ArticleThe Journal of allergy and clinical immunology2023
A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 29 citations in OpenAlex.
- Vitamin C supplementation to pregnant smokers alters asthma- and allergy-associated CpGs in child buccal DNA at 5 years of age.Clinical epigenetics · 2025Trial
- Immune pathways and prenatal/perinatal environmental exposures contribute to epigenetic gestational age prediction and acceleration.Epigenetics · 2026Article
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- Rhinovirus and interleukin-13 alter DNA methylation in bronchial epithelial cells at asthma loci.ERJ open research · 2026Article
- Th2 Cytokines Reshape the Transcriptome: Insights from a Canine Organoid Model of Atopic Dermatitis.International journal of molecular sciences · 2026Article
- Airway epithelial heterogeneity and mucus plugging in asthmatic bronchioles.American journal of respiratory and critical care medicine · 2026Article
- Deconvolution of DNA methylation data reveals cell type-specific epigenomic signatures in endometriosis and eutopic endometrium.Molecular human reproduction · 2026Article
- The epigenetic-immune-microbiome axis in early life: reprogramming the origins and endotypes of pediatric asthma.Frontiers in immunology · 2026Review
- Bronchial epithelial transcriptome reveals dysregulated interferon and inflammatory responses to rhinovirus in exacerbation-prone pediatric asthma.JCI insight · 2025Article
- Distinct DNA methylation in mother-infant dyads exposed to PM2.5 in pregnancy.Clinical epigenetics · 2025Article
- Epigenetic Alterations in Perioperative Anaphylaxis Among Chinese Patients: A Case-Control Study Protocol.Health science reports · 2025Article
- Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma.bioRxiv : the preprint server for biology · 2025Article
- Immune impacts of fire smoke exposure.Nature medicine · 2025Article
- Genetic contributions to epigenetic-defined endotypes of allergic phenotypes in children.American journal of human genetics · 2025Article
- Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations.Genome medicine · 2025Article
- A Phenotypically Distinct Human Th2 Cell Subpopulation Is Associated With Development of Allergic Disorders in Infancy.Allergy · 2025Article
- Precision medicine for asthma treatment: Unlocking the potential of the epigenome and microbiome.The Journal of allergy and clinical immunology · 2025Review
- Advancing therapeutic target discovery in pulmonary diseases: evolution and application of space exploration technologies.Frontiers in cell and developmental biology · 2025Review
- Prenatal ambient air pollution associations with DNA methylation in asthma- and allergy-relevant genes: findings from ECHO.Environmental epigenetics · 2025Article
- SilencingEnvironmental epigenetics · 2025Article
Corrections and comments
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Authors and funding
23 authors at 13 institutions in 2 countries.
Funding
Abstract
backgroundDNA methylation of cytosines at cytosine-phosphate-guanine (CpG) dinucleotides (CpGs) is a widespread epigenetic mark, but genome-wide variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high-throughput arrays.
objectivesTo explore this hidden portion of the epigenome, this study combined whole-genome bisulfite sequencing with in silico evidence of gene regulatory regions to design a custom array of high-value CpGs. This study focused on airway epithelial cells from children with and without allergic asthma because these cells mediate the effects of inhaled microbes, pollution, and allergens on asthma and allergic disease risk.
methodsThis study identified differentially methylated regions from whole-genome bisulfite sequencing in nasal epithelial cell DNA from a total of 39 children with and without allergic asthma of both European and African ancestries. This study selected CpGs from differentially methylated regions, previous allergy or asthma epigenome-wide association studies (EWAS), or genome-wide association study loci, and overlapped them with functional annotations for inclusion on a custom Asthma&Allergy array. This study used both the custom and EPIC arrays to perform EWAS of allergic sensitization (AS) in nasal epithelial cell DNA from children in the URECA (Urban Environment and Childhood Asthma) birth cohort and using the custom array in the INSPIRE [Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure] birth cohort. Each CpG on the arrays was assigned to its nearest gene and its promotor capture Hi-C interacting gene and performed expression quantitative trait methylation (eQTM) studies for both sets of genes.
resultsCustom array CpGs were enriched for intermediate methylation levels compared to EPIC CpGs. Intermediate methylation CpGs were further enriched among those associated with AS and for eQTMs on both arrays.
conclusionsThis study revealed signature features of high-value CpGs and evidence for epigenetic regulation of genes at AS EWAS loci that are robust to race/ethnicity, ascertainment, age, and geography.
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