Department of Human Genetics, University of Chicago, Chicago, Ill.
Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Ore.
J Allergy Clin Immunol. 2023 Jun;151(6):1609-1621. doi: 10.1016/j.jaci.2022.12.828. Epub 2023 Feb 6.
DNA 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.
To 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.
This 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.
Custom 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.
This 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.
胞嘧啶-磷酸-鸟嘌呤（CpG）二核苷酸（CpG）处的胞嘧啶 DNA 甲基化是一种广泛存在的表观遗传标记，但由于商业高通量阵列上可变 CpG 的代表性有限，全基因组变异相对来说尚未得到充分探索。
为了探索表观基因组的这一部分，本研究将全基因组亚硫酸氢盐测序与基因调控区域的计算机证据相结合，设计了一种高价值 CpG 的定制阵列。本研究集中于患有和不患有过敏性哮喘的儿童的气道上皮细胞，因为这些细胞介导吸入的微生物、污染和过敏原对哮喘和过敏性疾病风险的影响。
本研究从总共 39 名具有和不具有欧洲和非洲血统的过敏性哮喘儿童的鼻上皮细胞 DNA 中，从全基因组亚硫酸氢盐测序中鉴定出差异甲基化区域。本研究从差异甲基化区域、先前的过敏或哮喘表观基因组全基因组关联研究（EWAS）或全基因组关联研究位点中选择 CpG，并将其与功能注释重叠，以包含在定制的哮喘和过敏阵列上。本研究使用定制和 EPIC 阵列在 URECA（城市环境和儿童哮喘）出生队列的儿童的鼻上皮细胞 DNA 中进行过敏致敏（AS）的 EWAS，并在 INSPIRE [呼吸道合胞病毒暴露后婴儿对肺部感染和哮喘的易感性]出生队列中使用定制阵列进行研究。阵列上的每个 CpG 都被分配到其最近的基因及其启动子捕获 Hi-C 相互作用基因，并对这两组基因进行表达定量性状甲基化（eQTM）研究。
与 EPIC CpG 相比，定制阵列 CpG 富集了中等甲基化水平。中间甲基化的 CpG 进一步富集在与 AS 相关的 CpG 中，并在两个阵列上富集了 eQTM。
本研究揭示了高价值 CpG 的特征以及 AS EWAS 位点基因的表观遗传调控证据，这些证据不受种族/民族、鉴定、年龄和地理位置的影响。
