Culturing Mouse Embryonic Stem Cells in Serum May Provoke Gene Expression Variability

Culturing Mouse Embryonic Stem Cells in Serum May Provoke Gene Expression Variability

Previous studies suggest that mouse embryonic stem cells (ESCs) in culture are not homogeneous. Transcription factors associated with ESC identity may be expressed in a heterogeneous manner. For example, Nanog and Dppa3 are expressed in only a fraction of cells. Variation in expression of these individual genes has been implicated in controlling the differentiation potential of different subpopulations.However, the mechanisms responsible for global gene expression variation in ESCs are not fully understood.

Using single-cell technologies, several studies have reported transcriptomic analysis of mouse ESCs and uncovered signaling and microRNA pathways that influence heterogeneity of ESCs in culture.  More-recent studies have also examined transcriptional networks and cellcycle regulators that contribute to transcriptional variation. Epigenetic regulation, which may also contribute to overall variability, has not been adequately explored. Moreover, the relevance of ESC culture heterogeneity to early embryonic development has yet to be analyzed.

Researchers performed single-cell mRNA-seq analysis of mouse ESCs and uncovered significant heterogeneity in ESCs cultured in serum.

They define highly variable gene clusters with distinct chromatin states and show that bivalent genes are prone to expression variation. At the same time, authors identify an ESC-priming pathway that initiates the exit from the naive ESC state.

Finally, they provide evidence that a large proportion of intracellular network variability is due to the extracellular culture environment. Serum-free culture reduces cellular heterogeneity and transcriptome variation in ESCs.