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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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da Silva Rodrigues Marçal E, Borges JB, Bastos GM, Crespo Hirata TD, de Oliveira VF, Gonçalves RM, Faludi AA, Dias França JI, de Oliveira Silva DV, Malaquias VB, Luchessi AD, Silbiger VN, Nakazone MA, Carmo TS, Silva Souza DR, Sampaio MF, Crespo Hirata RD, Hirata MH. Methylation status of LDLR, PCSK9 and LDLRAP1 is associated with cardiovascular events in familial hypercholesterolemia. Epigenomics 2024; 16:809-820. [PMID: 38884343 PMCID: PMC11370914 DOI: 10.1080/17501911.2024.2351792] [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: 02/26/2024] [Accepted: 04/27/2024] [Indexed: 06/18/2024] Open
Abstract
Aim: Methylation of LDLR, PCSK9 and LDLRAP1 CpG sites was assessed in patients with familial hypercholesterolemia (FH). Methods: DNA methylation of was analyzed by pyrosequencing in 131 FH patients and 23 normolipidemic (NL) subjects.Results: LDLR, PCSK9 and LDLRP1 methylation was similar between FH patients positive (MD) and negative (non-MD) for pathogenic variants in FH-related genes. LDLR and PCSK9 methylation was higher in MD and non-MD groups than NL subjects (p < 0.05). LDLR, PCSK9 and LDLRAP1 methylation profiles were associated with clinical manifestations and cardiovascular events in FH patients (p < 0.05).Conclusion: Differential methylation of LDLR, PCSK9 and LDLRAP1 is associated with hypercholesterolemia and cardiovascular events. This methylation profile maybe useful as a biomarker and contribute to the management of FH.
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Affiliation(s)
- Elisangela da Silva Rodrigues Marçal
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil
| | - Jéssica Bassani Borges
- Department of Research, Hospital Beneficiencia Portuguesa de Sao Paulo, Sao Paulo, 01323-001, Brazil
| | - Gisele Medeiros Bastos
- Department of Research, Hospital Beneficiencia Portuguesa de Sao Paulo, Sao Paulo, 01323-001, Brazil
| | - Thiago Dominguez Crespo Hirata
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Victor Fernandes de Oliveira
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
| | | | - Andre Arpad Faludi
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo, 04012-909, Brazil
| | - João Italo Dias França
- Center for Clinical Trials & Pharmacovigilance, Butantan Institute, Sao Paulo, 05585-000, Brazil
| | - Daiana Vitor de Oliveira Silva
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Vanessa Barbosa Malaquias
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Andre Ducati Luchessi
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, 59012-570, Brazil
| | - Marcelo Arruda Nakazone
- Department of Cardiology & Cardiovascular Surgery, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto, 15090-000, Brazil
| | - Tayanne Silva Carmo
- Department of Biochemistry & Molecular Biology, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto, 15090-000, Brazil
| | - Dorotéia Rossi Silva Souza
- Department of Biochemistry & Molecular Biology, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto, 15090-000, Brazil
| | - Marcelo Ferraz Sampaio
- Department of Cardiology, Hospital Beneficencia Portuguesa de Sao Paulo, Sao Paulo, 01323-001, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical & Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, 05508-000, Brazil
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Lee HS, Kim B, Park T. Genome- and epigenome-wide association studies identify susceptibility of CpG sites and regions for metabolic syndrome in a Korean population. Clin Epigenetics 2024; 16:60. [PMID: 38685121 PMCID: PMC11059751 DOI: 10.1186/s13148-024-01671-5] [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: 11/14/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND While multiple studies have investigated the relationship between metabolic syndrome (MetS) and its related traits (fasting glucose, triglyceride, HDL cholesterol, blood pressure, waist circumference) and DNA methylation, our understanding of the epigenetic mechanisms in MetS remains limited. Therefore, we performed an epigenome-wide meta-analysis of blood DNA methylation to identify differentially methylated probes (DMPs) and differentially methylated regions (DMRs) associated with MetS and its components using two independent cohorts comprising a total of 2,334 participants. We also investigated the specific genetic effects on DNA methylation, identified methylation quantitative trait loci (meQTLs) through genome-wide association studies and further utilized Mendelian randomization (MR) to assess how these meQTLs subsequently influence MetS status. RESULTS We identified 40 DMPs and 27 DMRs that are significantly associated with MetS. In addition, we identified many novel DMPs and DMRs underlying inflammatory and steroid hormonal processes. The most significant associations were observed in 3 DMPs (cg19693031, cg26974062, cg02988288) and a DMR (chr1:145440444-145441553) at the TXNIP, which are involved in lipid metabolism. These CpG sites were identified as coregulators of DNA methylation in MetS, TG and FAG levels. We identified a total of 144 cis-meQTLs, out of which only 13 were found to be associated with DMPs for MetS. Among these, we confirmed the identified causal mediators of genetic effects at CpG sites cg01881899 at ABCG1 and cg00021659 at the TANK genes for MetS. CONCLUSIONS This study observed whether specific CpGs and methylated regions act independently or are influenced by genetic effects for MetS and its components in the Korean population. These associations between the identified DNA methylation and MetS, along with its individual components, may serve as promising targets for the development of preventive interventions for MetS.
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Affiliation(s)
- Ho-Sun Lee
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.
| | - Boram Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Taesung Park
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea
- Department of Statistics, Seoul National University, Seoul, 08826, Korea
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Zhang J, Cheng X, Wei Y, Zhang Z, Zhou Q, Guan Y, Yan Y, Wang R, Jia C, An J, He M. Epigenome-wide perspective of cadmium-associated DNA methylation and its mediation role in the associations of cadmium with lipid levels and dyslipidemia risk. Food Chem Toxicol 2024; 184:114409. [PMID: 38128686 DOI: 10.1016/j.fct.2023.114409] [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: 05/16/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Studies demonstrated the associations of cadmium (Cd) with lipid levels and dyslipidemia risk, but the mechanisms involved need further exploration. OBJECTIVES We aimed to explore the role of DNA methylation (DNAM) in the relationship of Cd with lipid levels and dyslipidemia risk. METHODS Urinary cadmium levels (UCd) were measured by inductively coupled plasma mass spectrometry, serum high-density lipoprotein (HDL), total cholesterol, triglyceride, and low-density lipoprotein were measured with kits, and DNAM was measured using the Infinium MethylationEPIC BeadChip. Robust linear regressions were conducted for epigenome-wide association study. Multivariate linear and logistic regressions were performed to explore the associations of UCd with lipid levels and dyslipidemia risk, respectively. Mediation analyses were conducted to explore potential mediating role of DNAM in the associations of Cd with lipid levels and dyslipidemia risk. RESULTS UCd was negatively associated with HDL levels (p = 0.01) and positively associated with dyslipidemia (p < 0.01). There were 92/11 DMPs/DMRs (FDR<0.05) associated with UCd. Cd-associated DNAM and pathways were connected with cardiometabolic diseases and immunity. Cg07829377 (LINC01060) mediated 42.05%/22.88% of the UCd-HDL/UCd-dyslipidemia associations (p = 0.02 and 0.01, respectively). CONCLUSIONS Cadmium caused site-specific DNAM alterations and the associations of UCd with lipid levels and dyslipidemia risk may be partially mediated by DNAM.
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Affiliation(s)
- Jiazhen Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xu Cheng
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yue Wei
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China; Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Zefang Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China; Department of Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Qihang Zhou
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Youbing Guan
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yan Yan
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ruixin Wang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chengyong Jia
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jun An
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [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: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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6
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Sarnowski C, Huan T, Ma Y, Joehanes R, Beiser A, DeCarli CS, Heard-Costa NL, Levy D, Lin H, Liu CT, Liu C, Meigs JB, Satizabal CL, Florez JC, Hivert MF, Dupuis J, De Jager PL, Bennett DA, Seshadri S, Morrison AC. Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer's disease at CPT1A locus. Clin Epigenetics 2023; 15:173. [PMID: 37891690 PMCID: PMC10612362 DOI: 10.1186/s13148-023-01589-4] [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: 07/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a major risk factor for Alzheimer's disease (AD) dementia. The mechanisms by which IR predisposes to AD are not well-understood. Epigenetic studies may help identify molecular signatures of IR associated with AD, thus improving our understanding of the biological and regulatory mechanisms linking IR and AD. METHODS We conducted an epigenome-wide association study of IR, quantified using the homeostatic model assessment of IR (HOMA-IR) and adjusted for body mass index, in 3,167 participants from the Framingham Heart Study (FHS) without type 2 diabetes at the time of blood draw used for methylation measurement. We identified DNA methylation markers associated with IR at the genome-wide level accounting for multiple testing (P < 1.1 × 10-7) and evaluated their association with neurological traits in participants from the FHS (N = 3040) and the Religious Orders Study/Memory and Aging Project (ROSMAP, N = 707). DNA methylation profiles were measured in blood (FHS) or dorsolateral prefrontal cortex (ROSMAP) using the Illumina HumanMethylation450 BeadChip. Linear regressions (ROSMAP) or mixed-effects models accounting for familial relatedness (FHS) adjusted for age, sex, cohort, self-reported race, batch, and cell type proportions were used to assess associations between DNA methylation and neurological traits accounting for multiple testing. RESULTS We confirmed the strong association of blood DNA methylation with IR at three loci (cg17901584-DHCR24, cg17058475-CPT1A, cg00574958-CPT1A, and cg06500161-ABCG1). In FHS, higher levels of blood DNA methylation at cg00574958 and cg17058475 were both associated with lower IR (P = 2.4 × 10-11 and P = 9.0 × 10-8), larger total brain volumes (P = 0.03 and P = 9.7 × 10-4), and smaller log lateral ventricular volumes (P = 0.07 and P = 0.03). In ROSMAP, higher levels of brain DNA methylation at the same two CPT1A markers were associated with greater risk of cognitive impairment (P = 0.005 and P = 0.02) and higher AD-related indices (CERAD score: P = 5 × 10-4 and 0.001; Braak stage: P = 0.004 and P = 0.01). CONCLUSIONS Our results suggest potentially distinct epigenetic regulatory mechanisms between peripheral blood and dorsolateral prefrontal cortex tissues underlying IR and AD at CPT1A locus.
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Affiliation(s)
- Chloé Sarnowski
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Alexa Beiser
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Nancy L Heard-Costa
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel Levy
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia L Satizabal
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Harvard University, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, Canada
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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7
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Luo M, Xie X, Wu J, Zhang L, Zheng X, Xie M, Lin N, Xiao H, Zeng J, Lan G, Lu X, Ye X, Huang Z, Xu T, Wang T, Lin K, Guo Y, Xie X. Association of ambient PM 10 and PM 2.5 with coronary stenosis measured using selective coronary angiography. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115338. [PMID: 37556955 DOI: 10.1016/j.ecoenv.2023.115338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/14/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Long-term ambient particulate matter (PM) exposure exerts detrimental effects on cardiovascular health. Evidence on the relation of chronically exposed ambient PM10 and PM2.5 with coronary stenosis remains lacking. Our aim was to investigate the association of PM10 and PM2.5 with coronary stenosis in patients undergoing coronary angiography. METHODS We performed a retrospective cohort study consisting of 7513 individuals who underwent coronary angiography in Fujian Province, China, from January 2019 to December 2021. We calculated a modified Gensini score (GS) to represent the degree of stenosis in coronary arteries by selective coronary angiography. We fitted linear regressions and logistic models to assess the association of PM10 and PM2.5 with coronary stenosis. We employed restricted cubic splines to describe the exposure-response curves. We performed mediation analyses to assess the potential mediators. RESULTS Long-term ambient PM10 and PM2.5 (prior three years average) exposure was significantly associated with the GS, with a breakpoint concentration of 47.5 μg/m3 and 25.8 μg/m3 for PM10 and PM2.5, respectively, above which we found a linear positive exposure-response relationship of ambient PM with GS. Each 10 µg /m3 increase in PM10 exposure (β: 4.81, 95 % CI: 0.44-9.19) and PM2.5 exposure [β: 10.50, 95 % CI: 3.14-17.86] were positively related to the GS. The adjusted odds ratio (OR) for each 10 µg/m3 increment in PM10 exposure on severe coronary stenosis was 1.33 (95 % CI: 1.04-1.76). Correspondingly, the adjusted OR for PM2.5 was 1.87 (95 % CI: 1.24-2.99). The mediation analysis indicated that the effect of PM10 on coronary stenosis may be partially mediated through total cholesterol, low-density lipoprotein cholesterol, apolipoprotein B, serum creatinine and blood urea nitrogen, and the effect of PM2.5 may be mediated in part by hemoglobin A1c. CONCLUSION Our study provides the first evidence that chronic ambient PM10 and PM2.5 exposure was associated with coronary stenosis assessed by GS in patients with suspected coronary artery disease and reveals its potential mediators.
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Affiliation(s)
- Manqing Luo
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Xiaowei Xie
- The First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Jieyu Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Liwei Zhang
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Xi Zheng
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Mengying Xie
- The Second Clinical Medical School, Nanchang University, Nanchang, China
| | - Na Lin
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Huazhen Xiao
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Jilang Zeng
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Guohui Lan
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiaoli Lu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiaoying Ye
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zelin Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Tingting Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Tinggui Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Kaiyang Lin
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China
| | - Yansong Guo
- Department of Cardiology, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China; Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Center for Geriatrics, Fujian Provincial Clinical Research Center for Severe Acute Cardiovascular Diseases, Fuzhou, China; Fujian Heart Failure Center Alliance, Fuzhou, China.
| | - Xiaoxu Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China; Clinical Research Unit, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.
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8
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Chan MHM, Merrill SM, Konwar C, Kobor MS. An integrative framework and recommendations for the study of DNA methylation in the context of race and ethnicity. DISCOVER SOCIAL SCIENCE AND HEALTH 2023; 3:9. [PMID: 37122633 PMCID: PMC10118232 DOI: 10.1007/s44155-023-00039-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Human social epigenomics research is critical to elucidate the intersection of social and genetic influences underlying racial and ethnic differences in health and development. However, this field faces major challenges in both methodology and interpretation with regard to disentangling confounded social and biological aspects of race and ethnicity. To address these challenges, we discuss how these constructs have been approached in the past and how to move forward in studying DNA methylation (DNAm), one of the best-characterized epigenetic marks in humans, in a responsible and appropriately nuanced manner. We highlight self-reported racial and ethnic identity as the primary measure in this field, and discuss its implications in DNAm research. Racial and ethnic identity reflects the biological embedding of an individual's sociocultural experience and environmental exposures in combination with the underlying genetic architecture of the human population (i.e., genetic ancestry). Our integrative framework demonstrates how to examine DNAm in the context of race and ethnicity, while considering both intrinsic factors-including genetic ancestry-and extrinsic factors-including structural and sociocultural environment and developmental niches-when focusing on early-life experience. We reviewed DNAm research in relation to health disparities given its relevance to race and ethnicity as social constructs. Here, we provide recommendations for the study of DNAm addressing racial and ethnic differences, such as explicitly acknowledging the self-reported nature of racial and ethnic identity, empirically examining the effects of genetic variants and accounting for genetic ancestry, and investigating race-related and culturally regulated environmental exposures and experiences. Supplementary Information The online version contains supplementary material available at 10.1007/s44155-023-00039-z.
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Affiliation(s)
- Meingold Hiu-ming Chan
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Chaini Konwar
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
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9
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van der Linden EL, Meeks KAC, Chilunga F, Hayfron-Benjamin C, Bahendeka S, Klipstein-Grobusch K, Venema A, van den Born BJ, Agyemang C, Henneman P, Adeyemo A. Epigenome-wide association study of plasma lipids in West Africans: the RODAM study. EBioMedicine 2023; 89:104469. [PMID: 36791658 PMCID: PMC10025759 DOI: 10.1016/j.ebiom.2023.104469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND DNA-methylation has been associated with plasma lipid concentration in populations of diverse ethnic backgrounds, but epigenome-wide association studies (EWAS) in West-Africans are lacking. The aim of this study was to identify DNA-methylation loci associated with plasma lipids in Ghanaians. METHODS We conducted an EWAS using Illumina 450k DNA-methylation array profiles of extracted DNA from 663 Ghanaian participants. Differentially methylated positions (DMPs) were examined for association with plasma total cholesterol (TC), LDL-cholesterol, HDL-cholesterol, and triglycerides concentrations using linear regression models adjusted for age, sex, body mass index, diabetes mellitus, and technical covariates. Findings were replicated in independent cohorts of different ethnicities. FINDINGS We identified one significantly associated DMP with triglycerides (cg19693031 annotated to TXNIP, regression coefficient beta -0.26, false discovery rate adjusted p-value 0.001), which replicated in-silico in South African Batswana, African American, and European populations. From the top five DMPs with the lowest nominal p-values, two additional DMPs for triglycerides (CPT1A, ABCG1), two DMPs for LDL-cholesterol (EPSTI1, cg13781819), and one for TC (TXNIP) replicated. With the exception of EPSTI1, these loci are involved in lipid transport/metabolism or are known GWAS-associated loci. The top 5 DMPs per lipid trait explained 9.5% in the variance of TC, 8.3% in LDL-cholesterol, 6.1% in HDL-cholesterol, and 11.0% in triglycerides. INTERPRETATION The top DMPs identified in this study are in loci that play a role in lipid metabolism across populations, including West-Africans. Future studies including larger sample size, longitudinal study design and translational research is needed to increase our understanding on the epigenetic regulation of lipid metabolism among West-African populations. FUNDING European Commission under the Framework Programme (grant number: 278901).
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Affiliation(s)
- Eva L van der Linden
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands; Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands.
| | - Karlijn A C Meeks
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands; Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Felix Chilunga
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Charles Hayfron-Benjamin
- Department of Physiology, University of Ghana Medical School, Accra, Ghana; Department of Anesthesia and Critical Care, Korle Bu Teaching Hospital, Accra, Ghana
| | | | - Kerstin Klipstein-Grobusch
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, the Netherlands; Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea Venema
- Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Reproduction & Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bert-Jan van den Born
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands; Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Peter Henneman
- Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Reproduction & Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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10
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Zhou J, Xiao L, Huang R, Song F, Li L, Li P, Fang Y, Lu W, Lv C, Quan M, Zhang D, Du Q. Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation. PLANT, CELL & ENVIRONMENT 2023; 46:479-497. [PMID: 36385613 DOI: 10.1111/pce.14490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Little information is known about DNA methylation variation in shaping environment-specific drought resistance and resilience for tree adaptation. In this study, we leveraged RNA sequencing and whole-genome bisulfite sequencing data to dissect the distinction of epigenetic regulation under drought stress and rewater condition of Populus tomentosa accessions from three geographical regions. We demonstrated low resistance and high resilience for accessions from South. Non-CG methylation levels in promoter regions of Southern accessions were lower than accessions from higher latitudes and negatively regulated gene expression. CHH context methylation was more sensitive to drought stress, and the geographical-specific differentially methylated regions were scarcely changed by environmental fluctuation. We identified 60 conserved hub genes within the co-expression networks that correlate with photosynthetic and stomatal morphological traits. Epigenome-wide association studies and genome-wide association studies of these 60 hub genes revealed the interdependency between genetic and epigenetic variation in GATA9 and LECRK-VIII.2, which was associated with stomatal morphology and chlorophyll content. The natural epigenetic variation in GATA9 was also faithfully transmitted to progenies in two family-based F1 populations. This study indicates a functional relationship of DNA methylation diversity with drought resistance and resilience which offers new insights into plants' local adaptation to a stressful environment.
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Affiliation(s)
- Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Rui Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yuanyuan Fang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
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11
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Wu Z, Chen L, Hong X, Si J, Cao W, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Cong L, Wang H, Wu X, Liu Y, Guo Y, Chen Z, Lv J, Gao W, Li L. Temporal associations between leukocytes DNA methylation and blood lipids: a longitudinal study. Clin Epigenetics 2022; 14:132. [PMID: 36274151 PMCID: PMC9588246 DOI: 10.1186/s13148-022-01356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/13/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The associations between blood lipids and DNA methylation have been investigated in epigenome-wide association studies mainly among European ancestry populations. Several studies have explored the direction of the association using cross-sectional data, while evidence of longitudinal data is still lacking. RESULTS We tested the associations between peripheral blood leukocytes DNA methylation and four lipid measures from Illumina 450 K or EPIC arrays in 1084 participants from the Chinese National Twin Registry and replicated the result in 988 participants from the China Kadoorie Biobank. A total of 23 associations of 19 CpG sites were identified, with 4 CpG sites located in or adjacent to 3 genes (TMEM49, SNX5/SNORD17 and CCDC7) being novel. Among the validated associations, we conducted a cross-lagged analysis to explore the temporal sequence and found temporal associations of methylation levels of 2 CpG sites with triglyceride and 2 CpG sites with high-density lipoprotein-cholesterol (HDL-C) in all twins. In addition, methylation levels of cg11024682 located in SREBF1 at baseline were temporally associated with triglyceride at follow-up in only monozygotic twins. We then performed a mediation analysis with the longitudinal data and the result showed that the association between body mass index and HDL-C was partially mediated by the methylation level of cg06500161 (ABCG1), with a mediation proportion of 10.1%. CONCLUSIONS Our study indicated that the DNA methylation levels of ABCG1, AKAP1 and SREBF1 may be involved in lipid metabolism and provided evidence for elucidating the regulatory mechanism of lipid homeostasis.
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Affiliation(s)
- Zhiyu Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Lu Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jiahui Si
- National Institute of Health Data Science at Peking University, Peking University, Beijing, 100191, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, 100191, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, 266033, China
| | - Liming Cong
- Zhejiang Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, 210008, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, 150090, China
| | - Yu Guo
- Fuwai hospital Chinese Academy of Medical Sciences, Beijing, 100037, China
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, 100191, China
- Key Laboratory of Molecular Cardiovascular Sciences (Peking University), Ministry of Education, Beijing, 100191, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, 100191, China.
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12
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Meloni M, Moll T, Issaka A, Kuzawa CW. A biosocial return to race? A cautionary view for the postgenomic era. Am J Hum Biol 2022; 34:e23742. [PMID: 35275433 PMCID: PMC9286859 DOI: 10.1002/ajhb.23742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies demonstrating epigenetic and developmental sensitivity to early environments, as exemplified by fields like the Developmental Origins of Health and Disease (DOHaD) and environmental epigenetics, are bringing new data and models to bear on debates about race, genetics, and society. Here, we first survey the historical prominence of models of environmental determinism in early formulations of racial thinking to illustrate how notions of direct environmental effects on bodies have been used to naturalize racial hierarchy and inequalities in the past. Next, we conduct a scoping review of postgenomic work in environmental epigenetics and DOHaD that looks at the role of race/ethnicity in human health (2000-2021). Although there is substantial heterogeneity in how race is conceptualized and interpreted across studies, we observe practices that may unwittingly encourage typological thinking, including: using DNA methylation as a novel marker of racial classification; neglect of variation and reversibility within supposedly homogenous racial groups; and a tendency to label and reify whole groups as pathologized or impaired. Even in the very different politico-economic and epistemic context of contemporary postgenomic science, these trends echo deeply held beliefs in Western thinking which claimed that different environments shape different bodies and then used this logic to argue for essential differences between Europeans and non-Europeans. We conclude with a series of suggestions on interpreting and reporting findings in these fields that we feel will help researchers harness this work to benefit disadvantaged groups while avoiding the inadvertent dissemination of new and old forms of stigma or prejudice.
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Affiliation(s)
- Maurizio Meloni
- Alfred Deakin Institute for Citizenship and GlobalisationDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
| | - Tessa Moll
- Alfred Deakin Institute for Citizenship and GlobalisationDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
- School of Public Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Ayuba Issaka
- School of Health and Social Development, Faculty of HealthDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
| | - Christopher W. Kuzawa
- Department of Anthropology and Institute for Policy ResearchNorthwestern UniversityEvanstonIllinoisUSA
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13
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Kim S, White SM, Radke EG, Dean JL. Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment. ENVIRONMENT INTERNATIONAL 2022; 164:107278. [PMID: 35537365 DOI: 10.1016/j.envint.2022.107278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response to some chemical exposures. Characterization of these methylation events is critical to understand the molecular consequences of chemical exposures. In this context, a novel workflow was developed to interrogate publicly available epidemiological transcriptomic and methylomic data to identify relevant pathway level changes in response to chemical exposure, using inorganic arsenic as a case study. Gene Set Enrichment Analysis (GSEA) was used to identify causal methylation events that result in concomitant downstream transcriptional deregulation. This analysis demonstrated an unequal distribution of differentially methylated regions across the human genome. After mapping these events to known genes, significant enrichment of a subset of these pathways suggested that arsenic-mediated methylation may be both specific and non-specific. Parallel GSEA performed on matched transcriptomic samples determined that a substantially reduced subset of these pathways are enriched and that not all chemically-induced methylation results in a downstream alteration in gene expression. The resulting pathways were found to be representative of well-established molecular events known to occur in response to arsenic exposure. The harmonization of enriched transcriptional patterns with those identified from the methylomic platform promoted the characterization of plausibly causal molecular signaling events. The workflow described here enables significant gene and methylation-specific pathways to be identified from whole blood samples of individuals exposed to environmentally relevant chemical levels. As future efforts solidify specific causal relationships between these molecular events and relevant apical endpoints, this novel workflow could aid risk assessments by identifying molecular targets serving as biomarkers of hazard, informing mechanistic understanding, and characterizing dose ranges that promote relevant molecular/epigenetic signaling events occuring in response to chemical exposures.
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Affiliation(s)
- Stephanie Kim
- Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USA.
| | - Shana M White
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
| | - Elizabeth G Radke
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C., USA.
| | - Jeffry L Dean
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
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14
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Peering into the crystal ball to predict plaque rupture. J Clin Lipidol 2022; 16:383-385. [DOI: 10.1016/j.jacl.2022.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/24/2022]
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15
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Atherosclerosis Development and Progression: The Role of Atherogenic Small, Dense LDL. Medicina (B Aires) 2022; 58:medicina58020299. [PMID: 35208622 PMCID: PMC8877621 DOI: 10.3390/medicina58020299] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 12/16/2022] Open
Abstract
Atherosclerosis is responsible for large cardiovascular mortality in many countries globally. It has been shown over the last decades that the reduction of atherosclerotic progression is a critical factor for preventing future cardiovascular events. Low-density lipoproteins (LDL) have been successfully targeted, and their reduction is one of the key preventing measures in patients with atherosclerotic disease. LDL particles are pivotal for the formation and progression of atherosclerotic plaques; yet, they are quite heterogeneous, and smaller, denser LDL species are the most atherogenic. These particles have greater arterial entry and retention, higher susceptibility to oxidation, as well as reduced affinity for the LDL receptor. Increased proportion of small, dense LDL particles is an integral part of the atherogenic lipoprotein phenotype, the most common form of dyslipidemia associated with insulin resistance. Recent data suggest that both genetic and epigenetic factors might induce expression of this specific lipid pattern. In addition, a typical finding of increased small, dense LDL particles was confirmed in different categories of patients with elevated cardiovascular risk. Small, dense LDL is an independent risk factor for cardiovascular diseases, which emphasizes the clinical importance of both the quality and the quantity of LDL. An effective management of atherosclerotic disease should take into account the presence of small, dense LDL in order to prevent cardiovascular complications.
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16
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Song N, Sim JA, Dong Q, Zheng Y, Hou L, Li Z, Hsu CW, Pan H, Mulder H, Easton J, Walker E, Neale G, Wilson CL, Ness KK, Krull KR, Srivastava DK, Yasui Y, Zhang J, Hudson MM, Robison LL, Huang IC, Wang Z. Blood DNA methylation signatures are associated with social determinants of health among survivors of childhood cancer. Epigenetics 2022; 17:1389-1403. [PMID: 35109748 PMCID: PMC9586655 DOI: 10.1080/15592294.2022.2030883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Social epigenomics is an emerging field in which social scientist collaborate with computational biologists, especially epigeneticists, to address the underlying pathway for biological embedding of life experiences. This social epigenomics study included long-term childhood cancer survivors enrolled in the St. Jude Lifetime Cohort. DNA methylation (DNAm) data were generated using the Illumina EPIC BeadChip, and three social determinants of health (SDOH) factors were assessed: self-reported educational attainment, personal income, and an area deprivation index based on census track data. An epigenome-wide association study (EWAS) was performed to evaluate the relation between DNAm at each 5’-cytosine-phosphate-guanine-3’ (CpG) site and each SDOH factor based on multivariable linear regression models stratified by ancestry (European ancestry, n = 1,618; African ancestry, n = 258). EWAS among survivors of European ancestry identified 130 epigenome-wide significant SDOH–CpG associations (P < 9 × 10−8), 25 of which were validated in survivors of African ancestry (P < 0.05). Thirteen CpGs were associated with all three SDOH factors and resided at pleiotropic loci in cigarette smoking–related genes (e.g., CLDND1 and CPOX). After accounting for smoking and body mass index, these associations remained significant with attenuated effect sizes. Seven of 13 CpGs were associated with gene expression level based on 57 subsamples with blood RNA sequencing data available. In conclusion, DNAm signatures, many resembling the effect of tobacco use, were associated with SDOH factors among survivors of childhood cancer, thereby suggesting that biologically distal SDOH factors influence health behaviours or related factors, the epigenome, and subsequently survivors’ health.
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Affiliation(s)
- Nan Song
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy, College of Pharmacy, Chungbuk National University, Cheongju, Chungcheongbuk-do, Korea
| | - Jin-Ah Sim
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,School of Ai Convergence, Hallym University, Chuncheon, Gangwon-do, Korea
| | - Qian Dong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Zhenghong Li
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chia-Wei Hsu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haitao Pan
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Mulder
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Walker
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,St. Jude Children's Research Hospital, Hartwell Center, Memphis, TN, USA
| | - Geoffrey Neale
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,St. Jude Children's Research Hospital, Hartwell Center, Memphis, TN, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kevin R Krull
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deo Kumar Srivastava
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - I-Chan Huang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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17
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Walker-Short E, Buckner T, Vigers T, Carry P, Vanderlinden LA, Dong F, Johnson RK, Yang IV, Kechris K, Rewers M, Norris JM. Epigenome-Wide Association Study of Infant Feeding and DNA Methylation in Infancy and Childhood in a Population at Increased Risk for Type 1 Diabetes. Nutrients 2021; 13:4057. [PMID: 34836312 PMCID: PMC8618577 DOI: 10.3390/nu13114057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
We assessed associations between infant diet (e.g., breastfeeding and introduction to solid foods) and DNA methylation in infancy and childhood. We measured DNA methylation in peripheral blood collected in infancy (9-15 months of age) in 243 children; and in a subset of 50 children, we also measured methylation in childhood (6-9 years of age) to examine persistence, and at birth (in cord blood) to examine temporality. We performed multivariable linear regression of infant diet on the outcome of methylation using epigenome-wide and candidate site approaches. We identified six novel CpG sites associated with breastfeeding duration using an EWAS approach. One differentially methylated site presented directionally consistent associations with breastfeeding (cg00574958, CPT1A) in infancy and childhood but not at birth. Two differentially methylated sites in infancy (cg19693031, TXNIP; cg23307264, KHSRP) were associated with breastfeeding and were not present at birth; however, these associations did not persist into childhood. Associations between infant diet and methylation in infancy at three sites (cg22369607, AP001525.1; cg2409200, TBCD; cg27173510, PGBD5) were also present at birth, suggesting the influence of exposures other than infant diet. Infant diet exposures are associated with persistent methylation differences in CPT1A, which may be one mechanism behind infant diet's long-term health effects.
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Affiliation(s)
- Elizabeth Walker-Short
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
| | - Timothy Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA; (T.V.); (K.K.)
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (F.D.); (M.R.)
| | - Patrick Carry
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
| | - Fran Dong
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (F.D.); (M.R.)
| | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ivana V. Yang
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA; (T.V.); (K.K.)
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (F.D.); (M.R.)
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA; (E.W.-S.); (T.B.); (P.C.); (L.A.V.); (R.K.J.); (I.V.Y.)
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