Stromal-based proteome data improve stratification of hormone receptor-positive breast cancer

Breast cancers are biologically and clinically diverse. While large-scale gene expression analyses have enabled epithelial-centered molecular classifications, studies of the tumor microenvironment (TME) remain limited, especially at the proteome level using tissue-specific resolution. By laser capture microdissection and mass spectrometry-based proteomics followed by unsupervised clustering of the stromal proteome, we discovered three patient subgroups. The largest cluster revealed the most discrete representation of stromal proteins, including a 35-protein (35P) panel linked to extracellular matrix biology, tumor progression programs, and increased abundance of tumor-associated macrophages (TAM) by single-cell profiling. Clinical validation of 35P, using whole tissue protein and mRNA values from different cohorts of ER+/HER2- breast cancer, including a large randomized controlled trial (STO), identified that more aggressive (or 'high-grade') stromal features were independent of current molecular subtypes. The 35P stromal panel may reflect important clinical information by improving patient stratification beyond current epithelial-based classification of breast cancer.