ArticleJournal of translational medicine2021
Identification of key methylation differentially expressed genes in posterior fossa ependymoma based on epigenomic and transcriptome analysis.
Article in Journal of translational medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 13 citations in OpenAlex.
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- Single-cell RNA sequencing of anaplastic ependymoma and H3K27M-mutant diffuse midline glioma.BMC neurology · 2024Article
- Identification of hub programmed cell death-related genes and immune infiltration in Crohn's disease using bioinformatics.Frontiers in genetics · 2024Article
- Drugging Hijacked Kinase Pathways in Pediatric Oncology: Opportunities and Current Scenario.Pharmaceutics · 2023Review
- Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis.American journal of cancer research · 2023Article
- The 2021 World Health Organization Classification of Tumors of the Central Nervous System: What Neuroradiologists Need to Know.AJNR. American journal of neuroradiology · 2022Review
- Systemic chemotherapy of pediatric recurrent ependymomas: results from the German HIT-REZ studies.Journal of neuro-oncology · 2021Article
- Review
- Phase II study of everolimus for recurrent or progressive pediatric ependymoma.Neuro-oncology advancesArticle
- The immunopeptidomic landscape of ependymomas provides actionable antigens for T-cell-based immunotherapy.Neuro-oncology advancesArticle
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPosterior fossa ependymoma (EPN-PF) can be classified into Group A posterior fossa ependymoma (EPN-PFA) and Group B posterior fossa ependymoma (EPN-PFB) according to DNA CpG island methylation profile status and gene expression. EPN-PFA usually occurs in children younger than 5 years and has a poor prognosis.
methodsUsing epigenome and transcriptome microarray data, a multi-component weighted gene co-expression network analysis (WGCNA) was used to systematically identify the hub genes of EPN-PF. We downloaded two microarray datasets (GSE66354 and GSE114523) from the Gene Expression Omnibus (GEO) database. The Limma R package was used to identify differentially expressed genes (DEGs), and ChAMP R was used to analyze the differential methylation genes (DMGs) between EPN-PFA and EPN-PFB. GO and KEGG enrichment analyses were performed using the Metascape database.
resultsGO analysis showed that enriched genes were significantly enriched in the extracellular matrix organization, adaptive immune response, membrane raft, focal adhesion, NF-kappa B pathway, and axon guidance, as suggested by KEGG analysis. Through WGCNA, we found that MEblue had a significant correlation with EPN-PF (R = 0.69, P = 1 × 10
conclusionssGSEA and GSVA analysis indicated that these five hub genes could lead to poor prognosis by inducing hypoxia, PI3K-Akt-mTOR, and TNFα-NFKB pathways. Further study of these dysmethylated hub genes in EPN-PF and the pathways they participate in may provides new ideas for EPN-PF treatment.
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