ArticleOncoTargets and therapy2020
Exploring DNA Methylation Profiles Altered in Cryptogenic Hepatocellular Carcinomas by High-Throughput Targeted DNA Methylation Sequencing: A Preliminary Study for Cryptogenic Hepatocellular Carcinoma.
Article in OncoTargets and therapy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- Genome-Wide DNA Methylation Markers Associated With Metabolic Liver Cancer.Gastro hep advances · 2025Article
- Transcriptome Profiling of Mouse Embryonic Fibroblast Spontaneous Immortalization: A Comparative Analysis.International journal of molecular sciences · 2024Article
- Introduction of a multiplex amplicon sequencing assay to quantify DNA methylation in target cytosine markers underlying four selected epigenetic clocks.Clinical epigenetics · 2023Article
- Differential methylation patterns in lean and obese non-alcoholic steatohepatitis-associated hepatocellular carcinoma.BMC cancer · 2022Article
- DNA Methylation Profiles of Ovarian Granular Cells from Fluorosis Female Patients Suffering Reproductive Dysfunctions.Biological trace element research · 2022Article
- The expression and prognostic value of Src homology 2 domain-containing transforming protein C3 (SHC3) and its potential role in colorectal cancer.Translational cancer research · 2021Article
- Differential DNA Methylation in Prostate Tumors from Puerto Rican Men.International journal of molecular sciences · 2021Article
- Potential Role of NEU1 in Hepatocellular Carcinoma: A Study Based on Comprehensive Bioinformatical Analysis.Frontiers in molecular biosciences · 2021Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHepatocellular carcinoma (HCC) includes cryptogenic hepatocellular carcinomas (CR-HCC) that lack a defined cause. Specific DNA methylation patterns and comparisons of the aberrant alterations in DNA methylation between CR-HCC and adjacent peritumor tissues (APTs) have not yet been reported.
methodsThe SureSelectXT Methyl-Seq Target Enrichment System was used to sequence targeted DNA methylation in three paired CR-HCC tissues and APTs. Gene Ontology (GO) enrichment and KEGG pathway analysis were performed to investigate the DNA methylation mechanism of CR-HCC. The mRNA expression levels of HOXB-AS3, HOXB6, HOXB3, USP18, MAP3K6, TIRAP, TNNI2, SHC3, CTTN, and TFAP2A, selected from the identified signaling pathways, were evaluated by quantitative real-time PCR (qPCR).
resultsA total of 1728 differentially methylated regions (DMRs) were identified in tumor tissues compared with non-tumor tissues, of which 868 DMRs were hypermethylated and 860 were hypomethylated. The DMRs were mapped within 2091 DMR-associated genes (DMGs). The mRNA expression of HOXB-AS3, HOXB3, and MAP3K6 was downregulated in CR-HCC tissues compared to the APTs. However, the mRNA expression of TIRAP, SHC3, and CTTN was upregulated in the CR-HCC tissues. Differences between the mRNA expression of HOXB6, USP18, TNNI2, and TFAP2A in the CR-HCC and APTS tissues were not statistically significant. GO analysis showed that the molecular functions of "binding", "protein binding", and "cytoskeletal protein binding" were the main categories for the hypermethylated DMGs. The hypomethylated DMGs were mostly enriched in the molecular functions "binding", "protein binding", "calcium ion binding", among others. KEGG pathway analysis showed that the hypermethylated DMGs were enriched in several pathways such as "estrogen signaling pathway", while hypomethylated DMGs were enriched in several pathways such as "proteoglycans in cancer", suggesting that epigenetic modifications play important roles in the cryptogenic hepatocarcinogenesis.
conclusionThese results provide useful information for future work to characterize the functions of epigenetic mechanisms on CR-HCC.
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