Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma

Abstract

findings, we were interested in examining whether methylation of specific CpG sites is 67 associated with expression of non-nearby cis-genes. We thus conducted an expression 68 quantitative trait methylation (eQTM) analysis in nasal airway epithelium from 455 Puerto 69Ricans ages 9 to 20 years, including 219 subjects with asthma (cases) and 236 control subjects. 70 71 Results 72Location of eQTM-methylation probes relative to paired genes 73 By testing associations between methylation probes within 1 Mb of transcription start sites (TSS) 74 of genes and gene expression, we identified 16,867 significant methylation-expression pairs 75 (FDR-P < 0.01, see Methods), comprising 9,103 methylation probes associated with expression 76 of 3,512 genes. We then investigated the position of significant methylation probes in this eQTM 77 analysis in relation to their paired genes. If a methylation probe was associated with expression 78 of multiple genes, we counted such probe for each gene. We found that 11% and 89% of 79 significant eQTM probes were located within and outside genes, respectively -including 4% of 80 eQTM probes in promoter regions (Figure 1a). Most eQTM methylation probes were distant 81 from their target genes (371,840 bp on average) (Figure 1b). 82 83 Because we found distant relationships between methylation and their target genes, we assessed 84 whether eQTM methylation probes in nasal epithelium are enriched in the enhancer regions of 85 their paired genes. For this, we checked the enhancer database for lung tissue 86 (http://enhanceratlas.org/) 3 , since nasal epithelial tissue was not available in that database, and 87 nasal and bronchial epithelial methylation and expression are well correlated 1 . We found that 88 eQTM methylation probes are more likely to be located in enhancer regions of their paired genes 89 than randomly selected control probes (p-value: 1.3x10 -213 ) (Figure 1c, Table 1). 90 91 While most methylation probes near TSS were negatively correlated with gene expression, more 92 distant pairs tended to be positively correlated (Figure 1d). Of the eQTM methylation probes 93 associated with expression of the gene they were located in, 81.9% were negatively correlated 94 with expression (85.3% if in promoter regions) (Figure 1e). In contrast, only 40.2 % of eQTM 95 methylation probes associated with expression of a distant gene (i.e. methylation probes outside 96 of the associated gene) were negatively correlated with expression levels (Figure 1f). 97 98 Most of the top eQTM genes (by eQTM P-value) have been implicated in lung disease (Figure 99 2). PAX8 is associated with bronchodilator response in children with asthma 4 , ECHDC3 is 100 associated with obesity and asthma in children 5 , LSP1 is associated with acute lung inflammation 101 6 , HLA-DQB1 is associated with asthma 7 and total IgE 8 , FRG1B is highly mutated in lung 102 adenocarcinoma 9 , and KANSL1 is associated with pulmonary function 10 . 103 104 Gene Ontology enrichment analysis 105We performed a Gene Ontology enrichment ...

Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood

“…genome-wide studies investigating the associations between DNA methylation levels and gene expression [9,10]. Several eQTM studies have been published in diverse cell types/tissues: whole blood [8,11], monocytes [11][12][13], lymphoblastoid cell lines, T-cells and fibroblasts derived from umbilical cords [14,15], fibroblasts [16], liver [17], skeletal muscle [18], nasal airway epithelium [19] and placenta [20]. As most of the EWAS are conducted in whole blood [6,21], there is a need for comprehensive eQTM studies in this tissue.…”

It’s in the (Epi)genetics

“…5 Their findings also show that the more distal relationships of DNA methylation and expression are often positively correlated as opposed to the canonical negative correlations observed in most promoters. Kim et al 7 further show that the top eQTMs are in genes and pathways of high relevance to asthma and atopy, with most enriched gene ontology pathways relating to immune processes and cell adhesion and activation. Furthermore, a little over a third of eQTM CpGs (5,934/ 16,867; Fig 1B) were shown to affect atopic asthma through altering gene expression, assessed by formal mediation analysis, providing statistical evidence for causality in these relationships.…”

“…To more comprehensively characterize the relationship of DNA methylation and gene expression in the nasal epithelium, Kim et al 7 in this issue of CHEST have reanalyzed their dataset by performing an expression quantitative trait methylation (eQTM) analysis in which they comprehensively map significant associations between gene expression and CpG methylation within 1 megabase (Mb) of the transcription start site of genes (generally referred to as cis relationships) (Fig 1A). Their main findings are in line with the emerging knowledge of how DNA methylation regulates gene expression in that most CpGs that are significantly associated with gene expression are heavily enriched within distal enhancer elements as opposed to promoters, with eQTM CpGs being on average 372 Kb from target genes.…”

“…There are many strengths of the study by Kim et al 7 The first one is the use of a well-characterized cohort of children with atopic asthma in Puerto Rico. Puerto Ricans have a disproportional burden of asthma, making studies in this cohort highly significant.…”

“…Relationships within 1 Mb distance on the same chromosome are referred to as cis-QTLs (red), whereas more distant relationships on the same chromosome or on two different chromosomes are referred to as trans-QTLs (not shown). B, Kim et al 7 identified 16,867 cis-eQTMs, 5,934 of which were shown as statistically significant effects of DNA methylation mediated through gene expression on allergic asthma in the nasal epithelium. mQTL and eQTLs in this same cohort were reported previously.…”