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Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation

AIMS/HYPOTHESIS: Several studies have identified associations between type 2 diabetes and DNA methylation (DNAm). However, the causal role of these associations remains unclear. This study aimed to provide evidence for a causal relationship between DNAm and type 2 diabetes. METHODS: We used bidirect...

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Autores principales: Juvinao-Quintero, Diana L., Sharp, Gemma C., Sanderson, Eleanor C. M., Relton, Caroline L., Elliott, Hannah R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244277/
https://www.ncbi.nlm.nih.gov/pubmed/37202507
http://dx.doi.org/10.1007/s00125-023-05914-7
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author Juvinao-Quintero, Diana L.
Sharp, Gemma C.
Sanderson, Eleanor C. M.
Relton, Caroline L.
Elliott, Hannah R.
author_facet Juvinao-Quintero, Diana L.
Sharp, Gemma C.
Sanderson, Eleanor C. M.
Relton, Caroline L.
Elliott, Hannah R.
author_sort Juvinao-Quintero, Diana L.
collection PubMed
description AIMS/HYPOTHESIS: Several studies have identified associations between type 2 diabetes and DNA methylation (DNAm). However, the causal role of these associations remains unclear. This study aimed to provide evidence for a causal relationship between DNAm and type 2 diabetes. METHODS: We used bidirectional two-sample Mendelian randomisation (2SMR) to evaluate causality at 58 CpG sites previously detected in a meta-analysis of epigenome-wide association studies (meta-EWAS) of prevalent type 2 diabetes in European populations. We retrieved genetic proxies for type 2 diabetes and DNAm from the largest genome-wide association study (GWAS) available. We also used data from the Avon Longitudinal Study of Parents and Children (ALSPAC, UK) when associations of interest were not available in the larger datasets. We identified 62 independent SNPs as proxies for type 2 diabetes, and 39 methylation quantitative trait loci as proxies for 30 of the 58 type 2 diabetes-related CpGs. We applied the Bonferroni correction for multiple testing and inferred causality based on p<0.001 for the type 2 diabetes to DNAm direction and p<0.002 for the opposing DNAm to type 2 diabetes direction in the 2SMR analysis. RESULTS: We found strong evidence of a causal effect of DNAm at cg25536676 (DHCR24) on type 2 diabetes. An increase in transformed residuals of DNAm at this site was associated with a 43% (OR 1.43, 95% CI 1.15, 1.78, p=0.001) higher risk of type 2 diabetes. We inferred a likely causal direction for the remaining CpG sites assessed. In silico analyses showed that the CpGs analysed were enriched for expression quantitative trait methylation sites (eQTMs) and for specific traits, dependent on the direction of causality predicted by the 2SMR analysis. CONCLUSIONS/INTERPRETATION: We identified one CpG mapping to a gene related to the metabolism of lipids (DHCR24) as a novel causal biomarker for risk of type 2 diabetes. CpGs within the same gene region have previously been associated with type 2 diabetes-related traits in observational studies (BMI, waist circumference, HDL-cholesterol, insulin) and in Mendelian randomisation analyses (LDL-cholesterol). Thus, we hypothesise that our candidate CpG in DHCR24 may be a causal mediator of the association between known modifiable risk factors and type 2 diabetes. Formal causal mediation analysis should be implemented to further validate this assumption. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s00125-023-05914-7) contains peer-reviewed but unedited supplementary material.
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spelling pubmed-102442772023-06-08 Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation Juvinao-Quintero, Diana L. Sharp, Gemma C. Sanderson, Eleanor C. M. Relton, Caroline L. Elliott, Hannah R. Diabetologia Article AIMS/HYPOTHESIS: Several studies have identified associations between type 2 diabetes and DNA methylation (DNAm). However, the causal role of these associations remains unclear. This study aimed to provide evidence for a causal relationship between DNAm and type 2 diabetes. METHODS: We used bidirectional two-sample Mendelian randomisation (2SMR) to evaluate causality at 58 CpG sites previously detected in a meta-analysis of epigenome-wide association studies (meta-EWAS) of prevalent type 2 diabetes in European populations. We retrieved genetic proxies for type 2 diabetes and DNAm from the largest genome-wide association study (GWAS) available. We also used data from the Avon Longitudinal Study of Parents and Children (ALSPAC, UK) when associations of interest were not available in the larger datasets. We identified 62 independent SNPs as proxies for type 2 diabetes, and 39 methylation quantitative trait loci as proxies for 30 of the 58 type 2 diabetes-related CpGs. We applied the Bonferroni correction for multiple testing and inferred causality based on p<0.001 for the type 2 diabetes to DNAm direction and p<0.002 for the opposing DNAm to type 2 diabetes direction in the 2SMR analysis. RESULTS: We found strong evidence of a causal effect of DNAm at cg25536676 (DHCR24) on type 2 diabetes. An increase in transformed residuals of DNAm at this site was associated with a 43% (OR 1.43, 95% CI 1.15, 1.78, p=0.001) higher risk of type 2 diabetes. We inferred a likely causal direction for the remaining CpG sites assessed. In silico analyses showed that the CpGs analysed were enriched for expression quantitative trait methylation sites (eQTMs) and for specific traits, dependent on the direction of causality predicted by the 2SMR analysis. CONCLUSIONS/INTERPRETATION: We identified one CpG mapping to a gene related to the metabolism of lipids (DHCR24) as a novel causal biomarker for risk of type 2 diabetes. CpGs within the same gene region have previously been associated with type 2 diabetes-related traits in observational studies (BMI, waist circumference, HDL-cholesterol, insulin) and in Mendelian randomisation analyses (LDL-cholesterol). Thus, we hypothesise that our candidate CpG in DHCR24 may be a causal mediator of the association between known modifiable risk factors and type 2 diabetes. Formal causal mediation analysis should be implemented to further validate this assumption. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s00125-023-05914-7) contains peer-reviewed but unedited supplementary material. Springer Berlin Heidelberg 2023-05-19 2023 /pmc/articles/PMC10244277/ /pubmed/37202507 http://dx.doi.org/10.1007/s00125-023-05914-7 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Juvinao-Quintero, Diana L.
Sharp, Gemma C.
Sanderson, Eleanor C. M.
Relton, Caroline L.
Elliott, Hannah R.
Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title_full Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title_fullStr Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title_full_unstemmed Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title_short Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation
title_sort investigating causality in the association between dna methylation and type 2 diabetes using bidirectional two-sample mendelian randomisation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244277/
https://www.ncbi.nlm.nih.gov/pubmed/37202507
http://dx.doi.org/10.1007/s00125-023-05914-7
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