3139 - Transcriptomic Analysis of a Tumor Microarray of Breast Cancers with BRCA1 vs. BRCA2 Mutations

Purpose/Objective(s): Mutations in BRCA1 and BRCA2 genes represent the most common hereditary changes that predispose to the development of breast cancer. These genes follow a dominant pattern of inheritance and act as tumor suppressors due to their crucial role in responding to and repairing DNA damage, particularly through homologous recombination. Despite both genes having critical roles in homologous recombination, BRCA1 mutations are associated with a higher likelihood of developing triple-negative breast cancer (TNBC), whereas BRCA2 tumors have a higher likelihood of forming hormone receptor-positive (HR+) breast cancers. Our goal was to compare the transcriptional profiles of breast tumors with BRCA1 versus BRCA2 mutations to better understand the differences in drivers of tumorigenesis.

Materials/Methods: Through the St. Louis Breast Tissue Registry, we accessed 100 de-identified, surgically resected breast tumors with BRCA mutations (40 BRCA1 and 60 BRCA2) stored in FFPE tissue blocks. Samples were processed for transcriptomic profiling and sequenced on an Illumina NovaSeq 6000. Gene counts were normalized using TMM factors in Edge R, excluding ribosomal genes and low-expressed genes. Differential expression analysis was performed in Limma, filtering results for genes with adjusted p-values <0.05. Subsequent functional analysis was performed using GSEA version 4.3.2.

Results: Gene set enrichment analysis (GSEA) demonstrated enrichment of transcripts involved in immune signaling and in E2F and MYC targets in BRCA1 mutated tumors, likely due to the predominance of highly proliferative TNBC within this subgroup. Conversely, BRCA2 mutated tumors had enrichment in transcripts upregulated in response to estrogen, a signature expected in HR+ tumors. We subsequently subdivided tumor samples by histologic subtypes and performed principal component analysis (PCA). GSEA comparing BRCA1 and BRCA2 HR+ tumors, still demonstrated upregulation of transcripts involved in estrogen response in BRCA2 tumors despite no difference in the number of patients who were pre- versus post-menopausal among the subgroups. BRCA1 and BRCA2 TNBCs clustered together on PCA, suggesting strong similarities between these two subgroups. Of all transcripts, only LGR5, a stem cell marker involved in WNT signaling and linked to poor-relapse free survival in TNBC, was significantly enriched in BRCA2 versus BRCA1 TNBC tumors.

Conclusion: Our findings suggest that histological subtype drives transcriptional differences more strongly than the difference between having a BRCA1 and BRCA2 mutation. Remarkably, BRCA1 and BRCA2 TNBC tumors are transcriptionally homogenous with only LGR5 demonstrating significant enrichment in BRCA2 TNBC tumors. Transcripts upregulated in response to estrogen response appear to be a hallmark of BRCA2 HR+ tumors even when comparing against HR+ BRCA1 tumors and after consideration of menopausal status.