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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. The aim of this study is to gain insight into the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. Protein and RNA were isolated from cultured parenchymal lung fibroblasts of 17 patients with stage IV COPD 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 were compared to investigate the overlap and correlation between both levels of data. 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. We hereby describe 40 DE proteins in COPD fibroblasts including 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.

Background: Changes in microRNA (miRNA) expression can contribute to the pathogenesis of many diseases, including asthma. We aimed to identify miRNAs that are differentially expressed between asthma patients and healthy controls, and explore their association with clinical and inflammatory parameters of asthma., Methods: Differentially expressed miRNAs were determined by small RNA sequencing on bronchial biopsies of 79 asthma patients and 82 healthy controls using linear regression models. Differentially expressed miRNAs were associated with clinical and inflammatory asthma features. Potential miRNA-mRNA interactions were analysed using mRNA data available from the same bronchial biopsies, and enrichment of pathways was identified with Enrichr and g:Profiler., Results: In total, 78 differentially expressed miRNAs were identified in bronchial biopsies of asthma patients compared with controls, of which 60 remained differentially expressed after controlling for smoking and inhaled corticosteroid treatment. We identified several asthma-associated miRNAs, including miR-125b-5p and miR-223-3p, based on a significant association with multiple clinical and inflammatory asthma features and their negative correlation with genes associated with the presence of asthma. The most enriched biological pathway(s) affected by miR-125b-5p and miR-223-3p were inflammatory response and cilium assembly/organisation. Of interest, we identified that lower expression of miR-26a-5p was linked to more severe eosinophilic inflammation as measured in blood, sputum as well as bronchial biopsies., Conclusion: Collectively, we identified miR-125b-5p, miR-223-3p and miR-26a-5p as potential regulators that could contribute to the pathogenesis of asthma., Competing Interests: Conflict of interest: M.P. Roffel has nothing to disclose. Conflict of interest: I.M. Boudewijn has nothing to disclose. Conflict of interest: J.L.L. van Nijnatten has nothing to disclose. Conflict of interest: A. Faiz has nothing to disclose. Conflict of interest: C.J. Vermeulen has nothing to disclose. Conflict of interest: A.J. van Oosterhout owns GlaxoSmithKline shares. Conflict of interest: K. Affleck is an employee of GlaxoSmithKline. Conflict of interest: W. Timens reports personal fees for consultancy from Roche Diagnostics/Ventana, Bristol-Myers-Squibb and Diaceutics, personal fees for consultancy and lectures from MSD, outside the submitted work. Conflict of interest: K.R. Bracke has nothing to disclose. Conflict of interest: T. Maes reports grants from Ghent University (BOF19-GOA-008, BOF U4 funding; 05U40516) and Fund for Scientific Research in Flanders, during the conduct of the study; personal fees for advisory board work from GlaxoSmithKline, grants from Chiesi, outside the submitted work; and is shareholder of Oryzon Genomics and Mendelion Lifesciences SL. Conflict of interest: I.H. Heijink has nothing to disclose. Conflict of interest: C-A. Brandsma has nothing to disclose. Conflict of interest: M. van den Berge reports research grants (Paid to institution) from GlaxoSmithKline, Sanofi, Novartis, Genentech and Roche, outside the submitted work., (Copyright ©The authors 2022. For reproduction rights and permissions contact permissions@ersnet.org.)