Transcriptome dataset of human corneal endothelium based on ribosomal RNA-depleted RNA-Seq data

Tokuda, Yoshiyuki; Okumura, Naoki; Komori, Yuya; Hanada, Naoya; Tashiro, Kei; Koizumi, Noriko; Nakano, Masakazu

doi:10.1038/s41597-020-00754-1

Cited by 17 publications

(20 citation statements)

References 36 publications

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“…The genes PTGDS and ALCAM ( CD166 ) are also reportedly highly expressed in HCECs. 41 , 42 , 44 , 45 Our gene ontology analysis rendered a network plot of highly expressed genes in the cHCECs ( Fig. 4 B).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis Identified the Circadian Clock and Global Circadian Gene Expression in Human Corneal Endothelial Cells

Nakai

Tsuchiya

Koike

et al. 2022

Invest. Ophthalmol. Vis. Sci.

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Purpose To investigate circadian clock oscillation and circadian global gene expression in cultured human corneal endothelial cells (cHCECs) to elucidate and assess the potential function of circadian regulation in HCECs. Methods In this study, we introduced a circadian bioluminescence reporter, Bmal1:luciferase ( Bmal1:luc ), into cHCECs and subsequently monitored real-time bioluminescence rhythms. RNA-sequencing data analysis was then performed using sequential time-course samples of the cHCECs to obtain a comprehensive understanding of the circadian gene expression rhythms. The potential relevance of rhythmically expressed genes was then assessed by systematic approaches using functional clustering and individual gene annotations. Results Bmal1:luc bioluminescence exhibited clear circadian oscillation in the cHCECs. The core clock genes and clock-related genes showed high-amplitude robust circadian messenger RNA (mRNA) expression rhythms in cHCECs after treatment with dexamethasone, and 329 genes that exhibited circadian mRNA expression rhythms were identified (i.e., genes involved in various physiological processes including glycolysis, mitochondrial function, antioxidative systems, hypoxic responses, apoptosis, and extracellular matrix regulation, which represent the physiological functions of HCECs). Conclusions Our findings revealed that cHCECs have a robust and functional circadian clock, and our discovery that a large number of genes exhibit circadian mRNA expression rhythms in cHCECs suggests a potential contribution of circadian regulation to fine-tune HCEC functions for daily changes in the environment.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis Identified the Circadian Clock and Global Circadian Gene Expression in Human Corneal Endothelial Cells

Nakai

Tsuchiya

Koike

et al. 2022

Invest. Ophthalmol. Vis. Sci.

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“…To assess RNA expression of genes in corneal tissue associated with SCCED, total RNA was extracted from corneal tissue gently debrided from four SCCED Boxer dogs with the NOG deletion and three affected non-Boxer dogs without the NOG deletion (Boston Terrier (2), Pomeranian) as has been described previously [ 25 ]. Using the Qiagen RNeasy Plus Universal mini kit (Qiagen, Germantown, MD) RNA was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA).…”

Section: Methodsmentioning

confidence: 99%

A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs

et al. 2021

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Background Superficial chronic corneal epithelial defects (SCCEDs) are spontaneous corneal defects in dogs that share many clinical and pathologic characteristics to recurrent corneal erosions (RCE) in humans. Boxer dogs are predisposed to SCCEDs, therefore a search for a genetic defect was performed to explain this susceptibility. DNA was extracted from blood collected from Boxer dogs with and without SCCEDs followed by whole genome sequencing (WGS). RNA sequencing of corneal tissue and immunostaining of corneal sections from affected SCCED Boxer dogs with a deletion in the NOG gene and affected non-Boxer dogs without the deletion were performed. Results A 30 base pair deletion at a splice site in Noggin (NOG) (Chr 9:31453999) was identified by WGS and was significantly associated (P < 0.0001) with Boxer SCCEDs compared to unaffected non-Boxer dogs. NOG, BMP4, MMP13, and NCAM1 all had significant fold reductions in expression and SHH was significantly increased in Boxers with the NOG deletion as identified by RNA-Seq. Corneal IHC from NOG deletion dogs with SCCEDs had lower NOG and significantly higher scores of BMP2. Conclusions Many Boxer dogs with SCCED have a genetic defect in NOG. NOG is a constitutive protein in the cornea which is a potent inhibitor of BMP, which likely regulate limbal epithelial progenitor cells (LEPC). Dysregulation of LEPC may play a role in the pathogenesis of RCE.

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“…The total RNA of CECs from 10 patients with FECD was isolated by the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, as described in our previous report [15]. Brie y, CECs lysed with QIAzol lysis reagent were thawed at 37˚C.…”

Section: Total Rna Preparationmentioning

confidence: 99%

“…1. We rst compared the gene expression levels in the corneal endothelium of patients with FECD (n = 10) with those of healthy control subjects previously described (n = 7) [15]. The 24,636 genes among the total reference 60,164 genes were extracted through the QC process using the Wald test.…”

Section: Identi Cation and Con Rmation Of Degsmentioning

confidence: 99%

RNA-Seq–Based Transcriptome Analysis of Corneal Endothelial Cells Derived from Patients with Fuchs Endothelial Corneal Dystrophy

Nakagawa

Tokuda

Nakano

et al. 2022

Preprint

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Fuchs endothelial corneal dystrophy (FECD) is the most common inherited corneal disease. Fibrillar focal excrescences called guttae and corneal edema due to corneal endothelial cell death result in progressive vision loss. Multiple genetic variants have been reported, but the pathogenesis of FECD is not fully understood. In this study, we used RNA-Seq to analyze differential gene expression in the corneal endothelium obtained from patients with FECD. Differential expression analysis of transcriptomic profiles revealed that expression of 2,366 genes (1,092 upregulated and 1,274 downregulated genes) was significantly altered in the corneal endothelium of the patients with FECD compared to healthy subjects. Gene ontology analysis demonstrated an enrichment of genes involved in extracellular matrix (ECM) organization, response to oxidative stress, and apoptotic signaling. Several pathway analyses consistently indicated the dysregulation of ECM-associated pathways. Our differential gene expression findings support the previously proposed underlying mechanisms, including oxidative stress and apoptosis of endothelial cells, as well as the phenotypic clinical FECD hallmark of ECM deposits. Further investigation focusing on differentially expressed genes related to these pathways might be beneficial for elucidating mechanisms and developing novel therapies.

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Transcriptome dataset of human corneal endothelium based on ribosomal RNA-depleted RNA-Seq data

Cited by 17 publications

References 36 publications

Comprehensive Analysis Identified the Circadian Clock and Global Circadian Gene Expression in Human Corneal Endothelial Cells

Comprehensive Analysis Identified the Circadian Clock and Global Circadian Gene Expression in Human Corneal Endothelial Cells

A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs

RNA-Seq–Based Transcriptome Analysis of Corneal Endothelial Cells Derived from Patients with Fuchs Endothelial Corneal Dystrophy

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