Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.
Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada.
Clin Epigenetics. 2021 Jun 26;13(1):131. doi: 10.1186/s13148-021-01114-5.
Epigenome-wide association studies (EWAS) have provided opportunities to understand the role of epigenetic mechanisms in development and pathophysiology of many chronic diseases. However, an important limitation of conventional EWAS is that profiles of epigenetic variability are often obtained in samples of mixed cell types. Here, we aim to assess whether changes in cord blood DNA methylation (DNAm) associated with gestational diabetes mellitus (GDM) exposure and early childhood growth markers occur in a cell type-specific manner.
We analyzed 275 cord blood samples collected at delivery from a prospective pre-birth cohort with genome-wide DNAm profiled by the Illumina MethylationEPIC array. We estimated proportions of seven common cell types in each sample using a cord blood-specific DNAm reference panel. Leveraging a recently developed approach named CellDMC, we performed cell type-specific EWAS to identify CpG loci significantly associated with GDM, or 3-year-old body mass index (BMI) z-score. A total of 1410 CpG loci displayed significant cell type-specific differences in methylation level between 23 GDM cases and 252 controls with a false discovery rate < 0.05. Gene Ontology enrichment analysis indicated that LDL transportation emerged from CpG specifically identified from B-cells DNAm analyses and the mitogen-activated protein kinase pathway emerged from CpG specifically identified from natural killer cells DNAm analyses. In addition, we identified four and six loci associated with 3-year-old BMI z-score that were specific to CD8+ T-cells and monocytes, respectively. By performing genome-wide permutation tests, we validated that most of our detected signals had low false positive rates.
Compared to conventional EWAS adjusting for the effects of cell type heterogeneity, the proposed approach based on cell type-specific EWAS could provide additional biologically meaningful associations between CpG methylation, prenatal maternal GDM or 3-year-old BMI. With careful validation, these findings may provide new insights into the pathogenesis, programming, and consequences of related childhood metabolic dysregulation. Therefore, we propose that cell type-specific analyses are worth cautious explorations.
全基因组关联研究（EWAS）为理解表观遗传机制在许多慢性疾病的发展和病理生理学中的作用提供了机会。然而，传统 EWAS 的一个重要局限性是，表观遗传变异性的图谱通常是在混合细胞类型的样本中获得的。在这里，我们旨在评估与妊娠糖尿病（GDM）暴露和儿童早期生长标志物相关的脐带血 DNA 甲基化（DNAm）变化是否以细胞类型特异性的方式发生。
我们分析了来自前瞻性产前队列的 275 个分娩时采集的脐带血样本，这些样本通过 Illumina MethylationEPIC 阵列进行了全基因组 DNAm 图谱分析。我们使用脐带血特异性 DNAm 参考面板估计了每个样本中七种常见细胞类型的比例。利用最近开发的一种名为 CellDMC 的方法，我们进行了细胞类型特异性 EWAS，以鉴定与 GDM 或 3 岁时体重指数（BMI）z 评分显著相关的 CpG 位点。共有 1410 个 CpG 位点在 23 例 GDM 病例和 252 例对照之间的甲基化水平显示出显著的细胞类型特异性差异，假发现率<0.05。基因本体论富集分析表明，LDL 转运从 B 细胞 DNAm 分析中特异性鉴定的 CpG 中出现，丝裂原激活蛋白激酶途径从自然杀伤细胞 DNAm 分析中特异性鉴定的 CpG 中出现。此外，我们还鉴定了与 3 岁时 BMI z 评分相关的四个和六个位点，分别与 CD8+T 细胞和单核细胞特异性相关。通过进行全基因组置换检验，我们验证了我们检测到的大多数信号具有较低的假阳性率。
与调整细胞类型异质性影响的传统 EWAS 相比，基于细胞类型特异性 EWAS 的方法可以提供 CpG 甲基化、产前母亲 GDM 或 3 岁时 BMI 之间的额外有生物学意义的关联。通过仔细验证，这些发现可能为相关儿童代谢失调的发病机制、编程和后果提供新的见解。因此，我们建议对细胞类型特异性分析进行谨慎探索。
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