Genomic Signatures Predict the Immunogenicity of BRCA-Deficient Breast Cancer

Breast cancers with alterations have a relatively high mutational load, suggesting that immune checkpoint blockade may be a potential treatment option. However, the degree of immune cell infiltration varies widely, and molecular features contributing to this variability remain unknown. We hypothesized that genomic signatures might predict immunogenicity in breast cancers. Using The Cancer Genome Atlas (TCGA) genomic data, we compared breast cancers with (89) and without (770) either germline or somatic alterations. We also studied 35 breast cancers with germline mutations from Penn using WES and IHC. We found that homologous recombination deficiency (HRD) scores were negatively associated with expression-based immune indices [cytolytic index ( = 0.04), immune ESTIMATE ( = 0.002), type II IFN signaling ( = 0.002)] despite being associated with a higher mutational/neoantigen burden, in mutant breast cancers. Further, absence of allele-specific loss of heterozygosity (LOH negative; = 0.01) or subclonality ( = 0.003) of germline and somatic mutations, respectively, predicted for heightened cytolytic activity. Gene set analysis found that multiple innate and adaptive immune pathways that converge on NF-κB may contribute to this heightened immunogenicity. IHC of Penn breast cancers demonstrated increased CD45 ( = 0.039) and CD8 infiltrates ( = 0.037) and increased PDL1 expression ( = 0.012) in HRD-low or LOH-negative cancers. Triple-negative cancers with low HRD had far greater CD8 T cells ( = 0.0011) and Perforin 1 expression ( = 0.014) compared with hormone receptor-positive HRD-high cancers. HRD scores and hormone receptor subtype are predictive of immunogenicity in breast cancers and may inform the design of optimal immune therapeutic strategies.