Changes In Gene Expression With Progression Of Emphysematous Destruction In COPD

Abstract

To gain insights into the pathogenesis of chronic obstructive pulmonary disease (COPD), we profiled gene expression in Introduction: regions with differing emphysema severity from six lungs with COPD and two donor lungs. Regional emphysema severity was Methods: determined using micro-CT and quantified as the mean linear intercept between alveolar septa (Lm). One μg of RNA was isolated from eight samples from each of eight lungs (8 x 8 = 64 total samples), processed, and hybridized onto the Affymetrix Human Exon 1.0 ST array. The Robust Multichip Average (RMA) algorithm was used to generate transcript-level expression values for 17881 genes. Differential expression was determined by linear mixed effect models that accounts for inter-individual differences in baseline gene-expression. One-hundred and twenty-seven genes had expression profiles significantly correlated with the degree of emphysema (FDR Results: q-value < 0.1). These genes are significantly enriched for those previously found to have COPD and/or COPD-severity associated expression profiles in cross-sectional studies that compared lung tissue from individuals with and without COPD. Gene set enrichment analysis demonstrated that the genes that decrease with increasing regional emphysema severity are enriched for genes with roles in cellular structure, integrin signaling, extracellular matrix, and focal adhesion as well as genes in the VEGF and TGFβ pathways, which are known to be involved in angiogenesis and extracellular matrix (ECM) remodeling, respectively. Genes induced by TGFβ1 in several publically available gene expression datasets were found to be enriched among the downregulated genes further implicating the TGFβ pathway in COPD pathogenesis. Immunohistochemistry showed that SMAD6, a member of the TGFβ family, is downregulated in endothelial cells in the lung vasculature. The Context Likelihood of Related (CLR) algorithm was used to infer a gene co-expression network in order to elucidate which transcription factors may be playing a role in emphysema progression. The Ingenuity Pathway Analysis (IPA) tool showed that genes connected to EPAS1 (HIF2-alpha) in the CLR network including KDR (VEGFR2) and TEK (TIE2) had supporting experimental evidence for transcriptional regulation. EPAS1 is a hypoxia inducible factor that was downregulated in regions of severe emphysema. We have identified gene expression patterns that correlate with the progression of emphysema. Our Conclusion: hope is that understanding the processes that promote emphysematous destruction of the alveolae will lead to a better understanding of the mechanisms responsible for COPD progression, as well as suggest targets for future development of more effective anti-COPD therapies.