Mitochondrial-derived vesicles compensate for loss of LC3-mediated mitophagy

Mitochondria are critical metabolic and signaling hubs, and dysregulated mitochondrial homeostasis is implicated in many diseases. Degradation of damaged mitochondria by selective GABARAP/LC3-dependent macro-autophagy (mitophagy) is critical for maintaining mitochondrial homeostasis. To identify alternate forms of mitochondrial quality control that functionally compensate if mitophagy is inactive, we selected for autophagy-dependent cancer cells that survived loss of LC3-dependent autophagosome formation caused by inactivation of ATG7 or RB1CC1/FIP200. We discovered rare surviving autophagy-deficient clones that adapted to maintain mitochondrial homeostasis after gene inactivation and identified two enhanced mechanisms affecting mitochondria including mitochondrial dynamics and mitochondrial-derived vesicles (MDVs). To further understand these mechanisms, we quantified MDVs via flow cytometry and confirmed an SNX9-mediated mechanism necessary for flux of MDVs to lysosomes. We show that the autophagy-dependent cells acquire unique dependencies on these processes, indicating that these alternate forms of mitochondrial homeostasis compensate for loss of autophagy to maintain mitochondrial health. [Display omitted] •Autophagy-dependent cells maintain functional mitochondria when mitophagy is blocked•Cancer cells can adapt to loss of canonical autophagy/mitophagy•Cancer cells upregulate mitochondrial dynamics to maintain mitochondrial homeostasis•ATG7 KO cells are dependent on mitochondrial-derived vesicles to degrade mitochondria Towers et al. show that autophagy-dependent cancer cells can survive loss of canonical mitochondrial recycling pathways, known as mitophagy. Rare surviving autophagy-deficient clones have upregulated mitochondrial dynamics to maintain mitochondrial homeostasis and become more dependent on mitochondrial-derived vesicles to degrade damaged mitochondria independent of LC3-conjugation.