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

Author

Listed:
  • Hyun Goo Woo

    (Ajou University School of Medicine
    Ajou University)

  • Ji-Hye Choi

    (Ajou University School of Medicine
    Ajou University)

  • Sarah Yoon

    (Ajou University School of Medicine)

  • Byul A. Jee

    (Ajou University School of Medicine
    Ajou University)

  • Eun Ju Cho

    (Seoul National University College of Medicine)

  • Jeong-Hoon Lee

    (Seoul National University College of Medicine)

  • Su Jong Yu

    (Seoul National University College of Medicine)

  • Jung-Hwan Yoon

    (Seoul National University College of Medicine)

  • Nam-Joon Yi

    (Seoul National University College of Medicine)

  • Kwang-Woong Lee

    (Seoul National University College of Medicine)

  • Kyung-Suk Suh

    (Seoul National University College of Medicine)

  • Yoon Jun Kim

    (Seoul National University College of Medicine)

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.

Suggested Citation

  • Hyun Goo Woo & Ji-Hye Choi & Sarah Yoon & Byul A. Jee & Eun Ju Cho & Jeong-Hoon Lee & Su Jong Yu & Jung-Hwan Yoon & Nam-Joon Yi & Kwang-Woong Lee & Kyung-Suk Suh & Yoon Jun Kim, 2017. "Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00991-w
    DOI: 10.1038/s41467-017-00991-w
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    Cited by:

    1. Ji-Hye Choi & Bok-Soon Lee & Jeon Yeob Jang & Yun Sang Lee & Hyo Jeong Kim & Jin Roh & Yoo Seob Shin & Hyun Goo Woo & Chul-Ho Kim, 2023. "Single-cell transcriptome profiling of the stepwise progression of head and neck cancer," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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