CRISPR Screening to Identify DNA Repair Pathways Used During Cancer Therapy
Undergraduates: Aihui (Alyssa) Guo, Dr. Wanjuan Feng
Faculty Advisor: Gaorav Gupta
Department: Biology
Background: DDR is crucial for maintaining genomic stability by detecting and repairing damage to cellular DNA, and by eliminating cells with irreparable DNA1. Disruption of the DDR is observed in many cancers and is hypothesized to contribute to the mutagenic processes driving tumorigenesis2. We propose to implement a customized CRISPR library targeting 310 DDR genes to identify the genes that are essential for viability after DNA damage induced by IR, different classes of chemotherapeutics, and various inhibitors in a uniform cancer cell line model. Methods: 1) CRISPR pooled screening and library preparation is used to allow for lentiviral-based delivery of individual small guide RNAs (sgRNAs) into cells in order to perform large-scale functional genetic screens. 2) Growth-dependent changes in sgRNA representation is used to for selected chemotherapeutic drugs and ionized radiation. 3) For genes that are identified as required for repair of damage induced by the different DDAs, we analyzed TCGA using the cbioportal. Results and Conclusion: Treatment group to the control samples are compared to identify sgRNA sequences that are depleted specifically in the treated sample(s); These depleted sgRNAs are predicted to target genes that are essential for repair of DNA damage induced by that treatment.