Transcriptomic Analysis of the Developmental Similarities and Differences Between the Native Retina and Retinal Organoids

Investigative Ophthalmology & Visual Science
Zekai CuiJiansu Chen

Abstract

We performed a bioinformatic transcriptome analysis to determine the alteration of gene expression between the native retina and retinal organoids in both mice and humans. The datasets of mouse native retina (GSE101986), mouse retinal organoids (GSE102794), human native retina (GSE104827), and human retinal organoids (GSE119320) were obtained from Gene Expression Omnibus. After normalization, a principal component analysis was performed to categorize the samples. The genes were clustered to classify them. A functional analysis was performed using the bioinformatics tool Gene ontology enrichment to analyze the biological processes of selected genes and cellular components. The development of retinal organoids is slower than that in the native retina. In the early stage, cell proliferation predominates. Subsequently, neural differentiation is dominant. In the later stage, the dominant differentiated cells are photoreceptors. Additionally, the fatty acid metabolic process and mitochondria-related genes are upregulated over time, and the glycogen catabolic process and activin receptors are gradually downregulated in human retinal organoids. However, these trends are opposite in mouse retinal organoids. There are two peaks in mitoch...Continue Reading

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Citations

Aug 23, 2020·Cancers·Rossukon Kaewkhaw, Duangnate Rojanaporn
Dec 29, 2020·Development·Michelle O'Hara-Wright, Anai Gonzalez-Cordero
May 18, 2021·Frontiers in Cell and Developmental Biology·Manuela VölknerMike O Karl
Jul 20, 2021·Frontiers in Cellular Neuroscience·Xuying LiXin Wei
Jul 27, 2021·Development·Michelle O'Hara-Wright, Anai Gonzalez-Cordero

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Datasets Mentioned

BETA
GSE101986
GSE102794
GSE104827
GSE119320

Methods Mentioned

BETA
RNA-seq
PCA
ubiquitination
dissection

Software Mentioned

Metascape
Search Tool for the Retrieval
iDEP
Sangerbox
SPSS

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