Abstract A12: Analysis of tumor immunogenicity in germline BRCA1/2 mutation associated breast and ovarian cancers
Authors: Kraya Adam , Maxwell Kara N. , Wenz Brandon M. , Wubbenhorst Bradley , Sloover Daniel De , Lunceford Nicole , Barrett Amanda , Morrissette Jennifer D. , Feldman Michael , Vonderheide Robert H. , Domcheck Susan M. , Nathanson Katherine L. 
Published: March 2017

Abstract
Germline mutations in BRCA1 or BRCA 2 can lead to increased genomic instability and mutational burden in mutation-associated breast and ovarian cancer. Given the association of tumor neoepitope load and clinical response to immune checkpoint therapy, we used whole exome sequencing (WES) to predict missense mutational burden and potential neoepitope expression in 34 breast and 71 ovarian tumors with germline BRCA1/2 mutations (combining Penn and TCGA cohorts). Analysis of WES data found that tumors from patients with BRCA1/2 mutations had significantly higher mutational burden than non-BRCA1/2 tumors (p&lt;0.01). Based on a novel bioinformatics pipeline for human leukocyte antigen (HLA) genotyping and MHC class I neoantigen prediction, we found that neoantigen load (predicted IC50 &lt;500 nM) varied across patients (breast: mean - 147, std. dev. – 127; ovarian: mean – 126, std. dev. – 96). While higher neoantigen load promotes cytotoxic CD8+ T-cell responses in a number of cancers, we found among the BRCA1/2 subset that neoantigen load did not correlate with cytolytic signature, an RNA-based metric of anti-tumor immune response. From TCGA RNA-seq data, immune pathways (q&lt;0.01) including PD-1 signaling, reflective of counter-regulatory responses often observed in response to immune pressure, positively correlated with cytolytic signature. Neoantigen load, however, correlated only with GPCR signaling and extracellular matrix (ECM) proteins (q&lt;0.01). By contrast, the expression of genes involved in ECM and angiogenesis, which are involved in tumor immune escape and suppression of immune cell infiltration, negatively correlated with cytolytic signature (q&lt;0.01). Increased PDL1 and PDL2 (p&lt;0.05) expression associated with copy number loss in PTEN. These data were confirmed by tissue microarray analysis, which found that levels of T cell infiltration did not associate with neoantigen load, whereas PTEN loss was associated with decreased T cell infiltration (p&lt;0.05). Our work demonstrates that neoantigen load alone is not sufficient to induce T-cell infiltration and cytotoxicity in tumors from patients with BRCA1/2 mutations, but rather points to tumor intrinsic pathways involving PTEN copy alterations and a dense extracellular matrix as determinants of tumor immunity, both of which may lead to novel opportunities for combination immune therapy in these cancers.
Citation Format: Adam Kraya, Kara N. Maxwell, Brandon M. Wenz, Bradley Wubbenhorst, Daniel De Sloover, Nicole Lunceford, Amanda Barrett, Jennifer D. Morrissette, Michael Feldman, Robert H. Vonderheide, Susan M. Domcheck, Katherine L. Nathanson. Analysis of tumor immunogenicity in germline BRCA1/2 mutation associated breast and ovarian cancers. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A12.