Author Correction: Analysis of DNA methylation in cancer: location revisited

Koch, Alexander; Joosten, Sophie C.; Feng, Zheng; Ruijter, Tim C. de; Draht, Muriel X.G.; Melotte, Veerle; Smits, Kim M.; Veeck, Jürgen; Herman, James G.; Neste, Leander Van; Criekinge, Wim Van; Meyer, Tim De; Engeland, Manon van

doi:10.1038/s41571-018-0028-9

Cited by 34 publications

(26 citation statements)

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“…Epigenetic changes are common markers of human cancers, including GBM ( Kim and Kim, 2008 ; Romani et al, 2018 ). DNA methylation is a core element of epigenetic alteration, an essential signaling tool for regulating genomic functions, and a key feature mediating tumorigenesis ( Koch et al, 2018 ; Muhammad et al, 2018 ; Yamashita et al, 2018 ). DNA methylation can provide biomarkers for the early diagnosis and prognosis of cancer and provide a new method for further clinical applications ( Lofton-Day and Lesche, 2003 ; Gustafsson et al, 2018 ; Kim et al, 2018 ; Li et al, 2018 , 2019 ; Pérez et al, 2018 .…”

Section: Molecular-based Gbm Classification In Diagnosis and Prognosimentioning

confidence: 99%

Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy

Zhang

Qin

Liu

et al. 2020

Front. Mol. Biosci.

105

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Glioblastoma (GBM) is highly invasive and the deadliest brain tumor in adults. It is characterized by inter-tumor and intra-tumor heterogeneity, short patient survival, and lack of effective treatment. Prognosis and therapy selection is driven by molecular data from gene transcription, genetic alterations and DNA methylation. The four GBM molecular subtypes are proneural, neural, classical, and mesenchymal. More effective personalized therapy heavily depends on higher resolution molecular subtype signatures, combined with gene therapy, immunotherapy and organoid technology. In this review, we summarize the principal GBM molecular classifications that guide diagnosis, prognosis, and therapeutic recommendations.

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Section: Molecular-based Gbm Classification In Diagnosis and Prognosimentioning

confidence: 99%

Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy

Zhang

Qin

Liu

et al. 2020

Front. Mol. Biosci.

105

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“…At least 17 and 160 types of chemical modifications have been discovered in DNA and RNA, respectively (Raiber et al, 2017 ; Boccaletto et al, 2018 ). DNA modification plays important roles in several biological processes and diseases, including development (Greenberg and Bourc’his, 2019 ), aging (Unnikrishnan et al, 2019 ), cancer (Koch et al, 2018 ), etc. These modifications would not interfere with Watson-Crick pairing but affect the DNA-protein interaction while in the major groove of the double helix.…”

Section: Introductionmentioning

confidence: 99%

Mapping the epigenetic modifications of DNA and RNA

et al. 2020

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Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.

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“…Previously, several genomic and transcriptome data have focused on exploring effective diagnostic or prognostic markers in STSs, including alternative splicing [8], copy number variation [9], and genes expression [10]. As one of the core elements in tumorigenesis progression, DNA methylation occurs early and frequently in regulating a variety of genomic functions [11][12][13]. DNA methylation is a posttranslational modification process, which are selectively occurred on the cytosines of 5′-CpG-3′ to generates 5-methyldeoxycytidine.…”

Section: Introductionmentioning

confidence: 99%

DNA methylation patterns–based subtype distinction and identification of soft tissue sarcoma prognosis

Fan

et al. 2020

Preprint

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Background: Soft tissue sarcomas (STSs) are heterogeneous at the clinical with a variable tendency of aggressive behavior. Methods: In this study, we constructed a specific DNA methylation-based classification to identify the distinct prognosis-subtypes of STSs based on the DNA methylation spectrum from the TCGA database.Results: Eventually, samples were clustered into four subgroups, and their survival curves were distinct from each other. Meanwhile, the samples in each subgroup reflected differentially in several clinical features. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was also conducted on the genes of the corresponding promoter regions of the above‐described specific methylation sites, revealing that these genes were mainly concentrated in certain cancer‑associated biological functions and pathways. In addition, we calculated the differences among clustered methylation sites and performed the specific methylation sites with LASSO algorithm. The selection operator algorithm was employed to derive a risk signature model, and a prognostic signature based on these methylation sites performed well for risk stratification in STSs patients. At last, a nomogram consisted of clinical features and risk score was developed for the survival prediction. Conclusion: In conclusion, this study declares that DNA methylation-based STSs subtype classification is highly relevant for future development of personalized therapy as it identifies the prediction value of patient prognosis.

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Author Correction: Analysis of DNA methylation in cancer: location revisited

Cited by 34 publications

References 0 publications

Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy

Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy

Mapping the epigenetic modifications of DNA and RNA

DNA methylation patterns–based subtype distinction and identification of soft tissue sarcoma prognosis

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