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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 Gata4/6, Dsp, Sla39a8, Actn3 and Pla2g1b (against the control) in the 14 days in three cell lines. The number following the gene name is the enrichment score
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Fig2: The expression of Gata4/6, Dsp, Sla39a8, Actn3 and Pla2g1b (against the control) in the 14 days in three cell lines. The number following the gene name is the enrichment score

Mentions: Two research groups reported that differentiation of mES cells is induced by Gata4/6 (Fujikura et al. 2002; Li et al. 2004), but it is not known when, and with what partners, Gata4/6 induce stem cell differentiation. It is interesting that Oct3/4 over-expression can induce Gata4 transcription, which in turn triggers differentiation (Fujikura et al. 2002; Li et al. 2004). As no knowledge of the Gata4/6 related signaling pathway was available, we simply checked the expression profile of these two genes. Gata4/6 expression was low at the early time points but became significantly higher at the last four (Fig. 2), with a large negative enrichment score (−1.387 and −1.273, respectively). The increase of expression began earlier in E201 (J1, without LIF) than in E113 and E165 (V6.5 and R1, with LIF), indicating that LIF may play some role in delaying cell differentiation. Nevertheless, we found that Gata4/6 were not the genes with the largest negative enrichment score. The largest and second largest scores, −2.392 and −1.915, came from Slc39a8 and Dsp. Whether the two play a more important role than Gata4/6 in stem cell differentiation and their relationship with Gata4/6 remain unknown. These results confirm that Gata4/6 can indeed reflect stem cell differentiation, but Slc39a8 and Dsp could be alternative, and possibly better, indicators. In addition, the most enriched single genes at the early time points were Actn3 and Pla2g1b, which do not appear in any of our defined gene sets (Fig. 2). Whether they are involved in self-renewal is not clear. These genes, with extraordinarily high enrichment scores, provide new and important clues for deciphering signaling in stem cell self-renewal and differentiation.Fig. 2


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 Gata4/6, Dsp, Sla39a8, Actn3 and Pla2g1b (against the control) in the 14 days in three cell lines. The number following the gene name is the enrichment score
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: The expression of Gata4/6, Dsp, Sla39a8, Actn3 and Pla2g1b (against the control) in the 14 days in three cell lines. The number following the gene name is the enrichment score
Mentions: Two research groups reported that differentiation of mES cells is induced by Gata4/6 (Fujikura et al. 2002; Li et al. 2004), but it is not known when, and with what partners, Gata4/6 induce stem cell differentiation. It is interesting that Oct3/4 over-expression can induce Gata4 transcription, which in turn triggers differentiation (Fujikura et al. 2002; Li et al. 2004). As no knowledge of the Gata4/6 related signaling pathway was available, we simply checked the expression profile of these two genes. Gata4/6 expression was low at the early time points but became significantly higher at the last four (Fig. 2), with a large negative enrichment score (−1.387 and −1.273, respectively). The increase of expression began earlier in E201 (J1, without LIF) than in E113 and E165 (V6.5 and R1, with LIF), indicating that LIF may play some role in delaying cell differentiation. Nevertheless, we found that Gata4/6 were not the genes with the largest negative enrichment score. The largest and second largest scores, −2.392 and −1.915, came from Slc39a8 and Dsp. Whether the two play a more important role than Gata4/6 in stem cell differentiation and their relationship with Gata4/6 remain unknown. These results confirm that Gata4/6 can indeed reflect stem cell differentiation, but Slc39a8 and Dsp could be alternative, and possibly better, indicators. In addition, the most enriched single genes at the early time points were Actn3 and Pla2g1b, which do not appear in any of our defined gene sets (Fig. 2). Whether they are involved in self-renewal is not clear. These genes, with extraordinarily high enrichment scores, provide new and important clues for deciphering signaling in stem cell self-renewal and differentiation.Fig. 2

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