ArticleGastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association2016
Establishment of a DNA methylation marker to evaluate cancer cell fraction in gastric cancer.
Article in Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 28 citations in OpenAlex.
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- Epigenetic disruption of adipogenic gene enhancers in dedifferentiated liposarcomas and its therapeutic value.Frontiers in oncology · 2025Article
- Clinicopathological Significances and Prognostic Value ofJournal of Cancer · 2023Article
- Consistent DNA Hypomethylations in Prostate Cancer.International journal of molecular sciences · 2022Article
- DNMT3B overexpression downregulates genes with CpG islands, common motifs, and transcription factor binding sites that interact with DNMT3B.Scientific reports · 2022Article
- Prediction of tissue origin of adenocarcinomas in the esophagogastric junction by DNA methylation.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2022Article
- DNA methylation marker to estimate ovarian cancer cell fraction.Medical oncology (Northwood, London, England) · 2022Article
- Eps15 Homology Domain-Containing Protein 3 Hypermethylation as a Prognostic and Predictive Marker for Colorectal Cancer.Biomedicines · 2021Article
- Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles.Frontiers in oncology · 2021Article
- The mMolecular therapy oncolytics · 2020Article
- RPL38 Regulates the Proliferation and Apoptosis of Gastric Cancer via miR-374b-5p/VEGF Signal Pathway.OncoTargets and therapy · 2020Article
- Novel prodrugs of decitabine with greater metabolic stability and less toxicity.Clinical epigenetics · 2019Article
- LINC00162 confers sensitivity to 5-Aza-2'-deoxycytidine via modulation of an RNA splicing protein, HNRNPH1.Oncogene · 2019Article
- Significance of molecular classification of ependymomas: C11orf95-RELA fusion-negative supratentorial ependymomas are a heterogeneous group of tumors.Acta neuropathologica communications · 2018Article
- DNA Methylation Biomarkers for the Diagnosis of Barrett's Oesophagus.The American journal of gastroenterology · 2018Article
- Hypermethylation ofOncotarget · 2017Article
- Genetic Alterations in Gastric Cancer Associated withFrontiers in medicine · 2017Review
- DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation.American journal of cancer research · 2017Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTumor samples are unavoidably contaminated with coexisting normal cells. Here, we aimed to establish a DNA methylation marker to estimate the fraction of gastric cancer (GC) cells in any DNA sample by isolating genomic regions specifically methylated in GC cells.
methodsGenome-wide and gene-specific methylation analyses were conducted with an Infinium HumanMethylation450 BeadChip array and by quantitative methylation-specific PCR, respectively. Purified cancer and noncancer cells were prepared by laser-capture microdissection. TP53 mutation data were obtained from our previous study using next-generation target sequencing.
resultsGenome-wide DNA methylation analysis of 12 GC cell lines, 30 GCs, six normal gastric mucosae, one sample of peripheral leukocytes, and four noncancerous gastric mucosae identified OSR2, PPFIA3, and VAV3 as barely methylated in normal cells and highly methylated in cancer cells. Quantitative methylation-specific PCR using 26 independent GCs validated that one or more of them was highly methylated in all of the GCs. Using four pairs of purified cells, we confirmed the three genes were highly methylated (85 % or more) in cancer cells and barely methylated (5 % or less) in noncancer cells. The cancer cell fraction assessed by the panel of the three genes showed good correlation with that assessed by the TP53 mutant allele frequency in 13 GCs (r = 0.77). After correction of the GC cell fraction, unsupervised clustering analysis of the genome-wide DNA methylation profiles yielded clearer clustering.
conclusionsA DNA methylation marker-namely, the panel of the three genes-is useful to estimate the cancer cell fraction in GCs.
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