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Goldsmith C, Thevin V, Fesneau O, Matias MI, Perrault J, Abid AH, Taylor N, Dardalhon V, Marie JC, Hernandez-Vargas H. Single-Molecule DNA Methylation Reveals Unique Epigenetic Identity Profiles of T Helper Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1029-1039. [PMID: 38284984 PMCID: PMC11002815 DOI: 10.4049/jimmunol.2300091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024]
Abstract
Both identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. However, a method that reliably and readily profiles DNA base modifications is still needed to finely study Th cell differentiation. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes, but their potential to characterize intermediate cell transitions has not yet been evaluated. To assess transition states in Th cells, we developed a method to profile Th cell identity using Cas9-targeted single-molecule nanopore sequencing. Targeting as few as 10 selected genomic loci, we were able to distinguish major in vitro polarized murine T cell subtypes, as well as intermediate phenotypes, by their native DNA 5mCpG patterns. Moreover, by using off-target sequences, we were able to infer transcription factor activities relevant to each cell subtype. Detection of 5mCpG and 5hmCpG was validated on intestinal Th17 cells escaping transforming growth factor β control, using single-molecule adaptive sampling. A total of 21 differentially methylated regions mapping to the 10-gene panel were identified in pathogenic Th17 cells relative to their nonpathogenic counterpart. Hence, our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological transition states of Th cells.
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Affiliation(s)
- Chloe Goldsmith
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Valentin Thevin
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Olivier Fesneau
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Maria I Matias
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Julie Perrault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Ali Hani Abid
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Pediatric Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Valérie Dardalhon
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Julien C Marie
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Hector Hernandez-Vargas
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
- Genomics Consulting, Bron, France
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Parks CG, Leyzarovich D, Love SA, Long S, Hofmann JN, Beane Freeman LE, Sandler DP. High pesticide exposures events, pesticide poisoning, and shingles: A medicare-linked study of pesticide applicators in the agricultural health study. ENVIRONMENT INTERNATIONAL 2023; 181:108251. [PMID: 37862860 PMCID: PMC10836588 DOI: 10.1016/j.envint.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
OBJECTIVES Self-reported shingles was associated with history of high pesticide exposure events (HPEE) in licensed pesticide applicators aged >60 years in the Agricultural Health Study (AHS). In the current study, using AHS-linked Medicare claims data, we examined incident shingles in relation to pesticide-related illness and pesticide poisoning, as well as HPEE. METHODS We studied 22,753 licensed private pesticide applicators (97% white males, enrolled in the AHS 1993-97), aged ≥66 years with >12 consecutive months of Medicare fee-for-service hospital and outpatient coverage between 1999 and 2016. Incident shingles was identified based on having ≥1 shingles claim(s) after 12 months without claims. At AHS enrollment, participants were asked if they ever sought medical care or were hospitalized for pesticide-related illness, and a supplemental questionnaire (completed by 51%) asked about HPEE and poisoning. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated using Cox proportional hazards regression, adjusted for age, sex, race, state, and education. RESULTS Over 192,053 person-years (PY), 2396 applicators were diagnosed with shingles (10.5%; age-standardized rate, 13.6 cases per 1,000PY), with higher rates among those reporting hospitalization for pesticide-related illness, pesticide poisoning, and HPEE (23.2, 22.5, and 16.6 per 1,000PY, respectively). In adjusted models, shingles was associated with hospitalization for pesticide-related illness (HR 1.69; 1.18, 2.39), poisoning (1.49; 1.08, 1.46), and HPEE (1.23; 95% CI = 1.03, 1.46), especially HPEE plus medical care/poisoning (1.78; 1.30, 2.43). CONCLUSION These novel findings suggest that acute, high-level, and clinically impactful pesticide exposures may increase risk of shingles in subsequent years to decades following exposure.
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Affiliation(s)
- Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | | | | | | | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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3
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Varshavsky M, Harari G, Glaser B, Dor Y, Shemer R, Kaplan T. Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm. CELL REPORTS METHODS 2023; 3:100567. [PMID: 37751697 PMCID: PMC10545910 DOI: 10.1016/j.crmeth.2023.100567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/18/2023] [Accepted: 08/03/2023] [Indexed: 09/28/2023]
Abstract
Chronological age prediction from DNA methylation sheds light on human aging, health, and lifespan. Current clocks are mostly based on linear models and rely upon hundreds of sites across the genome. Here, we present GP-age, an epigenetic non-linear cohort-based clock for blood, based upon 11,910 methylomes. Using 30 CpG sites alone, GP-age outperforms state-of-the-art models, with a median accuracy of ∼2 years on held-out blood samples, for both array and sequencing-based data. We show that aging-related changes occur at multiple neighboring CpGs, with implications for using fragment-level analysis of sequencing data in aging research. By training three independent clocks, we show enrichment of donors with consistent deviation between predicted and actual age, suggesting individual rates of biological aging. Overall, we provide a compact yet accurate alternative to array-based clocks for blood, with applications in longitudinal aging research, forensic profiling, and monitoring epigenetic processes in transplantation medicine and cancer.
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Affiliation(s)
- Miri Varshavsky
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil Harari
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Roy R, Kuo PL, Candia J, Sarantopoulou D, Ubaida-Mohien C, Hernandez D, Kaileh M, Arepalli S, Singh A, Bektas A, Kim J, Moore AZ, Tanaka T, McKelvey J, Zukley L, Nguyen C, Wallace T, Dunn C, Wood W, Piao Y, Coletta C, De S, Sen J, Weng NP, Sen R, Ferrucci L. Epigenetic signature of human immune aging in the GESTALT study. eLife 2023; 12:e86136. [PMID: 37589453 PMCID: PMC10506794 DOI: 10.7554/elife.86136] [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: 01/12/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
Age-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood-borne immune cell types (naive B, naive CD4+ and CD8+ T cells, granulocytes, monocytes, and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousands of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor (TF) motifs, respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to TF motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.
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Affiliation(s)
- Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Pei-Lun Kuo
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julián Candia
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | | | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Arsun Bektas
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Jaekwan Kim
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ann Z Moore
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julia McKelvey
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Linda Zukley
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Cuong Nguyen
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Tonya Wallace
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - William Wood
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Christopher Coletta
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Jyoti Sen
- Laboratory of Clinical Investigation, National Institute on AgingBaltimoreUnited States
| | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
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Shen X, Gao X, Luo Y, Xu Q, Fan Y, Hong S, Huang Z, Liu X, Wang Q, Chen Z, Wang D, Lu L, Wu C, Liang H, Wang L. Cxxc finger protein 1 maintains homeostasis and function of intestinal group 3 innate lymphoid cells with aging. NATURE AGING 2023; 3:965-981. [PMID: 37429951 DOI: 10.1038/s43587-023-00453-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 06/09/2023] [Indexed: 07/12/2023]
Abstract
Aging is accompanied by homeostatic and functional dysregulation of multiple immune cell subsets. Group 3 innate lymphoid cells (ILC3s) constitute a heterogeneous cell population that plays pivotal roles in intestinal immunity. In this study, we found that ILC3s in aged mice exhibited dysregulated homeostasis and function, leading to bacterial and fungal infection susceptibility. Moreover, our data revealed that the enrichment of the H3K4me3 modification in effector genes of aged gut CCR6+ ILC3s was specifically decreased compared to young mice counterparts. Disruption of Cxxc finger protein 1 (Cxxc1) activity, a key subunit of H3K4 methyltransferase, in ILC3s led to similar aging-related phenotypes. An integrated analysis revealed Kruppel-like factor 4 (Klf4) as a potential Cxxc1 target. Klf4 overexpression partially restored the differentiation and functional defects seen in both aged and Cxxc1-deficient intestinal CCR6+ ILC3s. Therefore, these data suggest that targeting intestinal ILC3s may provide strategies to protect against age-related infections.
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Affiliation(s)
- Xin Shen
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Co-Facility Center, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xianzhi Gao
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, China
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Yikai Luo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Qianying Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Fan
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Shenghui Hong
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | | | - Xiaoqian Liu
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Qianqian Wang
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Di Wang
- Zhejiang University School of Medicine, Hangzhou, China
| | - Linrong Lu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, China.
- Laboratory Animal Center, Zhejiang University, Hangzhou, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China.
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6
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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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7
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Liu Q, Zheng Y, Goronzy JJ, Weyand CM. T cell aging as a risk factor for autoimmunity. J Autoimmun 2023; 137:102947. [PMID: 36357240 PMCID: PMC10164202 DOI: 10.1016/j.jaut.2022.102947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/09/2022]
Abstract
Immune aging is a complex process rendering the host susceptible to cancer, infection, and insufficient tissue repair. Many autoimmune diseases preferentially occur during the second half of life, counterintuitive to the concept of excess adaptive immunity driving immune-mediated tissue damage. T cells are particularly susceptible to aging-imposed changes, as they are under extreme proliferative pressure to fulfill the demands of clonal expansion and of homeostatic T cell repopulation. T cells in older adults have a footprint of genetic and epigenetic changes, lack mitochondrial fitness, and fail to maintain proteostasis, diverging them from host protection to host injury. Here, we review recent progress in understanding how the human T-cell system ages and the evidence detailing how T cell aging contributes to autoimmune conditions. T cell aging is now recognized as a risk determinant in two prototypic autoimmune syndromes; rheumatoid arthritis and giant cell arteritis. The emerging concept adds susceptibility to autoimmune and autoinflammatory disease to the spectrum of aging-imposed adaptations and opens new opportunities for immunomodulatory therapy by restoring the functional intactness of aging T cells.
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Affiliation(s)
- Qingxiang Liu
- Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Yanyan Zheng
- Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA; Department of Cardiovascular Medicine, Mayo Alix School of Medicine, Rochester, MN, USA
| | - Jorg J Goronzy
- Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94306, USA
| | - Cornelia M Weyand
- Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA; Department of Cardiovascular Medicine, Mayo Alix School of Medicine, Rochester, MN, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94306, USA.
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8
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Househam AM. Effects of stress and mindfulness on epigenetics. VITAMINS AND HORMONES 2023; 122:283-306. [PMID: 36863798 DOI: 10.1016/bs.vh.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Epigenetics are heritable changes in the rate of gene expression without any modification of the DNA sequence and occur in response to environmental changes. Tangible changes to the external surroundings may be practical causes for epigenetic modifications, playing a potential evolutionary role. While fight, flight, or freeze responses once served a concrete role in survival, modern humans may not face similar existential threats that warrant psychological stress. Yet, chronic mental stress is predominant in modern life. This chapter elucidates the deleterious epigenetic changes that occur due to chronic stress. In an exploration of mindfulness-based interventions (MBIs) as a potential antidote to such stress-induced epigenetic modifications, several pathways of action are uncovered. The epigenetic changes that occur because of mindfulness practice are demonstrated across the hypothalamic-pituitary-adrenal axis, serotonergic transmission, genomic health and aging, and neurological biomarkers.
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Affiliation(s)
- Ayman Mukerji Househam
- Department of Social Work, New York University, New York, NY, United States; Department of Psychology, New York University, New York, NY, United States.
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9
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Zhai J, Kongsberg WH, Pan Y, Hao C, Wang X, Sun J. Caloric restriction induced epigenetic effects on aging. Front Cell Dev Biol 2023; 10:1079920. [PMID: 36712965 PMCID: PMC9880295 DOI: 10.3389/fcell.2022.1079920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Aging is the subject of many studies, facilitating the discovery of many interventions. Epigenetic influences numerous life processes by regulating gene expression and also plays a crucial role in aging regulation. Increasing data suggests that dietary changes can alter epigenetic marks associated with aging. Caloric restriction (CR)is considered an intervention to regulate aging and prolong life span. At present, CR has made some progress by regulating signaling pathways associated with aging as well as the mechanism of action of intercellular signaling molecules against aging. In this review, we will focus on autophagy and epigenetic modifications to elaborate the molecular mechanisms by which CR delays aging by triggering autophagy, epigenetic modifications, and the interaction between the two in caloric restriction. In order to provide new ideas for the study of the mechanism of aging and delaying aging.
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Affiliation(s)
| | | | | | | | | | - Jie Sun
- *Correspondence: Xiaojing Wang, ; Jie Sun,
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10
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Liotti A, Ferrara AL, Loffredo S, Galdiero MR, Varricchi G, Di Rella F, Maniscalco GT, Belardo M, Vastano R, Prencipe R, Pignata L, Romano R, Spadaro G, de Candia P, Pezone A, De Rosa V. Epigenetics: an Opportunity to Shape Innate and Adaptive Immune Responses. Immunol Suppl 2022; 167:451-470. [PMID: 36043705 DOI: 10.1111/imm.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
Epigenetics connects genetic and environmental factors: it includes DNA methylation, histone post-translational modifications and the regulation of chromatin accessibility by non-coding RNAs, all of which control constitutive or inducible gene transcription. This plays a key role in harnessing the transcriptional programs of both innate and adaptive immune cells due to its plasticity and environmental-driven nature, piloting myeloid and lymphoid cell fate decision with no change in their genomic sequence. In particular, epigenetic marks at the site of lineage specific transcription factors and maintenance of cell type-specific epigenetic modifications, referred to as "epigenetic memory", dictate cell differentiation, cytokine production and functional capacity following repeated antigenic exposure in memory T cells. Moreover, metabolic and epigenetic reprogramming occurring during a primary innate immune response leads to enhanced responses to secondary challenges, a phenomenon known as "trained immunity". Here we discuss how stable and dynamic epigenetic states control immune cell identity and plasticity in physiological and pathological conditions. Dissecting the regulatory circuits of cell fate determination and maintenance is of paramount importance for understanding the delicate balance between immune cell activation and tolerance, in healthy conditions and in autoimmune diseases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Antonietta Liotti
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Anne Lise Ferrara
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Stefania Loffredo
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Maria Rosaria Galdiero
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Gilda Varricchi
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Francesca Di Rella
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Naples, Italy
| | - Giorgia Teresa Maniscalco
- Neurological Clinic and Stroke Unit and Multiple Sclerosis Center "A. Cardarelli" Hospital, Naples, Italy
| | - Martina Belardo
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Roberta Vastano
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Rosaria Prencipe
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Pediatric Section, University of Naples "Federico II", Naples, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Paola de Candia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Veronica De Rosa
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
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11
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Garnica M, Aiello A, Ligotti ME, Accardi G, Arasanz H, Bocanegra A, Blanco E, Calabrò A, Chocarro L, Echaide M, Kochan G, Fernandez-Rubio L, Ramos P, Pojero F, Zareian N, Piñeiro-Hermida S, Farzaneh F, Candore G, Caruso C, Escors D. How Can We Improve the Vaccination Response in Older People? Part II: Targeting Immunosenescence of Adaptive Immunity Cells. Int J Mol Sci 2022; 23:9797. [PMID: 36077216 PMCID: PMC9456031 DOI: 10.3390/ijms23179797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
The number of people that are 65 years old or older has been increasing due to the improvement in medicine and public health. However, this trend is not accompanied by an increase in quality of life, and this population is vulnerable to most illnesses, especially to infectious diseases. Vaccination is the best strategy to prevent this fact, but older people present a less efficient response, as their immune system is weaker due mainly to a phenomenon known as immunosenescence. The adaptive immune system is constituted by two types of lymphocytes, T and B cells, and the function and fitness of these cell populations are affected during ageing. Here, we review the impact of ageing on T and B cells and discuss the approaches that have been described or proposed to modulate and reverse the decline of the ageing adaptive immune system.
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Affiliation(s)
- Maider Garnica
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Anna Aiello
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Mattia Emanuela Ligotti
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Giulia Accardi
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Hugo Arasanz
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Ana Bocanegra
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Ester Blanco
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
- Division of Gene Therapy and Regulation of Gene Expression, Centro de Investigación Médica Aplicada (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Anna Calabrò
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Luisa Chocarro
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Miriam Echaide
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Grazyna Kochan
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Leticia Fernandez-Rubio
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Pablo Ramos
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Fanny Pojero
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Nahid Zareian
- The Rayne Institute, School of Cancer and Pharmaceutical Sciences, King’s College London, London WC2R 2LS, UK
| | - Sergio Piñeiro-Hermida
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Farzin Farzaneh
- The Rayne Institute, School of Cancer and Pharmaceutical Sciences, King’s College London, London WC2R 2LS, UK
| | - Giuseppina Candore
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Calogero Caruso
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - David Escors
- Oncoimmunology Group, Navarrabiomed, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
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12
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Czaja AJ. Epigenetic Aspects and Prospects in Autoimmune Hepatitis. Front Immunol 2022; 13:921765. [PMID: 35844554 PMCID: PMC9281562 DOI: 10.3389/fimmu.2022.921765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
The observed risk of autoimmune hepatitis exceeds its genetic risk, and epigenetic factors that alter gene expression without changing nucleotide sequence may help explain the disparity. Key objectives of this review are to describe the epigenetic modifications that affect gene expression, discuss how they can affect autoimmune hepatitis, and indicate prospects for improved management. Multiple hypo-methylated genes have been described in the CD4+ and CD19+ T lymphocytes of patients with autoimmune hepatitis, and the circulating micro-ribonucleic acids, miR-21 and miR-122, have correlated with laboratory and histological features of liver inflammation. Both epigenetic agents have also correlated inversely with the stage of liver fibrosis. The reduced hepatic concentration of miR-122 in cirrhosis suggests that its deficiency may de-repress the pro-fibrotic prolyl-4-hydroxylase subunit alpha-1 gene. Conversely, miR-155 is over-expressed in the liver tissue of patients with autoimmune hepatitis, and it may signify active immune-mediated liver injury. Different epigenetic findings have been described in diverse autoimmune and non-autoimmune liver diseases, and these changes may have disease-specificity. They may also be responses to environmental cues or heritable adaptations that distinguish the diseases. Advances in epigenetic editing and methods for blocking micro-ribonucleic acids have improved opportunities to prove causality and develop site-specific, therapeutic interventions. In conclusion, the role of epigenetics in affecting the risk, clinical phenotype, and outcome of autoimmune hepatitis is under-evaluated. Full definition of the epigenome of autoimmune hepatitis promises to enhance understanding of pathogenic mechanisms and satisfy the unmet clinical need to improve therapy for refractory disease.
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Affiliation(s)
- Albert J. Czaja
- *Correspondence: Albert J. Czaja, ; orcid.org/0000-0002-5024-3065
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13
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Luo OJ, Lei W, Zhu G, Ren Z, Xu Y, Xiao C, Zhang H, Cai J, Luo Z, Gao L, Su J, Tang L, Guo W, Su H, Zhang ZJ, Fang EF, Ruan Y, Leng SX, Ju Z, Lou H, Gao J, Peng N, Chen J, Bao Z, Liu F, Chen G. Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty. NATURE AGING 2022; 2:348-364. [PMID: 37117750 DOI: 10.1038/s43587-022-00198-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 02/25/2022] [Indexed: 12/15/2022]
Abstract
Frailty is an intermediate status of the human aging process, associated with decompensated homeostasis and death. The immune phenotype of frailty and its underlying cellular and molecular processes remain poorly understood. We profiled 114,467 immune cells from cord blood, young adults and healthy and frail old adults using single-cell RNA and TCR sequencing. Here we show an age-dependent accumulation of transcriptome heterogeneity and variability in immune cells. Characteristic transcription factors were identified in given cell types of specific age groups. Trajectory analysis revealed cells from non-frail and frail old adults often fall into distinct paths. Numerous TCR clonotypes were shared among T-cell subtypes in old adults, indicating differential pluripotency and resilience capabilities of aged T cells. A frailty-specific monocyte subset was identified with exclusively high expression of long noncoding RNAs NEAT1 and MALAT1. Our study discovers human frailty-specific immune cell characteristics based on the comprehensive dimensions in the immune landscape of aging and frailty.
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14
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Perdaens O, van Pesch V. Molecular Mechanisms of Immunosenescene and Inflammaging: Relevance to the Immunopathogenesis and Treatment of Multiple Sclerosis. Front Neurol 2022; 12:811518. [PMID: 35281989 PMCID: PMC8913495 DOI: 10.3389/fneur.2021.811518] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2021] [Indexed: 12/18/2022] Open
Abstract
Aging is characterized, amongst other features, by a complex process of cellular senescence involving both innate and adaptive immunity, called immunosenescence and associated to inflammaging, a low-grade chronic inflammation. Both processes fuel each other and partially explain increasing incidence of cancers, infections, age-related autoimmunity, and vascular disease as well as a reduced response to vaccination. Multiple sclerosis (MS) is a lifelong disease, for which considerable progress in disease-modifying therapies (DMTs) and management has improved long-term survival. However, disability progression, increasing with age and disease duration, remains. Neurologists are now involved in caring for elderly MS patients, with increasing comorbidities. Aging of the immune system therefore has relevant implications for MS pathogenesis, response to DMTs and the risks mediated by these treatments. We propose to review current evidence regarding markers and molecular mechanisms of immunosenescence and their relevance to understanding MS pathogenesis. We will focus on age-related changes in the innate and adaptive immune system in MS and other auto-immune diseases, such as systemic lupus erythematosus and rheumatoid arthritis. The consequences of these immune changes on MS pathology, in interaction with the intrinsic aging process of central nervous system resident cells will be discussed. Finally, the impact of immunosenescence on disease evolution and on the safety and efficacy of current DMTs will be presented.
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Affiliation(s)
- Océane Perdaens
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Vincent van Pesch
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- *Correspondence: Vincent van Pesch
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15
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Abstract
Two vasculitides, giant cell arteritis (GCA) and Takayasu arteritis (TAK), are recognized as autoimmune and autoinflammatory diseases that manifest exclusively within the aorta and its large branches. In both entities, the age of the affected host is a critical risk factor. TAK manifests during the 2nd-4th decade of life, occurring while the immune system is at its height of performance. GCA is a disease of older individuals, with infrequent cases during the 6th decade and peak incidence during the 8th decade of life. In both vasculitides, macrophages and T cells infiltrate into the adventitia and media of affected vessels, induce granulomatous inflammation, cause vessel wall destruction, and reprogram vascular cells to drive adventitial and neointimal expansion. In GCA, abnormal immunity originates in an aged immune system and evolves within the aged vascular microenvironment. One hallmark of the aging immune system is the preferential loss of CD8+ T cell function. Accordingly, in GCA but not in TAK, CD8+ effector T cells play a negligible role and anti-inflammatory CD8+ T regulatory cells are selectively impaired. Here, we review current evidence of how the process of immunosenescence impacts the risk for GCA and how fundamental differences in the age of the immune system translate into differences in the granulomatous immunopathology of TAK versus GCA.
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Immune Memory in Aging: a Wide Perspective Covering Microbiota, Brain, Metabolism, and Epigenetics. Clin Rev Allergy Immunol 2021; 63:499-529. [PMID: 34910283 PMCID: PMC8671603 DOI: 10.1007/s12016-021-08905-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 11/06/2022]
Abstract
Non-specific innate and antigen-specific adaptive immunological memories are vital evolutionary adaptations that confer long-lasting protection against a wide range of pathogens. Adaptive memory is established by memory T and B lymphocytes following the recognition of an antigen. On the other hand, innate immune memory, also called trained immunity, is imprinted in innate cells such as macrophages and natural killer cells through epigenetic and metabolic reprogramming. However, these mechanisms of memory generation and maintenance are compromised as organisms age. Almost all immune cell types, both mature cells and their progenitors, go through age-related changes concerning numbers and functions. The aging immune system renders the elderly highly susceptible to infections and incapable of mounting a proper immune response upon vaccinations. Besides the increased infectious burden, older individuals also have heightened risks of metabolic and neurodegenerative diseases, which have an immunological component. This review discusses how immune function, particularly the establishment and maintenance of innate and adaptive immunological memory, regulates and is regulated by epigenetics, metabolic processes, gut microbiota, and the central nervous system throughout life, with a focus on old age. We explain in-depth how epigenetics and cellular metabolism impact immune cell function and contribute or resist the aging process. Microbiota is intimately linked with the immune system of the human host, and therefore, plays an important role in immunological memory during both homeostasis and aging. The brain, which is not an immune-isolated organ despite former opinion, interacts with the peripheral immune cells, and the aging of both systems influences the health of each other. With all these in mind, we aimed to present a comprehensive view of the aging immune system and its consequences, especially in terms of immunological memory. The review also details the mechanisms of promising anti-aging interventions and highlights a few, namely, caloric restriction, physical exercise, metformin, and resveratrol, that impact multiple facets of the aging process, including the regulation of innate and adaptive immune memory. We propose that understanding aging as a complex phenomenon, with the immune system at the center role interacting with all the other tissues and systems, would allow for more effective anti-aging strategies.
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Zhang H, Weyand CM, Goronzy JJ. Hallmarks of the aging T-cell system. FEBS J 2021; 288:7123-7142. [PMID: 33590946 PMCID: PMC8364928 DOI: 10.1111/febs.15770] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
The adaptive immune system has the enormous challenge to protect the host through the generation and differentiation of pathogen-specific short-lived effector T cells while in parallel developing long-lived memory cells to control future encounters with the same pathogen. A complex regulatory network is needed to preserve a population of naïve cells over lifetime that exhibit sufficient diversity of antigen receptors to respond to new antigens, while also sustaining immune memory. In parallel, cells need to maintain their proliferative potential and the plasticity to differentiate into different functional lineages. Initial signs of waning immune competence emerge after 50 years of age, with increasing clinical relevance in the 7th-10th decade of life. Morbidity and mortality from infections increase, as drastically exemplified by the current COVID-19 pandemic. Many vaccines, such as for the influenza virus, are poorly effective to generate protective immunity in older individuals. Age-associated changes occur at the level of the T-cell population as well as the functionality of its cellular constituents. The system highly relies on the self-renewal of naïve and memory T cells, which is robust but eventually fails. Genetic and epigenetic modifications contribute to functional differences in responsiveness and differentiation potential. To some extent, these changes arise from defective maintenance; to some, they represent successful, but not universally beneficial adaptations to the aging host. Interventions that can compensate for the age-related defects and improve immune responses in older adults are increasingly within reach.
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Affiliation(s)
- Huimin Zhang
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
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18
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Do Transgenerational Epigenetic Inheritance and Immune System Development Share Common Epigenetic Processes? J Dev Biol 2021; 9:jdb9020020. [PMID: 34065783 PMCID: PMC8162332 DOI: 10.3390/jdb9020020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications regulate gene expression for development, immune response, disease, and other processes. A major role of epigenetics is to control the dynamics of chromatin structure, i.e., the condensed packaging of DNA around histone proteins in eukaryotic nuclei. Key epigenetic factors include enzymes for histone modifications and DNA methylation, non-coding RNAs, and prions. Epigenetic modifications are heritable but during embryonic development, most parental epigenetic marks are erased and reset. Interestingly, some epigenetic modifications, that may be resulting from immune response to stimuli, can escape remodeling and transmit to subsequent generations who are not exposed to those stimuli. This phenomenon is called transgenerational epigenetic inheritance if the epigenetic phenotype persists beyond the third generation in female germlines and second generation in male germlines. Although its primary function is likely immune response for survival, its role in the development and functioning of the immune system is not extensively explored, despite studies reporting transgenerational inheritance of stress-induced epigenetic modifications resulting in immune disorders. Hence, this review draws from studies on transgenerational epigenetic inheritance, immune system development and function, high-throughput epigenetics tools to study those phenomena, and relevant clinical trials, to focus on their significance and deeper understanding for future research, therapeutic developments, and various applications.
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Gougourelas D, Tsentidis C, Koufadaki AM, Koutsovasilis A, Gougourela E, Karanasios S, Sotiropoulos A, Bousboulas S, Karavanaki KA. Associated autoimmunity in Type 1 Diabetes and latent autoimmune diabetes of adults: The role of glutamic-acid decarboxylase autoantibodies. Diabetes Res Clin Pract 2021; 175:108847. [PMID: 33945840 DOI: 10.1016/j.diabres.2021.108847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022]
Abstract
AIMS To determine the prevalence of Associated Autoimmune Diseases (AADs) in Latent Autoimmune Diabetes of Adults (LADA) versus autoimmune Type 1 Diabetes (T1D) and the role of glutamic-acid decarboxylase antibodies (GADA) and other factors. METHODS Adults with autoimmune diabetes mellitus (DM) were recruited from the Diabetes Center of Nikaia-Piraeus Hospital. Demographic and clinical parameters were recorded and anti-pancreatic and organ-specific antibodies were measured. RESULTS Of 160 patients, 33.75% had one AAD and 24.37% had two or more. Patients with LADA had higher overall prevalence of AADs, mainly autoimmune thyroiditis and gastritis. Celiac disease was present only in T1D. GADA positive patients had higher prevalence of AADs and multiple autoimmunity, especially thyroiditis and gastritis. Patients with LADA had higher rates of positive GADA or islet-cell antibodies (ICA). After controlling for LADA, GADA remained a significant predictor of AADs. Female gender and chronological age were also significant predictors of AADs. CONCLUSIONS AADs were present in 58.13% of patients. Patients with LADA were more prone to a generalized autoimmune disorder than those with T1D. AADs development was significantly associated with female sex, older age and positive GADA, which proved an independent marker of associated autoimmunity.
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Affiliation(s)
- Dimitrios Gougourelas
- Diabetes Center, General Hospital of Nikaia - Piraeus "Agios Panteleimon", Athens, Greece.
| | - Charalampos Tsentidis
- Department of Endocrinology, Metabolism & Diabetes Mellitus, General Hospital of Nikaia - Piraeus "Agios Panteleimon", Athens, Greece
| | - Athina Maria Koufadaki
- Diabetes and Metabolism Clinic, 2(nd) Department of Pediatrics, National and Kapodistrian University of Athens, "P&A Kyriakou" Children's Hospital, Athens, Greece
| | | | - Eupraxia Gougourela
- Diabetes Center, General Hospital of Nikaia - Piraeus "Agios Panteleimon", Athens, Greece
| | - Spyridon Karanasios
- Diabetes and Metabolism Clinic, 2(nd) Department of Pediatrics, National and Kapodistrian University of Athens, "P&A Kyriakou" Children's Hospital, Athens, Greece
| | - Alexios Sotiropoulos
- Diabetes Center, General Hospital of Nikaia - Piraeus "Agios Panteleimon", Athens, Greece
| | - Stavros Bousboulas
- Diabetes Center, General Hospital of Nikaia - Piraeus "Agios Panteleimon", Athens, Greece
| | - Kyriaki Athina Karavanaki
- Diabetes and Metabolism Clinic, 2(nd) Department of Pediatrics, National and Kapodistrian University of Athens, "P&A Kyriakou" Children's Hospital, Athens, Greece
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20
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Saul D, Kosinsky RL. Epigenetics of Aging and Aging-Associated Diseases. Int J Mol Sci 2021; 22:ijms22010401. [PMID: 33401659 PMCID: PMC7794926 DOI: 10.3390/ijms22010401] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Aging represents the multifactorial decline in physiological function of every living organism. Over the past decades, several hallmarks of aging have been defined, including epigenetic deregulation. Indeed, multiple epigenetic events were found altered across different species during aging. Epigenetic changes directly contributing to aging and aging-related diseases include the accumulation of histone variants, changes in chromatin accessibility, loss of histones and heterochromatin, aberrant histone modifications, and deregulated expression/activity of miRNAs. As a consequence, cellular processes are affected, which results in the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, and neurodegenerative disorders. In this review, we focus on epigenetic mechanisms underlying aging-related processes in various species and describe how these deregulations contribute to human diseases.
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Affiliation(s)
- Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-293-2386
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21
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Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features, immune infiltrates, and response prediction to immunotherapy in melanoma. EBioMedicine 2020; 52:102647. [PMID: 32028068 PMCID: PMC6997575 DOI: 10.1016/j.ebiom.2020.102647] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunotherapy, including checkpoint inhibition, has remarkably improved prognosis in advanced melanoma. Despite this success, acquired resistance is still a major challenge. The T cell costimulatory receptor TNFRSF9 (also known as 4-1BB and CD137) is a promising new target for immunotherapy and two agonistic antibodies are currently tested in clinical trials. However, little is known about epigenetic regulation of the encoding gene. In this study we investigate a possible correlation of TNFRSF9 DNA methylation with gene expression, clinicopathological parameters, molecular and immune correlates, and response to anti-PD-1 immunotherapy to assess the validity of TNFRSF9 methylation to serve as a biomarker. METHODS We performed a correlation analyses of methylation at twelve CpG sites within TNFRSF9 with regard to transcriptional activity, immune cell infiltration, mutation status, and survival in a cohort of N = 470 melanoma patients obtained from The Cancer Genome Atlas. Furthermore, we used quantitative methylation-specific PCR to confirm correlations in a cohort of N = 115 melanoma patients' samples (UHB validation cohort). Finally, we tested the ability of TNFRSF9 methylation and expression to predict progression-free survival (PFS) and response to anti-PD-1 immunotherapy in a cohort comprised of N = 121 patients (mRNA transcription), (mRNA ICB cohort) and a case-control study including N = 48 patients (DNA methylation, UHB ICB cohort). FINDINGS We found a significant inverse correlation between TNFRSF9 DNA methylation and mRNA expression levels at six of twelve analyzed CpG sites (P ≤ 0.005), predominately located in the promoter flank region. Consistent with its role as costimulatory receptor in immune cells, TNFRSF9 mRNA expression and hypomethylation positively correlated with immune cell infiltrates and an interferon-γ signature. Furthermore, elevated TNFRSF9 mRNA expression and TNFRSF9 hypomethylation correlated with superior overall survival. In patients receiving anti-PD-1 immunotherapy (mRNA ICB cohort), we found that TNFRSF9 hypermethylation and reduced mRNA expression correlated with poor PFS and response. INTERPRETATION Our study suggests that TNFRSF9 mRNA expression is regulated via DNA methylation. The observed correlations between TNFRSF9 DNA methylation or mRNA expression with known features of response to immune checkpoint blockage suggest TNFRSF9 methylation could serve as a biomarker in the context of immunotherapies. Concordantly, we identified a correlation between TNFRSF9 DNA methylation and mRNA expression with disease progression in patients under immunotherapy. Our study provides rationale for further investigating TNFRSF9 DNA methylation as a predictive biomarker for response to immunotherapy. FUNDING AF was partly funded by the Mildred Scheel Foundation. SF received funding from the University Hospital Bonn BONFOR program (O-105.0069). DN was funded in part by DFG Cluster of Excellence ImmunoSensation (EXC 1023). The funders had no role in study design, data collection and analysis, interpretation, decision to publish, or preparation of the manuscript; or any aspect pertinent to the study.
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Czaja AJ. Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions. World J Gastroenterol 2019; 25:6579-6606. [PMID: 31832000 PMCID: PMC6906207 DOI: 10.3748/wjg.v25.i45.6579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
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Abstract
PURPOSE OF REVIEW Epigenetics has been implicated in the pathogenesis of systemic sclerosis (SSc). In this review, the involvement of the three epigenetic mechanisms in SSc development and progression-DNA methylation, histone modifications, and non-coding RNAs-will be discussed. RECENT FINDINGS Alteration in epigenetics was observed in immune cells, dermal fibroblasts, and endothelial cells derived from SSc patients. Genes that are affected include those involved in immune cell function and differentiation, TGFβ and Wnt pathways, extracellular matrix accumulation, transcription factors, and angiogenesis. All the studies remain in the pre-clinical stage. Extensive research provides evidence that epigenetic alterations are critical for SSc pathogenesis. Future epigenomic studies will undoubtedly continue to broaden our understanding of disease pathogenesis and clinical heterogeneity. They will also provide the scientific basis for repurposing epigenetic-modifying agents for SSc patients.
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Affiliation(s)
- Pei-Suen Tsou
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, 109 Zina Pitcher Pl., 4025 BSRB, Ann Arbor, MI, 48109-2200, USA.
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Cao H, Li D, Lu H, Sun J, Li H. Uncovering potential lncRNAs and nearby mRNAs in systemic lupus erythematosus from the Gene Expression Omnibus dataset. Epigenomics 2019; 11:1795-1809. [PMID: 31755746 DOI: 10.2217/epi-2019-0145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: The aim of this study was to find potential differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in systemic lupus erythematosus. Materials & methods: Differentially expressed lncRNAs and mRNAs were obtained in the Gene Expression Omnibus dataset. Functional annotation of differentially expressed mRNAs was performed, followed by protein-protein interaction network analysis. Then, the interaction network of lncRNA-nearby targeted mRNA was built. Results: Several interaction pairs of lncRNA-nearby targeted mRNA including NRIR-RSAD2, RP11-153M7.5-TLR2, RP4-758J18.2-CCNL2, RP11-69E11.4-PABPC4 and RP11-496I9.1-IRF7/HRAS/PHRF1 were identified. Measles and MAPK were significantly enriched signaling pathways of differentially expressed mRNAs. Conclusion: Our study identified several differentially expressed lncRNAs and mRNAs. And their interactions may play a crucial role in the process of systemic lupus erythematosus.
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Affiliation(s)
- Haiyu Cao
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Dong Li
- Department of Dermatology & Sexology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei 430030, PR China
| | - Huixiu Lu
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Jing Sun
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Haibin Li
- Department of Medicine, The Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, PR China
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
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Crooke SN, Ovsyannikova IG, Poland GA, Kennedy RB. Immunosenescence: A systems-level overview of immune cell biology and strategies for improving vaccine responses. Exp Gerontol 2019; 124:110632. [PMID: 31201918 DOI: 10.1016/j.exger.2019.110632] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/30/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Immunosenescence contributes to a decreased capacity of the immune system to respond effectively to infections or vaccines in the elderly. The full extent of the biological changes that lead to immunosenescence are unknown, but numerous cell types involved in innate and adaptive immunity exhibit altered phenotypes and function as a result of aging. These manifestations of immunosenescence at the cellular level are mediated by dysregulation at the genetic level, and changes throughout the immune system are, in turn, propagated by numerous cellular interactions. Environmental factors, such as nutrition, also exert significant influence on the immune system during aging. While the mechanisms that govern the onset of immunosenescence are complex, systems biology approaches allow for the identification of individual contributions from each component within the system as a whole. Although there is still much to learn regarding immunosenescence, systems-level studies of vaccine responses have been highly informative and will guide the development of new vaccine candidates, novel adjuvant formulations, and immunotherapeutic drugs to improve vaccine responses among the aging population.
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Affiliation(s)
- Stephen N Crooke
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA.
| | | | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA.
| | - Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA.
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
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Aljadeff G, Longhi E, Shoenfeld Y. Bisphenol A: A notorious player in the mosaic of autoimmunity. Autoimmunity 2018; 51:370-377. [DOI: 10.1080/08916934.2018.1551374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gali Aljadeff
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
| | - Eleonora Longhi
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- University of Bologna School of Medicine, Bologna, Italy
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Tost J, Gay S, Firestein G. Epigenetics of the immune system and alterations in inflammation and autoimmunity. Epigenomics 2018; 9:371-373. [PMID: 28378617 DOI: 10.2217/epi-2017-0026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jorg Tost
- Laboratory for Epigenetics & Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich, Switzerland
| | - Gary Firestein
- Division of Rheumatology, Allergy & Immunology, University of California, San Diego School of Medicine, La Jolla, CA, USA
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Belot MP, Castell AL, Le Fur S, Bougnères P. Dynamic demethylation of the IL2RA promoter during in vitro CD4+ T cell activation in association with IL2RA expression. Epigenetics 2018; 13:459-472. [PMID: 30096258 DOI: 10.1080/15592294.2018.1469893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
IL2RA, a subunit of the high affinity receptor for interleukin-2 (IL2), plays a crucial role in immune homeostasis. Notably, IL2RA expression is induced in CD4+ T cells in response to various stimuli and is constitutive in regulatory T cells (Tregs). We selected for our study 18 CpGs located within cognate regulatory regions of the IL2RA locus and characterized their methylation in naive, regulatory, and memory CD4+ T cells. We found that 5/18 CpGs (notably CpG + 3502) show dynamic, active demethylation during the in vitro activation of naive CD4+ T cells. Demethylation of these CpGs correlates with appearance of IL2RA protein at the cell surface. We found no influence of cis located SNP alleles upon CpG methylation. Treg cells show constitutive demethylation at all studied CpGs. Methylation of 9/18 CpGs, including CpG +3502, decreases with age. Our data thus identify CpG +3502 and a few other CpGs at the IL2RA locus as coordinated epigenetic regulators of IL2RA expression in CD4+ T cells. This may contribute to unravel how the IL2RA locus can be involved in immune physiology and pathology.
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Affiliation(s)
- Marie-Pierre Belot
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France.,b Fondation de l'AP-HP pour la Recherche , Paris , France
| | - Anne-Laure Castell
- c Service de Médecine des Adolescents , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
| | - Sophie Le Fur
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
| | - Pierre Bougnères
- a Institut National de la Santé et de la Recherche Médicale UMR1169 , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France.,c Service de Médecine des Adolescents , Paris Sud University, Bicêtre Hospital , Le Kremlin-Bicêtre , France
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Czaja AJ. Under-Evaluated or Unassessed Pathogenic Pathways in Autoimmune Hepatitis and Implications for Future Management. Dig Dis Sci 2018; 63:1706-1725. [PMID: 29671161 DOI: 10.1007/s10620-018-5072-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/12/2018] [Indexed: 12/11/2022]
Abstract
Autoimmune hepatitis is a consequence of perturbations in homeostatic mechanisms that maintain self-tolerance but are incompletely understood. The goals of this review are to describe key pathogenic pathways that have been under-evaluated or unassessed in autoimmune hepatitis, describe insights that may shape future therapies, and encourage investigational efforts. The T cell immunoglobulin mucin proteins constitute a family that modulates immune tolerance by limiting the survival of immune effector cells, clearing apoptotic bodies, and expanding the population of granulocytic myeloid-derived suppressor cells. Galectins influence immune cell migration, activation, proliferation, and survival, and T cell exhaustion can be induced and exploited as a possible management strategy. The programmed cell death-1 protein and its ligands comprise an antigen-independent inhibitory axis that can limit the performance of activated T cells by altering their metabolism, and epigenetic changes can silence pro-inflammatory genes or de-repress anti-inflammatory genes that affect disease severity. Changes in the intestinal microbiota and permeability of the intestinal mucosal barrier can be causative or consequential events that affect the occurrence and phenotype of immune-mediated disease, and they may help explain the female propensity for autoimmune hepatitis. Perturbations within these homeostatic mechanisms have been implicated in experimental models and limited clinical experiences, and they have been favorably manipulated by monoclonal antibodies, recombinant molecules, pharmacological agents or dietary supplements. In conclusion, pathogenic mechanisms that have been implicated in other systemic immune-mediated and liver diseases but under-evaluated or unassessed in autoimmune hepatitis warrant consideration and rigorous evaluation.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street S.W., Rochester, MN, 55905, USA.
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Abstract
PURPOSE OF REVIEW The purpose of this review is to discuss recent observations of epigenetic changes related to the complex pathogenesis of systemic vasculitides and their contribution to the field. RECENT FINDINGS There have been new observations of epigenetic changes in vasculitis and their potential role in disease pathogenesis in antineutrophil cytoplasmic antibody-associated vasculitis, giant-cell arteritis, Kawasaki disease, Behçet's disease, and IgA vasculitis. Some of this recent work has focused on the efficacy of using DNA methylation and miRNA expression as clinical biomarkers for disease activity and how DNA methylation and histone modifications interact to regulate disease-related gene expression. SUMMARY DNA methylation, histone modification, and miRNA expression changes are all fruitful ground for biomarker discovery and therapeutic targets in vasculitis. Current knowledge has provided targeted and suggested effects, but in many cases, has relied upon small cohorts, cosmopolitan cell populations, and limited knowledge of functional interactions. Expanding our knowledge of how these epigenetic mechanisms interact in a disease-specific and cell-specific manner will help to better understand the pathogenesis of systemic vasculitis.
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Vogt TJ, Gevensleben H, Dietrich J, Kristiansen G, Bootz F, Landsberg J, Goltz D, Dietrich D. Detailed analysis of adenosine A2a receptor ( ADORA2A) and CD73 (5'-nucleotidase, ecto, NT5E) methylation and gene expression in head and neck squamous cell carcinoma patients. Oncoimmunology 2018; 7:e1452579. [PMID: 30221045 PMCID: PMC6136855 DOI: 10.1080/2162402x.2018.1452579] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/15/2022] Open
Abstract
Background: The adenosine A2a receptor (A2aR) and the adenosine synthesizing enzyme CD73 have recently evolved as a novel immunotherapeutic target. However, little is known about epigenetic modification of the encoding genes ADORA2A and NT5E. Methods: In the present study, we evaluated methylation at 23 loci of ADORA2A and 17 loci of NT5E with regard to transcriptional activity, human papilloma virus (HPV) status, immune cell infiltration, and outcome in a cohort of 279 head and neck squamous carcinoma (HNSCC) patients obtained from The Cancer Genome Atlas (TCGA). Methylation and mRNA expression were generated by the Infinium HumanMethylation450 BeadChip and Illumina HiSeq 2000 RNA Sequencing Version 2 analysis (Illumina, Inc., San Diego, CA, USA). HPV status was assessed by RNA-Seq data analysis of the viral genes E6 and E7. Results: Thirteen out of 23 ADORA2A loci and 15/17 NT5E loci were significantly correlated with mRNA levels (p < 0.05). Inverse correlations were predominately found in promoter regions, while positive correlations were more profound at intragenic loci. ADORA2A hypermethylation was significantly associated with poor overall survival (OS, p ≤ 0.030), whereas NT5E hypomethylation was associated with decreased OS in HPV-positive tumors (p ≤ 0.024) and increased OS in HPV-negative HNSCC (p ≤ 0.029). Further, we found significant correlations between methylation and immune cell infiltrates. Conclusion: Our data might point towards a significant role of the A2aR/CD73 axis during cancer progression in HNSCC.
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Affiliation(s)
- Timo J. Vogt
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Jörn Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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Ray D, Yung R. Immune senescence, epigenetics and autoimmunity. Clin Immunol 2018; 196:59-63. [PMID: 29654845 DOI: 10.1016/j.clim.2018.04.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]
Abstract
Aging of the immune system in humans and animals is characterized by a decline in both adaptive and innate immune responses. Paradoxically, aging is also associated with a state of chronic inflammation ("inflammaging") and an increased likelihood of developing autoimmune diseases. Epigenetic changes in non-dividing and dividing cells, including immune cells, due to environmental factors contribute to the inflammation and autoimmunity that characterize both the state and diseases of aging. Here, we review the epigenetic mechanisms involved in the development of immune senescence and autoimmunity in old age.
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Affiliation(s)
- Donna Ray
- Division of Rheumatology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Raymond Yung
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
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Czaja AJ. Epigenetic changes and their implications in autoimmune hepatitis. Eur J Clin Invest 2018; 48. [PMID: 29383703 DOI: 10.1111/eci.12899] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/25/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The genetic risk of autoimmune hepatitis is insufficient to explain the observed risk, and epigenetic changes may explain disparities in disease occurrence in different populations within and between countries. The goal of this review was to examine how epigenetic changes induced by the environment or inherited as a phenotypic trait may affect autoimmune hepatitis and be amenable to therapeutic intervention. MATERIALS AND METHODS Pertinent abstracts were identified in PubMed by multiple search terms. The number of abstracts reviewed was 1689, and the number of full-length articles reviewed exceeded 150. RESULTS Activation of pro-inflammatory genes in autoimmune disease is associated with hypomethylation of deoxyribonucleic acid and modification of histones within chromatin. Organ-specific microribonucleic acids can silence genes by marking messenger ribonucleic acids for degradation, and they can promote inflammatory activity or immunosuppression. High circulating levels of the microribonucleic acids 21 and 122 have been demonstrated in autoimmune hepatitis, and they may increase production of pro-inflammatory cytokines. Microribonucleic acids are also essential for maintaining regulatory T cells. Drugs, pollutants, infections, diet and ageing can induce inheritable epigenetic changes favouring autoimmunity. Reversal is feasible by manipulating enzymes, transcription factors, gene-silencing molecules and toxic exposures or by administering methyl donors and correcting vitamin D deficiency. Gene targets, site specificity, efficacy and consequences are uncertain. CONCLUSIONS Potentially reversible epigenetic changes may affect the occurrence and outcome of autoimmune hepatitis, and investigations are warranted to determine the nature of these changes, key genomic targets, and feasible interventions and their consequences.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
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Jasiulionis MG. Abnormal Epigenetic Regulation of Immune System during Aging. Front Immunol 2018; 9:197. [PMID: 29483913 PMCID: PMC5816044 DOI: 10.3389/fimmu.2018.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to the study of mechanisms controlling the chromatin structure, which has fundamental role in the regulation of gene expression and genome stability. Epigenetic marks, such as DNA methylation and histone modifications, are established during embryonic development and epigenetic profiles are stably inherited during mitosis, ensuring cell differentiation and fate. Under the effect of intrinsic and extrinsic factors, such as metabolic profile, hormones, nutrition, drugs, smoke, and stress, epigenetic marks are actively modulated. In this sense, the lifestyle may affect significantly the epigenome, and as a result, the gene expression profile and cell function. Epigenetic alterations are a hallmark of aging and diseases, such as cancer. Among biological systems compromised with aging is the decline of immune response. Different regulators of immune response have their promoters and enhancers susceptible to the modulation by epigenetic marks, which is fundamental to the differentiation and function of immune cells. Consistent evidence has showed the regulation of innate immune cells, and T and B lymphocytes by epigenetic mechanisms. Therefore, age-dependent alterations in epigenetic marks may result in the decline of immune function and this might contribute to the increased incidence of diseases in old people. In order to maintain health, we need to better understand how to avoid epigenetic alterations related to immune aging. In this review, the contribution of epigenetic mechanisms to the loss of immune function during aging will be discussed, and the promise of new means of disease prevention and management will be pointed.
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Affiliation(s)
- Miriam G Jasiulionis
- Laboratory of Ontogeny and Epigenetics, Pharmacology Department, Universidade Federal de São Paulo, São Paulo, Brazil
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Czaja AJ. Review article: next-generation transformative advances in the pathogenesis and management of autoimmune hepatitis. Aliment Pharmacol Ther 2017; 46:920-937. [PMID: 28901565 DOI: 10.1111/apt.14324] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/01/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Advances in autoimmune hepatitis that transform current concepts of pathogenesis and management can be anticipated as products of ongoing investigations driven by unmet clinical needs and an evolving biotechnology. AIM To describe the advances that are likely to become transformative in autoimmune hepatitis, based on the direction of current investigations. METHODS Pertinent abstracts were identified in PubMed by multiple search terms. Full-length articles were selected for review, and a secondary bibliography was developed. The discovery process was repeated, and a tertiary bibliography was identified. The number of abstracts reviewed was 2830, and the number of full-length articles reviewed exceeded 150. RESULTS Risk-laden allelic variants outside the major histocompatibility complex (rs3184504, r36000782) are being identified by genome-wide association studies, and their gene products are potential therapeutic targets. Epigenetic changes associated with environmental cues can enhance the transcriptional activity of genes, and chromatin re-structuring and antagonists of noncoding molecules of ribonucleic acid are feasible interventions. The intestinal microbiome is a discovery field for microbial products and activated immune cells that may translocate to the periphery and respond to manipulation. Epidemiological studies and controlled interview-based surveys may implicate environmental and xenobiotic factors that warrant evidence-based changes in lifestyle, and site-directed molecular and cellular interventions promise to change the paradigm of treatment from one of blanket immunosuppression. CONCLUSIONS Advances in genetics, epigenetics, pathophysiology, epidemiology, and site-directed molecular and cellular interventions constitute the next generation of transformative advances in autoimmune hepatitis.
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Affiliation(s)
- A J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
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Bhat J, Helmuth J, Chitadze G, Kouakanou L, Peters C, Vingron M, Ammerpohl O, Kabelitz D. Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity. Scand J Immunol 2017; 86:184-195. [PMID: 28799233 DOI: 10.1111/sji.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/06/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic marks including histone modifications and DNA methylation are associated with the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning. Thus, it provides information on two levels of epigenetic regulation. Development and differentiation of T cells into functional subset cells including memory T cells are dynamic processes driven by environmental signals. Here, we briefly review the current knowledge of how epigenetic regulation contributes to subset specification, differentiation and memory development in T cells. Specifically, we focus on epigenetic mechanisms differentially active in the two distinct T cell populations expressing αβ or γδ T cell receptors. We also discuss examples of epigenetic alterations of T cells in autoimmune diseases. DNA methylation and histone acetylation are subject to modification by several classes of 'epigenetic modifiers', some of which are in clinical use or in preclinical development. Therefore, we address the impact of some epigenetic modifiers on T-cell activation and differentiation, and discuss possible synergies with T cell-based immunotherapeutic strategies.
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Affiliation(s)
- J Bhat
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - J Helmuth
- Otto-Warburg-Laboratories: Epigenomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - G Chitadze
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - L Kouakanou
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - C Peters
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - O Ammerpohl
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - D Kabelitz
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
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