MicroRNA sequencing in ARCaPE and ARCaPM cells

ARCaPE and ARCaPM human prostate cancer cell lines are derivatives of the ARCaP cell line, with epithelial and mesenchymal characteristics respectively. Hence, they are a model of epithelial-mesenchymal transition in prostate cancer. The objective of this study was to identify differentially expressed microRNAs in these cell lines, which may be responsible for the EMT phenotype. Unsupervised hierarchical clustering confirmed that microRNA expression profiles are distinctly different between the two cell lines, with 119 miRNAs significantly increased and 81 microRNAs significantly decreased in ARCaPM cells as compared to ARCaPE. Further analysis revealed that many of the differentially expressed microRNAs belong to only a few microRNA families/clusters. Unsurprisingly, microRNAs in these clusters are co-expressed due to common promoters, which are known to be regulated by Wnt signalling and BMP signalling(33) pathways. The microRNAs that were most strikingly overexpressed in ARCaPE cells belong to the miR-372 and miR-302 clusters, which have been previously shown to be key regulators of EMT in embryonic stem cells and induced pluripotent stem cells. 3 biological replicates each of ARCaPE and ARCaPM compared. Adaptor sequences are as follows: 3' adaptor: AGATCGGAAGAGCACACGTCT 5' adaptor: GTTCAGAGTTCTACAGTCCGACGATC