Association of the 70-gene assay and homologous recombination deficiency in patients with high risk 2 breast cancers.

Abstract

561 Background: Homologous recombination deficiency (HRD) is a biomarker for impaired DNA repair proficiency and genomic instability, associated with sensitivity to DNA-damaging agents. MammaPrint (MP), a 70-gene assay, stratifies early breast cancer (EBC) by UltraLow, Low, High Risk 1 (H1) or High Risk 2 (H2) of recurrence. Compared to patients (pts) with H1 tumors, pts with H2 tumors derive greater benefit from anthracycline-based chemotherapy. Here we analyze HRD signatures to assess whether MP gene expression profiling may detect pathway activity in H2 tumors indicating DNA repair deficiency. Methods: We analyzed tumors from pts enrolled in the FLEX study who consented to full transcriptome and clinical data collection, with available MP and BluePrint (BP; Luminal or Basal) results (N=1298). HRD status assessed using a 228-gene signature was further refined into a 26-gene panel (Jacobson et al., 2023). The R-package Limma was used to preprocess gene expression data. For each gene, the median expression value of probes mapping to the gene was calculated. Differences in HRD scores were compared across MP and BP groups using a t-test. Results: Pts with HR+HER2- EBC HRD scores differed significantly by both MP and BP. Using the 228-gene HRD signature, H2 tumors were associated with higher HRD compared with H1 cancers (p<0.001). Luminal H2 tumors were also associated with higher HRD scores than Luminal H1 tumors (p<0.001). Basal tumors were associated with higher HRD compared with Luminal tumors within both H1 and H2 (Luminal H1 vs Basal H1 and Luminal H2 vs Basal H2; both p<0.001), and Basal H2 tumors had higher HRD scores than Basal H1 tumors (p<0.001). Similar patterns were observed within the 26-gene HRD panel. H2 tumors were associated with higher scores than MP H1 tumors (p<0.001), and Luminal H2 tumors were associated with higher scores than Luminal H1 tumors (p<0.001). Basal tumors were associated with higher HRD than Luminal tumors within both MP risk groups (Luminal H1 vs Basal H1, p=0.002; Luminal H2 vs Basal H2, p<0.001). Basal H2 tumors demonstrated numerically higher scores than Basal H1 tumors using the 26-gene panel, but did not reach statistical significance (p=0.062). Conclusions: In this real-world analysis, MP and BP identified differences in underlying HRD biology, with H2 tumors enriched for HRD and Luminal H1 tumors demonstrating relative homologous recombination proficiency. These findings may provide a biological rationale for the anthracycline chemotherapy and immunotherapy benefit observed in pts with H2 tumors and further evidence for MP as a tool for refined therapy selection. Additional research is warranted to examine MP as a biomarker for HRD-sensitive therapies such as PARP inhibitors and carboplatin. These results further highlight biological diversity within genomically high-risk tumors, uniquely detected by MP and BP. Clinical trial information: NCT03053193 .