Dataset Information

The proteome of normal human iris, ciliary body, retinal pigment epithelium, and choroid

ABSTRACT: The iris is a fine structure that controls the amount of light that enters the eye. The ciliary body controls the shape of the lens and produces aqueous humor. The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. In iris, ciliary body, and RPE/choroid, we identified 2,959, 2,867, and 2,755 non-redundant proteins with protein false positive rate <1%. There were 43 unambiguous protein isoforms identified in iris, ciliary body, and RPE/choroid. Four “missing proteins” were found in ciliary body. The MS proteome database of the human iris, ciliary body, and RPE/choroid may serve as a valuable resource for future investigations of the eye in health and disease. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001424.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Retinal Pigment Epithelium, Iris, Ciliary Body, Choroid

DISEASE(S): Disease Free

SUBMITTER: Pingbo Zhang

LAB HEAD: Richard D. Semba

PROVIDER: PXD002194 | Pride | 2016-02-04

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 482

Publications

Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid.

Zhang Pingbo P Kirby David D Dufresne Craig C Chen Yan Y Turner Randi R Ferri Sara S Edward Deepak P DP Van Eyk Jennifer E JE Semba Richard D RD

Proteomics 20160311 7

The iris is a fine structure that controls the amount of light that enters the eye. The ciliary body controls the shape of the lens and produces aqueous humor. The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/M ...[more]

PMID: 26834087

Similar Datasets

Project description:Ocular pigment epithelium (PE) cells promote the generation of T regulators (PE-induced Treg cells). Moreover, T cells exposed to PE acquire the capacity to suppress the activation of bystander T cells via TGFbeta. Membrane-bound TGFbeta on iris PE cells interacts with TGFbeta receptors on T cells, leading to the conversion of T cells to CD8(+) Treg cells via a cell contact-dependent mechanism. Conversely, soluble forms of TGFbeta produced by retinal PE cells can convert CD4(+) T cells into Treg cells in a manner that is independent of cell contact. In this study, we looked at the expression of immunoregulatory factors (TGFbeta, thrombospondins, CD59, IL-1 receptor antagonist, etc.) in PE cells as identified via an oligonucleotide microarray. Several thrombospondin-binding molecules were detected, and thus we focused subsequent analyses on thrombospondins. Via the conversion of latent TGFbeta to an active form that appears to be mediated by thrombospondin 1 (TSP-1), cultured iris PE and retinal PE cells induce a PE-induced Treg cell fate. After conversion, both ocular PE and PE-induced Treg cells express TSP-1. Regulatory T cell generation was amplified when the T cells also expressed TSP-1. In addition, PE-induced Treg cells significantly suppressed activation of bystander T cells via TSP-1. These results strongly suggest that the ability of ocular PE and PE-induced Treg cells to suppress bystander T cells depends on their capacity to produce TSP-1. Thus, intraocular TSP-1 produced by both ocular parenchymal cells and regulatory T cells is essential for immune regulation in the eye. Experiment Overall Design: Comparison of gene expression pattern in Mouse Primary Cultured Cell Lines (RPE, IPE, CBPE). Experiment Overall Design: Adult (6- to 8-week-old) C57BL/6 purchased from CLEA Japan Inc. (Tokyo, Japan) were used as donors ocular pigment epithelium (PE). To cultivate iris PE (IPE) and ciliary body PE (CBPE), iris and ciliary body tissues in the eyes were dissected out, and then incubated in 1 mg/ml Dispase and 0.05 mg/ml DNase I (both from Boehringer-Mannheim, Mannheim, Germany) for 1 hr. To cultivate retinal PE (RPE) Eyes were cut into two parts along a circumferential line posterior to the ciliary process, creating a ciliary body-deficient posterior eyecup. The eyecup was then incubated in 0.2% trypsin (Biowhitaker) for 1 hr. These tissues were triturated to make a single cell suspension, and then re-suspended in the medium.

Project description:The choroid is the vascular layer situated between the outer sclera and the inner retina. Together with the ciliary body and the iris it forms the uvea. Because of its rich blood supply it is also called the nutritive layer and it supplies oxygen and nutrition to the retinal pigment epithelium and the outer retina. Due to its vascular nature it acts as a heat sink and helps in thermoregulation within the eye. It also contains a pigment “melanin”, which absorbs excess light within the eye and prevents scattering. . The human choroid is thickest posteriorly where it measures 0.2 mm, whereas anteriorly it measures 0.1 mm.. The aim of this study was to characterize the choroid proteome to generate a resource for future studies on the choroid . The method used in this study combined bRPLC and LC-MS/MS analysis of the proteins isolated from the three cadaver samples of healthy donors. Subsequently, we classified the proteins based on gene ontology and pathway analysis. A total of 5,249 non redundant proteins were identified in the human choroid. Gene ontology classification pinpointed proteins involved in protein metabolism, regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, transport, cell growth and/or maintenance and immune response. Several proteins identified in normal choroid have previously been identified in human choroid where these proteins are related to glaucoma, ocular inflammation, toxoplasmic retinochoroiditis, diabetic retinopathy, open-angle glaucoma and Grave’s disease. The top canonical pathway in which the choroid proteins participated are EIF2 signaling, integrin signalling, mitochondrial dysfunction, regulation of eIF4 and p70S6K signaling and clathrin-mediated endocytosis signalling. Around 800 choroid proteins were related to infectious diseases. The results of this study illustrate the largest number of proteins identified in human choroid and may serve as a valuable resource for future investigations of choroid biology and disease. Proteomic analysis of choroid proteins could provide versatile information to understand choroidal functions and the underlying pathogenesis of choroidal pathologies.

Project description:Purpose: Age-related degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE)/choroid from early AMD and control maculas using exon-based arrays. Methods: Gene expression levels in nine early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using DAVID, and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. CFH genotype was also assessed and differential expression was analyzed with respect to high AMD risk (YH/HH) and low AMD risk (YY) genotypes. Results: Seventy-five genes were identified as differentially expressed (raw p-value < 0.01; >50% fold change, mean log2 expression level in AMD or control M-bM-^IM-% median of all average gene expression values); however, no genes were significant (adj. p-value < 0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change < 0.5; raw p-value < 0.01), 18 genes were identified by DAVID analysis as associated with vision or neurological processes. GSEA of RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis with respect to CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p-value = 0.0008). Conclusions: GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout occurs early in the pathogenesis of AMD. Using AltAnalyze (ver. 2.0.7 beta), we analyzed nine early AMD and nine control eyes using Affymetrix Human Exon ST 1.0 arrays. Following initial processing in AltAnalyze, two control arrays were identified as potential outliers by tests implement in arrayQualityMetrics, a package for R.

			Action	DRS
	0orHDJ8h-2509_01.mgf	Mgf
	0orHDJ8h-2509_02.mgf	Mgf
	0orHDJ8h-2509_03.mgf	Mgf
	0orHDJ8h-2509_04.mgf	Mgf
	0orHDJ8h-2509_05.mgf	Mgf