Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq

作者：Rebecca Kusko, John Brothers, Gang Liu, Lingqi Luo, Brenda Juan Guardela, John Tedrow, Yuriy Aleksyev, Ivana V. Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank C. Sciurba, Marc E. Lenburg, David A. Schwartz, Jennifer Beane, Naftali Kaminski, Avrum Spira · 发表于：BMC Proceedings · 年份：2012 · DOI：10.1186/1753-6561-6-s6-p21 · 被引用次数：3 · 研究领域：Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis、Medical Imaging and Pathology Studies、RNA modifications and cancer

As part of the Lung Genomics Research Consortium (LGRC), we sought to characterize transcriptomic alterations underlying the molecular pathogenesis of emphysema and idiopathic pulmonary fibrosis (IPF) using mRNA-Seq,and comparing to mRNAand microRNA microarray data obtained from the same samples. 87 LGRC lung tissue samples were sequenced on the Illumina GAIIx, generating 75 nt paired-end reads and approximately 30-40 million reads per sample. Using gapped aligner Tophat, an average of 85% of reads aligned to hg19. Gene expression was quantified using Cufflinks and Ensembl59 known gene annotation ( n = 24,249 genes). All lung tissue samples used in this study, as well as additional LGRC lung tissue samples, were run on Agilent V2 human whole genome arrays and Agilent V3 human miRNA microarrays. Using a mixture model, expression of 6,359 genes was detected, 9,538 genes were not detected, and 8,397 genes were variably detected across all lung tissue samples. Using a subset of 58 samples from subjects with IPF ( n = 19), emphysema ( n = 19) or control samples ( n = 20), differential gene expression was determined using a t test to compare each disease state with control. The expression levels of 1,770 genes differed between IPF and control, and 220 genes between emphysema and control ( P < 0.001). Genes that go up in both emphysema and IPF relative to control were enriched for the p53/hypoxia pathway (KEGG, Biocarta) by GSEA. Gene expression estimates were highly correlated betw...