July 2019
Volume 60, Issue 9
Open Access
ARVO Annual Meeting Abstract  |   July 2019
Identification of Key miRNAs and Genes for Mouse Retinal Development Using a Linear Model
Author Affiliations & Notes
  • Yi Shen Wang
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Mei Li
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Xiao Wang
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Jing Lu
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Lin Lu
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Yan Luo
    Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
  • Footnotes
    Commercial Relationships   Yi Shen Wang, None; Mei Li, None; Xiao Wang, None; Jing Lu, None; Lin Lu, None; Yan Luo, None
  • Footnotes
    Support  National Key Basic Research Program of China (973 Program: 2013CB967000); National Natural Science Foundation of China to YAN LUO (81371020); the Science and Technology Planning Projects of Guangdong Province (2014B030301040)
Investigative Ophthalmology & Visual Science July 2019, Vol.60, 6030. doi:
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    • Get Citation

      Yi Shen Wang, Mei Li, Xiao Wang, Jing Lu, Lin Lu, Yan Luo; Identification of Key miRNAs and Genes for Mouse Retinal Development Using a Linear Model. Invest. Ophthalmol. Vis. Sci. 2019;60(9):6030.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : miRNAs are upstream regulators of gene expression that are involved in many biological processes. The purpose of this study was to obtain a detailed spatiotemporal miRNA expression profile for mice, identify one or more miRNAs key to mouse retinal development, and explore the roles and mechanisms of these miRNAs

Methods : The miRNA expression pattern of the developing mouse retina was acquired from LNA microarrays. Data were processed to identify differentially-expressed miRNAs (DE-miRNAs) using the linear model by Python 3.6. Target genes of DE-miRNAs were predicted from TargetScan and miRDB databases. Subsequent functional analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment.

Results : The microarray data are accessible through Gene Expression Omnibus (GEO) Series accession number GSE115581. Nine miRNAs—miR-9-5p, miR-130a-3p, miR-181a/b-5p, miR-92a-3p, miR-20a-5p, miR-93-5p, miR-9-3p, and miR-124—were identified as key DE-miRNAs with low variability during mouse retinal development. After performing gene prediction, GO analysis results showed that target genes of the DE-miRNAs were enriched in cellular metabolic process-related terms. In KEGG analysis, target genes of DE-miRNAs were significantly enriched in PI3K/AKT/mTOR signaling, FOXO signaling, MAPK signaling, neurotrophin signaling, TGF-BETA signaling, focal adhesion, and the axon guidance pathway. PI3K, AKT, PTEN, MAPK1, SOS, SIPR1, BCL2L11, TGFBR1/2, and ITGA/ITGAB are essential factors in these pathways

Conclusions : By using a linear model, all involved developmental time points could be taken into account. Several DE-miRNAs and their target genes and pathways were identified that may play crucial roles in mouse retinal development. This study could provide the groundwork for further experiments.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.

 

The bar graph indicated the distribution of absolute values of slopes in order from the lowest to the highest of all mouse miRNAs. The horizontal axis represented different miRNAs, and the vertical axis represented the absolute value of slopes.

The bar graph indicated the distribution of absolute values of slopes in order from the lowest to the highest of all mouse miRNAs. The horizontal axis represented different miRNAs, and the vertical axis represented the absolute value of slopes.

 

miRNAs for which the absolute value of slope was in top 1% and R2 was over 0.6 were included. The horizontal axis represented the absolute value of slope, and the vertical axis represented the value of R2 . miRNAs closer to the upper right corner had greater changes and less variability during development.

miRNAs for which the absolute value of slope was in top 1% and R2 was over 0.6 were included. The horizontal axis represented the absolute value of slope, and the vertical axis represented the value of R2 . miRNAs closer to the upper right corner had greater changes and less variability during development.

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