Abstract / Summary
Background/Objectives: Homologous recombination deficiency (HRD) is an important feature of breast cancer, but the relationship between alternative splicing (AS) of homologous recombination (HR) genes and HRD remains poorly characterized. The study investigated whether coordinated HR-gene AS is associated with genomic HRD and immune phenotypes. Methods: Using The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) cohort, we developed a normal-referenced, module-balanced HR splicing disruption score (HRSD) from 186 AS events across 49 HR genes. Associations with HRD were evaluated across molecularly restricted subsets and by multivariable analysis. HRD-associated splicing features were assessed across six immune phenotypes. A prioritized RAD54B alternative termination event was characterized further and independently evaluated in the Sweden Cancerome Analysis Network-Breast (SCAN-B) cohort. Results: HRSD was positively associated with genomic HRD (ρ = 0.338, p = 1.64 × 10−21) and remained significant after restriction for HRD-associated molecular features and exclusion of basal tumors. In multivariable models, each 1-SD increase in HRSD was independently associated with higher HRD scores (β = 3.17, p = 7.08 × 10−7) and HRD-high status (OR = 1.6, p = 0.001). HRD-associated splicing converged with immunoregulatory phenotypes, particularly regulatory T-cells and checkpoint activity. RAD54B alternative termination (RAD54B|AT|84553) was higher in HRD-high tumors (p = 3.42 × 10−14) and remained independently associated with immunoregulatory phenotypes after adjustment. SCAN-B analysis validated the terminal-exon structure and reproduced subtype-specific termination patterns. Conclusions: HR-associated AS represents a transcript-level dimension of HRD biology in breast cancer. RAD54B alternative termination may provide a candidate link between HRD-associated splicing and immunoregulatory phenotypes, warranting further functional investigation.