Deciphering Spatially Resolved Pathway Heterogeneity in Ovarian Cancer Post-Neoadjuvant Chemotherapy

Abstract

High-grade serous ovarian cancer (HGSOC) is the most common and lethal subtype of ovarian cancer, characterized by high recurrence rates and limited treatment options following chemotherapy resistance. Its significant heterogeneity poses major challenges for effective therapy and clinical outcomes. In this study, we present a systems-level analysis of spatial transcriptomics data to characterize tumor heterogeneity in post-neoadjuvant chemotherapy HGSOC patients. By integrating gene expression profiles with spatial localization and histological context, we quantified hallmark pathway activities across tissue regions. The computed pathway scores were then used for clustering to investigate intra-tumoral heterogeneity. We also constructed gene co-expression network within tumor-enriched regions. Finally, we examined the association of these co-expressed modules with treatment response. Clustering based on pathway activity scores revealed spatially distinct regions enriched for different hallmark pathways, uncovering functionally diverse cellular subpopulations within the tumor microenvironment. Tumor cell-enriched clusters show difference in pathways related to proliferation, metabolism, immune signaling and stress response, while fibroblast-rich regions exhibit upregulation of epithelial-mesenchymal transition (EMT). Unsupervised co-expression analysis further revealed gene modules associated with both biological processes and clinical phenotypes. Poor responders exhibit higher expression of gene modules involved in stress response, ribosomal function, oxidative phosphorylation, and cell-cycle regulation. In contrast, good responders show elevated activity in modules enriched for immune activation, extracellular matrix (ECM) remodeling, and inflammatory signaling. Our findings provide insights into spatially resolved functional states, tumor heterogeneity, and molecular features associated with treatment response, offering a foundation for precision oncology approaches in ovarian cancer.