Conserved cell state dynamics reveal targetable resistance patterns in ovarian high-grade serous carcinoma

Abstract

Core homeostatic programs of tissues, reflected in gene expression modules, can persist through oncogenesis. To reveal how cell states of normal fallopian tube epithelia (FTE) transform into intra-tumoral heterogeneity in ovarian high-grade serous carcinoma (HGSC), we applied a continuous, multi-state approach on single-cell transcriptomes of treatment-naive tumors (n=50) and normal FTE (n=14). We found the gene modules conserved from normal FTE to cancer to be more diverse than those altered during tumorigenesis, wherein the pseudotime-late TNF/NF-{kappa}B-associated module was linked to poor prognosis. The modules showed biases in subclonal structures and homologous-recombination deficiency, suggesting that genetic drivers employ existing epithelial programs for oncogenic phenotypes. Finally, organoid experiments validated actionable non-genetic drivers of these cell states, allowing chemosensitization by modulating apoptosis and NF-{kappa}B pathways. In summary, we identified prognostic, continuous cell states that reconstitute fallopian tube dynamics in HGSC and offer actionable targets to improve platinum response.