ArticleBMC medical genomics2015
Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas.
Article in BMC medical genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Downregulated miR-23b-3p expression acts as a predictor of hepatocellular carcinoma progression: A study based on public data and RT-qPCR verification.International journal of molecular medicine · 2018Pooled it
- 14-CpG-Based Signature Improves the Prognosis Prediction of Hepatocellular Carcinoma Patients.BioMed research international · 2020Trial
- Whole-Genome Bisulfite Sequencing Identifies Blood-Based DNA Methylation Biomarker for Hepatocellular Carcinoma.Molecular carcinogenesis · 2026Article
- Integration of RASSF1A and TSPYL5 methylation and AFP protein as plasma biomarker for hepatocellular carcinoma diagnosis.Journal of cancer research and clinical oncology · 2025Article
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- Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2.ACS medicinal chemistry letters · 2024Article
- Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2.bioRxiv : the preprint server for biology · 2024Article
- The role of DNA methylation in human pancreatic neuroendocrine tumours.Endocrine oncology (Bristol, England) · 2023Review
- Assessment of the Feasibility of a Future Integrated Larger-Scale Epidemiological Study to Evaluate Health Risks of Air Pollution Episodes in Children.International journal of environmental research and public health · 2022Article
- A Study to Investigate the Role of Noncoding RNA miR146 Alpha as a Potential Biomarker in Prostate Cancer.Journal of analytical oncology · 2022Article
- DNA Methylation Profiling of Human Hepatocarcinogenesis.Hepatology (Baltimore, Md.) · 2021Observational
- HNF-4α inhibits hepatocellular carcinoma cell proliferation through mir-122-adam17 pathway.PloS one · 2020Article
- A health disparities study of MicroRNA-146a expression in prostate cancer samples derived from African American and European American patients.Journal of solid tumors · 2020Article
- The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity.Scientific reports · 2019Article
- Oncogenic value of microRNA-15b-5p in hepatocellular carcinoma and a bioinformatics investigation.Oncology letters · 2019Article
- The clinicopathological significance of decreased miR-125b-5p in hepatocellular carcinoma: evidence based on RT-qPCR, microRNA-microarray, and microRNA-sequencing.International journal of clinical and experimental pathology · 2019Article
- Article
- RGS17 inhibits tumorigenesis and improves 5-fluorouracil sensitivity in nasopharyngeal carcinoma.OncoTargets and therapy · 2018Article
- Identification of key genes in endometrioid endometrial adenocarcinoma via TCGA database.Cancer biomarkers : section A of Disease markers · 2017Article
- Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma.Hepatoma research · 2016Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEpigenome-wide studies in hepatocellular carcinoma (HCC) have identified numerous genes with aberrant DNA methylation. However, methods for triaging functional candidate genes as useful biomarkers for epidemiological study have not yet been developed.
methodsWe conducted targeted next-generation bisulfite sequencing (bis-seq) to investigate associations of DNA methylation and mRNA expression in HCC. Integrative analyses of epigenetic profiles with DNA copy number analysis were used to pinpoint functional genes regulated mainly by altered DNA methylation.
resultsSignificant differences between HCC tumor and adjacent non-tumor tissue were observed for 28 bis-seq amplicons, with methylation differences varying from 12% to 43%. Available mRNA expression data in Oncomine were evaluated. Two candidate genes (GRASP and TSPYL5) were significantly under-expressed in HCC tumors in comparison with precursor and normal liver tissues. The expression levels in tumor tissues were, respectively, 1.828 and - 0.148, significantly lower than those in both precursor and normal liver tissue. Validations in an additional 42 paired tissues showed consistent under-expression in tumor tissue for GRASP (-7.49) and TSPYL5 (-9.71). A highly consistent DNA hypermethylation and mRNA repression pattern was obtained for both GRASP (69%) and TSPYL5 (73%), suggesting that their biological function is regulated by DNA methylation. Another two genes (RGS17 and NR2E1) at Chr6q showed significantly decreased DNA methylation in tumors with loss of DNA copy number compared to those without, suggesting alternative roles of DNA copy number losses and hypermethylation in the regulation of RGS17 and NR2E1.
conclusionsThese results suggest that integrative analyses of epigenomic and genomic data provide an efficient way to filter functional biomarkers for future epidemiological studies in human cancers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.