Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

Abstract

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown.MethodsTo identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography–tandem mass spectrometry (LC–MS/MS) approach to examine protein expression in lung tissues from IPF patients.ResultsA total of 662 proteins with altered expression (455 upregulated proteins and 207 downregulated proteins) were identified in lung tissue of IPF patients compared with control. KEGG pathway enrichment analysis showed that the altered proteins in lung tissue mainly belonged to the PI3K-Akt signaling, focal adhesion, ECM-receptor interaction, and carbon metabolism pathways. According to the bioinformatic definition of the matrisome, 229 matrisome proteins were identified in lung tissue. These proteins comprised the ECM of lung, of which 104 were core matrisome proteins, and 125 were matrisome-associated proteins. Of the 229 ECM quantified proteins, 56 significantly differentially expressed proteins (19 upregulated proteins and 37 downregulated proteins) were detected in IPF lung tissue samples. In addition to proteins with well-known functions such as COL1A1, SCGB1A1, TAGLN, PSEN2, TSPAN1, CTSB, AGR2, CSPG2, and SERPINB3, we identified several novel ECM proteins with unknown function deposited in IPF lung tissue including LGALS7, ASPN, HSP90AA1 and HSP90AB1. Some of these differentially expressed proteins were further verified using Western blot analysis and immunohistochemical staining.ConclusionsThis study provides a list of proteomes that were detected in IPF lung tissue by iTRAQ technology combined with LC–MS/MS. The findings of this study will contribute better understanding to the pathogenesis of IPF and facilitate the development of therapeutic targets.Electronic supplementary materialThe online version of this article (10.1186/s12014-019-9226-4) contains supplementary material, which is available to authorized users.

Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues

“…This approach utilizes multi-steps to enrich for ECM proteins and we report that 11.1% of the proteins detected are ECM components. This is in accord with studies utilizing human lung specimens where the percentage of ECM components detected are reported as 5.4% [34], 7.2% [35], and 8.2% [36]; in mouse lungs, 5.2% is reported [37]. The protein gene names for these regions are shown in Fig.…”

HSP90 Inhibition and Modulation of the Proteome: Therapeutical Implications for Idiopathic Pulmonary Fibrosis (IPF)

“…Isobaric tag for relative and absolute quantitation (iTRAQ) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to analyze proteomic changes in lung tissue of IPF patients and controls [53]. From more than 4000 proteins analyzed, 600 were founded altered (455 upregulated and 207 downregulated) confirming previous results on extracellular matrix overexpression and defining new involved proteins.…”

“…From more than 4000 proteins analyzed, 600 were founded altered (455 upregulated and 207 downregulated) confirming previous results on extracellular matrix overexpression and defining new involved proteins. Among these, several collagens, glycoproteins, proteoglycans, and secretory and regulatory factor matrisomes were identified and validated by Western blotting, confirming the role of collagen 1, cathepsin B, AGR-2, galectin-7, HSP90α, and HSP90β [53]. In another study, functional proteomics was used to analyze differences in four diseases (idiopathic pulmonary fibrosis, sarcoidosis, systemic sclerosis, and pulmonary Langerhans sclerosis).…”

How the Pathological Microenvironment Affects the Behavior of Mesenchymal Stem Cells in the Idiopathic Pulmonary Fibrosis

“…Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease (ILD) [1], characterized by an increase of fibroblast proliferation, an excessive extracellular matrix (ECM) deposition [2], and distortion of lung architecture, eventually leading to respiratory failure [3]. To date, limited treatment options are available, and prognosis remains still poor [4]. Although the etiology of this disease is not completely known, some studies have shown how environmental factors (smoking and exposure to toxic agents), age, and genetic factors represent the main risk factors for IPF onset [5].…”