Distinct transcriptomic features of tumor and stromal cells in direct contact in luminal and triple-negative breast cancers

Abstract

Aim: The aim was to determine the transcriptomic features of tumor and stromal cells in direct contact within tumor nodules in luminal and triple-negative breast cancer.

Methods: Spatial transcriptomic profiling was performed using the Visium 10x platform on FFPE tumor tissue sections from 10 patients with luminal breast cancer and 9 patients with triple-negative breast cancer. Manual morphological annotation of spots and evaluation of differentially expressed genes (DEGs) in identified spot clusters were performed using Loupe Browser v8.0.0 (10X Genomics, USA). Activated biological processes were assessed using the Enrichr online resource and the GO Biological Process 2025 database. Ligand-receptor pairs were identified using the CellChat package (v2.0) in R (v4.4.2).

Results: In luminal breast cancer, mixed cluster (tumor cells colocalized with stromal cells) was characterized by overexpression of genes encoding S100A family Ca²⁺-binding proteins S100A4, S100A8, S100A9), matrix metalloproteinases MMP2, MMP7, MMP14), cytokeratins KRT5, KRT7, KRT15, KRT23, KRT81), the mesenchymal marker VIM, and epithelial-mesenchymal transition (EMT)-associated genes ICAM1, PRRX1) compared to tumor-only cluster. In triple-negative breast cancer, mixed cluster showed overexpression ofS100A2, S100A8, S100A9, the epithelial gene KRT6B, the cancer stem cell marker CD44, and NOTCH2, which is associated with negative regulation of EMT. In both breast cancer subtypes, mixed cluster showed transcriptomic enrichment of gene sets associated with regulation of the ERK/MAPK cascade, apoptosis, and cell adhesion and migration. Ligand-receptor pairs associated with cell-cell contact, EMT, and immune response were also detected in colocalized cells, with a broader spectrum of these pairs observed in luminal breast cancer.

Conclusions: This study assessed the transcriptomic characteristics of directly contacting tumor and stromal cells and identified the spectrum of ligand-receptor pairs mediating their interactions. Characterizing the properties of cells at the tumor-stroma interface helps unravel mechanisms of breast cancer progression and identify novel diagnostic markers and therapeutic targets.

Keywords

luminal breast cancer / triple-negative breast cancer / spatial transcriptomics / Visium 10x / tumor cells / tumor microenvironment / ligand-receptor pairs

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