Abstract 1073: Integrated single cell atlas of human breast cancer enables highly-resolved analysis of tumor heterogeneity and metabolic comorbidities

Abstract Single cell transcriptomics (scRNAseq) remains the method of choice to quantify and annotate cellular heterogeneity in the tumor and its microenvironment (TME), yet most studies are under-powered to associate changes in tumor heterogeneity with phenotypes such as tumor subtype, grade, and patient age, among others. In this study, we created an integrated atlas of human breast cancer (BC), the largest resource of its kind, totaling more than 700, 000 cells across 145 patients, and optimized computational methods to benchmark integration performance, and robustly perform hierarchical cell type annotation. By combining single profiles, a higher-resolution annotation of immune, stromal, and epithelial cell types was achieved. Further, using this integrated atlas, differential abundance analyses identified significant changes in immune and stromal cell type composition associated with tumor grade, subtype, and inferred metabolic comorbidities. For insulin resistance and obesity, we identified significant expansion in exhausted CD4 T Cell populations and interferon signalling in CD8 and macrophage populations. These changes in TME heterogeneity were not discernible or had effects in discordant directions when the analysis was limited to individual BC studies, highlighting the need for atlas-based mega-analysis approaches. This highly-resolved integrated scRNAseq BC atlas represents a valuable resource for hypothesis-driven analyses of tumor heterogeneity. Citation Format: Andrew D. Chen, Christina Ennis, Lina Kroehling, Gerald Denis, Stefano Monti. Integrated single cell atlas of human breast cancer enables highly-resolved analysis of tumor heterogeneity and metabolic comorbidities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1073.