Abstract 3691: Analysis of germline BRCA1/2 mutation associated breast and ovarian tumors reveals distinct pathways of immunosuppression
Authors: Kraya Adam , Maxwell Kara N. , Wenz Brandon M. , Wubbenhorst Bradley , Lunceford Nicole , Barrett Amanda , Morrissette Jennifer J. , Feldman Michael D. , Domchek Susan M. , Vonderheide Robert H. , Nathanson Katherine L. 
Published: July 2017

Abstract
BRCA1 and BRCA2 are essential homologous recombination (HR) repair proteins; germline mutations confer elevated risk for breast and ovarian cancer. Defects in BRCA can lead to immune-related effects including depletion of peripheral T-cell pools and increased somatic mutational burden. We investigated the immunophenotypic properties of breast and ovarian cancers associated with germline BRCA1/2 mutations. We determined neoantigen load in 16 breast and 26 ovarian tumors with germline BRCA1/2 mutations and 50 non-BRCA tumors for each disease using whole exome sequencing data from the TCGA. Although neoantigen load (IC50 &lt;500 nM) was variable across tumors, it did not differ between BRCA1/2 mutant and non-BRCA tumors. Leveraging RNAseq data from the TCGA, we investigated immune-related transcriptomic features within each disease. Cytolytic index, a measure of PRF1 and GZMA expression, was higher in non-BRCA tumors than BRCA1/2 mutant for breast (p&lt;0.01) tumors and correlated more closely with neoantigen load than in non-BRCA tumors (Breast: BRCA r2=-0.15, non-BRCA r2=0.237). Class I HLA expression also correlated with cytolytic index (p&lt;0.05) in non-BRCA tumors but not BRCA1/2 mutation associated tumors for both breast and ovarian cancers, suggesting more robust antigen-driven adaptive immunity in non-BRCA tumors. HLA expression was significantly lower (p&lt;0.01) among BRCA mutant breast tumors, indicating immune escape by HLA down-regulation. We classified non-BRCA breast tumors by their level of HR deficiency (HRD score), as HRD by both BRCA and non-BRCA mediated mechanisms can lead to increased somatic mutational burden. Non-BRCA breast tumors irrespective of HRD score exhibited evidence of a more inflamed phenotype than BRCA1/2 mutant tumors, indicated by higher inferred immune cell infiltration, immune checkpoint expression, and chemokine expression (all p&lt;0.01). To investigate potential mechanisms of immune escape in BRCA1/2 vs non-BRCA tumors, we compared canonical gene sets (MsigDb) across the two cohorts. Expression of extracellular matrix (ECM) proteins was higher in BRCA1/2 breast and ovarian tumors (q&lt;0.02), suggesting that BRCA1/2 tumors may exclude immune cells via a dense ECM as observed for colorectal cancer and melanoma. Among Penn BRCA1/2 tumors (19 breast, 20 ovarian), neoantigen load did not differ from TCGA BRCA1/2 tumors. We directly measured immune cell infiltration via tumor immunohistochemistry in 12 breast and 14 ovarian Penn BRCA1/2 tumors. We found that CD3+ and CD8+ T cell infiltration was significantly lower in BRCA1/2 tumors with PTEN deletion (p&lt;0.05), a known correlate of ECM remodeling in breast and ovarian cancer. Our work provides early evidence that BRCA1/2 breast and ovarian tumors mitigate intratumoral adaptive immunity by T-cell exclusion, so that despite higher mutational burden, they may not respond to checkpoint blockade.
Citation Format: Adam Kraya, Kara N. Maxwell, Brandon M. Wenz, Bradley Wubbenhorst, Nicole Lunceford, Amanda Barrett, Jennifer J. Morrissette, Michael D. Feldman, Susan M. Domchek, Robert H. Vonderheide, Katherine L. Nathanson. Analysis of germline BRCA1/2 mutation associated breast and ovarian tumors reveals distinct pathways of immunosuppression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3691. doi:10.1158/1538-7445.AM2017-3691