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DNA methylation analysis of the cell free DNA from Retinoblastoma

ABSTRACT: DNA methylation analysis of the cell free DNA from Retinoblastoma

PROVIDER: PRJNA804516 | ENA |

REPOSITORIES: ENA

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DNA methylation analysis of the cell free DNA from Retinoblastoma

Project description:Retinoblastoma (RB) is a primary intraocular cancer in infants and toddlers. Direct biopsy is contraindicated in RB due to the risks of provoking extraocular tumor spread. In this study, we demonstrated that DNA methylation profile can be obtained from the tumor-derived cell-free DNA in aqueous humor (AH) and is highly concordance with that directly from RB primary tumors. It is the first time to identify unique DNA methylation pattern from RB tumor before surgically removing the eye. We provde the evidence that DNA methylation from AH could not only be used for RB diagnosis, but also for the prognostic prediction and potential therapeutic targets by personalized approach.

2022-08-18 | GSE196363 | GEO

Functions of UHRF1 in the regulation of DNA methylation in retinoblastoma

Project description:UHRF1 (ubiquitin-like with PHD and ring finger domains 1) is an epigenetic regulator that is involved in the regulation of DNA and histone methylation and many other cellular events. The UHRF1 is frequently found to be overexpressed in various human cancers, and its overexpression has been associated with pro-tumorigenic effects such as inhibition of apoptosis and high metastatic potential. However, the molecular mechanisms underlying these pro-tumorigenic effects of UHRF1 overexpression in cancers still remain unclear. Retinoblastoma (Rb) is an intraocular tumor which arises from developing retina by biallelic inactivation of Rb1 gene. In this study, we uncovered that the UHRF1 is highly expressed in retinoblastoma, and genomes of retinoblastoma have differential DNA methylation patterns compared to those of normal retina, characterized by global hypomethylation and promoter hypermethylation at key tumor suppressor genes. Given the well-documented functions of UHRF1 in the regulation of DNA methylation, we hypothesized that the overexpressed UHRF1 may contribute to the aberrant DNA methylation in retinoblastoma genomes. To test our hypothesis, we profiled the genome-wide methylation patterns in normal retina and Y79 retinoblastoma cell line by MeDIP-seq, and then investigated how the methylation patterns in Y79 are affected by down-modulation of UHRF1. For identification of differentially methylated regions between the control and UHRF1 knockdown Y79 cells, we analysed three independent sets of sequencing data to unambiguously determine the effects of UHRF1 down-modulation on the methylome of Y79 retinoblastoma cells.

2017-03-30 | GSE92712 | GEO

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

Methylation profiles of cell-free DNA using nanopore sequencing

Project description:Methylation profiles of cell-free DNA using nanopore sequencing

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Methylation profiles of cell-free DNA using nanopore sequencing

Project description:Methylation profiles of cell-free DNA using nanopore sequencing

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Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA

Project description:Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA

| PRJNA493114 | ENA

Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy

Project description:DNA methylation progiling of circulaing cell-free DNA isolatated from serum of 12 MTLE patients and 11 healthy controls. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs.

2023-01-11 | GSE208758 | GEO

FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

Project description:FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

| PRJNA965897 | ENA

FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

Project description:FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

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QUANTITATIVE PHOSPHOPROTEOMIC PROFILING OF PRIMARY RETINOBLASTOMA TUMORS

Project description:Retinoblastoma is a malignant tumor of the retina which most often occurs in children below 5 years of age with an incident rate of about 1 in 15,000 to 18,000 live births. Retinoblastoma is the first ever cancer that was reported to have a genetic basis. It occurs widely due to inactivating mutations in RB1 gene. Gene expression studies, copy number variation analysis, epigenetic profiling including miRNA and methylation of retinoblastoma has been carried to understand the disease mechanism and key players in the disease. Our group has earlier performed differential proteomics of retinoblastoma to identify proteins of therapeutic importance. However, there are no studies to understand the signalling mechanisms associated with retinoblastoma. Hence, global phosphoproteomics of retinoblastoma was carried out to identify signalling events associated with this cancer. Our study identified stress response proteins to be hyper phosphorylated which included H2AFX and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma that indicated activation of DNA damage response pathways. We also observed activation of anti-apoptotic proteins in retinoblastoma compared to control. These observations showed activation of survival pathways and signalling networks activated in tumors.

2019-11-11 | PXD007228 | Pride

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