ArticlePloS one2012
Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
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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
72 citing papers in PubMed, 1 synthesis or guideline pooled it, 108 citations in OpenAlex.
- Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data.BMC medical genetics · 2014Pooled it
- Integrative machine learning and multi-omics identify a centromere gene signature and validate B3GALT4 as a tumor suppressor in osteosarcoma.Journal of bone oncology · 2026Article
- Transcriptome combined with single-cell data to construct a prognostic model for glycosylation-related genes in osteosarcoma.Discover oncology · 2026Article
- The Role of DNA Methylation in Osteosarcoma Pathogenesis and Therapy.OncoTargets and therapy · 2026Review
- WGCNA-identified COL13A1 drives osteosarcoma metastasis and progression via TGF-β signaling.Journal of bone oncology · 2025Article
- SETDB1 amplification in osteosarcomas: Insights from its role in healthy tissues and other cancer types.Oncotarget · 2025Review
- The osteosarcoma immune microenvironment in progression: PLEK as a prognostic biomarker and therapeutic target.Frontiers in immunology · 2025Article
- Feasibility and barriers to rapid establishment of patient-derived primary osteosarcoma cell lines in clinical management.iScience · 2024Review
- The expression and clinical significance of ARHGAP25 in osteosarcoma based on bioinformatics analysis.Scientific reports · 2024Article
- Targeting WNT5B and WNT10B in osteosarcoma.Oncotarget · 2024Review
- Bioinformatics analysis and validation of mesenchymal stem cells related gene MT1G in osteosarcoma.Aging · 2024Article
- Unveiling research trends in the prognosis of osteosarcoma: A bibliometric analysis from 2000 to 2022.Heliyon · 2024Article
- DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development.Molecular genetics and genomics : MGG · 2023Article
- Nuclear receptor modulators inhibit osteosarcoma cell proliferation and tumour growth by regulating the mTOR signaling pathway.Cell death & disease · 2023Article
- Longitudinal characterization of primary osteosarcoma and derived subcutaneous and orthotopic relapsed patient-derived xenograft models.Frontiers in oncology · 2023Article
- Review
- Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma.Communications biology · 2022Article
- miR-486-5p expression is regulated by DNA methylation in osteosarcoma.BMC genomics · 2022Article
- Identification of Small-Molecule Inhibitors for Osteosarcoma Targeted Therapy: SynchronizingFrontiers in bioengineering and biotechnology · 2022Article
- Targeting the NAD Salvage Synthesis Pathway as a Novel Therapeutic Strategy for Osteosarcomas with Low NAPRT Expression.International journal of molecular sciences · 2021Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOsteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. PRINCIPAL
findingsThe cell lines showed complex patterns of DNA copy number changes, where genomic copy number gains were significantly associated with gene-rich regions and losses with gene-poor regions. By integrating the datasets, 350 genes were identified as having two types of aberrations (gain/over-expression, hypo-methylation/over-expression, loss/under-expression or hyper-methylation/under-expression) using a recurrence threshold of 6/19 (>30%) cell lines. The genes showed in general alterations in either DNA copy number or DNA methylation, both within individual samples and across the sample panel. These 350 genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. The aberrations of three selected genes, CXCL5, DLX5 and RUNX2, were validated in five cell lines and five tumour samples using PCR techniques. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2'-deoxycytidine treatment for four genes tested; AKAP12, CXCL5, EFEMP1 and IL11RA. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for detrimental genes.
conclusionsIntegrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between DNA copy number, DNA methylation and mRNA expression in osteosarcomas, contributing to better understanding of osteosarcoma biology.
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Registered trials
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.