Cancer Biology Program, Rajiv Gandhi Center of Biotechnology, Thiruvananthapuram 695014, India
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 a master 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 [3, 4]. 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at-least, in-part, for the noted transcriptome of breast cancer cells as affected by ERBB2 (Mudavari and Kumar, unpublished findings). 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 [3, 4]. 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 [3, 4]. Because of the lab research interests, follow up studies independently verified that ERBB2-overexpression is accompanied by upregulation 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. (Studies supported by NIH Grant CA090970 and Catharine Birch Williams & McCormick Chair Funds to RK; also presented and shared at other scientific meetings).
 Mudvari P. and Kumar, R. Search for a triple negative breast cancer (TNBC) signature. M.S. Dissertation Research, 2009-2010.
 Mudvari P. et al., Genomic insights into triple-negative and HER2-positive breast cancers using isogenic model systems. PLoS One 8(9):e74993, 2013.
 Mudvari P. and Kumar, R. Dissecting the role of HER2 in breast cancer transcriptome using an isogenic cell line model, Doctoral Dissertation Research, 2010-July 2014.
 Toi, M. et al. The Global Cancer Genomics Consortium’s Symposium: New Era of Molecular Medicine and Epigenetic Cancer Medicine - Cross Section of Genomics and Epigenetics. Genes & Cancer 6(1-2), 1-8, 2015.