ArticlePLoS computational biology2017
Significant associations between driver gene mutations and DNA methylation alterations across many cancer types.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Genomic insights into uterine leiomyosarcoma: Unraveling KMT2D, CREBBP, NOTCH2, TSC2, ATM, and GNAS signatures.Clinics (Sao Paulo, Brazil) · 2026Article
- Molecular and bioinformatic analysis of apoptotic tumor suppressor genes in cervical cancer.Journal of applied genetics · 2026Article
- Aberrant DNA methylation as a key modulator of cell death pathways: insights into cancer progression and other diseases.Functional & integrative genomics · 2025Review
- Stochastic demethylation and redundant epigenetic suppressive mechanisms generate highly heterogeneous responses to pharmacological DNA methyltransferase inhibition.Journal of experimental & clinical cancer research : CR · 2025Article
- Sodium arsenite-induced DNA methylation alterations exacerbated by p53 knockout in MCF7 cells.Heliyon · 2024Article
- Comprehensive analysis of stearoyl-coenzyme A desaturase in prostate adenocarcinoma: insights into gene expression, immune microenvironment and tumor progression.Frontiers in immunology · 2024Article
- Methylomics and cancer: the current state of methylation profiling and marker development for clinical care.Cancer cell international · 2023Review
- Article
- Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin.Cancer cell · 2023Article
- Association of CDKN2A/B mutations, PD-1, and PD-L1 with the risk of acute lymphoblastic leukemia in children.Journal of cancer research and clinical oncology · 2023Article
- Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.PLoS computational biology · 2023Article
- Article
- Optimized screening of DNA methylation sites combined with gene expression analysis to identify diagnostic markers of colorectal cancer.BMC cancer · 2023Article
- Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas.Brain sciences · 2023Article
- Similarities and differences in gene expression profiles ofFrontiers in oncology · 2023Article
- Tumor Antigenicity and a Pre-Existing Adaptive Immune Response in Advanced BRAF Mutant Colorectal Cancers.Cancers · 2022Article
- Induction of the BRAFV600E Mutation in Thyroid Cells Leads to Frequent Hypermethylation.Clinical and experimental otorhinolaryngology · 2022Article
- Widespread redundancy in -omics profiles of cancer mutation states.Genome biology · 2022Article
- Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma.Computational and structural biotechnology journal · 2022Article
- Methylation Drivers and Prognostic Implications in Sinonasal Poorly Differentiated Carcinomas.Cancers · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Recent evidence shows that mutations in several driver genes can cause aberrant methylation patterns, a hallmark of cancer. In light of these findings, we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected. We measured this relationship using principal component analyses and methylation-mutation associations applied at the nucleotide level and with respect to genome-wide trends. We found that a few mutated driver genes were associated with genome-wide patterns of aberrant hypomethylation or CpG island hypermethylation in specific cancer types. In addition, we identified associations between 737 mutated driver genes and site-specific methylation changes. Moreover, using these mutation-methylation associations, we were able to distinguish between two uterine and two thyroid cancer subtypes. The driver gene mutation-associated methylation differences between the thyroid cancer subtypes were linked to differential gene expression in JAK-STAT signaling, NADPH oxidation, and other cancer-related pathways. These results establish that driver gene mutations are associated with methylation alterations capable of shaping regulatory network functions. In addition, the methodology presented here can be used to subdivide tumors into more homogeneous subsets corresponding to underlying molecular characteristics, which could improve treatment efficacy.
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