Abstract B042: Beyond genomics: Ex-vivo cytotoxicity and antiproliferation functional profiling revealed abemaciclib and entrectinib as potential actionable therapy options in recurrent brain cancers

Abstract Introduction. In primary brain cancers, actionable mutations and biomarkers often provide limited guidance for selecting the most effective therapy, and even when NCCN guideline recommended treatments are chosen, recurrence is common. We evaluated whether a rapid, multiplexed ex-vivo functional profiling assay using NCCN-recommended treatments can identify actionable treatment options beyond genomic and biomarker prediction in recurrent disease. Methods. Fresh surgical specimens from two recurrent brain tumors were processed into viable three-dimensional tumor microtissues and analyzed using a simultaneous cytotoxic and antiproliferative ex-vivo 3D functional profiling assay with results returned within 7-10 days. NCCN guideline–recommended agents were tested at standardized, clinically relevant concentrations covering four logs. Cytotoxicity (loss of viability) and antiproliferation (inhibition of DNA synthesis) were quantified as percent effect relative to untreated controls and categorized as resistant (<25%), intermediate (25–75%), or sensitive (>75%).[IT1] Results. In the recurrent oligosarcoma case (aggressive sarcomatoid variant of oligodendroglioma), the multiplexed assay confirmed resistance to prior therapies. Ivosidenib showed no cytotoxic activity (0.5, estimated 95% CI 0.0–ND) with modest growth inhibition (40.6 [37.8–42.6]), and temozolomide demonstrated low cytotoxicity (16.5 [16.4–16.6]) with limited antiproliferative effect (25.2 [25.1–25.2]). Lomustine or everolimus were considered as next NCCN-guideline recommended therapies, but neither showed significant cytotoxicity or antiproliferation. In contrast, abemaciclib showed some cytotoxicity (28.8 [28.5–30.0]) with strong antiproliferative effectiveness (84.8 [84.8–86.8]), and irinotecan demonstrated intermediate cytotoxicity (35.4 [33.8–37.2]) with strong growth inhibition (81.3 [ND–81.4]), identifying other NCCN-recommended options to consider. In a recurrent glioblastoma case following resection, chemoradiation, adjuvant temozolomide, and immunotherapy, temozolomide showed low cytotoxicity (21.9 [21.9–21.9) with limited antiproliferative activity (35.1 [34.6–37.4]), and procarbazine demonstrated no measurable activity (0.0 [0.0–ND]; 0.0 [0.0–ND]). Entrectinib exhibited strong cytotoxic activity (79.4 [79.4–79.4]) with robust growth inhibition (84.0 [84.0–84.0]), whereas larotrectinib showed neither cytotoxic nor antiproliferative effect (0.0 [0.0–ND]; 0.0 [0.0–ND]), despite both drugs targeting the TRK pathway. Conclusions. Simultaneous ex-vivo cytotoxicity and antiproliferation profiling using NCCN-recommended therapies can confirm resistance to prior treatments and identify potentially effective, CNS-penetrant cytotoxic and cytostatic options in recurrent primary brain cancers. This phenotype-driven approach complements molecular diagnostics and improves prioritization of guideline-based therapies in heavily pretreated patients within the clinical decision timeframe. Citation Format: Christian Apfel, Chiara Maestri, Rajeshwar Nitiyanandan, Ivan Trus, Ricardo Parker, William Cancer. Beyond genomics: Ex-vivo cytotoxicity and antiproliferation functional profiling revealed abemaciclib and entrectinib as potential actionable therapy options in recurrent brain cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Brain Cancer; 2026 Mar 23-25; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(6_Suppl):Abstract nr B042.