Time‐ and compartment‐resolved proteome profiling of the extracellular niche in lung injury and repair

Abstract

The extracellular matrix (ECM) is a key regulator of tissue morphogenesis and repair. However, its composition and architecture are not well characterized. Here, we monitor remodeling of the extracellular niche in tissue repair in the bleomycin-induced lung injury mouse model. Mass spectrometry quantified 8,366 proteins from total tissue and bronchoalveolar lavage fluid (BALF) over the course of 8 weeks, surveying tissue composition from the onset of inflammation and fibrosis to its full recovery. Combined analysis of proteome, secretome, and transcriptome highlighted post-transcriptional events during tissue fibrogenesis and defined the composition of airway epithelial lining fluid. To comprehensively characterize the ECM, we developed a quantitative detergent solubility profiling (QDSP) method, which identified Emilin-2 and collagen-XXVIII as novel constituents of the provisional repair matrix. QDSP revealed which secreted proteins interact with the ECM, and showed drastically altered association of morphogens to the insoluble matrix upon injury. Thus, our proteomic systems biology study assigns proteins to tissue compartments and uncovers their dynamic regulation upon lung injury and repair, potentially contributing to the development of anti-fibrotic strategies.

Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival

“…These findings are consistent with previous reports in which both proteins were found to be up-regulated in mouse and rat models of bleomycin-induced pulmonary fibrosis (22)(23)(24). Schiller et al (23) showed that Tnc is increased at both the protein and mRNA levels in the lungs of mice treated with bleomycin, and demonstrated that higher Tnc expression is associated with stiffer lung tissue, a feature of fibrosis. Furthermore, Tnc not only is a marker of pulmonary fibrosis, but also has been implicated in the pathogenesis of the disease.…”

“…Changes in ECM in Lung Fibrosis. Two recent studies have used proteomics to report changes occurring in bleomycin-induced fibrosis (22,23). Along with some overlapping findings, our study of the insoluble ECM has uncovered and quantified additional proteins.…”

Towards integrating extracellular matrix and immunological pathways

“…For example, Decaris et al characterized the alterations in ECM turnover following bleomycin-induced lung fibrosis, and Talmi-Frank et al measured changes in lung ECM protein abundance in the context of influenza infection (22,23). Proteomic analysis of samples after differential extraction and from different soluble fractions has the potential to provide improved resolution of the matrisome based on lung compartment (24). …”

“…In a recent study, Schiller et al . performed a comprehensive analysis of proteomic and transcriptomic changes in ECM following bleomycin-induced lung injury (24). Analysis of multiple time points, out to 56 days post-injury, and of multiple compartments of the lung, including soluble and insoluble fractions of total tissue and bronchoalveolar lavage fluid, provided a high-resolution data set to explore pathways involved in host response to injury.…”

“…‘Omics’ approaches to survey gene transcription profiles or protein profiles of extracellular matrices from different pathological contexts will be useful is assessing changes in the abundance of ECM-related proteins. Several recent studies have begun to utilize mass spectrometry to generate protein profiles in the context of viral infection, lung fibrosis, and cancer revealing major differences in ECM composition compared to healthy controls (16,21–24,27,28). Particularly promising is the approach taken by Schiller et al in a recent study combining mass spectrometry and RNAseq to identify ECM and immunological pathways contributing to resolution of bleomycin-induced lung injury (24).…”