RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

Abstract Background 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. Methods 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. Results 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. Conclusions 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.https://deepblue.lib.umich.edu/bitstream/2027.42/142723/1/12890_2018_Article_603.pd

Readings in European Security, Volume 3. CEPS Paperback. November 2005

The ambition of this latest volume of Readings in European Security is to serve as a prism, through which the EU’s external relations and security can be assessed, with contributions from its American and Russian partners. It contains the complete set of working papers (Nos. 16 through 20) during the period January 2003 to June 2005. International experts tackle strategic issues such as Russia’s relationship with the West, the rise of China (with special reference to arms supplies), Iran’s nuclear programme and European ‘homeland security’ against the background of global terrorism. On these issues and others, transatlantic relations continue to be more relevant than ever, with the US and the EU intertwined in the world’s tightest network of economic and societal relations. Further, Russia’s management of its security challenges also has an impact on its relations with the EU and the US. As the enlarging EU stretches to cover an expanding area of competence, its responses to these challenges affect not only its internal security, but increasingly that of its neighbours and other powerful actors on the world stage

RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

BACKGROUND: 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. METHODS: To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC \u3c 0.7, FEV1% \u3c 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. RESULTS: 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\u27 = 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\u27 = 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. CONCLUSIONS: 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

Additional file 1: of RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

Tables S1, S2, S3, S4, S5 and S6. Table S1. This table provides: a) Gene-specific assay information including SNP sites, primer and internal standard sequences, b) Subject-specific demographic information, and c) assay- and subject-specific transcript abundance values (target gene molecules/106 ACTB molecules). Table S2. Population used for allele specific expression analysis: Summary demographic characteristics of the study population of allele specific expression (subject total n = 180). Table S3. Transcription factor-target inter-gene correlation in Control, COPD, or All subjects (p-value < 0.05). Table S4. Analysis of covariance (ANCOVA). Gene expression values (Independent Variables) significantly correlated (positively or negatively) with COPD subjects (Dependent Variable) after control for expression values of other genes (Covariates). Table S5. ERCC5 SNPs linked to rs17655 and rs873601 (D > 0.95) and with p < 0.05 in LHS and COPDgene NHW CB cohorts. COPD GWAS p-values, population-specific genotype frequencies, and epigenetic annotation information from Haploreg/Encode. Table S6. Haplotype structure between COPDgene NHW1 associated SNP rs4150275, putative functional cis-rSNP rs873601, and DAE2 SNP rs17655. (XLSX 109 kb