151
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Martini E, Kunderfranco P, Peano C, Carullo P, Cremonesi M, Schorn T, Carriero R, Termanini A, Colombo FS, Jachetti E, Panico C, Faggian G, Fumero A, Torracca L, Molgora M, Cibella J, Pagiatakis C, Brummelman J, Alvisi G, Mazza EMC, Colombo MP, Lugli E, Condorelli G, Kallikourdis M. Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload-Driven Heart Failure Reveals Extent of Immune Activation. Circulation 2019; 140:2089-2107. [PMID: 31661975 DOI: 10.1161/circulationaha.119.041694] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Inflammation is a key component of cardiac disease, with macrophages and T lymphocytes mediating essential roles in the progression to heart failure. Nonetheless, little insight exists on other immune subsets involved in the cardiotoxic response. METHODS Here, we used single-cell RNA sequencing to map the cardiac immune composition in the standard murine nonischemic, pressure-overload heart failure model. By focusing our analysis on CD45+ cells, we obtained a higher resolution identification of the immune cell subsets in the heart, at early and late stages of disease and in controls. We then integrated our findings using multiparameter flow cytometry, immunohistochemistry, and tissue clarification immunofluorescence in mouse and human. RESULTS We found that most major immune cell subpopulations, including macrophages, B cells, T cells and regulatory T cells, dendritic cells, Natural Killer cells, neutrophils, and mast cells are present in both healthy and diseased hearts. Most cell subsets are found within the myocardium, whereas mast cells are found also in the epicardium. Upon induction of pressure overload, immune activation occurs across the entire range of immune cell types. Activation led to upregulation of key subset-specific molecules, such as oncostatin M in proinflammatory macrophages and PD-1 in regulatory T cells, that may help explain clinical findings such as the refractivity of patients with heart failure to anti-tumor necrosis factor therapy and cardiac toxicity during anti-PD-1 cancer immunotherapy, respectively. CONCLUSIONS Despite the absence of infectious agents or an autoimmune trigger, induction of disease leads to immune activation that involves far more cell types than previously thought, including neutrophils, B cells, Natural Killer cells, and mast cells. This opens up the field of cardioimmunology to further investigation by using toolkits that have already been developed to study the aforementioned immune subsets. The subset-specific molecules that mediate their activation may thus become useful targets for the diagnostics or therapy of heart failure.
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Affiliation(s)
- Elisa Martini
- Adaptive Immunity Laboratory (E.M., M.C., M.K.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Paolo Kunderfranco
- Bioinformatics Unit (P.K., R.C., A.T.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Clelia Peano
- Genomic Unit (C. Peano, J.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Italy (C. Peano, P.C., G.C.)
| | - Pierluigi Carullo
- Department of Cardiovascular Medicine (P.C., C. Panico, C. Pagiatakis, G.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Italy (C. Peano, P.C., G.C.)
| | - Marco Cremonesi
- Adaptive Immunity Laboratory (E.M., M.C., M.K.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Tilo Schorn
- Advanced Imaging Unit (T.S.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Roberta Carriero
- Bioinformatics Unit (P.K., R.C., A.T.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Alberto Termanini
- Bioinformatics Unit (P.K., R.C., A.T.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Federico Simone Colombo
- Flow Cytometry Core (F.S.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Elena Jachetti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy (E.J., M.P.C.)
| | - Cristina Panico
- Department of Cardiovascular Medicine (P.C., C. Panico, C. Pagiatakis, G.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Giuseppe Faggian
- Department of Cardiac Surgery, University of Verona, Italy (G.F.)
| | - Andrea Fumero
- Cardiac Surgery Division, Department of Cardiovascular Medicine (A.F., L.T.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Lucia Torracca
- Cardiac Surgery Division, Department of Cardiovascular Medicine (A.F., L.T.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Martina Molgora
- Laboratory of Experimental Immunopathology (M.M.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Javier Cibella
- Genomic Unit (C. Peano, J.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Christina Pagiatakis
- Department of Cardiovascular Medicine (P.C., C. Panico, C. Pagiatakis, G.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Jolanda Brummelman
- Laboratory of Translational Immunology (J.B., G.A., E.M.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Giorgia Alvisi
- Laboratory of Translational Immunology (J.B., G.A., E.M.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Emilia Maria Cristina Mazza
- Laboratory of Translational Immunology (J.B., G.A., E.M.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Mario Paolo Colombo
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy (E.J., M.P.C.)
| | - Enrico Lugli
- Flow Cytometry Core (F.S.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Laboratory of Translational Immunology (J.B., G.A., E.M.C., E.L.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Gianluigi Condorelli
- Department of Cardiovascular Medicine (P.C., C. Panico, C. Pagiatakis, G.C.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Italy (C. Peano, P.C., G.C.).,Humanitas University, Pieve Emanuele, Italy (G.C., M.K.)
| | - Marinos Kallikourdis
- Adaptive Immunity Laboratory (E.M., M.C., M.K.), Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Humanitas University, Pieve Emanuele, Italy (G.C., M.K.)
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152
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Morel D, Jeffery D, Aspeslagh S, Almouzni G, Postel-Vinay S. Combining epigenetic drugs with other therapies for solid tumours - past lessons and future promise. Nat Rev Clin Oncol 2019; 17:91-107. [PMID: 31570827 DOI: 10.1038/s41571-019-0267-4] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic dysregulation has long been recognized as a key factor contributing to tumorigenesis and tumour maintenance that can influence all of the recognized hallmarks of cancer. Despite regulatory approvals for the treatment of certain haematological malignancies, the efficacy of the first generation of epigenetic drugs (epi-drugs) in patients with solid tumours has been disappointing; however, successes have now been achieved in selected solid tumour subtypes, thanks to the development of novel compounds and a better understanding of cancer biology that have enabled precision medicine approaches. Several lines of evidence support that, beyond their potential as monotherapies, epigenetic drugs could have important roles in synergy with other anticancer therapies or in reversing acquired therapy resistance. Herein, we review the mechanisms by which epi-drugs can modulate the sensitivity of cancer cells to other forms of anticancer therapy, including chemotherapy, radiation therapy, hormone therapy, molecularly targeted therapy and immunotherapy. We provide a critical appraisal of the preclinical rationale, completed clinical studies and ongoing clinical trials relating to combination therapies incorporating epi-drugs. Finally, we propose and discuss rational clinical trial designs and drug development strategies, considering key factors including patient selection, tumour biomarker evaluation, drug scheduling and response assessment and study end points, with the aim of optimizing the development of such combinations.
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Affiliation(s)
- Daphné Morel
- ATIP-Avenir Group, UMR981, INSERM (French National Institute of Health and Medical Research), Gustave Roussy Cancer Campus, Villejuif, France
| | - Daniel Jeffery
- Nuclear Dynamics Unit - UMR3664, National Centre for Scientific Research, Institut Curie, Paris, France
| | | | - Geneviève Almouzni
- Nuclear Dynamics Unit - UMR3664, National Centre for Scientific Research, Institut Curie, Paris, France.
| | - Sophie Postel-Vinay
- ATIP-Avenir Group, UMR981, INSERM (French National Institute of Health and Medical Research), Gustave Roussy Cancer Campus, Villejuif, France. .,Drug Development Department (DITEP), Gustave Roussy Cancer Campus, Paris-Saclay University, Villejuif, France.
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153
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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154
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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: 2.0] [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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155
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Peng J, Sun BF, Chen CY, Zhou JY, Chen YS, Chen H, Liu L, Huang D, Jiang J, Cui GS, Yang Y, Wang W, Guo D, Dai M, Guo J, Zhang T, Liao Q, Liu Y, Zhao YL, Han DL, Zhao Y, Yang YG, Wu W. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res 2019; 29:725-738. [PMID: 31273297 DOI: 10.1038/s41422-019-0195-y] [Citation(s) in RCA: 758] [Impact Index Per Article: 126.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively delineate the PDAC intra-tumoral heterogeneity and the underlying mechanism for PDAC progression, we employed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomic atlas of 57,530 individual pancreatic cells from primary PDAC tumors and control pancreases, and identified diverse malignant and stromal cell types, including two ductal subtypes with abnormal and malignant gene expression profiles respectively, in PDAC. We found that the heterogenous malignant subtype was composed of several subpopulations with differential proliferative and migratory potentials. Cell trajectory analysis revealed that components of multiple tumor-related pathways and transcription factors (TFs) were differentially expressed along PDAC progression. Furthermore, we found a subset of ductal cells with unique proliferative features were associated with an inactivation state in tumor-infiltrating T cells, providing novel markers for the prediction of antitumor immune response. Together, our findings provide a valuable resource for deciphering the intra-tumoral heterogeneity in PDAC and uncover a connection between tumor intrinsic transcriptional state and T cell activation, suggesting potential biomarkers for anticancer treatment such as targeted therapy and immunotherapy.
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Affiliation(s)
- Junya Peng
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Chuan-Yuan Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jia-Yi Zhou
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu-Sheng Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hao Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Lulu Liu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Dan Huang
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Jialin Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Guan-Shen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Dan Guo
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China.,Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Menghua Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Junchao Guo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Quan Liao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Yi Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Da-Li Han
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China. .,Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China.
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156
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Nicetto D, Zaret KS. Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 2019; 55:1-10. [PMID: 31103921 DOI: 10.1016/j.gde.2019.04.013] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
Compacted, transcriptionally repressed chromatin, referred to as heterochromatin, represents a major fraction of the higher eukaryotic genome and exerts pivotal functions of silencing repetitive elements, maintenance of genome stability, and control of gene expression. Among the different histone post-translational modifications (PTMs) associated with heterochromatin, tri-methylation of lysine 9 on histone H3 (H3K9me3) is gaining increased attention. Besides its known role in repressing repetitive elements and non-coding portions of the genome, recent observations indicate H3K9me3 as an important player in silencing lineage-inappropriate genes. The ability of H3K9me3 to influence cell identity challenges the original concept of H3K9me3-marked heterochromatin as mainly a constitutive type of chromatin and provides a further level of understanding of how to modulate cell fate control. Here, we summarize the role of H3K9me3 marked heterochromatin and its dynamics in establishing and maintaining cellular identity.
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Affiliation(s)
- Dario Nicetto
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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157
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Regulation of T cell differentiation and function by epigenetic modification enzymes. Semin Immunopathol 2019; 41:315-326. [PMID: 30963214 DOI: 10.1007/s00281-019-00731-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Peripheral naive CD4+ and CD8+ cells are developed in the thymus and proliferate and differentiate into various specialized T cell subsets upon activation by peptide-major histocompatibility complexes in periphery to execute different functions during immune responses. Cytokines, transcription factors, and a large number of intracellular molecules have been shown to affect T cell development, activation, and function. In addition, epigenetic modifications, such as histone modification and DNA methylation, regulate T cell biology. The epigenetic modifications are regulated by a range of DNA methyltransferases, DNA demethylation enzymes, and histone modification enzymes. Dysregulations of epigenetic modifications are closely associated with autoimmune diseases and tumorigenesis. Here, we review the current literature about the functions of DNA and histone modification enzymes in T cell development, activation, differentiation, and function.
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158
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Affiliation(s)
- Francesc Baixauli
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Matteo Villa
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L. Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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159
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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: 1.8] [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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160
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Rodrigues C, Pattabiraman C, Vijaykumar A, Arora R, Narayana SM, Kumar RV, Notani D, Varga-Weisz P, Krishna S. A SUV39H1-low chromatin state characterises and promotes migratory properties of cervical cancer cells. Exp Cell Res 2019; 378:206-216. [PMID: 30772380 DOI: 10.1016/j.yexcr.2019.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
Metastatic progression is a major cause of mortality in cervical cancers, but factors regulating migratory and pre-metastatic cell populations remain poorly understood. Here, we sought to assess whether a SUV39H1-low chromatin state promotes migratory cell populations in cervical cancers, using meta-analysis of data from The Cancer Genome Atlas (TCGA), immunohistochemistry, genomics and functional assays. Cervical cancer cells sorted based on migratory ability in vitro have low levels of SUV39H1 protein, and SUV39H1 knockdown in vitro enhanced cervical cancer cell migration. Further, TCGA SUV39H1-low tumours correlated with poor clinical outcomes and showed gene expression signatures of cell migration. SUV39H1 expression was examined within biopsies, and SUV39H1low cells within tumours also demonstrated migratory features. Next, to understand genome scale transcriptional and chromatin changes in migratory populations, cell populations sorted based on migration in vitro were examined using RNA-Seq, along with ChIP-Seq for H3K9me3, the histone mark associated with SUV39H1. Migrated populations showed SUV39H1-linked migratory gene expression signatures, along with broad depletion of H3K9me3 across gene promoters. We show for the first time that a SUV39H1-low chromatin state associates with, and promotes, migratory populations in cervical cancers. Our results posit SUV39H1-low cells as key populations for prognosis estimation and as targets for novel therapies.
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Affiliation(s)
- Calvin Rodrigues
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India
| | - Chitra Pattabiraman
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India
| | - Anjali Vijaykumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India
| | - Reety Arora
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India
| | | | - Rekha V Kumar
- Department of Pathology, Kidwai Cancer Institute, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India
| | - Patrick Varga-Weisz
- The Babraham Institute, Cambridge, UK; School of Biological Sciences, University of Essex, Colchester, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bangalore 560065, Karnataka, India.
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161
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- 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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162
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Lu C, Yang D, Klement JD, Oh IK, Savage NM, Waller JL, Colby AH, Grinstaff MW, Oberlies NH, Pearce CJ, Xie Z, Kulp SK, Coss CC, Phelps MA, Albers T, Lebedyeva IO, Liu K. SUV39H1 Represses the Expression of Cytotoxic T-Lymphocyte Effector Genes to Promote Colon Tumor Immune Evasion. Cancer Immunol Res 2019; 7:414-427. [PMID: 30610059 DOI: 10.1158/2326-6066.cir-18-0126] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/07/2018] [Accepted: 12/18/2018] [Indexed: 01/23/2023]
Abstract
Despite the presence of CTLs in the tumor microenvironment, the majority of immunogenic human colon cancer does not respond to immune checkpoint inhibitor immunotherapy, and microsatellite instable (MSI) tumors are not naturally eliminated. The molecular mechanism underlying the inactivity of tumor-infiltrating CTLs is unknown. We report here that CTLs were present in both MSI and microsatellite stable colon tumors. The expression of the H3K9me3-specific histone methyltransferase SUV39H1 was significantly elevated in human colon carcinoma compared with normal colon tissues. Using a mouse colon carcinoma model, we further determined that tumor-infiltrating CTLs in the colon tumor microenvironment have high expression of SUV39H1. To target SUV39H1 in the tumor microenvironment, a virtual chemical library was screened on the basis of the SET (suppressor of variegation 3-9, enhancer of zeste and trithorax) domain structure of the human SUV39H1 protein. Functional enzymatic activity assays identified a small molecule that inhibits SUV39H1 enzymatic activity. On the basis of the structure of this small molecule, we modified it and chemically synthesized a small molecule, termed F5446, which has an EC50 of 0.496 μmol/L for SUV39H1 enzymatic activity. H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells. F5446 inhibited H3K9me3, thereby upregulating expression of these effectors in tumor-infiltrating CTLs and suppressing colon carcinoma growth in a CD8+ CTL-dependent manner in vivo Our data indicate that SUV39H1 represses CTL effector gene expression and, in doing so, confers colon cancer immune escape.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Cell Line, Tumor
- Colonic Neoplasms/drug therapy
- Colonic Neoplasms/immunology
- Colonic Neoplasms/metabolism
- Disease Models, Animal
- Enzyme Inhibitors/pharmacology
- Enzyme Inhibitors/therapeutic use
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/immunology
- Histones/metabolism
- Humans
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/immunology
- Methyltransferases/metabolism
- Mice
- Repressor Proteins/antagonists & inhibitors
- Repressor Proteins/immunology
- Repressor Proteins/metabolism
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Tumor Escape
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/immunology
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Affiliation(s)
- Chunwan Lu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia.
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Dafeng Yang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Il Kyu Oh
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
| | - Natasha M Savage
- Department of Pathology, Medical College of Georgia, Augusta, Georgia
| | - Jennifer L Waller
- Department of Population Health Sciences, Medical College of Georgia, Augusta, Georgia
| | - Aaron H Colby
- Ionic Pharmaceuticals, Brookline, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Mark W Grinstaff
- Ionic Pharmaceuticals, Brookline, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina
| | | | - Zhiliang Xie
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Samuel K Kulp
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Christopher C Coss
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Mitch A Phelps
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Thomas Albers
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia
| | - Iryna O Lebedyeva
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia.
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
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163
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A chemical biology toolbox to study protein methyltransferases and epigenetic signaling. Nat Commun 2019; 10:19. [PMID: 30604761 PMCID: PMC6318333 DOI: 10.1038/s41467-018-07905-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 12/04/2018] [Indexed: 12/11/2022] Open
Abstract
Protein methyltransferases (PMTs) comprise a major class of epigenetic regulatory enzymes with therapeutic relevance. Here we present a collection of chemical probes and associated reagents and data to elucidate the function of human and murine PMTs in cellular studies. Our collection provides inhibitors and antagonists that together modulate most of the key regulatory methylation marks on histones H3 and H4, providing an important resource for modulating cellular epigenomes. We describe a comprehensive and comparative characterization of the probe collection with respect to their potency, selectivity, and mode of inhibition. We demonstrate the utility of this collection in CD4+ T cell differentiation assays revealing the potential of individual probes to alter multiple T cell subpopulations which may have implications for T cell-mediated processes such as inflammation and immuno-oncology. In particular, we demonstrate a role for DOT1L in limiting Th1 cell differentiation and maintaining lineage integrity. This chemical probe collection and associated data form a resource for the study of methylation-mediated signaling in epigenetics, inflammation and beyond. Protein methyltransferases (PMTs) are epigenetic regulatory enzymes with significant therapeutic relevance. Here the authors describe a collection of chemical inhibitors and antagonists to modulate most of the key methylation marks on histones H3 and H4, and use the collection to study of the role of PMTs in mouse and human T cell differentiation.
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164
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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: 106] [Impact Index Per Article: 15.1] [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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165
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Long KB, Young RM, Boesteanu AC, Davis MM, Melenhorst JJ, Lacey SF, DeGaramo DA, Levine BL, Fraietta JA. CAR T Cell Therapy of Non-hematopoietic Malignancies: Detours on the Road to Clinical Success. Front Immunol 2018; 9:2740. [PMID: 30559740 PMCID: PMC6287001 DOI: 10.3389/fimmu.2018.02740] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Chimeric antigen receptor (CAR)-engineered T cells represent a breakthrough in personalized medicine. In this strategy, a patient's own T lymphocytes are genetically reprogrammed to encode a synthetic receptor that binds a tumor antigen, allowing T cells to recognize and kill antigen-expressing cancer cells. As a result of complete and durable responses in individuals who are refractory to standard of care therapy, CAR T cells directed against the CD19 protein have been granted United States Food and Drug Administration (FDA) approval as a therapy for treatment of pediatric and young adult acute lymphoblastic leukemia and diffuse large B cell lymphoma. Human trials of CAR T cells targeting CD19 or B cell maturation antigen in multiple myeloma have also reported early successes. However, a clear and consistently reproducible demonstration of the clinical efficacy of CAR T cells in the setting of solid tumors has not been reported to date. Here, we review the history and status of CAR T cell therapy for solid tumors, potential T cell-intrinsic determinants of response and resistance as well as extrinsic obstacles to the success of this approach for much more prevalent non-hematopoietic malignancies. In addition, we summarize recent strategies and innovations that aim to augment the potency of CAR T cells in the face of multiple immunosuppressive barriers operative within the solid tumor microenvironment. Advances in the field of CAR T cell biology over the coming years in the areas of safety, reliability and efficacy against non-hematopoietic cancers will ultimately determine how transformative adoptive T cell therapy will be in the broader battle against cancer.
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Affiliation(s)
- Kristen B Long
- Department of Biology, Mansfield University, Mansfield, PA, United States
| | - Regina M Young
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, United States
| | - Alina C Boesteanu
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Megan M Davis
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - J Joseph Melenhorst
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Simon F Lacey
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - David A DeGaramo
- Department of Biology, Mansfield University, Mansfield, PA, United States
| | - Bruce L Levine
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Joseph A Fraietta
- Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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166
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Yadav T, Quivy JP, Almouzni G. Chromatin plasticity: A versatile landscape that underlies cell fate and identity. Science 2018; 361:1332-1336. [PMID: 30262494 DOI: 10.1126/science.aat8950] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During development and throughout life, a variety of specialized cells must be generated to ensure the proper function of each tissue and organ. Chromatin plays a key role in determining cellular state, whether totipotent, pluripotent, multipotent, or differentiated. We highlight chromatin dynamics involved in the generation of pluripotent stem cells as well as their influence on cell fate decision and reprogramming. We focus on the capacity of histone variants, chaperones, modifications, and heterochromatin factors to influence cell identity and its plasticity. Recent technological advances have provided tools to elucidate the underlying chromatin dynamics for a better understanding of normal development and pathological conditions, with avenues for potential therapeutic application.
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Affiliation(s)
- Tejas Yadav
- Institut Curie, 75248 Paris Cedex 05, France
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167
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Shen J, Luo X, Wu Q, Huang J, Xiao G, Wang L, Yang B, Li H, Wu C. A Subset of CXCR5 +CD8 + T Cells in the Germinal Centers From Human Tonsils and Lymph Nodes Help B Cells Produce Immunoglobulins. Front Immunol 2018; 9:2287. [PMID: 30344522 PMCID: PMC6183281 DOI: 10.3389/fimmu.2018.02287] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/14/2018] [Indexed: 01/14/2023] Open
Abstract
Recent studies indicated that CXCR5+CD8+ T cells in lymph nodes could eradicate virus-infected target cells. However, in the current study we found that a subset of CXCR5+CD8+ T cells in the germinal centers from human tonsils or lymph nodes are predominately memory cells that express CD45RO and CD27. The involvement of CXCR5+CD8+ T cells in humoral immune responses is suggested by their localization in B cell follicles and by the concomitant expression of costimulatory molecules, including CD40L and ICOS after activation. In addition, CXCR5+CD8+ memory T cells produced significantly higher levels of IL-21, IFN-γ, and IL-4 at mRNA and protein levels compared to CXCR5−CD8+ memory T cells, but IL-21-expressing CXCR5+CD8+ T cells did not express Granzyme B and perforin. When cocultured with sorted B cells, sorted CXCR5+CD8+ T cells promoted the production of antibodies compared to sorted CXCR5−CD8+ T cells. However, fixed CD8+ T cells failed to help B cells and the neutralyzing antibodies against IL-21 or CD40L inhibited the promoting effects of sorted CXCR5+CD8+ T cells on B cells for the production of antibodies. Finally, we found that in the germinal centers of lymph nodes from HIV-infected patients contained more CXCR5+CD8+ T cells compared to normal lymph nodes. Due to their versatile functional capacities, CXCR5+CD8+ T cells are promising candidate cells for immune therapies, particularly when CD4+ T cell help are limited.
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Affiliation(s)
- Juan Shen
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Zhongshan School of Medicine, Institute of Immunology, Sun Yat-sen University, Guangzhou, China
| | - Xi Luo
- Affiliated Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiongli Wu
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Zhongshan School of Medicine, Institute of Immunology, Sun Yat-sen University, Guangzhou, China
| | - Jun Huang
- Department of Pathogenic Biology and Immunology, Institute of Immunology, Guangzhou Medical University, Guangzhou, China
| | - Guanying Xiao
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Liantang Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Binyan Yang
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Zhongshan School of Medicine, Institute of Immunology, Sun Yat-sen University, Guangzhou, China
| | - Huabin Li
- Eye and Ent Hospital of Fudan Hospital, Shanghai, China
| | - Changyou Wu
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Zhongshan School of Medicine, Institute of Immunology, Sun Yat-sen University, Guangzhou, China
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168
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Goronzy JJ, Hu B, Kim C, Jadhav RR, Weyand CM. Epigenetics of T cell aging. J Leukoc Biol 2018; 104:691-699. [PMID: 29947427 PMCID: PMC6162101 DOI: 10.1002/jlb.1ri0418-160r] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 02/06/2023] Open
Abstract
T cells are a heterogeneous population of cells that differ in their differentiation stages. Functional states are reflected in the epigenome that confers stability in cellular identity and is therefore important for naïve as well as memory T cell function. In many cellular systems, changes in chromatin structure due to alterations in histone expression, histone modifications and DNA methylation are characteristic of the aging process and cause or at least contribute to cellular dysfunction in senescence. Here, we review the epigenetic changes in T cells that occur with age and discuss them in the context of canonical epigenetic marks in aging model systems as well as recent findings of chromatin accessibility changes in T cell differentiation. Remarkably, transcription factor networks driving T cell differentiation account for many of the age-associated modifications in chromatin structures suggesting that loss of quiescence and activation of differentiation pathways are major components of T cell aging.
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Affiliation(s)
- Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Bin Hu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Chulwoo Kim
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Rohit R. Jadhav
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
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169
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Knochelmann HM, Smith AS, Dwyer CJ, Wyatt MM, Mehrotra S, Paulos CM. CAR T Cells in Solid Tumors: Blueprints for Building Effective Therapies. Front Immunol 2018; 9:1740. [PMID: 30140266 PMCID: PMC6094980 DOI: 10.3389/fimmu.2018.01740] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023] Open
Abstract
Genetic redirection of T lymphocytes with chimeric antigen receptors (CARs) has soared from treating cancers preclinically to FDA approval for hematologic malignancies and commercial-grade production scale in under 30 years. To date, solid tumors are less susceptible to CAR therapies and instead have been treated more successfully with immune checkpoint blockade or tumor-infiltrating lymphocyte therapy. Here, we discuss the current challenges in treating solid tumors with CAR T cells, and the obstacles within the host and tumor microenvironment hindering their efficacy. We present a novel three-pronged approach for enhancing the efficacy of CAR T cells whereby a single infusion product can synergize the power of an optimal CAR construct, a highly potent T cell subset, and rejuvenate the endogenous immune response to conquer therapeutically-resistant solid tumors.
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Affiliation(s)
- Hannah M Knochelmann
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, SC, United States
| | - Aubrey S Smith
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, SC, United States
| | - Connor J Dwyer
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, SC, United States
| | - Megan M Wyatt
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, SC, United States
| | - Shikhar Mehrotra
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Surgery, Medical University of South Carolina, Charleston, SC, United States
| | - Chrystal M Paulos
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States.,Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, SC, United States
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170
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Redd PS, Lu C, Klement JD, Ibrahim ML, Zhou G, Kumai T, Celis E, Liu K. H3K4me3 mediates the NF-κB p50 homodimer binding to the pdcd1 promoter to activate PD-1 transcription in T cells. Oncoimmunology 2018; 7:e1483302. [PMID: 30228953 DOI: 10.1080/2162402x.2018.1483302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/12/2018] [Accepted: 05/25/2018] [Indexed: 12/27/2022] Open
Abstract
PD-1 is a co-repressive receptor that curbs T cell activation and thereby serves as a protection mechanism against autoimmunity under physiological conditions. Under pathological conditions, tumor cells express PD-L1 as an adaptive resistant mechanism to suppress PD-1+ T cells to evade host immunosurveillance. PD-1 therefore is a key target in cancer immunotherapy. Despite the extensive studies of PD-1 expression regulation, the pdcd1 transcription machinery and regulatory mechanisms are still not fully understood. We report here that the NF-κB p50 homodimer is a transcription regulator of PD-1 in activated T cells. A putative κB sequence exists at the pdcd1 promoter. All five NF-κB Rel subunits are activated in activated T cells. However, only the p50 homodimer directly binds to the κB sequence at the pccd1 promoter in CD4+ and CD8+ T cells. Deficiency in p50 results in reduced PD-1 expression in both CD4+ and CD8+ T cells in vitro. Using an in vivo mixed bone marrow chimera mouse model, we show that p50 regulates PD-1 expression in a cell-intrinsic way and p50 deficiency leads to decreased PD-1 expression in both antigen-specific CD4+ and CD8+ T cells in vivo. The expression levels of H3K4me3-specific histone methyltransferase increased significantly, resulting in a significant increase in H3K4me3 deposition at the pdcd1 promoter in activated CD4+ and CD8+ T cells. Inhibition of H3K4me3 significantly decreased p50 binding to the pdcd1 promoter and PD-1 expression in a T cell line. Our findings determine that the p50-H3K4me3 axis regulates pdcd1 transcription activation in activated T cells.
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Affiliation(s)
- Priscilla S Redd
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Chunwan Lu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Mohammed L Ibrahim
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Gang Zhou
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Takumi Kumai
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Esteban Celis
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
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171
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Yeo L, Woodwyk A, Sood S, Lorenc A, Eichmann M, Pujol-Autonell I, Melchiotti R, Skowera A, Fidanis E, Dolton GM, Tungatt K, Sewell AK, Heck S, Saxena A, Beam CA, Peakman M. Autoreactive T effector memory differentiation mirrors β cell function in type 1 diabetes. J Clin Invest 2018; 128:3460-3474. [PMID: 29851415 DOI: 10.1172/jci120555] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/23/2018] [Indexed: 12/26/2022] Open
Abstract
In type 1 diabetes, cytotoxic CD8+ T cells with specificity for β cell autoantigens are found in the pancreatic islets, where they are implicated in the destruction of insulin-secreting β cells. In contrast, the disease relevance of β cell-reactive CD8+ T cells that are detectable in the circulation, and their relationship to β cell function, are not known. Here, we tracked multiple, circulating β cell-reactive CD8+ T cell subsets and measured β cell function longitudinally for 2 years, starting immediately after diagnosis of type 1 diabetes. We found that change in β cell-specific effector memory CD8+ T cells expressing CD57 was positively correlated with C-peptide change in subjects below 12 years of age. Autoreactive CD57+ effector memory CD8+ T cells bore the signature of enhanced effector function (higher expression of granzyme B, killer-specific protein of 37 kDa, and CD16, and reduced expression of CD28) compared with their CD57- counterparts, and network association modeling indicated that the dynamics of β cell-reactive CD57+ effector memory CD8+ T cell subsets were strongly linked. Thus, coordinated changes in circulating β cell-specific CD8+ T cells within the CD57+ effector memory subset calibrate to functional insulin reserve in type 1 diabetes, providing a tool for immune monitoring and a mechanism-based target for immunotherapy.
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Affiliation(s)
- Lorraine Yeo
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Alyssa Woodwyk
- Division of Epidemiology and Biostatistics, Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Sanjana Sood
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Anna Lorenc
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Martin Eichmann
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Irma Pujol-Autonell
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Rosella Melchiotti
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Ania Skowera
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Efthymios Fidanis
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Garry M Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Katie Tungatt
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Susanne Heck
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Alka Saxena
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Craig A Beam
- Division of Epidemiology and Biostatistics, Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom.,King's Health Partners Institute of Diabetes, Endocrinology and Obesity, London, United Kingdom
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172
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Peripheral Tissue Chemokines: Homeostatic Control of Immune Surveillance T Cells. Trends Immunol 2018; 39:734-747. [PMID: 30001872 DOI: 10.1016/j.it.2018.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/18/2018] [Accepted: 06/12/2018] [Indexed: 12/15/2022]
Abstract
Cellular immunity is governed by a complex network of migratory cues that enable appropriate immune cell responses in a timely and spatially controlled fashion. This review focuses on the chemokines and their receptors regulating the steady-state localisation of immune cells within healthy peripheral tissues. Steady-state immune cell traffic is not well understood but is thought to involve constitutive (homeostatic) chemokines. The recent discovery of tissue-resident memory T cells (TRM cells) illustrates our need for understanding how chemokines control immune cell mobilisation and/or retention. These studies will be critical to unravel novel pathways for preserving tissue function (aging) and preventing tissue disease (vaccination).
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173
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Smith-Raska MR, Arenzana TL, D'Cruz LM, Khodadadi-Jamayran A, Tsirigos A, Goldrath AW, Reizis B. The Transcription Factor Zfx Regulates Peripheral T Cell Self-Renewal and Proliferation. Front Immunol 2018; 9:1482. [PMID: 30022979 PMCID: PMC6039547 DOI: 10.3389/fimmu.2018.01482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/14/2018] [Indexed: 12/02/2022] Open
Abstract
Peripheral T lymphocytes share many functional properties with hematopoietic stem cells (HSCs), including long-term maintenance, quiescence, and latent proliferative potential. In addition, peripheral T cells retain the capacity for further differentiation into a variety of subsets, much like HSCs. While the similarities between T cells and HSC have long been hypothesized, the potential common genetic regulation of HSCs and T cells has not been widely explored. We have studied the T cell-intrinsic role of Zfx, a transcription factor specifically required for HSC maintenance. We report that T cell-specific deletion of Zfx caused age-dependent depletion of naïve peripheral T cells. Zfx-deficient T cells also failed to undergo homeostatic proliferation in a lymphopenic environment, and showed impaired antigen-specific expansion and memory response. In addition, the invariant natural killer T cell compartment was severely reduced. RNA-Seq analysis revealed that the most dysregulated genes in Zfx-deficient T cells were similar to those observed in Zfx-deficient HSC and B cells. These studies identify Zfx as an important regulator of peripheral T cell maintenance and expansion and highlight the common molecular basis of HSC and lymphocyte homeostasis.
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Affiliation(s)
- Matthew R Smith-Raska
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
| | - Teresita L Arenzana
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
| | - Louise M D'Cruz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Boris Reizis
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
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174
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Good-Jacobson KL. Strength in diversity: Phenotypic, functional, and molecular heterogeneity within the memory B cell repertoire. Immunol Rev 2018; 284:67-78. [DOI: 10.1111/imr.12663] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim L. Good-Jacobson
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology; Biomedicine Discovery Institute, Monash University; Clayton Vic. Australia
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175
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Abstract
Upon stimulation, small numbers of naive CD8+ T cells proliferate and differentiate into a variety of memory and effector cell types. CD8+ T cells can persist for years and kill tumour cells and virally infected cells. The functional and phenotypic changes that occur during CD8+ T cell differentiation are well characterized, but the epigenetic states that underlie these changes are incompletely understood. Here, we review the epigenetic processes that direct CD8+ T cell differentiation and function. We focus on epigenetic modification of DNA and associated histones at genes and their regulatory elements. We also describe structural changes in chromatin organization that affect gene expression. Finally, we examine the translational potential of epigenetic interventions to improve CD8+ T cell function in individuals with chronic infections and cancer.
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Affiliation(s)
- Amanda N Henning
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Nicholas P Restifo
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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176
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Abstract
Epigenetic repression is required for the generation of CD8
+
effector T cells
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Affiliation(s)
- Amanda N Henning
- Center for Cell-Based Therapy, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
- Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Christopher A Klebanoff
- Center for Cell Engineering and Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
- Parker Institute for Cancer Immunotherapy, MSKCC, New York, NY 10065, USA
| | - Nicholas P Restifo
- Center for Cell-Based Therapy, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
- Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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