The up-regulated pathways common to both cell lines include the metabolism-related such as steroids, pyruvate, glycolysis glutathione, or glycerolipid, and not directly related to the control of cellular proliferation.
In addition to genes with diverse functions that are not directly related to HH-dependent proliferation, up-regulated genes that influence the G1/S transition and subsequent cell cycle progression, and that are common to both cell lines, include CDKN1A, and the DNA-damage-inducible transcripts 3 and 4 (DDIT3 and DDIT4).
The derivation of EPT1 from EP156T was clearly verified by the similar expression levels of hTERT, the puromycin resistance and the very similar karyotypes of both cell lines, including a common derivative chromosome, der(20).
Other interesting expression changes that were common to both cell lines included the down-regulation of SCD.
Over-represented themes among the up-regulated genes in both cell lines included oncogenesis and cell cycle progression from G2 to M phase.
A number of genes involved in cell cycle regulation and proliferation were modulated in both cell lines, including CDKN1A and MAK.
Expression analysis showed an expected profile of gene expression in both cell lines, including known TGF-β targets (Additional file 7: Table S4, Additional file 8: Figure S4c for qRT-PCR validations).
A number of genes involved in xenobiotic metabolism and transcriptionally activated via the aryl hydrocarbon receptor (AHR) were up-regulated in both cell lines including NQO1, AKR1C3, AKR1C1, MGST1 and CPM.
Of these differentially expressed genes, 68 genes (39 62%) were commonly down- or up-regulated in both cell lines including RPS6KB1, ABL1, PPP1R12B, PRKCQ, and STK32B [see Additional File 1].
As2O3 markedly decreased protein levels of several EVI1 forms in both cell lines including MDS1/EVI1 (which consists of sequences derived from both EVI1 and the MDS1 gene, located telomeric to EVI1), 11 full-length EVI1, and EVI1Del190 515 (similar to the identified Δ324 isoform isolated from human endometrial carcinoma cells).
Expression changes observed in both cell lines included genes involved in xenobiotic metabolism (e.g., CYP1B1, NQO1, MGST1, AKR1C1, AKR1C3, CPM), cell cycle regulation (e.g., CDKN1A), apoptosis/anti-apoptosis (e.g., BAX, IER3), chromatin assembly (e.g., histone genes), and oxidative stress response (e.g., TXNRD1).
