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A high-throughput test enables specific detection of hepatocellular carcinoma

Author

Listed:
  • David Cheishvili

    (HKG Epitherapeutics Ltd. Unit 313-315, 3/F Biotech Center 2
    McGill University)

  • Chifat Wong

    (HKG Epitherapeutics Ltd. Unit 313-315, 3/F Biotech Center 2)

  • Mohammad Mahbubul Karim

    (International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B))

  • Mohammad Golam Kibria

    (International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B))

  • Nusrat Jahan

    (International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B))

  • Pappu Chandra Das

    (International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B))

  • Md. Abul Khair Yousuf

    (Bangabandhu Sheikh Mujib Medical University)

  • Md. Atikul Islam

    (Bangabandhu Sheikh Mujib Medical University)

  • Dulal Chandra Das

    (Bangabandhu Sheikh Mujib Medical University)

  • Sheikh Mohammad Noor-E-Alam

    (Bangabandhu Sheikh Mujib Medical University)

  • Moshe Szyf

    (McGill University)

  • Sarwar Alam

    (Bangabandhu Sheikh Mujib Medical University)

  • Wasif A. Khan

    (International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B))

  • Mamun Al Mahtab

    (Bangabandhu Sheikh Mujib Medical University)

Abstract

High-throughput tests for early cancer detection can revolutionize public health and reduce cancer morbidity and mortality. Here we show a DNA methylation signature for hepatocellular carcinoma (HCC) detection in liquid biopsies, distinct from normal tissues and blood profiles. We developed a classifier using four CpG sites, validated in TCGA HCC data. A single F12 gene CpG site effectively differentiates HCC samples from other blood samples, normal tissues, and non-HCC tumors in TCGA and GEO data repositories. The markers were validated in a separate plasma sample dataset from HCC patients and controls. We designed a high-throughput assay using next-generation sequencing and multiplexing techniques, analyzing plasma samples from 554 clinical study participants, including HCC patients, non-HCC cancers, chronic hepatitis B, and healthy controls. HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC. Implementing this assay for high-risk individuals could significantly decrease HCC morbidity and mortality.

Suggested Citation

  • David Cheishvili & Chifat Wong & Mohammad Mahbubul Karim & Mohammad Golam Kibria & Nusrat Jahan & Pappu Chandra Das & Md. Abul Khair Yousuf & Md. Atikul Islam & Dulal Chandra Das & Sheikh Mohammad Noo, 2023. "A high-throughput test enables specific detection of hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39055-7
    DOI: 10.1038/s41467-023-39055-7
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    References listed on IDEAS

    as
    1. Ryan Lister & Mattia Pelizzola & Robert H. Dowen & R. David Hawkins & Gary Hon & Julian Tonti-Filippini & Joseph R. Nery & Leonard Lee & Zhen Ye & Que-Minh Ngo & Lee Edsall & Jessica Antosiewicz-Bourg, 2009. "Human DNA methylomes at base resolution show widespread epigenomic differences," Nature, Nature, vol. 462(7271), pages 315-322, November.
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