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Lundin JI, Peters U, Hu Y, Ammous F, Avery CL, Benjamin EJ, Bis JC, Brody JA, Carlson C, Cushman M, Gignoux C, Guo X, Haessler J, Haiman C, Joehanes R, Kasela S, Kenny E, Lapalainien T, Levy D, Liu C, Liu Y, Loos RJ, Lu A, Matise T, North KE, Park SL, Ratliff SM, Reiner A, Rich SS, Rotter JI, Smith JA, Sotoodehnia N, Tracy R, Van den Berg D, Xu H, Ye T, Zhao W, Raffield LM, Kooperberg C. Methylation patterns associated with C-reactive protein in racially and ethnically diverse populations. Epigenetics 2024; 19:2333668. [PMID: 38571307 PMCID: PMC10996836 DOI: 10.1080/15592294.2024.2333668] [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: 11/30/2023] [Accepted: 03/17/2024] [Indexed: 04/05/2024] Open
Abstract
Systemic low-grade inflammation is a feature of chronic disease. C-reactive protein (CRP) is a common biomarker of inflammation and used as an indicator of disease risk; however, the role of inflammation in disease is not completely understood. Methylation is an epigenetic modification in the DNA which plays a pivotal role in gene expression. In this study we evaluated differential DNA methylation patterns associated with blood CRP level to elucidate biological pathways and genetic regulatory mechanisms to improve the understanding of chronic inflammation. The racially and ethnically diverse participants in this study were included as 50% White, 41% Black or African American, 7% Hispanic or Latino/a, and 2% Native Hawaiian, Asian American, American Indian, or Alaska Native (total n = 13,433) individuals. We replicated 113 CpG sites from 87 unique loci, of which five were novel (CADM3, NALCN, NLRC5, ZNF792, and cg03282312), across a discovery set of 1,150 CpG sites associated with CRP level (p < 1.2E-7). The downstream pathways affected by DNA methylation included the identification of IFI16 and IRF7 CpG-gene transcript pairs which contributed to the innate immune response gene enrichment pathway along with NLRC5, NOD2, and AIM2. Gene enrichment analysis also identified the nuclear factor-kappaB transcription pathway. Using two-sample Mendelian randomization (MR) we inferred methylation at three CpG sites as causal for CRP levels using both White and Black or African American MR instrument variables. Overall, we identified novel CpG sites and gene transcripts that could be valuable in understanding the specific cellular processes and pathogenic mechanisms involved in inflammation.
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Affiliation(s)
- Jessica I. Lundin
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yao Hu
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Christy L. Avery
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Emelia J. Benjamin
- Boston Medical Center, Boston University Chobanian and Avedisian School of Medicine, Boston University School of Public Health, Boston, MA, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT, USA
| | - Chris Gignoux
- Interdisciplinary Quantitative Biology, University of Colorado, Boulder, CO, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Chris Haiman
- Department of Environmental Medicine and Public Health, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD, USA
| | | | - Eimear Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yongmei Liu
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Ruth J.F. Loos
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ake Lu
- Department of Human Genetics, University of California LA, Los Angeles, CA, USA
| | - Tara Matise
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Kari E. North
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Sungshim L. Park
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, and Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Harborview Medical Center, Seattle, WA, USA
| | - Russell Tracy
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - David Van den Berg
- Department of Environmental Medicine and Public Health, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ting Ye
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - On Behalf of the PAGE Study
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Boston Medical Center, Boston University Chobanian and Avedisian School of Medicine, Boston University School of Public Health, Boston, MA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT, USA
- Interdisciplinary Quantitative Biology, University of Colorado, Boulder, CO, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Environmental Medicine and Public Health, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD, USA
- New York Genome Center, New York, NY
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Department of Human Genetics, University of California LA, Los Angeles, CA, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Epidemiology, School of Public Health, and Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Cardiovascular Health Research Unit, Harborview Medical Center, Seattle, WA, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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2
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Alsegehy S, Southey BR, Hernandez AG, Rund LA, Antonson AM, Nowak RA, Johnson RW, Rodriguez-Zas SL. Epigenetic disruptions in the offspring hypothalamus in response to maternal infection. Gene 2024; 910:148329. [PMID: 38431234 DOI: 10.1016/j.gene.2024.148329] [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: 01/11/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
DNA methylation is an epigenetic modification that can alter gene expression, and the incidence can vary across developmental stages, inflammatory conditions, and sexes. The effects of viral maternal viral infection and sex on the DNA methylation patterns were studied in the hypothalamus of a pig model of immune activation during development. DNA methylation at single-base resolution in regions of high CpG density was measured on 24 individual hypothalamus samples using reduced representation bisulfite sequencing. Differential over- and under-methylated sites were identified and annotated to proximal genes and corresponding biological processes. A total of 120 sites were differentially methylated (FDR-adjusted p-value < 0.05) between maternal infection or sex groups. Among the 66 sites differentially methylated between groups exposed to inflammatory signals and control, most sites were over-methylated in the challenged group and included sites in the promoter regions of genes SIRT3 and NRBP1. Among the 54 differentially methylated sites between females and males, most sites were over-methylated in females and included sites in the promoter region of genes TNC and EIF4G1. The analysis of the genes proximal to the differentially methylated sites suggested that biological processes potentially impacted include immune response, neuron migration and ensheathment, peptide signaling, adaptive thermogenesis, and tissue development. These results suggest that translational studies should consider that the prolonged effect of maternal infection during gestation may be enacted through epigenetic regulatory mechanisms that may differ between sexes.
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Affiliation(s)
- Samah Alsegehy
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauretta A Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adrienne M Antonson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rodney W Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sandra L Rodriguez-Zas
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
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3
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Chen J, Hui Q, Titanji BK, So-Armah K, Freiberg M, Justice AC, Xu K, Zhu X, Gwinn M, Marconi VC, Sun YV. A multi-trait epigenome-wide association study identified DNA methylation signature of inflammation among people with HIV. RESEARCH SQUARE 2024:rs.3.rs-4419840. [PMID: 38854093 PMCID: PMC11160930 DOI: 10.21203/rs.3.rs-4419840/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inflammation underlies many conditions causing excess morbidity and mortality among people with HIV (PWH). A handful of single-trait epigenome-wide association studies (EWAS) have suggested that inflammation is associated with DNA methylation (DNAm) among PWH. Multi-trait EWAS may further improve statistical power and reveal pathways in common between different inflammatory markers. We conducted single-trait EWAS of three inflammatory markers (soluble CD14, D-dimers, and interleukin 6) in the Veteran Aging Cohort Study (n = 920). The study population was all male PWH with an average age of 51 years, and 82.3% self-reported as Black. We then applied two multi-trait EWAS methods-CPASSOC and OmniTest-to combine single-trait EWAS results. CPASSOC and OmniTest identified 189 and 157 inflammation-associated DNAm sites respectively, of which 112 overlapped. Among the identified sites, 56% were not significant in any single-trait EWAS. Top sites were mapped to inflammation-related genes including IFITM1, PARP9 and STAT1. These genes were significantly enriched in pathways such as "type I interferon signaling" and "immune response to virus". We demonstrate that multi-trait EWAS can improve the discovery of inflammation-associated DNAm sites, genes, and pathways. These DNAm sites suggest molecular mechanisms in response to inflammation associated with HIV and might hold the key to addressing persistent inflammation in PWH.
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Affiliation(s)
| | | | | | - Kaku So-Armah
- Boston University Chobanian and Avedisian School of Medicine
| | - Matthew Freiberg
- Vanderbilt University School of Medicine and Tennessee Valley Healthcare System
| | | | - Ke Xu
- Connecticut Veteran Health System
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4
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Hillary RF, Ng HK, McCartney DL, Elliott HR, Walker RM, Campbell A, Huang F, Direk K, Welsh P, Sattar N, Corley J, Hayward C, McIntosh AM, Sudlow C, Evans KL, Cox SR, Chambers JC, Loh M, Relton CL, Marioni RE, Yousefi PD, Suderman M. Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts. CELL GENOMICS 2024; 4:100544. [PMID: 38692281 PMCID: PMC11099341 DOI: 10.1016/j.xgen.2024.100544] [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: 11/02/2023] [Revised: 02/09/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024]
Abstract
Chronic inflammation is a hallmark of age-related disease states. The effectiveness of inflammatory proteins including C-reactive protein (CRP) in assessing long-term inflammation is hindered by their phasic nature. DNA methylation (DNAm) signatures of CRP may act as more reliable markers of chronic inflammation. We show that inter-individual differences in DNAm capture 50% of the variance in circulating CRP (N = 17,936, Generation Scotland). We develop a series of DNAm predictors of CRP using state-of-the-art algorithms. An elastic-net-regression-based predictor outperformed competing methods and explained 18% of phenotypic variance in the Lothian Birth Cohort of 1936 (LBC1936) cohort, doubling that of existing DNAm predictors. DNAm predictors performed comparably in four additional test cohorts (Avon Longitudinal Study of Parents and Children, Health for Life in Singapore, Southall and Brent Revisited, and LBC1921), including for individuals of diverse genetic ancestry and different age groups. The best-performing predictor surpassed assay-measured CRP and a genetic score in its associations with 26 health outcomes. Our findings forge new avenues for assessing chronic low-grade inflammation in diverse populations.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; School of Psychology, University of Exeter, Exeter EX4 4QG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Felicia Huang
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
| | - Kenan Direk
- Imperial Clinical Trials Unit, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Paul Welsh
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Janie Corley
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, Edinburgh Imaging and UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; British Heart Foundation Data Science Centre, Health Data Research UK, London NW1 2BE, UK; Health Data Research UK, London NW1 2BE, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon R Cox
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK; National Skin Centre, Singapore 308205, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - Paul D Yousefi
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
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5
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Livshits G, Kalinkovich A. Restoration of epigenetic impairment in the skeletal muscle and chronic inflammation resolution as a therapeutic approach in sarcopenia. Ageing Res Rev 2024; 96:102267. [PMID: 38462046 DOI: 10.1016/j.arr.2024.102267] [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: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Sarcopenia is an age-associated loss of skeletal muscle mass, strength, and function, accompanied by severe adverse health outcomes, such as falls and fractures, functional decline, high health costs, and mortality. Hence, its prevention and treatment have become increasingly urgent. However, despite the wide prevalence and extensive research on sarcopenia, no FDA-approved disease-modifying drugs exist. This is probably due to a poor understanding of the mechanisms underlying its pathophysiology. Recent evidence demonstrate that sarcopenia development is characterized by two key elements: (i) epigenetic dysregulation of multiple molecular pathways associated with sarcopenia pathogenesis, such as protein remodeling, insulin resistance, mitochondria impairments, and (ii) the creation of a systemic, chronic, low-grade inflammation (SCLGI). In this review, we focus on the epigenetic regulators that have been implicated in skeletal muscle deterioration, their individual roles, and possible crosstalk. We also discuss epidrugs, which are the pharmaceuticals with the potential to restore the epigenetic mechanisms deregulated in sarcopenia. In addition, we discuss the mechanisms underlying failed SCLGI resolution in sarcopenia and the potential application of pro-resolving molecules, comprising specialized pro-resolving mediators (SPMs) and their stable mimetics and receptor agonists. These compounds, as well as epidrugs, reveal beneficial effects in preclinical studies related to sarcopenia. Based on these encouraging observations, we propose the combination of epidrugs with SCLI-resolving agents as a new therapeutic approach for sarcopenia that can effectively attenuate of its manifestations.
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Affiliation(s)
- Gregory Livshits
- Department of Morphological Sciences, Adelson School of Medicine, Ariel University, Ariel 4077625, Israel; Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel.
| | - Alexander Kalinkovich
- Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel
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6
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Ahmed IA, Liu M, Gomez D. Nuclear Control of Vascular Smooth Muscle Cell Plasticity during Vascular Remodeling. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:525-538. [PMID: 37820925 PMCID: PMC10988766 DOI: 10.1016/j.ajpath.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Control of vascular smooth muscle cell (SMC) gene expression is an essential process for establishing and maintaining lineage identity, contractility, and plasticity. Most mechanisms (epigenetic, transcriptional, and post-transcriptional) implicated in gene regulation occur in the nucleus. Still, intranuclear pathways are directly impacted by modifications in the extracellular environment in conditions of adaptive or maladaptive remodeling. Integration of extracellular, cellular, and genomic information into the nucleus through epigenetic and transcriptional control of genome organization plays a major role in regulating SMC functions and phenotypic transitions during vascular remodeling and diseases. This review aims to provide a comprehensive update on nuclear mechanisms, their interactions, and their integration in controlling SMC homeostasis and dysfunction. It summarizes and discusses the main nuclear mechanisms preponderant in SMCs in the context of vascular disease, such as atherosclerosis, with an emphasis on studies employing in vivo cell-specific loss-of-function and single-cell omics approaches.
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Affiliation(s)
- Ibrahim A Ahmed
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingjun Liu
- Department of Pathology, New York University, New York, New York
| | - Delphine Gomez
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
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7
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Kremer TL, Chen J, Buhl A, Berhe O, Bilek E, Geiger-Primo L, Ma R, Moessnang C, Reichert M, Reinhard I, Schwarz K, Schweiger JI, Streit F, Witt SH, Zang Z, Zhang X, Noethen MM, Rietschel M, Ebner-Priemer UW, Schwarz E, Meyer-Lindenberg A, Braun U, Tost H. Multimodal Associations of FKBP5 Methylation with Emotion-Regulatory Brain Circuits. Biol Psychiatry 2024:S0006-3223(24)01141-7. [PMID: 38460581 DOI: 10.1016/j.biopsych.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Understanding the biological processes underlying individual differences in emotion regulation and stress responsivity is a key challenge for translational neuroscience. The gene FKBP5 is a core regulator in molecular stress signaling that is implicated in the development of psychiatric disorders. Yet it remains unclear how FKBP5 DNA methylation (DNAm) in peripheral blood relates to individual differences in measures of neural structure and function, and their relevance to daily-life stress responsivity. METHODS Here, we characterize multimodal correlates of FKBP5 DNAm by combining epigenetic data with neuroimaging and Ambulatory Assessment in a sample of 395 healthy individuals. RESULTS First, we show that FKBP5 demethylation as a psychiatric risk factor relates to an anxiety-associated reduction of gray matter volume in the ventromedial prefrontal cortex (vmPFC), a brain area that is involved in emotion regulation and mental health risk and resilience. This effect of epigenetic upregulation of FKBP5 on neuronal structure is more pronounced where FKBP5 is epigenetically downregulated at baseline. Leveraging 208 functional MRI scans during a well-established emotion processing task we find that FKBP5 DNAm in peripheral blood is associated with functional difference of prefrontal-limbic circuits modulating affective responsivity to daily stressors, which we measured using ecological momentary assessment in daily life. CONCLUSIONS Overall, we demonstrate how FKBP5 contributes to interindividual differences in neural and real-life affect regulation via structural and functional changes in prefrontal-limbic brain circuits.
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Affiliation(s)
- Thomas L Kremer
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Junfang Chen
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Current address: Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, School of Life Sciences, Fudan University, Guangzhou, China
| | - Anais Buhl
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Oksana Berhe
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Edda Bilek
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lena Geiger-Primo
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ren Ma
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carolin Moessnang
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Current address: Faculty for Applied Psychology, SRH University Heidelberg, Heidelberg, Germany
| | - Markus Reichert
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mental mHealth Lab, Chair of Applied Psychology, Institute of Sports and Sports Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany; Department of eHealth and Sports Analytics, Ruhr University Bochum, Bochum, Germany
| | - Iris Reinhard
- Department of Biostatistics, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kristina Schwarz
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Current address: Institute of Clinical Psychology and Psychotherapy, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Janina I Schweiger
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhenxiang Zang
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Current address: Department of Radiology and Nuclear Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiaolong Zhang
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Markus M Noethen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ulrich W Ebner-Priemer
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mental mHealth Lab, Chair of Applied Psychology, Institute of Sports and Sports Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Emanuel Schwarz
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Meyer-Lindenberg
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Urs Braun
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Heike Tost
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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8
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Rath S, Hawsawi YM, Alzahrani F, Khan MI. Epigenetic regulation of inflammation: The metabolomics connection. Semin Cell Dev Biol 2024; 154:355-363. [PMID: 36127262 DOI: 10.1016/j.semcdb.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
Epigenetic factors are considered the regulator of complex machinery behind inflammatory disorders and significantly contributed to the expression of inflammation-associated genes. Epigenetic modifications modulate variation in the expression pattern of target genes without affecting the DNA sequence. The current knowledge of epigenetic research focused on their role in the pathogenesis of various inflammatory diseases that causes morbidity and mortality worldwide. Inflammatory diseases are categorized as acute and chronic based on the disease severity and are regulated by the expression pattern of various genes. Hence, understanding the role of epigenetic modifications during inflammation progression will contribute to the disease outcomes and therapeutic approaches. This review also focuses on the metabolomics approach associated with the study of inflammatory disorders. Inflammatory responses and metabolic regulation are highly integrated and various advanced techniques are adopted to study the metabolic signature molecules. Here we discuss several metabolomics approaches used to link inflammatory disorders and epigenetic changes. We proposed that deciphering the mechanism behind the inflammation-metabolism loop may have immense importance in biomarkers research and may act as a principal component in drug discovery as well as therapeutic applications.
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Affiliation(s)
- Suvasmita Rath
- Center of Environment, Climate Change and Public Health, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Yousef M Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 40047, Jeddah 21499, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia.
| | - Faisal Alzahrani
- Department of Biochemistry, King Abdulaziz University (KAU), Jeddah 21577, Saudi Arabia; Embryonic Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Department of Biochemistry, King Abdulaziz University (KAU), Jeddah 21577, Saudi Arabia; Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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9
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Petrache I, Riches DW. Reduced Bik expression drives low-grade airway inflammation and increased risk for COPD in females. J Clin Invest 2024; 134:e177753. [PMID: 38357926 PMCID: PMC10866644 DOI: 10.1172/jci177753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Chronic low-grade inflammation is increasingly recognized as a subtle yet potent risk factor for a multitude of age-related disorders, including respiratory diseases, cardiovascular conditions, metabolic syndromes, autoimmunity, and cancer. In this issue of the JCI, Mebratu, Jones, and colleagues shed new light on the mechanisms that promote low-grade airway inflammation and how this contributes to the development of chronic obstructive pulmonary disease (COPD). Their finding that Bik deficiency leads to spontaneous emphysema in female mice, but not in males, marks a notable advancement in our understanding of how inflammatory processes can diverge based on biological sex. This finding is of clinical relevance, given the vulnerability of women to developing COPD.
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Affiliation(s)
- Irina Petrache
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - David W.H. Riches
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Program in Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
- Department of Research, Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA
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10
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Tisato V, Silva JA, Scarpellini F, Capucci R, Marci R, Gallo I, Salvatori F, D'Aversa E, Secchiero P, Serino ML, Zauli G, Singh AV, Gemmati D. Epigenetic role of LINE-1 methylation and key genes in pregnancy maintenance. Sci Rep 2024; 14:3275. [PMID: 38332006 PMCID: PMC10853191 DOI: 10.1038/s41598-024-53737-2] [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: 09/29/2023] [Accepted: 02/04/2024] [Indexed: 02/10/2024] Open
Abstract
Spontaneous abortion is a pregnancy complication characterized by complex and multifactorial etiology. About 5% of childbearing women are globally affected by early pregnancy loss (EPL) and most of them experience recurrence (RPL). Epigenetic mechanisms and controlled inflammation are crucial for pregnancy maintenance and genetic predispositions may increase the risk affecting the maternal-fetal crosstalk. Combined analyses of global methylation, inflammation and inherited predispositions may contribute to define pregnancy loss etiopathogenesis. LINE-1 epigenetic regulation plays crucial roles during embryo implantation, and its hypomethylation has been associated with senescence and several complex diseases. By analysing a group of 230 women who have gone through pregnancy interruption and comparing those experiencing spontaneous EPL (n = 123; RPL, 54.5%) with a group of normal pregnant who underwent to voluntary interruption (VPI, n = 107), the single statistical analysis revealed significant lower (P < 0.00001) LINE-1 methylation and higher (P < 0.0001) mean cytokine levels (CKs: IL6, IL10, IL17A, IL23) in EPL. Genotyping of the following SNPs accounted for different EPL/RPL risk odds ratio: F13A1 rs5985 (OR = 0.24; 0.06-0.90); F13B rs6003 (OR = 0.23; 0.047-1.1); FGA rs6050 (OR = 0.58; 0.33-1.0); CRP rs2808635/rs876538 (OR = 0.15; 0.014-0.81); ABO rs657152 (OR = 0.48; 0.22-1.08); TP53 rs1042522 (OR = 0.54; 0.32-0.92); MTHFR rs1801133/rs1801131 (OR = 2.03; 1.2-3.47) and FGB rs1800790 (OR = 1.97; 1.01-3.87), although Bonferroni correction did not reach significant outputs. Principal Component Analysis (PCA) and logistic regression disclosed further SNPs positive/negative associations (e.g. APOE rs7412/rs429358; FGB rs1800790; CFH rs1061170) differently arranged and sorted in four significant PCs: PC1 (F13A, methylation, CKs); PC3 (CRP, MTHFR, age, methylation); PC4 (F13B, FGA, FGB, APOE, TP53, age, methylation); PC6 (F13A, CFH, ABO, MTHFR, TP53, age), yielding further statistical power to the association models. In detail, positive EPL risk association was with PC1 (OR = 1.81; 1.33-2.45; P < 0.0001) and negative associations with PC3 (OR = 0.489; 0.37-0.66; P < 0.0001); PC4 (OR = 0.72; 0.55-0.94; P = 0.018) and PC6 (OR = 0.61; 0.46-0.81; P = 0.001). Moreover, significant inverse associations were detected between methylation and CKs levels in the whole group (rIL10 = - 0.22; rIL17A = - 0.25; rIL23 = - 0.19; rIL6 = - 0.22), and methylation with age in the whole group, EPL and RPL subgroups (r2TOT = 0.147; r2EPL = 0.136; r2 RPL = 0.248), while VPI controls lost significance (r2VPI = 0.011). This study provides a valuable multilayer approach for investigating epigenetic abnormalities in pregnancy loss suggesting genetic-driven dysregulations and anomalous epigenetic mechanisms potentially mediated by LINE-1 hypomethylation. Women with unexplained EPL might benefit of such investigations, providing new insights for predicting the pregnancy outcome and for treating at risk women with novel targeted epidrugs.
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Affiliation(s)
- Veronica Tisato
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy.
- University Strategic Centre for Studies On Gender Medicine, University of Ferrara, 44121, Ferrara, Italy.
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy.
- LTTA Centre, University of Ferrara, 44121, Ferrara, Italy.
| | - Juliana A Silva
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | | | - Roberta Capucci
- Department of Medical Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Roberto Marci
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Ines Gallo
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Francesca Salvatori
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Elisabetta D'Aversa
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Paola Secchiero
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Maria L Serino
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy
| | - Giorgio Zauli
- Department of Environmental Sciences and Prevention, University of Ferrara, 44121, Ferrara, Italy
| | - Ajay V Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy.
- University Strategic Centre for Studies On Gender Medicine, University of Ferrara, 44121, Ferrara, Italy.
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy.
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11
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Cheng C, Yu F, Yuan G, Jia J. Update on N6-methyladenosine methylation in obesity-related diseases. Obesity (Silver Spring) 2024; 32:240-251. [PMID: 37989724 DOI: 10.1002/oby.23932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 11/23/2023]
Abstract
Obesity is a chronic metabolic disease that is closely related to type 2 diabetes mellitus, cardiovascular diseases, nonalcoholic fatty liver disease, obstructive sleep apnea, and osteoarthritis. The prevalence of obesity is increasing rapidly every year and is recognized as a global public health problem. In recent years, the role of epigenetics in the development of obesity and related diseases has been recognized and is currently a research hotspot. N6-methyladenosine (m6A) methylation is the most abundant epigenetic modification in the eukaryotic RNA, including mRNA and noncoding RNA. Several studies have shown that the m6A modifications in the target mRNA and the corresponding m6A regulators play a significant role in lipid metabolism and are strongly associated with the pathogenesis of obesity-related diseases. In this review, the latest research findings regarding the role of m6A methylation in obesity and related metabolic diseases are summarized. The authors' aim is to highlight evidence that suggests the clinical utility of m6A modifications and the m6A regulators as novel early prediction biomarkers and precision therapeutics for obesity and obesity-related diseases.
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Affiliation(s)
- Caiqin Cheng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Jiangsu University; Institute of Endocrine and Metabolic Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fan Yu
- Department of Endocrinology and Metabolism, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, Jiangsu, China
| | - Guoyue Yuan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Jiangsu University; Institute of Endocrine and Metabolic Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jue Jia
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Jiangsu University; Institute of Endocrine and Metabolic Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
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12
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Dessie EY, Ding L, Mersha TB. Integrative analysis identifies gene signatures mediating the effect of DNA methylation on asthma severity and lung function. Clin Epigenetics 2024; 16:15. [PMID: 38245772 PMCID: PMC10800055 DOI: 10.1186/s13148-023-01611-9] [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: 03/22/2023] [Accepted: 12/02/2023] [Indexed: 01/22/2024] Open
Abstract
DNA methylation (DNAm) changes play a key role in regulating gene expression in asthma. To investigate the role of epigenetics and transcriptomics change in asthma, we used publicly available DNAm (asthmatics, n = 96 and controls, n = 46) and gene expression (asthmatics, n = 79 and controls, n = 39) data derived from bronchial epithelial cells (BECs). We performed differential methylation/expression and weighted co-methylation/co-expression network analyses to identify co-methylated and co-expressed modules associated with asthma severity and lung function. For subjects with both DNAm and gene expression data (asthmatics, n = 79 and controls, n = 39), machine-learning technique was used to prioritize CpGs and differentially expressed genes (DEGs) for asthma risk prediction, and mediation analysis was used to uncover DEGs that mediate the effect of DNAm on asthma severity and lung function in BECs. Finally, we validated CpGs and their associated DEGs and the asthma risk prediction model in airway epithelial cells (AECs) dataset. The asthma risk prediction model based on 18 CpGs and 28 DEGs showed high accuracy in both the discovery BEC dataset with area under the receiver operating characteristic curve (AUC) = 0.99 and the validation AEC dataset (AUC = 0.82). Genes in the three co-methylated and six co-expressed modules were enriched in multiple pathways including WNT/beta-catenin signaling and notch signaling. Moreover, we identified 35 CpGs correlated with DEGs in BECs, of which 17 CpGs including cg01975495 (SERPINE1), cg10528482 (SLC9A3), cg25477769 (HNF1A) and cg26639146 (CD9), cg17945560 (TINAGL1) and cg10290200 (FLNC) were replicated in AECs. These DEGs mediate the association between DNAm and asthma severity and lung function. Overall, our study investigated the role of DNAm and gene expression change in asthma and provided an insight into the mechanisms underlying the effects of DNA methylation on asthma, asthma severity and lung function.
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Affiliation(s)
- Eskezeia Y Dessie
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lili Ding
- Division of Biostatistics and Epidemiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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13
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Geiger M, Gorica E, Mohammed SA, Mongelli A, Mengozi A, Delfine V, Ruschitzka F, Costantino S, Paneni F. Epigenetic Network in Immunometabolic Disease. Adv Biol (Weinh) 2024; 8:e2300211. [PMID: 37794610 DOI: 10.1002/adbi.202300211] [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: 06/08/2023] [Revised: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Although a large amount of data consistently shows that genes affect immunometabolic characteristics and outcomes, epigenetic mechanisms are also heavily implicated. Epigenetic changes, including DNA methylation, histone modification, and noncoding RNA, determine gene activity by altering the accessibility of chromatin to transcription factors. Various factors influence these alterations, including genetics, lifestyle, and environmental cues. Moreover, acquired epigenetic signals can be transmitted across generations, thus contributing to early disease traits in the offspring. A closer investigation is critical in this aspect as it can help to understand the underlying molecular mechanisms further and gain insights into potential therapeutic targets for preventing and treating diseases arising from immuno-metabolic dysregulation. In this review, the role of chromatin alterations in the transcriptional modulation of genes involved in insulin resistance, systemic inflammation, macrophage polarization, endothelial dysfunction, metabolic cardiomyopathy, and nonalcoholic fatty liver disease (NAFLD), is discussed. An overview of emerging chromatin-modifying drugs and the importance of the individual epigenetic profile for personalized therapeutic approaches in patients with immuno-metabolic disorders is also presented.
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Affiliation(s)
- Martin Geiger
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessia Mongelli
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessandro Mengozi
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Valentina Delfine
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- Department of Research and Education, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
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14
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Watkins SH, Testa C, Simpkin AJ, Smith GD, Coull B, De Vivo I, Tilling K, Waterman PD, Chen JT, Diez-Roux AV, Krieger N, Suderman M, Relton C. An epigenome-wide analysis of DNA methylation, racialized and economic inequities, and air pollution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570610. [PMID: 38105971 PMCID: PMC10723401 DOI: 10.1101/2023.12.07.570610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Importance DNA methylation (DNAm) provides a plausible mechanism by which adverse exposures become embodied and contribute to health inequities, due to its role in genome regulation and responsiveness to social and biophysical exposures tied to societal context. However, scant epigenome-wide association studies (EWAS) have included structural and lifecourse measures of exposure, especially in relation to structural discrimination. Objective Our study tests the hypothesis that DNAm is a mechanism by which racial discrimination, economic adversity, and air pollution become biologically embodied. Design A series of cross-sectional EWAS, conducted in My Body My Story (MBMS, biological specimens collected 2008-2010, DNAm assayed in 2021); and the Multi Ethnic Study of Atherosclerosis (MESA; biological specimens collected 2010-2012, DNAm assayed in 2012-2013); using new georeferenced social exposure data for both studies (generated in 2022). Setting MBMS was recruited from four community health centers in Boston; MESA was recruited from four field sites in: Baltimore, MD; Forsyth County, NC; New York City, NY; and St. Paul, MN. Participants Two population-based samples of US-born Black non-Hispanic (Black NH), white non-Hispanic (white NH), and Hispanic individuals (MBMS; n=224 Black NH and 69 white NH) and (MESA; n=229 Black NH, n=555 white NH and n=191 Hispanic). Exposures Eight social exposures encompassing racial discrimination, economic adversity, and air pollution. Main outcome Genome-wide changes in DNAm, as measured using the Illumina EPIC BeadChip (MBMS; using frozen blood spots) and Illumina 450k BeadChip (MESA; using purified monocytes). Our hypothesis was formulated after data collection. Results We observed the strongest associations with traffic-related air pollution (measured via black carbon and nitrogen oxides exposure), with evidence from both studies suggesting that air pollution exposure may induce epigenetic changes related to inflammatory processes. We also found suggestive associations of DNAm variation with measures of structural racial discrimination (e.g., for Black NH participants, born in a Jim Crow state; adult exposure to racialized economic residential segregation) situated in genes with plausible links to effects on health. Conclusions and Relevance Overall, this work suggests that DNAm is a biological mechanism through which structural racism and air pollution become embodied and may lead to health inequities.
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Affiliation(s)
- Sarah Holmes Watkins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian Testa
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Andrew J. Simpkin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
| | - George Davey Smith
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Brent Coull
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Pamela D. Waterman
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Jarvis T. Chen
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Ana V. Diez-Roux
- Department of Epidemiology and Biostatistics and Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, USA
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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15
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Santarelli R, Evangelista L, Pompili C, Lo Presti S, Rossi A, Arena A, Gaeta A, Gonnella R, Gilardini Montani MS, Cirone M. EBV infection of primary colonic epithelial cells causes inflammation, DDR and autophagy dysregulation, effects that may predispose to IBD and carcinogenesis. Virus Res 2023; 338:199236. [PMID: 37797746 PMCID: PMC10582763 DOI: 10.1016/j.virusres.2023.199236] [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: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
EBV is a gammaherpesvirus strongly associated to human cancer. The virus has been shown to play a role also in inflammatory diseases, including IBD, in the context of which colon cancer more frequently arise. In this study, we show for the first time that EBV infects primary colonic epithelial cells (HCoEpC), promotes pro-inflammatory cytokine secretion and activates molecular pathways bridging inflammation and cancer, such as ERK1/2. These effects, occurring in the course of the lytic phase of the viral life cycle, led to DDR and autophagy dysregulation. Such cellular responses, playing a key role in the maintenance of proteostasis and genome integrity, are essential to prevent carcinogenesis. Interestingly, we found that the use of the demethylating agent 5-AZA could counteract most of the effects induced by EBV infection in HCoEpC, suggesting that DNA hyper-methylation may strongly contribute to viral-driven inflammation and colon cancer predisposition.
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Affiliation(s)
- Roberta Santarelli
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Lorenzo Evangelista
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Chiara Pompili
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Salvatore Lo Presti
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Alberto Rossi
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Andrea Arena
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Aurelia Gaeta
- Department of Molecular Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Roberta Gonnella
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | | | - Mara Cirone
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy.
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16
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Baechle JJ, Chen N, Makhijani P, Winer S, Furman D, Winer DA. Chronic inflammation and the hallmarks of aging. Mol Metab 2023; 74:101755. [PMID: 37329949 PMCID: PMC10359950 DOI: 10.1016/j.molmet.2023.101755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Recently, the hallmarks of aging were updated to include dysbiosis, disabled macroautophagy, and chronic inflammation. In particular, the low-grade chronic inflammation during aging, without overt infection, is defined as "inflammaging," which is associated with increased morbidity and mortality in the aging population. Emerging evidence suggests a bidirectional and cyclical relationship between chronic inflammation and the development of age-related conditions, such as cardiovascular diseases, neurodegeneration, cancer, and frailty. How the crosstalk between chronic inflammation and other hallmarks of aging underlies biological mechanisms of aging and age-related disease is thus of particular interest to the current geroscience research. SCOPE OF REVIEW This review integrates the cellular and molecular mechanisms of age-associated chronic inflammation with the other eleven hallmarks of aging. Extra discussion is dedicated to the hallmark of "altered nutrient sensing," given the scope of Molecular Metabolism. The deregulation of hallmark processes during aging disrupts the delicate balance between pro-inflammatory and anti-inflammatory signaling, leading to a persistent inflammatory state. The resultant chronic inflammation, in turn, further aggravates the dysfunction of each hallmark, thereby driving the progression of aging and age-related diseases. MAIN CONCLUSIONS The crosstalk between chronic inflammation and other hallmarks of aging results in a vicious cycle that exacerbates the decline in cellular functions and promotes aging. Understanding this complex interplay will provide new insights into the mechanisms of aging and the development of potential anti-aging interventions. Given their interconnectedness and ability to accentuate the primary elements of aging, drivers of chronic inflammation may be an ideal target with high translational potential to address the pathological conditions associated with aging.
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Affiliation(s)
- Jordan J Baechle
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Nan Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada
| | - Priya Makhijani
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David Furman
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA; Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, CONICET, Pilar, Argentina.
| | - Daniel A Winer
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada; Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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17
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Rizo-Téllez SA, Sekheri M, Filep JG. C-reactive protein: a target for therapy to reduce inflammation. Front Immunol 2023; 14:1237729. [PMID: 37564640 PMCID: PMC10410079 DOI: 10.3389/fimmu.2023.1237729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
C-reactive protein (CRP) is well-recognized as a sensitive biomarker of inflammation. Association of elevations in plasma/serum CRP level with disease state has received considerable attention, even though CRP is not a specific indicator of a single disease state. Circulating CRP levels have been monitored with a varying degree of success to gauge disease severity or to predict disease progression and outcome. Elevations in CRP level have been implicated as a useful marker to identify patients at risk for cardiovascular disease and certain cancers, and to guide therapy in a context-dependent manner. Since even strong associations do not establish causality, the pathogenic role of CRP has often been over-interpreted. CRP functions as an important modulator of host defense against bacterial infection, tissue injury and autoimmunity. CRP exists in conformationally distinct forms, which exhibit distinct functional properties and help explaining the diverse, often contradictory effects attributed to CRP. In particular, dissociation of native pentameric CRP into its subunits, monomeric CRP, unmasks "hidden" pro-inflammatory activities in pentameric CRP. Here, we review recent advances in CRP targeting strategies, therapeutic lowering of circulating CRP level and development of CRP antagonists, and a conformation change inhibitor in particular. We will also discuss their therapeutic potential in mitigating the deleterious actions attributed to CRP under various pathologies, including cardiovascular, pulmonary and autoimmune diseases and cancer.
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Affiliation(s)
- Salma A. Rizo-Téllez
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Meriem Sekheri
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - János G. Filep
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
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18
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Valentini N, Requejo Cier CJ, Lamarche C. Regulatory T-cell dysfunction and its implication for cell therapy. Clin Exp Immunol 2023; 213:40-49. [PMID: 37158407 PMCID: PMC10324551 DOI: 10.1093/cei/uxad051] [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: 12/16/2022] [Revised: 03/04/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Regulatory T cells (Tregs) are a subtype of CD4+ T cells that can mediate immune tolerance by a multitude of immunomodulatory mechanisms. Treg-based adoptive immunotherapy is currently being tested in multiple phases I and II clinical trials in transplantation and autoimmune diseases. We have learned from the work done on conventional T cells that distinct mechanistic states can define their dysfunctions, such as exhaustion, senescence, and anergy. All three can negatively impact the therapeutic effectiveness of T-cell-based therapies. However, whether Tregs are susceptible to such dysfunctional states is not well studied, and results are sometimes found to be controversial. In addition, Treg instability and loss of FOXP3 expression is another Treg-specific dysfunction that can decreasein their suppressive potential. A better understanding of Treg biology and pathological states will be needed to compare and interpret the results of the different clinical and preclinical trials. We will review herein Tregs' mechanisms of action, describe different T-cell dysfunction subtypes and how and if they apply to Tregs (exhaustion, senescence, anergy, and instability), and finally how this knowledge should be taken into consideration when designing and interpreting Treg adoptive immunotherapy trials.
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Affiliation(s)
- Nicolas Valentini
- Medicine Department, Hôpital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
- Microbiology, Infectiology and Immunology Department, Université de Montréal, Montreal, QC, Canada
| | - Christopher J Requejo Cier
- Medicine Department, Hôpital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
- Microbiology, Infectiology and Immunology Department, Université de Montréal, Montreal, QC, Canada
| | - Caroline Lamarche
- Medicine Department, Hôpital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
- Medicine Department, Université de Montréal, Montreal, QC, Canada
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19
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Verschoor CP, Vlasschaert C, Rauh MJ, Paré G. A DNA methylation based measure outperforms circulating CRP as a marker of chronic inflammation and partly reflects the monocytic response to long-term inflammatory exposure: A Canadian longitudinal study of aging analysis. Aging Cell 2023:e13863. [PMID: 37139638 PMCID: PMC10352553 DOI: 10.1111/acel.13863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
A key hallmark in the age-related dysfunction of physiological systems is disruption related to the regulation of inflammation, often resulting in a chronic, low-grade inflammatory state (i.e., inflammaging). In order to understand the causes of overall system decline, methods to quantify the life-long exposure or damage related to chronic inflammation are critical. Here, we characterize a comprehensive epigenetic inflammation score (EIS) based on DNA methylation loci (CpGs) that are associated with circulating levels of C-reactive protein (CRP). In a cohort of 1446 older adults, we show that associations to age and health-related traits such as smoking history, chronic conditions, and established measures of accelerated aging were stronger for EIS than CRP, while the risk of longitudinal outcomes such as outpatient or inpatient visits and increased frailty were relatively similar. To determine whether variation in EIS actually reflects the cellular response to chronic inflammation we exposed THP1 myelo-monocytic cells to low levels of inflammatory mediators for 14 days, finding that EIS increased in response to both CRP (p = 0.011) and TNF (p = 0.068). Interestingly, a refined version of EIS based only on those CpGs that changed in vitro was more strongly associated with many of the aforementioned traits as compared to EIS. In conclusion, our study demonstrates that EIS outperforms circulating CRP with regard to its association to health-traits that are synonymous with chronic inflammation and accelerated aging, and substantiates its potential role as a clinically relevant tool for stratifying patient risk of adverse outcomes prior to treatment or following illness.
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Affiliation(s)
- Chris P Verschoor
- Health Sciences North Research Institute, Sudbury, Ontario, Canada
- Northern Ontario School of Medicine, Sudbury, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | | | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Guillaume Paré
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
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20
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Conole ELS, Vaher K, Cabez MB, Sullivan G, Stevenson AJ, Hall J, Murphy L, Thrippleton MJ, Quigley AJ, Bastin ME, Miron VE, Whalley HC, Marioni RE, Boardman JP, Cox SR. Immuno-epigenetic signature derived in saliva associates with the encephalopathy of prematurity and perinatal inflammatory disorders. Brain Behav Immun 2023; 110:322-338. [PMID: 36948324 DOI: 10.1016/j.bbi.2023.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Preterm birth is closely associated with a phenotype that includes brain dysmaturation and neurocognitive impairment, commonly termed Encephalopathy of Prematurity (EoP), of which systemic inflammation is considered a key driver. DNA methylation (DNAm) signatures of inflammation from peripheral blood associate with poor brain imaging outcomes in adult cohorts. However, the robustness of DNAm inflammatory scores in infancy, their relation to comorbidities of preterm birth characterised by inflammation, neonatal neuroimaging metrics of EoP, and saliva cross-tissue applicability are unknown. METHODS Using salivary DNAm from 258 neonates (n = 155 preterm, gestational age at birth 23.28 - 34.84 weeks, n = 103 term, gestational age at birth 37.00 - 42.14 weeks), we investigated the impact of a DNAm surrogate for C-reactive protein (DNAm CRP) on brain structure and other clinically defined inflammatory exposures. We assessed i) if DNAm CRP estimates varied between preterm infants at term equivalent age and term infants, ii) how DNAm CRP related to different types of inflammatory exposure (maternal, fetal and postnatal) and iii) whether elevated DNAm CRP associated with poorer measures of neonatal brain volume and white matter connectivity. RESULTS Higher DNAm CRP was linked to preterm status (-0.0107 ± 0.0008, compared with -0.0118 ± 0.0006 among term infants; p < 0.001), as well as perinatal inflammatory diseases, including histologic chorioamnionitis, sepsis, bronchopulmonary dysplasia, and necrotising enterocolitis (OR range |2.00 | to |4.71|, p < 0.01). Preterm infants with higher DNAm CRP scores had lower brain volume in deep grey matter, white matter, and hippocampi and amygdalae (β range |0.185| to |0.218|). No such associations were observed for term infants. Association magnitudes were largest for measures of white matter microstructure among preterms, where elevated epigenetic inflammation associated with poorer global measures of white matter integrity (β range |0.206| to |0.371|), independent of other confounding exposures. CONCLUSIONS Inflammatory-related DNAm captures the allostatic load of inflammatory burden in preterm infants. Such DNAm measures complement biological and clinical metrics when investigating the determinants of neurodevelopmental differences.
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Affiliation(s)
- Eleanor L S Conole
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Kadi Vaher
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Manuel Blesa Cabez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jill Hall
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael J Thrippleton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J Quigley
- Imaging Department, Royal Hospital for Children and Young People, Edinburgh, EH16 4TJ, UK
| | - Mark E Bastin
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James P Boardman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
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21
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Xiong P, Zhang F, Liu F, Zhao J, Huang X, Luo D, Guo J. Metaflammation in glucolipid metabolic disorders: Pathogenesis and treatment. Biomed Pharmacother 2023; 161:114545. [PMID: 36948135 DOI: 10.1016/j.biopha.2023.114545] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
The public health issue of glucolipid metabolic disorders (GLMD) has grown significantly, posing a grave threat to human wellness. Its prevalence is rising yearly and tends to affect younger people. Metaflammation is an important mechanism regulating body metabolism. Through a complicated multi-organ crosstalk network involving numerous signaling pathways such as NLRP3/caspase-1/IL-1, NF-B, p38 MAPK, IL-6/STAT3, and PI3K/AKT, it influences systemic metabolic regulation. Numerous inflammatory mediators are essential for preserving metabolic balance, but more research is needed to determine how they contribute to the co-morbidities of numerous metabolic diseases. Whether controlling the inflammatory response can influence the progression of GLMD determines the therapeutic strategy for such diseases. This review thoroughly examines the role of metaflammation in GLMD and combs the research progress of related therapeutic approaches, including inflammatory factor-targeting drugs, traditional Chinese medicine (TCM), and exercise therapy. Multiple metabolic diseases, including diabetes, non-alcoholic fatty liver disease (NAFLD), cardiovascular disease, and others, respond therapeutically to anti-inflammatory therapy on the whole. Moreover, we emphasize the value and open question of anti-inflammatory-based means for treating GLMD.
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Affiliation(s)
- Pingjie Xiong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
| | - Fan Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
| | - Fang Liu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
| | - Jiayu Zhao
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
| | - Xiaoqiang Huang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China.
| | - Duosheng Luo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
| | - Jiao Guo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China; Institute of Chinese Medicine, Guangdong Pharmaceutical University; Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou 510006, China.
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22
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Fernández-Carrión R, Sorlí JV, Asensio EM, Pascual EC, Portolés O, Alvarez-Sala A, Francès F, Ramírez-Sabio JB, Pérez-Fidalgo A, Villamil LV, Tinahones FJ, Estruch R, Ordovas JM, Coltell O, Corella D. DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3635. [PMID: 36834337 PMCID: PMC9964856 DOI: 10.3390/ijerph20043635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva M. Asensio
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Francesc Francès
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Laura V. Villamil
- Department of Physiology, School of Medicine, University Antonio Nariño, Bogotá 111511, Colombia
| | - Francisco J. Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, 29590 Málaga, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Jose M. Ordovas
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
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23
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Long-term variability in physiological measures in relation to mortality and epigenetic aging: prospective studies in the USA and China. BMC Med 2023; 21:20. [PMID: 36647101 PMCID: PMC9843964 DOI: 10.1186/s12916-022-02674-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/21/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Visit-to-visit body weight variability (BWV), pulse rate variability (PRV), and blood pressure variability (BPV) have been respectively linked to multiple health outcomes. The associations of the combination of long-term variability in physiological measures with mortality and epigenetic age acceleration (EAA) remain largely unknown. METHODS We constructed a composite score of physiological variability (0-3) of large variability in BWV, PRV, and BPV (the top tertiles) in 2006/2008-2014/2016 in the Health and Retirement Study (HRS) and 2011-2015 in the China Health and Retirement Longitudinal Study (CHARLS). All-cause mortality was documented through 2018. EAA was calculated using thirteen DNA methylation-based epigenetic clocks among 1047 participants in a substudy of the HRS. We assessed the relation of the composite score to the risk of mortality among 6566 participants in the HRS and 6906 participants in the CHARLS by Cox proportional models and then investigated its association with EAA using linear regression models. RESULTS A higher score of variability was associated with higher mortality risk in both cohorts (pooled hazard ratio [HR] per one-point increment, 1.27; 95% confidence interval [CI], 1.18, 1.39; P-heterogeneity = 0.344), after adjustment for multiple confounders and baseline physiological measures. Specifically, each SD increment in BWV, PRV, and BPV was related to 21% (95% CI: 15%, 28%), 6% (0%, 13%), and 12% (4%, 19%) higher hazard of mortality, respectively. The composite score was significantly related to EAA in second-generation clocks trained on health outcomes (e.g., standardized coefficient = 0.126 in the Levine clock, 95% CI: 0.055, 0.196) but not in most first-generation clocks trained on chronological age. CONCLUSIONS Larger variability in physiological measures was associated with a higher risk of mortality and faster EAA.
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Wang C, DeMeo DL, Kim ES, Cardenas A, Fong KC, Lee LO, Spiro A, Whitsel EA, Horvath S, Hou L, Baccarelli AA, Li Y, Stewart JD, Manson JE, Grodstein F, Kubzansky LD, Schwartz JD. Epigenome-Wide Analysis of DNA Methylation and Optimism in Women and Men. Psychosom Med 2023; 85:89-97. [PMID: 36201768 PMCID: PMC9771983 DOI: 10.1097/psy.0000000000001147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Higher optimism is associated with reduced mortality and a lower risk of age-related chronic diseases. DNA methylation (DNAm) may provide insight into mechanisms underlying these relationships. We hypothesized that DNAm would differ among older individuals who are more versus less optimistic. METHODS Using cross-sectional data from two population-based cohorts of women with diverse races/ethnicities ( n = 3816) and men (only White, n = 667), we investigated the associations of optimism with epigenome-wide leukocyte DNAm. Random-effects meta-analyses were subsequently used to pool the individual results. Significantly differentially methylated cytosine-phosphate-guanines (CpGs) were identified by the "number of independent degrees of freedom" approach: effective degrees of freedom correction using the number of principal components (PCs), explaining >95% of the variation of the DNAm data (PC-correction). We performed regional analyses using comb-p and pathway analyses using the Ingenuity Pathway Analysis software. RESULTS We found that essentially all CpGs (total probe N = 359,862) were homogeneous across sex and race/ethnicity in the DNAm-optimism association. In the single CpG site analyses based on homogeneous CpGs, we identified 13 significantly differentially methylated probes using PC-correction. We found four significantly differentially methylated regions and two significantly differentially methylated pathways. The annotated genes from the single CpG site and regional analyses are involved in psychiatric disorders, cardiovascular disease, cognitive impairment, and cancer. Identified pathways were related to cancer, and neurodevelopmental and neurodegenerative disorders. CONCLUSION Our findings provide new insights into possible mechanisms underlying optimism and health.
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Affiliation(s)
- Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Dawn L. DeMeo
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric S. Kim
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Psychology, University of British Columbia, BC V6T 1Z4, Canada
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Population Medicine, Division of Chronic Disease Research Across the Lifecourse, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Kelvin C. Fong
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Lewina O. Lee
- National Center for Posttraumatic Stress Disorder, VA Boston Healthcare System, Boston, MA 02130, USA
- Department Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Avron Spiro
- Department Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
- Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA 02130, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - James D. Stewart
- Cardiovascular Program, Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, 27599, USA
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Francine Grodstein
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Laura D. Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Joel D. Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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25
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Hernández Cordero AI, Yang CX, Yang J, Li X, Horvath S, Shaipanich T, MacIsaac J, Lin D, McEwen L, Kobor MS, Guillemi S, Harris M, Lam W, Lam S, Obeidat M, Novak RM, Hudson F, Klinker H, Dharan N, Montaner J, Man SP, Kunisaki K, Sin DD, Leung JM. The relationship between the epigenetic aging biomarker "grimage" and lung function in both the airway and blood of people living with HIV: An observational cohort study. EBioMedicine 2022; 83:104206. [PMID: 35944348 PMCID: PMC9379521 DOI: 10.1016/j.ebiom.2022.104206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/14/2022] [Accepted: 07/24/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Age-related comorbidities such as chronic obstructive pulmonary disease (COPD) are common in people living with human immunodeficiency virus (PLWH). We investigated the relationship between COPD and the epigenetic age of the airway epithelium and peripheral blood of PLWH. METHODS Airway epithelial brushings from 34 PLWH enrolled in the St. Paul's Hospital HIV Bronchoscopy cohort and peripheral blood from 378 PLWH enrolled in The Strategic Timing of Antiretroviral Treatment (START) study were profiled for DNA methylation. The DNA methylation biomarker of age and healthspan, GrimAge, was calculated in both tissue compartments. We tested the association of GrimAge with COPD in the airway epithelium and airflow obstruction as defined by an FEV1/FVC<0.70, and FEV1 decline over 6 years in blood. FINDINGS The airway epithelium of PLWH with COPD was associated with greater GrimAge residuals compared to PLWH without COPD (Beta=3.18, 95%CI=1.06-5.31, P=0.005). In blood, FEV1/FVC<LLN was associated with greater GrimAge residuals (Beta=1.74, 95%CI=0.37-3.24, P=0.019). FEV1 decline was inversely correlated with GrimAge residuals in blood (r=-0.13, P=0.012). PLWH who had normal lung function but who subsequently developed an FEV1/FVC<0.70 over the course of 6 years had higher GrimAge residuals at baseline (Beta=2.33, 95%CI=0.23-4.44, P=0.031). INTERPRETATION GrimAge may reflect lung and systemic epigenetic changes that occur with advanced airflow obstruction and may help to identify PLWH with a higher risk of developing COPD. FUNDING Canadian Institutes of Health Research and the British Columbia Lung Association. The START substudy was funded by NIH grants: UM1-AI068641, UM1-AI120197, and RO1HL096453.
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Affiliation(s)
- Ana I Hernández Cordero
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles (UCLA), Los Angeles, CA 90095, United States,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA 90095, United States
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada,Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada,Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan Lam
- British Columbia Cancer Research Centre and the University of British Columbia, Vancouver, British Columbia
| | - Stephen Lam
- British Columbia Cancer Research Centre and the University of British Columbia, Vancouver, British Columbia
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard M. Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, IL, United States
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, UK
| | - Hartwig Klinker
- Medizinische Klinik und Poliklinik II, Universitatsklinikum Wurzburg, Wurzburg, Germany
| | - Nila Dharan
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada,Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - S.F. Paul Man
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine and the Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Corresponding author at: Room 166-1081 Burrard St, Centre for Heart Lung Innovation, Vancouver, BC V6Z 1Y6.
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26
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Holloway JW, DeMeo DL. Omics and Lung Function: A Need for Integration. Am J Respir Crit Care Med 2022; 206:242-244. [PMID: 35608542 PMCID: PMC9890266 DOI: 10.1164/rccm.202205-0928ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
| | - Dawn L. DeMeo
- Department of Medicine,Division of Pulmonary and Critical Care MedicineBrigham and Women’s HospitalBoston, Massachusetts
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