Repeat expansions in the C9orf72 gene are a common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), two devastating neurodegenerative disorders. One of the proposed mechanisms of GGGGCC repeat expansion is their translation to produce unnatural dipeptide repeat (DPR) proteins that accumulate in aggregates and contribute to the pathology. There are 5 different DPRs poly(GA), poly(GR), poly(PR), poly(PA), poly(GP) which are neurotoxic in vitro. In our study, we identified the interactome of all five DPR proteins, consisting of 125 repeats, overexpressed in HEK293T cells using BioID2 proximity labeling. We identified 140 interacting partners for polyGR, 130 for polyGA, 138 for polyPR, 62 for polyPA, and 38 for polyGP. Gene ontology enrichment analysis of proteomic data identified interaction candidates involved in protein translation, signal transduction pathways, protein catabolic processes, amide metabolic processes, and RNA-binding. Through further analyses, we evaluated the interaction between polyGA and Valosin-containing protein (VCP) in HEK293T cells as well as in brains of C9orf72 patients. Furthermore, we are showing that polyGA sequester VCP in polyGA aggregates and hinders its function. Additionally, we analyzed the effect of decreased level of VCP on autophagic markers p62 and LC3.