SLC25A28 is a synthetic lethal target in nucleotide excision repair-deficient cancer

Background: Nucleotide excision repair-deficient (NER-D) cancers comprise approximately 10% of bladder urinary tract and uterine cancers. Platinum-based chemotherapy is the current standard of care for NER-D cancers; however, its nephrotoxicity limits applicability in patients with compromised renal function. No druggable targets have been identified for NER-D tumors. Genome-wide CRISPR screening offers a powerful strategy to identify synthetic lethal interactions. We performed a genome-wide screen to identify potential synthetic lethal targets in NER-deficient cells. Methods: An RT112/84 ERCC4 knockout ( ERCC4 -/- ) cell line was generated. ERCC4 status was examined by Sanger sequencing and Western blotting, and nucleotide excision repair activity was assessed using the Host Cell Reactivation Assay (HCRA). A genome-wide CRISPR screen was performed in RT112/84 wild-type (WT) and ERCC4 -/- cells to identify candidate synthetic lethal targets. Colony formation assays validated candidate interactions, and SLC25A28 was further tested for synthetic lethality with ERCC2 , ERCC3 , and ERCC5 . RNA sequencing was conducted to investigate the mechanism underlying SLC25A28-ERCC4 synthetic lethality. Results: Sanger sequencing and Western blot confirmed ERCC4 knockout in RT112/84 cells. HCRA demonstrated markedly reduced NER activity in ERCC4 -/- cells. Genome-wide CRISPR screening identified SLC25A28 as a top synthetic lethal candidate with ERCC4 . Colony assays validated the synthetic lethality between SLC25A28 and ERCC2 , ERCC3 , ERCC4 and ERCC5 . Conclusions: Our findings identify SLC25A28 as a novel synthetic lethal target in NER-deficient cancers, suggesting that inhibition of SLC25A28 may represent a potential therapeutic strategy for tumors harboring NER pathway mutations. This study was supported by STTR 1 R41 CA275627-01, the Niehaus Center for Inherited Cancer Genomics, and the Breast Cancer Research Foundation.