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Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation.

Nair G, Abranches E, Guedes AM, Henrique D, Raj A - Sci Rep (2015)

Bottom Line: Here, we show the transcriptome of Nanog-negative cells exhibits expression of classes of genes associated with differentiation that are not yet active in cells exposed to differentiation conditions for one day.These results are consistent with the concept that Nanog-negative cells may contain subpopulations of both lineage-primed and differentiated cells.Our results suggest that the observed enrichment of lineage-specific marker gene expression in Nanog-negative cells is associated with spontaneous differentiation of a subset of these cells rather than the more random expression that may be associated with reversible lineage priming.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.

ABSTRACT
Populations of cultured mouse embryonic stem cells (ESCs) exhibit a subfraction of cells expressing uncharacteristically low levels of pluripotency markers such as Nanog. Yet, the extent to which individual Nanog-negative cells are differentiated, both from ESCs and from each other, remains unclear. Here, we show the transcriptome of Nanog-negative cells exhibits expression of classes of genes associated with differentiation that are not yet active in cells exposed to differentiation conditions for one day. Long non-coding RNAs, however, exhibit more changes in expression in the one-day-differentiated cells than in Nanog-negative cells. These results are consistent with the concept that Nanog-negative cells may contain subpopulations of both lineage-primed and differentiated cells. Single cell analysis showed that Nanog-negative cells display substantial and coherent heterogeneity in lineage marker expression in progressively nested subsets of cells exhibiting low levels of Nanog, then low levels of Oct4, and then a set of lineage markers, which express intensely in a small subset of these more differentiated cells. Our results suggest that the observed enrichment of lineage-specific marker gene expression in Nanog-negative cells is associated with spontaneous differentiation of a subset of these cells rather than the more random expression that may be associated with reversible lineage priming.

No MeSH data available.


Related in: MedlinePlus

Distribution of Joint Hits and Differential Expression of lincRNA.(A) Joint distribution of fold changes for genes that turned up as 10% FDR hits for differential expression in heterogeneity (Nanog:VNP(+) vs Nanog:VNP(−)) and differentiation (Stem vs Diff). Text annotations for each quadrant note some genes found in it, as well as the top 3 GO terms and number of genes falling in them by the “greedy” method. (B) Differential expression analysis for lincRNA identified by22 as repressors of certain lineage programs in mouse ES-cells.
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f3: Distribution of Joint Hits and Differential Expression of lincRNA.(A) Joint distribution of fold changes for genes that turned up as 10% FDR hits for differential expression in heterogeneity (Nanog:VNP(+) vs Nanog:VNP(−)) and differentiation (Stem vs Diff). Text annotations for each quadrant note some genes found in it, as well as the top 3 GO terms and number of genes falling in them by the “greedy” method. (B) Differential expression analysis for lincRNA identified by22 as repressors of certain lineage programs in mouse ES-cells.

Mentions: To further dissect the differences between ESCs grown in 2i + LIF conditions and (1) cells grown in these conditions that exhibit low levels of Nanog expression vs. (2) cells subjected to a short period of differentiation, we compared the fold changes for genes that turned up as 10% FDR hits in both comparisons (Fig. 3A). Of the 1372 differentially expressed genes, about two-thirds were altered in “coherent” directions (genes both up- or down-regulated in Nanog:VNP(+)/VNP(−) and Stem/Diff - lower-left and upper-right quadrants), while the remaining one third are differentially expressed in “incoherent” directions.


Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation.

Nair G, Abranches E, Guedes AM, Henrique D, Raj A - Sci Rep (2015)

Distribution of Joint Hits and Differential Expression of lincRNA.(A) Joint distribution of fold changes for genes that turned up as 10% FDR hits for differential expression in heterogeneity (Nanog:VNP(+) vs Nanog:VNP(−)) and differentiation (Stem vs Diff). Text annotations for each quadrant note some genes found in it, as well as the top 3 GO terms and number of genes falling in them by the “greedy” method. (B) Differential expression analysis for lincRNA identified by22 as repressors of certain lineage programs in mouse ES-cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544010&req=5

f3: Distribution of Joint Hits and Differential Expression of lincRNA.(A) Joint distribution of fold changes for genes that turned up as 10% FDR hits for differential expression in heterogeneity (Nanog:VNP(+) vs Nanog:VNP(−)) and differentiation (Stem vs Diff). Text annotations for each quadrant note some genes found in it, as well as the top 3 GO terms and number of genes falling in them by the “greedy” method. (B) Differential expression analysis for lincRNA identified by22 as repressors of certain lineage programs in mouse ES-cells.
Mentions: To further dissect the differences between ESCs grown in 2i + LIF conditions and (1) cells grown in these conditions that exhibit low levels of Nanog expression vs. (2) cells subjected to a short period of differentiation, we compared the fold changes for genes that turned up as 10% FDR hits in both comparisons (Fig. 3A). Of the 1372 differentially expressed genes, about two-thirds were altered in “coherent” directions (genes both up- or down-regulated in Nanog:VNP(+)/VNP(−) and Stem/Diff - lower-left and upper-right quadrants), while the remaining one third are differentially expressed in “incoherent” directions.

Bottom Line: Here, we show the transcriptome of Nanog-negative cells exhibits expression of classes of genes associated with differentiation that are not yet active in cells exposed to differentiation conditions for one day.These results are consistent with the concept that Nanog-negative cells may contain subpopulations of both lineage-primed and differentiated cells.Our results suggest that the observed enrichment of lineage-specific marker gene expression in Nanog-negative cells is associated with spontaneous differentiation of a subset of these cells rather than the more random expression that may be associated with reversible lineage priming.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.

ABSTRACT
Populations of cultured mouse embryonic stem cells (ESCs) exhibit a subfraction of cells expressing uncharacteristically low levels of pluripotency markers such as Nanog. Yet, the extent to which individual Nanog-negative cells are differentiated, both from ESCs and from each other, remains unclear. Here, we show the transcriptome of Nanog-negative cells exhibits expression of classes of genes associated with differentiation that are not yet active in cells exposed to differentiation conditions for one day. Long non-coding RNAs, however, exhibit more changes in expression in the one-day-differentiated cells than in Nanog-negative cells. These results are consistent with the concept that Nanog-negative cells may contain subpopulations of both lineage-primed and differentiated cells. Single cell analysis showed that Nanog-negative cells display substantial and coherent heterogeneity in lineage marker expression in progressively nested subsets of cells exhibiting low levels of Nanog, then low levels of Oct4, and then a set of lineage markers, which express intensely in a small subset of these more differentiated cells. Our results suggest that the observed enrichment of lineage-specific marker gene expression in Nanog-negative cells is associated with spontaneous differentiation of a subset of these cells rather than the more random expression that may be associated with reversible lineage priming.

No MeSH data available.


Related in: MedlinePlus