Abstract 5187: Characterization and prediction of drug responses in NF1 patient-derived tumor organoids through multiplex phenotypic profiling

Abstract Neurofibromatosis Type I (NF1) is a tumor-predisposing genetic disorder driven by pathogenic variants in the NF1 gene. The development of neurofibromas, including cutaneous neurofibromas (cNFs) and plexiform neurofibromas (pNFs), constitutes a major challenge of NF1 management. Although cNFs do not carry a risk of malignant transformation, they are associated with significant comorbidities. Furthermore, benign pNFs have a risk of evolving into malignant peripheral nerve sheath tumors (MPNSTs), a rare type of soft tissue sarcoma, in ≈15% of patients. Current therapies for NF1 are limited. To date, there are no systemic treatment options for cNF lesions other than desiccation or surgical removal. For pNF management, selumetininb (a MEK1/2 inhibitor) is the only approved treatment for pediatric patients with inoperable, symptomatic lesions. However, treatment is not curative and requires continuous administration, with toxicity concerns. Lastly, MPNSTs are resistant to most systemic therapies, with surgery being the only available approach for treating localized lesions. NF1-associated tumors present a complex microenvironment that comprise different cell types including Schwann cells, fibroblasts, and mast cells. The identification of effective non-surgical treatments has been severely limited by the rarity of these tumors, their pronounced cellular heterogeneity, and the lack of patient-derived models that accurately replicate these complex characteristics. We have developed patient-derived organoids of both neurofibromas (Nguyen et al, Cell Reports Methods 2024) and MPNSTs (Al Shihabi et al, Cell Stem Cell 2024) that maintain cellular and molecular features of parental tumors, as novel tractable models for drug discovery studies. Here, we develop a modified, 3D-compatible Cell Painting assay (Bray et al, Nature Protocols 2016) to stain cellular structures and provide unbiased phenotypic readouts of NF1 patient-derived tumor organoids. We combined Cell Painting with our high throughput mini-ring organoid screening platform (Phan et al, Communications Biology 2019; Al Shihabi et al, Science Advances 2022) to rapidly screen FDA-approved drugs. We are developing a deep-learning based microscopy analysis framework to extract phenotypic features, which we will integrate with omic-based readouts to prioritize candidate therapeutic agents and establish phenotypic biomarkers that predict clinical outcomes, enabling precision medicine approaches for NF1 patients. Citation Format: Alberto Mendoza-Valderrey, Huyen T. Nguyen, Jenna Tomkinson, Cameron Mattson, Michael J. Lippincott, Summer Swearingen, Sara Gosline, Gregory P. Way, Alice Soragni. Characterization and prediction of drug responses in NF1 patient-derived tumor organoids through multiplex phenotypic profiling [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 5187.