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Combined microarray analysis uncovers self-renewal related signaling in mouse embryonic stem cells.

Zhu H, Yang H, Owen MR - Syst Synth Biol (2008)

Bottom Line: Albeit the expression of individual genes in signaling pathways was not noticeably different between cells cultivated with and without LIF, at gene-set level the expression of ERK/MAPK (but not JAK/STAT) and cell cycle related genes was found significantly enriched in cells cultivated with LIF.When data at the first 7 time points were compared with data at the last 4 time points, the expression of several cell cycle related gene sets was apparently enriched in all three cell lines, indicating the active cell proliferation in the first 2 days.When that mechanism weakens, cell differentiation begins.

View Article: PubMed Central - PubMed

Affiliation: Center for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK, Hao.Zhu@nottingham.ac.uk.

ABSTRACT
Due to the limited understanding of self-renewal and pluripotency related signaling in stem cells, extracting information from genome-wide expression data is not only important but also challenging. With the combined use of two methods, we analyzed a set of microarray data at 11 time points from three mouse embryonic stem cell lines cultivated with and without leukemia inhibitory factor (LIF) for 14 days. Albeit the expression of individual genes in signaling pathways was not noticeably different between cells cultivated with and without LIF, at gene-set level the expression of ERK/MAPK (but not JAK/STAT) and cell cycle related genes was found significantly enriched in cells cultivated with LIF. This indicates that the Ras/Raf/ERK pathway, in addition to JAK/STAT, may also be a key player to carry on external LIF signal into mouse embryonic stem cells to promote self-renewal. When data at the first 7 time points were compared with data at the last 4 time points, the expression of several cell cycle related gene sets was apparently enriched in all three cell lines, indicating the active cell proliferation in the first 2 days. Compared with the slight decay of Oct4/Nanog/Sox2 during the 14 days, the expression of cell differentiation genes such as Gata4/6 underwent a drastic increase, which indicates that the upregulated expression of cell differentiation genes may better reflect the loss of self renewal than the down regulated expression of the stemness indicators Oct4, Sox2 and Nanog. Apart from differential expression and gene set enrichment analyses, a clustering algorithm was also used to classify genes into co-expression clusters. The possible regulation of two clusters, whose expression was most changed during cell culture from very low to very high, was explored. The drastic changes of these genes, including Slc39a8 which was a potential indicator of cell differentiation, in contrast the slight changes of self-renewal genes, imply that differentiation may be the default fate of stem cells and self-renewal may rely on a maintenance mechanism. When that mechanism weakens, cell differentiation begins.

No MeSH data available.


Related in: MedlinePlus

The expression of Pou5f1, Nanog, Sox2, JAK1/2/3 and STAT3/4 (against the control) in the 14 days in three cell lines. Only Stat4 showed a clear down regulation
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Fig1: The expression of Pou5f1, Nanog, Sox2, JAK1/2/3 and STAT3/4 (against the control) in the 14 days in three cell lines. Only Stat4 showed a clear down regulation

Mentions: Assuming that LIF would significantly enhance the activity of some pathways, we first examined gene expression in the cells cultivated with and without LIF. Differentially expressed genes were identified according to their fold change compared with the control (see “Clustering” in Materials and methods). 2135 genes were differentially expressed in the two LIF-cultivated cell lines and 1716 genes in the one non-LIF-cultivated cell line (see Materials and methods). Of them, 1607 were shared by both. We then checked differentially expressed genes in known signaling pathways and functional modules, including those stemness specific genes (11 activated and 12 repressed, denoted as Boyer+ and Boyer− in Boyer et al. 2005). Unexpectedly, the expression of genes in these pathways and modules seemed not to be noticeably different (Table 1). Specifically, all the 7 positive indicators (Boyer+) and 3 of 4 negative indicators (Boyer-) of self-renewal were differentially expressed in all cell lines. Also, Nanog, Oct4 and Sox2 did not show a clear, LIF-dependent expression pattern (Fig. 1). These results suggest that LIF might not be the vital or sole factor for self-renewal under this culture condition. As conjectured (Dani et al. 1998), other factors may exist and play a role.Table 1


Combined microarray analysis uncovers self-renewal related signaling in mouse embryonic stem cells.

Zhu H, Yang H, Owen MR - Syst Synth Biol (2008)

The expression of Pou5f1, Nanog, Sox2, JAK1/2/3 and STAT3/4 (against the control) in the 14 days in three cell lines. Only Stat4 showed a clear down regulation
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2553326&req=5

Fig1: The expression of Pou5f1, Nanog, Sox2, JAK1/2/3 and STAT3/4 (against the control) in the 14 days in three cell lines. Only Stat4 showed a clear down regulation
Mentions: Assuming that LIF would significantly enhance the activity of some pathways, we first examined gene expression in the cells cultivated with and without LIF. Differentially expressed genes were identified according to their fold change compared with the control (see “Clustering” in Materials and methods). 2135 genes were differentially expressed in the two LIF-cultivated cell lines and 1716 genes in the one non-LIF-cultivated cell line (see Materials and methods). Of them, 1607 were shared by both. We then checked differentially expressed genes in known signaling pathways and functional modules, including those stemness specific genes (11 activated and 12 repressed, denoted as Boyer+ and Boyer− in Boyer et al. 2005). Unexpectedly, the expression of genes in these pathways and modules seemed not to be noticeably different (Table 1). Specifically, all the 7 positive indicators (Boyer+) and 3 of 4 negative indicators (Boyer-) of self-renewal were differentially expressed in all cell lines. Also, Nanog, Oct4 and Sox2 did not show a clear, LIF-dependent expression pattern (Fig. 1). These results suggest that LIF might not be the vital or sole factor for self-renewal under this culture condition. As conjectured (Dani et al. 1998), other factors may exist and play a role.Table 1

Bottom Line: Albeit the expression of individual genes in signaling pathways was not noticeably different between cells cultivated with and without LIF, at gene-set level the expression of ERK/MAPK (but not JAK/STAT) and cell cycle related genes was found significantly enriched in cells cultivated with LIF.When data at the first 7 time points were compared with data at the last 4 time points, the expression of several cell cycle related gene sets was apparently enriched in all three cell lines, indicating the active cell proliferation in the first 2 days.When that mechanism weakens, cell differentiation begins.

View Article: PubMed Central - PubMed

Affiliation: Center for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK, Hao.Zhu@nottingham.ac.uk.

ABSTRACT
Due to the limited understanding of self-renewal and pluripotency related signaling in stem cells, extracting information from genome-wide expression data is not only important but also challenging. With the combined use of two methods, we analyzed a set of microarray data at 11 time points from three mouse embryonic stem cell lines cultivated with and without leukemia inhibitory factor (LIF) for 14 days. Albeit the expression of individual genes in signaling pathways was not noticeably different between cells cultivated with and without LIF, at gene-set level the expression of ERK/MAPK (but not JAK/STAT) and cell cycle related genes was found significantly enriched in cells cultivated with LIF. This indicates that the Ras/Raf/ERK pathway, in addition to JAK/STAT, may also be a key player to carry on external LIF signal into mouse embryonic stem cells to promote self-renewal. When data at the first 7 time points were compared with data at the last 4 time points, the expression of several cell cycle related gene sets was apparently enriched in all three cell lines, indicating the active cell proliferation in the first 2 days. Compared with the slight decay of Oct4/Nanog/Sox2 during the 14 days, the expression of cell differentiation genes such as Gata4/6 underwent a drastic increase, which indicates that the upregulated expression of cell differentiation genes may better reflect the loss of self renewal than the down regulated expression of the stemness indicators Oct4, Sox2 and Nanog. Apart from differential expression and gene set enrichment analyses, a clustering algorithm was also used to classify genes into co-expression clusters. The possible regulation of two clusters, whose expression was most changed during cell culture from very low to very high, was explored. The drastic changes of these genes, including Slc39a8 which was a potential indicator of cell differentiation, in contrast the slight changes of self-renewal genes, imply that differentiation may be the default fate of stem cells and self-renewal may rely on a maintenance mechanism. When that mechanism weakens, cell differentiation begins.

No MeSH data available.


Related in: MedlinePlus