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Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing

  1. Author:
    Craig, Amanda J
    Silveira, Maruhen A Datsch
    Ma, Lichun
    Revsine, Mahler
    Wang, Limin
    Heinrich, Sophia
    Rae, Zachary
    Ruchinskas, Allison
    Dadkhah,Kimia
    Do, Whitney
    Behrens, Shay
    Mehrabadi, Farid R
    Dominguez, Dana A
    Forgues, Marshonna
    Budhu, Anuradha
    Chaisaingmongkol, Jittiporn
    Hernandez, Jonathan M
    Davis, Jeremy L
    Tran,Bao
    Marquardt, Jens U
    Ruchirawat, Mathuros
    Kelly, Michael
    Greten, Tim F
    Wang, Xin W

  2. Author Address

    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hanover Medical School, 30159 Hanover, Germany., Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 20701, USA., Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Department of Surgical Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA., Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10400, Thailand., Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Department of Medicine I, University of L 252;beck, 23552 L 252;beck, Germany., Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. Electronic address: xw3u@nih.gov.,
    1. Year: 2023
    2. Date: Nov 17
    3. Epub Date: 2023 11 17
  2. Journal: Cell Reports
    1. 42
    2. 11
    3. Pages: 113446
  4. Type of Article: Article
  5. Article Number: 113446
  1. Abstract:

    Primary liver cancer (PLC) consists of two main histological subtypes; hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). The role of transcription factors (TFs) in malignant hepatobiliary lineage commitment between HCC and iCCA remains underexplored. Here, we present genome-wide profiling of transcription regulatory elements of 16 PLC patients using single-cell assay for transposase accessible chromatin sequencing. Single-cell open chromatin profiles reflect the compositional diversity of liver cancer, identifying both malignant and microenvironment component cells. TF motif enrichment levels of 31 TFs strongly discriminate HCC from iCCA tumors. These TFs are members of the nuclear/retinoid receptor, POU, or ETS motif families. POU factors are associated with prognostic features in iCCA. Overall, nuclear receptors, ETS and POU TF motif families delineate transcription regulation between HCC and iCCA tumors, which may be relevant to development and selection of PLC subtype-specific therapeutics. Published by Elsevier Inc.

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External Sources

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  2. DOI: 10.1016/j.celrep.2023.113446
  3. PMID: 37980571
  4. PII : S2211-1247(23)01458-4

Library Notes

  1. Fiscal Year: FY2023-2024
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