title: Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes.
abstract: Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease of unknown cause that lacks a proven therapy for altering its high mortality rate. Microarrays have been employed to investigate the pathogenesis of IPF, but are presented mostly at the gene-expression level due to technologic limitations. In as much as, alternative RNA splicing isoforms are increasingly identified as potential regulators of human diseases, including IPF, we propose a new approach with the capacity to detect splicing variants using RNA-seq data. We conducted a joint analysis of differential expression and differential splicing on annotated human genes and isoforms, and identified 122 non-differentially expressed genes with a high degree of "switch" between major and minor isoforms. Three cases with variant mechanisms for alternative splicing were validated using qRT-PCR, among the group of genes in which expression was not significantly changed at the gene level. We also identified 35 novel transcripts that were unique to the fibrotic lungs using exon-exon junction evidence, and selected a representative for qRT-PCR validation. The results of our study are likely to provide new insight into the pathogenesis of pulmonary fibrosis and may eventuate in new treatment targets.
authors.affiliation: Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America.
authors.forename: Nan
authors.initials: N
authors.lastname: Deng
authors.forename: Cecilia G
authors.initials: CG
authors.lastname: Sanchez
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Lasky
authors.forename: Dongxiao
authors.initials: D
authors.lastname: Zhu
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000328:Adult; D000368:Aged; D005091:Exons / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D054990:Idiopathic Pulmonary Fibrosis / Q000235:genetics*; D008168:Lung / Q000378:metabolism* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011401:Promoter Regions, Genetic / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D020033:Protein Isoforms; D012333:RNA, Messenger