DDDR-09. FUNCTIONAL GENOMICS AND CHEMOTHERAPY RESISTANCE SCREENING IDENTIFIES BIOMARKERS AND TARGETABLE MECHANISMS OF CCNU RESISTANCE IN GLIOMAS

Abstract

Abstract The bifunctional alkylator lomustine (CCNU) remains widely but heterogeneously used as one of the few effective treatments in glioblastoma (GBM) and IDH mutant gliomas. Despite its widespread use, mechanisms of response and resistance to this agent are controversial and patients who benefit are poorly understood. To address this with next-generation patient models and functional genomics approaches, we generated and characterized CCNU response in a large cohort of 71 patient-derived glioma cell lines (PDCLs, spheroids/organoids). Models had fully defined clinical and molecular characteristics (WES, RNAseq, and patient and model MGMT). Patient models, including those derived from patients who acquired resistance to CCNU, exhibited a surprisingly wide range of differential response to CCNU (median IC50: 21.66uM; range: 1.52uM-159uM) using metabolic (CTG) as well as cell death readouts, with no lines showing complete resistance (EC100 < 291uM). MGMT promoter methylation status but not mismatch repair (MMR) trended, but did not reach, statistical significance as a predictor of CCNU sensitivity (p=0.053), in striking contrast to TMZ (p=0.01). Chronic CCNU exposure of two PDCLs led to acquired resistance to CCNU (IC50 increase from 5uM to 50uM on average). RNA sequencing showed 194 significantly differentially expressed genes while no mutations acquired in resistant models were identified in DNA sequencing. PRISM pooled screening of over 900 barcoded cancer cell lines and correlation with DepMap whole genome CRISPR-knockout data showed unique patterns of CCNU response and strong upregulation of DNA repair targets in the resistant state, which differed from TMZ. Shared targets were also identified in a CRISPR-activator screen performed on a CCNU sensitive cell line in the presence and absence of CCNU and converged on multiple mTOR pathway genes as top enriched targets and biomarkers of resistance in CCNU-resistant models. These druggable targets are currently being investigated for combination therapies with CCNU and potential to overcome resistance.