Starvation-induced FLCN association with lysosomes via a Rab34–RILP complex

Dynamic positioning of lysosomes in the cytoplasm plays an important role in their function and is, in part, regulated by cellular nutrient status. The FLCN/FNIP complex is known to be active on the lysosome surface, where it interacts with Rag GTPases, supports the nutrient‐dependent recruitment and activation of mTORC1, and regulates the localisation of lysosome associated transcription factors (Petit et al., 2013; Tsun et al., 2013). New research from Starling et al. (2016) now shows that folliculin (FLCN) also controls the dynamic cytoplasmic position of the lysosome itself.

Lysosomal positioning coordinates cellular nutrient responses (Korolchuk et al., 2011), and is affected by several components, including the GTPase Rab34 that can promote lysosome clustering in the peri-nuclear region (Wang et al., 2002). Nutrient starvation, which suppresses mTORC1 activity, can also promote peri-nuclear clustering of lysosomes in HeLa cells, while nutrient-abundance and high mTORC1 activity leads to dispersion and accumulation of lysosomes at the cell periphery. mTORC1 is activated on the lysosomal surface, via a signaling network composed of Rag GTPases, the FLCN/FNIP complex and other protein complexes. FLCN/FNIP complex receives signaling inputs from metabolic pathways via phosphorylation, upon activation of mTORC1 and AMPK (Baba et al., 2006).

Starling et al. (2016) present strong evidence for a model where starvation‐induced FLCN association with lysosomes drives the formation of contact sites between lysosomes and Rab34‐positive peri-nuclear membranes, by promoting the association of Rab34 with its effector RILP. This restricts lysosome motility and thus promotes their retention in the peri-nuclear region of the cell.

Figure obtained from Starling et al. (2016)

The group shows that FLCN/FNIP complex is required for starvation‐induced peri-nuclear lysosome clustering.  Depletion of FLCN or of both FNIP1 and FNIP2 proteins using siRNA strongly affects lysosome positioning under starvation conditions, suggesting a functional connection between FLCN/FNIP-lysosome association and lysosome dynamics. As small GTPases are known to play a role in lysosome dynamics the group considered, among other GTPases, Rab34 and its effector protein RILP. Rab34 itself contributes to starvation‐induced peri‐nuclear clustering of lysosomes. However, in HeLa cells, depletion of FLCN significantly suppresses this ability.  FLCN was shown to associate with mitochondrial targeted Rab34 and the FLCN C‐terminal DENN domain is necessary for this association. Pull down experiments show that the FLCN‐DENN domain directly promotes the formation of an active Rab34–RILP complex.

The same type of experiments examining Rab34 and lysosome distribution were conducted in the BHD kidney cancer cell line UOK257 (FLCN deficient) and UOK257‐2 (FLCN restored) with results showing reduction in lysosome dynamics in the FLCN expressing cells in a DENN domain‐dependent way through Rab34/RILP.  The results in UOK257 cells are nutrient-independent, which the authors suggest might be due to the complete long term loss of full FLCN compared with acute depletion, or perhaps due to metabolic changes in the UOK257 cells.

Overall, the study shows how, in HeLa cells, FLCN couples the lysosomal nutrient signalling network to the cellular machinery that controls the intracellular distribution of the lysosome itself. The functional relevance of the study is supported by similar results, although nutrient-independent, in the BHD kidney cancer cell line, suggesting that this pathway may play a role in the pathogenesis of BHD syndrome. Since UOK257 cells do not show large deficiencies in mTORC1 activity (Baba et al., 2006), authors suggest that expanding these studies to other BHD-relevant epithelial cell types to understand how FLCN/Rab34‐dependent changes in lysosome motility may contribute to BHD syndrome.

In summary, given the complex relationship between lysosome positioning, autophagy and mTORC1 activity (Korolchuk et al., 2011), and the emerging connections between FLCN and the same pathways (Petit et al., 2013; Tsun et al., 2013), the group suggests that the dysregulation of lysosome dynamics by disruption of FLCN may contribute to the dysregulated autophagy and mTORC1 activity phenotypes found in various BHD model systems studied. The study sheds light on the mechanisms of lysosome dysregulation and can be exploited to develop therapies for kidney cancer therapies.

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