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Comparative computational analysis of pluripotency in human and mouse stem cells.

Ernst M, Abu Dawud R, Kurtz A, Schotta G, Taher L, Fuellen G - Sci Rep (2015)

Bottom Line: Pluripotent cells can be subdivided into two distinct states, the naïve and the primed state, the latter being further advanced on the path of differentiation.Reprogramming of human stem cells into a more naïve-like state is an important research focus.The pipeline consists of identifying regulated start-ups/shut-downs in terms of molecular interactions, followed by functional annotation of the genes involved and aggregation of results across conditions, yielding sets of mechanisms that are consistently regulated in transitions towards similar states of pluripotency.

View Article: PubMed Central - PubMed

Affiliation: Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany.

ABSTRACT
Pluripotent cells can be subdivided into two distinct states, the naïve and the primed state, the latter being further advanced on the path of differentiation. There are substantial differences in the regulation of pluripotency between human and mouse, and in humans only stem cells that resemble the primed state in mouse are readily available. Reprogramming of human stem cells into a more naïve-like state is an important research focus. Here, we developed a pipeline to reanalyze transcriptomics data sets that describe both states, naïve and primed pluripotency, in human and mouse. The pipeline consists of identifying regulated start-ups/shut-downs in terms of molecular interactions, followed by functional annotation of the genes involved and aggregation of results across conditions, yielding sets of mechanisms that are consistently regulated in transitions towards similar states of pluripotency. Our results suggest that one published protocol for naïve human cells gave rise to human cells that indeed share putative mechanisms with the prototypical naïve mouse pluripotent cells, such as DNA damage response and histone acetylation. However, cellular response and differentiation-related mechanisms are similar between the naïve human state and the primed mouse state, so the naïve human state did not fully reflect the naïve mouse state.

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Heatmap of evidence for enrichment of KEGG pathways in target aggregates.The heatmap includes only KEGG pathways for which a significant enrichment in one of the block aggregates was determined using our statistical assessment. This aggregate is colour-coded to the left of the heatmap (green: naïve, red: primed, blue: NHPM, cyan: NMPH).
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f9: Heatmap of evidence for enrichment of KEGG pathways in target aggregates.The heatmap includes only KEGG pathways for which a significant enrichment in one of the block aggregates was determined using our statistical assessment. This aggregate is colour-coded to the left of the heatmap (green: naïve, red: primed, blue: NHPM, cyan: NMPH).

Mentions: In order to compare our findings to results based on a pathway-centric compendium of functional gene annotations, we repeated our analysis pipeline using the KEGG pathway database, instead of GOBP. Figure 9 summarizes the results, on the same analysis stage as Figure 6, featuring a heatmap of KEGG pathway enrichment evidence in target aggregates. The clustering of the target aggregates confirms the purported closeness of human and mouse naïvity. This clustering considers only significant KEGG pathways, i.e. pathways that were found to be specifically enriched in any of the four block aggregates, with a p-value threshold of 0.05. Yet, a number of KEGG terms resonate well with our previous findings. Base excision repair was identified as specific for the naïve block aggregate, corroborating the GOBP term signal transduction in response to DNA damage found above. Furthermore, glycolysis and valine, leucine, and isoleucine biosynthesis were among the naïve-specific terms. The former is consistent with ref. 21. With respect to the latter, it was shown that the metabolomes of hESCs and human embryonal carcinoma cells (hECCs), which are the malignant counterpart to the hESCs, share common signatures comprising amongst others also amino acid metabolism28. Further, mESCs cultured in 2i + Lif in comparison to Serum + Lif upregulate amino acid related metabolism21. However, the precise role of different amino acid pathways in pluripotency remains to be determined in detail. As for pathways that are shared between the target aggregates PH and PM, we found axon guidance, supporting our conclusion about the importance of neuron differentiation for the primed aggregate. Finally, the NHPM block aggregate features various signalling pathways involved in differentiation such as those related to TGF-beta, NOD-like and Jak/STAT, consistent with the GOBP analysis. In interpreting the results of the KEGG analysis, however, it should be noted that fewer genes could be annotated with KEGG pathways, compared to those with GOBP annotations.


Comparative computational analysis of pluripotency in human and mouse stem cells.

Ernst M, Abu Dawud R, Kurtz A, Schotta G, Taher L, Fuellen G - Sci Rep (2015)

Heatmap of evidence for enrichment of KEGG pathways in target aggregates.The heatmap includes only KEGG pathways for which a significant enrichment in one of the block aggregates was determined using our statistical assessment. This aggregate is colour-coded to the left of the heatmap (green: naïve, red: primed, blue: NHPM, cyan: NMPH).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4300513&req=5

f9: Heatmap of evidence for enrichment of KEGG pathways in target aggregates.The heatmap includes only KEGG pathways for which a significant enrichment in one of the block aggregates was determined using our statistical assessment. This aggregate is colour-coded to the left of the heatmap (green: naïve, red: primed, blue: NHPM, cyan: NMPH).
Mentions: In order to compare our findings to results based on a pathway-centric compendium of functional gene annotations, we repeated our analysis pipeline using the KEGG pathway database, instead of GOBP. Figure 9 summarizes the results, on the same analysis stage as Figure 6, featuring a heatmap of KEGG pathway enrichment evidence in target aggregates. The clustering of the target aggregates confirms the purported closeness of human and mouse naïvity. This clustering considers only significant KEGG pathways, i.e. pathways that were found to be specifically enriched in any of the four block aggregates, with a p-value threshold of 0.05. Yet, a number of KEGG terms resonate well with our previous findings. Base excision repair was identified as specific for the naïve block aggregate, corroborating the GOBP term signal transduction in response to DNA damage found above. Furthermore, glycolysis and valine, leucine, and isoleucine biosynthesis were among the naïve-specific terms. The former is consistent with ref. 21. With respect to the latter, it was shown that the metabolomes of hESCs and human embryonal carcinoma cells (hECCs), which are the malignant counterpart to the hESCs, share common signatures comprising amongst others also amino acid metabolism28. Further, mESCs cultured in 2i + Lif in comparison to Serum + Lif upregulate amino acid related metabolism21. However, the precise role of different amino acid pathways in pluripotency remains to be determined in detail. As for pathways that are shared between the target aggregates PH and PM, we found axon guidance, supporting our conclusion about the importance of neuron differentiation for the primed aggregate. Finally, the NHPM block aggregate features various signalling pathways involved in differentiation such as those related to TGF-beta, NOD-like and Jak/STAT, consistent with the GOBP analysis. In interpreting the results of the KEGG analysis, however, it should be noted that fewer genes could be annotated with KEGG pathways, compared to those with GOBP annotations.

Bottom Line: Pluripotent cells can be subdivided into two distinct states, the naïve and the primed state, the latter being further advanced on the path of differentiation.Reprogramming of human stem cells into a more naïve-like state is an important research focus.The pipeline consists of identifying regulated start-ups/shut-downs in terms of molecular interactions, followed by functional annotation of the genes involved and aggregation of results across conditions, yielding sets of mechanisms that are consistently regulated in transitions towards similar states of pluripotency.

View Article: PubMed Central - PubMed

Affiliation: Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany.

ABSTRACT
Pluripotent cells can be subdivided into two distinct states, the naïve and the primed state, the latter being further advanced on the path of differentiation. There are substantial differences in the regulation of pluripotency between human and mouse, and in humans only stem cells that resemble the primed state in mouse are readily available. Reprogramming of human stem cells into a more naïve-like state is an important research focus. Here, we developed a pipeline to reanalyze transcriptomics data sets that describe both states, naïve and primed pluripotency, in human and mouse. The pipeline consists of identifying regulated start-ups/shut-downs in terms of molecular interactions, followed by functional annotation of the genes involved and aggregation of results across conditions, yielding sets of mechanisms that are consistently regulated in transitions towards similar states of pluripotency. Our results suggest that one published protocol for naïve human cells gave rise to human cells that indeed share putative mechanisms with the prototypical naïve mouse pluripotent cells, such as DNA damage response and histone acetylation. However, cellular response and differentiation-related mechanisms are similar between the naïve human state and the primed mouse state, so the naïve human state did not fully reflect the naïve mouse state.

Show MeSH
Related in: MedlinePlus