari K Asou
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Toshihiro Ito
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Takeshi Yamamoto
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Toshio Kanno
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
- Laboratory of Medical Omics Research, KAZUSA DNA Research Institute, Kisarazu, Chiba, Japan
| | - Takahiro Nakajima
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
- Laboratory of Medical Omics Research, KAZUSA DNA Research Institute, Kisarazu, Chiba, Japan
| | - Kenji Ishiwata
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Damon J Tumes
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan.
- AMED-CREST, AMED, Chuo-ku, Chiba, Japan.
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66
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Chen Y, Zander R, Khatun A, Schauder DM, Cui W. Transcriptional and Epigenetic Regulation of Effector and Memory CD8 T Cell Differentiation. Front Immunol 2018; 9:2826. [PMID: 30581433 PMCID: PMC6292868 DOI: 10.3389/fimmu.2018.02826] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/15/2018] [Indexed: 12/25/2022] Open
Abstract
Immune protection and lasting memory are accomplished through the generation of phenotypically and functionally distinct CD8 T cell subsets. Understanding how these effector and memory T cells are formed is the first step in eventually manipulating the immune system for therapeutic benefit. In this review, we will summarize the current understanding of CD8 T cell differentiation upon acute infection, with a focus on the transcriptional and epigenetic regulation of cell fate decision and memory formation. Moreover, we will highlight the importance of high throughput sequencing approaches and single cell technologies in providing insight into genome-wide investigations and the heterogeneity of individual CD8 T cells.
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Affiliation(s)
- Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ryan Zander
- Blood Center of Wisconsin, Blood Research Institute, Milwaukee, WI, United States
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - David M Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.,Blood Center of Wisconsin, Blood Research Institute, Milwaukee, WI, United States
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67
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Understanding Subset Diversity in T Cell Memory. Immunity 2018; 48:214-226. [PMID: 29466754 DOI: 10.1016/j.immuni.2018.02.010] [Citation(s) in RCA: 334] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/05/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022]
Abstract
Considerable advances have been made in recent years in understanding the generation and function of memory T cells. Memory T cells are typically parsed into discreet subsets based on phenotypic definitions that connote distinct roles in immunity. Here we consider new developments in the field and focus on how emerging differences between memory cells with respect to their trafficking, metabolism, epigenetic regulation, and longevity may fail to fit into small groups of "memory subsets." Rather, the properties of individual memory T cells fall on a continuum within each of these and other parameters. We discuss how this continuum influences the way that the efficacy of vaccination is assessed, as well as the suitability of a memory population for protective immunity.
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68
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Horton MB, Prevedello G, Marchingo JM, Zhou JHS, Duffy KR, Heinzel S, Hodgkin PD. Multiplexed Division Tracking Dyes for Proliferation-Based Clonal Lineage Tracing. THE JOURNAL OF IMMUNOLOGY 2018; 201:1097-1103. [PMID: 29914887 DOI: 10.4049/jimmunol.1800481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 11/19/2022]
Abstract
The generation of cellular heterogeneity is an essential feature of immune responses. Understanding the heritability and asymmetry of phenotypic changes throughout this process requires determination of clonal-level contributions to fate selection. Evaluating intraclonal and interclonal heterogeneity and the influence of distinct fate determinants in large numbers of cell lineages, however, is usually laborious, requiring familial tracing and fate mapping. In this study, we introduce a novel, accessible, high-throughput method for measuring familial fate changes with accompanying statistical tools for testing hypotheses. The method combines multiplexing of division tracking dyes with detection of phenotypic markers to reveal clonal lineage properties. We illustrate the method by studying in vitro-activated mouse CD8+ T cell cultures, reporting division and phenotypic changes at the level of families. This approach has broad utility as it is flexible and adaptable to many cell types and to modifications of in vitro, and potentially in vivo, fate monitoring systems.
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Affiliation(s)
- Miles B Horton
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Victoria, Australia; and
| | - Giulio Prevedello
- Hamilton Institute, Maynooth University, Maynooth, County Kildare, Ireland
| | - Julia M Marchingo
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Victoria, Australia; and
| | - Jie H S Zhou
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Victoria, Australia; and
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, County Kildare, Ireland
| | - Susanne Heinzel
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Victoria, Australia; and
| | - Philip D Hodgkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia; .,Department of Medical Biology, The University of Melbourne, Parkville 3010, Victoria, Australia; and
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69
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Polonsky M, Rimer J, Kern-Perets A, Zaretsky I, Miller S, Bornstein C, David E, Kopelman NM, Stelzer G, Porat Z, Chain B, Friedman N. Induction of CD4 T cell memory by local cellular collectivity. Science 2018; 360:360/6394/eaaj1853. [DOI: 10.1126/science.aaj1853] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/19/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
Abstract
Cell differentiation is directed by signals driving progenitors into specialized cell types. This process can involve collective decision-making, when differentiating cells determine their lineage choice by interacting with each other. We used live-cell imaging in microwell arrays to study collective processes affecting differentiation of naïve CD4+ T cells into memory precursors. We found that differentiation of precursor memory T cells sharply increases above a threshold number of locally interacting cells. These homotypic interactions involve the cytokines interleukin-2 (IL-2) and IL-6, which affect memory differentiation orthogonal to their effect on proliferation and survival. Mathematical modeling suggests that the differentiation rate is continuously modulated by the instantaneous number of locally interacting cells. This cellular collectivity can prioritize allocation of immune memory to stronger responses.
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70
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Klann JE, Kim SH, Remedios KA, He Z, Metz PJ, Lopez J, Tysl T, Olvera JG, Ablack JN, Cantor JM, Boland BS, Yeo G, Zheng Y, Lu LF, Bui JD, Ginsberg MH, Petrich BG, Chang JT. Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. THE JOURNAL OF IMMUNOLOGY 2018; 200:4012-4023. [PMID: 29703862 DOI: 10.4049/jimmunol.1800112] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/09/2018] [Indexed: 12/22/2022]
Abstract
Maintenance of the regulatory T (Treg) cell pool is essential for peripheral tolerance and prevention of autoimmunity. Integrins, heterodimeric transmembrane proteins consisting of α and β subunits that mediate cell-to-cell and cell-to-extracellular matrix interactions, play an important role in facilitating Treg cell contact-mediated suppression. In this article, we show that integrin activation plays an essential, previously unappreciated role in maintaining murine Treg cell function. Treg cell-specific loss of talin, a β integrin-binding protein, or expression of talin(L325R), a mutant that selectively abrogates integrin activation, resulted in lethal systemic autoimmunity. This dysfunction could be attributed, in part, to a global dysregulation of the Treg cell transcriptome. Activation of integrin α4β1 led to increased suppressive capacity of the Treg cell pool, suggesting that modulating integrin activation on Treg cells may be a useful therapeutic strategy for autoimmune and inflammatory disorders. Taken together, these results reveal a critical role for integrin-mediated signals in controlling peripheral tolerance by virtue of maintaining Treg cell function.
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Affiliation(s)
- Jane E Klann
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Stephanie H Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Kelly A Remedios
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Patrick J Metz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Justine Lopez
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Jocelyn G Olvera
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Jailal N Ablack
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Joseph M Cantor
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Gene Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Ye Zheng
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Li-Fan Lu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093; and
| | - Mark H Ginsberg
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Brian G Petrich
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093;
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71
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Fuentes E, Fuentes M, Alarcón M, Palomo I. Immune System Dysfunction in the Elderly. AN ACAD BRAS CIENC 2018; 89:285-299. [PMID: 28423084 DOI: 10.1590/0001-3765201720160487] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/29/2016] [Indexed: 02/07/2023] Open
Abstract
Human aging is characterized by both physical and physiological frailty that profoundly affects the immune system. In this context aging is associated with declines in adaptive and innate immunity established as immunosenescence. Immunosenescence is a new concept that reflects the age-associated restructuring changes of innate and adaptive immune functions. Thus elderly individuals usually present chronic low-level inflammation, higher infection rates and chronic diseases. A study of alterations in the immune system during aging could provide a potentially useful biomarker for the evaluation of immune senescence treatment. The immune system is the result of the interplay between innate and adaptive immunity, yet the impact of aging on this function is unclear. In this article the function of the immune system during aging is explored.
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Affiliation(s)
- Eduardo Fuentes
- Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging/ PIEI-ES, Universidad de Talca, Postal Code 3460000, Casilla 747, Talca, Chile.,Núcleo Científico Multidisciplinario, Universidad de Talca, Postal Code 3460000, Casilla 747, Talca, Chile
| | - Manuel Fuentes
- Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging/ PIEI-ES, Universidad de Talca, Postal Code 3460000, Casilla 747, Talca, Chile
| | - Marcelo Alarcón
- Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging/ PIEI-ES, Universidad de Talca, Postal Code 3460000, Casilla 747, Talca, Chile
| | - Iván Palomo
- Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging/ PIEI-ES, Universidad de Talca, Postal Code 3460000, Casilla 747, Talca, Chile
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72
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Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity. Cell Rep 2018; 16:3311-3321. [PMID: 27653692 DOI: 10.1016/j.celrep.2016.08.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/21/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022] Open
Abstract
How functionally diverse populations of pathogen-specific killer T cells are generated during an immune response remains unclear. Here, we propose that fine-tuning of CD8αβ co-receptor levels via histone acetylation plays a role in lineage fate. We show that lysine acetyltransferase 6A (KAT6A) is responsible for maintaining permissive Cd8 gene transcription and enabling robust effector responses during infection. KAT6A-deficient CD8(+) T cells downregulated surface CD8 co-receptor expression during clonal expansion, a finding linked to reduced Cd8α transcripts and histone-H3 lysine 9 acetylation of the Cd8 locus. Loss of CD8 expression in KAT6A-deficient T cells correlated with reduced TCR signaling intensity and accelerated contraction of the effector-like memory compartment, whereas the long-lived memory compartment appeared unaffected, a result phenocopied by the removal of the Cd8 E8I enhancer element. These findings suggest a direct role of CD8αβ co-receptor expression and histone acetylation in shaping functional diversity within the cytotoxic T cell pool.
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73
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Flores-Santibáñez F, Cuadra B, Fernández D, Rosemblatt MV, Núñez S, Cruz P, Gálvez-Cancino F, Cárdenas JC, Lladser A, Rosemblatt M, Bono MR, Sauma D. In Vitro-Generated Tc17 Cells Present a Memory Phenotype and Serve As a Reservoir of Tc1 Cells In Vivo. Front Immunol 2018; 9:209. [PMID: 29472932 PMCID: PMC5809442 DOI: 10.3389/fimmu.2018.00209] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/24/2018] [Indexed: 11/13/2022] Open
Abstract
Memory CD8+ T cells are ideal candidates for cancer immunotherapy because they can mediate long-term protection against tumors. However, the therapeutic potential of different in vitro-generated CD8+ T cell effector subsets to persist and become memory cells has not been fully characterized. Type 1 CD8+ T (Tc1) cells produce interferon-γ and are endowed with high cytotoxic capacity, whereas IL-17-producing CD8+ T (Tc17) cells are less cytotoxic but display enhanced self-renewal capacity. We sought to evaluate the functional properties of in vitro-generated Tc17 cells and elucidate their potential to become long lasting memory cells. Our results show that in vitro-generated Tc17 cells display a greater in vivo persistence and expansion in response to secondary antigen stimulation compared to Tc1 cells. When transferred into recipient mice, Tc17 cells persist in secondary lymphoid organs, present a recirculation behavior consistent with central memory T cells, and can shift to a Tc1 phenotype. Accordingly, Tc17 cells are endowed with a higher mitochondrial spare respiratory capacity than Tc1 cells and express higher levels of memory-related molecules than Tc1 cells. Together, these results demonstrate that in vitro-generated Tc17 cells acquire a central memory program and provide a lasting reservoir of Tc1 cells in vivo, thus supporting the use of Tc17 lymphocytes in the design of novel and more effective therapies.
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Affiliation(s)
| | - Bárbara Cuadra
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dominique Fernández
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mariana V Rosemblatt
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Facultad de Medicina, Universidad San Sebastian, Santiago, Chile.,Programa de Doctorado en Ciencias Biomedicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sarah Núñez
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Cruz
- Anatomy and Developmental Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | | | - J César Cárdenas
- Anatomy and Developmental Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Geroscience Center for Brain Health and Metabolism, Santiago, Chile.,Buck Institute for Research on Aging, Novato, CA, United States.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, United States
| | | | - Mario Rosemblatt
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Fundacion Ciencia & Vida, Santiago, Chile.,Facultad de Ciencias Biologicas, Universidad Andrés Bello, Santiago, Chile
| | - María Rosa Bono
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniela Sauma
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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74
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Heinzel S, Marchingo JM, Horton MB, Hodgkin PD. The regulation of lymphocyte activation and proliferation. Curr Opin Immunol 2018; 51:32-38. [PMID: 29414529 DOI: 10.1016/j.coi.2018.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 01/10/2023]
Abstract
Activation induced proliferation and clonal expansion of antigen specific lymphocytes is a hallmark of the adaptive immune response to pathogens. Recent studies identify two distinct control phases. In the first T and B lymphocytes integrate antigen and additional costimuli to motivate a programmed proliferative burst that ceases with a return to cell quiescence and eventual death. This proliferative burst is autonomously timed, ensuring an appropriate response magnitude whilst preventing uncontrolled expansion. This initial response is subject to further modification and extension by a range of signals that modify, expand and direct the emergence of a rich array of new cell types. Thus, both robust clonal expansion of a small number of antigen specific T cells, and the concurrent emergence of extensive cellular diversity, confers immunity to a vast array of different pathogens. The in vivo response to a given pathogen is made up by the sum of all responding clones and is reproducible and pathogen specific. Thus, a precise description of the regulatory principles governing lymphocyte proliferation, differentiation and survival is essential to a unified understanding of the immune system.
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Affiliation(s)
- Susanne Heinzel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Julia M Marchingo
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Miles B Horton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Philip D Hodgkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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75
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76
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Backer RA, Hombrink P, Helbig C, Amsen D. The Fate Choice Between Effector and Memory T Cell Lineages: Asymmetry, Signal Integration, and Feedback to Create Bistability. Adv Immunol 2018; 137:43-82. [DOI: 10.1016/bs.ai.2017.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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77
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Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R. Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature 2017; 552:404-409. [PMID: 29236683 PMCID: PMC5965677 DOI: 10.1038/nature25144] [Citation(s) in RCA: 319] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/17/2017] [Indexed: 01/20/2023]
Abstract
Memory CD8 T cells that circulate in the blood and are present in lymphoid organs are an essential component of long-lived T cell immunity. These memory CD8 T cells remain poised to rapidly elaborate effector functions upon re-exposure to pathogens, but also have many properties in common with naive cells, including pluripotency and the ability to migrate to the lymph nodes and spleen. Thus, memory cells embody features of both naive and effector cells, fuelling a long-standing debate centred on whether memory T cells develop from effector cells or directly from naive cells. Here we show that long-lived memory CD8 T cells are derived from a subset of effector T cells through a process of dedifferentiation. To assess the developmental origin of memory CD8 T cells, we investigated changes in DNA methylation programming at naive and effector cell-associated genes in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection in mice. Methylation profiling of terminal effector versus memory-precursor CD8 T cell subsets showed that, rather than retaining a naive epigenetic state, the subset of cells that gives rise to memory cells acquired de novo DNA methylation programs at naive-associated genes and became demethylated at the loci of classically defined effector molecules. Conditional deletion of the de novo methyltransferase Dnmt3a at an early stage of effector differentiation resulted in reduced methylation and faster re-expression of naive-associated genes, thereby accelerating the development of memory cells. Longitudinal phenotypic and epigenetic characterization of the memory-precursor effector subset of virus-specific CD8 T cells transferred into antigen-free mice revealed that differentiation to memory cells was coupled to erasure of de novo methylation programs and re-expression of naive-associated genes. Thus, epigenetic repression of naive-associated genes in effector CD8 T cells can be reversed in cells that develop into long-lived memory CD8 T cells while key effector genes remain demethylated, demonstrating that memory T cells arise from a subset of fate-permissive effector T cells.
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Affiliation(s)
- Ben Youngblood
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - J. Scott Hale
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Haydn T. Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30322
| | - Eunseon Ahn
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Xiaojin Xu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Andreas Wieland
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Koichi Araki
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Erin E. West
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Hazem E. Ghoneim
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - Pranay Dogra
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - Carl W. Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Bogumila T. Konieczny
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Rustom Antia
- Department of Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
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78
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CD8 + T Lymphocyte Self-Renewal during Effector Cell Determination. Cell Rep 2017; 17:1773-1782. [PMID: 27829149 DOI: 10.1016/j.celrep.2016.10.032] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/03/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022] Open
Abstract
Selected CD8+ T cells must divide, produce differentiated effector cells, and self-renew, often repeatedly. We now show that silencing expression of the transcription factor TCF1 marks loss of self-renewal by determined effector cells and that this requires cell division. In acute infections, the first three CD8+ T cell divisions produce daughter cells with unequal proliferative signaling but uniform maintenance of TCF1 expression. The more quiescent initial daughter cells resemble canonical central memory cells. The more proliferative, effector-prone cells from initial divisions can subsequently undergo division-dependent production of a TCF1-negative effector daughter cell along with a self-renewing TCF1-positive daughter cell, the latter also contributing to the memory cell pool upon resolution of infection. Self-renewal in the face of effector cell determination may promote clonal amplification and memory cell formation in acute infections, sustain effector regeneration during persistent subclinical infections, and be rate limiting, but remediable, in chronic active infections and cancer.
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79
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Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Am J Hum Genet 2017; 101:686-699. [PMID: 29106824 PMCID: PMC5673624 DOI: 10.1016/j.ajhg.2017.09.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/13/2017] [Indexed: 01/09/2023] Open
Abstract
Previous studies have prioritized trait-relevant cell types by looking for an enrichment of genome-wide association study (GWAS) signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell populations. Measurement of single-cell gene expression has become a popular method for characterizing novel cell types, and yet limited work has linked single-cell RNA sequencing (RNA-seq) to phenotypes of interest. To address this deficiency, we present RolyPoly, a regression-based polygenic model that can prioritize trait-relevant cell types and genes from GWAS summary statistics and gene expression data. RolyPoly is designed to use expression data from either bulk tissue or single-cell RNA-seq. In this study, we demonstrated RolyPoly's accuracy through simulation and validated previously known tissue-trait associations. We discovered a significant association between microglia and late-onset Alzheimer disease and an association between schizophrenia and oligodendrocytes and replicating fetal cortical cells. Additionally, RolyPoly computes a trait-relevance score for each gene to reflect the importance of expression specific to a cell type. We found that differentially expressed genes in the prefrontal cortex of individuals with Alzheimer disease were significantly enriched with genes ranked highly by RolyPoly gene scores. Overall, our method represents a powerful framework for understanding the effect of common variants on cell types contributing to complex traits.
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Affiliation(s)
- Diego Calderon
- Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA.
| | - Anand Bhaskar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David A Knowles
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - David Golan
- Faculty of Industrial Engineering & Management, Technion, Haifa 3200003, Israel
| | - Towfique Raj
- Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Audrey Q Fu
- Department of Statistical Science, University of Idaho, Moscow, ID 83844, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
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80
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Capece T, Walling BL, Lim K, Kim KD, Bae S, Chung HL, Topham DJ, Kim M. A novel intracellular pool of LFA-1 is critical for asymmetric CD8 + T cell activation and differentiation. J Cell Biol 2017; 216:3817-3829. [PMID: 28954823 PMCID: PMC5674876 DOI: 10.1083/jcb.201609072] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/13/2017] [Accepted: 07/11/2017] [Indexed: 11/22/2022] Open
Abstract
The integrin lymphocyte function-associated antigen 1 (LFA-1; CD11a/CD18) is a key T cell adhesion receptor that mediates stable interactions with antigen-presenting cell (APC), as well as chemokine-mediated migration. Using our newly generated CD11a-mYFP knock-in mice, we discovered that naive CD8+ T cells reserve a significant intracellular pool of LFA-1 in the uropod during migration. Intracellular LFA-1 quickly translocated to the cell surface with antigenic stimulus. Importantly, the redistribution of intracellular LFA-1 at the contact with APC was maintained during cell division and led to an unequal inheritance of LFA-1 in divided T cells. The daughter CD8+ T cells with disparate LFA-1 expression showed different patterns of migration on ICAM-1, APC interactions, and tissue retention, as well as altered effector functions. In addition, we identified Rab27 as an important regulator of the intracellular LFA-1 translocation. Collectively, our data demonstrate that an intracellular pool of LFA-1 in naive CD8+ T cells plays a key role in T cell activation and differentiation.
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Affiliation(s)
- Tara Capece
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Brandon L Walling
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Kihong Lim
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Kyun-Do Kim
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Seyeon Bae
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Hung-Li Chung
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - David J Topham
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
| | - Minsoo Kim
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY
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81
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SIRT6 knockout cells resist apoptosis initiation but not progression: a computational method to evaluate the progression of apoptosis. Apoptosis 2017; 22:1336-1343. [DOI: 10.1007/s10495-017-1412-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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82
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Widjaja CE, Olvera JG, Metz PJ, Phan AT, Savas JN, de Bruin G, Leestemaker Y, Berkers CR, de Jong A, Florea BI, Fisch K, Lopez J, Kim SH, Garcia DA, Searles S, Bui JD, Chang AN, Yates JR, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT. Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J Clin Invest 2017; 127:3609-3623. [PMID: 28846070 PMCID: PMC5617668 DOI: 10.1172/jci90895] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 07/14/2017] [Indexed: 12/30/2022] Open
Abstract
During an immune response, CD8+ T lymphocytes can undergo asymmetric division, giving rise to daughter cells that exhibit distinct tendencies to adopt terminal effector and memory cell fates. Here we show that "pre-effector" and "pre-memory" cells resulting from the first CD8+ T cell division in vivo exhibited low and high rates of endogenous proteasome activity, respectively. Pharmacologic reduction of proteasome activity in CD8+ T cells early during differentiation resulted in acquisition of terminal effector cell characteristics, whereas enhancement of proteasome activity conferred attributes of memory lymphocytes. Transcriptomic and proteomic analyses revealed that modulating proteasome activity in CD8+ T cells affected cellular metabolism. These metabolic changes were mediated, in part, through differential expression of Myc, a transcription factor that controls glycolysis and metabolic reprogramming. Taken together, these results demonstrate that proteasome activity is an important regulator of CD8+ T cell fate and raise the possibility that increasing proteasome activity may be a useful therapeutic strategy to enhance the generation of memory lymphocytes.
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Affiliation(s)
| | | | | | - Anthony T Phan
- Division of Biological Sciences, UCSD, La Jolla, California, USA
| | - Jeffrey N Savas
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Gerjan de Bruin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Yves Leestemaker
- Division of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Celia R Berkers
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Utrecht, The Netherlands
| | - Annemieke de Jong
- Division of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bogdan I Florea
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kathleen Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, and
| | | | | | | | | | - Jack D Bui
- Department of Pathology, UCSD, La Jolla, California, USA
| | - Aaron N Chang
- Center for Computational Biology and Bioinformatics, Department of Medicine, and
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | | | | | - Huib Ovaa
- Division of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center, Leiden, The Netherlands
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83
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Shin HM, Kapoor VN, Kim G, Li P, Kim HR, Suresh M, Kaech SM, Wherry EJ, Selin LK, Leonard WJ, Welsh RM, Berg LJ. Transient expression of ZBTB32 in anti-viral CD8+ T cells limits the magnitude of the effector response and the generation of memory. PLoS Pathog 2017; 13:e1006544. [PMID: 28827827 PMCID: PMC5578684 DOI: 10.1371/journal.ppat.1006544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/31/2017] [Accepted: 07/20/2017] [Indexed: 01/02/2023] Open
Abstract
Virus infections induce CD8+ T cell responses comprised of a large population of terminal effector cells and a smaller subset of long-lived memory cells. The transcription factors regulating the relative expansion versus the long-term survival potential of anti-viral CD8+ T cells are not completely understood. We identified ZBTB32 as a transcription factor that is transiently expressed in effector CD8+ T cells. After acute virus infection, CD8+ T cells deficient in ZBTB32 showed enhanced virus-specific CD8+ T cell responses, and generated increased numbers of virus-specific memory cells; in contrast, persistent expression of ZBTB32 suppressed memory cell formation. The dysregulation of CD8+ T cell responses in the absence of ZBTB32 was catastrophic, as Zbtb32-/- mice succumbed to a systemic viral infection and showed evidence of severe lung pathology. We found that ZBTB32 and Blimp-1 were co-expressed following CD8+ T cell activation, bound to each other, and cooperatively regulated Blimp-1 target genes Eomes and Cd27. These findings demonstrate that ZBTB32 is a key transcription factor in CD8+ effector T cells that is required for the balanced regulation of effector versus memory responses to infection. CD8+ T lymphocytes are essential for immune protection against viruses. In response to an infection, these cells are activated, proliferate, and generate antiviral effector cells that eradicate the infection. Following this, the majority of these effector cells die, leaving a small subset of long-lived virus-specific memory T cells. Our study identifies a transcription factor, ZBTB32, that is required for the regulation of CD8+ T cell responses. In its absence, antiviral CD8+ T cell numbers increase to abnormally high levels, and generate an overabundance of memory T cells. When this dysregulated response occurs following infection with a virus that cannot be rapidly eliminated by the immune system, the infected animals die from immune-mediated tissue damage, indicating the importance of this pathway.
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Affiliation(s)
- Hyun Mu Shin
- Dept of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Anatomy and Cell Biology, Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Varun N. Kapoor
- Dept of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Gwanghun Kim
- Department of Anatomy and Cell Biology, Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hang-Rae Kim
- Department of Anatomy and Cell Biology, Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - M. Suresh
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susan M. Kaech
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - E. John Wherry
- Department of Microbiology and Institute for Immunology, University of Pennsylvania Perelman School Medicine, Philadelphia, Pennsylvania, United States of America
| | - Liisa K. Selin
- Dept of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Warren J. Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Raymond M. Welsh
- Dept of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Leslie J. Berg
- Dept of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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84
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Lymphocyte Fate and Metabolism: A Clonal Balancing Act. Trends Cell Biol 2017; 27:946-954. [PMID: 28818395 DOI: 10.1016/j.tcb.2017.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 01/16/2023]
Abstract
Activated lymphocytes perform a clonal balancing act, yielding a daughter cell that differentiates owing to intense PI3K signaling, alongside a self-renewing sibling cell with blunted anabolic signaling. Divergent cellular anabolism versus catabolism is emerging as a feature of several developmental and regenerative paradigms. Metabolism can dictate cell fate, in part, because lineage-specific regulators are embedded in the circuitry of conserved metabolic switches. Unequal transmission of PI3K signaling during regenerative divisions is reminiscent of compartmentalized PI3K activity during directed motility or polarized information flow in non-dividing cells. The diverse roles of PI3K pathways in membrane traffic, cell polarity, metabolism, and gene expression may have converged to instruct sibling cell feast and famine, thereby enabling clonal differentiation alongside self-renewal.
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85
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Hey-Nguyen WJ, Xu Y, Pearson CF, Bailey M, Suzuki K, Tantau R, Obeid S, Milner B, Field A, Carr A, Bloch M, Cooper DA, Kelleher AD, Zaunders JJ, Koelsch KK. Quantification of Residual Germinal Center Activity and HIV-1 DNA and RNA Levels Using Fine Needle Biopsies of Lymph Nodes During Antiretroviral Therapy. AIDS Res Hum Retroviruses 2017; 33:648-657. [PMID: 28287825 DOI: 10.1089/aid.2016.0171] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
HIV-1 reservoirs are most often studied in peripheral blood (PB), but not all lymphocytes recirculate, particularly T follicular helper (Tfh) CD4+ T cells, as well as germinal center (GC) B cells, in lymph nodes (LNs). Ultrasound-guided fine needle biopsies (FNBs) from inguinal LNs and PB samples were obtained from 10 healthy controls (HCs) and 21 HIV-1-infected subjects [11 antiretroviral therapy (ART) naive and 10 on ART]. Tfh cells and GC B cells were enumerated by flow cytometry. HIV-1 DNA and cell-associated (CA) RNA levels in LNs and PB were quantified by real-time polymerase chain reaction. FNBs were obtained without adverse events. Tfh cells and GC B cells were highly elevated in ART-naive subjects, with a median GC B cell count >300-fold higher than HCs, but also remained higher in 4 out of the 10 subjects on ART. GC B cell counts and Tfh cell counts were highly correlated with each other, and also with activated T cells in LNs but not in blood. Levels of HIV-1 DNA and CA RNA viral burden in highly purified CD4+ T cells from FNBs were significantly elevated compared with those in CD4+ T cells from PB in the ART-naive group, but only trended toward an increase in the ART patients. FNBs enabled minimally invasive access to, and parallel measurement of residual activated T and B cells and viral burden within LNs in HIV-1-infected patients. These FNBs revealed significant GC activity that was not apparent from corresponding PB samples.
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Affiliation(s)
| | - Yin Xu
- Kirby Institute, UNSW Sydney, Sydney, Australia
| | | | | | - Kazuo Suzuki
- Kirby Institute, UNSW Sydney, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
| | - Robyn Tantau
- Department of Medical Imaging, St. Vincent's Hospital, Darlinghurst, Australia
| | - Solange Obeid
- Department of Medical Imaging, St. Vincent's Hospital, Darlinghurst, Australia
| | - Brad Milner
- Department of Medical Imaging, St. Vincent's Hospital, Darlinghurst, Australia
| | - Andrew Field
- Department of Anatomical Pathology, St. Vincent's Hospital, Darlinghurst, Australia
| | - Andrew Carr
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
| | - Mark Bloch
- Holdsworth House Medical Practice, Darlinghurst, Australia
| | - David A. Cooper
- Kirby Institute, UNSW Sydney, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
| | - Anthony D. Kelleher
- Kirby Institute, UNSW Sydney, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
| | - John J. Zaunders
- Kirby Institute, UNSW Sydney, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
| | - Kersten K. Koelsch
- Kirby Institute, UNSW Sydney, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Darlinghurst, Australia
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86
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Klann JE, Remedios KA, Kim SH, Metz PJ, Lopez J, Mack LA, Zheng Y, Ginsberg MH, Petrich BG, Chang JT. Talin Plays a Critical Role in the Maintenance of the Regulatory T Cell Pool. THE JOURNAL OF IMMUNOLOGY 2017; 198:4639-4651. [PMID: 28515282 DOI: 10.4049/jimmunol.1601165] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/14/2017] [Indexed: 12/22/2022]
Abstract
Talin, a cytoskeletal protein essential in mediating integrin activation, has been previously shown to be involved in the regulation of T cell proliferation and function. In this study, we describe a role for talin in maintaining the homeostasis and survival of the regulatory T (Treg) cell pool. T cell-specific deletion of talin in Tln1fl/flCd4Cre mice resulted in spontaneous lymphocyte activation, primarily due to numerical and functional deficiencies of Treg cells in the periphery. Peripheral talin-deficient Treg cells were unable to maintain high expression of IL-2Rα, resulting in impaired IL-2 signaling and ultimately leading to increased apoptosis through downregulation of prosurvival proteins Bcl-2 and Mcl-1. The requirement for talin in maintaining high IL-2Rα expression by Treg cells was due, in part, to integrin LFA-1-mediated interactions between Treg cells and dendritic cells. Collectively, our data suggest a critical role for talin in Treg cell-mediated maintenance of immune homeostasis.
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Affiliation(s)
- Jane E Klann
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kelly A Remedios
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Stephanie H Kim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Patrick J Metz
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Justine Lopez
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lauren A Mack
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037; and
| | - Ye Zheng
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037; and
| | - Mark H Ginsberg
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Brian G Petrich
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA 30322
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
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87
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Kumagai J, Hirahara K, Nakayama T. Pathogenic Th cell subsets in chronic inflammatory diseases. ACTA ACUST UNITED AC 2017; 39:114-23. [PMID: 27212597 DOI: 10.2177/jsci.39.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
CD4(+) T cells play central roles to appropriate protection against pathogens. While, they can also be pathogenic driving inflammatory diseases. Besides the classical model of differentiation of T helper 1 (Th1) and Th2 cells, various CD4(+) T cell subsets, including Th17, Th9, T follicular helper (Tfh) and T regulatory (Treg) cells, have been recognized recently. In this review, we will focus on how these various CD4(+) T cell subsets contribute to the pathogenesis of immune-mediated inflammatory diseases. We will also discuss various unique subpopulations of T helper cells that have been identified. Recent advancement of the basic immunological research revealed that T helper cells are plastic than we imagined. So, we will focus on the molecular mechanisms underlying the generation of the plasticity and heterogeneity of T helper cell subsets. These latest finding regarding T helper cell subsets has pushed us to reconsider the etiology of immune-mediated inflammatory diseases beyond the model based on the conventional Th1/Th2 balance. Toward this end, we put forward another model, "the pathogenic Th population disease induction model", as a possible mechanism for the induction and/or persistence of immune-mediated inflammatory diseases.
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Affiliation(s)
- Jin Kumagai
- Department of Immunology, Graduate School of Medicine, Chiba University
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88
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Crauste F, Mafille J, Boucinha L, Djebali S, Gandrillon O, Marvel J, Arpin C. Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny. Cell Syst 2017; 4:306-317.e4. [PMID: 28237797 DOI: 10.1016/j.cels.2017.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/21/2016] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Primary immune responses generate short-term effectors and long-term protective memory cells. The delineation of the genealogy linking naive, effector, and memory cells has been complicated by the lack of phenotypes discriminating effector from memory differentiation stages. Using transcriptomics and phenotypic analyses, we identify Bcl2 and Mki67 as a marker combination that enables the tracking of nascent memory cells within the effector phase. We then use a formal approach based on mathematical models describing the dynamics of population size evolution to test potential progeny links and demonstrate that most cells follow a linear naive→early effector→late effector→memory pathway. Moreover, our mathematical model allows long-term prediction of memory cell numbers from a few early experimental measurements. Our work thus provides a phenotypic means to identify effector and memory cells, as well as a mathematical framework to investigate their genealogy and to predict the outcome of immunization regimens in terms of memory cell numbers generated.
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Affiliation(s)
- Fabien Crauste
- Team Dracula, Inria, 69603 Villeurbanne, France; Institut Camille Jordan, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5208, 43 Boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Julien Mafille
- CIRI, ICL, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR 5308, École Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France
| | - Lilia Boucinha
- CIRI, ICL, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR 5308, École Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France
| | - Sophia Djebali
- CIRI, ICL, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR 5308, École Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France
| | - Olivier Gandrillon
- Team Dracula, Inria, 69603 Villeurbanne, France; Laboratory of Biology and Modelling of the Cell, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 allée d'Italie Site Jacques Monod, 69007 Lyon, France
| | - Jacqueline Marvel
- CIRI, ICL, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR 5308, École Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France.
| | - Christophe Arpin
- CIRI, ICL, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR 5308, École Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France.
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89
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Kakaradov B, Arsenio J, Widjaja CE, He Z, Aigner S, Metz PJ, Yu B, Wehrens EJ, Lopez J, Kim SH, Zuniga EI, Goldrath AW, Chang JT, Yeo GW. Early transcriptional and epigenetic regulation of CD8 + T cell differentiation revealed by single-cell RNA sequencing. Nat Immunol 2017; 18:422-432. [PMID: 28218746 PMCID: PMC5360497 DOI: 10.1038/ni.3688] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 01/13/2017] [Indexed: 12/13/2022]
Abstract
During microbial infection, responding CD8+ T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA-sequencing approach and analyzed individual CD8+ T lymphocytes sequentially throughout the course of a viral infection in vivo. Our analyses revealed a striking transcriptional divergence among cells that had undergone their first division and identified previously unknown molecular determinants that controlled the fate specification of CD8+ T lymphocytes. Our findings suggest a model for the differentiation of terminal effector cells initiated by an early burst of transcriptional activity and subsequently refined by epigenetic silencing of transcripts associated with memory lymphocytes, which highlights the power and necessity of single-cell approaches.
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Affiliation(s)
- Boyko Kakaradov
- Department of Cellular and Molecular Medicine, University of California, San Diego, California, USA
| | - Janilyn Arsenio
- Department of Medicine, University of California, San Diego, California, USA
| | | | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, California, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, California, USA
| | - Patrick J Metz
- Department of Medicine, University of California, San Diego, California, USA
| | - Bingfei Yu
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Ellen J Wehrens
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Justine Lopez
- Department of Medicine, University of California, San Diego, California, USA
| | - Stephanie H Kim
- Department of Medicine, University of California, San Diego, California, USA
| | - Elina I Zuniga
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, California, USA.,Institute for Genomic Medicine, University of California, San Diego, California, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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90
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Abstract
Asymmetric cell division (ACD) controls cell fate decisions in model organisms such as Drosophila and C. elegans and has recently emerged as a mediator of T cell fate and hematopoiesis. The most appropriate methods for assessing ACD in T cells are still evolving. Here we describe the methods currently applied to monitor and measure ACD of developing and activated T cells. We provide an overview of approaches for capturing cells in the process of cytokinesis in vivo, ex vivo, or during in vitro culture. We provide methods for in vitro fixed immunofluorescent staining and for time-lapse analysis. We provide an overview of the different approaches for quantification of ACD of lymphocytes, discuss the pitfalls and concerns in interpretation of these analyses, and provide detailed methods for the quantification of ACD in our group.
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Affiliation(s)
- Mirren Charnley
- Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, Swinburne University of Technology, Mail No H74, PO Box 218, Hawthorn, VIC, 3122, Australia
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia
- Faculty of Science, Engineering and Technology, Biointerface Engineering, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Sarah M Russell
- Faculty of Science, Engineering and Technology, Centre for Micro-Photonics, Swinburne University of Technology, Mail No H74, PO Box 218, Hawthorn, VIC, 3122, Australia.
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
- Department of Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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91
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Richard A, Boullu L, Herbach U, Bonnafoux A, Morin V, Vallin E, Guillemin A, Papili Gao N, Gunawan R, Cosette J, Arnaud O, Kupiec JJ, Espinasse T, Gonin-Giraud S, Gandrillon O. Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process. PLoS Biol 2016; 14:e1002585. [PMID: 28027290 PMCID: PMC5191835 DOI: 10.1371/journal.pbio.1002585] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/22/2016] [Indexed: 12/31/2022] Open
Abstract
In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a “simple” program that all cells execute identically but results from the dynamical behavior of the underlying molecular network. A single-cell transcriptomics analysis offers a new dynamical view of the differentiation process, involving an increase in between-cell variability prior to commitment. The differentiation process has classically been seen as a stereotyped program leading from one progenitor toward a functional cell. This vision was based upon cell population-based analyses averaged over millions of cells. However, new methods have recently emerged that allow interrogation of the molecular content at the single-cell level, challenging this view with a new model suggesting that cell-to-cell gene expression stochasticity could play a key role in differentiation. We took advantage of a physiologically relevant avian cellular model to analyze the expression level of 92 genes in individual cells collected at several time-points during differentiation. We first observed that the process analyzed at the single-cell level is very different and much less well ordered than the population-based average view. Furthermore, we showed that cell-to-cell variability in gene expression peaks transiently before strongly decreasing. This rise in variability precedes two key events: an irreversible commitment to differentiation, followed by a significant increase in cell size variability. Altogether, our results support the idea that differentiation is not a “simple” series of well-ordered molecular events executed identically by all cells in a population but likely results from dynamical behavior of the underlying molecular network.
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Affiliation(s)
- Angélique Richard
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
| | - Loïs Boullu
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France
- Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France
- Département de Mathématiques et de statistiques de l’Université de Montréal, Pavillon André-Aisenstadt, 2920, chemin de la Tour, Montréal (Québec) H3T 1J4 Canada
| | - Ulysse Herbach
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France
- Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France
| | - Arnaud Bonnafoux
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France
- The CoSMo company. 5 passage du Vercors – 69007 LYON – France
| | - Valérie Morin
- Univ Lyon, Univ Claude Bernard, CNRS UMR 5310 - INSERM U1217, Institut NeuroMyoGène, F-69622 Villeurbanne-Cedex, France
| | - Elodie Vallin
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
| | - Anissa Guillemin
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
| | - Nan Papili Gao
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne Switzerland
| | - Rudiyanto Gunawan
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne Switzerland
| | - Jérémie Cosette
- Genethon – Institut National de la Santé et de la Recherche Médicale – INSERM, Université d’Evry-Val-d’Essone – 1 rue de l’internationale 91000 Evry, France
| | - Ophélie Arnaud
- RIKEN - Center for Life Science Technologies (Division of Genomic Technologies)—CLST (DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Thibault Espinasse
- Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France
| | - Sandrine Gonin-Giraud
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
| | - Olivier Gandrillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007, Lyon, France
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France
- * E-mail:
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92
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Gasteiger G, Ataide M, Kastenmüller W. Lymph node - an organ for T-cell activation and pathogen defense. Immunol Rev 2016; 271:200-20. [PMID: 27088916 DOI: 10.1111/imr.12399] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The immune system is a multicentered organ that is characterized by intimate interactions between its cellular components to efficiently ward off invading pathogens. A key constituent of this organ system is the distinct migratory activity of its cellular elements. The lymph node represents a pivotal meeting point of immune cells where adaptive immunity is induced and regulated. Additionally, besides barrier tissues, the lymph node is a critical organ where invading pathogens need to be eliminated in order to prevent systemic distribution of virulent microbes. Here, we explain how the lymph node is structurally and functionally organized to fulfill these two critical functions - pathogen defense and orchestration of adaptive immunity. We will discuss spatio-temporal aspects of cellular immune responses focusing on CD8 T cells and review how and where these cells are activated in the context of viral infections, as well as how viral antigen expression kinetics and different antigen presentation pathways are involved. Finally, we will describe how such responses are regulated and 'helped', and discuss how this relates to intranodal positioning and cellular migration of the various cellular components that are involved in these processes.
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Affiliation(s)
- Georg Gasteiger
- Institute of Medical Microbiology and Hygiene & FZI Research Center for Immunotherapy, University of Mainz Medical Center, Mainz, Germany
| | - Marco Ataide
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany
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93
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Ahmed R, Roger L, Costa Del Amo P, Miners KL, Jones RE, Boelen L, Fali T, Elemans M, Zhang Y, Appay V, Baird DM, Asquith B, Price DA, Macallan DC, Ladell K. Human Stem Cell-like Memory T Cells Are Maintained in a State of Dynamic Flux. Cell Rep 2016; 17:2811-2818. [PMID: 27974195 PMCID: PMC5186732 DOI: 10.1016/j.celrep.2016.11.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/23/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022] Open
Abstract
Adaptive immunity requires the generation of memory T cells from naive precursors selected in the thymus. The key intermediaries in this process are stem cell-like memory T (TSCM) cells, multipotent progenitors that can both self-renew and replenish more differentiated subsets of memory T cells. In theory, antigen specificity within the TSCM pool may be imprinted statically as a function of largely dormant cells and/or retained dynamically by more transitory subpopulations. To explore the origins of immunological memory, we measured the turnover of TSCM cells in vivo using stable isotope labeling with heavy water. The data indicate that TSCM cells in both young and elderly subjects are maintained by ongoing proliferation. In line with this finding, TSCM cells displayed limited telomere length erosion coupled with high expression levels of active telomerase and Ki67. Collectively, these observations show that TSCM cells exist in a state of perpetual flux throughout the human lifespan.
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Affiliation(s)
- Raya Ahmed
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Laureline Roger
- Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Pedro Costa Del Amo
- Department of Medicine, St. Mary's Hospital, Imperial College London, London W2 1PG, UK
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Rhiannon E Jones
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lies Boelen
- Department of Medicine, St. Mary's Hospital, Imperial College London, London W2 1PG, UK
| | - Tinhinane Fali
- Sorbonne Universités, UPMC Université Paris 06, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France; INSERM U1135, CIMI-Paris, 75013 Paris, France
| | - Marjet Elemans
- Department of Medicine, St. Mary's Hospital, Imperial College London, London W2 1PG, UK
| | - Yan Zhang
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Victor Appay
- Sorbonne Universités, UPMC Université Paris 06, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France; INSERM U1135, CIMI-Paris, 75013 Paris, France
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Becca Asquith
- Department of Medicine, St. Mary's Hospital, Imperial College London, London W2 1PG, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Derek C Macallan
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, UK; St. George's University Hospitals National Health Service Foundation Trust, Blackshaw Road, London SW17 0QT, UK.
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
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94
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Tyrakis PA, Palazon A, Macias D, Lee KL, Phan AT, Veliça P, You J, Chia GS, Sim J, Doedens A, Abelanet A, Evans CE, Griffiths JR, Poellinger L, Goldrath AW, Johnson RS. S-2-hydroxyglutarate regulates CD8 + T-lymphocyte fate. Nature 2016; 540:236-241. [PMID: 27798602 PMCID: PMC5149074 DOI: 10.1038/nature20165] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/18/2016] [Indexed: 12/28/2022]
Abstract
R-2-hydroxyglutarate accumulates to millimolar levels in cancer cells with gain-of-function isocitrate dehydrogenase 1/2 mutations. These levels of R-2-hydroxyglutarate affect 2-oxoglutarate-dependent dioxygenases. Both metabolite enantiomers, R- and S-2-hydroxyglutarate, are detectible in healthy individuals, yet their physiological function remains elusive. Here we show that 2-hydroxyglutarate accumulates in mouse CD8+ T cells in response to T-cell receptor triggering, and accumulates to millimolar levels in physiological oxygen conditions through a hypoxia-inducible factor 1-alpha (HIF-1α)-dependent mechanism. S-2-hydroxyglutarate predominates over R-2-hydroxyglutarate in activated T cells, and we demonstrate alterations in markers of CD8+ T-cell differentiation in response to this metabolite. Modulation of histone and DNA demethylation, as well as HIF-1α stability, mediate these effects. S-2-hydroxyglutarate treatment greatly enhances the in vivo proliferation, persistence and anti-tumour capacity of adoptively transferred CD8+ T cells. Thus, S-2-hydroxyglutarate acts as an immunometabolite that links environmental context, through a metabolic-epigenetic axis, to immune fate and function.
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Affiliation(s)
- Petros A. Tyrakis
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Asis Palazon
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - David Macias
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Kian. L. Lee
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | | | - Pedro Veliça
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
| | - Jia You
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | - Grace S. Chia
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | - Jingwei Sim
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Andrew Doedens
- Molecular Biology Section, UC San Diego, La Jolla, CA, USA
| | - Alice Abelanet
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Colin E. Evans
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - John R. Griffiths
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
| | | | - Randall S. Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
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95
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Blas-Rus N, Bustos-Morán E, Martín-Cófreces NB, Sánchez-Madrid F. Aurora-A shines on T cell activation through the regulation of Lck. Bioessays 2016; 39. [PMID: 27910998 DOI: 10.1002/bies.201600156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Different protein kinases control signaling emanating from the T cell receptor (TCR) during antigen-specific T cell activation. Mitotic kinases, e.g. Aurora-A, have been widely studied in the context of mitosis due to their role during microtubule (MT) nucleation, becoming critical regulators of cell cycle progression. We have recently described a specific role for Aurora-A kinase in antigenic T cell activation. Blockade of Aurora-A in T cells severely disrupts the dynamics of MTs and CD3ζ-bearing signaling vesicles during T cell activation. Furthermore, Aurora-A deletion impairs the activation of signaling molecules downstream of the TCR. Targeting Aurora-A disturbs the activation of Lck, which is one of the first signals that drive T cell activation in an antigen-dependent manner. This work describes possible models of regulation of Lck by Aurora-A during T cell activation. We also discuss possible roles for Aurora-A in other systems similar to the IS, and its putative functions in cell polarization.
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Affiliation(s)
- Noelia Blas-Rus
- Servicio de Inmunología, Hospital Universitario de la Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Madrid, Spain
| | - Eugenio Bustos-Morán
- Vascular Pathophysiology Area, Centro Nacional Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Noa B Martín-Cófreces
- Vascular Pathophysiology Area, Centro Nacional Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Francisco Sánchez-Madrid
- Servicio de Inmunología, Hospital Universitario de la Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Madrid, Spain.,Vascular Pathophysiology Area, Centro Nacional Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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96
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Ikebuchi R, Teraguchi S, Vandenbon A, Honda T, Shand FHW, Nakanishi Y, Watanabe T, Tomura M. A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response. Sci Rep 2016; 6:35002. [PMID: 27756896 PMCID: PMC5069467 DOI: 10.1038/srep35002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/22/2016] [Indexed: 01/23/2023] Open
Abstract
Foxp3+ regulatory T cells (Tregs) migrating from the skin to the draining lymph node (dLN) have a strong immunosuppressive effect on the cutaneous immune response. However, the subpopulations responsible for their inhibitory function remain unclear. We investigated single-cell gene expression heterogeneity in Tregs from the dLN of inflamed skin in a contact hypersensitivity model. The immunosuppressive genes Ctla4 and Tgfb1 were expressed in the majority of Tregs. Although Il10-expressing Tregs were rare, unexpectedly, the majority of Il10-expressing Tregs co-expressed Gzmb and displayed Th1-skewing. Single-cell profiling revealed that CD43+ CCR5+ Tregs represented the main subset within the Il10/Gzmb-expressing cell population in the dLN. Moreover, CD43+ CCR5+ CXCR3− Tregs expressed skin-tropic chemokine receptors, were preferentially retained in inflamed skin and downregulated the cutaneous immune response. The identification of a rare Treg subset co-expressing multiple immunosuppressive molecules and having tissue-remaining capacity offers a novel strategy for the control of skin inflammatory responses.
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Affiliation(s)
- Ryoyo Ikebuchi
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Laboratory of Immunology, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka, 584-8540, Japan.,Japan Society for the Promotion of Science, Japan
| | - Shunsuke Teraguchi
- Quantitative Immunology Research Unit, IFReC, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Alexis Vandenbon
- Immuno-Genomics Research Unit, IFReC, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuya Honda
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Francis H W Shand
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yasutaka Nakanishi
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Takeshi Watanabe
- The Tazuke-Kofukai Medical Research Institute, Kitano Hospital, Kita-ku, Osaka, 530-8480, Japan
| | - Michio Tomura
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Laboratory of Immunology, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka, 584-8540, Japan
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Cannoodt R, Saelens W, Saeys Y. Computational methods for trajectory inference from single-cell transcriptomics. Eur J Immunol 2016; 46:2496-2506. [DOI: 10.1002/eji.201646347] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Robrecht Cannoodt
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
- Center for Medical Genetics; Ghent University; Ghent Belgium
- Cancer Research Institute Ghent (CRIG); Ghent Belgium
| | - Wouter Saelens
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
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Gonzales C, Yoshihara HAI, Dilek N, Leignadier J, Irving M, Mieville P, Helm L, Michielin O, Schwitter J. In-Vivo Detection and Tracking of T Cells in Various Organs in a Melanoma Tumor Model by 19F-Fluorine MRS/MRI. PLoS One 2016; 11:e0164557. [PMID: 27736925 PMCID: PMC5063406 DOI: 10.1371/journal.pone.0164557] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/18/2022] Open
Abstract
Background 19F-MRI and 19F-MRS can identify specific cell types after in-vitro or in-vivo 19F-labeling. Knowledge on the potential to track in-vitro 19F-labeled immune cells in tumor models by 19F-MRI/MRS is scarce. Aim To study 19F-based MR techniques for in-vivo tracking of adoptively transferred immune cells after in-vitro 19F-labeling, i.e. to detect and monitor their migration non-invasively in melanoma-bearing mice. Methods Splenocytes (SP) were labeled in-vitro with a perfluorocarbon (PFC) and IV-injected into non-tumor bearing mice. In-vitro PFC-labeled ovalbumin (OVA)-specific T cells from the T cell receptor-transgenic line OT-1, activated with anti-CD3 and anti-CD28 antibodies (Tact) or OVA-peptide pulsed antigen presenting cells (TOVA-act), were injected into B16 OVA melanoma-bearing mice. The distribution of the 19F-labelled donor cells was determined in-vivo by 19F-MRI/MRS. In-vivo 19F-MRI/MRS results were confirmed by ex-vivo 19F-NMR and flow cytometry. Results SP, Tact, and TOVA-act were successfully PFC-labeled in-vitro yielding 3x1011-1.4x1012 19F-atoms/cell in the 3 groups. Adoptively transferred 19F-labeled SP, TOVA-act, and Tact were detected by coil-localized 19F-MRS in the chest, abdomen, and left flank in most animals (corresponding to lungs, livers, and spleens, respectively, with highest signal-to-noise for SP vs TOVA-act and Tact, p<0.009 for both). SP and Tact were successfully imaged by 19F-MRI (n = 3; liver). These in-vivo data were confirmed by ex-vivo high-resolution 19F-NMR-spectroscopy. By flow cytometric analysis, however, TOVA-act tended to be more abundant versus SP and Tact (liver: p = 0.1313; lungs: p = 0.1073; spleen: p = 0.109). Unlike 19F-MRI/MRS, flow cytometry also identified transferred immune cells (SP, Tact, and TOVA-act) in the tumors. Conclusion SP, Tact, and TOVA-act were successfully PFC-labeled in-vitro and detected in-vivo by non-invasive 19F-MRS/MRI in liver, lung, and spleen. The portion of 19F-labeled T cells in the adoptively transferred cell populations was insufficient for 19F-MRS/MRI detection in the tumor. While OVA-peptide-activated T cells (TOVA-act) showed highest infiltration into all organs, SP were detected more reliably by 19F-MRS/MRI, most likely explained by cell division of TOVA-act after injection, which dilutes the 19F content in the T cell-infiltrated organs. Non-dividing 19F-labeled cell species appear most promising to be tracked by 19F-MRS/MRI.
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Affiliation(s)
- Christine Gonzales
- Division of Cardiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Hikari A. I. Yoshihara
- Division of Cardiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nahzli Dilek
- Molecular Modeling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Ludwig Branch for Cancer Research of the University of Lausanne, Epalinges, Switzerland
| | - Julie Leignadier
- Ludwig Branch for Cancer Research of the University of Lausanne, Epalinges, Switzerland
| | - Melita Irving
- Ludwig Branch for Cancer Research of the University of Lausanne, Epalinges, Switzerland
| | - Pascal Mieville
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochime, Lausanne, Switzerland
| | - Lothar Helm
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochime, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Ludwig Branch for Cancer Research of the University of Lausanne, Epalinges, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Juerg Schwitter
- Division of Cardiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Cardiac Magnetic Resonance Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- * E-mail:
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Kamiński MM, Liedmann S, Milasta S, Green DR. Polarization and asymmetry in T cell metabolism. Semin Immunol 2016; 28:525-534. [DOI: 10.1016/j.smim.2016.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 12/31/2022]
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100
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Shao C, Höfer T. Robust classification of single-cell transcriptome data by nonnegative matrix factorization. Bioinformatics 2016; 33:235-242. [DOI: 10.1093/bioinformatics/btw607] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/14/2022] Open
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