A proteomics approach to identify COPD-related changes in lung fibroblasts

Abstract

Background: Lung fibroblasts are implicated in abnormal tissue repair in chronic obstructive pulmonary disease (COPD). The exact mechanisms are unknown and comprehensive analysis comparing COPD- and control fibroblasts is lacking. Aim: To gain insight in the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. Methods: Protein and RNA was isolated from cultured parenchymal lung fibroblasts of 17 stage IV COPD patients and 16 non-COPD controls. Proteins were analyzed using LC-MS/MS and RNA through RNA sequencing. Differential protein and gene expression in COPD was assessed via linear regression, followed by pathway enrichment, correlation analysis and immunohistological staining in lung tissue. Proteomic and transcriptomic data was compared to investigate the overlap and correlation between both levels of data. Results: We identified 40 differentially expressed (DE) proteins and zero DE genes between COPD and control fibroblasts. The most significant DE proteins were HNRNPA2B1 and FHL1. Thirteen of the 40 proteins were previously associated with COPD, including FHL1 and GSTP1. Six of the 40 proteins were related to telomere maintenance pathways, and were positively correlated with the senescence marker LMNB1. No significant correlation between gene and protein expression was observed for the 40 proteins. Conclusions: The 40 DE proteins in COPD fibroblasts include previously described COPD proteins (FHL1, GSTP1) and new COPD research targets like HNRNPA2B1. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis and indicates that different types of information are generated with both methods.

Lung Fibroblasts from Chronic Obstructive Pulmonary Disease Subjects Have a Deficient Gene Expression Response to Cigarette Smoke Extract Compared to Healthy

“…Other studies investigating only the differences between baseline healthy and COPD lung fibroblasts which can lead to inadequate conclusions that pathways involved are associated with COPD and not healthy. 18 Whereas differences found here at baseline reflected that the healthy lung fibroblast responded far more than the COPD. Therefore, it is important to assume that differences in biomarkers at baseline would not reflect targetable markers for COPD therapeutics.…”

“…Although several studies have compared large arrays/profiles of gene expression from cells of COPD subjects to control subjects, [13][14][15][16][17][18] no studies were found in regard to the effects of CSE stimulation. A broad and quantitative assessment of lung fibroblast expression should elucidate more accurate mechanisms that differentiate healthy and COPD responses to CSE giving insight into more targetable pathways for treatments.…”

“…International Journal of Chronic Obstructive Pulmonary Disease 2023:18 . CSE increased collagen production via the ERK-MAPK,…”