Abstract 3885: Mutational landscape and copy number alterations of mucinous breast carcinoma

Abstract

Abstract Background: Mucinous breast carcinoma (MBC) is a special histologic type of breast cancer, comprising 2% of invasive breast carcinomas. These tumors have a distinctive histologic appearance, characterized by clusters of tumor cells floating in large amounts of extracellular mucin. MBCs are preferentially of low histologic grade and almost invariably express estrogen receptor (ER) and lack HER2 overexpression. MBCs, however, are likely to be unrelated to other forms of low-grade ER-positive/ HER-negative breast cancers, given that the hallmark features of low-grade ER-positive invasive carcinoma of no special type (IC-NST), namely 1q gains and 16q losses, are not found in MBCs. Here we sought to characterize the mutational landscape and copy number alterations (CNA) of MBCs by high-depth whole exome sequencing analysis. Material and Methods: Eighteen MBCs, of which 6 were mucinous A (paucicellular), 7 were mucinous B (hypercellular), and 5 were of mixed phenotype (mucinous admixed with adjacent IC-NST), were retrieved from the authors’ institutions. Sections from frozen blocks were microdissected to ensure a tumor cell content >60%. DNA samples extracted from tumor and matched normal tissues were subjected to high-depth (250x) whole exome sequencing. Single nucleotide variants (SNVs) were called using MuTect, and somatic insertions and deletions (indels) were called using Strelka and Varscan2. Potentially pathogenic mutations were defined using computational algorithms including PolyPhen-2, MutationTaster, Mutation Assessor, CHASM and FATHMM. Somatic CNAs were determined using VarScan2. Selected SNVs and indels were validated with Sanger sequencing. Results: A median of 30 (range 13-65) SNVs and indels were identified per MBC. The only significantly mutated gene as defined by MutSigCV (q<0.1) was GATA3, which was mutated in 39% of cases. The repertoire of somatic mutations found in MBCs was distinct from that of IC-NSTs of luminal molecular subtype analyzed in The Cancer Genome Atlas project. In fact, MBCs were found to harbor mutations in TP53 (0%) and PIK3CA (5.5%) at significantly lower frequencies than IC-NSTs of luminal subtype (19% and 40.6%, respectively; p<0.001). A comparison between mucinous subtypes (A and B) did not show any significant differences in terms of mutations and/ or CNAs, whereas mixed MBC/IC-NSTs were found to have more complex genomes. In mixed cases, the mucinous and adjacent IC-NST components shared mutations and CNAs; however, also CNAs and mutations restricted to one of the components were found. CNA analysis confirmed our previous observations that MBCs, contrary of low-grade ER-positive IC-NSTs, lack concurrent copy number gains of 1q and 16p and losses of 16q and 22q. Conclusions: The repertoire of somatic mutations and CNAs found in MBCs is distinct from that of luminal IC-NSTs, suggesting that MBCs likely evolve through genetic pathways distinct from those of low-grade ER-positive IC-NSTs. Citation Format: Salvatore Piscuoglio, Charlotte Ng, Carey A. Eberle, Elena Guerini-Rocco, Caterina Marchio, Odette Mariani, Anne Vincent-Salomon, Britta Weigelt, Jorge S. Reis-Filho. Mutational landscape and copy number alterations of mucinous breast carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3885. doi:10.1158/1538-7445.AM2015-3885