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 treatment at relapse, complementary strategies like drug screening are urgently needed. We evaluated short-term drug screening as a rapid, reliable method to assess drug sensitivities in pediatric solid tumors using ex vivo cultures from previously established patient-derived xenograft (PDX) models. Ex vivo drug screening was performed within 14 days of receipt across two institutes, testing 77-224 compounds depending on cell availability. Drug responses were consistent across institutes (n = 6), and effective compounds were reproducibly identified in a replicate model. Tumor type-specific responses were observed. In neuroblastoma, ALK-mutation status did not correlate with ALK-inhibitor response, whereas correlations with transcriptomic changes were observed. Timepoint-specific drug sensitivities were observed in serial Ewing sarcoma models. Overall, drug hits were identified in 94% of screens (n = 63), broadening treatment options for 88% of cases without targetable alterations (n = 11). In case of a targetable event, drug screening refined compound choice. Ex vivo drug screening is a fast and feasible method, providing insights into compound efficacy and enabling quick identification of functional treatment suggestions. Ex vivo drug screening should be integrated into a future next-generation diagnostic platform for pediatric solid tumors, combined with genomics and transcriptomics.
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Data availability
The data presented in this study are available via the R2 Genomics Analysis and Visualization Platform (https://hgserver2.amc.nl/).
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Acknowledgements
We thank all patients and their parents for providing samples that made this research possible. We appreciate the support given by the following core facilities: High Throughput Screening Facility in the Princess Máxima Center and BioPhenics High-Content Screening Laboratory in the Curie Institute, and FIMM High Throughput Biomedicine Core unit (supported by EU OPENSCREEN and BioCenter Finland). We would like to thank our collaborators of the ITCCP4 consortium for sharing their knowledge and resources. The part of this work that is performed in the Máxima was supported within the framework of the IMI2 ITCC-P4 program (grant agreement no. 116064). In addition, the molecular characterization of some PDX models and the IRCCS—Istituto Ortopedico Rizzoli, Experimental Oncology Laboratory, Bologna, Italy, (K.S.), was supported by the IMI2 ITCC-P4 program (grant agreement no. 116064). We acknowledge the role of the Italian Alliance against Cancer for coordinating the participation in the ITCC-P4 project. E.C. is supported by the EuReCa international PhD program granted to Institut Curie. At Institut Curie, this study was supported by the Ligue contre le Cancer (Projet de Recherche Enfants, Adolescents et Cancer de la Ligue Contre le Cancer), the Annenberg Foundation, the Association Hubert Gouin Enfance et Cancer, Imagine for Margo, the Fondation ARC pour la Recherche contre le Cancer (ARC), Agence Nationale de la Recherche (ANR) and the EraPerMed2018 funding call. Establishment of some PDX models was performed under the MAPPYACTS protocol (clinicaltrial.gov: NCT02613962). Part of this work was supported by the Aamu Foundation and the Cancer Foundation. The FIMM High Throughput Biomedicine unit is supported by the University of Helsinki and Biocenter Finland, Finnish Cultural Foundation, and Väre Foundation (VP). Figure 1A was created in BioRender (Molenaar, J., 2025; https://BioRender.com/002la1z).
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Marlinde C. Schoonbeek: conceptualization, data curation, analyses, investigation, methodology, writing—original draft, visualization, and project administration. Pierre Gestraud: data curation, analyses, visualization, and writing—original draft. Lindy Vernooij: investigation and project administration. Arjan Boltjes: analyses and visualization. Vicky Amo-Addae: methodology and resources (Máxima library). Marloes van Luik: analyses and visualization. Elaine Del Nery: methodology and investigation. Angela Bellini: investigation and methodology. Ellora Chua: data curation, analyses, visualization, and original draft. Sarah Swaak: investigation. Eleonora Looze: investigation and writing—review & editing. Vilja M. Pietiäinen, Laura L. Turunen, and Jani S. Saarela: methodology and resources (COMPASS drug library). Julia Schueler, Emilie Indersie, Dennis Gürgen, Katia Scotlandi, Angelika Eggert, Rachida Bouarich, Franck Bourdeaut, Sakina Zaidi, Didier Surdez, Ángel M. Carcaboso, and Birgit Geoerger: methodology and resources (PDX models). Elnaz Saberi-Ansari: data curation and analyses. Yasmine Iddir and Alexandra Saint-Charles: project administration. Florence Cavalli: supervision and writing—review & editing. Apurva Gopisetty and Eva Maria Rief: project administration (ITCCP4). Hubert N. Caron, Lou Stancato, Gilles Vassal, and Stefan Pfister: supervision (ITCCP4) and writing—review & editing. Jan Koster: resources (R2 platform). Selma Eising: methodology, supervision, conceptualization, and writing—review & editing. Sander R. van Hooff and Marlinde L. van den Boogaard: supervision and writing—review & editing. Gudrun Schleiermacher and J.J. Molenaar: conceptualization, supervision, and writing—review & editing.
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G.S. receives research funding from Roche, BMS, Pfizer and MSD. The other authors declare no further competing interests related to this study.
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Schoonbeek, M.C., Gestraud, P., Vernooij, L. et al. Ex vivo drug sensitivity profiling to complement molecular profiling in pediatric precision oncology. npj Precis. Onc. (2026). https://doi.org/10.1038/s41698-025-01266-0
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DOI: https://doi.org/10.1038/s41698-025-01266-0
