ArticleNature communications2017
Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
75 citing papers in PubMed, 129 citations in OpenAlex.
- CPNE1 promotes stemness and confers resistance to GPC3 CAR-T cell therapy in hepatocellular carcinoma via the STAT3-TGF-β signaling pathway.Journal for immunotherapy of cancer · 2026Article
- Integrated Bioinformatics and Multi-Omics Analysis of ZBTB40 Expression, Prognostic Relevance, and Regulatory Networks in Hepatocellular Carcinoma.Medicina (Kaunas, Lithuania) · 2026Article
- Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.Genome biology · 2026Article
- CYSTM1 is a potential diagnostic and prognostic biomarker and correlated with immune infiltrates in hepatocellular carcinoma.Journal of gastrointestinal oncology · 2025Article
- Comprehensive transcriptomic analysis of hepatocellular Carcinoma: Uncovering shared and unique molecular signatures across diverse etiologies.Biochemistry and biophysics reports · 2025Article
- Statistical and machine learning based platform-independent key genes identification for hepatocellular carcinoma.PloS one · 2025Article
- CEP55: Implications for Immunotherapy and Survival in Hepatocellular Carcinoma.Combinatorial chemistry & high throughput screening · 2025Article
- Review
- Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework.Cancer gene therapy · 2024Article
- DecipheringEpigenomics · 2024Article
- Integrated bioinformatics analysis and experimental validation to understand tryptophan metabolism-related genes in hepatocellular carcinoma.Journal of Cancer · 2024Article
- Multi-omics integration analysis unveils heterogeneity in breast cancer at the individual level.Cell cycle (Georgetown, Tex.) · 2023Article
- Cell line-specific features of 3D chromatin organization in hepatocellular carcinoma.Genomics & informatics · 2023Article
- TP53 mutation-related senescence is an indicator of hepatocellular carcinoma patient outcomes from multiomics profiles.Smart medicine · 2023Article
- Genetic heterogeneity of liver cancer stem cells.Anatomy & cell biology · 2023Article
- Single-cell transcriptome profiling of the stepwise progression of head and neck cancer.Nature communications · 2023Article
- The mFrontiers in immunology · 2023Article
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- DNA methylation-based predictors of health: applications and statistical considerations.Nature reviews. Genetics · 2022Review
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hepatocellular carcinoma harbors numerous genomic and epigenomic aberrations of DNA copy numbers and DNA methylation. Transcriptomic deregulation by these aberrations plays key driver roles in heterogeneous progression of cancers. Here, we profile DNA copy numbers, DNA methylation, and messenger RNA expression levels from 64 cases of hepatocellular carcinoma specimens. We find that the frequencies of the aberrancies of the DNA copy-number-correlated (CNVcor) expression genes and the methylation-correlated expression (METcor) genes are co-regulated significantly. Multi-omics integration of the CNVcor and METcor genes reveal three prognostic subtypes of hepatocellular carcinoma, which can be validated by an independent data. The most aggressive subtype expressing stemness genes has frequent BAP1 mutations, implying its pivotal role in the aggressive tumor progression. In conclusion, our integrative analysis of genomic and epigenomic regulation provides new insights on the multi-layered pathobiology of hepatocellular carcinoma, which might be helpful in developing precision management for hepatocellular carcinoma patients.Hepatocellular carcinoma is known to harbour numerous genomic and epigenomic aberrations, driving transcriptomic deregulation. Here, the authors integrate genomic, epigenomic, and expression data to reveal three prognostic subtypes, providing insight to the pathobiology of hepatocellular carcinoma.
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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.