The lysosome is canonically known as a major organelle for protein degradation and nutrient sensing in the cell. Mutations in lysosomal enzymes and membrane proteins often result in neurological disease, demonstrating the critical role for this organelle in neuronal function and homeostasis. However, little is known about why diseases that impair this ubiquitous organelle often give rise to neuron-specific deficits. Given the selective vulnerability of neurons to lysosomal dysfunction, a better understanding of the unique functions of lysosomes in neurons is necessary.

To gain deeper insight into the biochemistry of neuronal lysosomes, we developed methods to engineer and culture human iPSC-derived neurons. Within this system, we used proximity labeling proteomics to profile the lysosomal surface proteome. We discovered that annexin A11 (ANXA11), a protein linked to familial amyotrophic lateral sclerosis (ALS), is a novel component of the lysosomal surface. ANXA11 is also a component of RNA granules, and its bipartite domain organization allows it to act as a tether between RNA granules (N-terminal phase separation) and the lysosomal surface (C-terminal phospholipid binding). We find that ANXA11 enables RNA granule hitchhiking on motile lysosomes, promoting the long-distance transport of RNA within neuronal processes. Critically, disease-linked mutations in ANXA11 disrupt this transport, providing support for failed RNA transport as a pathogenic mechanism in neurodegenerative disease. We identified ALG-2 and calcyclin (CACY) as two important modifiers of ANXA11 phase separation properties, and find that ALG-2 in particular restricts ANXA11-RNA granule contact and RNA granule-lysosome contact.

Finally, we identify an unexpected interaction between a ribosome biogenesis protein (NOP14) and endosomal SNARE proteins (STX7, STX8, STX12, and VTI1B) on the surface of lysosomes, and provide some evidence that this interaction mediates ribosome-lysosome tethering. Disrupting these interactions is linked with a depletion of stalled ribosomes in neurites, potentially providing a mechanism for ribosome hitchhiking on lysosomes for neuritic transport.

Together, this work illuminates a previously unknown dimension of lysosome biology in neurons, and positions the lysosome as a broadly important organelle for multiple aspects of protein and RNA trafficking and metabolism.