Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA.
Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA.
BMC Pulm Med. 2018 Mar 5;18(1):42. doi: 10.1186/s12890-018-0603-y.
There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD.
To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0.7, FEV1% < 80%), and 30 non-COPD controls. Targeted next generation sequencing was used to measure total and allele-specific expression of 35 genes in genome maintenance (GM) genes pathways linked to COPD pathogenesis, including seven TP53 and CEBP transcription factor family members. Shrinkage linear discriminant analysis (SLDA) was used to identify COPD-classification models. COPD GWAS were queried for putative cis-regulatory SNPs in the targeted genes.
On a network basis, TP53 and CEBP transcription factor pathway gene pair network connections, including key DNA repair gene ERCC5, were significantly different in COPD subjects (e.g., Wilcoxon rank sum test for closeness, p-value = 5.0E-11). ERCC5 SNP rs4150275 association with chronic bronchitis was identified in a set of Lung Health Study (LHS) COPD GWAS SNPs restricted to those in putative regulatory regions within the targeted genes, and this association was validated in the COPDgene non-hispanic white (NHW) GWAS. ERCC5 SNP rs4150275 is linked (D' = 1) to ERCC5 SNP rs17655 which displayed differential allelic expression (DAE) in BEC and is an expression quantitative trait locus (eQTL) in lung tissue (p = 3.2E-7). SNPs in linkage (D' = 1) with rs17655 were predicted to alter miRNA binding (rs873601). A classifier model that comprised gene features CAT, CEBPG, GPX1, KEAP1, TP73, and XPA had pooled 10-fold cross-validation receiver operator characteristic area under the curve of 75.4% (95% CI: 66.3%-89.3%). The prevalence of DAE was higher than expected (p = 0.0023) in the classifier genes.
GM genes comprised by COPD-associated BEC expression patterns were enriched for SNPs with cis-regulatory function, including a putative cis-rSNP in ERCC5 that was associated with COPD risk. These findings support additional total and allele-specific expression analysis of gene pathways with high prior likelihood for involvement in COPD pathogenesis.
需要更强大的方法来识别导致遗传性 COPD 发病机制的低效应 SNP。我们假设，通过顺式调控作用导致 COPD 风险的 SNP 在与 COPD 相关的支气管上皮细胞 (BEC) 表达模式所包含的基因中更为丰富。
为了验证这一假设，我们通过支气管镜从 60 名受试者中获得了正常的 BEC 标本：30 名受试者通过肺活量测定法（FEV1/FVC < 0.7，FEV1% < 80%）定义为 COPD，30 名非 COPD 对照。靶向下一代测序用于测量与 COPD 发病机制相关的基因组维持 (GM) 基因途径中的 35 个基因的总表达和等位基因特异性表达，包括七个 TP53 和 CEBP 转录因子家族成员。收缩线性判别分析 (SLDA) 用于识别 COPD 分类模型。对靶向基因中的假定顺式调控 SNP 进行 COPD GWAS 查询。
基于网络，TP53 和 CEBP 转录因子途径基因对网络连接，包括关键的 DNA 修复基因 ERCC5，在 COPD 患者中存在显著差异（例如，Wilcoxon 秩和检验的接近度，p 值 = 5.0E-11）。在一组肺健康研究 (LHS) COPD GWAS SNP 中，发现 ERCC5 SNP rs4150275 与慢性支气管炎相关，这些 SNP 仅限于靶向基因中假定的调控区域，并且在 COPDgene 非西班牙裔白人 (NHW) GWAS 中得到了验证。ERCC5 SNP rs4150275 与 ERCC5 SNP rs17655 相关（D' = 1），后者在 BEC 中显示出不同的等位基因表达（DAE），并且是肺组织中的表达数量性状基因座（eQTL）（p = 3.2E-7）。与 rs17655 连锁（D' = 1）的 SNP 预计会改变 miRNA 结合（rs873601）。包含基因特征 CAT、CEBPG、GPX1、KEAP1、TP73 和 XPA 的分类器模型在 10 倍交叉验证中具有 75.4%（95%CI：66.3%-89.3%）的接收器操作特征曲线下面积。DAE 的发生率高于预期（p = 0.0023）。
由 COPD 相关的 BEC 表达模式组成的 GM 基因富含具有顺式调控功能的 SNP，包括与 COPD 风险相关的 ERCC5 中的假定顺式 rSNP。这些发现支持对参与 COPD 发病机制的高先验可能性的基因途径进行额外的总表达和等位基因特异性表达分析。
