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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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Related in: MedlinePlus

Distribution of the Fisher statistic of GOBP terms.Selection of GOBP terms was based on specificity; only terms that were found to be specific for one of the block aggregates are included. Fisher statistics of association p-values were computed to evaluate the enrichment of GOBP terms in block aggregates. Background distributions of Fisher statistics (i.e. its distribution for all possible 4-tupels of comparisons, see text for details) are shown in a series of boxplots. Overlaid on each boxplot are the Fisher statistics that were computed for the four block aggregates. The terms are grouped based on the block aggregate for which they were found to be specifically significant. Panels A and B contain terms that are significant for the naïve and primed block aggregate, respectively. Terms in panel C, in turn, support the mixed block aggregate NHPM. In each panel the terms are ordered by the median of the background distribution.
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f8: Distribution of the Fisher statistic of GOBP terms.Selection of GOBP terms was based on specificity; only terms that were found to be specific for one of the block aggregates are included. Fisher statistics of association p-values were computed to evaluate the enrichment of GOBP terms in block aggregates. Background distributions of Fisher statistics (i.e. its distribution for all possible 4-tupels of comparisons, see text for details) are shown in a series of boxplots. Overlaid on each boxplot are the Fisher statistics that were computed for the four block aggregates. The terms are grouped based on the block aggregate for which they were found to be specifically significant. Panels A and B contain terms that are significant for the naïve and primed block aggregate, respectively. Terms in panel C, in turn, support the mixed block aggregate NHPM. In each panel the terms are ordered by the median of the background distribution.

Mentions: Applying a PCA to the matrix of aggregated evidence highlights the relationships between the target aggregates as well as the relative importance (loadings) of the single GOBP terms for the target aggregates (Figure 7). Here, the first PC clearly separates the target aggregates PM and PH (which have positive scores) from the target aggregates NM and NH (negative scores), with both groups having a lower intragroup than intergroup distance. Again, we conclude that there are functional similarities between the naïve states in mouse (represented by the target aggregate NM) and human (NH). Moreover, since the first PC accounts for 74% of the variance, these similarities are substantial. However, Figure 4 indicated that the naïve block aggregate is characterized by depletion of GOBP terms that are enriched elsewhere; yet the aggregation procedure that underlies the PCA considers enriched GOBP terms only. We investigated this issue further using a statistical approach, determining how many and which GOBP terms and, hence, biological processes are in fact common between NM and NH (see Figure 8 below). While the first PC in Figure 7 seems to capture functional and species-independent characteristics of naïve and primed pluripotency, the second PC, explaining roughly 17% of total variance, has a different interpretation. Here, the target aggregates NH and PM have strikingly similar scores, hinting at some biological process similarity between the claimed naïve state in human and the primed state in mouse. This finding prompted us to define the (additional) block aggregate NHPM (see Figure 3). In the next section we will use this aggregate to decipher the GOBP terms that might underlie this finding and that calls for improvements of protocols for human naïvity.


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)

Distribution of the Fisher statistic of GOBP terms.Selection of GOBP terms was based on specificity; only terms that were found to be specific for one of the block aggregates are included. Fisher statistics of association p-values were computed to evaluate the enrichment of GOBP terms in block aggregates. Background distributions of Fisher statistics (i.e. its distribution for all possible 4-tupels of comparisons, see text for details) are shown in a series of boxplots. Overlaid on each boxplot are the Fisher statistics that were computed for the four block aggregates. The terms are grouped based on the block aggregate for which they were found to be specifically significant. Panels A and B contain terms that are significant for the naïve and primed block aggregate, respectively. Terms in panel C, in turn, support the mixed block aggregate NHPM. In each panel the terms are ordered by the median of the background distribution.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8: Distribution of the Fisher statistic of GOBP terms.Selection of GOBP terms was based on specificity; only terms that were found to be specific for one of the block aggregates are included. Fisher statistics of association p-values were computed to evaluate the enrichment of GOBP terms in block aggregates. Background distributions of Fisher statistics (i.e. its distribution for all possible 4-tupels of comparisons, see text for details) are shown in a series of boxplots. Overlaid on each boxplot are the Fisher statistics that were computed for the four block aggregates. The terms are grouped based on the block aggregate for which they were found to be specifically significant. Panels A and B contain terms that are significant for the naïve and primed block aggregate, respectively. Terms in panel C, in turn, support the mixed block aggregate NHPM. In each panel the terms are ordered by the median of the background distribution.
Mentions: Applying a PCA to the matrix of aggregated evidence highlights the relationships between the target aggregates as well as the relative importance (loadings) of the single GOBP terms for the target aggregates (Figure 7). Here, the first PC clearly separates the target aggregates PM and PH (which have positive scores) from the target aggregates NM and NH (negative scores), with both groups having a lower intragroup than intergroup distance. Again, we conclude that there are functional similarities between the naïve states in mouse (represented by the target aggregate NM) and human (NH). Moreover, since the first PC accounts for 74% of the variance, these similarities are substantial. However, Figure 4 indicated that the naïve block aggregate is characterized by depletion of GOBP terms that are enriched elsewhere; yet the aggregation procedure that underlies the PCA considers enriched GOBP terms only. We investigated this issue further using a statistical approach, determining how many and which GOBP terms and, hence, biological processes are in fact common between NM and NH (see Figure 8 below). While the first PC in Figure 7 seems to capture functional and species-independent characteristics of naïve and primed pluripotency, the second PC, explaining roughly 17% of total variance, has a different interpretation. Here, the target aggregates NH and PM have strikingly similar scores, hinting at some biological process similarity between the claimed naïve state in human and the primed state in mouse. This finding prompted us to define the (additional) block aggregate NHPM (see Figure 3). In the next section we will use this aggregate to decipher the GOBP terms that might underlie this finding and that calls for improvements of protocols for human naïvity.

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