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Transcriptome sequencing in serum exosomes from proliferative diabetic retinopathy (PDR)

ABSTRACT: Transcriptome sequencing in serum exosomes from proliferative diabetic retinopathy (PDR)

PROVIDER: PRJNA740192 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14887177_1.fastq.gz	Fastqsanger.gz
	SRR14887177_2.fastq.gz	Fastqsanger.gz
	SRR14887178_1.fastq.gz	Fastqsanger.gz
	SRR14887178_2.fastq.gz	Fastqsanger.gz

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Transcriptome sequencing in serum exosomes from proliferative diabetic retinopathy (PDR)

Project description:Purpose: To detect serum exosomal ncRNA profiles of proliferative diabetic retinopathy (PDR) by High-throughput sequencing Methods: serum exosomal non-coding RNA (ncRNA) profiles profiles of PDR and MH were generated by deep sequencing, only in once, using IlluminaHiSeq 3000. After analyzing the base composition and quality of the data, according to the analysis results of the original data, the data were filtered to remove the joint sequence and the contaminated part, and to remove low-quality base sequences.If it is paired-ended sequencing data, the filtered data should be further screened to retain the paired sequences and obtain clean data. Conclusions: Our study represents the first detailed analysis of serum exosomal transcriptomes from PDR patients by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

2021-06-24 | GSE178721 | GEO

Vitreous of proliferative diabetic retinopathy patients

Project description:We identified lncRNA expression profiles in vitreous samples between proliferative diabetic retinopathy (PDR) patients and idiopathic macular hole (IMH) patients, and between PDR patients who had received preoperative anti-vascular endothelial growth factor (anti-VEGF) therapy and PDR patients who had received surgery alone. There had been the systemic expression differences in vitreous at the microarray level from PDR patients and IMH patients, and from PDR patients after anti-VEGF treatment and untreated PDR patients.

2022-07-15 | GSE191210 | GEO

Gene Expression Profile of Fibrovascular Membrane Associated with Proliferative Diabetic Retinopathy

2014-08-16 | GSE60436 | GEO

Gene Expression Profile of Fibrovascular Membrane Associated with Proliferative Diabetic Retinopathy

Project description:Proliferative diabetic retinopathy (PDR) is a vision-threatening disorder characterized by the formation of cicatricial fibrovascular membranes leading to traction retinal detachment. Despite the recent advance in the treatment of PDR such as vitreoretinal surgery with use of anti-vascular endothelial growth factor (VEGF) drug as an adjunct, it still remains vision-threatening disease. In order to identify genes associated with the pathogenesis of PDR, we performed gene expression analyses in fibrovascular membrane in patients with PDR using DNA microarray technology. This study was approved by the Ethics Committee of the Kyushu University Hospital and Fukuoka University Chikushi Hospital, and the surgical specimens were handled in accordance with the ethical standards of the 1989 Declaration of Helsinki. All patients gave informed consent before inclusion in the study. Fibrovascular membranes (FVMs) were surgically dissected from the retinal surface with horizontal scissors of patients with PDR undergoing pars plana vitrectomy. These specimens were classified into active and inactive according to the clinical findings of neovascularization (NV) in the FVMs.Total RNA were extracted from the FVMs. RNA from human retina was obtained from Clontech (Palo Alto, CA).

2014-08-16 | E-GEOD-60436 | biostudies-arrayexpress

Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy

Project description:Proliferative diabetic retinopathy (PDR) is the advanced stage of diabetic retinopathy (DR), coupling with irregular neovascularization, and is the leading cause of blindness in working-age people; but the molecular mechanism of vascular differentiation in PDR remains poorly characterized. In our study, we obtained the transcriptome profile of neovascular proliferative membrane specimens from patients with PDR via high-throughput sequencing and advanced bioinformatics. Marker genes of neovascularization were validated and distinct gene expression patterns were formed of PDR compared with normal retina. We also discovered gene sets that were co-expressed with vascular endothelial growth factor A (VEGFA), including transcription factors (TFs) that dysregulate VEGFA. In particular, ETS transcription factors family could negatively regulate VEGFA. We also detected a set of genes related to PDR was dramatically changed from pre-mRNA to mature mRNA. In summary, our study firstly presented the profile of neovascular proliferative membrane and identified new marker genes and key regulators of VEGFA, which could contribute the molecular therapy of PDR in the future.

2020-08-10 | GSE102485 | GEO

Altered expressions of transfer RNA-derived small RNAs and microRNAs in the vitreous humour of proliferative diabetic retinopathy.

Project description:To reveal the expression profiles of transfer RNA-derived small RNA (tsRNA)s and microRNA (miRNA)s in the vitreous humour of proliferative diabetic retinopathy (PDR).

2022-06-10 | GSE199852 | GEO

Differences in Aqueous Humor Protein Profiles in Patients With Proliferative Diabetic Retinopathy Before and After Aflibercept Treatment

Project description:To investigate the changes in aqueous humor (AH) protein profiles before and after intravitreal aflibercept (IVA) treatment in patients with proliferative diabetic retinopathy (PDR) patients. 5 PDR patients provided 10 samples of AH before and after IVA treatment (pre-group vs post-group). Proteins were identified using liquid chromatography-tandem mass spectrometry. Then, bioinformatics was employed to investigate the functional significance of differentially expressed proteins (DEPs) and hub proteins.

2024-05-21 | PXD039210 | Pride

The Multifaceted Role of Vitreous Hyalocytes: Orchestrating Inflammation, Angiomodulation, and Erythrophagocytosis in Proliferative Diabetic Retinopathy

Project description:Despite great advancements in proliferative diabetic retinopathy (PDR) therapy over the last decades, one third of treated patients continue to lose vision. Vitreous macrophages called hyalocytes have been implied in the pathogenesis of vitreoretinal proliferative disease previously but little is known about their role in PDR. In this study, we address molecular and cellular alterations of the PDR vitreous, in order to assess the potential contribution of hyalocytes to PDR development. A total of 55 patients were included in this study encompassing RNA-Sequencing analysis of vitreous hyalocytes from PDR and control patients, multiplex immunoassay and ELISA analysis of undiluted vitreous samples and isolation and immunohistochemical staining of cultured porcine hyalocytes. Our transcriptional analysis revealed an enhanced inflammatory signature of hyalocytes contributing to the cytokine pool within the PDR vitreous by expressing, among others, interleukin-6. The data further indicate an expression shift, involving angiopoietin-2, in PDR hyalocytes converting them to a proangiogenic cellular component, which may mediate formation of retinal neovascularization, hallmark of PDR. Finally, our data suggest a role of vitreous macrophages in erythrophagocytosis and, thereby, removal of vitreous hemorrhage, a severe complication of PDR. Immunomodulation of hyalocytes may thus prove an essential novel therapeutical approach in diabetic vitreoretinal disease.

2024-12-06 | GSE276892 | GEO

Proteomics of Vitreous Humor Reveals Upstream Regulators of Proliferative Diabetic Retinopathy

Project description:To investigate the key regulators of the disease by comparing the abundance of vitreous proteins between the patients with proliferative diabetic retinopathy (PDR) and the controls with idiopathic epiretinal membrane (iERM).

2021-07-26 | PXD027556 |

Single-cell RNA-sequencing reveals the heterogeneity of microglia in fibrous membrane derived from proliferative diabetic retinopathy and proliferative vitreoretinopathy

Project description:Fibrous membrane (FM), the hallmark for proliferative diabetic retinopathy (PDR) and proliferative vitreoretinopathy (PVR), can cause hemorrhages and retinal detachment, which may lead to blindness if not properly treated. However, little is known about the pathophysiology of FM. In this study, we successfully employed single-cell RNA sequencing on the small-sized vitreous FMs, and generated a comprehensive cell atlas of FMs derived from PVR and PDR. Distinct cell compositions were identified in the FMs, with microglia as the major cell population. Additionally, our analysis revealed a spectrum of microglia activation states with distinct molecular signatures and intercellular interactions in disease-specific microenvironment. This description of microglia phenotypes in the FM of PVR and PDR may offer insight into the activation of microglia in the FM pathogenesis, as well as potential signaling pathways amenable to disease-specific intervention.

2022-01-27 | GSE165784 | GEO

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