Mixed Molecular Subtypes Coexist in Estrogen Receptor Heterogeneous Primary Breast Cancers

We performed spatial transcriptomics of estrogen receptor (ER)-negative, ER-low, and ER-high tumor regions of breast cancers that were intermediate (10%-60%) ER-positive by immunohistochemistry to better understand the intratumor heterogeneity in ER expression and to elucidate whether cells of different molecular subtypes (ie, Luminal A [LumA], Luminal B [LumB], human epidermal growth factor receptor 2-enriched, or Basal-like) can coexist in the same tumor.

Digital spatial profiling was performed on 10 ER-heterogeneous (10%-60% ER+) and 10 ER-high (>60% ER+) primary breast cancers using the NanoString GeoMx platform with the Human Whole Transcriptome Atlas probe set.

LumA and LumB molecular subtypes were intermixed, but there were no Basal-like populations in these ER-heterogeneous tumors. The ER-negative (ER-) regions were LumB-like and showed lower expression of ESR1 and endocrine therapy sensitivity gene signatures but higher expression of immune-related genes and higher recurrence scores, indicating a more endocrine-resistant but chemotherapy-sensitive phenotype. We also found that ESR1 strongly positive cells enriched after preoperative chemotherapy in clinical trial tissues.

This study demonstrates mixed Lum-A and Lum-B molecular subtypes within ER-intermediate primary breast cancers and reveals that ER- tumor cell populations have molecular features of endocrine resistance but chemotherapy sensitivity. These findings may explain the worse clinical outcomes of patients with ER-heterogeneous breast cancers and suggest benefit from combined endocrine and chemotherapy strategies.