Beyond tumors: uninvolved breast tissue of breast cancer patients with adverse prognoses is enriched for pathogenic PIK3CA and TP53 post-zygotic variants

BACKGROUND: Histologically normal mammary tissue from breast cancer patients can harbor significant genetic alterations that could precede visible tumor development and influence disease progression. METHODS: Whole-exome sequencing was performed on 408 samples from 77 breast cancer patients with poor prognosis, 49 patients recruited without prognosis-based selection, and 15 individuals undergoing non-cancer-related mammoplasty. Paired primary tumor and histologically normal mammary gland tissues were analyzed. Variant classification adhered to strict filtering criteria, incorporating allele frequency thresholds, multiple annotation databases, and in silico prediction tools. Duplex sequencing was employed to detect and confirm pathogenic PIK3CA and TP53 variants in normal mammary tissue samples from 11 breast cancer patients with unfavorable prognosis. Statistical analyses included hypergeometric testing, Kaplan-Meier survival analysis, and Cox proportional hazards modeling. RESULTS: Post-zygotic pathogenic variants in cancer-associated genes were significantly more prevalent in normal mammary tissue of poor-prognosis patients (29%) than in unselected patients (12.5%) (p = 0.0008578). Variant presence and per-individual burden were similar across age-matched cohorts and intrinsic subtypes, indicating that subtype composition, germline predisposition and age do not account for the excess UM variant load in BCAP. Truncating variants were exclusive to poor-prognosis cases. Frequently altered genes included AKT1, PIK3CA, PTEN, TBX3, and TP53, with TP53 variants detected only in patients with adverse outcomes. Duplex sequencing confirmed the presence of low-frequency variants (as low as 1.34%) in regions of histologically normal breast tissue from patients with a poor prognosis. Notably, nearly one-quarter of all identified cases (24%, 12/49) harbored pathogenic variants in normal tissue absent from corresponding primary tumors, suggesting that at least some mosaic clones in uninvolved mammary tissue represent independent evolutionary events rather than residual tumor cells. CONCLUSIONS: Post-zygotic pathogenic variants are frequent in histologically normal mammary tissue from breast cancer patients, including alterations in key cancer-associated genes. These findings indicate that mosaic clonal changes outside the tumor are more common than previously appreciated and warrant further investigation. Assessing such variants in non-tumorous tissue may, in the future, help refine approaches to breast cancer risk evaluation and management.