1
|
Pan X, Chen Y, Yang Y, Kidambi S, Liang M, Liu P. Mediating effects of BMI on the association between DNA methylation regions and 24-h blood pressure in African Americans. J Hypertens 2024; 42:1750-1756. [PMID: 38973536 PMCID: PMC11361834 DOI: 10.1097/hjh.0000000000003796] [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] [Indexed: 07/09/2024]
Abstract
BACKGROUND DNA methylation is an important epigenetic mechanism that may influence blood pressure (BP) regulation and hypertension risk. Obesity, a major lifestyle factor associated with hypertension, may interact with DNA methylation to affect BP. However, the indirect effect of DNA methylation on 24-h BP measurements mediated by obesity-related phenotypes such as BMI has not been investigated. METHODS Causal mediation analysis was applied to examine the mediating role of BMI in the relation between DNA methylation and 24-h BP phenotypes, including SBP, DBP and mean arterial blood pressure (MAP), in 281 African American participants. RESULTS Analysis of 38 215 DNA methylation regions, derived from 1 549 368 CpG sites across the genome, identified up to 138 methylation regions that were significantly associated with 24-h BP measurements through BMI mediation. Among them, 38 (19.2%) methylation regions were concurrently associated with SBP, DBP and MAP. Genes associated with BMI-mediated methylation regions are potentially involved in various chronic diseases such as coronary artery disease and renal disease, which are often caused or exacerbated by hypertension. Notably, three genes ( CDH4 , NOTCH1 and COLGALT1 ) showed both direct associations with 24-h BP measurements and indirect associations through BMI after adjusting for age and sex covariates. CONCLUSION Our findings suggest that DNA methylation may contribute to the regulation of 24-h BP in African Americans both directly and indirectly through BMI mediation.
Collapse
Affiliation(s)
- Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yuru Chen
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yifan Yang
- Department of Mathematics, Shanghai Normal University, Shanghai, China
- Transwarp Technology Co., LTD, Shanghai, China
| | - Srividya Kidambi
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mingyu Liang
- Department of Physiology, University of Arizona, Tucson, AZ, USA
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
2
|
Shen Y, Domingo-Relloso A, Kupsco A, Kioumourtzoglou MA, Tellez-Plaza M, Umans JG, Fretts AM, Zhang Y, Schnatz PF, Casanova R, Martin LW, Horvath S, Manson JE, Cole SA, Wu H, Whitsel EA, Baccarelli AA, Navas-Acien A, Gao F. AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease. Brief Bioinform 2024; 25:bbae479. [PMID: 39323093 PMCID: PMC11424508 DOI: 10.1093/bib/bbae479] [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: 03/22/2024] [Revised: 08/17/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024] Open
Abstract
Coronary heart disease (CHD) is one of the leading causes of mortality and morbidity in the United States. Accurate time-to-event CHD prediction models with high-dimensional DNA methylation and clinical features may assist with early prediction and intervention strategies. We developed a state-of-the-art deep learning autoencoder survival analysis model (AESurv) to effectively analyze high-dimensional blood DNA methylation features and traditional clinical risk factors by learning low-dimensional representation of participants for time-to-event CHD prediction. We demonstrated the utility of our model in two cohort studies: the Strong Heart Study cohort (SHS), a prospective cohort studying cardiovascular disease and its risk factors among American Indians adults; the Women's Health Initiative (WHI), a prospective cohort study including randomized clinical trials and observational study to improve postmenopausal women's health with one of the main focuses on cardiovascular disease. Our AESurv model effectively learned participant representations in low-dimensional latent space and achieved better model performance (concordance index-C index of 0.864 ± 0.009 and time-to-event mean area under the receiver operating characteristic curve-AUROC of 0.905 ± 0.009) than other survival analysis models (Cox proportional hazard, Cox proportional hazard deep neural network survival analysis, random survival forest, and gradient boosting survival analysis models) in the SHS. We further validated the AESurv model in WHI and also achieved the best model performance. The AESurv model can be used for accurate CHD prediction and assist health care professionals and patients to perform early intervention strategies. We suggest using AESurv model for future time-to-event CHD prediction based on DNA methylation features.
Collapse
Affiliation(s)
- Yike Shen
- Department of Earth and Environmental Sciences, University of Texas at Arlington, 500 Yates Street, Arlington, TX, 76019, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Arce Domingo-Relloso
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, C. de Melchor Fernández Almagro, 5, Fuencarral-El Pardo, 5, Madrid, 28029, Spain
- Department of Statistics and Operations Research, University of Valencia, Carrer del Dr. Moliner, 50, Valencia, 46100, Spain
- Department of Biostatistics, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Marianthi-Anna Kioumourtzoglou
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, C. de Melchor Fernández Almagro, 5, Fuencarral-El Pardo, 5, Madrid, 28029, Spain
| | - Jason G Umans
- Department of Medicine, Georgetown-Howard Universities Center for Clinical and Translational Science, 4000 Reservoir Road NW, Washington, DC, 20007, USA
| | - Amanda M Fretts
- Department of Epidemiology, University of Washington, 3980 15th Ave NE, Seattle, WA, 98195, USA
| | - Ying Zhang
- Center for American Indian Health Research, Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, 801 N.E. 13th Street, Oklahoma City, OK, 73104, USA
| | - Peter F Schnatz
- Department of OB/GYN and Internal Medicine, Reading Hospital/Tower Health & Drexel University, 301 S 7th Ave, West Reading, PA, 19611, USA
| | - Ramon Casanova
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, 475 Vine St, Winston Salem, NC, 27101, USA
| | - Lisa Warsinger Martin
- Department of Medicine, Division of Cardiology, George Washington University, 2300 Eye Street, NW, Washington, DC, 20037, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), 695 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Altos Lab Inc, Granta Park, Little Abington, Cambridge, CB21 6GQ, United Kingdom
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 900 Commonwealth Ave, Boston, MA, 02215, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX, 78227, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health and Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
- Harvard T.H. Chan School of Public Health, Harvard University, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Feng Gao
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| |
Collapse
|
3
|
Wang Z, Wallace DA, Spitzer BW, Huang T, Taylor K, Rotter JI, Rich SS, Liu PY, Daviglus ML, Hou L, Ramos AR, Kaur S, Durda JP, González HM, Fornage M, Redline S, Isasi CR, Sofer T. Analysis of C-reactive protein omics-measures associates methylation risk score with sleep health and related health outcomes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.04.24313008. [PMID: 39281736 PMCID: PMC11398435 DOI: 10.1101/2024.09.04.24313008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Introduction DNA methylation (DNAm) predictors of high sensitivity C-reactive protein (CRP) offer a stable and accurate means of assessing chronic inflammation, bypassing the CRP protein fluctuations secondary to acute illness. Poor sleep health is associated with elevated inflammation (including elevated blood CRP levels) which may explain associations of sleep insufficiency with metabolic, cardiovascular and neurological diseases. Our study aims to characterize the relationships among sleep health phenotypes and CRP markers -blood, genetic, and epigenetic indicators-within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Methods In HCHS/SOL, methylation risk scores (MRS)-CRP and polygenetic risk score (PRS)-CRP were constructed separately as weighted sums of methylation beta values or allele counts, respectively, for each individual. Sleep health phenotypes were measured using self-reported questionnaires and objective measurements. Survey-weighted linear regression established the association between the multiple sleep phenotypes (obstructive sleep apnea (OSA), sleep duration, insomnia and excessive sleepiness symptom), cognitive assessments, diabetes and hypertension with CRP markers while adjusting for age, sex, BMI, study center, and the first five principal components of genetic ancestry in HCHS/SOL. Results We included 2221 HCHS/SOL participants (age range 37-76 yrs, 65.7% female) in the analysis. Both the MRS-CRP (95% confidence interval (CI): 0.32-0.42, p = 3.3 × 10-38) and the PRS-CRP (95% CI: 0.15-0.25, p = 1 × 10-14) were associated with blood CRP level. Moreover, MRS-CRP was associated with sleep health phenotypes (OSA, long sleep duration) and related conditions (diabetes and hypertension), while PRS-CRP markers were not associated with these traits. Circulating CRP level was associated with sleep duration and diabetes. Associations between OSA traits and metabolic comorbidities weakened after adjusting for MRS-CRP, most strongly for diabetes, and least for hypertension. Conclusions MRS-CRP is a promising estimate for systemic and chronic inflammation as reflected by circulating CRP levels, which either mediates or serves as a common cause of the association between sleep phenotypes and related comorbidities, especially in the presence of diabetes.
Collapse
Affiliation(s)
- Ziqing Wang
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Danielle A Wallace
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Brian W Spitzer
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tianyi Huang
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Baltimore, MD, USA
| | - Kent Taylor
- 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
| | - 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
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Peter Y Liu
- Division of Genetics, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Martha L Daviglus
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alberto R Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sonya Kaur
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J Peter Durda
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Hector M González
- Department of Neurosciences and Shiley-Marcos Alzheimer's Disease Center, University of California, San Diego, La Jolla, CA, USA
| | - Myriam Fornage
- 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
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carmen R Isasi
- Department of Epidemiology & Population Health, Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tamar Sofer
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
4
|
Skovgaard AC, Mohammadnejad A, Beck HC, Tan Q, Soerensen M. Multi-omics association study of DNA methylation and gene expression levels and diagnoses of cardiovascular diseases in Danish Twins. Clin Epigenetics 2024; 16:117. [PMID: 39187864 PMCID: PMC11348607 DOI: 10.1186/s13148-024-01727-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Cardiovascular diseases (CVDs) are major causes of mortality and morbidity worldwide; yet the understanding of their molecular basis is incomplete. Multi-omics studies have significant potential to uncover these mechanisms, but such studies are challenged by genetic and environmental confounding-a problem that can be effectively reduced by investigating intrapair differences in twins. Here, we linked data on all diagnoses of the circulatory system from the nationwide Danish Patient Registry (spanning 1977-2022) to a study population of 835 twins holding genome-wide DNA methylation and gene expression data. CVD diagnoses were divided into prevalent or incident cases (i.e., occurring before or after blood sample collection (2007-2011)). The diagnoses were classified into four groups: cerebrovascular diseases, coronary artery disease (CAD), arterial and other cardiovascular diseases (AOCDs), and diseases of the veins and lymphatic system. Statistical analyses were performed by linear (prevalent cases) or cox (incident cases) regression analyses at both the individual-level and twin pair-level. Significant genes (p < 0.05) in both types of biological data and at both levels were inspected by bioinformatic analyses, including gene set enrichment analysis and interaction network analysis. RESULTS In general, more genes were found for prevalent than for incident cases, and bioinformatic analyses primarily found pathways of the immune system, signal transduction and diseases for prevalent cases, and pathways of cell-cell communication, metabolisms of proteins and RNA, gene expression, and chromatin organization groups for incident cases. This potentially reflects biology related to response to CVD (prevalent cases) and mechanisms related to regulation and development of disease (incident cases). Of specific genes, Myosin 1E was found to be central for CAD, and DEAD-Box Helicase 5 for AOCD. These genes were observed in both the prevalent and the incident analyses, potentially reflecting that their DNA methylation and gene transcription levels change both because of disease (prevalent cases) and prior disease (incident cases). CONCLUSION We present novel biomarkers for CVD by performing multi-omics analysis in twins, hereby lowering the confounding due to shared genetics and early life environment-a study design that is surprisingly rare in the field of CVD, and where additional studies are highly needed.
Collapse
Affiliation(s)
- Asmus Cosmos Skovgaard
- The Danish Twin Registry and the Research Unit for Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| | - Afsaneh Mohammadnejad
- The Danish Twin Registry and the Research Unit for Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Hans Christian Beck
- Center for Individualized Medicine in Arterial Diseases, Department of Biochemistry, Odense University Hospital, J.B. Winsloews Vej 4, 5000, Odense C, Denmark
| | - Qihua Tan
- The Danish Twin Registry and the Research Unit for Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Mette Soerensen
- The Danish Twin Registry and the Research Unit for Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, J.B. Winsloews Vej 4, 5000, Odense C, Denmark
| |
Collapse
|
5
|
Wu J, Palasantzas V, Andreu-Sánchez S, Plösch T, Leonard S, Li S, Bonder MJ, Westra HJ, van Meurs J, Ghanbari M, Franke L, Zhernakova A, Fu J, Hoogerland JA, Zhernakova DV. Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation. Clin Epigenetics 2024; 16:104. [PMID: 39138531 PMCID: PMC11323446 DOI: 10.1186/s13148-024-01718-7] [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: 12/14/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND The plasma metabolome reflects the physiological state of various biological processes and can serve as a proxy for disease risk. Plasma metabolite variation, influenced by genetic and epigenetic mechanisms, can also affect the cellular microenvironment and blood cell epigenetics. The interplay between the plasma metabolome and the blood cell epigenome remains elusive. In this study, we performed an epigenome-wide association study (EWAS) of 1183 plasma metabolites in 693 participants from the LifeLines-DEEP cohort and investigated the causal relationships in DNA methylation-metabolite associations using bidirectional Mendelian randomization and mediation analysis. RESULTS After rigorously adjusting for potential confounders, including genetics, we identified five robust associations between two plasma metabolites (L-serine and glycine) and three CpG sites located in two independent genomic regions (cg14476101 and cg16246545 in PHGDH and cg02711608 in SLC1A5) at a false discovery rate of less than 0.05. Further analysis revealed a complex bidirectional relationship between plasma glycine/serine levels and DNA methylation. Moreover, we observed a strong mediating role of DNA methylation in the effect of glycine/serine on the expression of their metabolism/transport genes, with the proportion of the mediated effect ranging from 11.8 to 54.3%. This result was also replicated in an independent population-based cohort, the Rotterdam Study. To validate our findings, we conducted in vitro cell studies which confirmed the mediating role of DNA methylation in the regulation of PHGDH gene expression. CONCLUSIONS Our findings reveal a potential feedback mechanism in which glycine and serine regulate gene expression through DNA methylation.
Collapse
Affiliation(s)
- Jiafei Wu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Victoria Palasantzas
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Perinatal Neurobiology Research Group, Department of Pediatrics, School of Medicine and Health Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sam Leonard
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shuang Li
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Joanne A Hoogerland
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| |
Collapse
|
6
|
Huang S, Wei X, Qin F, Yuan Z, Mo C, Kang Y, Huang C, Jiang J, Ye L. Assessing causal association of circulating micronutrients and systemic lupus erythematosus susceptibility: a Mendelian randomization study. Front Nutr 2024; 11:1359697. [PMID: 39161911 PMCID: PMC11333035 DOI: 10.3389/fnut.2024.1359697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/04/2024] [Indexed: 08/21/2024] Open
Abstract
Background Previous studies showed the conflicting associations between circulating micronutrient levels and systemic lupus erythematosus (SLE). Therefore, we aimed to clarify the causal association between circulating micronutrient levels and the risk of SLE by two-sample Mendelian randomization (MR) analysis. Methods 56 single nucleotide polymorphisms (SNPs) significantly associated with 14 circulating micronutrients (vitamin A, B6, B9, B12, C, D and E, phosphorus, calcium, magnesium, copper, iron, zinc, and selenium) in published genome-wide association studies (GWAS) were used as instrumental variables (IVs). And summary statistics related to SLE were obtained from the IEU OpenGWAS database. We used the MR Steiger test to estimate the possible causal direction between circulating micronutrients and SLE. In the MR analysis, inverse variance weighting (IVW) method and the Wald ratio was as the main methods., Moreover, the MR-Pleiotropy residuals and outliers method (MR-PRESSO), Cochrane's Q-test, MR-Egger intercept method and leave-one-out analyses were applied as sensitivity analyses. Additionally, we conducted a retrospective analysis involving the 20,045 participants from the Third National Health and Nutritional Examination Survey (NHANES III). Weight variables were provided in the NHANES data files. Univariate and multivariate logistic regression analyses were performed to determine the associations between circulating micronutrients and SLE. Results The MR estimates obtained from the IVW method revealed potential negative correlations between circulating calcium (OR: 0.06, 95% CI: 0.01-0.49, P = 0.009), iron levels (OR: 0.63, 95% CI: 0.43-0.92, P = 0.016) and the risk of SLE. The results remained robust, even under various pairs of sensitivity analyses. Our retrospective analysis demonstrated that the levels of vitamin D, serum total calcium, and serum iron were significantly lower in SLE patients (N = 40) when compared to the control group (N = 20,005). Multivariate logistic regression analysis further established that increased levels of vitamin D and serum total calcium served as protective factors against SLE. Conclusion Our results provided genetic evidence supporting the potential protective role of increasing circulating calcium in the risk of SLE. Maintaining adequate levels of calcium may help reduce the risk of SLE.
Collapse
Affiliation(s)
- Shihui Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Xuemei Wei
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Fang Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Zongxiang Yuan
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuye Mo
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yiwen Kang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Chunlin Huang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Life Science Institute, Guangxi Medical University, Nanning, China
| |
Collapse
|
7
|
Huang D, Shang W, Xu M, Wan Q, Zhang J, Tang X, Shen Y, Wang Y, Yu Y. Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension. Circ Res 2024; 135:e76-e93. [PMID: 38841840 DOI: 10.1161/circresaha.124.324455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. METHODS We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. RESULTS We discovered that DNA methylation-associated genetic effects, especially in non-cytosine-phosphate-guanine (non-CpG) island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 (nuclear receptor subfamily 2 group F member 2) binding at the enhancer locus. CONCLUSIONS Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.
Collapse
Affiliation(s)
- Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
- School of Food Science and Technology, Jiangnan University, Wuxi, China (D.H.)
| | - Wenlong Shang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Mengtong Xu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Qiangyou Wan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine (Q.W.)
| | - Jin Zhang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Xiaofeng Tang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Yan Wang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| |
Collapse
|
8
|
Carbonneau M, Li Y, Prescott B, Liu C, Huan T, Joehanes R, Murabito JM, Heard‐Costa NL, Xanthakis V, Levy D, Ma J. Epigenetic Age Mediates the Association of Life's Essential 8 With Cardiovascular Disease and Mortality. J Am Heart Assoc 2024; 13:e032743. [PMID: 38808571 PMCID: PMC11255626 DOI: 10.1161/jaha.123.032743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/25/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Life's Essential 8 (LE8) is an enhanced metric for cardiovascular health. The interrelations among LE8, biomarkers of aging, and disease risks are unclear. METHODS AND RESULTS LE8 score was calculated for 5682 Framingham Heart Study participants. We implemented 4 DNA methylation-based epigenetic age biomarkers, with older epigenetic age hypothesized to represent faster biological aging, and examined whether these biomarkers mediated the associations between the LE8 score and cardiovascular disease (CVD), CVD-specific mortality, and all-cause mortality. We found that a 1 SD increase in the LE8 score was associated with a 35% (95% CI, 27-41; P=1.8E-15) lower risk of incident CVD, a 36% (95% CI, 24-47; P=7E-7) lower risk of CVD-specific mortality, and a 29% (95% CI, 22-35; P=7E-15) lower risk of all-cause mortality. These associations were partly mediated by epigenetic age biomarkers, particularly the GrimAge and the DunedinPACE scores. The potential mediation effects by epigenetic age biomarkers tended to be more profound in participants with higher genetic risk for older epigenetic age, compared with those with lower genetic risk. For example, in participants with higher GrimAge polygenic scores (greater than median), the mean proportion of mediation was 39%, 39%, and 78% for the association of the LE8 score with incident CVD, CVD-specific mortality, and all-cause mortality, respectively. No significant mediation was observed in participants with lower GrimAge polygenic score. CONCLUSIONS DNA methylation-based epigenetic age scores mediate the associations between the LE8 score and incident CVD, CVD-specific mortality, and all-cause mortality, particularly in individuals with higher genetic predisposition for older epigenetic age.
Collapse
Affiliation(s)
- Madeleine Carbonneau
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
- Framingham Heart StudyFraminghamMA
| | - Yi Li
- Department of BiostatisticsBoston University School of Public HealthBostonMA
| | - Brenton Prescott
- Section of Preventive Medicine and EpidemiologyBoston University School of MedicineBostonMA
| | - Chunyu Liu
- Department of BiostatisticsBoston University School of Public HealthBostonMA
| | - Tianxiao Huan
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
- Framingham Heart StudyFraminghamMA
| | - Roby Joehanes
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
- Framingham Heart StudyFraminghamMA
| | - Joanne M. Murabito
- Framingham Heart StudyFraminghamMA
- Department of MedicineSection of General Internal Medicine Boston University Chobanian & Avedisian School of Medicine, Boston, MA and Boston Medical CenterBostonMA
| | - Nancy L. Heard‐Costa
- Department of MedicineSection of General Internal Medicine Boston University Chobanian & Avedisian School of Medicine, Boston, MA and Boston Medical CenterBostonMA
| | - Vanessa Xanthakis
- Framingham Heart StudyFraminghamMA
- Department of BiostatisticsBoston University School of Public HealthBostonMA
- Section of Preventive Medicine and EpidemiologyBoston University School of MedicineBostonMA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMD
- Framingham Heart StudyFraminghamMA
| | - Jiantao Ma
- Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and PolicyTufts UniversityBostonMA
| |
Collapse
|
9
|
Drouard G, Mykkänen J, Heiskanen J, Pohjonen J, Ruohonen S, Pahkala K, Lehtimäki T, Wang X, Ollikainen M, Ripatti S, Pirinen M, Raitakari O, Kaprio J. Exploring machine learning strategies for predicting cardiovascular disease risk factors from multi-omic data. BMC Med Inform Decis Mak 2024; 24:116. [PMID: 38698395 PMCID: PMC11064347 DOI: 10.1186/s12911-024-02521-3] [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: 11/04/2022] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Machine learning (ML) classifiers are increasingly used for predicting cardiovascular disease (CVD) and related risk factors using omics data, although these outcomes often exhibit categorical nature and class imbalances. However, little is known about which ML classifier, omics data, or upstream dimension reduction strategy has the strongest influence on prediction quality in such settings. Our study aimed to illustrate and compare different machine learning strategies to predict CVD risk factors under different scenarios. METHODS We compared the use of six ML classifiers in predicting CVD risk factors using blood-derived metabolomics, epigenetics and transcriptomics data. Upstream omic dimension reduction was performed using either unsupervised or semi-supervised autoencoders, whose downstream ML classifier performance we compared. CVD risk factors included systolic and diastolic blood pressure measurements and ultrasound-based biomarkers of left ventricular diastolic dysfunction (LVDD; E/e' ratio, E/A ratio, LAVI) collected from 1,249 Finnish participants, of which 80% were used for model fitting. We predicted individuals with low, high or average levels of CVD risk factors, the latter class being the most common. We constructed multi-omic predictions using a meta-learner that weighted single-omic predictions. Model performance comparisons were based on the F1 score. Finally, we investigated whether learned omic representations from pre-trained semi-supervised autoencoders could improve outcome prediction in an external cohort using transfer learning. RESULTS Depending on the ML classifier or omic used, the quality of single-omic predictions varied. Multi-omics predictions outperformed single-omics predictions in most cases, particularly in the prediction of individuals with high or low CVD risk factor levels. Semi-supervised autoencoders improved downstream predictions compared to the use of unsupervised autoencoders. In addition, median gains in Area Under the Curve by transfer learning compared to modelling from scratch ranged from 0.09 to 0.14 and 0.07 to 0.11 units for transcriptomic and metabolomic data, respectively. CONCLUSIONS By illustrating the use of different machine learning strategies in different scenarios, our study provides a platform for researchers to evaluate how the choice of omics, ML classifiers, and dimension reduction can influence the quality of CVD risk factor predictions.
Collapse
Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Juha Mykkänen
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Jarkko Heiskanen
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Joona Pohjonen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Saku Ruohonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Katja Pahkala
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Paavo Nurmi Centre & Unit for Health and Physical Activity, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Xiaoling Wang
- Georgia Prevention Institute, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Bui H, Keshawarz A, Wang M, Lee M, Ratliff SM, Lin L, Birditt KS, Faul JD, Peters A, Gieger C, Delerue T, Kardia SLR, Zhao W, Guo X, Yao J, Rotter JI, Li Y, Liu X, Liu D, Tavares JF, Pehlivan G, Breteler MMB, Karabegovic I, Ochoa-Rosales C, Voortman T, Ghanbari M, van Meurs JBJ, Nasr MK, Dörr M, Grabe HJ, London SJ, Teumer A, Waldenberger M, Weir DR, Smith JA, Levy D, Ma J, Liu C. Association analysis between an epigenetic risk score and blood pressure. RESEARCH SQUARE 2024:rs.3.rs-4243866. [PMID: 38699335 PMCID: PMC11065078 DOI: 10.21203/rs.3.rs-4243866/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: 05/05/2024]
Abstract
Background Epigenome-wide association studies have revealed multiple DNA methylation sites (CpGs) associated with alcohol consumption, an important lifestyle risk factor for cardiovascular diseases. Results We generated an alcohol consumption epigenetic risk score (ERS) based on previously reported 144 alcohol-associated CpGs and examined the association of the ERS with systolic blood pressure (SBP), diastolic blood pressure (DBP), and hypertension (HTN) in 3,898 Framingham Heart Study (FHS) participants. We found an association of alcohol intake with the ERS in the meta-analysis with 0.09 units higher ERS per drink consumed per day (p < 0.0001). Cross-sectional analyses in FHS revealed that a one-unit increment of the ERS was associated with 1.93 mm Hg higher SBP (p = 4.64E-07), 0.68 mm Hg higher DBP (p = 0.006), and an odds ratio of 1.78 for HTN (p < 2E-16). Meta-analysis of the cross-sectional association of the ERS with BP traits in eight independent external cohorts (n = 11,544) showed similar relationships with blood pressure levels, i.e., a one-unit increase in ERS was associated with 0.74 (p = 0.002) and 0.50 (p = 0.0006) mm Hg higher SBP and DBP, but could not confirm the association with hypertension. Longitudinal analyses in FHS (n = 3,260) and five independent external cohorts (n = 4,021) showed that the baseline ERS was not associated with a change in blood pressure over time or with incident HTN. Conclusions Our findings provide proof-of-concept that utilizing an ERS is a useful approach to capture the recent health consequences of lifestyle behaviors such as alcohol consumption.
Collapse
Affiliation(s)
| | | | | | - Mikyeong Lee
- National Institute of Environmental Health Sciences
| | | | | | | | | | - Annette Peters
- Helmholtz Munich, German Research Center for Environmental Health
| | - Christian Gieger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance
| | - Thomas Delerue
- Helmholtz Munich, German Research Center for Environmental Health
| | | | | | - Xiuqing Guo
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | - Jie Yao
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | - Jerome I Rotter
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | - Yi Li
- Boston University School of Public Health
| | - Xue Liu
- Boston University School of Public Health
| | - Dan Liu
- German Center for Neurodegenerative Diseases
| | | | | | | | | | | | | | | | | | | | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald
| | | | | | | | - Melanie Waldenberger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance
| | | | | | | | | | | |
Collapse
|
12
|
Bui H, Keshawarz A, Wang M, Lee M, Ratliff SM, Lin L, Birditt KS, Faul JD, Peters A, Gieger C, Delerue T, Kardia SLR, Zhao W, Guo X, Yao J, Rotter JI, Li Y, Liu X, Liu D, Tavares JF, Pehlivan G, Breteler MM, Karabegovic I, Ochoa-Rosales C, Voortman T, Ghanbari M, van Meurs JB, Nasr MK, Dörr M, Grabe HJ, London SJ, Teumer A, Waldenberger M, Weir DR, Smith JA, Levy D, Ma J, Liu C. Association analysis between an epigenetic alcohol risk score and blood pressure. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.29.24303545. [PMID: 38464320 PMCID: PMC10925472 DOI: 10.1101/2024.02.29.24303545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Epigenome-wide association studies have revealed multiple DNA methylation sites (CpGs) associated with alcohol consumption, an important lifestyle risk factor for cardiovascular diseases. Results We generated an alcohol consumption epigenetic risk score (ERS) based on previously reported 144 alcohol-associated CpGs and examined the association of the ERS with systolic blood pressure (SBP), diastolic blood pressure (DBP), and hypertension (HTN) in 3,898 Framingham Heart Study (FHS) participants. We found an association of alcohol intake with the ERS in the meta-analysis with 0.09 units higher ERS per drink consumed per day (p < 0.0001). Cross-sectional analyses in FHS revealed that a one-unit increment of the ERS was associated with 1.93 mm Hg higher SBP (p = 4.64E-07), 0.68 mm Hg higher DBP (p = 0.006), and an odds ratio of 1.78 for HTN (p < 2E-16). Meta-analysis of the cross-sectional association of the ERS with BP traits in eight independent external cohorts (n = 11,544) showed similar relationships with blood pressure levels, i.e., a one-unit increase in ERS was associated with 0.74 (p = 0.002) and 0.50 (p = 0.0006) mm Hg higher SBP and DBP, but could not confirm the association with hypertension. Longitudinal analyses in FHS (n = 3,260) and five independent external cohorts (n = 4,021) showed that the baseline ERS was not associated with a change in blood pressure over time or with incident HTN. Conclusions Our findings provide proof-of-concept that utilizing an ERS is a useful approach to capture the recent health consequences of lifestyle behaviors such as alcohol consumption.
Collapse
Affiliation(s)
- Helena Bui
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Amena Keshawarz
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Mengyao Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Lisha Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Kira S. Birditt
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, German
- Institute for Medical Informatics, Biometrics and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Gieger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Bavaria, Germany
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Bavaria, Germany
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Xiuqing Guo
- The Institute for Translational Genomics and Populations, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jie Yao
- The Institute for Translational Genomics and Populations, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Populations, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yi Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Xue Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Dan Liu
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Juliana F. Tavares
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Gökhan Pehlivan
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Monique M.B. Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Irma Karabegovic
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Centro de Vida Saludable de la Universidad de Concepción, Concepción, Chile
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Joyce B.J. van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Mohamed Kamal Nasr
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine, Greifswald, Germany
- German Center of Neurodegenerative Diseases (DZNE), Rostock/Greifswald, site Greifswald, Germany
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Melanie Waldenberger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Bavaria, Germany
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Jiantao Ma
- Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| |
Collapse
|
13
|
Guirette M, Lan J, McKeown NM, Brown MR, Chen H, de Vries PS, Kim H, Rebholz CM, Morrison AC, Bartz TM, Fretts AM, Guo X, Lemaitre RN, Liu CT, Noordam R, de Mutsert R, Rosendaal FR, Wang CA, Beilin LJ, Mori TA, Oddy WH, Pennell CE, Chai JF, Whitton C, van Dam RM, Liu J, Tai ES, Sim X, Neuhouser ML, Kooperberg C, Tinker LF, Franceschini N, Huan T, Winkler TW, Bentley AR, Gauderman WJ, Heerkens L, Tanaka T, van Rooij J, Munroe PB, Warren HR, Voortman T, Chen H, Rao DC, Levy D, Ma J. Genome-Wide Interaction Analysis With DASH Diet Score Identified Novel Loci for Systolic Blood Pressure. Hypertension 2024; 81:552-560. [PMID: 38226488 PMCID: PMC10922535 DOI: 10.1161/hypertensionaha.123.22334] [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: 11/10/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND The Dietary Approaches to Stop Hypertension (DASH) diet score lowers blood pressure (BP). We examined interactions between genotype and the DASH diet score in relation to systolic BP. METHODS We analyzed up to 9 420 585 single nucleotide polymorphisms in up to 127 282 individuals of 6 population groups (91% of European population) from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (n=35 660) and UK Biobank (n=91 622) and performed European population-specific and cross-population meta-analyses. RESULTS We identified 3 loci in European-specific analyses and an additional 4 loci in cross-population analyses at Pinteraction<5e-8. We observed a consistent interaction between rs117878928 at 15q25.1 (minor allele frequency, 0.03) and the DASH diet score (Pinteraction=4e-8; P for heterogeneity, 0.35) in European population, where the interaction effect size was 0.42±0.09 mm Hg (Pinteraction=9.4e-7) and 0.20±0.06 mm Hg (Pinteraction=0.001) in Cohorts for Heart and Aging Research in Genomic Epidemiology and the UK Biobank, respectively. The 1 Mb region surrounding rs117878928 was enriched with cis-expression quantitative trait loci (eQTL) variants (P=4e-273) and cis-DNA methylation quantitative trait loci variants (P=1e-300). Although the closest gene for rs117878928 is MTHFS, the highest narrow sense heritability accounted by single nucleotide polymorphisms potentially interacting with the DASH diet score in this locus was for gene ST20 at 15q25.1. CONCLUSIONS We demonstrated gene-DASH diet score interaction effects on systolic BP in several loci. Studies with larger diverse populations are needed to validate our findings.
Collapse
Affiliation(s)
- Mélanie Guirette
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA (M.G., J.L., J.M.)
| | - Jessie Lan
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA (M.G., J.L., J.M.)
| | - Nicola M McKeown
- Programs of Nutrition, Department of Health Sciences, Sargent College of Health & Rehabilitation Sciences, Boston University, MA (N.M.M.)
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (M.R.B., H.C., P.S.d.V., A.C.M.)
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (M.R.B., H.C., P.S.d.V., A.C.M.)
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (M.R.B., H.C., P.S.d.V., A.C.M.)
| | - Hyunju Kim
- Department of Epidemiology (H.K., A.M.F.), Cardiovascular Health Research Unit, University of Washington, Seattle, WA
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (C.M.R.)
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston (M.R.B., H.C., P.S.d.V., A.C.M.)
| | - Traci M Bartz
- Departments of Biostatistics and Medicine (T.M.B.), Cardiovascular Health Research Unit, University of Washington, Seattle, WA
| | - Amanda M Fretts
- Department of Epidemiology (H.K., A.M.F.), Cardiovascular Health Research Unit, University of Washington, Seattle, WA
| | - Xiuqing Guo
- The Lundquist Institute at Harbor-University of California, Los Angeles, Torrance, CA (X.G.)
| | - Rozenn N Lemaitre
- Department of Medicine (R.N.L.), Cardiovascular Health Research Unit, University of Washington, Seattle, WA
| | - Ching-Ti Liu
- Biostatistics, Boston University School of Public Health, MA (C.-T.L.)
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics (R.N.), Leiden University Medical Center, the Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology (R.d.M., F.R.R.), Leiden University Medical Center, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology (R.d.M., F.R.R.), Leiden University Medical Center, the Netherlands
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, NSW, Australia (C.A.W., C.E.P)
- Mothers' and Babies' Research Program, Hunter Medical Research Institute, NSW, Australia (C.A.W., C.E.P.)
| | - Lawrence J Beilin
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Crawley (L.J.B., T.A.M.)
| | - Trevor A Mori
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Crawley (L.J.B., T.A.M.)
| | - Wendy H Oddy
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia (W.H.O.)
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, NSW, Australia (C.A.W., C.E.P)
- Mothers' and Babies' Research Program, Hunter Medical Research Institute, NSW, Australia (C.A.W., C.E.P.)
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System (J.F.C., C.W., R.M.v.D., E.S.T., X.S.)
| | - Clare Whitton
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System (J.F.C., C.W., R.M.v.D., E.S.T., X.S.)
- School of Population Health, Curtin University, Perth, Western Australia, Australia (C.W.)
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System (J.F.C., C.W., R.M.v.D., E.S.T., X.S.)
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University (R.M.v.D.)
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research (J.L.)
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System (J.F.C., C.W., R.M.v.D., E.S.T., X.S.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore (E.S.T.)
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System (J.F.C., C.W., R.M.v.D., E.S.T., X.S.)
| | - Marian L Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA (M.L.N., C.K., L.F.T.)
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA (M.L.N., C.K., L.F.T.)
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA (M.L.N., C.K., L.F.T.)
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill (N.F.)
| | - TianXiao Huan
- Framingham Heart Study and Population Sciences Branch, National Heart, Lung, and Blood Institute, MA (T.H., D.L.)
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Germany (T.W.W.)
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD (A.R.B.)
| | - W James Gauderman
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California (W.J.G.)
| | - Luc Heerkens
- Division of Human Nutrition and Health, Wageningen University & Research, the Netherlands (L.H.)
| | - Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD (T.T.)
| | - Jeroen van Rooij
- Department of Internal Medicine (J.v.R.), Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Patricia B Munroe
- Centre of Clinical Pharmacology & Precision Medicine, William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, United Kingdom (P.B.M., H.R.W.)
| | - Helen R Warren
- Centre of Clinical Pharmacology & Precision Medicine, William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, United Kingdom (P.B.M., H.R.W.)
| | - Trudy Voortman
- Department of Epidemiology (T.V.), Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Honglei Chen
- Department of Epidemiology and Biostatistics College of Human Medicine, Michigan State University, East Lansing (H.C.)
| | - D C Rao
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University School of Medicine, St. Louis, MO (D.C.R.)
| | - Daniel Levy
- Framingham Heart Study and Population Sciences Branch, National Heart, Lung, and Blood Institute, MA (T.H., D.L.)
| | - Jiantao Ma
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA (M.G., J.L., J.M.)
| |
Collapse
|
14
|
Domínguez-Barragán J, Fernández-Sanlés A, Hernáez Á, Llauradó-Pont J, Marrugat J, Robinson O, Tzoulaki I, Elosua R, Lassale C. Blood DNA methylation signature of diet quality and association with cardiometabolic traits. Eur J Prev Cardiol 2024; 31:191-202. [PMID: 37793095 PMCID: PMC10809172 DOI: 10.1093/eurjpc/zwad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
AIMS Diet quality might influence cardiometabolic health through epigenetic changes, but this has been little investigated in adults. Our aims were to identify cytosine-phosphate-guanine (CpG) dinucleotides associated with diet quality by conducting an epigenome-wide association study (EWAS) based on blood DNA methylation (DNAm) and to assess how diet-related CpGs associate with inherited susceptibility to cardiometabolic traits: body mass index (BMI), systolic blood pressure (SBP), triglycerides, type 2 diabetes (T2D), and coronary heart disease (CHD). METHODS AND RESULTS Meta-EWAS including 5274 participants in four cohorts from Spain, the USA, and the UK. We derived three dietary scores (exposures) to measure adherence to a Mediterranean diet, to a healthy plant-based diet, and to the Dietary Approaches to Stop Hypertension. Blood DNAm (outcome) was assessed with the Infinium arrays Human Methylation 450K BeadChip and MethylationEPIC BeadChip. For each diet score, we performed linear EWAS adjusted for age, sex, blood cells, smoking and technical variables, and BMI in a second set of models. We also conducted Mendelian randomization analyses to assess the potential causal relationship between diet-related CpGs and cardiometabolic traits. We found 18 differentially methylated CpGs associated with dietary scores (P < 1.08 × 10-7; Bonferroni correction), of which 12 were previously associated with cardiometabolic traits. Enrichment analysis revealed overrepresentation of diet-associated genes in pathways involved in inflammation and cardiovascular disease. Mendelian randomization analyses suggested that genetically determined methylation levels corresponding to lower diet quality at cg02079413 (SNORA54), cg02107842 (MAST4), and cg23761815 (SLC29A3) were causally associated with higher BMI and at cg05399785 (WDR8) with greater SBP, and methylation levels associated with higher diet quality at cg00711496 (PRMT1) with lower BMI, T2D risk, and CHD risk and at cg0557921 (AHRR) with lower CHD risk. CONCLUSION Diet quality in adults was related to differential methylation in blood at 18 CpGs, some of which related to cardiometabolic health.
Collapse
Affiliation(s)
- Jorge Domínguez-Barragán
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
| | - Alba Fernández-Sanlés
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0463, Norway
- Blanquerna School of Health Sciences, Universitat Ramon Llull, 08025 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
| | - Joana Llauradó-Pont
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Jaume Marrugat
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Oliver Robinson
- μedical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ioanna Tzoulaki
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Roberto Elosua
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic—Central University of Catalunya, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Camille Lassale
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003, Barcelona, Spain
| |
Collapse
|
15
|
Akhouri V, Majumder S, Gaikwad AB. Targeting DNA methylation in diabetic kidney disease: A new perspective. Life Sci 2023; 335:122256. [PMID: 37949210 DOI: 10.1016/j.lfs.2023.122256] [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: 09/20/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Diabetic kidney disease (DKD) is a leading diabetic complication causing significant mortality among people around the globe. People with poor glycemic control accompanied by hyperinsulinemia, dyslipidemia, hypertension, and obesity develop diabetic complications. These diabetic patients develop epigenetic changes and suffer from diabetic kidney complications even after subsequent glucose control, the phenomenon that is recognized as metabolic memory. DNA methylation is an essential epigenetic modification that contributes to the development and progression of several diabetic complications, including DKD. The aberrant DNA methylation pattern at CpGs sites within several genes, such as mTOR, RPTOR, IRS2, GRK5, SLC27A3, LCAT, and SLC1A5, associated with the accompanying risk factors exacerbate the DKD progression. Although drugs such as azacytidine and decitabine have been approved to target DNA methylation for diseases such as hematological malignancies, none have been approved for the treatment of DKD. More importantly, no DNA hypomethylation-targeting drugs have been approved for any disease conditions. Understanding the alteration in DNA methylation and its association with the disease risk factors is essential to target DKD effectively. This review has discussed the abnormal DNA methylation pattern and the kidney tissue-specific expression of critical genes involved in DKD onset and progression. Moreover, we also discuss the new possible therapeutic approach that can be exploited for treating DNA methylation aberrancy in a site-specific manner against DKD.
Collapse
Affiliation(s)
- Vivek Akhouri
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Anil Bhanudas Gaikwad
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
| |
Collapse
|
16
|
Keshawarz A, Joehanes R, Ma J, Lee GY, Costeira R, Tsai PC, Masachs OM, Bell JT, Wilson R, Thorand B, Winkelmann J, Peters A, Linseisen J, Waldenberger M, Lehtimäki T, Mishra PP, Kähönen M, Raitakari O, Helminen M, Wang CA, Melton PE, Huang RC, Pennell CE, O’Sullivan TA, Ochoa-Rosales C, Voortman T, van Meurs JB, Young KL, Graff M, Wang Y, Kiel DP, Smith CE, Jacques PF, Levy D. Dietary and supplemental intake of vitamins C and E is associated with altered DNA methylation in an epigenome-wide association study meta-analysis. Epigenetics 2023; 18:2211361. [PMID: 37233989 PMCID: PMC10228397 DOI: 10.1080/15592294.2023.2211361] [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: 08/11/2022] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Dietary intake of antioxidants such as vitamins C and E protect against oxidative stress, and may also be associated with altered DNA methylation patterns. METHODS We meta-analysed epigenome-wide association study (EWAS) results from 11,866 participants across eight population-based cohorts to evaluate the association between self-reported dietary and supplemental intake of vitamins C and E with DNA methylation. EWAS were adjusted for age, sex, BMI, caloric intake, blood cell type proportion, smoking status, alcohol consumption, and technical covariates. Significant results of the meta-analysis were subsequently evaluated in gene set enrichment analysis (GSEA) and expression quantitative trait methylation (eQTM) analysis. RESULTS In meta-analysis, methylation at 4,656 CpG sites was significantly associated with vitamin C intake at FDR ≤ 0.05. The most significant CpG sites associated with vitamin C (at FDR ≤ 0.01) were enriched for pathways associated with systems development and cell signalling in GSEA, and were associated with downstream expression of genes enriched in the immune response in eQTM analysis. Furthermore, methylation at 160 CpG sites was significantly associated with vitamin E intake at FDR ≤ 0.05, but GSEA and eQTM analysis of the top most significant CpG sites associated with vitamin E did not identify significant enrichment of any biological pathways investigated. CONCLUSIONS We identified significant associations of many CpG sites with vitamin C and E intake, and our results suggest that vitamin C intake may be associated with systems development and the immune response.
Collapse
Affiliation(s)
| | - Roby Joehanes
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiantao Ma
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Gha Young Lee
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Olatz M. Masachs
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Chair of Neurogenetics, School of Medicine, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Chair of Epidemiology, Medical Faculty, Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Cardiovascular Research (DZHK), München Heart Alliance, Munich, Germany
| | - Jakob Linseisen
- Chair of Epidemiology, University Augsburg at University Hospital Augsburg, Augsburg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), München Heart Alliance, Munich, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Mika Helminen
- Tays Research Services, Tampere University Hospital, Tampere, Finland
- Faculty of Social Sciences, Health Sciences, Tampere University, Tampere, Finland
| | - Carol A. Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Phillip E. Melton
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- School of Population and Global Health, University of Western Australia, Perth, Australia
| | - Rae-Chi Huang
- Nutrition & Health Innovation Research Institute, Edith Cowan University, Perth, Australia
| | - Craig E. Pennell
- Faculty of Social Sciences, Health Sciences, Tampere University, Tampere, Finland
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | | | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Centro de Vida Saludable, Universidad de Concepción, Concepción, Chile
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Joyce B.J. van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Kristin L. Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Hebrew Senior Life, Chapel Hill, North Carolina, USA
| | - Douglas P. Kiel
- Department of Medicine, Beth Israel Deaconess Medical Center, Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Caren E. Smith
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Paul F. Jacques
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
17
|
Foster C, Mamaeva O, Shrestha S, Hidalgo B. Epigenetic age in African American adolescents with type 2 diabetes: A cross-sectional case-control study protocol. Health Sci Rep 2023; 6:e1747. [PMID: 38078300 PMCID: PMC10702396 DOI: 10.1002/hsr2.1747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 02/12/2024] Open
Abstract
Background and Aims Type 2 diabetes (T2D) is a disease caused by a relative insulin deficiency compared to the significant insulin requirement needed by the body to achieve glycemic control. T2D in adolescence appears to be increasing in prevalence over the past several decades, necessitating studies to understand for the onset of the disease to occur early in the lifespan. Given the high burden of disease, specifically in young African American adolescents, our study chose to focus initially on feasibility of recruitment of this population. Methods Data was collected at a single study center at Children's of Alabama. The protocol was completed as part of routine care or at a study visit. The study team was able to leverage the Electronic Medical Record to prescreen eligible patients to discuss the study. A variety of times of day were utilized to improve likely of success with reaching potential participants. Inclusion criteria for patients with T2D was focused on the adolescent population (ages 12-18 years), with no history of an obesity syndrome. DNA methylation age will be calculated using the EPIC 850K array. Statistical analysis will be done using linear regression analysis, adjusting for covariates. Conclusions This study's aim was to screen and enroll young African American adolescents for a study investigating epigenetic aging and T2D. Our study found that more direct contact (face-to-face- or phone call) improve success of recruitment. Leveraging the electronic medical record also helped improve success with pre-screening participants. Challenges included recruiting participants who might come from long distances to a tertiary care center. Consolidating appointments helped improve the success of reaching these participants. Other challenges included frequent address changes and changed phone numbers. Close attention to the barriers as well as the successes will aid in understanding effective strategies for this important population.
Collapse
Affiliation(s)
- Christy Foster
- Division of Pediatric EndocrinologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Olga Mamaeva
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Sadeep Shrestha
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Bertha Hidalgo
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| |
Collapse
|
18
|
Carreras-Gallo N, Dwaraka VB, Cáceres A, Smith R, Mendez TL, Went H, Gonzalez JR. Impact of tobacco, alcohol, and marijuana on genome-wide DNA methylation and its relationship with hypertension. Epigenetics 2023; 18:2214392. [PMID: 37216580 DOI: 10.1080/15592294.2023.2214392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/13/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Tobacco, alcohol, and marijuana consumption is an important public health problem because of their high use worldwide and their association with the risk of mortality and many health conditions, such as hypertension, which is the commonest risk factor for death throughout the world. A likely pathway of action of substance consumption leading to persistent hypertension is DNA methylation. Here, we evaluated the effects of tobacco, alcohol, and marijuana on DNA methylation in the same cohort (N = 3,424). Three epigenome-wide association studies (EWAS) were assessed in whole blood using the InfiniumHumanMethylationEPIC BeadChip. We also evaluated the mediation of the top CpG sites in the association between substance consumption and hypertension. Our analyses showed 2,569 CpG sites differentially methylated by alcohol drinking and 528 by tobacco smoking. We did not find significant associations with marijuana consumption after correcting for multiple comparisons. We found 61 genes overlapping between alcohol and tobacco that were enriched in biological processes involved in the nervous and cardiovascular systems. In the mediation analysis, we found 66 CpG sites that significantly mediated the effect of alcohol consumption on hypertension. The top alcohol-related CpG site (cg06690548, P-value = 5.9·10-83) mapped to SLC7A11 strongly mediated 70.5% of the effect of alcohol consumption on hypertension (P-value = 0.006). Our findings suggest that DNA methylation should be considered for new targets in hypertension prevention and management, particularly concerning alcohol consumption. Our data also encourage further research into the use of methylation in blood to study the neurological and cardiovascular effects of substance consumption.
Collapse
Affiliation(s)
| | | | - Alejandro Cáceres
- Epidemiology, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya, Barcelona, Spain
| | | | | | | | - Juan R Gonzalez
- Epidemiology, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
19
|
Guirette M, Lan J, McKeown N, Brown MR, Chen H, DE Vries PS, Kim H, Rebholz CM, Morrison AC, Bartz TM, Fretts AM, Guo X, Lemaitre RN, Liu CT, Noordam R, DE Mutsert R, Rosendaal FR, Wang CA, Beilin L, Mori TA, Oddy WH, Pennell CE, Chai JF, Whitton C, VAN Dam RM, Liu J, Tai ES, Sim X, Neuhouser ML, Kooperberg C, Tinker L, Franceschini N, Huan T, Winkler TW, Bentley AR, Gauderman WJ, Heerkens L, Tanaka T, van Rooij J, Munroe PB, Warren HR, Voortman T, Chen H, Rao DC, Levy D, Ma J. Genome-Wide Interaction Analysis with DASH Diet Score Identified Novel Loci for Systolic Blood Pressure. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.10.23298402. [PMID: 37986948 PMCID: PMC10659476 DOI: 10.1101/2023.11.10.23298402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Objective We examined interactions between genotype and a Dietary Approaches to Stop Hypertension (DASH) diet score in relation to systolic blood pressure (SBP). Methods We analyzed up to 9,420,585 biallelic imputed single nucleotide polymorphisms (SNPs) in up to 127,282 individuals of six population groups (91% of European population) from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (CHARGE; n=35,660) and UK Biobank (n=91,622) and performed European population-specific and cross-population meta-analyses. Results We identified three loci in European-specific analyses and an additional four loci in cross-population analyses at P for interaction < 5e-8. We observed a consistent interaction between rs117878928 at 15q25.1 (minor allele frequency = 0.03) and the DASH diet score (P for interaction = 4e-8; P for heterogeneity = 0.35) in European population, where the interaction effect size was 0.42±0.09 mm Hg (P for interaction = 9.4e-7) and 0.20±0.06 mm Hg (P for interaction = 0.001) in CHARGE and the UK Biobank, respectively. The 1 Mb region surrounding rs117878928 was enriched with cis-expression quantitative trait loci (eQTL) variants (P = 4e-273) and cis-DNA methylation quantitative trait loci (mQTL) variants (P = 1e-300). While the closest gene for rs117878928 is MTHFS, the highest narrow sense heritability accounted by SNPs potentially interacting with the DASH diet score in this locus was for gene ST20 at 15q25.1. Conclusion We demonstrated gene-DASH diet score interaction effects on SBP in several loci. Studies with larger diverse populations are needed to validate our findings.
Collapse
Affiliation(s)
- Mélanie Guirette
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Jessie Lan
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Nicola McKeown
- Programs of Nutrition, Department of Health Sciences, Sargent College of Health & Rehabilitation Sciences, Boston University, Boston, MA, USA
| | - Michael R Brown
- 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
| | - Han Chen
- 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
| | - Paul S DE Vries
- 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
| | - Hyunju Kim
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 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
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, Seattle, WA, USA
| | - Amanda M Fretts
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- The Lundquist Institute at Harbor-UCLA, Torrance, CA, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ching-Ti Liu
- Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Renée DE Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, NSW, Australia
- Hunter Medical Research Institute, NSW, Australia
| | - Lawrence Beilin
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Crawley, Western Australia, Australia
| | - Trevor A Mori
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Crawley, Western Australia, Australia
| | - Wendy H Oddy
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia Saw Swee Hock, School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, NSW, Australia
- Hunter Medical Research Institute, NSW, Australia
| | - Jin Fang Chai
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Clare Whitton
- School of Population Health, Curtin University, Perth, Western Australia, Australia
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Rob M VAN Dam
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - E Shyong Tai
- School of Population Health, Curtin University, Perth, Western Australia, Australia
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xueling Sim
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Marian L Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lesley Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Tianxiao Huan
- Framingham Heart Study and Population Sciences Branch, NHLBI, Framingham, MA, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg; Regensburg, Germany
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - W James Gauderman
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California; CA, USA
| | - Luc Heerkens
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Patricia B Munroe
- Centre of Clinical Pharmacology & Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Helen R Warren
- Centre of Clinical Pharmacology & Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Honglei Chen
- Department of Epidemiology and Biostatistics College of Human Medicine, Michigan State University, East Lansing, Michigan, USA
| | - D C Rao
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Levy
- Framingham Heart Study and Population Sciences Branch, NHLBI, Framingham, MA, USA
| | - Jiantao Ma
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Costeira R, Evangelista L, Wilson R, Yan X, Hellbach F, Sinke L, Christiansen C, Villicaña S, Masachs OM, Tsai PC, Mangino M, Menni C, Berry SE, Beekman M, van Heemst D, Slagboom PE, Heijmans BT, Suhre K, Kastenmüller G, Gieger C, Peters A, Small KS, Linseisen J, Waldenberger M, Bell JT. Metabolomic biomarkers of habitual B vitamin intakes unveil novel differentially methylated positions in the human epigenome. Clin Epigenetics 2023; 15:166. [PMID: 37858220 PMCID: PMC10588110 DOI: 10.1186/s13148-023-01578-7] [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: 07/03/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND B vitamins such as folate (B9), B6, and B12 are key in one carbon metabolism, which generates methyl donors for DNA methylation. Several studies have linked differential methylation to self-reported intakes of folate and B12, but these estimates can be imprecise, while metabolomic biomarkers can offer an objective assessment of dietary intakes. We explored blood metabolomic biomarkers of folate and vitamins B6 and B12, to carry out epigenome-wide analyses across up to three European cohorts. Associations between self-reported habitual daily B vitamin intakes and 756 metabolites (Metabolon Inc.) were assessed in serum samples from 1064 UK participants from the TwinsUK cohort. The identified B vitamin metabolomic biomarkers were then used in epigenome-wide association tests with fasting blood DNA methylation levels at 430,768 sites from the Infinium HumanMethylation450 BeadChip in blood samples from 2182 European participants from the TwinsUK and KORA cohorts. Candidate signals were explored for metabolite associations with gene expression levels in a subset of the TwinsUK sample (n = 297). Metabolomic biomarker epigenetic associations were also compared with epigenetic associations of self-reported habitual B vitamin intakes in samples from 2294 European participants. RESULTS Eighteen metabolites were associated with B vitamin intakes after correction for multiple testing (Bonferroni-adj. p < 0.05), of which 7 metabolites were available in both cohorts and tested for epigenome-wide association. Three metabolites - pipecolate (metabolomic biomarker of B6 and folate intakes), pyridoxate (marker of B6 and folate) and docosahexaenoate (DHA, marker of B6) - were associated with 10, 3 and 1 differentially methylated positions (DMPs), respectively. The strongest association was observed between DHA and DMP cg03440556 in the SCD gene (effect = 0.093 ± 0.016, p = 4.07E-09). Pyridoxate, a catabolic product of vitamin B6, was inversely associated with CpG methylation near the SLC1A5 gene promoter region (cg02711608 and cg22304262) and with SLC7A11 (cg06690548), but not with corresponding changes in gene expression levels. The self-reported intake of folate and vitamin B6 had consistent but non-significant associations with the epigenetic signals. CONCLUSION Metabolomic biomarkers are a valuable approach to investigate the effects of dietary B vitamin intake on the human epigenome.
Collapse
Affiliation(s)
- Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
| | - Laila Evangelista
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Xinyu Yan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Fabian Hellbach
- Epidemiology, Medical Faculty, University Augsburg, University Hospital Augsburg, 86156, Augsburg, Germany
| | - Lucy Sinke
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Olatz M Masachs
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, SE1 9NH, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Karsten Suhre
- Department of Biophysics and Physiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jakob Linseisen
- Epidemiology, Medical Faculty, University Augsburg, University Hospital Augsburg, 86156, Augsburg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
| |
Collapse
|
22
|
Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep 2023; 13:17680. [PMID: 37848499 PMCID: PMC10582077 DOI: 10.1038/s41598-023-44806-z] [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: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
Collapse
Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeongok G Logan
- School of Nursing, University of Virginia, Charlottesville, VA, USA
| | - Younghoon Kwon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joao A C Lima
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Jacobs
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Duprez
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, USA
| | - Lyndia Brumback
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- 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
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, 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
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, NC, USA
| | - Russell P Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Thomas W Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, 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
| | - David J Van Den Berg
- Department of Preventive Medicine and Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julio A Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Hughes
- Department of Internal Medicine - Section of Gerontology and Geriatric Medicine, and Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, Department of Medicine, University of Virginia, 1340 Jefferson Park Ave., Pinn hall 6054, Charlottesville, VA, 22908, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
23
|
Zhang Y, Yang H, Jiang M, Nie X. Exploring the pathogenesis and treatment of IgA nephropathy based on epigenetics. Epigenomics 2023; 15:1017-1026. [PMID: 37909120 DOI: 10.2217/epi-2023-0318] [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] [Indexed: 11/02/2023] Open
Abstract
IgA nephropathy is the most common primary glomerulonephritis worldwide. However, its exact cause remains unclear, with known genetic factors explaining only 11% of the variation. Recently, researchers have turned their attention to epigenetic abnormalities in immune-related diseases, recognizing their significance in IgA nephropathy's development and progression. This emerging field has revolutionized our understanding of epigenetics in IgA nephropathy research. Though in its early stages, studying IgA nephropathy's epigenetics holds promise for unraveling its pathogenesis and identifying new biomarkers and therapies. This review aims to comprehensively analyze epigenetics' role in IgA nephropathy's development and suggest avenues for potential therapeutic interventions. In the future, assessing and modulating epigenetics may become integral in diagnosing, tailoring treatments and assessing prognoses for IgA nephropathy.
Collapse
Affiliation(s)
- Yunfan Zhang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Huanhuan Yang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Ming Jiang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Xiaojing Nie
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
- Department of Pediatrics, Affiliated Dongfang Hospital, Xiamen University, Fuzhou, 350025, China
| |
Collapse
|
24
|
Keshawarz A, Bui H, Joehanes R, Ma J, Liu C, Huan T, Hwang SJ, Tejada B, Sooda M, Courchesne P, Munson PJ, Demirkale CY, Yao C, Heard-Costa NL, Pitsillides AN, Lin H, Liu CT, Wang Y, Peloso GM, Lundin J, Haessler J, Du Z, Cho M, Hersh CP, Castaldi P, Raffield LM, Wen J, Li Y, Reiner AP, Feolo M, Sharopova N, Vasan RS, DeMeo DL, Carson AP, Kooperberg C, Levy D. Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: the Framingham Heart Study. Sci Rep 2023; 13:12952. [PMID: 37563237 PMCID: PMC10415314 DOI: 10.1038/s41598-023-39936-3] [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: 05/03/2022] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
Expression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression. The present study describes an eQTM resource of CpG-transcript pairs derived from whole blood DNA methylation and RNA sequencing gene expression data in 2115 Framingham Heart Study participants. We identified 70,047 significant cis CpG-transcript pairs at p < 1E-7 where the top most significant eGenes (i.e., gene transcripts associated with a CpG) were enriched in biological pathways related to cell signaling, and for 1208 clinical traits (enrichment false discovery rate [FDR] ≤ 0.05). We also identified 246,667 significant trans CpG-transcript pairs at p < 1E-14 where the top most significant eGenes were enriched in biological pathways related to activation of the immune response, and for 1191 clinical traits (enrichment FDR ≤ 0.05). Independent and external replication of the top 1000 significant cis and trans CpG-transcript pairs was completed in the Women's Health Initiative and Jackson Heart Study cohorts. Using significant cis CpG-transcript pairs, we identified significant mediation of the association between CpG sites and cardiometabolic traits through gene expression and identified shared genetic regulation between CpGs and transcripts associated with cardiometabolic traits. In conclusion, we developed a robust and powerful resource of whole blood eQTM CpG-transcript pairs that can help inform future functional studies that seek to understand the molecular basis of disease.
Collapse
Affiliation(s)
- Amena Keshawarz
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Helena Bui
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roby Joehanes
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiantao Ma
- Framingham Heart Study, Framingham, MA, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, MA, USA
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brandon Tejada
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meera Sooda
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Courchesne
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter J Munson
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cumhur Y Demirkale
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA
| | - Chen Yao
- Framingham Heart Study, Framingham, MA, USA
| | - Nancy L Heard-Costa
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Achilleas N Pitsillides
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Honghuang Lin
- Framingham Heart Study, Framingham, MA, USA
- Division of Clinical Informatics, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yuxuan Wang
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gina M Peloso
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | | | | | - Zhaohui Du
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- General Medicine and Primary Care, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mike Feolo
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Nataliya Sharopova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA.
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
25
|
Jin J, Zhao X, Zhu C, Li M, Wang J, Fan Y, Liu C, Shen C, Yang R. Hypomethylation of ABCG1 in peripheral blood as a potential marker for the detection of coronary heart disease. Clin Epigenetics 2023; 15:120. [PMID: 37507725 PMCID: PMC10375639 DOI: 10.1186/s13148-023-01533-6] [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: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Novel molecular biomarkers for the risk assessment and early detection of coronary heart disease (CHD) are urgently needed for disease prevention. Altered methylation of ATP-binding cassette subfamily G member 1 (ABCG1) has been implicated in CHD but was mostly studied in Caucasians. Exploring the potential relationship between ABCG1 methylation in blood and CHD among the Chinese population would yield valuable insights. METHODS Peripheral blood samples were obtained from a case-control study (287 CHD patients vs. 277 controls) and a prospective nested case-control study (171 CHD patients and 197 matched controls). DNA extraction and bisulfite-specific PCR amplification techniques were employed for sample processing. Quantitative assessment of methylation levels was conducted using mass spectrometry. Statistical analyses involved the utilization of logistic regression and nonparametric tests. RESULTS We found hypomethylation of ABCG1 in whole blood was associated with the risk of CHD in both studies, which was enhanced in heart failure (HF) patients, female and younger subjects. When combined with baseline characteristics, altered ABCG1 methylation showed improved predictive effect for differentiating CHD cases, ischemic cardiomyopathy (ICM) cases, younger than 60 years CHD cases, and female CHD cases from healthy controls (area under the curve (AUC) = 0.68, 0.71, 0.74, and 0.73, respectively). CONCLUSIONS We demonstrated a robust link between ABCG1 hypomethylation in whole blood and CHD risk in the Chinese population and provided novel evidence indicating that aberrant ABCG1 methylation in peripheral blood can serve as an early detection biomarker for CHD patients.
Collapse
Affiliation(s)
- Jialie Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Xiaojing Zhao
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
- Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100000, People's Republic of China
| | - Mengxia Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Jinxin Wang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, 100000, People's Republic of China
| | - Yao Fan
- Division of Clinical Epidemiology, Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, 211166, Nanjing, China.
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.
| |
Collapse
|
26
|
Manichaikul A, Hu X, Logan J, Kwon Y, Lima J, Jacobs D, Duprez D, Brumback L, Taylor K, Durda P, Johnson C, Cornell E, Guo X, Liu Y, Tracy R, Blackwell T, Papanicolaou G, Mitchell G, Rich S, Rotter J, Van Den Berg D, Chirinos J, Hughes T, Garrett-Bakelman F. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. RESEARCH SQUARE 2023:rs.3.rs-3125948. [PMID: 37502922 PMCID: PMC10371087 DOI: 10.21203/rs.3.rs-3125948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Kent Taylor
- The Institute for Translational Genomics and Population Sciences
| | | | | | | | | | | | | | | | | | | | - Stephen Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia
| | - Jerome Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | | | | | | | | |
Collapse
|
27
|
Shi J, Wu L, Chen Y, Zhang M, Yu J, Ren L, He Y, Li J, Ma S, Hu W, Peng H. Association between CORIN methylation and hypertension in Chinese adults. Postgrad Med J 2023; 99:753-762. [DOI: https:/doi.org/10.1136/pmj-2022-141802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Abstract
Background
Corin, a physical activator of atrial natriuretic peptide, has been associated with hypertension with unclear mechanisms. Here, we aimed to examine whether CORIN gene methylation was involved in the underlying molecular mechanisms.
Methods
DNA methylation levels of CORIN were measured by target bisulfite sequencing using genomic DNA isolated from peripheral blood mononuclear cells in 2498 participants in the Gusu cohort (discovery sample) and 1771 independent participants (replication sample). We constructed a mediation model with DNA methylation as the predictor, serum corin as the mediator, and hypertension as the outcome, adjusting for covariates. Multiple testing was controlled by false discovery rate (FDR) approach.
Results
Of the 9 CpGs assayed, hypermethylation at all CpGs were significantly associated with a lower level of blood pressure in the discovery sample and eight associations were also significant in the replication sample (all FDR-adjusted p<0.05). Serum corin mediated approximately 3.07% (p=0.004), 6.25% (p=0.002) and 10.11% (p=0.034) of the associations of hypermethylation at one CpG (Chr4:47840096) with systolic and diastolic blood pressure, and hypertension, respectively. All these mediations passed the causal inference test.
Conclusions
These results suggest that hypermethylation in the CORIN gene is associated with a lower odds of prevalent hypertension and may be involved in the role of corin in blood pressure regulation.
Collapse
Affiliation(s)
- Jijun Shi
- Department of Neurology , , Suzhou , China
- Second Affiliated Hospital of Soochow University , , Suzhou , China
| | - Lei Wu
- Department of Maternal and Child Health , , Suzhou, Jiangsu , China
- Suzhou Industrial Park Center for Disease Control and Prevention , , Suzhou, Jiangsu , China
| | - Yan Chen
- Department of Nephrology , , Jiangyin, Jiangsu , China
- The Affiliated Jiangyin Hospital of Southeast University Medical College , , Jiangyin, Jiangsu , China
| | - Mingzhi Zhang
- Department of Epidemiology , , Suzhou , China
- Soochow University Medical College , , Suzhou , China
| | - Jia Yu
- Department of Epidemiology , , Suzhou, Jiangsu , China
- School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases of Soochow University , , Suzhou, Jiangsu , China
| | - Liyun Ren
- Department of Epidemiology , , Suzhou , China
- Soochow University Medical College , , Suzhou , China
| | - Yan He
- Department of Epidemiology , , Suzhou , China
- Soochow University Medical College , , Suzhou , China
| | - Jing Li
- Department of Epidemiology , , Suzhou, Jiangsu , China
- School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases of Soochow University , , Suzhou, Jiangsu , China
| | - Shengqi Ma
- Department of Epidemiology , , Suzhou, Jiangsu , China
- School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases of Soochow University , , Suzhou, Jiangsu , China
| | - Weidong Hu
- Department of Neurology , , Suzhou , China
- Second Affiliated Hospital of Soochow University , , Suzhou , China
| | - Hao Peng
- Department of Epidemiology , , Suzhou, Jiangsu , China
- School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases of Soochow University , , Suzhou, Jiangsu , China
| |
Collapse
|
28
|
Abstract
Epigenetics has transformed our understanding of the molecular basis of complex diseases, including cardiovascular and metabolic disorders. This review offers a comprehensive overview of the current state of knowledge on epigenetic processes implicated in cardiovascular and metabolic diseases, highlighting the potential of DNA methylation as a precision medicine biomarker and examining the impact of social determinants of health, gut bacterial epigenomics, noncoding RNA, and epitranscriptomics on disease development and progression. We discuss challenges and barriers to advancing cardiometabolic epigenetics research, along with the opportunities for novel preventive strategies, targeted therapies, and personalized medicine approaches that may arise from a better understanding of epigenetic processes. Emerging technologies, such as single-cell sequencing and epigenetic editing, hold the potential to further enhance our ability to dissect the complex interplay between genetic, environmental, and lifestyle factors. To translate research findings into clinical practice, interdisciplinary collaborations, technical and ethical considerations, and accessibility of resources and knowledge are crucial. Ultimately, the field of epigenetics has the potential to revolutionize the way we approach cardiovascular and metabolic diseases, paving the way for precision medicine and personalized health care, and improving the lives of millions of individuals worldwide affected by these conditions.
Collapse
Affiliation(s)
- Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, New York (A.A.B.)
| | - José Ordovás
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, at Tufts University, Boston, MA (J.O.)
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain (J.O.)
- Consortium CIBERObn, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (J.O.)
| |
Collapse
|
29
|
Kou M, Li X, Shao X, Grundberg E, Wang X, Ma H, Heianza Y, Martinez JA, Bray GA, Sacks FM, Qi L. DNA Methylation of Birthweight-Blood Pressure Genes and Changes of Blood Pressure in Response to Weight-Loss Diets in the POUNDS Lost Trial. Hypertension 2023; 80:1223-1230. [PMID: 37039021 PMCID: PMC10192077 DOI: 10.1161/hypertensionaha.123.20864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/26/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND DNA methylation (DNAm) may play a critical role in bridging prenatal adverse events and cardiometabolic disorders including hypertension in later life. METHODS We included 672 adult participants with overweight or obesity, who participated in a 2-year randomized weight-loss dietary intervention study. We defined the regional DNAm levels as the average methylation level of 5'-cytosine-phosphate-guanine-3' within 500 bp of LINC00319 (cg01820192), ATP2B1 (cg00508575), and LMNA (cg12593793), respectively. Generalized linear regression models were used to assess the association between the regional DNAm and 2-year blood pressure changes. Trajectory analysis was used to identify subgroups that shared a similar underlying trajectory of 2-year blood pressure changes. RESULTS The regional DNAm at LINC00319, showed significantly different associations with 2-year changes in systolic blood pressure and diastolic blood pressure among participants assigned to low- or high-fat diets (P for interaction<0.05 for all). In response to the low-fat diet, per SD higher regional DNAm at LINC00319 was associated with greater reductions in both 2-year changes in systolic blood pressure (β, -1.481; P=0.020) and diastolic blood pressure (β, -1.096; P=0.009). Three trajectories of changes in systolic blood pressure or diastolic blood pressure were identified, and participants with higher regional DNAm at LINC00319 were more likely to experience and maintain decreased systolic blood pressure and diastolic blood pressure (odds ratio of being in decrease-stable versus stable [95% CI], 1.542 [1.146-2.076] and 1.463 [1.125-1.902]). CONCLUSIONS Our findings suggest that DNAm could be a metabolic memory bridging early and later life, and an indicator of more benefits from eating a low-fat weight-loss diet.
Collapse
Affiliation(s)
- Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, United States
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - J. Alfredo Martinez
- Madrid Institute of Advance Studies (IMDEA), Research Institute on Food & Health Sciences, Precision Nutrition Program, Madrid, Spain
| | - George A. Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
| | - Frank M. Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| |
Collapse
|
30
|
Colicino E, Fiorito G. DNA methylation-based biomarkers for cardiometabolic-related traits and their importance for risk stratification. CURRENT OPINION IN EPIDEMIOLOGY AND PUBLIC HEALTH 2023; 2:25-31. [PMID: 38601732 PMCID: PMC11003758 DOI: 10.1097/pxh.0000000000000020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Recent findings The prevalence of cardiometabolic syndrome in adults is increasing worldwide, highlighting the importance of biomarkers for individuals' classification based on their health status. Although cardiometabolic risk scores and diagnostic criteria have been developed aggregating adverse health effects of individual conditions on the overall syndrome, none of them has gained unanimous acceptance. Therefore, novel molecular biomarkers have been developed to better understand the risk, onset and progression of both individual conditions and the overall cardiometabolic syndrome. Summary Consistent associations between whole blood DNA methylation (DNAm) levels at several single genomic (i.e. CpG) sites and both individual and aggregated cardiometabolic conditions supported the creation of second-generation DNAm-based cardiometabolic-related biomarkers. These biomarkers linearly combine individual DNAm levels from key CpG sites, selected by a two-step machine learning procedures. They can be used, even retrospectively, in populations with extant whole blood DNAm levels and without observed cardiometabolic phenotypes. Purpose of review Here we offer an overview of the second-generation DNAm-based cardiometabolic biomarkers, discussing methodological advancements and implications on the interpretation and generalizability of the findings. We finally emphasize the contribution of DNAm-based biomarkers for risk stratification beyond traditional factors and discuss limitations and future directions of the field.
Collapse
Affiliation(s)
- Elena Colicino
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | |
Collapse
|
31
|
Wang W, Yao J, Li W, Wu Y, Duan H, Xu C, Tian X, Li S, Tan Q, Zhang D. Epigenome-wide association study in Chinese monozygotic twins identifies DNA methylation loci associated with blood pressure. Clin Epigenetics 2023; 15:38. [PMID: 36869404 PMCID: PMC9985232 DOI: 10.1186/s13148-023-01457-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Hypertension is a crucial risk factor for developing cardiovascular disease and reducing life expectancy. We aimed to detect DNA methylation (DNAm) variants potentially related to systolic blood pressure (SBP) and diastolic blood pressure (DBP) by conducting epigenome-wide association studies in 60 and 59 Chinese monozygotic twin pairs, respectively. METHODS Genome-wide DNA methylation profiling in whole blood of twins was performed using Reduced Representation Bisulfite Sequencing, yielding 551,447 raw CpGs. Association between DNAm of single CpG and blood pressure was tested by applying generalized estimation equation. Differentially methylated regions (DMRs) were identified by comb-P approach. Inference about Causation through Examination of Familial Confounding was utilized to perform the causal inference. Ontology enrichment analysis was performed using Genomic Regions Enrichment of Annotations Tool. Candidate CpGs were quantified using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data. RESULTS The median age of twins was 52 years (95% range 40, 66). For SBP, 31 top CpGs (p < 1 × 10-4) and 8 DMRs were identified, with several DMRs within NFATC1, CADM2, IRX1, COL5A1, and LRAT. For DBP, 43 top CpGs (p < 1 × 10-4) and 12 DMRs were identified, with several DMRs within WNT3A, CNOT10, and DAB2IP. Important pathways, such as Notch signaling pathway, p53 pathway by glucose deprivation, and Wnt signaling pathway, were significantly enriched for SBP and DBP. Causal inference analysis suggested that DNAm at top CpGs within NDE1, MYH11, SRRM1P2, and SMPD4 influenced SBP, while SBP influenced DNAm at CpGs within TNK2. DNAm at top CpGs within WNT3A influenced DBP, while DBP influenced DNAm at CpGs within GNA14. Three CpGs mapped to WNT3A and one CpG mapped to COL5A1 were validated in a community population, with a hypermethylated and hypomethylated direction in hypertension cases, respectively. Gene expression analysis by WGCNA further identified some common genes and enrichment terms. CONCLUSION We detect many DNAm variants that may be associated with blood pressure in whole blood, particularly the loci within WNT3A and COL5A1. Our findings provide new clues to the epigenetic modification underlying hypertension pathogenesis.
Collapse
Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 308 Ningxia Road, Qingdao, 266021, Shandong, China
| | - Jie Yao
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 308 Ningxia Road, Qingdao, 266021, Shandong, China
- Jiangsu Health Development Research Center, Nanjing, Jiangsu, China
| | - Weilong Li
- Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 308 Ningxia Road, Qingdao, 266021, Shandong, China
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention/Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 308 Ningxia Road, Qingdao, 266021, Shandong, China.
| |
Collapse
|
32
|
Fragoso-Bargas N, Elliott HR, Lee-Ødegård S, Opsahl JO, Sletner L, Jenum AK, Drevon CA, Qvigstad E, Moen GH, Birkeland KI, Prasad RB, Sommer C. Cross-Ancestry DNA Methylation Marks of Insulin Resistance in Pregnancy: An Integrative Epigenome-Wide Association Study. Diabetes 2023; 72:415-426. [PMID: 36534481 PMCID: PMC9935495 DOI: 10.2337/db22-0504] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Although there are some epigenome-wide association studies (EWAS) of insulin resistance, for most of them authors did not replicate their findings, and most are focused on populations of European ancestry, limiting the generalizability. In the Epigenetics in Pregnancy (EPIPREG; n = 294 Europeans and 162 South Asians) study, we conducted an EWAS of insulin resistance in maternal peripheral blood leukocytes, with replication in the Born in Bradford (n = 879; n = 430 Europeans and 449 South Asians), Methyl Epigenome Network Association (MENA) (n = 320), and Botnia (n = 56) cohorts. In EPIPREG, we identified six CpG sites inversely associated with insulin resistance across ancestry, of which five were replicated in independent cohorts (cg02988288, cg19693031, and cg26974062 in TXNIP; cg06690548 in SLC7A11; and cg04861640 in ZSCAN26). From methylation quantitative trait loci analysis in EPIPREG, we identified gene variants related to all five replicated cross-ancestry CpG sites, which were associated with several cardiometabolic phenotypes. Mediation analyses suggested that the gene variants regulate insulin resistance through DNA methylation. To conclude, our cross-ancestry EWAS identified five CpG sites related to lower insulin resistance.
Collapse
Affiliation(s)
- Nicolas Fragoso-Bargas
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hannah R. Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Sindre Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Julia O. Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Anne Karen Jenum
- General Practice Research Unit (AFE), Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Christian A. Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Vitas Ltd. Analytical Services, Oslo Science Park, Oslo, Norway
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kåre I. Birkeland
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rashmi B. Prasad
- Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
33
|
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).
Collapse
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
| |
Collapse
|
34
|
Gumz ML, Shimbo D, Abdalla M, Balijepalli RC, Benedict C, Chen Y, Earnest DJ, Gamble KL, Garrison SR, Gong MC, Hogenesch JB, Hong Y, Ivy JR, Joe B, Laposky AD, Liang M, MacLaughlin EJ, Martino TA, Pollock DM, Redline S, Rogers A, Dan Rudic R, Schernhammer ES, Stergiou GS, St-Onge MP, Wang X, Wright J, Oh YS. Toward Precision Medicine: Circadian Rhythm of Blood Pressure and Chronotherapy for Hypertension - 2021 NHLBI Workshop Report. Hypertension 2023; 80:503-522. [PMID: 36448463 PMCID: PMC9931676 DOI: 10.1161/hypertensionaha.122.19372] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Healthy individuals exhibit blood pressure variation over a 24-hour period with higher blood pressure during wakefulness and lower blood pressure during sleep. Loss or disruption of the blood pressure circadian rhythm has been linked to adverse health outcomes, for example, cardiovascular disease, dementia, and chronic kidney disease. However, the current diagnostic and therapeutic approaches lack sufficient attention to the circadian rhythmicity of blood pressure. Sleep patterns, hormone release, eating habits, digestion, body temperature, renal and cardiovascular function, and other important host functions as well as gut microbiota exhibit circadian rhythms, and influence circadian rhythms of blood pressure. Potential benefits of nonpharmacologic interventions such as meal timing, and pharmacologic chronotherapeutic interventions, such as the bedtime administration of antihypertensive medications, have recently been suggested in some studies. However, the mechanisms underlying circadian rhythm-mediated blood pressure regulation and the efficacy of chronotherapy in hypertension remain unclear. This review summarizes the results of the National Heart, Lung, and Blood Institute workshop convened on October 27 to 29, 2021 to assess knowledge gaps and research opportunities in the study of circadian rhythm of blood pressure and chronotherapy for hypertension.
Collapse
Affiliation(s)
- Michelle L Gumz
- Department of Physiology and Aging; Center for Integrative Cardiovascular and Metabolic Disease, Department of Medicine, Division of Nephrology, Hypertension and Renal Transplantation, University of Florida, Gainesville, FL (M.L.G.)
| | - Daichi Shimbo
- Department of Medicine, The Columbia Hypertension Center, Columbia University Irving Medical Center, New York, NY (D.S.)
| | - Marwah Abdalla
- Department of Medicine, Center for Behavioral Cardiovascular Health, Columbia University Irving Medical Center, New York, NY (M.A.)
| | - Ravi C Balijepalli
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD (R.C.B., Y.H., J.W., Y.S.O.)
| | - Christian Benedict
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Sweden (C.B.)
| | - Yabing Chen
- Department of Pathology, University of Alabama at Birmingham, and Research Department, Birmingham VA Medical Center, AL (Y.C.)
| | - David J Earnest
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University, Bryan, TX (D.J.E.)
| | - Karen L Gamble
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, AL (K.L.G.)
| | - Scott R Garrison
- Department of Family Medicine, University of Alberta, Canada (S.R.G.)
| | - Ming C Gong
- Department of Physiology, University of Kentucky, Lexington, KY (M.C.G.)
| | | | - Yuling Hong
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD (R.C.B., Y.H., J.W., Y.S.O.)
| | - Jessica R Ivy
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, United Kingdom (J.R.I.)
| | - Bina Joe
- Department of Physiology and Pharmacology and Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, OH (B.J.)
| | - Aaron D Laposky
- National Center on Sleep Disorders Research, Division of Lung Diseases, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD (A.D.L.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI (M.L.)
| | - Eric J MacLaughlin
- Department of Pharmacy Practice, Texas Tech University Health Sciences Center, Amarillo, TX (E.J.M.)
| | - Tami A Martino
- Center for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Ontario, Canada (T.A.M.)
| | - David M Pollock
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, AL (D.M.P.)
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (S.R.)
| | - Amy Rogers
- Division of Molecular and Clinical Medicine, University of Dundee, United Kingdom (A.R.)
| | - R Dan Rudic
- Department of Pharmacology and Toxicology, Augusta University, GA (R.D.R.)
| | - Eva S Schernhammer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (E.S.S.)
| | - George S Stergiou
- Hypertension Center, STRIDE-7, National and Kapodistrian University of Athens, School of Medicine, Third Department of Medicine, Sotiria Hospital, Athens, Greece (G.S.S.)
| | - Marie-Pierre St-Onge
- Division of General Medicine, Department of Medicine, Columbia University Irving Medical Center' New York, NY (M.-P.S.-O.)
| | - Xiaoling Wang
- Georgia Prevention Institute, Department of Medicine, Augusta University, GA (X.W.)
| | - Jacqueline Wright
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD (R.C.B., Y.H., J.W., Y.S.O.)
| | - Young S Oh
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD (R.C.B., Y.H., J.W., Y.S.O.)
| |
Collapse
|
35
|
Yang Y, Knol MJ, Wang R, Mishra A, Liu D, Luciano M, Teumer A, Armstrong N, Bis JC, Jhun MA, Li S, Adams HHH, Aziz NA, Bastin ME, Bourgey M, Brody JA, Frenzel S, Gottesman RF, Hosten N, Hou L, Kardia SLR, Lohner V, Marquis P, Maniega SM, Satizabal CL, Sorond FA, Valdés Hernández MC, van Duijn CM, Vernooij MW, Wittfeld K, Yang Q, Zhao W, Boerwinkle E, Levy D, Deary IJ, Jiang J, Mather KA, Mosley TH, Psaty BM, Sachdev PS, Smith JA, Sotoodehnia N, DeCarli CS, Breteler MMB, Ikram MA, Grabe HJ, Wardlaw J, Longstreth WT, Launer LJ, Seshadri S, Debette S, Fornage M. Epigenetic and integrative cross-omics analyses of cerebral white matter hyperintensities on MRI. Brain 2023; 146:492-506. [PMID: 35943854 PMCID: PMC9924914 DOI: 10.1093/brain/awac290] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Cerebral white matter hyperintensities on MRI are markers of cerebral small vessel disease, a major risk factor for dementia and stroke. Despite the successful identification of multiple genetic variants associated with this highly heritable condition, its genetic architecture remains incompletely understood. More specifically, the role of DNA methylation has received little attention. We investigated the association between white matter hyperintensity burden and DNA methylation in blood at ∼450 000 cytosine-phosphate-guanine (CpG) sites in 9732 middle-aged to older adults from 14 community-based studies. Single CpG and region-based association analyses were carried out. Functional annotation and integrative cross-omics analyses were performed to identify novel genes underlying the relationship between DNA methylation and white matter hyperintensities. We identified 12 single CpG and 46 region-based DNA methylation associations with white matter hyperintensity burden. Our top discovery single CpG, cg24202936 (P = 7.6 × 10-8), was associated with F2 expression in blood (P = 6.4 × 10-5) and co-localized with FOLH1 expression in brain (posterior probability = 0.75). Our top differentially methylated regions were in PRMT1 and in CCDC144NL-AS1, which were also represented in single CpG associations (cg17417856 and cg06809326, respectively). Through Mendelian randomization analyses cg06809326 was putatively associated with white matter hyperintensity burden (P = 0.03) and expression of CCDC144NL-AS1 possibly mediated this association. Differentially methylated region analysis, joint epigenetic association analysis and multi-omics co-localization analysis consistently identified a role of DNA methylation near SH3PXD2A, a locus previously identified in genome-wide association studies of white matter hyperintensities. Gene set enrichment analyses revealed functions of the identified DNA methylation loci in the blood-brain barrier and in the immune response. Integrative cross-omics analysis identified 19 key regulatory genes in two networks related to extracellular matrix organization, and lipid and lipoprotein metabolism. A drug-repositioning analysis indicated antihyperlipidaemic agents, more specifically peroxisome proliferator-activated receptor-alpha, as possible target drugs for white matter hyperintensities. Our epigenome-wide association study and integrative cross-omics analyses implicate novel genes influencing white matter hyperintensity burden, which converged on pathways related to the immune response and to a compromised blood-brain barrier possibly due to disrupted cell-cell and cell-extracellular matrix interactions. The results also suggest that antihyperlipidaemic therapy may contribute to lowering risk for white matter hyperintensities possibly through protection against blood-brain barrier disruption.
Collapse
Affiliation(s)
- Yunju Yang
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science at Houston, Houston, TX 77030, USA
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ruiqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Aniket Mishra
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Dan Liu
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Michelle Luciano
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17475, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald 17475, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, 15-269, Poland
| | - Nicola Armstrong
- Mathematics and Statistics, Curtin University, 6845 Perth, Australia
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 02115, USA
| | - Min A Jhun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48104, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Hieab H H Adams
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Nasir Ahmad Aziz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, 53127 Bonn, Germany
| | - Mark E Bastin
- Centre for Clinical Brain Sciences, Department of Neuroimaging Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Quebec, Canada H3A 0G1
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, Quebec, Canada H3A 0G1
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 02115, USA
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald 17475, Germany
| | - Rebecca F Gottesman
- Stroke Branch, National Institutes of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Norbert Hosten
- Department of Radiology and Neuroradiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48104, USA
| | - Valerie Lohner
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Pascale Marquis
- Canadian Centre for Computational Genomics, McGill University, Montréal, Quebec, Canada H3A 0G1
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, Quebec, Canada H3A 0G1
| | - Susana Muñoz Maniega
- Centre for Clinical Brain Sciences, Department of Neuroimaging Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases and Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX 78229, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02115, USA
| | - Farzaneh A Sorond
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Maria C Valdés Hernández
- Centre for Clinical Brain Sciences, Department of Neuroimaging Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Nuffield Department of Population Health, Oxford University, Oxford, OX3 7LF, UK
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald 17475, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Rostock, Germany
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48104, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA 01701, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Jiyang Jiang
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
- Neuroscience Research Australia, Sydney, NSW 2031, Australia
| | - Thomas H Mosley
- The Memory Impairment Neurodegenerative Dementia (MIND) Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 02115, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98104, USA
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, University of New South Wales, Randwick, NSW 2031, Australia
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48104, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 02115, USA
| | - Charles S DeCarli
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA 95816, USA
| | - Monique M B Breteler
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, 53127 Bonn, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald 17475, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Rostock, Germany
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, Department of Neuroimaging Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - W T Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA 98104, USA
- Department of Neurology, University of Washington, Seattle, WA 98104, USA
| | - Lenore J Launer
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases and Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX 78229, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02115, USA
| | - Stephanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, MA 02115, USA
- CHU de Bordeaux, Department of Neurology, F-33000 Bordeaux, France
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science at Houston, Houston, TX 77030, USA
| |
Collapse
|
36
|
Nagamatsu ST, Pietrzak RH, Xu K, Krystal JH, Gelernter J, Montalvo-Ortiz JL. Dissecting the epigenomic differences between smoking and nicotine dependence in a veteran cohort. Addict Biol 2023; 28:e13259. [PMID: 36577721 DOI: 10.1111/adb.13259] [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: 01/14/2022] [Revised: 08/26/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022]
Abstract
Smoking is a serious public health issue linked to more than 8 million deaths per year worldwide and may lead to nicotine dependence (ND). Although the epigenomic literature on smoking is well established, studies evaluating the role of epigenetics in ND are limited. In this study, we examined the epigenomic signatures of ND and how these differ from smoking exposure to identify biomarkers specific to ND. We investigated the peripheral epigenetic profile of smoking status (SS) and ND in a US male veteran cohort. DNA from saliva was collected from 1135 European American (EA) male US military veterans. DNAm was assessed using the Illumina Infinium Human MethylationEPIC BeadChip array. SS was evaluated as current smokers (n = 137; 12.1%) and non-current smokers (never and former; n = 998; 87.9%). NDFTND was assessed as a continuous variable using the Fagerström Test for ND (FTND; n = 1135; mean = 2.54 ± 2.29). Epigenome-wide association studies (EWAS) and co-methylation analyses were conducted for SS and NDFTND . A total of 450 and 22 genome-wide significant differentially methylated sites (DMS) were associated with SS and NDFTND , respectively (15 overlapped DMS). We identified 97 DMS (43 genes) in SS-EWAS previously reported in the literature, including AHRR and F2RL3 genes (p-value: 1.95 × 10-83 to 4.55 × 10-33 ). NDFTND novel DMS mapped to NEUROG1, ANPEP, and SLC29A1. Co-methylation analysis identified 386 modules (11 SS-related and 19 NDFTND -related). SS-related modules showed enrichment for alcoholism, while NDFTND -related modules were enriched for nicotine addiction. This study confirms previous findings associated with SS and identifies novel and-potentially specific-epigenetic biomarkers of ND that may inform prognosis and novel treatment strategies.
Collapse
Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
| | - Robert H Pietrzak
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Ke Xu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - John H Krystal
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Janitza Liz Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| |
Collapse
|
37
|
Hong X, Miao K, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Yu M, Wang H, Wu X, Liu Y, Gao W, Li L. Association Between DNA Methylation and Blood Pressure: A 5-Year Longitudinal Twin Study. Hypertension 2023; 80:169-181. [PMID: 36345830 DOI: 10.1161/hypertensionaha.122.19953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Previous EWASs (Epigenome-Wide Association Studies) have reported hundreds of blood pressure (BP) associated 5'-cytosine-phosphate-guanine-3' (CpG) sites. However, their results were inconsistent. Longitudinal observations on the temporal relationship between DNA methylation and BP are lacking. METHODS A candidate CpG site association study for BP was conducted on 1072 twins in the Chinese National Twin Registry. PubMed and EMBASE were searched for candidate CpG sites. Cross-lagged models were used to assess the temporal relationship between BP and DNA methylation in 308 twins who completed 2 surveys in 2013 and 2018. Then, the significant cross-lagged associations were validated by adopting the Inference About Causation From Examination of Familial Confounding approach. Finally, to evaluate the cumulative effects of DNA methylation on the progression of hypertension, we established methylation risk scores based on BP-associated CpG sites and performed Markov multistate models. RESULTS 16 and 20 CpG sites were validated to be associated with systolic BP and diastolic BP, respectively. In the cross-lagged analysis, we detected that methylation of 2 CpG sites could predict subsequent systolic BP, and systolic BP predicted methylation at another 3 CpG sites. For diastolic BP, methylation at 3 CpG sites had significant cross-lagged effects for predicting diastolic BP levels, while the prediction from the opposite direction was observed at one site. Among these, 3 associations were validated in the Inference About Causation From Examination of Familial Confounding analysis. Using the Markov multistate model, we observed that methylation risk scores were associated with the development of hypertension. CONCLUSIONS Our findings suggest the significance of DNA methylation in the development of hypertension.
Collapse
Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Ke Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, China (Z.P.)
| | - Min Yu
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China (M.Y.)
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China (H.W.)
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China (X.W.)
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China (Y.L.)
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| |
Collapse
|
38
|
Taylor JY, Huang Y, Zhao W, Wright ML, Wang Z, Hui Q, Potts‐Thompson S, Barcelona V, Prescott L, Yao Y, Crusto C, Kardia SLR, Smith JA, Sun YV. Epigenome-wide association study of BMI in Black populations from InterGEN and GENOA. Obesity (Silver Spring) 2023; 31:243-255. [PMID: 36479596 PMCID: PMC10107734 DOI: 10.1002/oby.23589] [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: 08/24/2021] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Obesity is a significant public health concern across the globe. Research investigating epigenetic mechanisms related to obesity and obesity-associated conditions has identified differences that may contribute to cellular dysregulation that accelerates the development of disease. However, few studies include Black women, who experience the highest incidence of obesity and early onset of cardiometabolic disorders. METHODS The association of BMI with epigenome-wide DNA methylation (DNAm) was examined using the 850K Illumina EPIC BeadChip in two Black populations (Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure [InterGEN], n = 239; and The Genetic Epidemiology Network of Arteriopathy [GENOA] study, n = 961) using linear mixed-effects regression models adjusted for batch effects, cell type heterogeneity, population stratification, and confounding factors. RESULTS Cross-sectional analysis of the InterGEN discovery cohort identified 28 DNAm sites significantly associated with BMI, 24 of which had not been previously reported. Of these, 17 were replicated using the GENOA study. In addition, a meta-analysis, including both the InterGEN and GENOA cohorts, identified 658 DNAm sites associated with BMI with false discovery rate < 0.05. In a meta-analysis of Black women, we identified 628 DNAm sites significantly associated with BMI. Using a more stringent significance threshold of Bonferroni-corrected p value 0.05, 65 and 61 DNAm sites associated with BMI were identified from the combined sex and female-only meta-analyses, respectively. CONCLUSIONS This study suggests that BMI is associated with differences in DNAm among women that can be identified with DNA extracted from salivary (discovery) and peripheral blood (replication) samples among Black populations across two cohorts.
Collapse
Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Yunfeng Huang
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Wei Zhao
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Zeyuan Wang
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Qin Hui
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | | | - Veronica Barcelona
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Laura Prescott
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Yutong Yao
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Cindy Crusto
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
- Survey Research CenterInstitute for Social Research, University of MichiganAnn ArborMichiganUSA
| | - Yan V. Sun
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
- Atlanta VA Healthcare SystemDecaturGeorgiaUSA
| |
Collapse
|
39
|
Xu X, Xu H, Zhang Z. Cerebral amyloid angiopathy-related cardiac injury: Focus on cardiac cell death. Front Cell Dev Biol 2023; 11:1156970. [PMID: 36910141 PMCID: PMC9998697 DOI: 10.3389/fcell.2023.1156970] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/16/2023] [Indexed: 03/14/2023] Open
Abstract
Cerebral amyloid angiopathy (CAA) is a kind of disease in which amyloid β (Aβ) and other amyloid protein deposits in the cerebral cortex and the small blood vessels of the brain, causing cerebrovascular and brain parenchymal damage. CAA patients are often accompanied by cardiac injury, involving Aβ, tau and transthyroxine amyloid (ATTR). Aβ is the main injury factor of CAA, which can accelerate the formation of coronary artery atherosclerosis, aortic valve osteogenesis calcification and cardiomyocytes basophilic degeneration. In the early stage of CAA (pre-stroke), the accompanying locus coeruleus (LC) amyloidosis, vasculitis and circulating Aβ will induce first hit to the heart. When the CAA progresses to an advanced stage and causes a cerebral hemorrhage, the hemorrhage leads to autonomic nervous function disturbance, catecholamine surges, and systemic inflammation reaction, which can deal the second hit to the heart. Based on the brain-heart axis, CAA and its associated cardiac injury can create a vicious cycle that accelerates the progression of each other.
Collapse
Affiliation(s)
- Xiaofang Xu
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huikang Xu
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhaocai Zhang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of the Diagnosis and Treatment for Severe Trauma and Burn of Zhejiang Province, Hangzhou, China.,Zhejiang Province Clinical Research Center for Emergency and Critical care medicine, Hangzhou, China
| |
Collapse
|
40
|
Smyth LJ, Dahlström EH, Syreeni A, Kerr K, Kilner J, Doyle R, Brennan E, Nair V, Fermin D, Nelson RG, Looker HC, Wooster C, Andrews D, Anderson K, McKay GJ, Cole JB, Salem RM, Conlon PJ, Kretzler M, Hirschhorn JN, Sadlier D, Godson C, Florez JC, Forsblom C, Maxwell AP, Groop PH, Sandholm N, McKnight AJ. Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease. Nat Commun 2022; 13:7891. [PMID: 36550108 PMCID: PMC9780337 DOI: 10.1038/s41467-022-34963-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Type 1 diabetes affects over nine million individuals globally, with approximately 40% developing diabetic kidney disease. Emerging evidence suggests that epigenetic alterations, such as DNA methylation, are involved in diabetic kidney disease. Here we assess differences in blood-derived genome-wide DNA methylation associated with diabetic kidney disease in 1304 carefully characterised individuals with type 1 diabetes and known renal status from two cohorts in the United Kingdom-Republic of Ireland and Finland. In the meta-analysis, we identify 32 differentially methylated CpGs in diabetic kidney disease in type 1 diabetes, 18 of which are located within genes differentially expressed in kidneys or correlated with pathological traits in diabetic kidney disease. We show that methylation at 21 of the 32 CpGs predict the development of kidney failure, extending the knowledge and potentially identifying individuals at greater risk for diabetic kidney disease in type 1 diabetes.
Collapse
Affiliation(s)
- Laura J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Katie Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Jill Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eoin Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Christopher Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kerry Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Gareth J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital and Department of Medicine Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alexander P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
| | - Amy Jayne McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| |
Collapse
|
41
|
A comparison of the genes and genesets identified by GWAS and EWAS of fifteen complex traits. Nat Commun 2022; 13:7816. [PMID: 36535946 PMCID: PMC9763500 DOI: 10.1038/s41467-022-35037-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Identifying genomic regions pertinent to complex traits is a common goal of genome-wide and epigenome-wide association studies (GWAS and EWAS). GWAS identify causal genetic variants, directly or via linkage disequilibrium, and EWAS identify variation in DNA methylation associated with a trait. While GWAS in principle will only detect variants due to causal genes, EWAS can also identify genes via confounding, or reverse causation. We systematically compare GWAS (N > 50,000) and EWAS (N > 4500) results of 15 complex traits. We evaluate if the genes or gene ontology terms flagged by GWAS and EWAS overlap, and find substantial overlap for diastolic blood pressure, (gene overlap P = 5.2 × 10-6; term overlap P = 0.001). We superimpose our empirical findings against simulated models of varying genetic and epigenetic architectures and observe that in most cases GWAS and EWAS are likely capturing distinct genesets. Our results indicate that GWAS and EWAS are capturing different aspects of the biology of complex traits.
Collapse
|
42
|
Majarian TD, Bentley AR, Laville V, Brown MR, Chasman DI, de Vries PS, Feitosa MF, Franceschini N, Gauderman WJ, Marchek C, Levy D, Morrison AC, Province M, Rao DC, Schwander K, Sung YJ, Rotimi CN, Aschard H, Gu CC, Manning AK. Multi-omics insights into the biological mechanisms underlying statistical gene-by-lifestyle interactions with smoking and alcohol consumption. Front Genet 2022; 13:954713. [PMID: 36544485 PMCID: PMC9760722 DOI: 10.3389/fgene.2022.954713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Though both genetic and lifestyle factors are known to influence cardiometabolic outcomes, less attention has been given to whether lifestyle exposures can alter the association between a genetic variant and these outcomes. The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium's Gene-Lifestyle Interactions Working Group has recently published investigations of genome-wide gene-environment interactions in large multi-ancestry meta-analyses with a focus on cigarette smoking and alcohol consumption as lifestyle factors and blood pressure and serum lipids as outcomes. Further description of the biological mechanisms underlying these statistical interactions would represent a significant advance in our understanding of gene-environment interactions, yet accessing and harmonizing individual-level genetic and 'omics data is challenging. Here, we demonstrate the coordinated use of summary-level data for gene-lifestyle interaction associations on up to 600,000 individuals, differential methylation data, and gene expression data for the characterization and prioritization of loci for future follow-up analyses. Using this approach, we identify 48 genes for which there are multiple sources of functional support for the identified gene-lifestyle interaction. We also identified five genes for which differential expression was observed by the same lifestyle factor for which a gene-lifestyle interaction was found. For instance, in gene-lifestyle interaction analysis, the T allele of rs6490056 (ALDH2) was associated with higher systolic blood pressure, and a larger effect was observed in smokers compared to non-smokers. In gene expression studies, this allele is associated with decreased expression of ALDH2, which is part of a major oxidative pathway. Other results show increased expression of ALDH2 among smokers. Oxidative stress is known to contribute to worsening blood pressure. Together these data support the hypothesis that rs6490056 reduces expression of ALDH2, which raises oxidative stress, leading to an increase in blood pressure, with a stronger effect among smokers, in whom the burden of oxidative stress is greater. Other genes for which the aggregation of data types suggest a potential mechanism include: GCNT4×current smoking (HDL), PTPRZ1×ever-smoking (HDL), SYN2×current smoking (pulse pressure), and TMEM116×ever-smoking (mean arterial pressure). This work demonstrates the utility of careful curation of summary-level data from a variety of sources to prioritize gene-lifestyle interaction loci for follow-up analyses.
Collapse
Affiliation(s)
- Timothy D. Majarian
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, United States
| | - Vincent Laville
- Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Michael R. Brown
- 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, United States
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Paul S. de Vries
- 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, United States
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - W. James Gauderman
- Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Casey Marchek
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MA, United States
| | - 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, United States
| | - Michael Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Dabeeru C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Karen Schwander
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, United States
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - C. Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Alisa K. Manning
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine and Harvard Medical School, Boston, MA, United States
| | | |
Collapse
|
43
|
van der Linden EL, Halley A, Meeks KAC, Chilunga F, Hayfron-Benjamin C, Venema A, Garrelds IM, Danser AHJ, van den Born BJ, Henneman P, Agyemang C. An explorative epigenome-wide association study of plasma renin and aldosterone concentration in a Ghanaian population: the RODAM study. Clin Epigenetics 2022; 14:159. [PMID: 36457109 PMCID: PMC9714193 DOI: 10.1186/s13148-022-01378-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The epigenetic regulation of the renin-angiotensin-aldosterone system (RAAS) potentially plays a role in the pathophysiology underlying the high burden of hypertension in sub-Saharan Africans (SSA). Here we report the first epigenome-wide association study (EWAS) of plasma renin and aldosterone concentrations and the aldosterone-to-renin ratio (ARR). METHODS Epigenome-wide DNA methylation was measured using the Illumina 450K array on whole blood samples of 68 Ghanaians. Differentially methylated positions (DMPs) were assessed for plasma renin concentration, aldosterone, and ARR using linear regression models adjusted for age, sex, body mass index, diabetes mellitus, hypertension, and technical covariates. Additionally, we extracted methylation loci previously associated with hypertension, kidney function, or that were annotated to RAAS-related genes and associated these with renin and aldosterone concentration. RESULTS We identified one DMP for renin, ten DMPs for aldosterone, and one DMP associated with ARR. Top DMPs were annotated to the PTPRN2, SKIL, and KCNT1 genes, which have been reported in relation to cardiometabolic risk factors, atherosclerosis, and sodium-potassium handling. Moreover, EWAS loci previously associated with hypertension, kidney function, or RAAS-related genes were also associated with renin, aldosterone, and ARR. CONCLUSION In this first EWAS on RAAS hormones, we identified DMPs associated with renin, aldosterone, and ARR in a SSA population. These findings are a first step in understanding the role of DNA methylation in regulation of the RAAS in general and in a SSA population specifically. Replication and translational studies are needed to establish the role of these DMPs in the hypertension burden in SSA populations.
Collapse
Affiliation(s)
- Eva L. van der Linden
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.7177.60000000084992262Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Adrienne Halley
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Karlijn A. C. Meeks
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.280128.10000 0001 2233 9230Center 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, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Charles Hayfron-Benjamin
- grid.8652.90000 0004 1937 1485Department of Physiology, University of Ghana Medical School, Accra, Ghana ,grid.415489.50000 0004 0546 3805Department of Anesthesia and Critical Care, Korle Bu Teaching Hospital, Accra, Ghana
| | - Andrea Venema
- grid.7177.60000000084992262Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Ingrid M. Garrelds
- grid.5645.2000000040459992XDivision of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Amsterdam, The Netherlands
| | - A. H. Jan Danser
- grid.5645.2000000040459992XDivision of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Amsterdam, The Netherlands
| | - Bert-Jan van den Born
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands ,grid.7177.60000000084992262Department of Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Peter Henneman
- grid.7177.60000000084992262Department of Human Genetics, Genome Diagnostics Laboratory Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Location AMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| |
Collapse
|
44
|
Armignacco R, Reel PS, Reel S, Jouinot A, Septier A, Gaspar C, Perlemoine K, Larsen CK, Bouys L, Braun L, Riester A, Kroiss M, Bonnet-Serrano F, Amar L, Blanchard A, Gimenez-Roqueplo AP, Prejbisz A, Januszewicz A, Dobrowolski P, Davies E, MacKenzie SM, Rossi GP, Lenzini L, Ceccato F, Scaroni C, Mulatero P, Williams TA, Pecori A, Monticone S, Beuschlein F, Reincke M, Zennaro MC, Bertherat J, Jefferson E, Assié G. Whole blood methylome-derived features to discriminate endocrine hypertension. Clin Epigenetics 2022; 14:142. [PMCID: PMC9635165 DOI: 10.1186/s13148-022-01347-y] [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: 05/11/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Arterial hypertension represents a worldwide health burden and a major risk factor for cardiovascular morbidity and mortality. Hypertension can be primary (primary hypertension, PHT), or secondary to endocrine disorders (endocrine hypertension, EHT), such as Cushing's syndrome (CS), primary aldosteronism (PA), and pheochromocytoma/paraganglioma (PPGL). Diagnosis of EHT is currently based on hormone assays. Efficient detection remains challenging, but is crucial to properly orientate patients for diagnostic confirmation and specific treatment. More accurate biomarkers would help in the diagnostic pathway. We hypothesized that each type of endocrine hypertension could be associated with a specific blood DNA methylation signature, which could be used for disease discrimination. To identify such markers, we aimed at exploring the methylome profiles in a cohort of 255 patients with hypertension, either PHT (n = 42) or EHT (n = 213), and at identifying specific discriminating signatures using machine learning approaches. Results Unsupervised classification of samples showed discrimination of PHT from EHT. CS patients clustered separately from all other patients, whereas PA and PPGL showed an overall overlap. Global methylation was decreased in the CS group compared to PHT. Supervised comparison with PHT identified differentially methylated CpG sites for each type of endocrine hypertension, showing a diffuse genomic location. Among the most differentially methylated genes, FKBP5 was identified in the CS group. Using four different machine learning methods—Lasso (Least Absolute Shrinkage and Selection Operator), Logistic Regression, Random Forest, and Support Vector Machine—predictive models for each type of endocrine hypertension were built on training cohorts (80% of samples for each hypertension type) and estimated on validation cohorts (20% of samples for each hypertension type). Balanced accuracies ranged from 0.55 to 0.74 for predicting EHT, 0.85 to 0.95 for predicting CS, 0.66 to 0.88 for predicting PA, and 0.70 to 0.83 for predicting PPGL. Conclusions The blood DNA methylome can discriminate endocrine hypertension, with methylation signatures for each type of endocrine disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01347-y.
Collapse
Affiliation(s)
- Roberta Armignacco
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Parminder S. Reel
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK
| | - Smarti Reel
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK
| | - Anne Jouinot
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.440907.e0000 0004 1784 3645Institut Curie, INSERM U900, MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Amandine Septier
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Cassandra Gaspar
- Sorbonne Université, INSERM, UMS Production et Analyse de données en Sciences de la vie et en Santé, PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, 75013 Paris, France
| | - Karine Perlemoine
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Casper K. Larsen
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France
| | - Lucas Bouys
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Leah Braun
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Riester
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Kroiss
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fidéline Bonnet-Serrano
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Hormonologie, AP-HP, Hôpital Cochin, F-75014 Paris, France
| | - Laurence Amar
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Unité Hypertension Artérielle, AP-HP, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Anne Blanchard
- grid.414093.b0000 0001 2183 5849Centre d’Investigations Cliniques 9201, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Anne-Paule Gimenez-Roqueplo
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Département de Médecine Génomique des Tumeurs et des Cancers, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Aleksander Prejbisz
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Andrzej Januszewicz
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Piotr Dobrowolski
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Eleanor Davies
- grid.8756.c0000 0001 2193 314XBHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Scott M. MacKenzie
- grid.8756.c0000 0001 2193 314XBHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Gian Paolo Rossi
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, Padua, Italy
| | - Livia Lenzini
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, Padua, Italy
| | - Filippo Ceccato
- grid.411474.30000 0004 1760 2630UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Carla Scaroni
- grid.411474.30000 0004 1760 2630UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Paolo Mulatero
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Tracy A. Williams
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Alessio Pecori
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Silvia Monticone
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Felix Beuschlein
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany ,grid.412004.30000 0004 0478 9977Klinikfür Endokrinologie, Diabetologie Und Klinische Ernährung, UniversitätsSpital Zürich (USZ) and Universität Zürich (UZH), Raemistrasse 100, 8091 Zurich, Switzerland
| | - Martin Reincke
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maria-Christina Zennaro
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Service de Génétique, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Jérôme Bertherat
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, F-75014 Paris, France
| | - Emily Jefferson
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK ,grid.8756.c0000 0001 2193 314XInstitute of Health and Wellbeing, University of Glasgow, Glasgow, G12 8RZ UK
| | - Guillaume Assié
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, F-75014 Paris, France
| |
Collapse
|
45
|
Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics 2022; 17:1357-1372. [PMID: 35030986 PMCID: PMC9586592 DOI: 10.1080/15592294.2022.2026591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
The role of DNA methylation and its interplay with gene expression in the susceptibility to pancreatic cancer (PanC) remains largely unexplored. To fill in this gap, we conducted an integrative two-phase epigenome-wide association study (EWAS) of PanC using genomic DNA from 44 cases and 556 controls (20 local controls and 536 public controls in the Framingham Heart Study) in phase 1 and 23 cases and 22 controls in phase 2. We validated the findings using pre-diagnostic blood samples from 13 cases and 26 controls in the Women's Health Initiative (WHI) Study. We further examined gene expression in peripheral leukocytes of 47 cases and 31 controls involved in the methylation study using RNA sequencing and performed bidirectional Mendelian randomization (MR) analysis using existing single nucleotide polymorphism (SNP) data. In phase 1, we identified 2776 significantly differentially methylated CpG sites (DMPs) and 154 significantly differentially methylated regions (DMRs). In phase 2, we validated six DMPs (in or near AIM2, DGKA, STK39, and TNFSF8) and three DMRs (in or near nc886, LY6G5C, and HLA-DPB1). The DMR near nc886 was further validated in the WHI samples (P = 6.69 × 10-5). MR analysis suggested that the CpG sites cg00308130 and cg16684184 for nc886 and cg16875057 for STK39 were causally related to PanC susceptibility and that PanC influenced methylation of cg15354065 for DGKA. This first integrative EWAS of PanC provides novel insights into the role of DNA methylation and its interplay with SNPs and gene expression in the disease susceptibility.
Collapse
Affiliation(s)
- Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Research Center at the University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Myriam Fornage
- IBrown Foundation Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Research Center at the University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
46
|
Bai C, Su M, Zhang Y, Lin Y, Sun Y, Song L, Xiao N, Xu H, Wen H, Zhang M, Ping J, Liu J, Hui R, Li H, Chen J. Oviductal Glycoprotein 1 Promotes Hypertension by Inducing Vascular Remodeling Through an Interaction With MYH9. Circulation 2022; 146:1367-1382. [PMID: 36172862 DOI: 10.1161/circulationaha.121.057178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Hypertension is a common cardiovascular disease that is related to genetic and environmental factors, but its mechanisms remain unclear. DNA methylation, a classic epigenetic modification, not only regulates gene expression but is also susceptible to environmental factors, linking environmental factors to genetic modification. Therefore, globally screening differential genomic DNA methylation in patients with hypertension is important for investigating hypertension mechanisms. METHODS Differential genomic DNA methylation in patients with hypertension, individuals with prehypertension, and healthy control individuals was screened using Illumina 450K BeadChip and verified by pyrosequencing. Plasma OVGP1 (oviduct glycoprotein 1) levels were determined using an enzyme-linked immunosorbent assay. Ovgp1 transgenic and knockout mice were generated to analyze the function of OVGP1. The blood pressure levels of the mouse models were measured using the tail-cuff system and radiotelemetry methods. The role of OVGP1 in vascular remodeling was determined by vascular relaxation studies. Protein-protein interactions were investigated using a pull-down/mass spectrometry assay and verified with coimmunoprecipitation and pull-down assays. RESULTS We found a hypomethylated site at cg20823859 in the promoter region of OVGP1 and plasma OVGP1 levels were significantly increased in patients with hypertension. This finding indicates that OVGP1 is associated with hypertension. In Ovgp1 transgenic mice, OVGP1 overexpression caused an increase in blood pressure, dysfunctional vasoconstriction and vasodilation, remodeling of arterial walls, and increased vascular superoxide stress and inflammation, and these phenomena were exacerbated by angiotensin II infusion. In contrast, OVGP1 deficiency attenuated angiotensin II-induced vascular oxidase stress, inflammation, and collagen deposition. These findings indicate that OVGP1 is a prohypertensive factor that directly promotes vascular remodeling. Pull-down and coimmunoprecipitation assays showed that MYH9 (nonmuscle myosin heavy chain IIA) interacted with OVGP1, whereas inhibition of MYH9 attenuated OVGP1-induced hypertension and vascular remodeling. CONCLUSIONS Hypomethylation at cg20823859 in the promoter region of OVGP1 is associated with hypertension and induces upregulation of OVGP1. The interaction between OVGP1 and MYH9 contributes to vascular remodeling and dysfunction. Therefore, OVGP1 is a prohypertensive factor that promotes vascular remodeling by binding with MYH9.
Collapse
Affiliation(s)
- Congxia Bai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China (C.B.)
| | - Ming Su
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China (M.S.)
| | - Yaohua Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China (Y.Z.)
| | - Yahui Lin
- Center of Laboratory Medicine, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases (Y.L.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingying Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Xiao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haochen Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongyan Wen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiedan Ping
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingzhou Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital (C.B., Y.Z., Y.S., L.S., N.X., H.X., H.W., M.Z., J.P., J.L., R.H., H.L., J.C.), National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China (J.C.)
| |
Collapse
|
47
|
Zhang X, Ammous F, Lin L, Ratliff SM, Ware EB, Faul JD, Zhao W, Kardia SLR, Smith JA. The Interplay of Epigenetic, Genetic, and Traditional Risk Factors on Blood Pressure: Findings from the Health and Retirement Study. Genes (Basel) 2022; 13:1959. [PMID: 36360196 PMCID: PMC9689874 DOI: 10.3390/genes13111959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/21/2023] Open
Abstract
The epigenome likely interacts with traditional and genetic risk factors to influence blood pressure. We evaluated whether 13 previously reported DNA methylation sites (CpGs) are associated with systolic (SBP) or diastolic (DBP) blood pressure, both individually and aggregated into methylation risk scores (MRS), in 3070 participants (including 437 African ancestry (AA) and 2021 European ancestry (EA), mean age = 70.5 years) from the Health and Retirement Study. Nine CpGs were at least nominally associated with SBP and/or DBP after adjusting for traditional hypertension risk factors (p < 0.05). MRSSBP was positively associated with SBP in the full sample (β = 1.7 mmHg per 1 standard deviation in MRSSBP; p = 2.7 × 10-5) and in EA (β = 1.6; p = 0.001), and MRSDBP with DBP in the full sample (β = 1.1; p = 1.8 × 10-6), EA (β = 1.1; p = 7.2 × 10-5), and AA (β = 1.4; p = 0.03). The MRS and BP-genetic risk scores were independently associated with blood pressure in EA. The effects of both MRSs were weaker with increased age (pinteraction < 0.01), and the effect of MRSDBP was higher among individuals with at least some college education (pinteraction = 0.02). In AA, increasing MRSSBP was associated with higher SBP in females only (pinteraction = 0.01). Our work shows that MRS is a potential biomarker of blood pressure that may be modified by traditional hypertension risk factors.
Collapse
Affiliation(s)
- Xinman Zhang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| |
Collapse
|
48
|
Elliott HR, Burrows K, Min JL, Tillin T, Mason D, Wright J, Santorelli G, Davey Smith G, Lawlor DA, Hughes AD, Chaturvedi N, Relton CL. Characterisation of ethnic differences in DNA methylation between UK-resident South Asians and Europeans. Clin Epigenetics 2022; 14:130. [PMID: 36243740 PMCID: PMC9571473 DOI: 10.1186/s13148-022-01351-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Ethnic differences in non-communicable disease risk have been described between individuals of South Asian and European ethnicity that are only partially explained by genetics and other known risk factors. DNA methylation is one underexplored mechanism that may explain differences in disease risk. Currently, there is little knowledge of how DNA methylation varies between South Asian and European ethnicities. This study characterised differences in blood DNA methylation between individuals of self-reported European and South Asian ethnicity from two UK-based cohorts: Southall and Brent Revisited and Born in Bradford. DNA methylation differences between ethnicities were widespread throughout the genome (n = 16,433 CpG sites, 3.4% sites tested). Specifically, 76% of associations were attributable to ethnic differences in cell composition with fewer effects attributable to smoking and genetic variation. Ethnicity-associated CpG sites were enriched for EWAS Catalog phenotypes including metabolites. This work highlights the need to consider ethnic diversity in epigenetic research.
Collapse
Affiliation(s)
- Hannah R. Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Josine L. Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Tillin
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Alun D. Hughes
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Nishi Chaturvedi
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| |
Collapse
|
49
|
Ma J, Chen X. Advances in pathogenesis and treatment of essential hypertension. Front Cardiovasc Med 2022; 9:1003852. [PMID: 36312252 PMCID: PMC9616110 DOI: 10.3389/fcvm.2022.1003852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Hypertension is a significant risk factor for cardiovascular and cerebrovascular diseases and the leading cause of premature death worldwide. However, the pathogenesis of the hypertension, especially essential hypertension, is complex and requires in-depth studies. Recently, new findings about essential hypertension have emerged, and these may provide important theoretical bases and therapeutic tools to break through the existing bottleneck of essential hypertension. In this review, we demonstrated important advances in the different pathogenesis areas of essential hypertension, and highlighted new treatments proposed in these areas, hoping to provide insight for the prevention and treatment of the essential hypertension.
Collapse
|
50
|
Lakshmanan AP, Murugesan S, Al Khodor S, Terranegra A. The potential impact of a probiotic: Akkermansia muciniphila in the regulation of blood pressure—the current facts and evidence. Lab Invest 2022; 20:430. [PMID: 36153618 PMCID: PMC9509630 DOI: 10.1186/s12967-022-03631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
Abstract
Akkermansia muciniphila (A. muciniphila) is present in the human gut microbiota from infancy and gradually increases in adulthood. The potential impact of the abundance of A. muciniphila has been studied in major cardiovascular diseases including elevated blood pressure or hypertension (HTN). HTN is a major factor in premature death worldwide, and approximately 1.28 billion adults aged 30–79 years have hypertension. A. muciniphila is being considered a next-generation probiotic and though numerous studies had highlighted the positive role of A. muciniphila in lowering/controlling the HTN, however, few studies had highlighted the negative impact of increased abundance of A. muciniphila in the management of HTN. Thus, in the review, we aimed to discuss the current facts, evidence, and controversy about the role of A. muciniphila in the pathophysiology of HTN and its potential effect on HTN management/regulation, which could be beneficial in identifying the drug target for the management of HTN.
Collapse
|