PO-461 A transcriptomic and molecular approach to uncovering achaete-scute complex homolog 2 (ASCL2) as a potential novel driver gene in breast cancer

Abstract

IntroductionBreast cancer is highly heterogeneous and despite ongoing advancements in diagnostics and targeted therapeutics, incidence and mortality continues to rise. Thus, there is a need for greater characterisation of driver genes to understand their mechanistic role in breast carcinogenesis and their respective signalling pathways.With the advent of high-throughput technologies in transcriptomics, it is now possible to examine thousands of genes in parallel, generating an unprecedented amount of information. However, the task of synthesising the vast amount of ‘OMICs’ data produced and extracting the clinically significant results is a prominent challenge. The aim of this study was to use in silico and in vitro methods to identify and functionally investigate a novel genetic driver gene that plays a key role in breast carcinogenesis.Material and methodsGene expression profiles were obtained from public databases (Array Express and Gene Expression Omnibus) and subjected to an extreme variation analysis. Pathway analysis tools were used to identify a novel potential candidate gene for further investigation. Gene expression was assessed in vitro by quantitative real-time RT-PCR (qRT-PCR) to ensure concordance with transcriptomic data. siRNA knockdown was carried out in breast cancer cells, and sufficient knockdown was validated using qRT-PCR. Subsequently, to assess the effect of gene knockdown, assays were used to measure proliferation, wound-healing and apoptosis.Results and discussionsWe have established a basic, novel and user-friendly pipeline for in silico pathway analysis of transcriptomic data. This has allowed for selection and in vitro validation of a candidate driver gene, Achaete-scute complex homolog 2 (ASCL2), seen to be elevated in breast cancer. This gene is a transcription factor and regulator of stem cell identity, as well as a known Wnt-target gene. Functional work has suggested that ASCL2 may be involved in the migration of breast cancer cells, as upon siRNA knockdown of ASCL2, cellular migration was inhibited compared to negative controls. Additional analysis has revealed that ASCL2 knockdown alters the expression of various Wnt-associated genes, such as Survivin (BIRC5) and CD44.ConclusionThis work suggests that ASCL2, functioning within the Wnt signalling pathway, may be a potential novel driver of breast tumourigenesis. Investigation using both in vitro methods and data mining, will continue to further elucidate the functional role of ASCL2 in breast cancer tumourigenesis.