Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy

In metastatic cancer, the role of heterogeneity at the tumor-immune microenvironment interface and its clinical relevance remain largely unexplored. Furthermore, the degree of tumor microenvironmental heterogeneity and its molecular underpinnings are unknown. To estimate tumor-immune heterogeneity and understand tumor-immune dynamics at baseline and upon treatment with chemotherapy, we performed unbiased pathway and cell type-specific immunogenomics analysis of treatment-naive (38 samples from 8 patients) and paired chemotherapy treated (80 paired samples from 40 patients) high-grade serous ovarian cancer (HGSOC) samples. Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumours revealed pervasive variability in immune signaling and distinct immune microenvironments co-existing within the same individuals, and within tumor deposits at diagnosis. To systematically explore cell type composition of the tumor microenvironment using bulk mRNA, we derived consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods, providing improved accuracy and sensitivity when compared to HGSOC immunostaining and leukocyte methylation data sets. The integration of pathway and cell type deconvolution analyses revealed that Myc and Wnt signaling associate with immune cell exclusion in untreated HGSOC samples. To evaluate the effect of chemotherapy on the intrinsic tumor-immune heterogeneity, we compared site-matched and site-unmatched tumors before and after neoadjuvant chemotherapy. Transcriptomic and T-cell receptor sequencing analyses showed that site-matched samples had increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, an effect not seen in site-unmatched samples. These results demonstrate that the tumor-immune interface in advanced disseminated HGSOC is intrinsically heterogeneous and thus requires site-specific analysis to reliably unmask chemotherapy’s impact on the tumor-immune microenvironment.