Global proteomic comparison highlights an extracellular-matrix and basement-membrane program in nonmalignant breast tissue from cancer-free BRCA1/2 carriers

Abstract Background Protein-level differences in nonmalignant breast tissue from cancer-free BRCA1/2 carriers have not been well characterized. We compared bulk-tissue proteomes from cancer-free carriers and noncarrier controls and evaluated potential prevention-relevant pathways and cellular contexts. Methods We applied data-independent acquisition mass spectrometry to 72 nonmalignant breast tissue samples spanning noncarrier controls, cancer-free BRCA1/2 carriers, and cancer-history carriers. Sixty-nine samples and 4,749 proteins passed quality control. Differential abundance was tested with age- and Site/Bank-adjusted linear models and prespecified model checks. Preranked gene-set enrichment and recurrent leading-edge analyses defined tissue programs that were compared with a published single-cell breast atlas and annotated against public HLA ligand and T-cell assay resources. Results Compared with noncarrier controls, cancer-free carriers had 435 differentially abundant proteins at FDR < 0.10 in the primary age- and Site/Bank-adjusted model; this number decreased to 49 after additional surgery-year adjustment. The most consistent pathway-level finding involved ECM and basement-membrane organization, including laminin interactions, ECM proteoglycans, and non-integrin membrane–ECM interactions; laminin interactions remained enriched at FDR < 0.10 in the surgery-year-adjusted model. Secondary exploratory patterns involved mitochondrial respiration and hypoxia/glycolysis, hemostatic and innate-immune pathways, and relative reductions in trafficking, proteostatic, and mitotic programs. Comparison with cancer-history carriers showed directional concordance and external single-cell and immune-resource analyses provided contextual annotation. Conclusions Nonmalignant breast tissue from cancer-free BRCA1/2 carriers differed from noncarrier control tissue most clearly in ECM and basement-membrane organization, with metabolic, stress-response, hemostatic/innate-immune, trafficking, proteostatic, and mitotic differences as secondary exploratory observations. Because surgical indication and specimen context were aligned with biological group and quantitative tissue composition was unavailable, this exploratory comparison cannot isolate a germline BRCA1/2 effect or determine cellular origin, causality, or individual cancer risk. This molecular-pathology framework provides a foundation for spatial validation, direct HLA immunopeptidomics, and prevention-oriented biomarkers and interventions.