ArticleGenome biology2015
An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Mapping the temporal landscape of breast cancer using epigenetic entropy.Communications biology · 2025Article
- Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity.Briefings in bioinformatics · 2025Article
- Sodium arsenite-induced DNA methylation alterations exacerbated by p53 knockout in MCF7 cells.Heliyon · 2024Article
- Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.Scientific reports · 2024Article
- Identification of DNA methylation characteristics associated with metastasis and prognosis in colorectal cancer.BMC medical genomics · 2024Article
- Pan-cancer landscape of epigenetic factor expression predicts tumor outcome.Communications biology · 2023Article
- An effective prognostic model in colon adenocarcinoma composed of cuproptosis-related epigenetic regulators.Frontiers in pharmacology · 2023Article
- CancerNet: a unified deep learning network for pan-cancer diagnostics.BMC bioinformatics · 2022Article
- Inference of age-associated transcription factor regulatory activity changes in single cells.Nature aging · 2022Article
- Oncogenomic Changes in Pancreatic Cancer and Their Detection in Stool.Biomolecules · 2022Review
- Interplay between chromatin marks in development and disease.Nature reviews. Genetics · 2022Review
- A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.Nature methods · 2022Article
- Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies.Clinical epigenetics · 2022Article
- Novel epigenetic network biomarkers for early detection of esophageal cancer.Clinical epigenetics · 2022Article
- The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines.Computational and structural biotechnology journal · 2022Article
- Analysis of DNA Repair-Related Prognostic Function and Mechanism in Gastric Cancer.Frontiers in cell and developmental biology · 2022Article
- DNA methylation-based profiling reveals distinct clusters with survival heterogeneity in high-grade serous ovarian cancer.Clinical epigenetics · 2021Article
- Targeting Epigenetics in Lung Cancer.Cold Spring Harbor perspectives in medicine · 2021Review
- Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation.EBioMedicine · 2021Article
- RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators.Leukemia · 2021Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the most important recent findings in cancer genomics is the identification of novel driver mutations which often target genes that regulate genome-wide chromatin and DNA methylation marks. Little is known, however, as to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types.
resultsHere we conduct an integrative pan-cancer-wide analysis of matched RNA-Seq and DNA methylation data across ten different cancer types. We identify seven tumor suppressor and eleven oncogenic epigenetic enzymes which display patterns of deregulation and association with genome-wide cancer DNA methylation patterns, which are largely independent of cancer type. In doing so, we provide evidence that genome-wide cancer hyper- and hypo- DNA methylation patterns are independent processes, controlled by distinct sets of epigenetic enzyme genes. Using causal network modeling, we predict a number of candidate drivers of cancer DNA hypermethylation and hypomethylation. Finally, we show that the genomic loci whose DNA methylation levels associate most strongly with expression of these putative drivers are highly consistent across cancer types.
conclusionsThis study demonstrates that there exist universal patterns of epigenomic deregulation that transcend cancer types, and that intra-tumor levels of genome-wide DNA hypomethylation and hypermethylation are controlled by distinct processes.
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