Idiopathic pulmonary fibrosis bronchoalveolar lavage cells RNA-seq indicates macrophage expression of pro-inflammatory M1/M2 activation concomitant with radical species metabolism inhibition. Homo sapiens

Current concepts of idiopathic pulmonary fibrosis (IPF) are that microscopic injury drives alveolar epithelial cell dysregulated activation and epithelial mesenchymal transition, ensuing fibrocyte recruitment, fibroblast proliferation and ECM deposition. With the background that IPF is also characterized by chronic accumulation of activated alveolar macrophages (aMAC) in the lower respiratory tract, we assessed IPFaMAC gene expression to identify patterns of activation, by RNA-seq using Illumina platform. To this we evaluated a population of 7 normal smoking controls and 16 IPF smoking patients. All IPFs had abnormal lung function and bronchoalveolar lavage (BAL) showing >80% macrophage counts and augmented spontaneous O2 radical release. RNA was extracted from whole BAL cells. Reads were mapped onto the UCSC mRNA database (GRCh37/hg19 version), and transcripts were aggregated by gene symbol, obtaining a final 19,723 unique protein-coding gene ID list, used for further analysis. Overall design: RNA-seq transcriptomics of idiopathic pulmonary fibrosis (IPF) patients vs controls: RNA samples were extracted from macrophages obtained from bronchoalveolar lavage (BAL)