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An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [ATAC-seq]

ABSTRACT: An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [ATAC-seq]

PROVIDER: PRJNA1135952 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29830191_1.fastq.gz	Fastqsanger.gz
	SRR29830191_2.fastq.gz	Fastqsanger.gz
	SRR29830192_1.fastq.gz	Fastqsanger.gz
	SRR29830192_2.fastq.gz	Fastqsanger.gz
	SRR29830193_1.fastq.gz	Fastqsanger.gz

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An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [RNA-seq]

Project description:Previous Genome-wide association studies (GWASs) have identified susceptibility loci of primary angle closure glaucoma (PACG), but applicating these findings is difficult. Although shallow anterior chamber depth (ACD) and short axial length (AL) are characteristic phenotypes of PACG, current GWAS variants do not show any correlation with these features, calling for the identification of more risk factors . Here, thicker and enlarged iris was identified as a significant independent risk factors. By employing allelic-specific STARR-seq and assay for transposase-accessible chromatin using sequencing (ATAC-seq), we screened disease-related variants in linkage disequilibrium and identified 2 causative variants in iris. Alterations in these variants may contribute to the pathogenic iris phenotype by upregulating the expression of PLEKHA7 and C10orf53, potentially regulating PACG development and progression. Our efforts nominate the important role of iris and identify pathogenic SNP-target gene interactions for PACG, providing a potentially powerful approach for interpreting noncoding variation of diseases.

2024-07-22 | GSE272250 | GEO

An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [ATAC-seq]

2024-07-22 | GSE272247 | GEO

An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [STARR-seq]

2024-07-22 | GSE272251 | GEO

Primary angle closure glaucoma is characterized by altered extracellular matrix homeostasis in the iris

Project description:Purpose. To characterize the proteome of the iris in primary angle closure glaucoma (PACG). Experimental Design. In this cross-sectional study, iris samples were obtained from surgical iridectomy of 48 adults with PACG and five normal controls. Peptides from iris were analyzed using liquid chromatography-tandem mass spectrometry on an Orbitrap Q Exactive Plus mass spectrometer. Verification of proteins of interest was conducted using selected reaction monitoring on a triple quadrupole mass spectrometer. The main outcome was proteins with a log2 two-fold difference in expression in iris between PACG and controls. Results. There were 3,446 non-redundant proteins identified in human iris, of which 165 proteins were upregulated and 251 proteins were downregulated in PACG compared with controls. Thirty-two upregulated proteins were either components of the extracellular matrix (ECM) (fibrillar collagens, EMILIN-2, fibrinogen, fibronectin, matrilin-2), matricellular proteins (thrombospondin-1), proteins involved in cell-matrix interactions (integrins, laminin, histidine-rich glycoprotein, paxillin), or protease inhibitors known to modulate ECM turnover (-2 macroglobulin, tissue factor pathway inhibitor 2, papilin). Two giant proteins, titin and obscurin, were up- and down-regulated, respectively, in the iris in PACG compared with controls. Conclusions and Clinical Relevance. This proteomic study shows that ECM composition and homeostasis is altered in the iris in PACG.

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Aqueous humour proteomic analysis of acute angle-closure glaucoma with visual field loss

Project description:original data of Aqueous humour proteomic analysis of acute angle-closure glaucoma with visual field loss.

2021-02-05 | PXD024028 |

An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [STARR-seq]

Project description:An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [STARR-seq]

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An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [RNA-seq]

Project description:An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [RNA-seq]

| PRJNA1135949 | ENA

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

Project description:The iris is a fine structure that controls the amount of light that enters the eye. Iris diseases that result in visual disability and blindness include iritis, primary angle closure glaucoma, and pigment dispersion syndrome. A detailed investigation of the proteome of the normal human iris may provide a foundation for new investigations into the iris biology and pathophysiology. We conducted an in-depth proteomic analysis of five normal irides. Proteins were fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. We identified 3,000 non-redundant proteins in the human iris, including 26 unambiguous protein isoforms. The proteins identified in the iris included numerous proteins involved in smooth muscle motility, melanosome development, extracellular matrix, and selenoproteins involved in redox signaling. The MS proteome database of the human iris may serve as a valuable resource for future investigations of the eye in health and disease.

2016-07-18 | PXD001424 | Pride

Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma

Project description:To better understand the molecular changes in the aqueous humor (AH) content with glaucoma, we analyzed the microRNA (miRNA) profiles of AH samples from patients with Primary Open Angle Glaucoma (POAG) and Exfoliation Glaucoma (XFG) compared to non-glaucoma controls.

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The potential role of long noncoding RNAs in primary open angle glaucoma

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2019-09-28 | GSE138125 | GEO

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