Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis

• Published in: BMC pulmonary medicine 2017-01, Vol.17 (1), p.15-15, Article 15
• Main Authors: Vukmirovic, Milica, Herazo-Maya, Jose D, Blackmon, John, Skodric-Trifunovic, Vesna, Jovanovic, Dragana, Pavlovic, Sonja, Stojsic, Jelena, Zeljkovic, Vesna, Yan, Xiting, Homer, Robert, Stefanovic, Branko, Kaminski, Naftali
• Format: Article
• Language: English
• Subjects: Case-Control Studies; Child; Freezing; Gene expression; Gene Expression Profiling; Gene Regulatory Networks; Genetic aspects; Health aspects; Humans; Idiopathic Pulmonary Fibrosis - genetics; Idiopathic Pulmonary Fibrosis - pathology; Lung - pathology; Matrix Metalloproteinase 7 - genetics; Methods; Microarray Analysis; Paraffin Embedding; Pulmonary fibrosis; Pulmonology; RNA - analysis; RNA sequencing; Sequence Analysis, RNA; United States; Wnt Signaling Pathway
• ISSN: 1471-2466; 1471-2466
• DOI: 10.1186/s12890-016-0356-4

Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR