Abstract 5076: Integrative genomic and transcriptomic analysis of metaplastic carcinomas of the breast
Authors: Mackay Alan G. , Natrajan Rachael , Maher Christopher , Lambros Maryou , Weigelt Britta , Nava-Rodrigues Daniel , Wilkerson Paul , CampionFlora Adriana , Kozarewa Iwanka , Fenwick Kerry , Campbell James , Chen Lina , Lord Christopher J. , Gauthier Arnaud , Pawar Vidya , Mariani Odette , Vincent-Salomon Anne , Reis-Filho Jorge 
Published: August 2012

Abstract
Background Metaplastic breast carcinomas (MBCs) are characterised by neoplastic cells that display differentiation towards squamous epithelium or mesenchymal elements. These tumours are of triple-negative phenotype and have an aggressive clinical behaviour. The aims of this study were to characterise a series of MBCs at the genomic and transcriptomic level to identify potential drivers of this breast cancer special type. Design Twenty-five frozen MBCs and two MBC cell lines (HCC1569 and Hs578T) were subjected to genotyping (Affymetrix SNP6), 32K BAC microarray comparative genomic hybridisation (aCGH), microarray gene expression profiling (Illumina HT12) and massively parallel mRNA-sequencing (RNA-seq, Illumina GAII). Novel chimaeric transcripts were identified using Chimerascan v0.4.3. 10 cases with available germline DNA were subjected to targeted exomic sequencing (Illumina HiSeq). Somatic variants were called using the Genome Analysis Toolkit (GATK) using best practice guidelines. Fusion genes and mutations were validated using (RT)-PCR and Sanger sequencing, respectively. Results MBCs displayed a complex pattern of gene copy number aberrations, with multiple copy number gains and losses throughout the genome. Recurrent amplifications/ high-level gains at 3q25.2-q27.1, 8p11.21-q24.3 and 12p13.33 and recurrent homozygous deletions on 9p21.3 (CDKN2A/2B) and 10q23.31 (PTEN) were found. Unsupervised clustering of gene expression showed that MBCs associated with chondroid differentiation separated into a distinct cluster, whereas MBC's with spindle and epithelial morphology did not cluster apart. Integration of SNP6 copy number and gene expression data identified 198 genes overexpressed when amplified. RNA-seq revealed 1025 unique nominated fusion gene events (43-119 per tumour), including 254 fusions predicted to be in-frame. These included a promoter swap involving TBXLR1 fused to PIK3CA and a recurrent promoter swap involving NF1 that was also seen in the MBC cell line Hs578T. Targeted exome sequencing identified 402 somatic coding variants (12-96 per tumour), including recurrent mutations in TP53 (5/10) and genes involved in PI3K signaling. Conclusion Our results demonstrate that MBCs have complex genomes and are heterogeneous at both the genomic and transcriptomic levels. TP53, CDKN2A/2B and PTEN mutations and/ or homozygous deletions, and activation of the PI3K pathway are recurrent events in these tumours.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5076. doi:1538-7445.AM2012-5076