Cellular Depletion of Major Cathepsin Proteases in HeLa and SH-SY5Y Cells

Proteins delivered by endocytosis or autophagy to lysosomes are degraded by exo- and endoproteases. In humans there are 15 lysosomal cathepsins (CTS) that act as important physiological regulators. The cysteine proteases CTSB and CTSL and the aspartic protease CTSD are the most abundant lysosomal proteinases and are often linked to autophagy, lysosomal storage and neurodegenerative diseases. Their concerted functions in proteolysis in the lysosome, their individual substrates, cleavage specificity, functional redundancy, and possible sequential action on substrate proteins are not well understood. To address these open points, we generated CTSB-, CTSD-, CTSL-, and CTSBDL-triple deficient (KO) human neuroblastoma-derived SH-SY5Y cells and CTSB-, CTSD-, CTSL-, CTSZ and CTSBDLZ-quadruple deficient (KO) HeLa cells. Proteome analyses of parental and CTS-depleted cells revealed an enrichment of semitryptic peptides and of lysosome/autophagy-associated proteins but also of potentially endocytosed membrane proteins like the amyloid precursor protein (APP). Amino- and carboxyterminal APP fragments accumulated in the multiple CTS-deficient cells, suggesting that APP is regularly processed by multiple CTS-mediated cleavage events.