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Deduction of Novel Genes Potentially Involved in the Effects of Very Low Dose Atropine (0.003%) Treatment on Corneal Epithelial Cells Using Next-Generation Sequencing and Bioinformatics Approaches

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Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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Department of Medical Education, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
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Department of Ophthalmology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
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Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
*
Author to whom correspondence should be addressed.
Medicina 2019, 55(9), 589; https://doi.org/10.3390/medicina55090589
Received: 30 July 2019 / Revised: 6 September 2019 / Accepted: 10 September 2019 / Published: 13 September 2019
Background and Objectives: Atropine is a nonselective muscarinic antagonist which has been used to prevent worsening of myopia in children. Different concentrations of atropine were used for myopia, ranging from 0.01% to 1.0%. However, there are still potential toxicity of different doses of atropine to the cornea. Here, we present a study of investigating novel genes potentially involved in the effects of very low dose atropine treatment (0.003%) on corneal epithelial cells using next-generation sequencing (NGS) and bioinformatics approaches. Materials and Methods: Human corneal epithelial cells were treated with 0.003% atropine, cultured until confluence, and RNA extracted for differential expression profiling of mRNA and microRNA (miRNA) between control and atropine-treated corneal epithelial cells. The functional enrichment analysis for differentially expressed genes was performed using two bioinformatics databases, including Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity® Pathway Analysis (IPA). In addition, potential miRNA-mRNA interactions involved in atropine-treated corneal epithelial cells were predicted and validated using different miRNA target prediction databases. Results: Our results showed 0.003% atropine might suppress the apoptosis of corneal epithelial cells, potentially through Ras and protein kinase A signaling pathways. We also validated the possible miRNA regulations by using TargetScan and miRDB databases. Hsa-miR-651-3p-EPHA7, hsa-miR-3148-TMEM108 and hsa-miR-874-5p-TBX6 were validated as possible miRNA regulations involved in corneal epithelial cells treated with 0.003% atropine. Conclusions: These findings may contribute novel insights into therapeutic strategies for treating cornea with 0.003% atropine. View Full-Text
Keywords: corneal epithelial cells; atropine; apoptosis; next-generation sequencing; bioinformatics corneal epithelial cells; atropine; apoptosis; next-generation sequencing; bioinformatics
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Chang, W.-A.; Hsiao, Y.-T.; Lin, H.-C.; Jian, S.-F.; Chen, Y.-J.; Kuo, P.-L. Deduction of Novel Genes Potentially Involved in the Effects of Very Low Dose Atropine (0.003%) Treatment on Corneal Epithelial Cells Using Next-Generation Sequencing and Bioinformatics Approaches. Medicina 2019, 55, 589.

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