Abstract PD4-4: Whole exome sequencing of aggressive rare breast cancers histologic subtypes reveals novel pathway for breast cancer progression
Authors: Dieci MV , Lefebvre C , Viehl P , Mathieu M-C , Laporte M , Scott V , Marty V , Drusch F , Guarneri V , Conte P , Lacroix L , Delaloge S , André F 
Published: August 2014

Abstract
Background: Rare cancers sometimes present clonal evolution. Genomic characterisation of these rare entities could lead to identify new genes involved in the progression of more frequent cancers. In the present study, we have performed whole exome sequencing of three rare and aggressive histological subtypes in order to identify new targets that could subsequently be validated in common breast cancers.
Methods: Whole exome sequencing was applied in ten pleiomorphic lobular carcinoma, seven micropapillary BC and eight metaplastic BC. Each cancer sample was matched with normal DNA from the same patient. Overall 50 samples were therefore sequenced. Tumor samples were selected to present &gt;30% cancer cells. Histological diagnosis was confirmed by a BC pathologist. Whole exome sequencing (WES) was performed by BGI (Bejing Genomic Institute, Hong-Kong, China) using the Illumina Hiseq2000 platform (90bp paired-end reads, depth ≥80x). Genes recurrently mutated (with somatic mutations in &gt;2 cases) were selected for validation. The validation by IonTorrent target sequencing was performed on additional formalin-fixed paraffin-embedded (FFPE) tumor samples (&gt;30% of tumor cells).
Results: Complete results of both WES and targeted resequencing validation are available for pleiomorphic lobular carcinoma. Nine of the 10 DNA pairs were eligible for WES. Genes already implicated in BC were significantly mutated: PIK3CA (3/9), TP53 (3/9) and CDH1 (3/9). Novel significantly mutated genes were identified: PYGM (2/9), EMR1 (2/9), ALDH1A2 (2/9), and DCLK1 (2/9). The validation using target gene sequencing was performed on the same 9 cases and on 19 additional confirmed pleiomorphic lobular BC cases (n = 28). For 8 out of the 9 cases with WES data, the results were reproducible on FFPE samples. Validation set confirmed recurrent mutations on PYGM genes (25%). PYGM is involved in glycogen metabolism. Further analyses on gene expression array revealed that PYGM is downregulated in most of the common BC samples, as compared to normal tissue, suggesting a role for this gene in the metabolism of common BC.
WES data are available for micropapillary and metaplastic BC. HSPA8 (coding for a Heat shock protein) was found mutated in 3/7 of micropapillary samples. Validation on additional FFPE samples is ongoing and will be presented. WES of metaplastic BC revealed a high frequency of TP53 and PIK3CA mutations (50% in both cases).
Conclusions: A novel mutated gene was identified in PLBC. PYGM is a gene involved in glycogen metabolism and was found downregulated in most of the common breast cancer. WES of micropapillary cancers suggests mutations on HSPA8, a gene encoding for a chaperon protein. Validation is ongoing. Deeper sequencing is ongoing for metaplastic BC that may help identifying new mutated genes in this multiclonal disease. Results will be presented.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD4-4.