Abstract 2408: Bioinformatics analysis of genes that confers apoptosis resistance to EGFR-PI3K co-targeting

Abstract Background: Large scale genomic studies have identified the overexpression of epidermal growth factor receptor (EGFR) and constitutive activation of the phosphoinositide-3-kinase/protein kinase B (PI3K/AKT) pathway as common genetic aberrations in head and neck cancer. Previously, we reported that the combination of EGFR inhibitor erlotinib with PI3K inhibitor BKM120 had synergistic effects and induced efficient apoptosis in a panel of head and neck cancer cell lines, but some cells were still resistant. The purpose of the current study is to identify molecular pathways that confer resistance to EGFR and PI3-K co-targeting through RNA-Seq and bioinformatics analysis. Methods: JHU022, a cell line resistant to EGFR and PI3K co-targeting was treated with the combination of erlotinib and BKM120 ± dasatinib (Src inhibitor) or crizotinib (Met inhibitor) for 24h. Total RNA was isolated and used for RNASeq analysis. In order to identify major pathways that were associated with resistance to EGFR and PI3K co-targeting, bioinformatics pathway analysis was conducted using 2-folds differentially expressed genes. The mRNA expression levels of selected differentially expressed genes were confirmed by qPCR. Results: FDR of ≥0.1% and fold-change of ≥2.0 were used as cut-off for selecting differentially expressed genes. A total of 961 genes were modulated by the combination of erlotinib and BKM120, 2205 by the combination of erlotinib, BKM120 and dasatinib, and 2251 by the combination of erlotinib, BKM120 and crizotinib when compared with untreated control. The addition of crizotinib to the combination of erlotinib and BKM120 resulted in the modulation of 624 genes, while the addition of dasatinib to erlotinib and BKM120 modulated 555 genes. KEGG pathway analysis identified DNA replication, cell cycle, mismatch repair, base excision repair, homologous recombination etc. as the major pathways affected by double and/or triple drug treatment. E2F targets, G2-M checkpoint, Myc targets were the common pathways identified by MSigDB analysis using differentially expressed genes. These pathways were also identified as major affected pathways in GO_Biological_Processes_2021 analysis. Conclusions: SRC-Met signaling confers resistance to EGFR and PI3K co-targeting by modulating genes associated with cell cycle, DNA replication, and cellular response to DNA damage. Grant Support: R15DE032063 and P20GM103434 Citation Format: Adeoluwa Adeluola, Humaira Noor, A.R.M. Ruhul Amin. Bioinformatics analysis of genes that confers apoptosis resistance to EGFR-PI3K co-targeting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2408.