Plasma-Derived Extracellular Vesicle-Enriched Fractions as a Potential Source of Biomarkers for Systemic Sclerosis-Associated Interstitial Lung Disease (SSc-ILD): A Shotgun Proteomic Exploration Analysis

Background: Systemic sclerosis (SSc)-associated interstitial lung disease (SSc-ILD) is the leading cause of morbidity and mortality in patients with SSc, with an unmet need for validated, minimally invasive biomarkers for early detection. Extracellular vesicles (EVs) present underexplored pathogenic players and potential biomarker sources in SSc-ILD. We performed a proteomic shotgun study aiming to identify disease-specific protein signatures and potential biomarker candidates. Methods: The study included 30 SSc patients divided into SSc-ILD and SSc w/o ILD groups and 20 matched controls. Plasma-derived EV-enriched fractions were analysed using liquid chromatography–mass spectrometry. Bioinformatic analysis, including differentially expressed proteins (DEPs), functional enrichment, protein–protein interaction network and Markov Cluster (MCL) analysis was performed. Results: Analysis of DEPs showed 14 significantly upregulated and 1 downregulated protein when comparing the SSc-ILD to the SSc w/o ILD group, 222 upregulated and 257 downregulated proteins between the SSc-ILD and control group, as well as 362 upregulated and 492 downregulated proteins between the SSc w/o ILD and control group. Functional enrichment analysis and MCL analysis pointed to disease-specific processes of extracellular matrix (ECM) and immune dysregulation, which largely overlapped between SSc-ILD and SSc w/o ILD groups. Among identified DEPs, SP-B, Cav-1 and Siglec-5 emerged as potential candidate biomarkers for SSc-ILD. Conclusions: Proteomic analysis of plasma-derived EV-enriched fractions shows potential EV involvement in pathogenic SSc processes, mainly related to ECM and immune dysregulation, as well as potential candidate biomarkers for SSc-ILD. Further studies are required to validate these results and assess biomarker potential and translational applicability of identified proteins.