Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing

BACKGROUND: EMT is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore it has been implicated in physiological processes like wound healing, and pathological conditions e.g. organ fibrosis and cancer. In late stage tumorigenesis, cells that underwent EMT are motile and may invade other parts of the body to form distant metastases. Madin-Darby Canine Kidney (MDCK) cells are widely used as a model to study epithelial polarity and EMT.OBSERVATIONS: We performed deep sequencing to build the transcriptome and miRNAome of epithelial and mesenchymal states in MDCK cells. With RNA-Seq, half of the genes known in the dog genome were detected, of which one third were differentially expressed during the process of EMT. Novel differentially regulated genes include interferon-stimulated genes and those involved in slit and netrin signaling. Gene set enrichment analysis of differentially expressed genes revealed TGFß1 as a central signaling factor. With miRNA-Seq, miRNAs that are known to be important regulators of EMT were detected and new candidates were predicted. miRNA target prediction combined with pathway analysis allowed us to identify additional pathways: Jak-Stat signaling and Pancreatic cancer. We also identified clusters (based on genomic coordinates) and families (based on sequence similarity) of significantly differentially expressed miRNAs, of which some were regulated by TGFß. Additionally we identified 25 completely novel miRNAs with a stable hairpin structure. One of the mesenchymal specific novel miRNAs was predicted to target genes involved in cell division, growth factor activity, and cellular adhesion complexes.CONCLUSIONS: We present the transcriptome and miRNAome of EMT in MDCK cells. We also investigated gene signatures and the interplay between miRNA and mRNA expression levels. Thereby, we increase the knowledge on the transcriptional landscape of mRNAs and miRNAs during the process of EMT.