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MiRNA profiles of natural recovery in vitreous humor after NAION induction in rat

ABSTRACT: We collected some vitreous humors from rat eyes through a photolabile paper based chip which experienced different natural recovery processes at day 0, 0.25, 1, 3, 7 day after eye stroke by laser induced in rat. These mirs samples were collected from extracelluar vesicles of vitreous humor in rat. We used microarray to find some new miRNAs that may participate in the natural recovery process after experience eye stroke.

ORGANISM(S): synthetic construct Rattus norvegicus

PROVIDER: GSE154312 | GEO | 2023/06/30

REPOSITORIES: GEO

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Proteomic analysis of human vitreous humor

Project description:In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. We identified 1269 proteins. This largest catalog of vitreous proteins to date should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.

2014-08-08 | PXD000957 | Pride

Protein composition of the subretinal fluid suggest selective diffusion of vitreous proteins in retinal detachment

Project description:Purpose: To study the proteome of the subretinal fluid (SRF) from rhegmatogenous retinal detachment (RRD) in search for novel markers for improved diagnosis and prognosis of RRD. Methods: Human undiluted SRF obtained during vitrectomy for primary RRD using a 41G needle (n = 24) was analyzed and compared to vitreous humor from 2-days post-mortem eyes (n = 20). Sample preparation underwent nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS). Label-free quantification (LFQ) using MaxQuant was used to determine differential expressed proteins between SRF and vitreous humor. The intensity-based absolute quantification (iBAQ) was used to rank proteins according to their molar fractions within groups. Identification of proteins beyond the quantitative level was performed using the Mascot search engine. Results: The protein concentration of the control vitreous humor was lower and more consistent (1.2 ± 0.4 mg) than that of the SRF (17.9 ± 22 mg). The iBAQ analysis showed high resemblance between SRF and vitreous humor, except for crystallins solely identified in vitreous humor. The LFQ analysis found 37 protein misregulations between SRF and vitreous humor of which the blood coagulation pathway was found to be enriched using the PANTHER Classification System. Combined, the iBAQ, LFQ and Mascot analysis found an overlap only in chitinase-3-like protein 1 and galectin-3-binding protein unique to the SRF. Conclusions: The proteome of the SRF was highly represented by proteins involved in proteolysis. Such proteins can possibly serve as targets in modulating the effects of SRF in RD.

2020-10-20 | PXD019159 | Pride

A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (ATAC-Seq)

Project description:Lens epithelial explants consist of lens epithelial cells (P8 FVB/N mice) grown in vitro on their native basement membrane, the lens capsule. For decades, biologists have used lens epithelial explants to study lens fiber cell differentiation. However, the global change in the accessibility of the chromatin and transcriptome during the process of explanting and culture is unknown. Therefore, P8 FVB/N lens epithelial explants cultured in either unsupplemented media or media containing 50% bovine vitreous humor for one or five days were collected. Chromatin and RNA was collected for ATAC-sequencing and RNA-sequencing respectively. Differentially accessible regions and differentially expressed genes were identified for each condition to provide a genome wide view of chromatin architecture and gene expression during fiber cell differentiation in vitro. Vitreous humor generally increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had relatively little effect on the accessibility of most of the genes highly expressed in the lens epithelium despite dramatic reductions in the transcript levels of these genes.

2023-02-15 | GSE215952 | GEO

A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (RNA-Seq)

2023-02-15 | GSE215950 | GEO

Proteomics of aqueous humor for biomarkers discovery in retinoblastoma

Project description:Background: Recent therapeutic advances have greatly improved the eye preservation rate in patients affected by retinoblastoma (RB), however local tumor control remains more difficult in the presence of resistant and/or relapsing retinal or vitreous disease. Thus, the identification of new biomarkers is crucial to design more effective treatment approaches. Recently, technological advances have allowed to safely recover aqueous humor (AH) from patients affected by RB undergoing local treatment. Methods: in order to identify specific proteins associated to active vitreous seeding, we have performed proteomic analysis of AH samples derived from patients affected by RB in different disease stages. Fifty-five AH samples were firstly included in this study. A new widened cohort was then used to validate the proteins identified in the previous discovery set. Results: a total of 808 and 630 proteins were identified in the two analysis, respectively. Five proteins resulted more expressed in the active vitreous seeding group: C19orf57, Girdin, SRFBP, GULP-1 and DCD. These proteins are involved in cytoskeleton regulation, tumor proliferation and growth, invasion and migration of cancer cells. Conclusion: reliable prognostic biomarkers are needed to guide RB management. Proteomic analysis of AH provide a unique opportunity to identify tumor associated biomarkers in patients with RB.

2023-03-10 | PXD022218 | Pride

In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection

Project description:S. aureus SA564 and SA564-codY-mutant were grown in bovine aqueous humor, bovine vitreous humor and a chemically defined medium. Samples were extracted in midlog phase and affymetrix microarray processing was performed.

2015-09-12 | E-MTAB-2928 | biostudies-arrayexpress

Proteomics of aqueous humor for biomarkers discovery in retinoblastoma (pt2)

2023-03-10 | PXD022256 | Pride

Comparative shotgun proteomics of aqueous humor for cataract, glaucoma and pseudoexfoliation eye disorders.

Project description:The aim of this work was to characterize proteome of aqueous humor from subjects with various eye conditions such as cataract, glaucoma and pseudoexfoliation syndrome by high-resolution chromate-mass-spectrometry. Twenty nine human aqueous humor samples were processed by shotgun proteomics. Data was searched using MaxQuant package. Totally, 263 protein groups were identified. Label-free quantitation reported some differentially expressed proteins in aqueous humor proteome for the aforementioned eye diseases.

2016-05-23 | PXD002623 | Pride

The Constitutive Proteome of Human Aqueous Humor

Project description:Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging mainly due to low sample volume and protein concentration. In this study, by utilizing state of the art technology, we performed Liquid-Chromatography Mass spectrometry (LC-MS/MS) analysis of 88 aqueous humor samples from subjects undergoing cataract surgery.

2021-09-09 | PXD022463 | Pride

RNA-sequencing uncovers transcriptomic changes in retinal tissues after vitreous substitution with a thermogelling polymer

Project description:We developed a thermogelling polymer with intrinsic anti-scarring properties on retinal cells in-vitro. To study its mechanism of action in-vivo, this thermogelling polymer was injected into the rabbit eye as a vitreous substitute and the retinal tissues were harvested for RNA-sequencing to understand transcriptomic changes induced by the polymer.

2022-04-09 | GSE200476 | GEO

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