Background
In development, inducing pluripotency and differentiation into different cell types results in global epigenetic changes, although the extent this occurs in induced pluripotent stem cell (iPSC)‐based neuronal models has not been extensively characterized.
Method
Human fibroblast cells were reprogrammed using lentiviral transfection. The resulting iPSC colonies were expanded, differentiated and collected at three different time points: day0 (iPSCs), day16 (neuronal progenitor cells), day37 and day58 (mature neurons). DNA methylation was assessed using the Illumina EPIC array. Using WGCNA, trajectory inference modelling and pathway analysis we identified loci undergoing dynamic changes during differentiation and the pathways these loci are associated with.
Result
This study has identified methylomic variation associated with neuronal differentiation and maturation. We identified 5,866 Bonferroni‐significant loci during differentiation using lineage modelling and noted that these loci are involved in pathways associated with head development, transcriptional regulation and cellular signalling. A gene‐gene interaction network analysis identified 50 densely connected genes that are influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity. Finally, we demonstrated that despite being functionally mature these iPSC‐derived neurons have a fetal epigenome.
Conclusion
We have shown that there are large epigenetic changes occurring throughout neuronal differentiation. These changes are within pathways that are key to neuronal development. Alongside this we have also identified an epigenetic trajectory signature associated with maturation and shown that neurons derived from iPSCs have a fetal epigenome.