Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts

Abstract

Fibroblasts/myofibroblasts are the key effector cells responsible for excessive extracellular matrix (ECM) deposition and fibrosis progression in both idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc) patient lungs, thus it is critical to understand the transcriptomic and proteomic programs underlying their fibrogenic activity. We conducted the first integrative analysis of the fibrotic programming in these cells at the levels of gene and microRNA (miRNA) expression, as well as deposited ECM protein to gain insights into how fibrotic transcriptional programs culminate in aberrant ECM protein production/deposition. We identified messenger RNA (mRNA), miRNA, and deposited matrisome protein signatures for IPF and SSc fibroblasts obtained from lung transplants using next-generation sequencing and mass spectrometry. SSc and IPF fibroblast transcriptional signatures were remarkably similar, with enrichment of WNT, TGF-β, and ECM genes. miRNA-seq identified differentially regulated miRNAs, including downregulation of miR-29b-3p, miR-138-5p and miR-146b-5p in disease fibroblasts and transfection of their mimics decreased expression of distinct sets of fibrotic signature genes as assessed using a Nanostring fibrosis panel. Finally, proteomic analyses uncovered a distinct “fibrotic” matrisome profile deposited by IPF and SSc fibroblasts compared to controls that highlights the dysregulated ECM production underlying their fibrogenic activities. Our comprehensive analyses of mRNA, miRNA, and matrisome proteomic profiles in IPF and SSc lung fibroblasts revealed robust fibrotic signatures at both the gene and protein expression levels and identified novel fibrogenesis-associated miRNAs whose aberrant downregulation in disease fibroblasts likely contributes to their fibrotic and ECM gene expression.

Prediction of severity and subtype of fibrosing disease using model informed by inflammation and extracellular matrix gene index

“…In several cases, our methodology confirmed associations that had previously been noted. We found Wnt signaling, TGF-β signaling, and ECM associated genes to be upregulated ( Table 1 ), which has been confirmed at the mRNA and miRNA level in SSc fibroblasts [ 40 ]. The Wnt/β -catenin signaling pathway is over activated in SSc patients and expression of WIF1 , a Wnt pathway antagonist, is decreased in SSc patients [ 41 ], likely through a reactive oxygen species-dependent transcriptional repression mechanism [ 42 ].…”

Analysis of the Interaction Network of Hub miRNAs-Hub Genes, Being Involved in Idiopathic Pulmonary Fibers and Its Emerging Role in Non-small Cell Lung Cancer

“…Previous studies have revealed that ECM protein expression plays an important role in the fibrotic process in IPF lungs (Vicens-Zygmunt et al, 2015). Excessive accumulation of ECM in the alveolar parenchyma and progressive scarring of lung tissue are major characteristics of IPF (Knudsen et al, 2017), and some studies have used this protein expression level as a criterion for evaluating treatment outcomes (Molina-Molina et al, 2018;Mullenbrock et al, 2018). Altogether, migration is strongly influenced by topology and composition of the ECM including integrin ligands, and the hub gens and hub miRNAs might play an important role in IPF progression with the change of ECM.…”

A noble TGF beta biogenesis inhibitor exhibits both potent anti-fibrotic and anti-inflammatory capabilities

“…Many of those genes were previously found to be fibrogenic, including those encoding NOX4, CTGF, PERIOSTIN, LOX, and CDH2. [15][16][17] Induction of NOX4, which encodes NADPH oxidase 4, is associated with the production of reactive oxygen species (ROS) and with several important signaling events, including LPS signaling and inflammasome activation. 18 These findings suggested that NOX4 plays an important role in the pathogenesis of myofibroblasts.…”