Differentially Expressed Proteins in Plasma-Derived Extracellular Vesicles from Chronic Myeloid Leukemia Patients

Chronic myeloid leukemia (CML) is driven by the BCR::ABL1 fusion gene. Although tyrosine kinase inhibitors (TKIs) have transformed outcomes, treatment resistance persists. Plasma extracellular vesicles (EVs) reflect their cell of origin and may serve as stable biomarkers. To characterize the plasma EV proteome in CML patients with distinct treatment responses and T315I mutation status. EVs were isolated from the plasma of healthy controls (HC) and CML patients classified as good (GTR) or poor (PTR) treatment responders, treatment-free remission (TFR), and T315I or pre-T315I mutation carriers. EVs were purified by size-exclusion chromatography, characterized by NTA and TEM, and analyzed by label-free mass spectrometry, followed by differential expression, enrichment, and protein–protein interaction analyses. A total of 598 proteins were identified, 257 retained after quality and abundance filtering. Forty-two proteins were differentially expressed among HC, GTR, and PTR groups (p < 0.01), with PTR samples showing marked downregulation of cytoskeletal and chaperone proteins (such as MYH9, HSP90AB1, FERMT3). TFR patients exhibited distinct enrichment in complement and coagulation cascades (C3, C4B, F9, F11) and metabolic pathways. Plasma EV proteomes reflect CML clinical status, revealing immune and cytoskeletal alterations associated with treatment response, remission, and resistance, suggesting potential biomarkers for disease monitoring.