Converging roles of PSENEN/PEN2 and CLN3 in the autophagy-lysosome system

PSENEN/PEN2 is the smallest subunit of the gamma-secretase complex, an intramembrane protease that cleaves proteins within their transmembrane domains. Mutations in components of the gamma-secretase underlie familial Alzheimer disease. In addition to its proteolytic activity, supplementary, gamma-secretase independent, functions in the macroautophagy/autophagy-lysosome system have been proposed. Here, we screened for PSENEN-interacting proteins and identified CLN3. Mutations in CLN3 are causative for juvenile neuronal ceroid lipofuscinosis, a rare lysosomal storage disorder considered the most common neurodegenerative disease in children. As mutations in the PSENEN and CLN3 genes cause different neurodegenerative diseases, understanding shared cellular functions of both proteins might be pertinent for understanding general cellular mechanisms underlying neurodegeneration. We hypothesized that CLN3 modulates gamma-secretase activity and that PSENEN and CLN3 play associated roles in the autophagy-lysosome system. We applied CRISPR gene-editing and obtained independent isogenic HeLa knockout cell lines for PSENEN and CLN3. Following previous studies, we demonstrate that PSENEN is essential for forming a functional gamma-secretase complex and is indispensable for gamma-secretase activity. In contrast, CLN3 does not modulate gamma-secretase activity to a significant degree. We observed in PSENEN- and CLN3-knockout cells corresponding alterations in the autophagy-lysosome system. These include reduced activity of lysosomal enzymes and lysosome number, an increased number of autophagosomes, increased lysosome-autophagosome fusion, and elevated levels of TFEB (transcription factor EB). Our study strongly suggests converging roles of PSENEN and CLN3 in the autophagy-lysosome system in a gamma-secretase activity-independent manner, supporting the idea of common cytopathological processes underlying different neurodegenerative diseases.

Automated summary

The study suggests that PSENEN and CLN3 may play important roles in the autophagy-lysosome system in a gamma-secretase activity-independent manner, indicating common cytopathological processes underlying different neurodegenerative diseases. The findings reveal a potential link between these two proteins in regulating cellular functions related to neurodegeneration.