Integration of Transcriptomic and Proteomic Profiles Identifies Potential Biomarkers in Idiopathic Pulmonary Fibrosis

Abstract Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Till now, no studies have been reported on revealing mechanisms and identifying biomarkers by integratively analyzing transcriptome and proteomes of IPF patients. Here we examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways of immune system activities and inflammatory responses, while DE proteins are associated with extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of BTNL9 and PLLP and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.