Abstract A054: Functional precision oncology in recurrent ependymoma: Multiplexed functional profiling reveals unexpected cytotoxic and anti-proliferative drug activity

Abstract Background: Recurrent pediatric ependymoma remains a major therapeutic challenge with few evidence-based systemic options. NCCN guidelines emphasize maximal safe resection and radiotherapy, without systemic chemotherapy and which should generally be reserved for recurrence due to limited and unpredictable benefit. However, personalized functional profiling may provide actionable, patient-specific evidence by directly measuring tumor drug sensitivity and resistance ex vivo. Methods: Fresh surgical specimens from three pediatric recurrent ependymomas were processed into viable tumor fragments and 3D microtumors analyzed using the SAGE Oncotest™, a multiplexed ex- vivo functional profiling assay measuring both cytotoxicity and antiproliferation. NCCN-relevant agents were tested at standardized and physiologically representative concentrations over several logs. Cytotoxicity (loss of viability) and antiproliferation (inhibition of DNA synthesis) were quantified using our proprietary algorithmic drug sensitivity score (DSS) with percent effect relative to untreated controls. Results: Responses were highly patient-specific and frequently uncoupled between growth arrest and cell death, indicating distinct underlying dependencies. Cytotoxic chemotherapies: Topoisomerase I–based therapy showed the most consistent dual activity, consistent with replication stress vulnerability. Irinotecan produced cytotoxicity across cases (20–77%) with strong antiproliferation (85–99%). Gemcitabine produced strong antiproliferation (96–99%) with variable cytotoxicity (0–45%), consistent with S-phase suppression without uniform tumor kill. CDK4/6 inhibitors: Intra-class divergence suggested differences in target selectivity and pathway reliance. Ribociclib produced strong antiproliferation (72–96%) with minimal cytotoxicity (5–33%), consistent with cytostatic CDK4/6 blockade, whereas abemaciclib showed in one tumor a striking dual activity (cytotoxicity 81%, antiproliferation 97%), consistent with broader kinase activity beyond CDK4/6. With the exception of venetoclax, most other targeted agents were largely inactive or cytostatic only. Combinations: Combinations did not reliably exceed the best single agent and occasionally reduced cytotoxicity, consistent with independent and sometimes antagonistic interactions. Conclusions: Current NCCN guidelines for ependymoma emphasize surgical resection and radiotherapy without routine systemic therapy, a strategy supported by broad drug resistance across most tumors. However, multiplex ex vivo profiling revealed patient-specific vulnerabilities, including strong antiproliferative effects and, in selected cases, measurable cytotoxicity. Functional profiling may therefore enable rational selection of individualized systemic therapies in recurrent ependymoma, with the potential to improve quality of life, prolong progression-free survival, and possibly overall survival. Citation Format: Rajeshwar Nitiyanandan, Ivan Trus, Chiara Maestri, Shawn Mahoney, Ricardo J. Parker, John Norko, Sheila Singh, William Cance, Chris Apfel. Functional precision oncology in recurrent ependymoma: Multiplexed functional profiling reveals unexpected cytotoxic and anti-proliferative drug activity [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 A054.