Tumor Immune Microenvironment and VAF-inferred BRCA1/2 Loss of Heterozygosity in Japanese Patients With Germline BRCA1/2 -mutated Breast Cancer

Background/Aim: Germline BRCA1/2 mutations (gBRCA1/2m) confer a markedly increased lifetime risk of breast cancer. Although diverse second-hit mechanisms lead to biallelic inactivation of BRCA1/2, their relationship with the immune microenvironment remains poorly understood, particularly in Japanese populations. Patients and Methods: We retrospectively analyzed 22 Japanese patients with gBRCA1/2m breast cancer who underwent curative surgery. Pathological evaluation included assessment of tumor-infiltrating lymphocytes (TILs), CD4+, CD8+, and FOXP3+ T-cell infiltration, and PD-L1 expression. Targeted next-generation sequencing of tumor samples identified somatic alterations. Loss of heterozygosity (LOH) at the BRCA1/2 locus was assessed using tumor-only sequencing data based on variant allele frequency (VAF). After adjustment for tumor cellularity, LOH was stringently defined as a modified VAF ≥0.90; cases not meeting this threshold were classified as non-LOH. Results: Twelve patients carried gBRCA1m and 10 carried gBRCA2m. High immune infiltration and frequent PD-L1 expression (68.2%) were observed, with a trend toward greater immune activity in BRCA1-mutated tumors. Of 14 cases with reportable sequencing results, LOH status was evaluable in 13. LOH was identified in 6 (46.2%) cases. LOH was more frequent in BRCA2-mutated tumors (75.0%) than in BRCA1-mutated tumors (33.3%). No differences were observed between LOH and non-LOH groups in CD4+, FOXP3+, or CD8+ T-cell infiltration, stromal TIL levels, PD-L1 expression, or disease-free survival. Conclusion: In this Japanese cohort of BRCA-mutated breast cancer, integrated genomic and pathological analyses revealed heterogeneity in second-hit mechanisms and immune microenvironment features and suggested that detectable LOH does not fully account for immune activation in these tumors.