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Quantifying the role of transcript levels in mediating DNA methylation effects on complex traits and diseases

Author

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  • Marie C. Sadler

    (University Center for Primary Care and Public Health
    Swiss Institute of Bioinformatics
    University of Lausanne)

  • Chiara Auwerx

    (University Center for Primary Care and Public Health
    Swiss Institute of Bioinformatics
    University of Lausanne
    Center for Integrative Genomics, University of Lausanne)

  • Kaido Lepik

    (University Center for Primary Care and Public Health
    Swiss Institute of Bioinformatics
    University of Lausanne)

  • Eleonora Porcu

    (University Center for Primary Care and Public Health
    Swiss Institute of Bioinformatics
    University of Lausanne
    Center for Integrative Genomics, University of Lausanne)

  • Zoltán Kutalik

    (University Center for Primary Care and Public Health
    Swiss Institute of Bioinformatics
    University of Lausanne)

Abstract

High-dimensional omics datasets provide valuable resources to determine the causal role of molecular traits in mediating the path from genotype to phenotype. Making use of molecular quantitative trait loci (QTL) and genome-wide association study (GWAS) summary statistics, we propose a multivariable Mendelian randomization (MVMR) framework to quantify the proportion of the impact of the DNA methylome (DNAm) on complex traits that is propagated through the assayed transcriptome. Evaluating 50 complex traits, we find that on average at least 28.3% (95% CI: [26.9%–29.8%]) of DNAm-to-trait effects are mediated through (typically multiple) transcripts in the cis-region. Several regulatory mechanisms are hypothesized, including methylation of the promoter probe cg10385390 (chr1:8’022’505) increasing the risk for inflammatory bowel disease by reducing PARK7 expression. The proposed integrative framework can be extended to other omics layers to identify causal molecular chains, providing a powerful tool to map and interpret GWAS signals.

Suggested Citation

  • Marie C. Sadler & Chiara Auwerx & Kaido Lepik & Eleonora Porcu & Zoltán Kutalik, 2022. "Quantifying the role of transcript levels in mediating DNA methylation effects on complex traits and diseases," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35196-3
    DOI: 10.1038/s41467-022-35196-3
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