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Hypermethylation at the CXCR5 gene locus limits trafficking potential of CD8+ T cells into B-cell follicles during HIV-1 infection. Blood Adv 2022; 6:1904-1916. [PMID: 34991160 PMCID: PMC8941472 DOI: 10.1182/bloodadvances.2021006001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
CD8+ T-cells play an important role in HIV control. However, in human lymph nodes (LNs), only a small subset of CD8+ T-cells expresses CXCR5, the chemokine receptor required for cell migration into B cell follicles, which are major sanctuaries for HIV persistence in individuals on therapy. Here, we investigate the impact of HIV infection on follicular CD8+ T-cells (fCD8s) frequencies, trafficking pattern and CXCR5 regulation. We show that, although HIV infection results in a marginal increase of fCD8s in LN, the majority of HIV-specific CD8+ T-cells are CXCR5 negative (non-fCD8s) (p<0.003). Mechanistic investigations using ATAC-seq showed that non-fCD8s have closed chromatin at the CXCR5 transcriptional start site (TSS). DNA bisulfite sequencing identified DNA hypermethylation at the CXCR5 TSS as the most probable cause of closed chromatin. Transcriptional factor footprints analysis revealed enrichment of transforming growth factors (TGFs) at the TSS of fCD8s. In-vitro stimulation of non-fCD8s with recombinant TGF-β resulted in significant increase in CXCR5 expression (fCD8s). Thus, this study identifies TGF-β signaling as a viable strategy for increasing fCD8s frequencies in follicular areas of the LN where they are needed to eliminate HIV infected cells, with implications for HIV cure strategies.
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2
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Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses. Genome Med 2021; 13:94. [PMID: 34034819 PMCID: PMC8145796 DOI: 10.1186/s13073-021-00907-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/11/2021] [Indexed: 01/26/2023] Open
Abstract
Background The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this pathway underlies various inflammation-mediated diseases, but the role of rare variants relative to common variants in immune response variability in healthy individuals remains unclear. Methods We performed molecular inversion probe sequencing on 48 IL-1 pathway-related genes in 463 healthy individuals from the Human Functional Genomics Project. We functionally grouped common and rare variants, over gene, subpathway, and inflammatory levels and performed the Sequence Kernel Association Test to test for association with in vitro stimulation-induced cytokine responses; specifically, IL-1β and IL-6 cytokine measurements upon stimulations that represent an array of microbial infections: lipopolysaccharide (LPS), phytohaemagglutinin (PHA), Candida albicans (C. albicans), and Staphylococcus aureus (S. aureus). Results We identified a burden of NCF4 rare variants with PHA-induced IL-6 cytokine and showed that the respective carriers are in the 1% lowest IL-6 producers. Collapsing rare variants in IL-1 subpathway genes produces a bidirectional association with LPS-induced IL-1β cytokine levels, which is reflected by a significant Spearman correlation. On the inflammatory level, we identified a burden of rare variants in genes encoding for proteins with an anti-inflammatory function with S. aureus-induced IL-6 cytokine. In contrast to these rare variant findings which were based on different types of stimuli, common variant associations were exclusively identified with C. albicans-induced cytokine over various levels of grouping, from the gene, to subpathway, to inflammatory level. Conclusions In conclusion, this study shows that functionally grouping common and rare genetic variants enables the elucidation IL-1-mediated biological mechanisms, specifically, for IL-1β and IL-6 cytokine responses induced by various stimuli. The framework used in this study may allow for the analysis of rare and common genetic variants in a wider variety of (non-immune) complex phenotypes and therefore has the potential to contribute to better understanding of unresolved, complex traits and diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00907-w.
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3
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Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR. A Beginner's Guide to Analysis of RNA Sequencing Data. Am J Respir Cell Mol Biol 2019; 59:145-157. [PMID: 29624415 DOI: 10.1165/rcmb.2017-0430tr] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Since the first publications coining the term RNA-seq (RNA sequencing) appeared in 2008, the number of publications containing RNA-seq data has grown exponentially, hitting an all-time high of 2,808 publications in 2016 (PubMed). With this wealth of RNA-seq data being generated, it is a challenge to extract maximal meaning from these datasets, and without the appropriate skills and background, there is risk of misinterpretation of these data. However, a general understanding of the principles underlying each step of RNA-seq data analysis allows investigators without a background in programming and bioinformatics to critically analyze their own datasets as well as published data. Our goals in the present review are to break down the steps of a typical RNA-seq analysis and to highlight the pitfalls and checkpoints along the way that are vital for bench scientists and biomedical researchers performing experiments that use RNA-seq.
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Affiliation(s)
- Clarissa M Koch
- 1 Division of Pulmonary and Critical Care, Department of Medicine
| | - Stephen F Chiu
- 1 Division of Pulmonary and Critical Care, Department of Medicine.,2 Division of Thoracic Surgery, Department of Surgery
| | | | - Ankit Bharat
- 1 Division of Pulmonary and Critical Care, Department of Medicine.,2 Division of Thoracic Surgery, Department of Surgery
| | - Karen M Ridge
- 1 Division of Pulmonary and Critical Care, Department of Medicine.,3 Department of Cell and Molecular Biology
| | | | - Deborah R Winter
- 5 Division of Rheumatology, Department of Medicine, Northwestern University, Chicago, Illinois
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4
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Wang Z, Liu S, Tao Y. Regulation of chromatin remodeling through RNA polymerase II stalling in the immune system. Mol Immunol 2019; 108:75-80. [PMID: 30784765 DOI: 10.1016/j.molimm.2019.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
RNA polymerase II (Pol II) binds to promoter-proximal regions of inducible target genes that are controlled and not transcribed by several negative elongation factors, which is known as Pol II stalling. The occurrence of stalling is due to particular modification signatures and structural conformations of chromatin that affect Pol II elongation. The existence and physiological importance of Pol II stalling implies that there is a dynamic balance in chromatin regulation prior to endogenous or exogenous stimulation. In this review, we discuss the effects of ATP-dependent chromatin remodeling complexes and histone modification via transcriptional machinery Pol II C-terminal domain phosphorylated at serine 5 (S5P RNAPII) initiation and S2P RNAPII elongation on the expression or silence of specific genes after the production of activated or differentiated signals or cytokines. The response occurs immediately during immune cell development and function, and it also includes the generation of immunological memories. This summary suggests that the host immune response genes involve a novel mechanism of selectively regulatory chromatin remodeling, a fundamental and crucial aspect of epigenetic regulation.
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Affiliation(s)
- Zuli Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuang Liu
- Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
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5
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Iannello A, Rolla S, Maglione A, Ferrero G, Bardina V, Inaudi I, De Mercanti S, Novelli F, D'Antuono L, Cardaropoli S, Todros T, Turrini MV, Cordioli C, Puorro G, Marsili A, Lanzillo R, Brescia Morra V, Cordero F, De Bortoli M, Durelli L, Visconti A, Cutrupi S, Clerico M. Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis. Front Immunol 2019; 9:3075. [PMID: 30671056 PMCID: PMC6331474 DOI: 10.3389/fimmu.2018.03075] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence supports the anti-inflammatory role of estrogens in Multiple Sclerosis (MS), originating from the observation of reduction in relapse rates among women with MS during pregnancy, but the molecular mechanisms are still not completely understood. Using an integrative data analysis, we identified T helper (Th) 17 and T regulatory (Treg) cell-type-specific regulatory regions (CSR) regulated by estrogen receptor alpha (ERα). These CSRs were validated in polarized Th17 from healthy donors (HD) and in peripheral blood mononuclear cells, Th17 and Treg cells from relapsing remitting (RR) MS patients and HD during pregnancy. 17β-estradiol induces active histone marks enrichment at Forkhead Box P3 (FOXP3)-CSRs and repressive histone marks enrichment at RAR related orphan receptor C (RORC)-CSRs in polarized Th17 cells. A disease-associated epigenetic profile was found in RRMS patients during pregnancy, suggesting a FOXP3 positive regulation and a RORC negative regulation in the third trimester of pregnancy. Altogether, these data indicate that estrogens act as immunomodulatory factors on the epigenomes of CD4+ T cells in RRMS; the identified CSRs may represent potential biomarkers for monitoring disease progression or new potential therapeutic targets.
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Affiliation(s)
- Andrea Iannello
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Simona Rolla
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Alessandro Maglione
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giulio Ferrero
- Department of Computer Science, University of Turin, Turin, Italy
| | - Valentina Bardina
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Ilenia Inaudi
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Stefania De Mercanti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Healthy Sciences, University of Turin, Turin, Italy
| | - Lucrezia D'Antuono
- Obstetric and Gynecologic Department, OIRM-Sant'Anna Hospital, Città della Salute e della Scienza, Turin, Italy
| | | | - Tullia Todros
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Maria Vittoria Turrini
- Multiple Sclerosis Center, Ospedali Civili di Brescia, Montichiari Hospital, Montichiari, Italy
| | - Cinzia Cordioli
- Multiple Sclerosis Center, Ospedali Civili di Brescia, Montichiari Hospital, Montichiari, Italy
| | - Giorgia Puorro
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, Naples, Italy
| | - Angela Marsili
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, Naples, Italy
| | - Roberta Lanzillo
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, Naples, Italy
| | - Vincenzo Brescia Morra
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, Naples, Italy
| | | | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Luca Durelli
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | - Santina Cutrupi
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Marinella Clerico
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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6
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Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility. J Allergy Clin Immunol 2018; 142:1793-1807. [DOI: 10.1016/j.jaci.2017.12.1006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 12/19/2022]
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7
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Tsagaratou A. TET mediated epigenetic regulation of iNKT cell lineage fate choice and function. Mol Immunol 2018; 101:564-573. [PMID: 30176520 DOI: 10.1016/j.molimm.2018.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/19/2018] [Accepted: 08/18/2018] [Indexed: 12/14/2022]
Abstract
During the last years, intensive research has shed light in the transcriptional networks that shape the invariant NKT (iNKT) cell lineage and guide the choices towards functionally distinct iNKT cell subsets (Constantinides and Bendelac, 2013; Engel and Kronenberg, 2014; Gapin, 2016; Kim et al., 2015). However, the epigenetic players that regulate gene expression and orchestrate the iNKT cell lineage choices remain poorly understood. Here, we summarize recent advances in our understanding of epigenetic regulation of iNKT cell development and lineage choice. Particular emphasis is placed on DNA modifications and the Ten Eleven Translocation (TET) family of DNA demethylases.
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Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, San Diego, CA, 92037, USA.
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8
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9
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Abstract
High-throughput sequencing assays have become an increasingly common part of biological research across multiple fields. Even as the resulting sequences pile up in public databases, it is not always obvious how to make use of these data sets. Functional genomics offers approaches to integrate these "big" data into our understanding of rheumatic diseases. This review aims to provide a primer on thinking about big data from functional genomics in the context of rheumatology, using examples from the field's literature as well as the author's own work to illustrate the execution of functional genomics research. Study design is crucial to ensure the right samples are used to address the question of interest. In addition, sequencing assays produce a variety of data types, from gene expression to 3D chromatin structure and single-cell technologies, that can be integrated into a model of the underlying gene regulatory networks. The best approach for this analysis uses the scientific process: bioinformatic methods should be used in an iterative, hypothesis-driven manner to uncover the disease mechanism. Finally, the future of functional genomics will see big data fully integrated into rheumatology, leading to computationally trained researchers and interactive databases. The goal of this review is not to provide a manual, but to enhance the familiarity of readers with functional genomic approaches and provide a better sense of the challenges and possibilities.
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Affiliation(s)
- Deborah R Winter
- Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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10
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Abstract
Macrophages play essential roles in the response to injury and infection and contribute to the development and/or homeostasis of the various tissues they reside in. Conversely, macrophages also influence the pathogenesis of metabolic, neurodegenerative, and neoplastic diseases. Mechanisms that contribute to the phenotypic diversity of macrophages in health and disease remain poorly understood. Here we review the recent application of genome-wide approaches to characterize the transcriptomes and epigenetic landscapes of tissue-resident macrophages. These studies are beginning to provide insights into how distinct tissue environments are interpreted by transcriptional regulatory elements to drive specialized programs of gene expression.
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11
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Keren-Shaul H, Spinrad A, Weiner A, Matcovitch-Natan O, Dvir-Szternfeld R, Ulland TK, David E, Baruch K, Lara-Astaiso D, Toth B, Itzkovitz S, Colonna M, Schwartz M, Amit I. A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease. Cell 2017; 169:1276-1290.e17. [PMID: 28602351 DOI: 10.1016/j.cell.2017.05.018] [Citation(s) in RCA: 2738] [Impact Index Per Article: 391.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Accepted: 05/11/2017] [Indexed: 01/23/2023]
Abstract
Alzheimer's disease (AD) is a detrimental neurodegenerative disease with no effective treatments. Due to cellular heterogeneity, defining the roles of immune cell subsets in AD onset and progression has been challenging. Using transcriptional single-cell sorting, we comprehensively map all immune populations in wild-type and AD-transgenic (Tg-AD) mouse brains. We describe a novel microglia type associated with neurodegenerative diseases (DAM) and identify markers, spatial localization, and pathways associated with these cells. Immunohistochemical staining of mice and human brain slices shows DAM with intracellular/phagocytic Aβ particles. Single-cell analysis of DAM in Tg-AD and triggering receptor expressed on myeloid cells 2 (Trem2)-/- Tg-AD reveals that the DAM program is activated in a two-step process. Activation is initiated in a Trem2-independent manner that involves downregulation of microglia checkpoints, followed by activation of a Trem2-dependent program. This unique microglia-type has the potential to restrict neurodegeneration, which may have important implications for future treatment of AD and other neurodegenerative diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amit Spinrad
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), and University Medical Center, Cancer Genomics Netherlands, 3584 CG Utrecht, the Netherlands.
| | - Orit Matcovitch-Natan
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raz Dvir-Szternfeld
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tyler K Ulland
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kuti Baruch
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Lara-Astaiso
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Beata Toth
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michal Schwartz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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12
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Yu B, Zhang K, Milner JJ, Toma C, Chen R, Scott-Browne JP, Pereira RM, Crotty S, Chang JT, Pipkin ME, Wang W, Goldrath AW. Epigenetic landscapes reveal transcription factors that regulate CD8 + T cell differentiation. Nat Immunol 2017; 18:573-582. [PMID: 28288100 PMCID: PMC5395420 DOI: 10.1038/ni.3706] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/07/2017] [Indexed: 12/14/2022]
Abstract
Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8+ T cell differentiation.
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Affiliation(s)
- Bingfei Yu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Kai Zhang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - J Justin Milner
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Clara Toma
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Runqiang Chen
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - James P Scott-Browne
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Renata M Pereira
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - Wei Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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13
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Zhu L, Jiang K, Webber K, Wong L, Liu T, Chen Y, Jarvis JN. Chromatin landscapes and genetic risk for juvenile idiopathic arthritis. Arthritis Res Ther 2017; 19:57. [PMID: 28288683 PMCID: PMC5348874 DOI: 10.1186/s13075-017-1260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 02/07/2023] Open
Abstract
Background The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci. Methods We analyzed RNA sequencing (RNA-Seq) data, H3K27ac and H3K4me1 chromatin immunoprecipitation-sequencing (ChIP-Seq) data, and previously published chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data to characterize the chromatin landscapes within the known JIA-associated risk loci. Results In both neutrophils and primary CD4+ T cells, the majority of the JIA-associated linkage disequilibrium (LD) blocks contained H3K27ac and/or H3K4me1 marks. These LD blocks were also binding sites for a small group of transcription factors, particularly in neutrophils. Furthermore, these regions showed abundant intronic and intergenic transcription in neutrophils. In neutrophils, none of the genes that were differentially expressed between untreated patients with JIA and healthy children were located within the JIA-risk LD blocks. In CD4+ T cells, multiple genes, including HLA-DQA1, HLA-DQB2, TRAF1, and IRF1 were associated with the long-distance interacting regions within the LD regions as determined from ChIA-PET data. Conclusions These findings suggest that genetic risk contributes to the aberrant transcriptional control observed in JIA. Furthermore, these findings demonstrate the challenges of identifying the actual causal variants within complex genomic/chromatin landscapes. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1260-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisha Zhu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kaiyu Jiang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Karstin Webber
- Graduate Program in Biological Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yanmin Chen
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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14
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Barski A, Cuddapah S, Kartashov AV, Liu C, Imamichi H, Yang W, Peng W, Lane HC, Zhao K. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Sci Rep 2017; 7:39785. [PMID: 28054639 PMCID: PMC5215294 DOI: 10.1038/srep39785] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022] Open
Abstract
Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both naïve and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the naïve cells. The mechanisms behind this rapid recall response of the memory cells are still not completely understood. Here, we performed epigenetic profiling of human resting naïve, central and effector memory T cells using ChIP-Seq and found that unlike the naïve cells, the regulatory elements of the cytokine genes in the memory T cells are marked by activating histone modifications even in the resting state. Therefore, the ability to induce expression of rapid recall genes upon activation is associated with the deposition of positive histone modifications during memory T cell differentiation. We propose a model of T cell memory, in which immunological memory state is encoded epigenetically, through poising and transcriptional memory.
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Affiliation(s)
- Artem Barski
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, NY, 10987, USA
| | - Andrey V Kartashov
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Chong Liu
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Hiromi Imamichi
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wenjing Yang
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - H Clifford Lane
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1024:63-90. [PMID: 28921465 DOI: 10.1007/978-981-10-5987-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Macrophages and dendritic cells initiate the innate immune response to infection and injury and contribute to inflammatory signaling to maintain the homeostasis of various tissues, which includes resident macrophages for the elimination of invading microorganisms and tissue damage. Inappropriate inflammatory signaling can lead to persistent inflammation and further develop into autoimmune and inflammation-associated diseases. Inflammatory signaling pathways have been well characterized, but how these signaling pathways are converted into sustained and diverse patterns of expression of cytokines, chemokines, and other genes in response to environmental challenges is unclear. Emerging evidence suggests the important role of epigenetic mechanisms in finely tuning the outcome of the host innate immune response. An understanding of epigenetic regulation of innate immune cell identity and function will enable the identification of the mechanism between gene-specific host defenses and inflammatory disease and will also allow for exploration of the program of innate immune memory in health and disease. This information could be used to develop therapeutic agents to enhance the host response, preventing chronic inflammation through preserving tissues and signaling integrity.
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16
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Hutter C, Minkov M. Insights into the pathogenesis of Langerhans cell histiocytosis: the development of targeted therapies. Immunotargets Ther 2016; 5:81-91. [PMID: 27785447 PMCID: PMC5066850 DOI: 10.2147/itt.s91058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
More than a century after its first description, Langerhans cell histiocytosis (LCH) still remains an intriguing disease. Considerable progress in understanding its biology has been achieved recently. Description of the V600E BRAF mutation in samples of LCH tissue in 2010 was followed by description of additional mutations, all leading to constitutive ERK activation. Current experimental data suggest that LCH is a myeloid neoplasia with inflammatory properties, yet the exact pathophysiology remains poorly understood. Disease management paradigms have changed over time, closely reflecting the evolving view of the nature of the disease. The international Histiocyte Society have conducted three prospective clinical studies on multisystem LCH since the early 1990s. The standard frontline therapy for patients with multisystem LCH based on the cumulative knowledge of those trials consists of 6–12 weeks of initial therapy (daily oral steroids and weekly vinblastine injections), followed by pulses of prednisolone/vinblastine every 3 weeks, for a total treatment duration of 12 months. A currently ongoing study (LCH-IV) with a complex design (five interventional and two observational strata) targets further reduction of mortality and morbidity by tailoring treatment intensity depending on expected risk, as well as by exploring treatment regimens for special locations. Current knowledge on LCH pathobiology opens opportunities for improvement in the patient outcome. The activating BRAF and MAP2K1 mutations collectively accounting for about 75% of the LCH population as well as the resulting constitutive activation of downstream ERK offer an opportunity for targeted treatment. Related issues (eg, finding most effective and less toxic drugs or combinations, appropriate dosage, and optimal treatment duration) must be addressed in controlled prospective trials. Additional mechanisms, such as the interactions of the mutated dendritic cell clone with other inflammatory cells and key cytokines and chemokines, still remain attractive targets for therapeutic intervention, particularly in patients with localized, less aggressive disease.
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Affiliation(s)
- Caroline Hutter
- International LCH Study Reference Center, Children's Cancer Research Institute, Vienna, Austria; St. Anna Children's Hospital, University Clinic of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Milen Minkov
- International LCH Study Reference Center, Children's Cancer Research Institute, Vienna, Austria; St. Anna Children's Hospital, University Clinic of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; Department of Pediatrics, Adolescent Medicine and Neonatology, Rudolfstiftung Hospital, Vienna, Austria
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17
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Mathematical Models for Immunology: Current State of the Art and Future Research Directions. Bull Math Biol 2016; 78:2091-2134. [PMID: 27714570 PMCID: PMC5069344 DOI: 10.1007/s11538-016-0214-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/26/2016] [Indexed: 01/01/2023]
Abstract
The advances in genetics and biochemistry that have taken place over the last 10 years led to significant advances in experimental and clinical immunology. In turn, this has led to the development of new mathematical models to investigate qualitatively and quantitatively various open questions in immunology. In this study we present a review of some research areas in mathematical immunology that evolved over the last 10 years. To this end, we take a step-by-step approach in discussing a range of models derived to study the dynamics of both the innate and immune responses at the molecular, cellular and tissue scales. To emphasise the use of mathematics in modelling in this area, we also review some of the mathematical tools used to investigate these models. Finally, we discuss some future trends in both experimental immunology and mathematical immunology for the upcoming years.
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18
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Withoff S, Li Y, Jonkers I, Wijmenga C. Understanding Celiac Disease by Genomics. Trends Genet 2016; 32:295-308. [PMID: 26972670 DOI: 10.1016/j.tig.2016.02.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we need to better understand to translate genetic knowledge into clinical practice. New genomic technologies and resources are permitting a systematic analysis of the functional elements in the non-coding part of the genome. Here we explain how investigating the regulatory and epigenomic landscape will help to pinpoint the cell types involved in CeD, and the driver genes and gene regulatory networks that are affected by CeD-associated SNPs.
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Affiliation(s)
- Sebo Withoff
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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19
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Swift SL, Stojdl DF. Big Data Offers Novel Insights for Oncolytic Virus Immunotherapy. Viruses 2016; 8:v8020045. [PMID: 26861383 PMCID: PMC4776200 DOI: 10.3390/v8020045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/15/2016] [Accepted: 01/27/2016] [Indexed: 12/20/2022] Open
Abstract
Large-scale assays, such as microarrays, next-generation sequencing and various “omics” technologies, have explored multiple aspects of the immune response following virus infection, often from a public health perspective. Yet a lack of similar data exists for monitoring immune engagement during oncolytic virus immunotherapy (OVIT) in the cancer setting. Tracking immune signatures at the tumour site can create a snapshot or longitudinally analyse immune cell activation, infiltration and functionality within global populations or individual cells. Mapping immune changes over the course of oncolytic biotherapy—from initial infection to tumour stabilisation/regression through to long-term cure or escape/relapse—has the potential to generate important therapeutic insights around virus-host interactions. Further, correlating such immune signatures with specific tumour outcomes has significant value for guiding the development of novel oncolytic virus immunotherapy strategies. Here, we provide insights for OVIT from large-scale analyses of immune populations in the infection, vaccination and immunotherapy setting. We analyse several approaches to manipulating immune engagement during OVIT. We further explore immunocentric changes in the tumour tissue following immunotherapy, and compile several immune signatures of therapeutic success. Ultimately, we highlight clinically relevant large-scale approaches with the potential to strengthen future oncolytic strategies to optimally engage the immune system.
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Affiliation(s)
- Stephanie L Swift
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada.
| | - David F Stojdl
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada.
- Department of Biology, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Pediatrics, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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