Abstract P2-05-06: Identification of specific gene signatures and alternative splice variants using exon array in Inflammatory breast Cancer
Authors: Lerebours Florence , Vacher Sophie , Le Cann Marie , Rondeau Sophie , Gentien David , Van Laere Steven , Bertucci François , de la Grange Pierre , Bieche Ivan 
Published: May 2015

Abstract
Inflammatory Breast Cancer (IBC) is a rare form of breast cancer with a particular phenotype and aggressiveness. Although significant progress has been made in the management of IBC, the prognosis remains poor. Intensive research on IBC has allowed identification of several candidate genes and pathways, but molecular findings unique to IBC have yet to be identified to improve treatment and survival. Transcriptomic studies have revealed a marked heterogeneity of IBC with limited gene overlap between studies, preventing the identification of a sensitive and specific signature in IBC.
In order to detect both gene expression levels and alternate RNA splice isoforms, we chose to perform splice-sensitive array profiling using Affymetrix Exon Array in a well-defined series of 33 IBC (core biopsies from previously untreated T4d carcinomas) compared with 28 stage I to non-inflammatory stage III breast cancers.
Gene expression analysis allowed the identification of classical molecular subtypes in both IBC and non-IBC, with overrepresentation of basal-like (17/33 vs 9/28) but no luminal A in IBC (vs 11/28). Based on Fold-Change (FC) &gt; 1.5 and p-value &lt; 0.05, 495 genes were significantly dysregulated between IBC and non-IBC, including in particular up-regulated hemoglobin genes and down-regulated ER-related genes in IBC compared to non-IBC. Most activated pathways were hematopoeitic cell lineage, cytokine-cytokine receptor interaction, chemokine signalling pathway and complement and coagulation cascade. We defined a 21-gene signature discriminating IBC from non-IBC with 8% error rate. To get rid of genes associated with molecular subtypes like ER-related genes, an analysis restricted to basal-like BC (17 IBC compared to 9 non-IBC) was performed allowing the definition of a 29-gene signature discriminating the whole groups of IBC from non-IBC with 3.3% error rate. Validation of this signature in the gene expression datasets from the World IBC Consortium will be presented.
Specific exon expression analysis revealed that when based on FC splicing-index and p-value, 266 exons representing 177 distinct genes were differentially regulated between IBC and non-IBC. After manually curation of results, 13 splice events representing 12 distinct genes were retained as good candidates for alternative splicing in IBC (EVL, RPL10, MYH10, HSPA8, DOCK7, DIDO1, RPL4, TRAK1, RGS1, LMO4, SMARCA4, ZNF337).
To confirm gene-signatures specific to IBC, altered pathways and major splice variants, we are performing a validation study using quantitative RT-PCR in the screening set (n=33) and in an independent series of 140 IBC compared to 200 non-stage-matched non-IBC. Finally the most dysregulated genes will also be studied at the protein level using immunohistochemistry.
Citation Format: Florence Lerebours, Sophie Vacher, Marie Le Cann, Sophie Rondeau, David Gentien, Steven Van Laere, François Bertucci, Pierre de la Grange, Ivan Bieche. Identification of specific gene signatures and alternative splice variants using exon array in Inflammatory breast Cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-06.