Insights from RNA-sequencing of bronchoalveolar lavage cells in a large sarcoidosis cohort

Abstract

Introduction: We analyzed the transcriptome of bronchoalveolar lavage cells (BAL) in a large cohort of well characterized sarcoidosis subjects by RNA-sequencing to better understand disease progression and severity, and potentially identify novel molecular phenotypes. Methods: BAL was performed on subjects enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis study (GRADS) as described (Moller et al., Ann Am Thorac Soc, 2015 PMID: 26193069). cDNA libraries were prepared from 1ug of RNA and sequenced by Ion Torrent Proton Sequencer. Cufflinks calculated Fragments per Kilobase of exon per Million (FPKM) values. Non-parametric correlation methods and Metacore identified significant genes and pathways. Weighted gene co-expression network analysis (WGCNA) revealed correlation networks between gene expression and clinical traits. Multiple hypothesis testing was controlled at FDR Results: 199 samples from 24 stage I, 33 stage II-III treated, 40 stage II-III untreated, 17 stage IV treated, and 12 stage IV untreated subjects were available (53.2% females, 23.1% blacks). Correlation analysis revealed that 65 genes were increased with advanced Scadding stage and 24 were decreased (FDR Conclusion: RNA-sequencing of BAL in sarcoidosis patients identified novel genes associated with features of disease. Preliminary analysis suggests the presence of molecular disease endotypes.