Fernando Perez-Villatoro, Aleksandra Shabanova, Lilian van Wagensveld, Ada Junquera, Iga Niemiec, María Mercedes Hincapié-Otero, Ziqi Kang, Matías Marín Falco, Kürşat Birgin, Sarah Wolf, Ella Anttila, Gayani Anandagoda, Julia Casado, Eric Marcus, Duco Gaillard, Essi Kahelin, Foteini Chamchougia, Matilda Salko, Saundarya Shah, Salvatore Russo, Jacopo Chiaro, Mikaela Grönholm, Joseph Ndika, Otto K. Kari, Ican Ican, Gabe S. Sonke, Koen K Van de Vijver, Rutgerus Fpm Kruitwagen, Maaike van der Aa, Anni Virtanen, Vincenzo Cerullo, Anna Vähärautio, P. Sorger, Hugo M. Horlings, Anniina Färkkilä
The tumor microenvironment in high-grade serous ovarian carcinoma (HGSC) is a complex network of malignant-host cell interactions, yet its orchestration remains poorly understood. We present a single-cell spatial atlas of metastatic HGSC from 280 patients, integrating high-dimensional imaging and molecular profiling. Analyzing 929 single-cell maps, we identify spatial domains with diverse cell compositions and show that immune cell coinfiltration at the tumor-stroma interface affects clinical outcomes. Using Cell Feature Importance Identification by RAndom forest (CEFIIRA), we find that tumor cell MHC class II (MHCII) expression is a key predictor of prolonged survival. Validation with deconvoluted single-cell and two distinct spatial transcriptomic datasets, along with immunopeptidomic analysis, confirms that MHCII expression correlates with immune activation, antigen presentation, and T-cell receptor clonality. Using a patient-derived immuno-oncology platform, we demonstrate that tumor MHCII expression associates with increased CD8+ T-cell cytotoxicity after PD-1 blockade, whereas blocking MHCII inhibits this activation. Our atlas offers new insights into immune activation, potentially improving patient stratification in HGSC. SIGNIFICANCE: This study delivers the first large-scale single-cell spatial atlas of HGSC, revealing how tumor-immune organization shapes outcomes. We identify tumor-intrinsic MHCII as a key driver of local immune activation and immunotherapy responsiveness, providing a mechanistic biomarker that can immediately inform improved patient stratification and therapeutic decision-making in ovarian cancer. See related commentary by Conejo-Garcia and Dangaj Laniti, p. 1041.