Abstract 1328: Using whole-genome CRISPR-Cas9 screening to identify resistance networks in glioblastoma

Abstract

Glioblastoma (GBM) is the most aggressive and common type of adult malignant brain tumor, with 12,000 new diagnoses each year. Even with the current standard of care—surgical resection, radiation, and temozolomide (TMZ)-based chemotherapy—the median survival is about 20 months. This is partly due to the high rate of resistance to conventional therapy, including TMZ, leading to recurrence rates close to 100%. It remains largely unknown what drives the development of this resistance. Many studies have shown differences between primary and recurrent tumors, but a deeper understanding of resistance mechanisms is needed. CRISPR-Cas9 screening is a powerful tool for systematic and unbiased genetic analysis, which we applied to understand TMZ resistance. We performed a genome-wide CRISPR knockout screen in H4 human GBM cells, encompassing over 17,000 genes. A DMSO-treated population was compared with a TMZ-treated population over 14 days. In this drug sensitivity screen, depletion of guides corresponds to a TMZ-resistance gene, whereas enrichment of guides corresponds to a TMZ-sensitivity gene. Analysis showed that there was significant enrichment in guides for known TMZ-sensitivity genes that have been highly cited—ATG14, MSH6, MLH1, and PMS2—thus validating our screen results. However, more importantly, we were able to identify a list of 200 novel genes implicated in TMZ resistance. Pathway analysis revealed that these genes were enriched in Hippo and Notch signaling, both known to play a role in chemoresistance. From this list of novel genes, we identified 4 previously unstudied genes. These genes showed significant elevations in RNA expression (p Citation Format: Shreya Budhiraja, Shivani Baisiwala, Ella Perrault, Li Chen, Cheol Park, Chidiebere Awah, Crismita Dmello, Andrew Zolp, Adam Sonabend, Atique Ahmed. Using whole-genome CRISPR-Cas9 screening to identify resistance networks in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1328.