ArticleEpigenetics2015
Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas.
Article in Epigenetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 38 citations in OpenAlex.
- Comparative analysis of surgical outcomes and prognostic factors between primary and recurrent sacral chordomas.European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society · 2026Article
- From Histology to Multi-Omics: Review of Chordoma Classification and Its Clinical Implications.Cells · 2026Review
- Epigenetic Alterations Beyond CpG Islands in Periodontitis: In Silico Study of DNA Methylation Data.Clinical and experimental dental research · 2026Article
- Radiogenomic method combining DNA methylation profiles and magnetic resonance imaging radiomics predicts patient prognosis in skull base chordoma.Clinical epigenetics · 2025Article
- DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment.Acta neuropathologica communications · 2023Article
- Donor T cell DNMT3a regulates alloreactivity in mouse models of hematopoietic stem cell transplantation.The Journal of clinical investigation · 2022Article
- DNA methylation-based prognostic subtypes of chordoma tumors in tissue and plasma.Neuro-oncology · 2022Article
- Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities.Frontiers in oncology · 2022Article
- Methylation-based reclassification and risk stratification of skull-base chordomas.Frontiers in oncology · 2022Article
- A chronicle review of new techniques that facilitate the understanding and development of optimal individualized therapeutic strategies for chordoma.Frontiers in oncology · 2022Review
- DNA methylation changes in infants between 6 and 52 weeks.Scientific reports · 2019Article
- Paraoxonase 3 is involved in the multi-drug resistance of esophageal cancer.Cancer cell international · 2018Article
- Identification of Predictive DNA Methylation Biomarkers for Chemotherapy Response in Colorectal Cancer.Frontiers in pharmacology · 2017Article
- Chordoma: an update on the pathophysiology and molecular mechanisms.Current reviews in musculoskeletal medicine · 2015Article
- Epigenetic deregulations in chordoma.Cell proliferation · 2015Review
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1-4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2'-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (>0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted P < 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
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