Machine Learning-Driven Extracellular Vesicles Peptidomics Powers Precision Classification of Endometrial Cancer

Endometrial cancer (EC) molecular subtyping is critical for prognosis and treatment but remains hindered by reliance on invasive tissue biopsies and time-consuming genomic sequencing. Here, we present a minimally invasive approach integrating MALDI-TOF mass spectrometry and LC-MS/MS-based peptidomic profiling of plasma extracellular vesicles (EVs) with machine learning for rapid EC screening and subtyping. EVs were isolated from EC patients and controls, and their peptidome fingerprints were analyzed. A machine learning model utilizing 12 discriminative MALDI-TOF MS features, the levels of CA125 and HE4, and clinical features related to cancer risk achieved an AUC of 0.867 in distinguishing EC from the controls. For molecular subtyping (POLE mutant, NSMP, MMRd, P53-abnormal), a multiclassification model demonstrated micro/macro-averaged AUCs of 0.91/0.90. LC-MS/MS identified 7,479 peptides, with fibrinogen α chain (FGA), protease serine 3 (PRSS3), and apolipoprotein A-I (APOA1) emerging as key biomarkers linked to specific subtypes. This study establishes a high-throughput, cost-effective platform for EC management, bridging translational gaps in precision oncology.