Abstract PR05: Spatial transcriptomics of ductal carcinoma in situ reveal subtype specific differences in tumoral and stromal cell compartments
Authors: Bergholtz Helga , Norum Jens Henrik , Lien Tonje G , Schandiz Hossein , Sauer Torill , Geisler Jürgen , Sørlie Therese 
Published: February 2024

Abstract
Up to 50% of patients diagnosed with ductal carcinoma in situ (DCIS) never experience progression to invasive disease, even if left untreated. Current knowledge of what makes DCIS become invasive is limited and we lack diagnostic tools to predict which patients can be spared treatment. Escape of tumor cells from the breast ducts is influenced by characteristics of the tumor cells, the microenvironment surrounding the ducts, and the interplay between the two. Intraductal tumor cells in DCIS are not physically in contact with extraductal stromal cells. Until now, analyses of DCIS tissue have mainly been performed on bulk tissue, however, this approach does not take into consideration the unique morphology of DCIS. We used the Nanostring GeoMX® digital spatial profiling platform to determine the transcriptome of DCIS tumor cells and the surrounding stromal cells separately. From a large cohort of &gt;500 DCIS cases from Akershus and Oslo University Hospitals, we selected 23 pure DCIS cases, grade 3, of different molecular subtypes: triple negative (TN), Luminal A (LumA) and HER2-enriched. At least four tumor-stroma pairs were selected from each case. Bioinformatic analyses were used to explore both tumor and stroma expression data and the interplay between the two cellular compartments. There were distinct gene expression differences between DCIS of different subtypes. Intertumoral heterogeneity was larger than intratumoral heterogeneity in all subtypes. This was also apparent in stromal cell compartments, although less pronounced. Gene ontology analyses of DCIS tumor cells from each of the three subtypes showed several overlapping biological processes, suggesting common mechanisms for regulating tumor cell growth in DCIS. We also found subtype specific differences: Tumor cells of the TN subtype showed upregulation of protein synthesis. Processes associated with RNA splicing were upregulated in tumor cells of the LumA subtype, whereas the HER2-enriched subtype showed increased DNA repair activity. The immune microenvironment differed between the subtypes: LumA DCIS were characterized by lower immune cell infiltration than TN and HER2-enriched, however, there was variation between and within the cases. Using in silico cell deconvolution, we found that B-cells were more abundant in HER2-enriched tumors, while T-cells were more common in TN and LumA. T-regulatory cells were found in all subtypes. The GeoMX® digital spatial profiling platform is well suited for exploring the transcriptome of DCIS samples. We found biologically relevant differences between tumor cells of the different molecular subtypes already at the DCIS stage in breast cancer progression. The immune cell composition surrounding DCIS lesions also differed between the subtypes. Further studies of the tumor-stroma interplay are required to understand the processes involved in progression of DCIS to invasive disease.
Citation Format: Helga Bergholtz, Jens Henrik Norum, Tonje G Lien, Hossein Schandiz, Torill Sauer, Jürgen Geisler, Therese Sørlie. Spatial transcriptomics of ductal carcinoma in situ reveal subtype specific differences in tumoral and stromal cell compartments [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr PR05.