| Using an isogenic cell line based model system, we characterized a comparative transcriptomic profile of Triple Negative Breast Cancer (TNBC) and non--TNBC human epidermal growth factor receptor 2 positive (HER2+) breast cancer subtypes. We identified several differentially expressed genes between TNBC and HER2+ samples in MDA--MB--231 and MDA--MB--468 cell lines, including a shared signature of 49 and 933 candidates, using microarray and RNA-sequencing respectively. Some of the biological processes that were enriched among deregulated genes included cell cycle regulation, proliferation, apoptosis, DNA damage checkpoint regulation and adhesion. Additionally, we identified several transcription factors and splicing associated proteins with deregulated expression between the subtypes. Using qPCR, we validated expression deregulation of LUM, LIPG, CTSB, LOXL2, ABCC3, ALCAM, DHCR24, FASN, SCNN1A and ZNF91 in the isogenic cells. Interestingly, among the deregulated candidates were genes with similar trends in patient samples with analogous breast cancer subtypes or were associated to specific subtypes through previous studies.;Probing at the transcript level expression, we identified number of both cell line specific and common candidates that were deregulated between TNBC and HER2+ isogenic cells. Interestingly, a subset of these candidates didn't present the same trend of modulation at the gene expression levels and could be regulated either via alternative promoter usage or alternative splicing. Through isoform and exon-centric analyses, we identified 22 and 248 genes (416 exons), respectively, that presented similar trend of deregulation between TNBC and HER2+ subtypes in both cell lines and are potentially regulated via post-transcriptional splicing. Using qPCR we were able to validate the up-regulation (or higher inclusion level) of an alternate exonic region of ATF4 in HER2+ cells compared to TNBC. Furthermore, we identified several motifs to be enriched within 2kb upstream and downstream region of the commonly deregulated exons between the subtypes. Among them 12 were enriched in at least 5% of our targets and included a highly enriched motif similar to a binding site recognized by SRSF1 splicing factor.;Thus our results comprehensively identified genes that present deregulation in breast cancer transcriptomes in relation to HER2 expression. Some of these may represent key molecules in the biology of breast cancer subtypes that present variable levels of HER2 expression including TNBC or HER2+ subtypes. In depth studies are required for understanding the implication of differential expression of these molecules and their role in breast cancer. |
