Genome-Wide Transcriptome Analysis of Estrogen Receptor-Positive and Human Epithelial Growth Factor Receptor 2-Positive Breast Cancers by Ribonucleic Acid Sequencing.

OBJECTIVE

The aim is to identify complex pathogenesis of breast cancer subtypes and disclose the whole landscape of altered transcriptional activities in these cancers.

METHODS

We downloaded raw expression data from public database, and performed transcriptome analysis of 8 estrogen receptor-positive (ER+) breast cancer tissue samples, 8 human epithelial growth factor receptor 2-positive (HER2+) breast cancer tissue samples, and 3 normal breast tissues by identification, functional annotation, and prediction of upstream regulators and cell-surface biomarkers of differentially expressed genes (DEGs).

RESULTS

We identified over 5,000 DEGs in each of ER+ and HER2+ breast cancers compared to normal tissues. Functional enrichment analysis of shared DEGs indicated significant changes in the regulation of immune -systems in the 2 subtypes. We further identified 1,871 DEGs between the 2 subtypes and disclosed great tumor heterogeneity. We identified 533 shared upregulated genes and predicted 17 upstream transcription factors, as well as identified differentially expressed cell-surface biomarkers for distinguishing our ER+ and HER2+ breast cancers. Further analysis also highlighted the limitation of the usage of HER2 alone in breast cancer classification.

CONCLUSIONS

Our findings in ER+ and HER2+ breast cancers provided novel insights into heterogeneous transcriptional activities underlying complex mechanisms of oncogenesis in breast cancers.