ArticleClinical epigenetics2020
A DNA methylation signature to improve survival prediction of gastric cancer.
Article in Clinical epigenetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 75 citations in OpenAlex.
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- Hypermethylation of the sodium channel beta subunit gene promoter is associated with colorectal cancer.Hereditas · 2024Article
- Methods for the Analysis of Multiple Epigenomic Mediators in Environmental Epidemiology.Current environmental health reports · 2024Review
- Identification of a novel m6A-related lncRNAs signature and immunotherapeutic drug sensitivity in pancreatic adenocarcinoma.BMC cancer · 2024Article
- New insight into the CNC-bZIP member, NFE2L3, in human diseases.Frontiers in cell and developmental biology · 2024Review
- Inactivation of epithelial sodium ion channel molecules serves as effective diagnostic biomarkers in clear cell renal cell carcinoma.Genes & genomics · 2023Article
- Predictive value of DNA methylation in the efficacy of chemotherapy for gastric cancer.Frontiers in oncology · 2023Article
- Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis.Journal of computational biology : a journal of computational molecular cell biology · 2022Review
- Downregulation of epithelial sodium channel (ENaC) activity in cystic fibrosis cells by epigenetic targeting.Cellular and molecular life sciences : CMLS · 2022Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe current Union International Committee on Cancer or the American Joint Committee on Cancer TNM stage system has shown valuable but insufficient estimation for subsets of gastric cancer and prediction for prognosis patients. Thus, there is an urgent need to identify diagnostic, prognostic, and predictive biomarkers to improve patients' outcomes. Our aim was to perform an integrative analysis on publicly available datasets to identify epigenetic changes that may play key role in the initiation and progression of gastric cancer, based on which we set to develop a DNA methylation signature to improve survival prediction of gastric cancer.
resultsA total of 340 methylation-related differentially expression genes (mrDEGs) were screened in gastric cancer patients from The Cancer Genome Atlas (TCGA) project. Pathway enrichment analysis revealed that they were involved in the biological process related to initiation and progression of gastric cancer. Based on the mrDEGs identified, we developed a DNA methylation signature consisting of ten gene members (SCNN1B, NFE2L3, CLDN2, RBPMS2, JPH2, GBP6, COL4A5, SMKR1, PPP1R14A, and ARL4D) according to their methylation β value. This innovative DNA methylation signature was associated with cancer recurrence, while it showed independence of cancer recurrence and TNM stage for survival prediction. Combination of this DNA methylation signature and TNM stage improved overall survival prediction in the receiver operating characteristic analysis. We also verified that two individual genes (PPP1R14A and SCNN1B) of the identified prognostic signature were regulated by promoter region methylation in a panel of gastric cell lines.
conclusionsThis study presents a powerful DNA methylation signature by performing analyses integrating multi-source data including transcriptome, methylome, and clinical outcome of gastric cancer patients from TCGA. The identified DNA methylation signature may be used to refine the current prognostic model and facilitate further stratification of patients in the future clinical trials. Further experimental studies are warranted to unveil the regulatory mechanism and functional role of all the individual genes of the DNA methylation signature. Also, clinical investigations in large GC patient cohorts are greatly needed to validate our findings.
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