Multi‑scale immune and spatial profiling of sclerosing adenosis and surrounding breast tissue identifies an immune‑cold field phenotype associated with breast cancer risk

BACKGROUND: Benign breast disease (BBD) is common and confers heterogeneous increases in breast cancer risk; however, risk prediction relies mainly on histopathology and clinical factors. Sclerosing adenosis (SA) is a proliferative BBD lesion associated with an approximately two-fold increase in risk, yet most women with SA never develop breast cancer. We hypothesize that the immune-stromal microenvironment of SA and its surrounding lobular field relates to subsequent invasive breast cancer. METHODS: In a nested case-control study within a BBD cohort, we profiled 24 sclerosing adenosis (SA) biopsies (9 developing invasive breast cancer within 15 years, cases; 15 cancer-free at ≥ 15 years, controls). We integrated whole-tissue NanoString gene-expression profiling with multiplex immunofluorescence (MxIF) imaging of SA lesions and surrounding morphologically normal lobules. We measured immune and stromal biomarkers in SA lesions and adjacent lobules, with image analysis masked to case-control status, integrated these data with whole-tissue gene expression, and summarized both microenvironment patterns and the proximity of immune cells to proliferating epithelium. RESULTS: SA biopsies from women who later developed cancer showed a low-immune, high-stromal gene-expression program, whereas controls were enriched for immune signatures. Stromal densities of CD8⁺, CD68⁺ and RUNX3⁺ cells in both lobular stroma and SA lesions mirrored this axis and were markedly lower in cases than controls. Unsupervised clustering identified immune-cold and immune-hot lobule types and four SA lesion field archetypes; immune-hot lobules and immune-hot/epithelium-proliferative lesion fields were enriched in controls. Spatial analyses further showed that immune-hot lobules have stromal immune cells positioned closer to proliferating epithelium and enriched CD27-CD8 microclusters, whereas SA lesions from cases exhibit greater immune-to-Ki67 distances, fewer boundary-proximal CD8⁺ sentinels, and depletion of CD27-RUNX3 and RUNX3-CD8 microclusters. CONCLUSIONS: These findings support an association of an immune-cold SA lesion embedded within an immune-cold lobular field phenotype with subsequent invasive breast cancer risk in women with SA, and suggest that spatially organized, RUNX3-rich immune microenvironments may contribute to epithelial surveillance. Validation in larger cohorts will be needed to confirm generalizability and clarify lesion-specific versus field-wide contributions.