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Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy

ABSTRACT: Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy

PROVIDER: PRJNA858063 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20105049.fastq.gz	Fastqsanger.gz
	SRR20105050.fastq.gz	Fastqsanger.gz
	SRR20105051.fastq.gz	Fastqsanger.gz
	SRR20105052.fastq.gz	Fastqsanger.gz
	SRR20105053.fastq.gz	Fastqsanger.gz

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Retinoblastoma Aqueous Humor Liquid Biopsy Repository

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Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy: moving beyond genomics

Project description:Identify DNA methylation change in retinoblastoma using aqueous humor cfDNA

2022-08-18 | GSE208053 | GEO

Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy: moving beyond genomics

Project description:Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy: moving beyond genomics

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Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy.

Project description:Retinoblastoma (RB) is a cancer that forms in the developing retina of babies and toddlers. The goal of therapy is to cure the tumor, save the eye and maximize vision. However, it is difficult to predict which eyes are likely to respond to therapy. Predictive molecular biomarkers are needed to guide prognosis and optimize treatment decisions. Direct tumor biopsy is not an option for this cancer; however, the aqueous humor (AH) is an alternate source of tumor-derived cell-free DNA (cfDNA). Here we show that DNA methylation profiling of the AH is a valid method to identify the methylation status of RB tumors. We identify 294 genes directly regulated by methylation that are implicated in p53 tumor suppressor (RB1, p53, p21, and p16) and oncogenic (E2F) pathways. Finally, we use AH to characterize molecular subtypes that can potentially be used to predict the likelihood of treatment success for retinoblastoma patients.

| S-EPMC9492718 | biostudies-literature

Characterizing DNA methylation signatures of retinoblastoma using the aqueous humor liquid biopsy

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-08-17 | GSE208055 | GEO

microRNA profiling in the aqueous humor of highly myopic eyes by next generation sequencing

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

Effect of prostaglandin analogs on aqueous humor outflow

Project description:The purpose of this study is to discover genes that might increase aqueous humor outflow when human ciliary muscle or human trabecular meshwork cells are treated with the prostaglandin analogues latanoprost free acid or prostaglandin F2alpha. Five tissue donors were pooled on each chip. Keywords: other

2003-07-16 | GSE492 | 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

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

2023-03-10 | PXD022256 | Pride