BACKGROUND: DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach.
METHODS: The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses.
RESULTS: We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development.
CONCLUSIONS: We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context.
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This study was supported by the National Institutes of Health R01- MD012765, R01-DK117445, and R21-HL140385 to NF. The TRANSLATE studies and MT are supported by British Heart Foundation project grants PG/17/35/33001 and PG/19/16/34270, Kidney Research UK grant RP_017_20180302, and Medical University of Silesia grants KNW-1-152/N/7/K and KNW-1-171/N/6/K. WT206194. DLM and REM are supported by Alzheimer’s Research UK major project grant ARUK-PG2017B-10. CH is supported by an MRC University Unit Programme Grant MC_UU_00007/10 (QTL in Health and Disease). SJL and MKL are supported by the Intramural Program of the NIH, National Institute of Environmental Health Sciences (ZO1 ES043012). SB acknowledges funding from the Wellcome Trust (218274/Z/19/Z). CEB and SIB are supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH.
The CATHGEN study was supported by NIH grants HL095987 and HL036587.
Generation Scotland (GS) received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and DNA methylation profiling of the GS samples was carried out by the Genetics Core Laboratory at the Clinical Research Facility, University of Edinburgh, Edinburgh, Scotland, and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL; Reference 104036/Z/14/Z)).
Support for the Multi-Ethnic Study of Atherosclerosis (MESA) projects are conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support for MESA is provided by contracts 75N92020D00001, HHSN268201500003I, N01-HC-95159, 75N92020D00005, N01-HC-95160, 75N92020D00002, N01-HC-95161, 75N92020D00003, N01-HC-95162, 75N92020D00006, N01-HC-95163, 75N92020D00004, N01-HC-95164, 75N92020D00007, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, and UL1-TR-001420. Also supported in part by the National Center for Advancing Translational Sciences, CTSI grant UL1TR001881, and the National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC) grant DK063491 to the Southern California Diabetes Endocrinology Research Center. The TOPMed MESA Multi-Omics project was conducted by the University of Washington and LABioMed (HHSN2682015000031/HHSN26800004).
The Jackson Heart Study (JHS) is supported and conducted in collaboration with Jackson State University (HHSN268201800013I), Tougaloo College (HHSN268201800014I), the Mississippi State Department of Health (HHSN268201800015I), and the University of Mississippi Medical Center (HHSN268201800010I, HHSN268201800011I, and HHSN268201800012I) contracts from the National Heart, Lung, and Blood Institute (NHLBI) and the National Institute for Minority Health and Health Disparities (NIMHD). The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the US Department of Health and Human Services. The funders had no role in the design and conduct of the study; in the collection, analysis, and interpretation of the data; and in the preparation, review, or approval of the manuscript.
The WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, US Department of Health and Human Services, through contracts HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C. A full listing of WHI investigators can be found at http://www.whi.org/researchers/Documents%20%20Write%20a%20Paper/WHI%20Investigator%20Long%20List.pdf”.
The Hypertension Genetic Epidemiology Network (HyperGEN) Study is part of the National Heart, Lung, and Blood Institute (NHLBI) Family Blood Pressure Program; collection of the data represented here was supported by grants U01 HL054472, U01 HL054473, U01 HL054495, and U01 HL054509. The HyperGEN: Genetics of Left Ventricular Hypertrophy Study was supported by NHLBI grant R01 HL055673 with whole-genome sequencing made possible by supplement -18S1. The epigenetic data in HyperGEN was funded by an American Heart Association Cardiovascular Genome-Phenome Study Pathway Grant Award 15GPSPG23890000.
Investigators interested in retrieving the controlled-access data at dbGap for WHI-BAA23 and MESA should apply using identifiers phs000200.v10.p3 and phs001416.v1.p, respectively (available online at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000200.v10.p3 and https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001416.v1.p1). The summary results from this study are placed in dbGaP with accession number phs000930.v8.p1. While awaiting data release via dbGaP, data are available at https://sph.unc.edu/wp-content/uploads/sites/112/2021/02/EWAS_COGENT.tar. Access to the WHI-EMPC DNA methylation dataset is available upon request to www.whi.org. DNA methylation datasets from JHS and HyperGEN have been recently generated and upload to dbGap is ongoing. JHS data are available on request from www.jacksonheartstudy.org and HyperGEN data are available from the corresponding author from Ammous et al. Currently, JHS and WHI datasets are available through a scientific review application process directed to each respective study publication and presentation committee. Data can be obtained from the coordinating center of WHI and JHS after signing a data use agreement with the study. For research projects that meet the rules for access, CATHGEN data are available from the CATHGEN Steering Committee. Relevant requests are to be sent to the contact person at the CATHGEN Steering Committee, Melissa Hurdle. According to the terms of consent for GS participants, access to individual-level data (omics and phenotypes) must be reviewed by the GS Access Committee. Applications should be made to firstname.lastname@example.org. The source code used for the eFORGE analyses is publicly available at https://github.com/charlesbreeze/eFORGE and https://github.com/charlesbreeze/eFORGE-TF.
Breeze, Charles E.; Batorsky, Anna; Lee, Mi Kyeong; Szeto, Mindy D.; Xu, Xiaoguang; McCartney, Daniel L.; Jiang, Rong; Patki, Amit; Kramer, Holly J.; Eales, James M.; Raffield, Laura; Lange, Leslie; Lange, Ethan; Durda, Peter; Liu, Yongmei; Tracy, Russ P.; Van Den Berg, David; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed MESA Multi-Omics Working Group; Evans, Kathryn L.; Kraus, William E.; and Arnett, Donna K., "Epigenome-Wide Association Study of Kidney Function Identifies Trans-Ethnic and Ethnic-Specific Loci" (2021). Epidemiology Faculty Publications. 75.
Additional file 1: Supplementary Figures. Figure S1 to S7. Study design, QQ plots, Manhattan plots, forest plots and eFORGE/FORGE2 analyses.
13073_2021_877_MOESM2_ESM.docx (321 kB)
Additional file 2: Supplementary Methods. Description of different constituent cohorts and studies, in addition to power analyses.
13073_2021_877_MOESM3_ESM.xlsx (148 kB)
Additional file 3: Supplementary Tables. Tables S1 to S5. Descriptive characteristics, quality control and processing, and results.