Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: The Framingham Heart Study

Abstract

Background. Expression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression and may reveal molecular mechanisms of disease. The present study describes an eQTM resource of CpG-transcript pairs. Methods. DNA methylation was measured in blood samples from 1,045 Framingham Heart Study (FHS) participants using the Illumina 450K BeadChip and in 1,070 FHS participants using the Illumina EPIC array. Blood gene expression data were collected from all 2,115 participants using RNA sequencing (RNA-seq). The association between DNA methylation and gene expression was quantified for all cis (i.e., within 1Mb) and trans (>1Mb) CpG-transcript pairs. Significant results (p<1E-7 for cis and <1E-14 for trans) were subsequently tested for enrichment of biological pathways and of clinical traits. Results. We identified 70,047 significant cis CpG-transcript pairs 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 1,208 clinical traits (enrichment false discovery rate [FDR] ≤ 0.05). We also identified 246,667 significant trans CpG-transcript pairs where the top most significant eGenes were enriched in biological pathways related to activation of the immune response, and for 1,191 clinical traits (enrichment FDR ≤ 0.05). 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 these cardiometabolic traits. Conclusions. We developed a robust and powerful resource of eQTM CpG-transcript pairs that can help inform future functional studies that seek to understand the molecular basis of disease.

Epigenetic Biomarkers of Socioeconomic Status are Associated with Age-Related Chronic Diseases and Mortality in Older Adults

“…A CpG site was in the promoter region if it was located 0-1500 bases upstream of a transcription start site. To identify CpGs associated with gene expression, we used results from expression quantitative trait methylation (eQTM) analysis performed using the 450k chip (101) and the EPIC (102) in the Framingham Heart Study (FHS). For each set of CpGs selected for a given biomarker, we compared whether the set of CpGs were more likely to be eQTMs than CpGs that were not selected by comparing the proportion of eQTMs in the two groups.…”

“…After FDR correction, gene-set enrichment of GO Biological Processes (BP) terms and KEGG pathways were not observed for either set of CpGs when mapped to their proximal genes (FDR q<0.01). When utilizing eQTM data from Keshawarz et al (2023), CpGs selected for the aSES-BIO and cSES-BIO mapped to the expression of 230 and 66 genes, respectively, in cis or in trans. Additionally, CpGs selected for aSES-BIO were associated with the expression of genes enriched for 8 GO BP terms related to cell death, T cell differentiation and activation, cell migration, and cell-cell signaling (SI Appendix, Table S12 and Figure S3).…”

Dietary and supplemental intake of vitamins C and E is associated with altered DNA methylation in an epigenome-wide association study meta-analysis

“…CpG sites that were significantly associated with vitamin C or E intake at a FDR ≤ 0.01 were used in expression quantitative trait methylation (eQTM) analysis within the FHS cohort to identify downstream effects of DNA methylation on gene expression. eQTM analysis in the FHS has used DNA methylation data and RNA sequencing data to quantify the association between DNA methylation and gene expression independent of age, sex, white blood cell count, blood cell fraction, platelet count, genetic principal components (PCs), and DNA methylation PCs [ 45 ]. We identified significant cis associations between CpG sites and gene transcripts (i.e., associations where the CpG site was within 1Mb of the transcription start site) at a p-value of 1.0 × 10 −7 [ 46 ].…”

A novel statistical framework for meta-analysis of total mediation effect with high dimensional omics mediators in large-scale genomic consortia

“…In the FHS Offspring and Third-Generation cohorts, expression profiling for 17,873 genes/transcripts was conducted using the Affymetrix Human Exon 1.0 ST GeneChip, derived from whole blood mRNA (Joehanes et al, 2012). On the other hand, as part of the TOPMed program, RNA-seq was performed on whole blood in these FHS cohorts using the Illumina NovaSeq system profiling expression of over 40,000 transcripts (Keshawarz et al, 2023). In the meta analysis, we only included nonoverlapping participants between the microarray and RNAseq platforms.…”