Abstract 4829: Massively parallel RNA sequencing analysis of micropapillary carcinomas of the breast
Authors: Natrajan Rachael , Maher Christopher A. , Lambros Maryou BK , Pawar Vidya , Wetterskog Daniel , Marchio Caterina , Barbashina Violetta , Geyer Felipe C. , Fenwick Kerry , Kozarewa Iwanka , Mackay Alan , Hakas Jarle , Mitsopoulos Konstantinos , Hardisson David , Sapino Anna , Vincent-Salomon Anne , Lord Christopher J. , Chinniayan Arul , Ashworth Alan , Reis-Filho Jorge S. 
Published: June 2012

Abstract
Micropapillary carcinomas of the breast are a special type of breast cancer that account for up to 3% of breast cancers and which have an aggressive clinical behaviour. They are preferentially of intermediate to high histological grade and consistently express oestrogen receptor (ER). Previous genomic studies have demonstrated that micropapillary carcinomas are characterized by a constellation of genetic aberrations that is distinct from that of grade and ER-matched ductal carcinomas of the breast. Akin to sarcomas and leukaemias, it has recently been demonstrated that some special types of breast cancer (e.g. secretory and adenoid cystic carcinomas) are characterised by recurrent specific chromosomal translocations leading to the formation of oncogenic fusion genes. The aim of this study was to investigate whether micropapillary carcinomas of the breast harbour novel recurrent fusion genes. A series of six pure micropapillary carcinomas and two secretory carcinomas (positive controls harbouring the ETV6-NTRK3 translocation) were subjected to paired-end massively parallel RNA sequencing (RNA-seq). cDNA libraries were prepared according to standard mRNA prep Illumina protocols and run on the GAII sequencers (read length of each mate pair = 54bp; 2 lanes per sample). Data were aligned to the genome and transcriptome using Eland and mate-pairs supporting novel chimeras identified using previously validated pipelines. Fusion genes identified were validated using reverse transcription PCR (RT-PCR), Sanger sequencing and investigated in separate cohorts of micropapillary carcinomas (n=25) and other types of breast cancer (n=163) using fluorescence in situ hybridisation and RT-PCR. The sensitivity of the approach was validated by the analysis of the two secretory carcinomas, as the ETV6-NTRK3 reciprocal fusion gene was identified using our pipeline. Analysis of micropapillary carcinomas identified four novel intra-chromosomal fusion genes. Three of the fusions; SLC2A1-FAF1, ELMO2-RAE1, BCAS4-AURKA were present in a single tumour and spanned breakpoints of amplification. A fourth, TSPAN14-DYDC2, was a copy neutral event in a separate tumour sample. We also observed that the three fusions from a single patient were also present in the lymph node metastasis. All fusions were validated with RT-PCR, Sanger sequencing and/or FISH. One of the fusion genes was shown to be recurrent (index case and a mixed micropapillary carcinoma). Our results demonstrate that a proportion of micropapillary carcinomas of the breast harbour fusion transcripts. Further investigations are being undertaken to determine the functionality of these fusion genes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4829. doi:10.1158/1538-7445.AM2011-4829