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Imran S, Neeland MR, Martino DJ, Peng S, Koplin J, Dharmage SC, Tang MLK, Sawyer S, Dang T, McWilliam V, Peters RL, Prescott S, Perrett KP, Novakovic B, Saffery R. Epigenomic variability is associated with age-specific naïve CD4 T cell response to activation in infants and adolescents. Immunol Cell Biol 2023; 101:397-411. [PMID: 36760028 PMCID: PMC10952707 DOI: 10.1111/imcb.12628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Childhood is a critical period of immune development. During this time, naïve CD4 (nCD4) T cells undergo programmed cell differentiation, mediated by epigenetic changes, in response to external stimuli leading to a baseline homeostatic state that may determine lifelong disease risk. However, the ontogeny of epigenetic signatures associated with CD4 T cell activation during key developmental periods are yet to be described. We investigated genome-wide DNA methylation (DNAm) changes associated with nCD4 T activation following 72 h culture in media+anti-CD3/CD28 beads in healthy infants (aged 12 months, n = 18) and adolescents (aged 10-15 years, n = 15). We integrated these data with transcriptomic and cytokine profiling from the same samples. nCD4 T cells from both age groups show similar extensive epigenetic reprogramming following activation, with the majority of genes involved in the T cell receptor signaling pathway associated with differential methylation. Additionally, we identified differentially methylated probes showing age-specific responses, that is, responses in only infants or adolescents, including within a cluster of T cell receptor (TCR) genes. These encoded several TCR alpha joining (TRAJ), and TCR alpha variable (TRAV) genes. Cytokine data analysis following stimulation revealed enhanced release of IFN-γ, IL-2 and IL-10, in nCD4 T cells from adolescents compared with infants. Overlapping differential methylation and cytokine responses identified four probes potentially underpinning these age-specific responses. We show that DNAm in nCD4T cells in response to activation is dynamic in infancy and adolescence, with additional evidence for age-specific effects potentially driving variation in cytokine responses between these ages.
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Affiliation(s)
- Samira Imran
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Melanie R Neeland
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - David J. Martino
- Wal‐yan Respiratory Research Centre, Telethon Kids InstitutePerthAustralia
- University of Western AustraliaPerthWAAustralia
| | - Stephen Peng
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Jennifer Koplin
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Shyamali C Dharmage
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Allergy and Lung Health UnitMelbourne School of Population and Global HealthUniversity of MelbourneMelbourneVICAustralia
| | - Mimi LK Tang
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Susan Sawyer
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Centre for Adolescent HealthRoyal Children's Hospital MelbourneMelbourneVICAustralia
| | - Thanh Dang
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Vicki McWilliam
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Rachel L Peters
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Susan Prescott
- School of MedicineThe University of Western Australia35 Stirling HighwayCrawleyWAAustralia
- Telethon Kids Institute15 Hospital AvenueNedlandsWAAustralia
- Department of ImmunologyPerth Children's Hospital15 Hospital AvenueNedlandsWAAustralia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Boris Novakovic
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Richard Saffery
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
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Zhong F, Lin Y, Zhao L, Yang C, Ye Y, Shen Z. Reshaping the tumour immune microenvironment in solid tumours via tumour cell and immune cell DNA methylation: from mechanisms to therapeutics. Br J Cancer 2023:10.1038/s41416-023-02292-0. [PMID: 37117649 DOI: 10.1038/s41416-023-02292-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
In recent years, the tumour microenvironment (TME) of solid tumours has attracted more and more attention from researchers, especially those non-tumour components such as immune cells. Infiltration of various immune cells causes tumour immune microenvironment (TIME) heterogeneity, and results in different therapeutic effects. Accumulating evidence showed that DNA methylation plays a crucial role in remodelling TIME and is associated with the response towards immune checkpoint inhibitors (ICIs). During carcinogenesis, DNA methylation profoundly changes, specifically, there is a global loss of DNA methylation and increased DNA methylation at the promoters of suppressor genes. Immune cell differentiation is disturbed, and exclusion of immune cells from the TME occurs at least in part due to DNA methylation reprogramming. Therefore, pharmaceutical interventions targeting DNA methylation are promising. DNA methyltransferase inhibitors (DNMTis) enhance antitumor immunity by inducing transcription of transposable elements and consequent viral mimicry. DNMTis upregulate the expression of tumour antigens, mediate immune cells recruitment and reactivate exhausted immune cells. In preclinical studies, DNMTis have shown synergistic effect when combined with immunotherapies, suggesting new strategies to treat refractory solid tumours.
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Affiliation(s)
- Fengyun Zhong
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China.
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China.
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Cassiano LMG, Cavalcante-Silva V, Oliveira MS, Prado BVO, Cardoso CG, Salim ACM, Franco GR, D’Almeida V, Francisco SC, Coimbra RS. Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic markings. Front Immunol 2023; 14:1048790. [PMID: 36993968 PMCID: PMC10040807 DOI: 10.3389/fimmu.2023.1048790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, that regulates the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic markings in leukocytes favorably regulates central components of COVID-19 physiopathology.
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Affiliation(s)
- Larissa M. G. Cassiano
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vanessa Cavalcante-Silva
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marina S. Oliveira
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
| | | | | | - Anna C. M. Salim
- Plataforma de Sequenciamento NGS (Next Generation Sequencing), Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
| | - Gloria R. Franco
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vânia D’Almeida
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Roney S. Coimbra
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
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Li M, Li Q, Dong H, Zhao S, Ning J, Bai X, Yue X, Xie A. Pilose antler polypeptides enhance chemotherapy effects in triple-negative breast cancer by activating the adaptive immune system. Int J Biol Macromol 2022; 222:2628-2638. [DOI: 10.1016/j.ijbiomac.2022.10.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
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de Vos L, Carrillo Cano TM, Zarbl R, Klümper N, Ralser DJ, Franzen A, Herr E, Gabrielpillai J, Vogt TJ, Dietrich J, Strieth S, Landsberg J, Dietrich D. CTLA4 , PD-1 , PD-L1 , PD-L2 , TIM-3 , TIGIT , and LAG3 DNA Methylation Is Associated With BAP1 -Aberrancy, Transcriptional Activity, and Overall Survival in Uveal Melanoma. J Immunother 2022; 45:324-334. [PMID: 35862127 DOI: 10.1097/cji.0000000000000429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022]
Abstract
Uveal melanoma (UM) is an aggressive disease with poor response to oncological treatment, including immunotherapy. Loss of the epigenetic modifier BRCA1-associated protein 1 (BAP1) function drives UM oncogenesis and is associated with an immune-suppressive tumor microenvironment, poor prognosis, and a distinct DNA methylation and gene expression profile. Our study aimed to analyze comprehensively the DNA methylation status of the immune checkpoint genes PD-1 , PD-L1 , PD-L2 , CTLA4, TIM-3 ( HAVCR2 ), TIGIT , and LAG3 and its association with mRNA expression, BAP1 -aberrancy, and patients' survival. We analyzed the DNA methylation landscape of immune checkpoint genes at single CpG resolution in N=80 UM samples provided by The Cancer Genome Atlas. We analyzed CpG methylation levels of the immune checkpoints with regard to their transcriptional signatures and patient outcomes.Methylation of specific CpG sites within the immune checkpoint genes PD-1 , PD-L1 , PD-L2 , CTLA4 , TIM-3 , TIGIT , and LAG3 correlated strongly with mRNA expression levels, indicating a strong regulation of gene expression through DNA methylation. Moreover, immune checkpoint gene methylation was strongly associated with BAP1 -mutation status and associated with overall survival in UM. Our data indicate an epigenetic regulation of immune checkpoints through DNA methylation in UM. Further, our data highlight the prognostic significance of DNA methylation of immune checkpoint genes in UM thereby providing a rationale for methylation testing as predictive biomarkers for immunotherapy response.
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Affiliation(s)
| | | | | | | | | | | | - Emmanuelle Herr
- Dermatology and Allergy, University Medical Center Bonn (UKB), Bonn, Germany
| | | | | | | | | | - Jennifer Landsberg
- Dermatology and Allergy, University Medical Center Bonn (UKB), Bonn, Germany
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Iwaszkiewicz-Grzes D, Piotrowska M, Gliwinski M, Urban-Wójciuk Z, Trzonkowski P. Antigenic Challenge Influences Epigenetic Changes in Antigen-Specific T Regulatory Cells. Front Immunol 2021; 12:642678. [PMID: 33868279 PMCID: PMC8044853 DOI: 10.3389/fimmu.2021.642678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Background Human regulatory T cells (Tregs) are the fundamental component of the immune system imposing immune tolerance via control of effector T cells (Teffs). Ongoing attempts to improve Tregs function have led to the creation of a protocol that produces antigen-specific Tregs, when polyclonal Tregs are stimulated with monocytes loaded with antigens specific for type 1 diabetes. Nevertheless, the efficiency of the suppression exerted by the produced Tregs depended on the antigen with the best results when insulin β chain peptide 9-23 was used. Here, we examined epigenetic modifications, which could influence these functional differences. Methods The analysis was pefromed in the sorted specific (SPEC, proliferating) and unspecific (UNSPEC, non-proliferating) subsets of Tregs and Teffs generated by the stimulation with monocytes loaded with either whole insulin (INS) or insulin β chain peptide 9-23 (B:9-23) or polyclonal cells stimulated with anti-CD3/anti-CD28 beads (POLY). A relative expression of crucial Tregs genes was determined by qRT-PCR. The Treg-specific demethylated region (TSDR) in FoxP3 gene methylation levels were assessed by Quantitative Methylation Specific PCR (qMSP). ELISA was used to measure genomic DNA methylation and histone H3 post-translational modifications (PTMs). Results Tregs SPECB:9-23 was the only subset expressing all assessed genes necessary for regulatory function with the highest level of expression among all analyzed conditions. The methylation of global DNA as well as TSDR were significantly lower in Tregs SPECB:9-23 than in Tregs SPECINS. When compared to Teffs, Tregs were characterized by a relatively lower level of PTMs but it varied in respective Tregs/Teffs pairs. Importantly, whenever the difference in PTM within Tregs/Teffs pair was significant, it was always low in one subset from the pair and high in the other. It was always low in Tregs SPECINS and high in Teffs SPECINS, while it was high in Tregs UNSPECINS and low in Teffs UNSPECINS. There were no differences in Tregs/Teffs SPECB:9-23 pair and the level of modifications was low in Tregs UNSPECB:9-23 and high in Teffs UNSPECB:9-23. The regions of PTMs in which differences were significant overlapped only partially between particular Tregs/Teffs pairs. Conclusions Whole insulin and insulin β chain peptide 9-23 affected epigenetic changes in CD4+ T cells differently, when presented by monocytes. The peptide preferably favored specific Tregs, while whole insulin activated both Tregs and Teffs.
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Affiliation(s)
| | | | - Mateusz Gliwinski
- Department of Medical Immunology, Medical University of Gdansk, Gdańsk, Poland
| | - Zuzanna Urban-Wójciuk
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Piotr Trzonkowski
- Department of Medical Immunology, Medical University of Gdansk, Gdańsk, Poland
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Burke CG, Myers JR, Post CM, Boulé LA, Lawrence BP. DNA Methylation Patterns in CD4+ T Cells of Naïve and Influenza A Virus-Infected Mice Developmentally Exposed to an Aryl Hydrocarbon Receptor Ligand. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:17007. [PMID: 33449811 PMCID: PMC7810290 DOI: 10.1289/ehp7699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/08/2020] [Accepted: 12/22/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Early life environmental exposures can have lasting effects on the function of the immune system and contribute to disease later in life. Epidemiological studies have linked early life exposure to xenobiotics that bind the aryl hydrocarbon receptor (AhR) with dysregulated immune responses later in life. Among the immune cells influenced by developmental activation of the AhR are CD 4 + T cells. Yet, the underlying affected cellular pathways via which activating the AhR early in life causes the responses of CD 4 + T cells to remain affected into adulthood remain unclear. OBJECTIVE Our goal was to identify cellular mechanisms that drive impaired CD 4 + T-cell responses later in life following maternal exposure to an exogenous AhR ligand. METHODS C57BL/6 mice were vertically exposed to the prototype AhR ligand, 2,3,7,8-tetrachlorodibenzo-p -dioxin (TCDD), throughout gestation and early postnatal life. The transcriptome and DNA methylation patterns were evaluated in CD 4 + T cells isolated from naïve and influenza A virus (IAV)-infected adult mice that were developmentally exposed to TCDD or vehicle control. We then assessed the influence of DNA methylation-altering drug therapies on the response of CD 4 + T cells from developmentally exposed mice to infection. RESULTS Gene and protein expression showed that developmental AhR activation reduced CD 4 + T-cell expansion and effector functions during IAV infection later in life. Furthermore, whole-genome bisulfite sequencing analyses revealed that developmental AhR activation durably programed DNA methylation patterns across the CD 4 + T-cell genome. Treatment of developmentally exposed offspring with DNA methylation-altering drugs alleviated some, but not all, of the impaired CD 4 + T-cell responses. DISCUSSION Taken together, these results indicate that skewed DNA methylation is one of the mechanisms by which early life exposures can durably change the function of T cells in mice. Furthermore, treatment with DNA methylation-altering drugs after the exposure restored some aspects of CD 4 + T-cell functional responsiveness. https://doi.org/10.1289/EHP7699.
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Affiliation(s)
- Catherine G. Burke
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jason R. Myers
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Christina M. Post
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Lisbeth A. Boulé
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - B. Paige Lawrence
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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Hiam D, Simar D, Laker R, Altıntaş A, Gibson-Helm M, Fletcher E, Moreno-Asso A, Trewin AJ, Barres R, Stepto NK. Epigenetic Reprogramming of Immune Cells in Women With PCOS Impact Genes Controlling Reproductive Function. J Clin Endocrinol Metab 2019; 104:6155-6170. [PMID: 31390009 DOI: 10.1210/jc.2019-01015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is a chronic disease affecting reproductive function and whole-body metabolism. Although the etiology is unclear, emerging evidence indicates that the epigenetics may be a contributing factor. OBJECTIVE To determine the role of global and genome-wide epigenetic modifications in specific immune cells in PCOS compared with controls and whether these could be related to clinical features of PCOS. DESIGN Cross-sectional study. PARTICIPANTS Women with (n = 17) or without PCOS (n = 17). SETTING Recruited from the general community. MAIN OUTCOME MEASURES Isolated peripheral blood mononuclear cells were analyzed using multicolor flow cytometry methods to determine global DNA methylation levels in a cell-specific fashion. Transcriptomic and genome-wide DNA methylation analyses were performed on T helper cells using RNA sequencing and reduced representation bisulfite sequencing. RESULTS Women with PCOS had lower global DNA methylation in monocytes (P = 0.006) and in T helper (P = 0.004), T cytotoxic (P = 0.004), and B cells (P = 0.03). Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5581 differentially methylated CpG sites. Functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. However, these genes were not altered at the transcriptomic level. CONCLUSIONS It was shown that PCOS is associated with global and gene-specific DNA methylation remodeling in a cell type-specific manner. Further investigation is warranted to determine whether epigenetic reprogramming of immune cells is important in determining the different phenotypes of PCOS.
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Affiliation(s)
- Danielle Hiam
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Rhianna Laker
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Gibson-Helm
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Elly Fletcher
- Baker Heart and Disease Institute, Melbourne, Victoria, Australia
| | - Alba Moreno-Asso
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Adam J Trewin
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Romain Barres
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Nigel K Stepto
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Medicine-Western Health, School of Medicine, Faculty of Medicine, Dentistry, and Health Science, Melbourne, Australia
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Zhou J, Wu YC, Xiao BJ, Guo XD, Zheng QX, Wu B. Age-related Changes in the Global DNA Methylation Profile of Oligodendrocyte Progenitor Cells Derived from Rat Spinal Cords. Curr Med Sci 2019; 39:67-74. [PMID: 30868493 DOI: 10.1007/s11596-019-2001-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Indexed: 01/12/2023]
Abstract
Demyelination of axons plays an important role in the pathology of many spinal cord diseases and injuries. Remyelination in demyelinated lesions is primarily performed by oligodendrocyte progenitor cells (OPCs), which generate oligodendrocytes in the developing and mature central nervous system. The efficiency of remyelination decreases with age. Many reports suggest that this decline in remyelination results from impaired OPC recruitment and differentiation during aging. Of the various molecular mechanisms involved in aging, changes in epigenetic modifications have received particular attention. Global DNA methylation is a major epigenetic modification that plays important roles in cellular senescence and organismal aging. Thus, we aimed to evaluate the dynamic changes in the global DNA methylation profiles of OPCs derived from rat spinal cords during the aging process. We separated and cultured OPCs from the spinal cords of neonatal, 4-month-old, and 16-month-old rats and investigated the age-related alterations of genomic DNA methylation levels by using quantitative colorimetric analysis. To determine the potential cause of dynamic changes in global DNA methylation, we further analyzed the activity of DNA methyltransferases (DNMTs) and the expression of DNMT1, DNMT3a, DNMT3b, TET1, TET2, TET3, MBD2, and MeCP2 in the OPCs from each group. Our results showed the genomic DNA methylation level and the activity of DNMTs from OPCs derived from rat spinal cords decreased gradually during aging, and OPCs from 16-month-old rats were characterized by global hypomethylation. During OPC aging, the mRNA and protein expression levels of DNMT3a, DNMT3b, and MeCP2 were significantly elevated; those of DNMT1 were significantly down-regulated; and no significant changes were observed in those for TET1, TET2, TET3, or MBD2. Our results indicated that global DNA hypomethylation in aged OPCs is correlated with DNMT1 downregulation. Together, these data provide important evidence for partly elucidating the mechanism of age-related impaired OPC recruitment and differentiation and assist in the development of new treatments for promoting efficient remyelination.
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Affiliation(s)
- Jing Zhou
- Department of General Surgery, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yong-Chao Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bao-Jun Xiao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao-Dong Guo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qi-Xin Zheng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bin Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Roles of SMC Complexes During T Lymphocyte Development and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:17-42. [DOI: 10.1016/bs.apcsb.2016.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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LaMere SA, Thompson RC, Komori HK, Mark A, Salomon DR. Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells. Genes Immun 2016; 17:283-97. [PMID: 27170561 PMCID: PMC4956548 DOI: 10.1038/gene.2016.19] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 12/28/2022]
Abstract
The epigenetic determinants driving the responses of CD4 T cells to antigen are currently an area of active research. Much has been done to characterize helper T-cell subsets and their associated genome-wide epigenetic patterns. In contrast, little is known about the dynamics of histone modifications during CD4 T-cell activation and the differential kinetics of these epigenetic marks between naive and memory T cells. In this study, we have detailed the dynamics of genome-wide promoter H3K4me2 and H3K4me3 over a time course during activation of human naive and memory CD4 T cells. Our results demonstrate that changes to H3K4 methylation occur relatively late after activation (5 days) and reinforce activation-induced upregulation of gene expression, affecting multiple pathways important to T-cell activation, differentiation and function. The dynamics and mapped pathways of H3K4 methylation are distinctly different in memory cells, which have substantially more promoters marked by H3K4me3 alone, reinforcing their more differentiated state. Our study provides the first data examining genome-wide histone modification dynamics during CD4 T-cell activation, providing insight into the cross talk between H3K4 methylation and gene expression, and underscoring the impact of these marks upon key pathways integral to CD4 T-cell activation and function.
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Affiliation(s)
- S A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - R C Thompson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - H K Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - A Mark
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - D R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Wiencke JK, Butler R, Hsuang G, Eliot M, Kim S, Sepulveda MA, Siegel D, Houseman EA, Kelsey KT. The DNA methylation profile of activated human natural killer cells. Epigenetics 2016; 11:363-80. [PMID: 26967308 DOI: 10.1080/15592294.2016.1163454] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., TNFA, LTA, IL13, CSF2). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. BHLHE40 was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
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Affiliation(s)
- John K Wiencke
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Rondi Butler
- b Brown University , Department of Epidemiology , Providence , RI
| | - George Hsuang
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Melissa Eliot
- b Brown University , Department of Epidemiology , Providence , RI
| | - Stephanie Kim
- b Brown University , Department of Epidemiology , Providence , RI
| | - Manuel A Sepulveda
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - Derick Siegel
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - E Andres Houseman
- e University of Oregon, College of Public Health and Human Science , Corvallis , OR
| | - Karl T Kelsey
- b Brown University , Department of Epidemiology , Providence , RI.,c Department of Laboratory Medicine and Pathology , Providence , RI
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Trejbalová K, Kovářová D, Blažková J, Machala L, Jilich D, Weber J, Kučerová D, Vencálek O, Hirsch I, Hejnar J. Development of 5' LTR DNA methylation of latent HIV-1 provirus in cell line models and in long-term-infected individuals. Clin Epigenetics 2016; 8:19. [PMID: 26900410 PMCID: PMC4759744 DOI: 10.1186/s13148-016-0185-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) latency represents the major barrier to virus eradication in infected individuals because cells harboring latent HIV-1 provirus are not affected by current antiretroviral therapy (ART). We previously demonstrated that DNA methylation of HIV-1 long terminal repeat (5' LTR) restricts HIV-1 reactivation and, together with chromatin conformation, represents an important mechanism of HIV-1 latency maintenance. Here, we explored the new issue of temporal development of DNA methylation in latent HIV-1 5' LTR. RESULTS In the Jurkat CD4(+) T cell model of latency, we showed that the stimulation of host cells contributed to de novo DNA methylation of the latent HIV-1 5' LTR sequences. Consecutive stimulations of model CD4(+) T cell line with TNF-α and PMA or with SAHA contributed to the progressive accumulation of 5' LTR DNA methylation. Further, we showed that once established, the high DNA methylation level of the latent 5' LTR in the cell line model was a stable epigenetic mark. Finally, we explored the development of 5' LTR DNA methylation in the latent reservoir of HIV-1-infected individuals who were treated with ART. We detected low levels of 5' LTR DNA methylation in the resting CD4(+) T cells of the group of patients who were treated for up to 3 years. However, after long-term ART, we observed an accumulation of 5' LTR DNA methylation in the latent reservoir. Importantly, within the latent reservoir of some long-term-treated individuals, we uncovered populations of proviral molecules with a high density of 5' LTR CpG methylation. CONCLUSIONS Our data showed the presence of 5' LTR DNA methylation in the long-term reservoir of HIV-1-infected individuals and implied that the transient stimulation of cells harboring latent proviruses may contribute, at least in part, to the methylation of the HIV-1 promoter.
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Affiliation(s)
- Kateřina Trejbalová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Denisa Kovářová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Jana Blažková
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Ladislav Machala
- Department of Infectious Diseases, Third Faculty of Medicine, Charles University and Hospital Na Bulovce in Prague, Budínova 67/2, CZ-18081 Prague 8, Czech Republic
| | - David Jilich
- Department of Infectious, Tropical and Parasitic Diseases, First Faculty of Medicine, Charles University in Prague and Hospital Na Bulovce, Budínova 67/ 2, CZ-18081 Prague 8, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Dana Kučerová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Ondřej Vencálek
- Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science of the Palacky University in Olomouc, Olomouc, CZ-77146 Czech Republic
| | - Ivan Hirsch
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic ; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic ; Faculty of Science, Department of Genetics and Microbiology, Charles University in Prague, Viničná 5, CZ-12844 Prague 2, Czech Republic ; Inserm, Centre de Recherche en Cancérologie de Marseille (CRCM), F-13273 Marseille, France ; Institut Paoli-Calmettes, F-13009 Marseille, France ; Aix-Marseille Univ., F-13284 Marseille, France ; CNRS, UMR7258, CRCM, F-13009 Marseille, France
| | - Jiří Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
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Bailey LB, Stover PJ, McNulty H, Fenech MF, Gregory JF, Mills JL, Pfeiffer CM, Fazili Z, Zhang M, Ueland PM, Molloy AM, Caudill MA, Shane B, Berry RJ, Bailey RL, Hausman DB, Raghavan R, Raiten DJ. Biomarkers of Nutrition for Development-Folate Review. J Nutr 2015; 145:1636S-1680S. [PMID: 26451605 PMCID: PMC4478945 DOI: 10.3945/jn.114.206599] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 12/13/2022] Open
Abstract
The Biomarkers of Nutrition for Development (BOND) project is designed to provide evidence-based advice to anyone with an interest in the role of nutrition in health. Specifically, the BOND program provides state-of-the-art information and service with regard to selection, use, and interpretation of biomarkers of nutrient exposure, status, function, and effect. To accomplish this objective, expert panels are recruited to evaluate the literature and to draft comprehensive reports on the current state of the art with regard to specific nutrient biology and available biomarkers for assessing nutrients in body tissues at the individual and population level. Phase I of the BOND project includes the evaluation of biomarkers for 6 nutrients: iodine, iron, zinc, folate, vitamin A, and vitamin B-12. This review represents the second in the series of reviews and covers all relevant aspects of folate biology and biomarkers. The article is organized to provide the reader with a full appreciation of folate's history as a public health issue, its biology, and an overview of available biomarkers (serum folate, RBC folate, and plasma homocysteine concentrations) and their interpretation across a range of clinical and population-based uses. The article also includes a list of priority research needs for advancing the area of folate biomarkers related to nutritional health status and development.
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Affiliation(s)
- Lynn B Bailey
- Department of Foods and Nutrition, University of Georgia, Athens, GA;
| | - Patrick J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Helene McNulty
- Northern Ireland Centre for Food and Health, Biomedical Sciences Research Institute, University of Ulster, Londonderry, United Kingdom
| | - Michael F Fenech
- Genome Health Nutrigenomics Laboratory, Food, Nutrition, and Bioproducts Flagship, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | | | - Zia Fazili
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Mindy Zhang
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Per M Ueland
- Department of Clinical Science, Univeristy of Bergen, Bergen, Norway
| | - Anne M Molloy
- Institute of Molecular Medicine, Trinity College, Dublin, Ireland
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA
| | - Robert J Berry
- National Center on Birth Defects and Developmental Disabilities, CDC, Atlanta, GA; and
| | | | - Dorothy B Hausman
- Department of Foods and Nutrition, University of Georgia, Athens, GA
| | - Ramkripa Raghavan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | - Daniel J Raiten
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD;
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15
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Li D, Guo B, Wu H, Tan L, Chang C, Lu Q. Interleukin-17 in systemic lupus erythematosus: A comprehensive review. Autoimmunity 2015; 48:353-61. [DOI: 10.3109/08916934.2015.1037441] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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16
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Dynamic regulation of the angiotensinogen gene by DNA methylation, which is influenced by various stimuli experienced in daily life. Hypertens Res 2015; 38:519-27. [PMID: 25809578 DOI: 10.1038/hr.2015.42] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 12/17/2022]
Abstract
Angiotensinogen (AGT) has a central role in maintaining blood pressure and fluid balance. DNA methylation is an epigenomic modification maintaining a steady pattern in somatic cells. Herein we summarize the link between AGT regulation and DNA methylation. DNA methylation negatively regulates AGT expression and dynamically changes in response to continuous AGT promoter stimulation. High-salt intake and excess circulating aldosterone cause DNA demethylation around the CCAAT enhancer-binding protein-binding sites, thereby converting the phenotype of AGT expression from an inactive to an active state in visceral adipose tissue. Salt-dependent hypertension may be partially affected by increased adipose AGT expression. Because angiotensin II is a well-established aldosterone-releasing hormone, stimulation of adipose AGT by aldosterone creates a positive feedback loop. This effect is pathologically associated with obesity-related hypertension, although it would be physiologically favorable for humans to efficiently retain their body fluid. The clear difference in DNA demethylation patterns between aldosterone and cortisol indicates a difference in the respective target DNA-binding sites between mineralocorticoid and glucocorticoid receptors in the AGT promoter. Stimulation-induced interactions between transcription factors and target DNA-binding sites trigger DNA demethylation. Dynamic changes in DNA methylation occur in relaxed chromatin regions both where transcription factors actively interact and where transcription is initiated. In contrast to rapid histone modifications, DNA demethylation and remethylation will progress relatively slowly over days or years. A wide variety of stimuli in daily life will continue to slowly and dynamically change DNA methylation patterns throughout life. Wise choices of beneficial stimuli will improve health.
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17
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Komori HK, Hart T, LaMere SA, Chew PV, Salomon DR. Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. THE JOURNAL OF IMMUNOLOGY 2015; 194:1565-79. [PMID: 25576597 DOI: 10.4049/jimmunol.1401162] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpGs) mapped by deep sequencing of T cell activation in human naive and memory CD4 T cells. Four hundred sixty-six CpGs (132 genes) displayed differential methylation between naive and memory cells. Twenty-one genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 of 21 genes encode proteins closely studied in T cells, whereas 15 genes represent novel targets for further study. Eighty-four genes demonstrated differential methylation between memory and naive cells that correlated to differential gene expression following activation, of which 39 exhibited reduced methylation in memory cells coupled with increased gene expression upon activation compared with naive cells. These reveal a class of primed genes more rapidly expressed in memory compared with naive cells and putatively regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells that correlates with activation-induced gene expression.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Traver Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Pamela V Chew
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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18
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LaMere SA, Komori HK, Salomon DR. New opportunities for organ transplantation research: epigenetics is likely to be an important determinant of the host immune response. Epigenomics 2013; 5:243-6. [PMID: 23750639 DOI: 10.2217/epi.13.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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19
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Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells. Blood 2013; 122:2823-36. [PMID: 23974203 DOI: 10.1182/blood-2013-02-481788] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulatory T cells (Treg) prevent the emergence of autoimmune disease. Prototypic natural Treg (nTreg) can be reliably identified by demethylation at the Forkhead-box P3 (FOXP3) locus. To explore the methylation landscape of nTreg, we analyzed genome-wide methylation in human naive nTreg (rTreg) and conventional naive CD4(+) T cells (Naive). We detected 2315 differentially methylated cytosine-guanosine dinucleotides (CpGs) between these 2 cell types, many of which clustered into 127 regions of differential methylation (RDMs). Activation changed the methylation status of 466 CpGs and 18 RDMs in Naive but did not alter DNA methylation in rTreg. Gene-set testing of the 127 RDMs showed that promoter methylation and gene expression were reciprocally related. RDMs were enriched for putative FOXP3-binding motifs. Moreover, CpGs within known FOXP3-binding regions in the genome were hypomethylated. In support of the view that methylation limits access of FOXP3 to its DNA targets, we showed that increased expression of the immune suppressive receptor T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT), which delineated Treg from activated effector T cells, was associated with hypomethylation and FOXP3 binding at the TIGIT locus. Differential methylation analysis provides insight into previously undefined human Treg signature genes and their mode of regulation.
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Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. eLife 2013; 2:e00523. [PMID: 23755361 PMCID: PMC3673336 DOI: 10.7554/elife.00523] [Citation(s) in RCA: 304] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/29/2013] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression. DOI:http://dx.doi.org/10.7554/eLife.00523.001 Variations occur throughout our genome. These variations can cause genes to be expressed (switched on) in slightly different ways among individuals. Moreover, the same gene can also be expressed in different ways in different cells within an individual. A third level of variation is supplied by epigenetic markers: these are molecules that bind to the DNA at specific points and can have profound effects on the expression of nearby genes. One such epigenetic marker is the addition of a methyl group to a cytosine base, a process that is known as DNA methylation. DNA methylation usually happens when a cytosine base is next to a guanine base, forming a CpG site. In mammals, most CpG sites have methyl groups attached, although regions with a lot of CpG sites (called CpG islands) are mostly unmethylated. Initial studies suggested that methylation prevented particular genes from being expressed, but more recent work has indicated that methylation can be associated with both reduced and increased expression of genes. Moreover, it is not clear if this association is active (i.e., changes in methylation drive changes in gene expression) or passive (DNA methylation is the result of gene regulation). Now, Gutierrez-Arcelus et al. have carried out a large-scale study to clarify the relationships between three different types of gene-related variations among individuals. They extracted fibroblasts, T-cells and lymphoblastoid cells from the umbilical cords of 204 babies, and analysed them for variations in DNA sequence, gene expression and DNA methylation. Their results show that the associations between the three are more complex than was previously thought. Gutierrez-Arcelus et al. show that the mechanisms that control the association between the variations in DNA methylation and gene expression in individuals are likely to be different to those that are responsible for the establishment of methylation patterns during the process of cell differentiation. They also find that the association between DNA methylation and gene expression can be either active or passive, and can depend on the context in which they occur in our genome. Finally, where the two copies or alleles of a gene are not equally expressed in a given cell, the difference in expression is primarily regulated by DNA sequence variation, with DNA methylation having little or no role on its own. Equally complex interactions and effects are expected in further studies of genetic and epigenetic variation. DOI:http://dx.doi.org/10.7554/eLife.00523.002
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Affiliation(s)
- Maria Gutierrez-Arcelus
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, Geneva, Switzerland [corrected]; Swiss Institute of Bioinformatics, Geneva, Switzerland
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Abstract
In this review, we introduce the IPEX syndrome and its relationship with germline mutations of the FOXP3 gene. We then describe the multiple functional roles of FOXP3 in regulatory T cells and epithelial cells as well as in IPEX syndrome and tumor progression. Potential mechanisms of FOXP3 inactivation and transcriptional regulation are discussed with recent advances. Finally, we point out current issues and a potential FOXP3-mediated therapeutic strategy as well as the reactivation of FOXP3 in patients with IPEX syndrome and cancer.
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Affiliation(s)
- Runhua Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Silin Li
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Wei-Hsiung Yang
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia 31404, USA
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Jacoby M, Gohrbandt S, Clausse V, Brons NH, Muller CP. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 2012; 7:1421-34. [PMID: 23151460 DOI: 10.4161/epi.22845] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation regulates gene expression in a cell-type specific way. Although peripheral blood mononuclear cells (PBMCs) comprise a heterogeneous cell population, most studies of DNA methylation in blood are performed on total mononuclear cells. In this study, we investigated high resolution methylation profiles of 58 CpG sites dispersed over eight immune response genes in multiple purified blood cells from healthy adults and newborns. Adjacent CpG sites showed methylation levels that were increasingly correlated in adult blood vs. cord blood. Thus, while interindividual variability increases from newborn to adult blood, the underlying methylation changes may not be merely stochastic, but seem to be orchestrated as clusters of adjacent CpG sites. Multiple linear regression analysis showed that interindividual methylation variability was influenced by distance of average methylation levels to the closest border (0 or 100%), presence of transcription factor binding sites, CpG conservation across species and age. Furthermore, CD4+ and CD14+ cell types were negative predictors of methylation variability. Concerns that PBMC methylation differences may be confounded by variations in blood cell composition were justified for CpG sites with large methylation differences across cell types, such as in the IFN-γ gene promoter. Taken together, our data suggest that unsorted mononuclear cells are reasonable surrogates of CD8+ and, to a lesser extent, CD4+ T cell methylation in adult peripheral, but not in neonatal, cord blood.
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Affiliation(s)
- Monique Jacoby
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
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