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MCs (mast cells) adversely affect atherosclerosis by promoting the progression of lesions and plaque destabilization. MC chymase cleaves apoA-I (apolipoprotein A-I), the main protein component of HDL (high-density lipoprotein). We previously showed that C-terminally truncated apoA-I (cleaved at the carboxyl side of Phe(225)) is present in normal human serum using a newly developed specific mAb (monoclonal antibody). In the present study, we aimed to identify chymase-induced cleavage sites in both lipid-free and lipid-bound (HDL(3)) forms of apoA-I. Lipid-free apoA-I was preferentially digested by chymase, at the C-terminus rather than the N-terminus. Phe(229) and Tyr(192) residues were the main cleavage sites. Interestingly, the Phe(225) residue was a minor cleavage site. In contrast, the same concentration of chymase failed to digest apoA-I in HDL(3); however, a 100-fold higher concentration of chymase modestly digested apoA-I in HDL(3) at only the N-terminus, especially at Phe(33). CPA (carboxypeptidase A) is another MC protease, co-localized with chymase in severe atherosclerotic lesions. CPA, in vitro, further cleaved C-terminal Phe(225) and Phe(229) residues newly exposed by chymase, but did not cleave Tyr(192). These results indicate that several forms of C-terminally and N-terminally truncated apoA-I could exist in the circulation. They may be useful as new biomarkers to assess the risk of CVD (cardiovascular disease).