N-Terminal proteomics reveals distinct protein degradation patterns in different types of human atherosclerotic plaques

BACKGROUND Destabilization and rupture of atherosclerotic plaques is a major cause of acute atherosclerotic cardiovascular events, including heart attack, ischemic stroke and peripheral arterial disease. Plaque destabilization is associated with extracellular matrix (ECM) modification and remodelling involving protease activity. Enzymatic cleavage generates protein fragments with new ‘ends’ (N-termini). We hypothesized that plaques susceptible to rupture would contain elevated levels of fragmented proteins with new N-termini. Identification of active proteases and their target proteins might allow categorization of plaque stability. METHODS Plaques from 21 patients who underwent carotid surgery due to symptomatic carotid artery stenosis were examined in an observational/cross-sectional study. The plaques were solubilized, digested, enriched for N-terminal fragments and analyzed by liquid chromatography-mass spectrometry. RESULTS The above methodology detected 35349 peptides, with 19543 being N-terminal species; 6561 were subsequently identified and quantified. Multidimensional scaling analysis and hierarchical clustering indicate the presence of three distinct clusters, which correlate with gross macroscopic plaque morphology (soft, mixed, and hard), ultrasound classification (echolucent/echogenic) and presence of hemorrhage/ulceration. Major differences were identified in the complement of peptide fragments, consistent with alternative turnover and degradation pathways dependent on plaque type. Identified peptides include signal and pro-peptides from ECM synthesis/turnover, and many from protein fragmentation. Sequence analysis indicates the targeted proteins (including ECM species) and the proteases (including meprins, cathepsins, matrix metalloproteinases, elastase, kallikreins) involved in fragment generation. CONCLUSIONS This study provides a large dataset of peptide fragments and proteases involved in plaque stability, mechanistic insights into remodelling, and possible biomarkers for improved atherosclerosis risk profiling. GRAPHICAL ABSTRACT