In sum, we establish an in vitro reconstituted proteoliposome system bearing mammalian autophagic SNAREs, HOPS, and Rab GTPases to illustrate the cooperative function between human HOPS and Rab GTPases to promote autophagic membrane fusion and propose that the C9orf72-Rab39A-HOPS axis links autophagosome-lysosome fusion with ALS/FTD pathology. This evidence concerns the gene C9orf72 and frontotemporal dementia.