Effects of adipocyte ablation on RPE/choroid complex in mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE261183 | GEO | 2025/03/31
REPOSITORIES: GEO
Similar Datasets
Project description:Young mice were compared to old mice (2 month vs 24 month) to determine gene changes that occur with aging in the mouse retinal pigmented epithelium/choroid of the eye. Keywords = retinal pigmented epithelium Keywords = aging Keywords = choroid
2010-06-05 | E-GEOD-565 | biostudies-arrayexpress
Project description:Young mice were compared to old mice (2 month vs 24 month) to determine gene changes that occur with aging in the mouse retinal pigmented epithelium/choroid of the eye. Keywords = retinal pigmented epithelium Keywords = aging Keywords = choroid Keywords: other
2003-09-30 | GSE565 | GEO
Project description:Effects of adipocyte ablation on RPE/choroid complex in mice
| PRJNA1085718 | ENA
Project description:We present a joint scRNA-seq and scATAC-seq atlas of adult human retinal pigment epithelium (RPE) and choroid. We integrate this atlas with a HiChIP enhancer connectome to predict noncoding variants with causal roles in age-related macular degeneration (AMD).
2025-03-25 | GSE262151 | GEO
Project description:<p>Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes. </p> <p>Reprinted from <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25446321">Whitmore, S.S., Wagner, A.H., DeLuca, A.P., Drack, A.V., Stone, E.M., Tucker, B.A., Zeng, S., Braun, T.A., Mullins, R.F., Scheetz, T.E., 2014. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research</a>. Used under <a href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported </a>license.</p> <p>Additional RNA sequencing was performed on temporal, macular, nasal, inferior, and superior retina from a fifth subject and is included in this dataset. See original publication for details.</p>
| phs001151 | dbGaP
Project description: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.
2016-02-04 | PXD002194 | Pride
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.
2018-04-25 | PXD002273 | Pride
Project description: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.
2017-11-29 | MSV000081766 | MassIVE
Project description:To characterize underlying changes in the retinal pigment epithelium (RPE)/choroid with age, we produced gene expression profiles for the RPE/choroid and compared the transcriptional profiles of the RPE/choroid from young and old mice. The changes in the aged RPE/choroid suggest that the tissue has become immunologically active. Such phenotypic changes in the normal aged RPE/choroid may provide a background for the development of age-related macular degeneration. Experiment Overall Design: We compared the gene expression of retinal pigmental epithelium/choroid from young and old animals. There were 4 samples from young mice and 4 samples from old mice. Each sample contained 4 retinal pigmental epithelium/choroid from 2 animals
2008-06-11 | E-GEOD-10965 | biostudies-arrayexpress
Project description:Purpose To examine how circulating immune mediators in vivo may affect gene and protein expression at the retinal pigment epithelium (RPE)/choroid interface. Methods Young mice were systemically infected with lymphocytic choriomeningitis virus (LCMV) or continuously infused with interferon (IFN)γ. RPE/choroid was isolated and analyzed with whole-transcriptome gene expression microarrays. Selected gene expression findings were validated at the protein level. Results Both the systemic immune activation from virus infection and the sterile systemically increased level of IFNγ resulted in increased expression of chemokine ligands, chemokine receptors and early complement components in isolates of RPE/choroid. These findings were largely absent from LCMV-infected mice deficient in either the interferon α/β receptor or IFNγ. Conclusions Together, these findings demonstrate that acute systemic immune activation results in a local response at the RPE/choroid interface that may include chemokine-dependent recruitment of inflammatory cells and engagement of the complement system. This may represent a link between the systemic low-grade inflammation and the retinal pathology observed in several multifactorial entities such as aging, age-related macular degeneration (AMD) and diabetes.
2018-12-31 | GSE73519 | GEO