A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells

Abstract

It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells.We initially identified putative direct downstream targets of OCT4 by employing CHIP-on-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes.A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Over-expression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells.In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.

Growth and Differentiation Factor 3 Is Transcriptionally Regulated by OCT4 in Human Embryonic Carcinoma Cells

“…It was also reported that RNA interference-mediated silencing of OCT4 reduces GDF3 expression in NCCIT cells. 42) Therefore, these data suggest that OCT4 is involved in the regulation of GDF3 expression in NCCIT cells.…”

Oct-4+/Tenascin C+ neuroblastoma cells serve as progenitors of tumor-derived endothelial cells

“…The relations between Oct-4 + cells present at the latter site and those found in perivascular areas are so far unknown, but it is tempting to speculate that the perinecrotic Oct-4 + NB cells are more stem-like cells than the perivascular ones, which have moved to a less hypoxic area and may be prone to differentiation. On the other hand, perivascular Oct-4 + cells can migrate back to the perinecrotic putative niche and revert to a cancer-stem cell-like phenotype likely through epigenetic mechanisms [62]. In this respect, the possibility that TECs can de-differentiate back to progenitor state under the influence of stimuli like hypoxia cannot be excluded and warrants further investigation.…”

“…TNC expression, which is under the control of Oct-4 [62], is low in normal brain tissue and upregulated in several malignant brain tumors in association with increased vascularity, short time to relapse, and poor prognosis [26,63]. Little information was so far available on TNC expression in human NB.…”

CD44hiCD24lo mammosphere-forming cells from primary breast cancer display resistance to multiple chemotherapeutic drugs

“…Nanog, Oct4, Sox2 and Klf4 are the most widely studied transcription factors in maintaining self-renewal and pluripotency of embryonic stem cells with transcriptional regulation network (39)(40)(41)(42). The stem cell phenotypes of human embryonic cells are maintained by a self-stabilizing network of transcription factors, such as Nanog, Oct4 and Sox2 (43).…”

“…Klf4 has been demonstrated to be expressed in adult somatic tissues with a higher rate of cell proliferation (44) and is an upstream regulator of a feed-forward loop that contains Nanog, Oct4 and Sox2 (45,46). These factors are also demonstrated to play important roles in the tumorigenesis of prostate cancer (47), colorectal cancer (48) and bladder carcinomas (49) and correlate with poor prognosis (39)(40)(41)(42). In mammosphere-forming cells from the breast cancer, the expression level of Sox2 was low whereas the expression levels of Klf4, Nanog and Oct4 were detectable.…”