MicroRNA and protein-coding gene expression analysis in idiopathic pulmonary fibrosis yields novel biomarker signatures associated to survival

• Published in: Translational research : the journal of laboratory and clinical medicine Vol. 228; pp. 1 - 12
• Main Authors: Casanova, Nancy G., Zhou, Tong, Gonzalez-Garay, Manuel L., Lussier, Yves A., Sweiss, Nadera, Ma, Shwu-Fan, Noth, Imre, Knox, Kenneth S., Garcia, Joe G.N.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2021
• Subjects: Aged; Biomarkers - metabolism; Case-Control Studies; Female; Gene Expression Profiling; Humans; Idiopathic Pulmonary Fibrosis - genetics; Leukocytes, Mononuclear - metabolism; Male; MicroRNAs - genetics; Middle Aged; Prognosis; Proteins - genetics; Reproducibility of Results; Survival Analysis; FVC; DLCO; RMA; KEGG; miRNA; DABG; PBMC; IPF; COPD
• ISSN: 1931-5244; 1878-1810
• DOI: 10.1016/j.trsl.2020.07.009

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease of unknown etiology that poses significant challenges in early diagnosis and prediction of progression. Analyses of microRNA and gene expression in IPF have yielded potentially predictive information. However, the relationship between microRNA/gene expression and quantitative phenotypic value in IPF remains controversial, as is the added value of this approach to current molecular signatures in IPF. To identify biomarkers predictive of survival in IPF via a microRNA-driven strategy. We profiled microRNA and protein-coding gene expression in peripheral blood mononuclear cells from 70 IPF subjects in a discovery cohort. We linked the microRNA/gene expression level with the quantitative phenotypic variation in IPF, including diffusing capacity of the lung for carbon monoxide and the forced vital capacity percent predicted. In silico analyses of expression profiles and quantitative phenotypic data allowed the generation of 2 sets of IPF molecular signatures (unique for microRNAs and protein-coding genes) that predict IPF survival. Each signature performed well in a validation cohort comprised of IPF patients aggregated from distinct patient populations recruited from different sites. Resampling test suggests that the protein-coding gene based signature is comparable and potentially superior to published IPF prognostic gene signatures. In conclusion, these results highlight the utility of microRNA-driven peripheral blood molecular signatures as valuable and novel biomarkers associated to individuals at high survival risk and for potentially facilitating individualized therapies in this enigmatic disorder.