Opening the Black Box: Spatial Transcriptomics and the Relevance of Artificial Intelligence–Detected Prognostic Regions in High-Grade Serous Carcinoma

Abstract

Image-based deep learning models are used to extract new information from standard hematoxylin and eosin pathology slides; however, biological interpretation of the features detected by artificial intelligence (AI) remains a challenge. High-grade serous ovarian carcinoma (HGSC) is characterized by not only aggressive behavior and chemotherapy resistance but also striking variability in outcome. Our understanding of this disease is limited, partly due to considerable tumor heterogeneity. We previously trained an AI model to identify HGSC tumor regions that are highly associated with outcome status but are indistinguishable from conventional morphologic methods. Here, we applied spatial transcriptomics to further profile the AI-identified tumor regions in 16 patients (8 per outcome group) and identify molecular features related to disease outcome in patients who underwent primary debulking surgery and platinum-based chemotherapy. We examined formalin-fixed paraffin-embedded tissue from (1) regions identified by the AI model as highly associated with short or extended chemotherapy response and (2) background tumor regions (not identified by the AI model as highly associated with outcome status) from the same tumors. We show that the transcriptomics profiles of AI-identified regions are more distinct than background regions from the same tumors, are superior in predicting outcomes, and differ in several pathways including those associated with chemoresistance in HGSC. Furthermore, we find that poor outcome and good outcome regions are enriched by different tumor subpopulations, suggesting distinctive interaction patterns. In summary, our work presents proof of concept that AI-guided spatial transcriptomics analysis improves the recognition of biologic features relevant to patient outcomes.