Whole genome expression profiling of normal human fetal and adult ocular tissues

Young, Terri L.; Hawthorne, Felicia; Feng, Sheng; Luo, Xiaoyan; St.Germain, Elizabeth; Wang, Minyue; Metlapally, Ravikanth

doi:10.1016/j.exer.2013.08.009

Cited by 17 publications

(15 citation statements)

References 26 publications

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“…Although not widely studied in sclera, some keratins have been previously reported in normal human sclera (see supplemental information in Young et al 54 ). They also hold the potential to influence scleral extracellular matrix because they are part of important intermediate filament network machinery that connects the cell periphery/extracellular matrix to the nuclear matrix via the actin microfilaments.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Scleral Micro- and Messenger-RNA Regulation During Myopia Development in the Mouse

Metlapally

Park

Chakraborty

et al. 2016

Invest. Ophthalmol. Vis. Sci.

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PurposeMicroRNA (miRNAs) have been previously implicated in scleral remodeling in normal eye growth. They have the potential to be therapeutic targets for prevention/retardation of exaggerated eye growth in myopia by modulating scleral matrix remodeling. To explore this potential, genome-wide miRNA and messenger RNA (mRNA) scleral profiles in myopic and control eyes from mice were studied.MethodsC57BL/6J mice (n = 7; P28) reared under a 12L:12D cycle were form-deprived (FD) unilaterally for 2 weeks. Refractive error and axial length changes were measured using photorefraction and 1310-nm spectral-domain optical coherence tomography, respectively. Scleral RNA samples from FD and fellow control eyes were processed for microarray assay. Statistical analyses were performed using National Institute of Aging array analysis tool; group comparisons were made using ANOVA, and gene ontologies were identified using software available on the Web. Findings were confirmed using quantitative PCR in a separate group of mice (n = 7).ResultsForm-deprived eyes showed myopic shifts in refractive error (−2.02 ± 0.47 D; P < 0.01). Comparison of the scleral RNA profiles of test eyes with those of control eyes revealed 54 differentially expressed miRNAs and 261 mRNAs fold-change >1.25 (maximum fold change = 1.63 and 2.7 for miRNAs and mRNAs, respectively) (P < 0.05; minimum, P = 0.0001). Significant ontologies showing gene over-representation (P < 0.05) included intermediate filament organization, scaffold protein binding, detection of stimuli, calcium ion, G protein, and phototransduction. Significant differential expression of Let-7a and miR-16-2, and Smok4a, Prph2, and Gnat1 were confirmed.ConclusionsScleral mi- and mRNAs showed differential expression linked to myopia, supporting the involvement of miRNAs in eye growth regulation. The observed general trend of relatively small fold-changes suggests a tightly controlled, regulatory mechanism for scleral gene expression.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Scleral Micro- and Messenger-RNA Regulation During Myopia Development in the Mouse

Metlapally

Park

Chakraborty

et al. 2016

Invest. Ophthalmol. Vis. Sci.

Self Cite

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“…compared gene expression patterns in normal human fetal (N=9) and adult retinas (N=6) using Illumina HumanHT-12 v4 Expression BeadChips [30]. A significant number of differentially expressed genes (N=1185, fold change ≥1.5) were found between adult and fetal retina.…”

Section: Exploring the Human Retina Transcriptomementioning

confidence: 99%

Transcriptome of the human retina, retinal pigmented epithelium and choroid

et al. 2015

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The retina and its adjacent supporting tissues -- retinal pigmented epithelium (RPE) and choroid -- are critical structures in human eyes required for normal visual perception. Abnormal changes in these layers have been implicated in diseases such as age-related macular degeneration and glaucoma. With the advent of high-throughput methods, such as serial analysis of gene expression, cDNA microarray, and RNA sequencing, there is unprecedented opportunity to facilitate our understanding of the normal retina, RPE, and choroid. This information can be used to identify dysfunction in age-related macular degeneration and glaucoma. In this review, we describe the current status in our understanding of these transcriptomes through the use of high throughput techniques.

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“…Additionally, MXRA5 is expressed in fetal optic nerve tissue and continues to be expressed in adult optic nerve tissue at a relatively lower level. 46 …”

Section: Resultsmentioning

confidence: 99%

The Role of Chromosome X in Intraocular Pressure Variation and Sex-Specific Effects

Simcoe

Khawaja

Mahroo

et al. 2020

Invest. Ophthalmol. Vis. Sci.

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Purpose The purpose of this study was to identify genetic variants on chromosome X associated with intraocular pressure (IOP) and determine if they possess any sex-specific effects. Methods Association analyses were performed across chromosome X using 102,407 participants from the UK Biobank. Replication and validation analyses were conducted in an additional 6599 participants from the EPIC-Norfolk cohort, and an independent 331,682 participants from the UK Biobank. Results We identified three loci associated with IOP at genomewide significance ( P < 5 × 10 −8 ), located within or near the following genes: MXRA5 (rs2107482, P = 7.1 × 10 −11 ), GPM6B (rs66819623, P = 6.9 × 10 −10 ), NDP , and EFHC2 (rs12558081, P = 4.9 × 10 −11 ). Alleles associated with increased IOP were also associated with increased risk for primary open-angle glaucoma in an independent sample. Finally, our results indicate that chromosome X genetics most likely do not illicit sex-specific effects on IOP. Conclusions In this study, we report the results of genomewide levels of association of three loci on chromosome X with IOP, and provide a framework to include chromosome X in large-scale genomewide association analyses for complex phenotypes.

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Whole genome expression profiling of normal human fetal and adult ocular tissues

Cited by 17 publications

References 26 publications

Genome-Wide Scleral Micro- and Messenger-RNA Regulation During Myopia Development in the Mouse

Genome-Wide Scleral Micro- and Messenger-RNA Regulation During Myopia Development in the Mouse

Transcriptome of the human retina, retinal pigmented epithelium and choroid

The Role of Chromosome X in Intraocular Pressure Variation and Sex-Specific Effects

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