Expression Profiling of Cell-intrinsic Regulators in the Process of Differentiation of Human IPSCs into Retinal Lineages

Overview

Journal Stem Cell Res Ther

Publisher Biomed Central

Date 2018 May 13

PMID 29751772

Citations 12

Authors

Jen-Hua Chuang

Aliaksandr A Yarmishyn

De-Kuang Hwang

Chih-Chien Hsu

Mong-Lien Wang

Yi-Ping Yang

Ke-Hung Chien

Shih-Hwa Chiou

Chi-Hsien Peng

Shih-Jen Chen

Affiliations

Soon will be listed here.

Abstract

Background: 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.

Methods: 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.

Results: 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 RGCs. EBF1 was shown to act upstream of ISL1 and BRN3A, the well-characterized regulators of RGC lineage specification. TF-encoding genes DLX1, DLX2 and INSM1 were the most highly overexpressed genes in the OVs, indicating their important role in the early stages of retinal differentiation. Along with MITF, the two paralogs, BHLHE41 and BHLHE40, were the most robust TF markers of RPE cells. The markedly contrasted expression of ACTL6B, encoding the component of chromatin remodeling complex SWI/SNF, discriminated hiPSC-derived OV/RGC and RPE lineages.

Conclusions: We identified novel, potentially important intrinsic regulators of RGC and RPE cell lineage specification in the process of differentiation from hiPSCs. We demonstrated the crucial role played by EBF1 in differentiation of RGCs. We identified intrinsic regulator biomarker signatures of these two retinal cell types that can be applied with high confidence to confirm the cell lineage identities.

Citing Articles

Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina.

Zeng X, Gyoja F, Cui Y, Loza M, Kusakabe T, Nakai K NAR Genom Bioinform. 2024; 6(4):lqae149.

PMID: 39534499 PMC: 11555436. DOI: 10.1093/nargab/lqae149.

BHLHE41, a transcriptional repressor involved in physiological processes and tumor development.

Bret C, Desmots-Loyer F, Moreaux J, Fest T Cell Oncol (Dordr). 2024; 48(1):43-66.

PMID: 39254779 PMC: 11850569. DOI: 10.1007/s13402-024-00973-3.

Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina.

Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M Nat Commun. 2024; 15(1):3567.

PMID: 38670973 PMC: 11053058. DOI: 10.1038/s41467-024-47933-x.

Integrative Single-Cell Transcriptomics and Epigenomics Mapping of the Fetal Retina Developmental Dynamics.

Li R, Liu J, Yi P, Yang X, Chen J, Zhao C Adv Sci (Weinh). 2023; 10(16):e2206623.

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Whole Exome Sequencing Reveals Novel Candidate Genes in Familial Forms of Glaucomatous Neurodegeneration.

Narta K, Teltumbade M, Vishal M, Sadaf S, Faruq M, Jama H Genes (Basel). 2023; 14(2).

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