ABSTRACT: To understand how CK2M-NM-2 silencing promotes a mesenchymal phenotype in human epithelial cells, like TGFM-NM-2 does, we have employed whole genome microarray expression profiling as a discovery platform to compare genes regulated in CK2M-NM-2-depleted cells and in TGFM-NM-2-treated cells. To do so, we began by deriving individual gene expression signatures of WT-, TGFM-NM-2-treated, CK2M-NM-2-depleted or CK2M-NM-2-depleted and rescued with chicken CK2M-NM-2, whose expression is not affected by the shRNA in MCF10A cells, and cataloguing genes exhibiting at least a 1.5-fold up- or down-regulation under each experimental condition. We observed that EMT triggered by TGFM-NM-21 or CK2M-NM-2-depletion induced an overlapping set of changes in gene expression. Of ~25,000 unique genes tested, we found ~1,200 genes whose expression was significantly modulated in TGFM-NM-21-treated or CK2M-NM-2-depleted cells as compared to Mock-cells. Of the 439 genes down-regulated in TGFM-NM-21-treated cells, 74 genes (17%) were also repressed in CK2M-NM-2-depleted MCF10A cells and 45 genes (10%) were commonly up-regulated. As expected, among commonly regulated genes, several mesenchymal genes (CDH2, FN1, MYL9, VIM) were upregulated, whereas epithelial genes such as CDH1, CDH3, CLDN1, CLDN7, OCLN, KRT5, KRT6B, COL2A1 and MUC1, were inversely turned down. The expression of the EMT-inducing transcription factors, Snail and Zeb, was also significantly up-regulated in accordance with the repression of their known target genes. While showing similar phenotypes, the genetic program of TGFM-NM-21-treated or CK2M-NM-2-depleted MCF10A cells also exhibited distinct features. These results highlight that in addition to TGFM-NM-21-regulated genes, CK2M-NM-2-depletion may affect alternative pathways. The microarray analysis was performed with RNAs isolated from parental MCF10A cells and the following MCF10A-derived cells: M-NM-^TCK2M-NM-2- and TGFM-NM-21-treated cells (2ng/ml for 72h) and each from two independent cell cultures (duplicates).
