Reprogramming of the stromal and immune microenvironment in preinvasive breast cancer

Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer. However, our knowledge of the DCIS tumor microenvironment (TME) remains limited. Here, we investigated the TME of estrogen receptor positive DCIS using fresh tissues samples from DCIS, invasive breast cancers and normal breast tissues. In total, 795,585 cells were analyzed from 153 patients by single cell RNA sequencing and 39 samples were profiled with spatial transcriptomics methods (Visium, Xenium). Our data identified reprogrammed vascular cells, fibroblasts and basal cells that encircled the DCIS regions, forming cancer stromal loops (CSL) that support the preinvasive cancer cells. The DCIS regions were highly immunosuppressive, and only lipomacrophages (APOC1+) and interferon T-cells infiltrated. The preinvasive cancer cells showed activation of cell cycling and interferon signaling, while reducing cell growth regulation, RNA processing, secretion and cell adhesion. Collectively, these data show extensive remodeling of the TME in DCIS that persists during invasive progression.