ArticleThe Journal of allergy and clinical immunology2023
Cis- and trans-eQTM analysis reveals novel epigenetic and transcriptomic immune markers of atopic asthma in airway epithelium.
Article in The Journal of allergy and clinical immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The trial behind it
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Who cites it
7 citing papers in PubMed, 9 citations in OpenAlex.
- eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.bioRxiv : the preprint server for biology · 2026Article
- Estimating in silico causal effects of DNA methylation on gene expression through genetic anchors in airway epithelium in asthma.Science advances · 2026Article
- The epigenetic-immune-microbiome axis in early life: reprogramming the origins and endotypes of pediatric asthma.Frontiers in immunology · 2026Review
- Pathway information on methylation analysis using deep neural network (PROMINENT): An interpretable deep learning method with pathway prior for phenotype prediction using gene-level DNA methylation.Artificial intelligence in medicine · 2025Article
- Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis reflecting disease severity and recovery.Communications biology · 2025Article
- MOSES: a methylation-based gene association approach for unveiling environmentally regulated genes linked to a trait or disease.Clinical epigenetics · 2024Article
- Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA.American journal of human genetics · 2024Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundExpression quantitative trait methylation (eQTM) analyses uncover associations between DNA methylation markers and gene expression. Most eQTM analyses of complex diseases have focused on cis-eQTM pairs (within 1 megabase).
objectivesThis study sought to identify cis- and trans-methylation markers associated with gene expression in airway epithelium from youth with and without atopic asthma.
methodsIn this study, the investigators conducted both cis- and trans-eQTM analyses in nasal (airway) epithelial samples from 158 Puerto Rican youth with atopic asthma and 100 control subjects without atopy or asthma. The investigators then attempted to replicate their findings in nasal epithelial samples from 2 studies of children, while also examining whether their results in nasal epithelium overlap with those from an eQTM analysis in white blood cells from the Puerto Rican subjects.
resultsThis study identified 9,108 cis-eQTM pairs and 2,131,500 trans-eQTM pairs. Trans-associations were significantly enriched for transcription factor and microRNA target genes. Furthermore, significant cytosine-phosphate-guanine sites (CpGs) were differentially methylated in atopic asthma and significant genes were enriched for genes differentially expressed in atopic asthma. In this study, 50.7% to 62.6% of cis- and trans-eQTM pairs identified in Puerto Rican youth were replicated in 2 smaller cohorts at false discovery rate-adjusted P < .1. Replicated genes in the trans-eQTM analysis included biologically plausible asthma-susceptibility genes (eg, HDC, NLRP3, ITGAE, CDH26, and CST1) and are enriched in immune pathways.
conclusionsStudying both cis- and trans-epigenetic regulation of airway epithelial gene expression can identify potential causal and regulatory pathways or networks for childhood asthma. Trans-eQTM CpGs may regulate gene expression in airway epithelium through effects on transcription factor and microRNA target genes.
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