Abstract 3999: Single cell transcriptomic comparison of patient derived ovarian cancer organoids and primary tumor epithelial signatures

Abstract High-grade serous ovarian cancer (HGSOC) is a rare but deadly disease. Platinum-based therapy along with PARPi maintenance therapy, is recommended to 80% of patients. However, acquired resistance to platinum and PARPi remains an ongoing clinical challenge, highlighting the need for the development of targeted therapies. To address this, there is a need for better in vitro models that mimic the tumor microenvironment (TME). Unlike traditional 2D culturing methods, patient-derived ovarian cancer organoids (PDOs) form 3D structures that more accurately recapitulate multilayered, multicellular tissue. The overall objective of this study is to examine how HGSOC PDOs can be used better understand tumor reprograming and how this relates to patient tumor behavior and response to therapy. Primary and metastatic tumor samples were collected from diagnosed HGSOC patients for organoid generation. Organoids were cultured for 1-5 passages before being submitted for sc-RNAseq. In addition to organoid samples, matched tumor FFPE samples were submitted for comparison. Our pilot study revealed that PDOs contain a mixture of epithelial, stromal, and immune cells. Using Monocle3, we assessed epithelial cell development and differentiation over time and identified distinct cell trajectory projections across all samples. We identified three distinct cell states: early, intermediate, and late. Our PDO sample exhibited multiple branch points within the intermediate cell state, which reflects different cell fate decisions. These findings suggest the presence of sub-populations within the intermediate cell state that are not detectable or are masked in whole tumor FFPE samples. Additionally, we examined cell-to-cell interactions using CellChat. Fibroblast cells were the most prolific producers of signaling messages across all cell types, while dendritic cells and macrophages received the highest volume of incoming signals. In conclusion, PDOs recapitulate key aspects of the TME, and can be used to investigate cell fate decisions of epithelial tumor cells, and cell-to-cell communications. This platform offers a promising tool for studying tumor behavior, therapeutic resistance, and developing more targeted and effective treatments. Citation Format: Bisiayo Fashemi, Vijayalaxmi Gupta, Yukihidi Ota, Moreniola Akande, Mary Mullen, Dineo Khabele. Single cell transcriptomic comparison of patient derived ovarian cancer organoids and primary tumor epithelial signatures [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 3999.