Single-cell and spatial technologies are revolutionizing the study of molecular states in clinical samples. This study combines single-cell (scFFPE-seq), spatial (Visium CytAssist), and in situ (Xenium) technologies to analyze FFPE human breast cancer sections. Integration of these technologies reveals molecular differences between tumor regions, identifies biomarkers involved in cancer progression, and identifies rare boundary cells at the myoepithelial border. The authors demonstrate that integrating these technologies provides deeper insights than using each technology alone, advancing oncology research and the development of diagnostics and therapeutics.

Amanda Janesick, Robert Shelansky, Andrew D. Gottscho, Florian Wagner, Stephen R. Williams, Morgane Rouault, Ghezal Beliakoff, Carolyn A. Morrison, Michelli F. Oliveira, Jordan T. Sicherman, Andrew Kohlway, Jawad Abousoud, Tingsheng Yu Drennon, Seayar H. Mohabbat, 10x Development Teams, Sarah E. B. Taylor