DNA methylation biomarkers for hepatocellular carcinoma

Cancer Cell International
Guorun FanXiong Cai

Abstract

Aberrant methylation of DNA is a key driver of hepatocellular carcinoma (HCC). In this study, we sought to integrate four cohorts profile datasets to identify such abnormally methylated genes and pathways associated with HCC. To this end, we downloaded microarray datasets examining gene expression (GSE84402, GSE46408) and gene methylation (GSE73003, GSE57956) from the GEO database. Abnormally methylated differentially expressed genes (DEGs) were sorted and pathways were analyzed. The String database was then used to perform enrichment and functional analysis of identified pathways and genes. Cytoscape software was used to create a protein-protein interaction network, and MCODE was used for module analysis. Finally, overall survival analysis of hub genes was performed by the OncoLnc online tool. In total, we identified 19 hypomethylated highly expressed genes and 14 hypermethylated lowly expressed genes at the screening step, and finally found six mostly changed hub genes including MAD2L1, CDC20, CCNB1, CCND1, AR and ESR1. Pathway analysis showed that aberrantly methylated-DEGs mainly associated with the cell cycle process, p53 signaling, and MAPK signaling in HCC. After validation in TCGA database, the methylation and expressio...Continue Reading

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Citations

Mar 28, 2020·United European Gastroenterology Journal
Feb 6, 2021·Journal of Clinical Medicine·Tom Domovitz, Meital Gal-Tanamy
Jul 3, 2021·International Journal of Molecular Sciences·Patricia de la Cruz-OjedaJordi Muntané
Aug 16, 2021·Journal of Biochemical and Molecular Toxicology·Salwa M Abo El-KhairAyman Z Elsamanoudy
Aug 28, 2021·Cancers·Ewa Wolinska, Maciej Skrzypczak
Oct 8, 2021·Frontiers in Oncology·Fang MiaoChenggang Yang

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Datasets Mentioned

BETA
GSE46408
GSE57956
GSE84402
GSE73003

Methods Mentioned

BETA
methylation profiling
ESR

Software Mentioned

GEO2R
MEXPRESS
STRING
CytoHubba
Search Tool for the Retrieval of Interacting Genes ( STRING
OncoLnc
Cytoscape
Funrich

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