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Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis

Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g. DNA methylation). Here we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individ...

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Autores principales: Tang, Guoping, Sun, Chen, Lv, Hongchao, Zhang, Mingming, Jiang, Yongshuai, Xu, Jing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9714356/
https://www.ncbi.nlm.nih.gov/pubmed/36342317
http://dx.doi.org/10.1002/2211-5463.13517
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author Tang, Guoping
Sun, Chen
Lv, Hongchao
Zhang, Mingming
Jiang, Yongshuai
Xu, Jing
author_facet Tang, Guoping
Sun, Chen
Lv, Hongchao
Zhang, Mingming
Jiang, Yongshuai
Xu, Jing
author_sort Tang, Guoping
collection PubMed
description Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g. DNA methylation). Here we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individual genetic variation and DNAm data. Epigenome‐wide meQTL (methylation quantitative trait loci) analysis was performed on 354 RA patients and 335 controls, scanning 30,101,744 relationships between 62 SNPs and 485,512 DNA methylation sites. Two regulatory relationship pairs (FDR < 0.05) showed very strong associations with RA risk. One was rs10796216‐cg00475509, and the DNAm decreased by 0.0168 per addition of allele rs10796216‐A. The other was rs6546473‐cg13358873, for which a 0.0365 reduction of DNAm at cg13358873 was observed for each addition of allele rs6546473‐A, and lower DNAm was found to be significantly associated with RA risk (P = 2.0407e‐28). Moreover, both pairs of meQTL showed a strong regulatory relationship only in RA samples, so they can be subsequently considered as risk markers for RA. In conclusion, our integrated analysis of genetic and epigenetic variation suggests that genetic variation may affect the risk of RA by regulating DNA methylation levels. Alterations of DNAm at cg00475509 and cg13358873 loci conferred by rs10796216‐A and rs6546473‐A allele may suggest a potential risk for RA. Our results deepen our understanding of the genetic and epigenetic mechanisms of RA and provide novel associations that can be further investigated in future studies.
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spelling pubmed-97143562022-12-02 Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis Tang, Guoping Sun, Chen Lv, Hongchao Zhang, Mingming Jiang, Yongshuai Xu, Jing FEBS Open Bio Research Articles Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g. DNA methylation). Here we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individual genetic variation and DNAm data. Epigenome‐wide meQTL (methylation quantitative trait loci) analysis was performed on 354 RA patients and 335 controls, scanning 30,101,744 relationships between 62 SNPs and 485,512 DNA methylation sites. Two regulatory relationship pairs (FDR < 0.05) showed very strong associations with RA risk. One was rs10796216‐cg00475509, and the DNAm decreased by 0.0168 per addition of allele rs10796216‐A. The other was rs6546473‐cg13358873, for which a 0.0365 reduction of DNAm at cg13358873 was observed for each addition of allele rs6546473‐A, and lower DNAm was found to be significantly associated with RA risk (P = 2.0407e‐28). Moreover, both pairs of meQTL showed a strong regulatory relationship only in RA samples, so they can be subsequently considered as risk markers for RA. In conclusion, our integrated analysis of genetic and epigenetic variation suggests that genetic variation may affect the risk of RA by regulating DNA methylation levels. Alterations of DNAm at cg00475509 and cg13358873 loci conferred by rs10796216‐A and rs6546473‐A allele may suggest a potential risk for RA. Our results deepen our understanding of the genetic and epigenetic mechanisms of RA and provide novel associations that can be further investigated in future studies. John Wiley and Sons Inc. 2022-11-19 /pmc/articles/PMC9714356/ /pubmed/36342317 http://dx.doi.org/10.1002/2211-5463.13517 Text en © 2022 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Tang, Guoping
Sun, Chen
Lv, Hongchao
Zhang, Mingming
Jiang, Yongshuai
Xu, Jing
Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title_full Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title_fullStr Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title_full_unstemmed Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title_short Identification of novel meQTLs strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
title_sort identification of novel meqtls strongly associated with rheumatoid arthritis by large‐scale epigenome‐wide analysis
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9714356/
https://www.ncbi.nlm.nih.gov/pubmed/36342317
http://dx.doi.org/10.1002/2211-5463.13517
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