CRISPR-Cas9 Genome and Double-Knockout Screening to Identify Novel Therapeutic Targets for Chemoresistance in Triple-Negative Breast Cancer

Background/Objectives: Triple-negative breast cancer (TNBC) accounts for 15 to 20% of breast cancer cases and contributes to a disproportionate 35% of breast cancer deaths. Its resistance to chemotherapy presents a significant challenge. Methods: We firstly compared transcriptomic profiles between TNBC cell lines and patient samples and inferred the MDA-MB-231 cell line as the most representative model for TNBC with poor response to chemotherapy. We then conducted a genome-wide CRISPR-Cas9 screening and RNA-seq analysis in MDA-MB-231. Results: This analysis revealed 96 and 93 genes that could re-sensitize cisplatin and doxorubicin treatment, respectively, with 19 overlapping genes. Among these genes, 28 have been studied and published previously in chemoresistance research. MCM9 was found as a new TNBC chemoresistance target. Its target drug, KPT-185, showed an additive effect with cisplatin in treating TNBC cells. In the follow-up gene combination double-knockout experiment among 65 genes selected from cell death pathways, 242 synthetic lethal gene pairs were discovered to overcome chemoresistance in TNBC. Conclusions: In this study, we identified synthetic lethal targets in treating TNBC with cisplatin and doxorubicin through a genome-wide CRISPR-Cas9 screening and gene combination double-knockout screening.