Evolving Transcriptomic Signature of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cells With Age

We differentiated the human embryonic stem cell line H9 into retinal pigment epithelium (RPE) cells to assess temporal changes in transcriptomic profiles of cells. We performed single cell RNA-Sequencing of a total of 16,576 cells, and analysed the resulting data to access the molecular changes of RPE cells across two culture time points (1 and 12 months). Our results indicate the stability of the RPE transcriptomic signature over time in culture, with results indicating maturing populations of RPE could be observed over time, with no evidence of an epithelial mesenchymal transition. Assessment of gene ontology (GO) pathways reveals that as cell cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions, which might reflect an increased ability to handle oxidative stress as cells mature. Comparison with the transcriptional profiles of native RPE identified a progression towards a maturing RPE profile. These results suggest that in vitro long-term culture of RPE cells allow the modelling of phenotypes observed in native mature tissue. Our work highlights the changing transcriptional landscape of hPSC-derived RPE as they age in culture, which provides a reference for native and patient- samples to be benchmarked against.