Identifying protein signatures in vesicles associated with treatment response in pulmonary sarcoidosis

Approximately 30% of patients with sarcoidosis require immunosuppressive therapy to relieve symptoms or prevent organ damage. Prednisone and methotrexate (MTX) are the most commonly used therapies; however, treatment response varies considerably between patients. This study aimed to identify extracellular vesicle (EV) protein signatures associated with treatment response. Proteomic analysis (LC–MS/MS) was performed in sarcoidosis patients treated with either prednisone (n = 20) or MTX (n = 20). Ten candidate proteins (five per treatment group) were selected for replication in a large retrospective cohort (n = 90) and subsequent validation in a prospective cohort (n = 22). We identified 67 differentially expressed proteins (DEPs) between responders and non-responders to prednisone and 38 DEPs for MTX. Reactome pathway analysis indicated that DEPs associated with prednisone response were primarily involved in metalloproteinase activity and Toll-like receptor signaling, whereas DEPs associated with MTX response were linked to GPCR signaling and hemostasis. Complement factor I (CFI) remained significantly different at baseline in prednisone responders (replication p < 0.001; validation p = 0.023). Complement component C8 (C8) showed differential expression in MTX responders (replication p = 0.032; validation p = 0.066). These findings indicate that EV protein profiles differ between responders and non-responders to prednisone or MTX in pulmonary sarcoidosis and may support future personalized treatment selection