alexa ERBB2 Transcriptome: From Biology To Genomics To Biology
ISSN: 1747-0862

Journal of Molecular and Genetic Medicine
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9th International Conference on Genomics & Pharmacogenomics
June 15-16, 2017 London, UK

Rakesh Kumar
George Washington University, USA
Posters & Accepted Abstracts: J Mol Genet Med
DOI: 10.4172/1747-0862-C1-016
Abstract
In recent years, Kumar’s lab has used high-throughput whole genome sequencing to gain genomic insights of the estrogen receptor positive, HER2 positive and triple-negative breast cancer (TNBC). Results from these, and those from other laboratories have provided unprecedented insights into the pathobiology of breast cancer as well an inter- and intra-tumor genomic heterogeneity due to differential expression of transcripts, splicing and promoter switching. However, these studies provided very little details of the influence of transcriptome as affected by the lost receptors. To address this research question, the laboratory decided to generate isogenic clones of TNBC breast cancer cells, MDA-MB231 and MDA-MB468, stably expressing ERBB2. These TNBC and ERBB2- positive non-TNBC clones also offered an opportunity to study the nature of ERBB2-transcriptome in an isogenic background. The clones were initially characterized through a microarray based platform as a part of Master’s dissertation project. This led to identification of ERBB2-modulated genes with some degree of overlap in gene expression profiles of ERBB2-positive human tumors through microarray analysis. To gain a deeper insight of ERBB2-transcriptome and to study the influence of ERBB2 on TNBC biology, the project was advanced to a Doctoral degree dissertation project and isogenic clones were subjected to RNA-sequencing analysis. A large volume of work over the years led to identification of differential expressed genes, alternative spliced transcripts, predicted transcription and splicing factors which we presumed to be responsible, at-least, in-part, for the noted transcriptome of breast cancer cells as affected by ERBB2. RNA-sequencing analysis of isogenic clones identified 933 ERBB2-regulated genes shared between two model systems. Mining of the RNA-seq data identified differentially spliced transcripts as affected by ERBB2 overexpression in two isogenic systems. Analysis of differential exon usage between TNBC and non-TNBC cells also identified 416 deregulated exons. Next analysis of the flanking regions of deregulated exons for splicing factors motifs recognized shared motifs for a set of splicing factors including, SF2/SRSF1. Because of the lab research interests, follow up studies independently verified that ERBB2-overexpression is accompanied by up-regulation of ABCC3 as well as SF2 proteins as new targets of ERBB2. This is particularly exciting as ABCC3 has been implicated in multidrug resistance associated with HER2 overexpression. On-going collaborative studies are designed to understand the role of ERBB2 in the regulation of ABCC3 and SF2, and potential cross-talk among all three molecules-all residing on the same chromosome 17.
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