Prognostic value of germline variants in luminal HER2-negative and triple negative breast cancer

Background and Objectives Germline pathogenic or likely pathogenic (P/LP) variants account for 5–10% of all breast cancer (BC) cases, with a higher prevalence of 10–20% observed in specific BC molecular subtypes, such as triple-negative breast cancer (TNBC). P/LP variants in established BC susceptibility genes are associated with an increased risk of BC and may contribute to distinct tumor phenotypes and clinical outcomes. This study aimed to evaluate the distribution of germline P/LP variants and their associations with clinicopathological features and clinical outcomes in BC patients. Material and Method A total of 85 female patients with stage I-II BC, including hormone receptor-positive (HR+)/HER2-negative (HER2−) (n=60) and TNBC (n=25), were included. Inclusion criteria required complete clinicopathological data (age at diagnosis, tumor size, tumor histological grade, lymph node involvement, and clinical outcomes) and absence of clinically significant comorbidities. Exome sequencing of germline DNA from peripheral blood was performed to identify variants in 13 BC susceptibility genes (BRCA1, BRCA2, CDH1, PTEN, STK11, TP53, ATM, CHEK2, PALB2, RAD51C, RAD51D, BARD1, and NF1). Variant analysis was conducted using the Franklin platform (Qiagen), and pathogenicity was re-evaluated according to current ENIGMA, ClinGen, and CanVIG guidelines. For statistical analysis, patients were stratified into P/LP variant carriers and non-carriers. Associations with clinicopathological features and clinical outcomes were assessed, with age included as a continuous covariate for adjustment. The study was approved by the Kaunas Regional Biomedical Research Ethical Committee (Nos. BE-2-10 and P1-BE-2-10/2014). Results Overall, 11 distinct P/LP variants were identified (six in BRCA1, three in CHEK2, and one each in BRCA2 and ATM). These variants were detected in 20/85 patients (23.5%), including 10/60 (16.7%) with HR+/HER2− BC and 10/25 (40%) with TNBC. Only one HR+/HER2− BC patient carried two variants; all others had a single variant. P/LP variants were significantly associated with BC molecular subtype (p=0.021), with carriers more likely to have TNBC (OR=3.33, 95% CI 1.17−9.52, p=0.025), although this was not significant after age adjustment (p=0.158). Carrier status was also associated with tumor grade (p=0.039), disease progression (p=0.007), and distant metastasis (p=0.035), but only the association for increased risk of disease progression for patients carrying P/LP variants remained significant after age adjustment (OR=3.09, 95% CI 1.01–9.43, p=0.048). In the TNBC subgroup, P/LP variant carrier status was statistically associated with lymph node involvement (p=0.009), with carriers having higher odds of lymph node involvement, even after age adjustment (OR=15.18, 95% CI 2.01–113.35, p=0.008), although this finding should be interpreted cautiously due to the small sample size. Survival analysis showed a significant association between P/LP variant carrier status and progression-free survival (PFS) in the overall cohort (p=0.011), which was likely driven by the HR+/HER2− BC subgroup (p=0.030) but not TNBC (p=0.154). In HR+/HER2− patients, carriers had a higher risk of shorter PFS in univariate analysis (HR=2.8, 95% CI 1.05–7.54, p=0.039), which was not significant after age adjustment (p=0.084). For metastasis-free survival (MFS), a significant difference was observed in the overall cohort (p = 0.039), but not in subtype-specific analyses. Although carriers showed a higher risk of shorter MFS in univariate analysis (HR=2.41, 95% CI 1.02– 5.72, p=0.046), this did not remain significant after adjustment for age (p=0.073). Conclusions and Recommendations Germline P/LP variants were identified in a substantial proportion of BC patients, with a higher prevalence in TNBC. Although carrier status was associated with more aggressive disease features, particularly disease progression, most associations did not remain significant after adjustment for age. These findings suggest that P/LP variants may contribute to BC heterogeneity, although their independent prognostic value appears limited and requires further investigation in larger cohorts.