Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death

An intronic expansion of GGGGCC repeats within the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS‐FTD). Ataxin‐2 with intermediate length of polyglutamine expansions (Ataxin‐2 Q30x) is a genetic modifier of the disease. Here, we found that C9ORF72 forms a complex with the WDR41 and SMCR8 proteins to act as a GDP/GTP exchange factor for RAB8a and RAB39b and to thereby control autophagic flux. Depletion of C9orf72 in neurons partly impairs autophagy and leads to accumulation of aggregates of TDP‐43 and P62 proteins, which are histopathological hallmarks of ALS‐FTD. SMCR8 is phosphorylated by TBK1 and depletion of TBK1 can be rescued by phosphomimetic mutants of SMCR8 or by constitutively active RAB39b, suggesting that TBK1, SMCR8, C9ORF72, and RAB39b belong to a common pathway regulating autophagy. While depletion of C9ORF72 only has a partial deleterious effect on neuron survival, it synergizes with Ataxin‐2 Q30x toxicity to induce motor neuron dysfunction and neuronal cell death. These results indicate that partial loss of function of C9ORF72 is not deleterious by itself but synergizes with Ataxin‐2 toxicity, suggesting a double‐hit pathological mechanism in ALS‐FTD. Synopsis Expansion of GGGGCC repeats in the C9ORF72 gene is the major genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS‐FTD). Here, we report that decreased expression of C9ORF72 impairs autophagy, but does not promote major neuronal cell death. In contrast, reduced levels of C9ORF72 enhance the aggregation and toxicity of the ALS‐linked factor Ataxin‐2 ( ATXN2 ). A video synopsis is available online at http://embopress.org/video_EMBOJ-2015-93350 C9ORF72 forms a complex with SMCR8 and WDR41. This complex acts as a GDP/GTP exchange factors for RAB8a and RAB39b. The kinase TBK1 phosphorylates and regulates SMCR8. C9ORF72 in complex with SMCR8 and WDR41 regulates formation of the autophagosome. Synergic toxicity between loss of C9ORF72 and expression of Ataxin‐2 with intermediate size of polyQ suggests a two‐hit mechanism in ALS‐FTD. Graphical Abstract The ALS‐linked factor C9orf72 forms a novel complex with SMCR8 and WDR41 to regulate GEF activity for Rab8a and Rab39b and autophagy. Loss of function of C9ORF72 synergizes with Ataxin‐2 toxicity, suggesting a double‐hit pathological mechanism in ALS‐FTD.