Abstract 1249: Chemotherapy enriches one of two pre-existing coordinated cellular programs characterized by inflammatory and stress pathways in high grade serous ovarian cancer

Women diagnosed with high grade serous ovarian cancer (HGSOC) often respond to initial rounds of neoadjuvant chemotherapy, but then undergo multiple rounds of relapse and regression before acquiring resistance. This pattern of response and relapse suggests that transient, non-genetic resistance mechanisms are engaged by a subpopulation of tumor cells allowing them to survive and re-form a tumor. To elucidate the mechanisms underlying this transient resistance, we performed scRNASeq and cyclic immunofluorescence (CyCIF) on matched pre- and post-treatment tissues from seven patients. Our transcriptomics data revealed that the interferon (IFN) pathways, IFNα and IFNγ, and the tumor necrosis factor alpha (TNFα) pathway were enriched following therapy in six out of the seven patients. The enrichment of the IFN and TNFα pathways following chemotherapy exposure suggested that tumor cells expressing these programs may survive treatment and thus contribute to relapse, prompting us to study this population further. Spatial analysis of three interferon-stimulated genes (ISGs) revealed that a large proportion of ISG+ tumor cells appear to occupy specific niches containing ISG+ immune cells, while other ISG+ tumor cells were not adjacent to ISG+ immune cells, suggesting both intrinsic and extrinsic mechanisms of IFN pathway activation. It has been reported that IFN is activated in the early lesions of HGSOC known as serous tubule intraepithelial carcinomas (STICs). To investigate whether the IFN pathway activity early in tumorigenesis may be associated with reactivation of retroviral DNA, we performed CyCIF on samples containing STICs and found correlated expression of ISGs and the LINE1 protein product, ORF1P. These STIC areas were typically not associated with immune cells. Similarly, we detected correlated expression of ORF1P with ISGs in invasive tumor cells. Together, our findings suggest that endogenous retroviral reactivation may activate the cGAS/STING pathway, turning on IFN and establishing an IFN+ tumor cell population. To further investigate the cellular heterogeneity of HGSOC and identify pathways that are co-expressed with the inflammatory pathways, we sub-clustered individual patients’ tumors. This analysis revealed two distinct tumor cell states: one associated with high expression of the inflammatory pathways with additional stress-related programs and EMT, and the other with MYC pathway, cellular proliferation, and metabolic pathways. We were able to confirm this coordinated expression in an additional 40 pre-treatment samples. Using an independent cohort from the TRIO14 ovarian cancer trial, we found the same pattern in HGSOC tumors from 46 patients. Future studies of this population aim to understand the functional importance of the IFN/inflammatory/stress state and to identify targetable vulnerabilities. Citation Format: Nomeda Girnius, Muyi Liu, Laura M. Selfors, Jaeyoung Kang, Linna Lahmadi, Mayura Thomas, Aylin Z. Henstridge, Morgan Gruner, Jordan Mattson, Dennis J. Slamon, Gottfried E. Koneckny, Andrew C. Nelson, Timothy K. Starr, Ronny Drapkin, Boris J. Winterhoff, Joan S. Brugge. Chemotherapy enriches one of two pre-existing coordinated cellular programs characterized by inflammatory and stress pathways in high grade serous ovarian cancer [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 1249.