PT - JOURNAL ARTICLE AU - Fredrik Salmén AU - Sanja Vickovic AU - Ludvig Larsson AU - Linnea Stenbeck AU - Johan Vallon-Christersson AU - Anna Ehinger AU - Jari Häkkinen AU - Åke Borg AU - Jonas Frisén AU - Patrik L Ståhl AU - Joakim Lundeberg TI - Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors AID - 10.1101/358937 DP - 2018 Jan 01 TA - bioRxiv PG - 358937 4099 - http://biorxiv.org/content/early/2018/06/30/358937.short 4100 - http://biorxiv.org/content/early/2018/06/30/358937.full AB - The comprehensive analysis of tumor tissue heterogeneity is crucial for determining specific disease states and establishing suitable treatment regimes. Here, we analyze tumor tissue sections from ten patients diagnosed with HER2+ breast cancer. We obtain and analyze multidimensional, genome-wide transcriptomics data to resolve spatial immune cell distribution and identity within the tissue sections. Furthermore, we determine the extent of immune cell infiltration in different regions of the tumor tissue, including invasive cancer regions. We combine cross-sectioning and computational alignment to build three-dimensional images of the transcriptional landscape of the tumor and its microenvironment. The three-dimensional data clearly demonstrates the heterogeneous nature of tumor-immune interactions and reveal interpatient differences in immune cell infiltration patterns. Our study shows the potential for an improved stratification and description of the tumor-immune interplay, which is likely to be essential in treatment decisions.