Degradomics for large‐scale mechanistic insights on proteases and proteolysis in human health

Tissue breakdown, especially extracellular matrix or secretome breakdown is a significant aspect of physiological remodeling and disease processes in solid organs, with profound structural and regulatory impact. Tissue and circulating proteins undergo breakdown through a chemical process mediated by proteases, that is, hydrolysis of peptide bonds. Proteolysis has immense biological impact because it is irreversible, results in protein inactivation or activation, and can generate fragments with new functions to expand the functional genome. The traditional focus on a few proteases of interest against candidate substrates provided limited insights into the proteolytic landscape of human diseases. In contrast, innovations in protein terminomics workflows, tandem mass spectrometry and data handling now routinely permit identification of proteolytic events and proteases on the proteome scale, the degradome. The unbiased, de novo elucidation of disease degradomes, termed forward degradomics, has increased the number of known in vivo proteolytic events, despite only limited application to human disease to date. In reverse degradomics, activities of proteases are elucidated individually, but also at the proteome scale by digesting protein libraries sourced from tissues and cell secretomes, or by comparing the degradomes of protease-deficient/overexpressing and parental cells. Integration of forward and reverse degradomes precisely defines protease primary mechanisms in disease. Cross-disease degradome analysis can define disease-relevant, protease-specific biomarkers, identify proteases as appropriate therapeutic targets, and predict cross-organ impact of protease inhibitors. A systematic effort to map disease degradomes, that is, a prospective human degradome project would generate a comprehensive proteolysis knowledgebase for diagnostics and therapeutics.