ArticleGenome biology2013
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 110 citations in OpenAlex.
- Epigenetic paradigm of DNA methylation for understanding the pathophysiology, diagnostics, and therapeutics in sarcomas.Epigenomics · 2025Review
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- Epigenetic disruption of adipogenic gene enhancers in dedifferentiated liposarcomas and its therapeutic value.Frontiers in oncology · 2025Article
- Identification of NINJ1 as a novel prognostic predictor for retroperitoneal liposarcoma.Discover oncology · 2024Article
- The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling.Journal of nanobiotechnology · 2024Article
- The Future of Targeted Therapy for Leiomyosarcoma.Cancers · 2024Review
- Methylation and Molecular Profiling to Aid in Diagnosis and Radiation Treatment for an Intracranial Ewing Sarcoma in a Pediatric Patient: A Case Report.Advances in radiation oncology · 2024Article
- Genetic, Epigenetic and Transcriptome Alterations in Liposarcoma for Target Therapy Selection.Cancers · 2024Review
- Article
- Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity.iScience · 2023Article
- The prognostic value of RASGEF1A RNA expression and DNA methylation in cytogenetically normal acute myeloid leukemia.Cancer biomarkers : section A of Disease markers · 2023Article
- Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data.Frontiers in bioinformatics · 2023Article
- The Intricate Interplay between the ZNF217 Oncogene and Epigenetic Processes Shapes Tumor Progression.Cancers · 2022Review
- Comparative oncology reveals DNMT3B as a molecular vulnerability in undifferentiated pleomorphic sarcoma.Cellular oncology (Dordrecht, Netherlands) · 2022Article
- Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome.Epigenetics · 2022Article
- Novel feature selection methods for construction of accurate epigenetic clocks.PLoS computational biology · 2022Article
- Comprehensive genomic profiling of EWSR1/FUS::CREB translocation-associated tumors uncovers prognostically significant recurrent genetic alterations and methylation-transcriptional correlates.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- In Silico Identification of Key Genes and Immune Infiltration Characteristics in Epicardial Adipose Tissue from Patients with Coronary Artery Disease.BioMed research international · 2022Article
- Identification of Methylation Signatures and Rules for Sarcoma Subtypes by Machine Learning Methods.BioMed research international · 2022Article
- Immunologic constant of rejection signature is prognostic in soft-tissue sarcoma and refines the CINSARC signature.Journal for immunotherapy of cancer · 2022Article
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Authors and funding
21 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-grade soft tissue sarcomas are a heterogeneous, complex group of aggressive malignant tumors showing mesenchymal differentiation. Recently, soft tissue sarcomas have increasingly been classified on the basis of underlying genetic alterations; however, the role of aberrant DNA methylation in these tumors is not well understood and, consequently, the usefulness of methylation-based classification is unclear.
resultsWe used the Infinium HumanMethylation27 platform to profile DNA methylation in 80 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 14 representative sarcoma cell lines. The primary samples were partitioned into seven stable clusters. A classification algorithm identified 216 CpG sites, mapping to 246 genes, showing different degrees of DNA methylation between these seven groups. The differences between the clusters were best represented by a set of eight CpG sites located in the genes SPEG, NNAT, FBLN2, PYROXD2, ZNF217, COL14A1, DMRT2 and CDKN2A. By integrating DNA methylation and mRNA expression data, we identified 27 genes showing negative and three genes showing positive correlation. Compared with non-neoplastic fat, NNAT showed DNA hypomethylation and inverse gene expression in myxoid liposarcomas, and DNA hypermethylation and inverse gene expression in dedifferentiated and pleomorphic liposarcomas. Recovery of NNAT in a hypermethylated myxoid liposarcoma cell line decreased cell migration and viability.
conclusionsOur analysis represents the first comprehensive integration of DNA methylation and transcriptional data in primary high-grade soft tissue sarcomas. We propose novel biomarkers and genes relevant for pathogenesis, including NNAT as a potential tumor suppressor in myxoid liposarcomas.
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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.