Abstract
Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%), and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%). We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10) and POSTN (RNA-Seq adjusted pval = 2.06e-09), which encode the extracellular matrix proteins collagen alpha-3(VI) and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.
Highlights
Idiopathic pulmonary fibrosis (IPF) is a progressive disease of unknown aetiology, characterized by fibrotic scarring in the lungs which leads to shortness of breath and eventual respiratory failure
We believe these results indicate a potential role for alternative splicing of periostin and collagen VI alpha-3 in IPF, but more investigation is needed to determine the cell types in which alternative splicing is operative, and to identify causal
Description ribosomal protein S24 collagen, type VI, alpha 3 periostin, osteoblast specific factor deleted in liver cancer 1 collagen, type III, alpha 1 ZFP36 ring finger protein-like 1 collagen, type III, alpha 1 GM2 ganglioside activator collagen, type III, alpha 1 transformer 2 beta homolog (Drosophila) down-regulated down-regulated down-regulated up-regulated down-regulated down-regulated down-regulated up-regulated down-regulated down-regulated variants and mechanisms of this effect and their relationship to IPF
Summary
Idiopathic pulmonary fibrosis (IPF) is a progressive disease of unknown aetiology, characterized by fibrotic scarring in the lungs which leads to shortness of breath and eventual respiratory failure. Current theory of pathogenesis in IPF holds that chronic injury to alveolar epithelial cells induces aberrant activation of woundhealing pathways, leading to an increase in inflammatory signals and subsequent differentiation of fibroblasts, epilthelial-mesenchymal transition in alveolar cells, and accumulation of myofibroblasts. This results in the formation of fibroblastic foci and deposition of collagen, fibronectin, and other extracellular matrix (EM) components. In contrast with normal wound-healing and for unknown reasons, apoptosis is not properly initiated in myofibroblasts, and secretion of EM proteins does not terminate This results in contraction and destruction of the lung parenchyma [3], [4]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
