Abstract Background Changes in microenvironment cell-cell interactions (CCI) during the progression from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) are poorly understood. Gene expression studies are confounded by cellular heterogeneity and few separate stromal and epithelial contributions, resulting in a lack of reliable prognostic biomarker to guide treatment decisions. Methods The gene expression of 293 microdissected regions from DCIS (92 epithelial, 31 stromal) and IDC (78 epithelial, 30 stromal) cases was aggregated from 6 datasets. Expression signatures of 6 cell lineages extracted from normal breast single-cell profiling were used to correct for differences in cell abundance. Subtype-specific functional differences between DCIS and IDC were measured for each region type using Gene Set Enrichment Analysis (GSEA). DCIS-IDC stromal-epithelial interactions were compared using the expression product of 139 ligand-receptor (LR) pairs permuting the DCIS-IDC labels to assess significance. Results Variation in cell-lineage abundance separated epithelial regions into 4 clusters, including one enriched for DCIS (Myoepi-Enriched) and two for IDC (Infiltrated, Vascularized). GSEA on cell lineage normalized expression data identified subtype-independent changes in epithelial regions (induction of Extracellular Matrix maintenance genes, reduction of Tp53 signaling in IDC), as well as subtype-specific changes (proliferation in ER- and Her2-IDC, reduction in Nucleotide Excision Repair in ER+ IDC). In the stroma, Notch and Rho-GTPase signaling were induced in IDC irrespective of subtype. The stromal-epithelial interaction level of 6 and 4 LR pairs were significantly enriched in DCIS and IDC, respectively. Five of the 6 DCIS-enriched LR pairs involved ephrin interactions, with interaction level progressively decreasing from normal to DCIS to IDC. In contrast, 2 IDC-enriched LR pairs involved T-cell activity likely regulating Treg proliferation ( CD28-CD86 ) or T and NK cells stimulation ( CD226-PVR ). Notably, the bulk expression product of one identified LR pair ( EPHB4-EFNB1 ) was associated with poor survival in IDC (HR=1.47, p=0.04) suggesting that early remodeling of this stromal-epithelial interaction may have long-lasting impact on disease severity. Conclusions The observed changes in cell states and stromal-epithelial interactions, beyond those driven by difference in cell abundance, may lead to new biomarkers for prognosis and targets for secondary prevention.

Differential Analysis of Stromal-Epithelial Interactions between In Situ and Invasive Breast Cancer using Gene Expression Profiling