Genomic and Immune Characterization of Triple-Negative Breast Cancer Brain Metastases

Abstract Introduction: Triple negative breast cancer (TNBC) is an aggressive subset of BC with high metastatic potential. Once metastatic, half of patients (pts) with TNBC will develop brain metastases (BM), commonly with progressive extracranial disease. While TNBC BM are routinely treated with radiotherapy, survival is generally less than one year. There are no approved systemic therapies to treat TNBC BM. Both the blood brain barrier and paucity of data on the biologic underpinnings and immune response of BCBM contribute to inadequate therapies for this disease. We sought to characterize the genomic and immune landscape of TNBC BM to foster the development of effective brain permeable anti-cancer agents. Experimental Procedures: A clinically-annotated BCBM biobank of archival brain metastases and primary BC that eventually metastasize to the brain was created under IRB approval (LCCC1419). DNA (tumor/normal) and RNA (tumor only) was extracted. Following library preparation, whole exome (WES) and RNA sequencing (RNASeq) was performed. Common mutations were determined from WES as those co-identified by two variant callers (Strelka, Cadabra), while immune gene signature expression, molecular subtype identification, and B and T cell receptor repertoires were inferred from RNAseq data. Results: Of the 26 enrolled pts, median age at BCBM diagnosis was 52 years (35-72); 23% were African American and 57% Caucasian. Additional non-brain metastatic sites included bone (23%), liver (20%), and lung (35%); 23% had a solitary BCBM. 35% of pts received chemotherapy after BCBM diagnosis, while 92% received radiation to the brain (21% WBRT, 5% SRS, 25% SRS plus WBRT and resection). The median survival from BCBM was 6 months. 40 (93%) of the tissues (21 primaries, 22 BCBM) were characterized as basal-like by PAM50; 1 HER2-enriched and 2 Luminal A. 34 genes were mutated in ≥20% of BCBMs, while only 8 were mutated in at least 25% of primaries. Commonly mutated BCBM genes included TP53, ATM and MYH9; in primaries only TP53. Many immune gene signatures were lower in BCBM compared to primary BC including B cell, dendritic cell, regulatory T cell, and IgG cluster (p<0.05). A signature of responsiveness to PD1 inhibition in melanoma was higher in BCBM compared with primary BC (p<0.05). Globally, the BCBM T cell receptor repertoires showed higher diversity (TCR evenness, p=0.006) and lower read count (TCR total read count, p=0.0267) compared to primary BC. Conclusions: TNBC BM compared to primary BC that metastasize to the brain had more significantly mutated genes, lower immune gene signature expression, higher PD1 inhibition response signature expression, and T cell receptor repertoire features less characteristic of an active antigen-specific response. Given that checkpoint inhibitors are showing response in non-BCBM (i.e. lung and melanoma), these findings indicate that immunotherapy to treat patients with TNBC BM is worthy of exploration. Citation Format: Benjamin G. Vincent, Maria Sambade, Shengjie Chai, Marni B. Siegel, Luz Cuaboy, Alan Hoyle, Joel Parker, Charles M. Perou, Carey K. Anders. Genomic and immune characterization of triple-negative breast cancer brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4055.