Abstract B031: Enhancing clinical decision-making: <i>ex vivo</i> drug sensitivity profiling to rapidly complement molecular profiling in pediatric precision medicine
Authors: Marlinde C. Schoonbeek, Pierre Gestraud, Lindy Vernooij, Eleonora J. Looze, Sarah E. M. Swaak, Vicky Amo-Addae, Elaine Del Nery, Angela Bellini, Jan Koster, Selma Eising, Sander Van Hooff, Marlinde L. van den Boogaard, Gudrun Schleiermacher, Jan J Molenaar
Journal: Cancer Research (2025)

Abstract Pediatric patients with high-risk extra-cranial solid tumors face a 5-year survival rate below 50%. As molecular profiling alone is insufficient to guide clinical decisions, functional profiling is essential to improve precision medicine. Current pre-clinical models are costly and too slow to benefit patients. We propose ex vivo short-term drug screening of tumor material as feasible model for predicting drug sensitivities in solid tumors, providing rapid, actionable insights to guide treatment. The ITCC-P4 consortium established 350 pediatric cancer PDX models. The Princess Máxima Center selected 37 models for ex vivo short-term screens, where the fresh tissue is cultured for a short period of time before drug sensitivity testing. In the Curie institute, an additional 33 models were selected. Drug sensitivity was assessed for 77-224 compounds, depending on the cell number. Whole genome sequencing, RNA sequencing, and methylation profiling were performed on the original patient tumor and PDX models. Drug sensitivity profiling of 70 pediatric pan-cancer models was successfully performed within 14 days after receiving the sample. The profiles demonstrate reliable, clinically relevant drug responses. In addition to identifying effective compounds for individual tumor types, biomarkers of response were identified within subgroups. For example, TP53 inactivation corresponded to significantly decreased sensitivity to idasanutlin and selinexor, and ALK-inhibitor sensitivity was confirmed in cases with increased ALK expression. Interestingly, sensitivity to cytotoxic compounds that target the cytoskeleton and topoisomerase inhibitors both show a strong dependency on the growth rate of the models. Importantly, screening results from both institutes consistently identified top effective drugs for models from the same patient (n = 6). Serial in vitro models of two Ewing patients, including primary and progression under treatment samples, show tumor progression and shifting therapeutic windows. Our results indicate that functional profiling can expand treatment possibilities found by molecular profiling. By determining drug hits using AUC and IC50 based criteria, we identified drug hits for 95% of samples (n=35) from the Princess Maxima Cohort. This includes 7 patients for whom molecular profiling failed to identify targetable alterations. Additionally, functional profiling refines drug choice by testing multiple therapeutic options for a genetic alteration. Ex vivo short-term screening is a feasible and rapid method to determine drug sensitivities of fresh tumor tissue. It confirms known genetic-drug response associations and provides novel insights into compound effectiveness in pediatric tumors. Shifting therapeutic responses in serial models highlight the importance of functional profiling at different timepoints. Currently, this method is expanded to include fresh patient samples. Ex vivo short-term screens offer a valuable tool for clinical decision-making, enabling precise, individualized treatments for high-risk pediatric solid tumors. Citation Format: Marlinde C. Schoonbeek, Pierre Gestraud, Lindy Vernooij, Eleonora J. Looze, Sarah E. M. Swaak, Vicky Amo-Addae, Elaine Del Nery, Angela Bellini, Jan Koster, Selma Eising, Sander Van Hooff, Marlinde L. van den Boogaard, Gudrun Schleiermacher, Jan J Molenaar. Enhancing clinical decision-making: ex vivo drug sensitivity profiling to rapidly complement molecular profiling in pediatric precision medicine [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals; 2025 Mar 11-13; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(5 Suppl):Abstract nr B031.