Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation

Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation of cell types derived from all three germ layers. Current gastruloid protocols display considerable heterogeneity between experiments in terms of morphology, elongation efficiency, and cell type composition. We therefore investigated whether altering the mESC pluripotency state would provide more consistent results. By growing three mESC lines from two different genetic backgrounds in different intervals of ESLIF and 2i medium the pluripotency state of cells was modulated, and mESC culture as well as the resulting gastruloids were analysed. Microscopic analysis showed a pre-culture-specific effect on gastruloid formation, in terms of aspect ratio and reproducibility. RNA-seq analysis of the mESC start population confirmed that short-term pulses of 2i and ESLIF modulate the pluripotency state, and result in different cellular states. Since multiple epigenetic regulators were detected among the top differentially expressed genes, we further analysed genome-wide DNA methylation and H3K27me3 distributions. We observed epigenetic differences between conditions, most dominantly in the promoter regions of developmental regulators. Lastly, when we investigated the cell type composition of gastruloids grown from these different pre-cultures, we observed that mESCs subjected to 2i-ESLIF preceding aggregation generated gastruloids more consistently, including more complex mesodermal contributions as compared to the ESLIF-only control. These results indicate that optimisation of the mESCs pluripotency state allows the modulation of cell differentiation during gastruloid formation.