Genome-wide transcriptome profiling of NEDD9-regulated genes using RNA-seq

Purpose:This study is to examine NEDD9-regulated and aldosterone-induced gene expression to understand the roles of NEDD9 and aldosterone in pulmonary arterial hypertension and pulmonary arterial fibrosis. The hypothesis tested here is whether there is a cross-talk between NEDD9 regulation and aldosterone signaling pathway in human pulmonary artery endothelial cells. Methods: mRNA profiles of human pulmonary artery endothelial cells were generated by deep sequencing, in triplicate, using Ilumina Hiseq 2000. The sequence reads that passed quality filters were aligned to the human reference genome (hg19) using Tophat2. Results: RNA-seq based transcriptome characterization revealed a number of NEDD9-regulated and aldosterone-induced profibrotic genes. Conclusions: RNA-seq based transcriptome analysis helps to make biological discoveries and decipher complex biological functions. Overall design: Transcriptome analysis was performed on human pulmonary artery endothelial cells. Six samples were transfected with NEDD9 siRNA and treated with aldosterone or vehicle control. 12 additional samples were directly treated with aldosterone or vehicle control.