Transcriptomic Comparison of RPE Derived from Two Human Embryonic Stem Cell Lines with Human Fetal RPE

Abstract

Purpose: : There is wide variety in the transcriptomes of human embryonic stem cells (hESC). This study asks whether there is also variability in the transcriptomes of retinal pigment epithelia (RPE) derived from two common hESC lines, H1 and H9, with an emphasis on genes for RPE functions.

Methods: : Human fetal RPE (hfRPE) and hESC-derived RPE were adapted to a serum-free medium that promotes differentiation. Cultures with a high, stable transepithelial electrical resistance were selected for analysis. The mRNA was isolated from three biological repeats and sequenced using the Illumina deep-sequencing platform. Following statistical analysis of the primary data, pair-wise comparisons were made between H1- or H9-derived RPE and hfRPE.

Results: : Overall, the transcriptome of H1-derived RPE showed greater overlap with hfRPE. Of 38,198 transcripts expressed by hfRPE, 82% were expressed by H1-derived RPE in amounts that were statistically equivalent to hfRPE. The others were overexpressed or underexpressed. Only 60% were expressed in similar amounts by H9-derived RPE. For RPE signature genes, the overlap for equivalent expression was 73% for H1-derived RPE and 56% for H9-derived RPE. For barrier-function related mRNAs there were some differences. Expression of transcripts relative to hfRPE for H1 vs H9 was 69% vs 60% (transporters) and 46% vs 41% (adherens junctions). However, there was minimal difference for ion channels (47% vs 44%) or tight junctions (56 vs 57%). Notably, there was a difference for autophagy- (72% vs 56%) and lysosomal- (70% vs 58%) related mRNAs.

Conclusions: : Although the H9 hESC line yields more RPE than the H1 line, the transcriptome of H1-derived RPE more closely approximates the transcriptome of hfRPE.

Keywords: retinal pigment epithelium • gene microarray • differentiation