Background Hexanucleotide repeat expansion in the C9ORF72 gene is the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One potential pathogenic mechanism is the aberrant accumulation of dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG (RAN) translation in all six reading frames (poly-GA, poly-GR, poly-PA, poly-PR, and poly-PG) of both sense and antisense RNAs. Abnormal cytoplasmic inclusions of these DPR proteins have been found in C9ORF72-ALS/FTD patient tissues and cells. Many studies revealed potential toxicities by different DPRs, especially poly-GR/PR, which were reported to be the most toxic DPRs to neurons. In particular, poly-GR has been shown to correlate with neurodegeneration in C9ORF72-related ALS/FTD, implicating the contribution of poly-GR to the disease etiology. Objective Our goal is to identify genetic modifiers that regulate the poly-GR mediated toxicity in human neurons which will provide novel insights into disease mechanisms and therapy development. Results We recently built a CRISPRi-based screening system in scalable human neurons (i3Neuron) to comprehensively decipher the toxic pathways induced by poly-GR and identify the modifiers that improve neuron survival as novel therapeutic targets. The pilot screening using a druggable CRISPRi library identified a receptor-type tyrosine-protein phosphatase as a strong candidate modifier. The survival of the GR-expressing i3Neurons is significantly improved when the gene is knocked down, probably via restoring the phosphatidylinositol 3-phosphate (PI3P) level. More importantly, reduction of the phosphatase by shRNA is sufficient to rescue the glutamate-induced excitotoxicity in the C9ORF72-ALS/FTD patient-derived induced pluripotent stem cell (iPSC)-differentiated neurons (C9 iPSNs). Conclusions We found PI3P is critical for cell survival in both poly-GR expressing neurons and C9 iPSNs. Our finding provides novel insights into the molecular pathways that contribute to poly-GR mediated toxicity and reveals a novel potential therapeutic target in C9ORF72-ALS/FTD patients.