Spatial Transcriptomic Mapping of the Breast Cancer Tumour Microenvironment Reveals Region-Specific Immune Checkpoint Gene Expression and Prognostic CD8+ T Cell Topography

Abstract

The spatial organisation of immune cells within the breast cancer tumour microenvironment (TME) is a critical but incompletely characterised determinant of immunotherapy response and patient prognosis. This study employed the Visium 10x Genomics spatial transcriptomics platform to simultaneously map gene expression and cellular topology in treatment-naive invasive ductal carcinoma specimens from eight patients recruited through the Karolinska University Hospital and NKI-AVL breast cancer biobank networks. Spatial deconvolution identified four major cellular regions—tumour core, peritumoral zone, immune infiltrate, and stroma—with distinct transcriptomic identities. Immune checkpoint genes including PDCD1 (PD-1), CD274 (PD-L1), and FOXP3 showed marked regional heterogeneity: PD-L1 was predominantly elevated in the tumour core (7.8-fold vs. normal adjacent tissue), while PD-1 was highest in the immune infiltrate (6.5-fold). CD8+ T cell density was highest in peritumoral zones (28.7 cells/mm²) but markedly depleted in the tumour core (12.4 cells/mm²). PD-1 expression on CD8+ T cells was highest in the immune infiltrate (84% PD-1+), indicating T cell exhaustion. These findings have implications for optimising spatial biopsy sampling strategies in Scandinavian and European immunotherapy biomarker trials.