Aqueous microRNA profiling in age-related macular degeneration and polypoidal choroidal vasculopathy by next-generation sequencing
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE221905 | GEO | 2022/12/29
REPOSITORIES: GEO
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Project description:Aqueous microRNA profiling in age-related macular degeneration and polypoidal choroidal vasculopathy by next-generation sequencing
| PRJNA916689 | ENA
Project description:Purpose: The goals of this study were to identify expression patterns in a large population of human donor choroids, including donors with early atrophic AMD Methods: Independent libraries were prepared for choroidal cells from twenty human donors. Macular samples from donors 1,2,3,5, 11, and 12 were acquired, analyzed, and uploaded in previous experiments (GSE135922 - donors 1,2, 11, and 12; GSE149100- donors 3 and 5). Choroidal punches were gently dissociated in collagenase II for 1 hour before cryopreservation. Thawed cells underwent endothelial cell enrichment by incubating with anti-CD31-microbeads. Final libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build hg38 with CellRanger(v6.0.0) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v4). Results: A total of 30416 cells were recovered after filtering with 5,607,479,828 corresponding reads. A total of 17097 cells were recovered from AMD donor libraries while 13319 cells were recovered from control donors. Clusters were assigned to known choroidal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from AMD versus control libraries. Particular emphasis was given to choriocapillaris endothelial cells. Conclusions: This study characterizes new gene expression signatures for several choroidal cells, including tissue resident macrophages, inflammatory macrophages, arterioles, and venules.
2022-02-21 | GSE183320 | GEO
Project description:To investigate the proteomic profiles of the aqueous humor (AH) of individuals with diabetic macular edema (DME).
2022-04-24 | PXD033404 |
Project description:Age-related macular degeneration (AMD) is a common, blinding disease of the elderly in which macular photoreceptor cells, retinal pigment epithelium, and choriocapillaris endothelial cells ultimately degenerate. Recent studies have found that degeneration of the choriocapillaris occurs early in this disease and that this endothelial cell dropout is concomitant with increased deposition of the complement membrane attack complex (MAC) at the choroidal endothelium. However, the impact of MAC injury to choroidal endothelial cells is poorly understood. To model this event in vitro, and to study the downstream consequences of MAC injury, endothelial cells were exposed to complement from human serum, compared to heat inactivated serum which lacks complement components. Cells exposed to complement components in human serum showed increased labeling with antibodies directed against the MAC, time and dose dependent cell death as assessed by lactate dehydrogenase assay, and increased permeability. RNA-Seq analysis following complement injury revealed increased expression of genes associated with angiogenesis including matrix metalloproteases (MMPs) 3 and 9, and VEGF-A. The MAC-induced increase in MMP9 RNA expression was validated using C5 depleted serum compared to C5 reconstitited serum. Increased levels of MMP9 were also determined using Western blot and zymography. These data suggest that, in addition to cell lysis, complement attack on choroidal endothelial cells promotes an angiogenic phenotype in surviving cells. RNA-Seq of RF/6A (cultured choroidal endothelial cells from Rhesus macaque) treated with either 50% heat-inactivated human serum ([CONTROL], n=3) or 50% normal human serum (active complement membrane attack complex [MAC], n=3)
2015-11-04 | E-GEOD-70806 | biostudies-arrayexpress
Project description:Although genome-wide association studies, animal models, and cell culture systems have yielded important insights into the pathogenesis of neovascular age-related macular degeneration (nAMD), the underlying molecular pathways remain ill defined. Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) of body donor eyes and were thus limited by the time span from death to preservation and the associated rapid 5'-RNA degradation. In this study, CNVs were therefore formalin-fixed immediately after surgical extraction from patients with nAMD and analyzed using a 3’ RNA sequencing approach called Massive Analysis of cDNA Ends (MACE). Age-matched formalin-fixed paraffin-embedded (FFPE) RPE-choroidal specimens obtained from the macular region of enucleated eyes with ciliary body melanoma served as controls. Transcriptome profiles were generated and disease-associated gene signatures were identified using statistical and bioinformatic methods. Calprotectin (S100A8/A9) protein expression was investigated by immunohistochemistry and ELISA.We identified 158 differentially-expressed genes (DEG) that were significantly increased in CNV compared to control tissue. Gene ontology enrichment analysis demonstrated that these DEG contributed to biological processes, such as Blood Vessel Development, Extracellular Structure Organization, Response to Wounding and several immune-related terms. The S100 calcium-binding protein A8 (S100A8) and S100A9 emerged among the top DEG, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples from nAMD patients and controls. This study provides a high-resolution RNA-sequencing-based transcriptional signature of choroidal neovascular membranes in AMD patients and reveals S100A8/A9 as a novel biomarker and promising target for AMD-directed therapeutics and diagnostics.
2020-04-09 | GSE146887 | GEO
Project description:Polypoidal choroidal vasculopathy (PCV) is characterized by polyp-like dilatation of blood vessels and turbulent blood flow in the choroid of the eye. Here, we cultivated blood outgrowth endothelial cells (BOECs) from PCV patients and normal controls. When BOECs were exposed to heterogeneous flow, single-cell analysis revealed that PCV BOECs preferentially adopted migratory-angiogenic cell state, while normal BOECs undertook proinflammatory cell state. PCV BOECs also had a repressed protective response to flow stress by demonstrating lower mitochondrial functions. We uncovered that elevated hyaluronidase-1 in PCV BOECs led to increased degradation of hyaluronan, a major component of endothelial glycocalyx. Hyaluronidase-1 was correspondingly detected in PCV patient vitreous humor and plasma samples. Notably, knockdown of hyaluronidase-1 in PCV BOECs modulated their abnormal cell migration and barrier permeability due to glycocalyx impairment. Therefore, hyaluronidase-1 inhibition could be a potential therapeutic modality in preserving glycocalyx integrity and endothelial stability in ocular diseases with vascular origin.
2022-01-20 | GSE179631 | GEO
Project description:Purpose: To characterize microRNAs (miRNAs) and their possible roles in high myopia by using next generation sequencing Methods: Aqueous humor samples were obtained from 15 highly myopic eyes and 15 cataract eyes at the onset of surgery. miRNA next generation sequencing and bioinformatics analyses were performed using RNA extracted from aqueous humor samples. Results: A total of 341 miRNAs were detected in the aqueous humor samples of highly myopic eyes; 201 miRNAs were detected in the aqueous humor samples of cataractous control eyes. A total of 249 mature miRNAs and 17 novel miRNAs were differentially expressed during myopia. Possible pathways regulated by these aberrantly expressed miRNAs included the TNF, MAPK, PI3K-Akt, and HIF-1 signaling pathways. Conclusions: The current study provided an overall view of miRNA profiling in the aqueous humor of highly myopic eyes. These profiles may be associated with myopia pathogenesis, and are potential biomarkers.
2021-12-15 | GSE142359 | GEO
Project description:We profiled using single cell RNA sequencing the immune cells of the aqueous humor from patients with uveitis.
2023-12-14 | GSE229166 | GEO
Project description:Previous studies on the biomarkers of pathologic myopia choroidal neovascularization (pmCNV) development merely detected limited types of proteins and provide a meagre illustration of the underlying pathways. Hence, an intact picture of molecular changes in the aqueous humor (AH) of pmCNV patients is lacking. Here, to explore the potential mechanisms and biomarkers of pmCNV, we analyzed the correlation between atrophic (A) lesions and neovascular (N) lesions in a myopic cohort based on the ATN grading system for myopic maculopathy (MM). In a quantitative proteomics test of AH profile of our patients, a significant correlation was found between A and N lesions (R = 0.5753, P < 0.0001). Accordingly, groups were divided into patients without MM, patients with myopic atrophic maculopathy (MAM), and patients with pmCNV (N2a lesion). In proteomics analysis, the existence of GFAP and complement-associated molecules in AH samples of the 3 groups also supported that MAM and pmCNV shared similar characteristics. Analyses of the differentially expressed proteins between the pmCNV group and two controls were performed. We identified several potential biomarkers for pmCNV, including FCN3, GFAP, EGFR, SFRP3, PPP2R1A, SLIT2, and CD248. Taken together, our study provides new insights for further research on pmCNV development.
2024-01-26 | PXD038430 | Pride
Project description:To investigate the differences in gene expression between matched human macular and peripheral choroidal endothelial cells (CEC) and matched human macular inner and outer CEC. The gene expression profiles of the unpassaged cell types were compared using Affymetrix GeneChip arrays. 9 arrays are included. 6mm diameter samples were dissected from 3 regions of the eye: peripheral inner choroid, macular outer choroid and macular inner choroid. RNA extracts from cells were hybridised to Affymetrix HGU133plus2 arrays in triplicate.
2013-12-31 | E-GEOD-51246 | biostudies-arrayexpress