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Updated: Jan 9, 2026
Pooled CRISPR-Based Genetic Screens in Mammalian Cells
Published on: September 4, 2019
CRISPR-Cas9 Genome and Double-Knockout Screening to Identify Novel Therapeutic Targets for Chemoresistance in
Shuai Shao1,2, Shangjia Li1, Yang Huo1
1Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
Abstract:
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.
Insights
Triple-negative breast cancer (TNBC) is deadly due to chemotherapy resistance. This study identified new gene targets and synthetic lethal pairs to overcome resistance to cisplatin and doxorubicin treatments in TNBC.
Area of Science:
- Oncology
- Genomics
- Cancer Research
Background:
- Triple-negative breast cancer (TNBC) accounts for a significant portion of breast cancer cases and deaths.
- Chemotherapy resistance is a major challenge in treating TNBC.
Purpose of the Study:
- To identify novel therapeutic targets and strategies to overcome chemoresistance in TNBC.
- To find genes that re-sensitize TNBC cells to cisplatin and doxorubicin.
Main Methods:
- Transcriptomic profiling to select a representative TNBC cell line (MDA-MB-231).
- Genome-wide CRISPR-Cas9 screening and RNA-seq analysis.
- Gene combination double-knockout screening in cell death pathways.
Main Results:
- Identified 96 and 93 genes that re-sensitize TNBC to cisplatin and doxorubicin, respectively.
- Discovered MCM9 as a novel TNBC chemoresistance target, with its drug KPT-185 showing additive effects with cisplatin.
- Uncovered 242 synthetic lethal gene pairs to combat TNBC chemoresistance.
Conclusions:
- Genome-wide and gene-combination screenings successfully identified synthetic lethal targets for TNBC treatment.
- This research provides new targets and strategies to improve chemotherapy efficacy in TNBC.
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