ArticleGenome medicine2016
The multi-omic landscape of transcription factor inactivation in cancer.
Article in Genome medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 34 citations in OpenAlex.
- The advances of DNA methylation in the liquid biopsy for the detection of lung cancer.Frontiers in oncology · 2025Review
- Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets.Signal transduction and targeted therapy · 2024Review
- On epigenetic stochasticity, entropy and cancer risk.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Transcription factor HOXB2 upregulates NUSAP1 to promote the proliferation, invasion and migration of nephroblastoma cells via the PI3K/Akt signaling pathway.Molecular medicine reports · 2022Article
- A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.Nature methods · 2022Article
- Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma.Signal transduction and targeted therapy · 2022Article
- Novel epigenetic network biomarkers for early detection of esophageal cancer.Clinical epigenetics · 2022Article
- Charting differentially methylated regions in cancer with Rocker-meth.Communications biology · 2021Article
- DNA Methylation Markers in Lung Cancer.Current genomics · 2021Review
- EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data.Genome biology · 2020Article
- Epigenetic Aging: More Than Just a Clock When It Comes to Cancer.Cancer research · 2020Review
- Improved detection of tumor suppressor events in single-cell RNA-Seq data.NPJ genomic medicine · 2020Article
- Epigenetics of lung cancer: a translational perspective.Cellular oncology (Dordrecht, Netherlands) · 2019Review
- Tensorial blind source separation for improved analysis of multi-omic data.Genome biology · 2018Article
- DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants.EBioMedicine · 2018Article
- Statistical and integrative system-level analysis of DNA methylation data.Nature reviews. Genetics · 2018Review
- Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development.Genome biology · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHypermethylation of transcription factor promoters bivalently marked in stem cells is a cancer hallmark. However, the biological significance of this observation for carcinogenesis is unclear given that most of these transcription factors are not expressed in any given normal tissue.
methodsWe analysed the dynamics of gene expression between human embryonic stem cells, fetal and adult normal tissue, as well as six different matching cancer types. In addition, we performed an integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for these six cancer types.
resultsWe here demonstrate that bivalently and PRC2 marked transcription factors highly expressed in a normal tissue are more likely to be silenced in the corresponding tumour type compared with non-housekeeping genes that are also highly expressed in the same normal tissue. Integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for six different matching cancer types reveals that in-cis promoter hypermethylation, and not in-cis genomic loss or genetic mutation, emerges as the predominant mechanism associated with silencing of these transcription factors in cancer. However, we also observe that some silenced bivalently/PRC2 marked transcription factors are more prone to copy number loss than promoter hypermethylation, pointing towards distinct, mutually exclusive inactivation patterns.
conclusionsThese data provide statistical evidence that inactivation of cell fate-specifying transcription factors in cancer is an important step in carcinogenesis and that it occurs predominantly through a mechanism associated with promoter hypermethylation.
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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.