Identifying Novel Therapeutic Targets for Overcoming TNBC Chemo Resistance Through Comprehensive CRISPR-Cas9 Genome Screening

Abstract

Triple-negative breast cancer (TNBC) represents 15-20% of cases but disproportionately contributes to 35% of breast cancer deaths. Chemotherapy resistance remains a significant challenge in TNBC treatment. In this study, we identified the MDA-MB-231 cell line as the most representative model for TNBC chemotherapy-poor responders by comparing genomic profiles from TNBC cell lines and patient samples. We performed a genome-wide CRISPR-Cas9 screen and RNAseq analysis in MDA-MB-231 cells to uncover potential synthetic lethal targets for cisplatin/doxorubicin treatment. Our analysis confirmed the involvement of known essential genes in DNA damage repair and regulation of DNA replication pathways, such as BCL2L1, ATM, CDC25B, and NBN, in sensitizing cells to cisplatin/doxorubicin. Additionally, We identified hundreds of previously unrecognized genes and pathways related to DNA repair, G2/M DNA damage checkpoint, AMPK signaling, and mTOR signaling. The observed differences between transcriptomic responses and essential pathways from the CRISPR screen suggest a complex regulatory system in cellular response to DNA damage drugs. By combining various data analysis methods and biological experimental approaches, we have pinpointed several promising genes, such as MCM9 and NEPPS, which could serve as potential drug targets to overcome chemoresistance. Overall, our approach efficiently identified essential genes with potential synthetic lethal interactions with cisplatin/doxorubicin, offering new possibilities for combination therapies in chemo resistant TNBC patients.