Functional annotation of the human retinal pigment epithelium transcriptome

Booij, Judith C.; Soest, S. van; Swagemakers, Sigrid; Essing, Anke H. W.; Verkerk, Annemieke J.M.H.; Spek, Peter J. van der; Gorgels, Theo G. M. F.; Bergen, Arthur A. B.

doi:10.1186/1471-2164-10-164

Cited by 47 publications

(77 citation statements)

References 36 publications

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“…Human gene expression data were obtained essentially as described 37 . In short, postmortem eye bulbs (retinal pigment epithelium was obtained from six donor eyes, choroid was obtained from three donor eyes and photoreceptors were obtained from three donor eyes), provided by the Corneabank Amsterdam, were rapidly frozen using liquid nitrogen.…”

Section: Methodsmentioning

confidence: 99%

A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14

et al. 2010

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Refractive errors are the most common ocular disorders worldwide and may lead to blindness. Although this trait is highly heritable, identification of susceptibility genes has been challenging. We conducted a genome-wide association study for refractive error in 5,328 individuals from a Dutch population-based study with replication in four independent cohorts (combined 10,280 individuals in the replication stage). We identified a significant association at chromosome 15q14 (rs634990, P = 2.21 × 10−14). The odds ratio of myopia compared to hyperopia for the minor allele (minor allele frequency = 0.47) was 1.41 (95% CI 1.16–1.70) for individuals heterozygous for the allele and 1.83 (95% CI 1.42–2.36) for individuals homozygous for the allele. The associated locus is near two genes that are expressed in the retina, GJD2 and ACTC1, and appears to harbor regulatory elements which may influence transcription of these genes. Our data suggest that common variants at 15q14 influence susceptibility for refractive errors in the general population.

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Section: Methodsmentioning

confidence: 99%

A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14

et al. 2010

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“…used microarray to assess the expression profile of the RPE from six eyes of normal donors between the ages of 63 and 78 [36]. Using six 22k custom arrays on laser dissected macular RPE cells they found that the highly expressed genes in the RPE represented functional categories in oxidative phosphorylation, ribosome pathway, and ATP synthesis.…”

Section: Exploring the Human Rpe/choroid 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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“…The n5-derived fibroblasts closely resembled MRC5 (human lung fibroblasts), BJ1 (human foreskin fibroblasts) and human skin fibroblasts; 20,21 the n5-derived neurons corresponded to the human gray and white matter brain cells; 22 and the transcriptome of our RPE cells was similar to previously published hRPE cells. 23,24,25 (for details see Supplemental Experimental Procedures Fig. S2).…”

Section: Establishment Of the Hesm01-oskmn-dox Isogenic Systemmentioning

confidence: 99%

“…We decided to follow up changes that occurred during culturing and estimate their possible input in the iPCS molecular signature. Gene expression and DNA methylation patterns of fibroblast-derived iPSC lines from early (4-12) and late (25)(26)(27)(28)(29) passages were examined (Fig. 5B, Table S4).…”

Section: Establishment Of the Hesm01-oskmn-dox Isogenic Systemmentioning

confidence: 99%

An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

et al. 2016

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Kiselev (2016) An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion, Cell Cycle, 15:7, 986-997, DOI: 10.1080/15384101.2016 ABSTRACTThe pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the 3 germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the "gold standard" of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, 3 types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and 3 pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that 5 iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of "the best iPSC line" selection and confirmed it on an independent dataset.

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Functional annotation of the human retinal pigment epithelium transcriptome

Cited by 47 publications

References 36 publications

A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14

A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14

Transcriptome of the human retina, retinal pigmented epithelium and choroid

An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

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