Expression profiling of cell-intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages

Stem Cell Research & Therapy
Jen-Hua ChuangShih-Jen Chen

Abstract

Differentiation of human induced pluripotent stem cells (hiPSCs) into retinal lineages offers great potential for medical application. Therefore, it is of crucial importance to know the key intrinsic regulators of differentiation and the specific biomarker signatures of cell lineages. In this study, we used microarrays to analyze transcriptomes of terminally differentiated retinal ganglion cell (RGC) and retinal pigment epithelium (RPE) lineages, as well as intermediate retinal progenitor cells of optic vesicles (OVs) derived from hiPSCs. In our analysis, we specifically focused on the classes of transcripts that encode intrinsic regulators of gene expression: the transcription factors (TFs) and epigenetic chromatin state regulators. We applied two criteria for the selection of potentially important regulators and markers: firstly, the magnitude of fold-change of upregulation; secondly, the contrasted pattern of differential expression between OV, RGC and RPE lineages. We found that among the most highly overexpressed TF-encoding genes in the OV/RGC lineage were three members of the Collier/Olfactory-1/Early B-cell family: EBF1, EBF2 and EBF3. Knockdown of EBF1 led to significant impairment of differentiation of hiPSCs into RGC...Continue Reading

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Datasets Mentioned

BETA
GSE96853

Methods Mentioned

BETA
dissection
PCR
confocal microscopy
transfection
acetylation
ubiquitination

Software Mentioned

GO
affy package
limma
pCLAMP
R
PANTHER
Bioconductor
Slim
Gene Ontology Slim - Slim

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