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Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer

Authors
Woo, HG; Choi, JH; Yoon, S; Jee, BA; Cho, EJ; Lee, JH; Yu, SJ; Yoon, JH; Yi, NJ; Lee, KW; Suh, KS; Kim, YJ
Citation
Nature communications, 8(1):839-839, 2017
Journal Title
Nature communications
ISSN
2041-1723
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.
MeSH terms
AgedCarcinoma, Hepatocellular/genetics*Carcinoma, Hepatocellular/mortalityDNA Copy Number VariationsDNA MethylationDatabases, GeneticEpigenesis, Genetic*FemaleGene Expression Regulation, Neoplastic*HumansLiver Neoplasms/genetics*Liver Neoplasms/mortalityMaleMiddle AgedTranscriptome
DOI
10.1038/s41467-017-00991-w
PMID
29018224
Appears in Collections:
Journal Papers > School of Medicine / Graduate School of Medicine > Physiology
AJOU Authors
우, 현구최, 지혜윤, 사라지, 별아
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