A phosphoinositide signalling pathway mediates rapid lysosomal repair

Abstract

Lysosomal dysfunction has been increasingly linked to disease and normal ageing 1 , 2 . Lysosomal membrane permeabilization (LMP), a hallmark of lysosome-related diseases, can be triggered by diverse cellular stressors 3 . Given the damaging contents of lysosomes, LMP must be rapidly resolved, although the underlying mechanisms are poorly understood. Here, using an unbiased proteomic approach, we show that LMP stimulates a phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway for rapid lysosomal repair. Upon LMP, phosphatidylinositol-4 kinase type 2α (PI4K2A) accumulates rapidly on damaged lysosomes, generating high levels of the lipid messenger phosphatidylinositol-4-phosphate. Lysosomal phosphatidylinositol-4-phosphate in turn recruits multiple oxysterol-binding protein (OSBP)-related protein (ORP) family members, including ORP9, ORP10, ORP11 and OSBP, to orchestrate extensive new membrane contact sites between damaged lysosomes and the endoplasmic reticulum. The ORPs subsequently catalyse robust endoplasmic reticulum-to-lysosome transfer of phosphatidylserine and cholesterol to support rapid lysosomal repair. Finally, the lipid transfer protein ATG2 is also recruited to damaged lysosomes where its activity is potently stimulated by phosphatidylserine. Independent of macroautophagy, ATG2 mediates rapid membrane repair through direct lysosomal lipid transfer. Together, our findings identify that the PITT pathway maintains lysosomal membrane integrity, with important implications for numerous age-related diseases characterized by impaired lysosomal function.

Lysosome repair by ER-mediated cholesterol transfer

“…The latter two mechanisms appear to be independent (Niekamp et al, 2022), and both we and others (Tan & Finkel, 2022) have found that activation of the ESCRTand ER-mediated repair occurs independently of each other. However, independent activation mechanisms do not exclude the possibility that the alternative repair mechanisms cross-talk at some level.…”

“…It also needs to be explained exactly how transfer of PS and cholesterol from the ER would mediate lysosome repair, and a relevant question is how the ER-mediated repair relates to the previously identified ESCRT- and ceramide-dependent repair mechanisms (Niekamp et al ., 2022; Radulovic et al ., 2018; Skowyra et al ., 2018). The latter two mechanisms appear to be independent (Niekamp et al ., 2022), and both we and others (Tan & Finkel, 2022) have found that activation of the ESCRT- and ER-mediated repair occurs independently of each other. However, independent activation mechanisms do not exclude the possibility that the alternative repair mechanisms cross-talk at some level.…”

“…We found that OSBP depletion causes a strong accumulation of PtdIns4P on damaged lysosomes, suggesting that OSBP performs a similar function in ER-lysosome contact sites. Therefore, OSBP not only mediates cholesterol transfer as proposed (Tan & Finkel, 2022), but also serves to balance lysosomal PtdIns4P levels.…”

“…While this manuscript was in preparation, another paper reporting the involvement of PI4K2A, PtdIns4P and ER contacts in lysosome repair was published (Tan & Finkel, 2022). This paper identified three PS transfer proteins, ORP9, ORP10 and ORP11, as being recruited to damaged lysosomes by PtdIns4P, and also made the interesting observation that the lipid channel protein ATG2 is activated by PS for repair of damaged lysosomes.…”

The PITT pathway: Keeping lysosomes young

“…This approach led to our recent discovery of the phosphoinositide‐initiated membrane tethering and lipid transport (PITT) pathway that is essential for rapid lysosomal membrane repair (Figure 1). 10 The PITT pathway is quickly triggered by LMP and it relies on new de novo membrane contacts between two organelles, namely damaged lysosomes and the endoplasmic reticulum (ER). In particular, we found that LMP stimulates rapid lysosomal recruitment of type II alpha phosphatidylinositol‐4 kinase (PI4K2A), leading to the production of phosphatidylinositol‐4‐phosphate (PtdIns4P, PI4P) on damaged lysosomes.…”