Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics

Vulnerable atherosclerotic plaques, especially hemorrhaged lesions, are the major cause of mortalities related to vascular pathologies. The early identification of vulnerable plaques helps to stratify patients at risk of developing acute vascular events. In this study, proteomics analyses of human carotid artery samples collected from patients with atheromatous plaques and complicated lesions, respectively, as well as from healthy controls were performed. The proteins isolated from the carotid artery samples were analyzed by a bottom-up shotgun approach that relied on nanoflow liquid chromatography–tandem mass spectrometry analyses (LC–MS/MS) using both data-dependent (DDA) and data-independent (DIA) acquisitions. The data obtained by high-resolution DIA analyses displayed a stronger distinction among groups compared to DDA analyses. Differentially expressed proteins were further examined using Ingenuity Pathway Analysis® with focus on pathological and molecular processes driving atherosclerosis. From the more than 150 significantly regulated canonical pathways, atherosclerosis signaling and neutrophil extracellular trap signaling were verified by protein-targeted data extraction. The results of our study are expected to facilitate a better understanding of the disease progression’s molecular drivers and provide inspiration for further multiomics and hypothesis-driven studies.