Dataset Information

Genome-wide methylation analysis of circulating tumor DNA: A new biomarker for recurrent glioblastom.

ABSTRACT:

Background

Glioblastoma (GBM) is a malignant tumor with a short survival and poor prognosis and a lack of clinically validated biomarkers for diagnosis and prognosis.

Methods

We collected cerebrospinal fluid (CSF) samples and normal CSF sample from recurrent GBM patients and paired tissue samples. Methylation profiles of CSF circulating tumor DNA (ctDNA) and transcriptional profiles of tumor tissues were analyzed. The China Glioma Genome Atlas (CGGA) database and Gene Expression Omnibus (GEO) was used for data analysis.

Results

Lasso analysis and multiplex Cox analysis were performed using intersecting genes of differentially methylated regions and differentially expressed genes. 8 hub genes were screened to construct diagnostic and prognostic models. Based on these 8 hub genes, the diagnostic (AUC = 0.944) and prognostic (3-years, AUC = 0.876) models were accurate.

Conclusions

In this study, 8 hub genes were identified for the diagnosis and prognosis of recurrent GBM, providing new biomarkers for the clinical study of recurrent GBM.

SUBMITTER: Dai L

PROVIDER: S-EPMC10031355 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide methylation analysis of circulating tumor DNA: A new biomarker for recurrent glioblastom.

Dai Lin L Liu Zhihui Z Zhu Yi Y Ma Lixin L

Heliyon 20230315 3

<h4>Background</h4>Glioblastoma (GBM) is a malignant tumor with a short survival and poor prognosis and a lack of clinically validated biomarkers for diagnosis and prognosis.<h4>Methods</h4>We collected cerebrospinal fluid (CSF) samples and normal CSF sample from recurrent GBM patients and paired tissue samples. Methylation profiles of CSF circulating tumor DNA (ctDNA) and transcriptional profiles of tumor tissues were analyzed. The China Glioma Genome Atlas (CGGA) database and Gene Expression O ...[more]

PMID: 36967887

Similar Datasets

Project description:Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1-4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2'-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (>0.2 average ?-value difference) between chordomas and nucleus pulposus samples (adjusted P < 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.

Dataset Information

Genome-wide methylation analysis of circulating tumor DNA: A new biomarker for recurrent glioblastom.

Background

Methods

Results

Conclusions

Publications

Genome-wide methylation analysis of circulating tumor DNA: A new biomarker for recurrent glioblastom.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets