Immune landscape in ER+ breast cancer subtypes identifies a differential role for macrophages

Current immunotherapies are ineffective for estrogen receptor positive (ER+) breast cancers, which account for nearly 70% of all breast cancers. Amongst the ER+ breast cancers, the major subtypes are invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). We utilized droplet-based single-cell RNAseq (10X Genomics) to analyzed the immune landscape of both peripheral blood and tumor infiltrating immune populations in both IDC and ILC. These analyses demonstrated substantial heterogeneity of macrophage within the tumor microenvironment. Overall design: Single-cell RNAseq was performed on paired peripheral blood samples and tissue samples from patients with ER+ breast cancers to assess the transcriptional immune landscape. Live immune cells were sorted from peripheral blood and single cell suspensions generated from tumor specimens. Both 3'-based and 5'-based single-cell RNAseq protocols from 10X Genomics were utilized. Samples were collected from a total of 15 patients (6 IDC and 9 ILC).