Transcriptome Analysis of the Human Corneal Endothelium
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE58315 | GEO | 2014/11/12
SECONDARY ACCESSION(S): PRJNA251984
REPOSITORIES: GEO
Similar Datasets
Project description:Mutations in the solute-linked carrier family 4 member 11 (SLC4A11) gene are associated with several corneal endothelial dystrophies, in all of which visually significant cornea edema may require corneal transplantation. To elucidate the pathogenesis of SLC4A11 associated corneal endothelial dystrophies, we analyzed the transcriptome of SLC4A11 knock-down primary human corneal endothelium (SLC4A11 KD pHCEnC) and scrambled RNA treated pHCEnC as controls.
2020-08-13 | GSE142636 | GEO
Project description:Mutations in the solute-linked carrier family 4 member 11 (SLC4A11) gene are associated with several corneal endothelial dystrophies, in all of which visually significant cornea edema may require corneal transplantation. To elucidate the pathogenesis of SLC4A11 associated corneal endothelial dystrophies, we analyzed the transcriptome of immortalized mouse corneal endothelial cells (Slc4a11-/- MCEnC) and Slc4a11+/+ MCEnC as controls.
2020-08-13 | GSE142635 | GEO
Project description:TGFBI associated Corneal Dystrophies (CD) are a group of inherited protein folding disorders linked to the mutation in the TGFBI gene. The resultant mutant protein (TGFBIp) is deposited as insoluble protein aggregates in various layers of the cornea leading to corneal opacity and poor vision. Depending on the type of mutation the deposits may be classified as amyloid fibrillar type, amorphous globular aggregates or a mixed form of both fibrils and amorphous aggregates. However, the molecular mechanism of the mutant-induced amyloidosis is not fully understood. This study aimsto characterize truncated peptides enriched in the amyloid aggregates and to identify the protein composition of the corneal aggregates derived from dystrophic patients using LC-MS/MS and compare the data with normal control cornea. We have identified several amyloid associated proteins, non-fibrillar amyloid associated proteins and TGFBIp as the major component of the corneal deposits. The results suggest that Apolipoprotein A-IV, Apolipoprotein E and Serine protease HtrA1 to be significantly enriched in the corneal deposits compared to the normal cornea. Comparative analysis of peptides from corneal deposits of patient and control identified several peptides of TGFBIp which are enriched in patient tissue and may form the core of corneal amyloids. Most of the peptides represent the 4th FAS-1 domain of the protein. Biophysical studies of two such peptides (G515DNRFSMLVAAIQSAGLTETLNR533 and Y571HIGDEILVSGGIGALVR588) demonstrate that they readily form amyloid fibrils under physiological conditions, confirming their intrinsic propensity to form amyloid fibrils. The identification of proteins which are involved in other protein misfolding disorders as well as identification of peptides from TGFBIp which form -amyloid core highlight that the mechanism of amyloid formation may share common molecular pathways.
2022-02-28 | PXD006640 | Pride
Project description:Genome wide DNA methylation profiling of normal human corneal endothelium and human corneal endothelium from FECD cases. The Illumina Infinium MethylationEPIC 850K BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in genomic DNA from human corneal endothelium samples. Samples included 11 non-FECD donors, 17 FECD cases.
2023-02-15 | GSE198917 | GEO
Project description:The corneal endothelium plays a primary role in maintaining corneal homeostasis and clarity, and must be surgically replaced with allogenic donor corneal endothelium in the event of visually significant dysfunction. However, a worldwide shortage of donor corneal tissue has led to a search for alternative sources of transplantable tissue. Cultured human corneal endothelial cells (HCEnC) have been shown to restore corneal clarity in experimental models of corneal endothelial dysfunction in animal models, but characterization of cultured HCEnC remains incomplete. To this end, we utilized next-generation RNA sequencing technology to compare the transcriptomic profile of ex vivo human corneal endothelium (evHCEnC) with that of primary HCEnC and HCEnC lines, and to determine the utility of cultured and immortalized corneal endothelial cells as models of in vivo corneal endothelium. Multidimensional analyses of the transcriptome datasets demonstrated that primary HCEnC have a closer relationship to evHCEnC than do immortalized HCEnC. Subsequent analyses showed that the majority of the genes specifically expressed in HCEnC (not expressed in ex vivo corneal epithelium or fibroblasts) demonstrated a marked variability of expression in cultured cells compared with evHCEnC. In addition, genes associated with either corneal endothelial cell function or corneal endothelial dystrophies were investigated. Significant differences in gene expression and protein levels were observed in the cultured cells compared with evHCEnC for each of the genes tested except for AGBL1 and LOXHD1, which were not detected by RNA-seq or qPCR. Our transcriptomic analysis suggests that at a molecular level primary HCEnC most closely resemble evHCEC and thus represent a viable therapeutic option for managing corneal endothelial dysfunction. Our findings also suggest that investigators should perform an assessment of the entire transcriptome of cultured HCEnC prior to determination of the potential clinical utility of the cultured HCEnC for the management of corneal endothelial cell failure. Transcriptomes from ex vivo corneal endothelium, primary cultures and three cell lines were compared. Three samples of each endothelial cell group were submitted for RNA sequencing for a total of 15 samples. The transcriptome for the ex vivo corneal endothelium was used as the reference (i.e., proxy for in vivo corneal endothelium). Transcript abundances for a subset of genes associated with corneal endothelial cell function or disease were validated with qPCR and western blot. Samples of ex vivo endothelium used for validation were independent replicates not used for RNA-sequencing.
2015-09-04 | E-GEOD-65991 | biostudies-arrayexpress
Project description:Corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs) in the inner layer of cornea, which is essential for maintaining corneal transparency. In order to better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other types of tissues, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are characteristic of CECs, involving in cell adhesion, proteoglycan and sulfur metabolic process. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. By comparing fetal and adult CECs, we also identified stage-specific markers associated with CEC maturation, such as the activation of the Wnt pathway genes in fetal, but not in adult CECs. Lastly, by immunohistochemistry of ocular tissues, we further confirmed the unique protein expression patterns for Wnt5a, S100A4, S100A6, and IER3, the four novel markers for either fetal or adult CECs. The identification of a new panel of molecular markers for fetal and mature CECs would be very useful for characterizing and quality controlling CECs through ex vivo expansion or stem cell differentiation for cell replacement therapy. mRNA profile between adult and fetal CECs by high-throughput sequencing
2013-01-08 | E-GEOD-41616 | biostudies-arrayexpress
Project description:Aim: To generate human embryonic stem cell-derived corneal endothelial cells (hESC-CECs) for transplantation in patients with corneal endothelial dystrophies.
2017-02-09 | GSE70954 | GEO
Project description:Fuchs’ endothelial corneal dystrophy is major corneal disorder in the western world affecting the innermost part of the cornea, which leads to visual impairment. The morphological changes observed in Fuchs’ endothelial corneal dystrophy is well described, however, much less in known of the pathology at the molecular level. As the morphological changes observed in the cornea is profound in the extracellular matrix we sought to determine in protein profiles and changes herein in the Descement’s membrane and endothelium layer of Fuchs’ endothelial conrneal dystrophy patients when compared to healthy control tissue. Using the extracted ion chromatogram label-free MS based quantification method we quantified approximately the 50 most abundant proteins of the Descemet’s membrane and endothelial layer in in patient and control tissue. In addition, using the isobaric tag for relative and absolute quantification MS method resulted in a total of 22 regulated proteins of which the majority were extracellular proteins known to be involved in proper assembly and modulation of the basement membrane in other tissues. Many of the regulated proteins were furthermore among the most abundant proteins quantified. The two MS methods performed here suggest altered arrangement of the extracellular matrix in Fuchs’ endothelial corneal dystrophy and provide new candidate proteins that may be involved in molecular mechanism of this disease.
2014-05-27 | PXD000746 | Pride
Project description:Purpose: Slc4a11 KO mice show significant edema and altered corneal endothelial morphology at an early age with concomitant increased mitochondrial ROS and oxidative damage relative to wild type. Here we used RNA-Seq with the goal of finding pathways related to corneal endothelial metabolic, pump and barrier function alterations. Methods: Corneal endothelium-Descemet’s membrane (CEDM) samples were from WT and Slc4a11 KO mice at 12 weeks of age. RNA sequencing data was subjected to Ingenuity Pathway Analysis and QPCR for validation. Results: The RNA sequencing IPA analysis predicted activation, inhibition or differential regulation of several pathways. We validated downregulation of Glycolytic enzymes, Mitochondrial complex components and Ion transporters. We observed upregulation of genes of cholesterol biosynthesis, GSH metabolism and tight and adherens junctions. Conclusions: Slc4a11 KO induces a coordinated decrease in glycolysis, glutaminolysis, oxygen consumption, lactate transporters and Na-K-ATPase. These changes together with the altered barrier function cause an accumulation of stromal lactate in Slc4a11 KO mice leading to chronic corneal edema.
2022-02-02 | GSE174586 | GEO
Project description:The corneal endothelium plays a primary role in maintaining corneal homeostasis and clarity, and must be surgically replaced with allogenic donor corneal endothelium in the event of visually significant dysfunction. However, a worldwide shortage of donor corneal tissue has led to a search for alternative sources of transplantable tissue. Cultured human corneal endothelial cells (HCEnC) have been shown to restore corneal clarity in experimental models of corneal endothelial dysfunction in animal models, but characterization of cultured HCEnC remains incomplete. To this end, we utilized next-generation RNA sequencing technology to compare the transcriptomic profile of ex vivo human corneal endothelium (evHCEnC) with that of primary HCEnC and HCEnC lines, and to determine the utility of cultured and immortalized corneal endothelial cells as models of in vivo corneal endothelium. Multidimensional analyses of the transcriptome datasets demonstrated that primary HCEnC have a closer relationship to evHCEnC than do immortalized HCEnC. Subsequent analyses showed that the majority of the genes specifically expressed in HCEnC (not expressed in ex vivo corneal epithelium or fibroblasts) demonstrated a marked variability of expression in cultured cells compared with evHCEnC. In addition, genes associated with either corneal endothelial cell function or corneal endothelial dystrophies were investigated. Significant differences in gene expression and protein levels were observed in the cultured cells compared with evHCEnC for each of the genes tested except for AGBL1 and LOXHD1, which were not detected by RNA-seq or qPCR. Our transcriptomic analysis suggests that at a molecular level primary HCEnC most closely resemble evHCEC and thus represent a viable therapeutic option for managing corneal endothelial dysfunction. Our findings also suggest that investigators should perform an assessment of the entire transcriptome of cultured HCEnC prior to determination of the potential clinical utility of the cultured HCEnC for the management of corneal endothelial cell failure.
2015-09-04 | GSE65991 | GEO