Gene expression profiles of C57BL/6 murine hepatocytes, murine embryonic stem cells (D3) and murine hepatocyte-reprogrammed induced Tissue Stem cells (iTSCs)
ABSTRACT: We have recently developed a new generation of induced stem cells that we have called “induced Tissue Stem cells” (iTSCs) which are generated by using low doses of non-integrative vectors encoding several embryonic reprogramming factors permitting to de-differentiate the cells without passing through a pluripotent state. ITSCs are thus multipotent stem cells rather than pluripotent stem cells. Using this technology we have produced endodermic iTSCs by de-differentiation of murine hepatocytes and shown that they are able to differentiate in vitro and in vivo into tissues restricted to endodermic layers. We report the gene expression profiles of two subclones of murine hepatocytes-reprogrammed iTSCs and of hepatocytes parental cells and murine embryonic stem cells (D3). Adherent liver cultures were established from 6 to 8 week old mice and one million of hepatocytes were infected with adenovirus encoding Oct4, Sox2, cMyc and Klf4. After 5 days of infections, cells were manually pooled and plated on mitomycin C-arrested Mouse Embryonic fibroblasts (MEF) in daily changed ES cell culture medium. In this manner, more than 50 colonies have been isolated and for two of them (clones 3 and 6), single cells were added in a 96-well cell culture plate for subcloning. Two subclones ; 6.6 and 3.8 were evaluated by microarray. The transcriptome was analyzed with Affymetrix microarray technology (GeneChip ® Mouse Gene 2.0 ST Array) and the data were normalized by the RMA method and annotated with Partek GS and R Bioconductor softwares.
Project description:Chavez2009 - a core regulatory network of OCT4 in human embryonic stem cells
A core OCT4-regulated network has been identified as a test case, to analyase stem cell characteristics and cellular differentiation.
This model is described in the article:
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R
BMC Genomics, 2009, 10:314
BACKGROUND: The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.
RESULTS: We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.
CONCLUSION: Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.
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Project description:Recent advances towards the efficient and reproducible differentiation of stem cells into hepatocyte-like cells (HLC) have created potential opportunities in clinical transplantation. For this approach to be successfully translated, however, it is necessary to understand the immune response to stem cell-derived cellular products. Whereas both embryonic stem cells and induced pluripotent stem cells have been utilized as cellular sources for differentiation and lineage specification, their relative ability to be recognized by immune effector cells is unclear. Here we determine the expression of immune recognition molecules on HLC generated from murine embryonic stem cells and induced pluripotent stem cells, compared to adult hepatocytes, and we evaluate the impact on recognition by NK cells. We report that HLC lack MHC class I expression, and that embryonic stem cell derived-HLC have higher expression of the NK cell activating ligands Rae1, H60, and Mult1 than induced pluripotent stem cell-derived HLC and adult hepatocytes. Moreover, the lack of MHC class I render embryonic stem cell derived-HLC, and induced pluripotent stem cell derived-HLC, susceptible to killing by syngeneic and allogeneic NK cells. Both embryonic stem cell derived-HLC, and induced pluripotent stem cell derived-HLC, are killed by NK cells at higher levels than adult hepatocytes. Finally, we demonstrate that the NK cell activation receptor, NKG2D, plays a key role in NK cell killing of embryonic stem cell derived-HLC, but not induced pluripotent stem cell-derived HLC. Hepatocytes were isolated from FVB/NJ mice and C57Bl/6 mice using a modification of the Seglen’s perfusion technique. Overall design: Undifferentiated embryonic stem cells ESC (n=4), Adult Hepatocytes (AD-Hep) (n = 3), mESC differentiated into hepatocyte like cells (n =3).
Project description:There are a total of four samples each for this analysis. Each sample consists of the cells grown on three 10 cm culture plates. Each plate should have 2x106 cells for a total of 6x106 cells per sample when all three plates are combined. The first sample is undifferentiated human embryonic stem cells, the second sample is human glutamatergic neurons derived from those human embryonic stem cells, the third sample is undifferentiated human induced pluripotent stem cells and the fourth sample is human glutamatergic neurons derived from those human induced pluripotent stem cells.
Project description:Reprogrammed somatic cells offer a valuable source of pluripotent cells that have the potential to differentiate into many cells types and provide a new tool for regenerative medicine. In the present study we differentiated induced pluripotent stem cells (iPS cells) into hepatic cells. We first showed that mouse iPS cells could from a complete liver in mouse embryo (E14.5) including hepatocytes, endothelial cells, sinusoidal cells and resident macrophages. We then designed a highly efficient hepatocyte differentiation protocol using defined factors on human embryonic stem cells (ES cells). This protocol was found to generate more than 80% albumin expressing cells that show hepatic functions and express most of liver genes as shown by microarray analyses. Similar results were obtained when human iPS cells were induced to differentiate following the same procedure. Overall design: Total RNA was harvested from the following sources and used for Affymetrix array analysis following manufacturer defined protocols: 1) human foreskin fibroblasts, ATCC cell line CRL2097, 3 independent cultures 2) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent undifferentiated cultures 3) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol 4) WAO9 human embryonic stem cells, 3 independent undifferentiated cultures 5) WAO9 human embryonic stem cells, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol
Project description:Reprogrammed somatic cells offer a valuable source of pluripotent cells that have the potential to differentiate into many cells types and provide a new tool for regenerative medicine. In the present study we differentiated induced pluripotent stem cells (iPS cells) into hepatic cells. We first showed that mouse iPS cells could from a complete liver in mouse embryo (E14.5) including hepatocytes, endothelial cells, sinusoidal cells and resident macrophages. We then designed a highly efficient hepatocyte differentiation protocol using defined factors on human embryonic stem cells (ES cells). This protocol was found to generate more than 80% albumin expressing cells that show hepatic functions and express most of liver genes as shown by microarray analyses. Similar results were obtained when human iPS cells were induced to differentiate following the same procedure. Experiment Overall Design: Total RNA was harvested from the following sources and used for Affymetrix array analysis following manufacturer defined protocols: Experiment Overall Design: 1) human foreskin fibroblasts, ATCC cell line CRL2097, 3 independent cultures Experiment Overall Design: 2) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent undifferentiated cultures Experiment Overall Design: 3) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol Experiment Overall Design: 4) WAO9 human embryonic stem cells, 3 independent undifferentiated cultures Experiment Overall Design: 5) WAO9 human embryonic stem cells, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol. <br><br>This experiment was reloaded in November 2010 after additional curation
Project description:Germline cell-derived pluripotent stem cells (GPSCs) are similar to embryonic stem (ES) cells in that they can proliferate intensively and differentiate into a variety of cell types, including cardiomyocytes and neurons. In this report, mouse GPSCs were induced to differentiate into hepatocytes with very high efficiency, and demonstrated, for the first time, to be functional. These hepatocytes were characterised at cellular and molecular levels. The GPSC-derived hepatocytes not only expressed hepatic markers, but were also metabolically active as shown by albumin and haptoglobin secretion, urea synthesis, glycogen storage and indocyanine green uptake. Previous studies have revealed some inherent differences in gene expression between undifferentiated mouse ES cells and GPSCs. We wanted to investigate whether this difference may impact on the hepatocyte differentiation capacity of the GPSCs. Large-scale gene expression profiling revealed a strong similarity between GPSC and ES cells at different stages of induced hepatic differentiation. Moreover, Pearson correlation analysis of the microarray datasets revealed that, at late hepatic differentiation stages, the in vitro-derived cells were closer to fetal mouse primary hepatocytes. Thus, adult GPSCs offer great potential for cell ment therapy for a wide variety of liver diseases. Overall design: Mouse ES cells and GPSCs at various times of hepatocyte differentiation, compared to embryonal (E16) and postnatal (PN1) mouse primary hepatocytes. The supplementary file 'GSE19044_non-normalized.txt' contains non-normalized data for Samples GSM471318-GSM471359.
Project description:Embryonic stem (ES) cells and trophoblast stem (TS) cells are both derived from early embryos, yet these cells have distinct differentiation properties. ES cells can differentiate into all three germ layer cell types, whereas TS cells can only differentiate into placental cells. It has not been determined whether TS cells can be converted into ES-like pluripotent stem (PS) cells. Here we report that overexpression of a single transcription factor, Oct4, in TS cells is sufficient to convert TS cells into a pluripotent state. These Oct4 induced pluripotent stem (OiPS) cells have the epigenetic characteristics of ES cells, including X chromosome reactivation and elevated H3K27 me3 modifications. The gene expression profile of OiPS cells and ES cells was very similar. Moreover, OiPS cells can differentiate into the three germ layer cell types in vitro and in vivo. More importantly, chimeric mice with germline transmission could be efficiently produced from OiPS cells. To our knowledge, this is the first evidence showing that only one single transcription factor could convert the non-embryonic TS cells into pluripotent stem cells with pluripotency. Gene expression profile of iPS cells and trophoblast stem cells were generated by Affymetrix Mouse Gene 1.0 ST Array. The Gene expression profile of ES cell R1 in GSE17004 was used as control. Three biological repeats were included for each line.