Gastroenterology

Gastroenterology

Volume 132, Issue 1, January 2007, Pages 330-342
Gastroenterology

Basic–liver, pancreas, and biliary tract
Characterization of HULC, a Novel Gene With Striking Up-Regulation in Hepatocellular Carcinoma, as Noncoding RNA

https://doi.org/10.1053/j.gastro.2006.08.026Get rights and content

Background & Aims: Recent studies have highlighted the role of noncoding RNAs (ncRNAs) in carcinogenesis, and suggested that this class of genes might be used as biomarkers in cancer. We searched the human genome for novel genes including ncRNAs related to hepatocellular carcinoma (HCC). Methods: An HCC-specific gene library was generated and screened for deregulated genes with 46 HCCs, 4 focal nodular hyperplasias, and 7 cirrhoses utilizing cDNA arrays. Sequencing of library clones identified a novel ncRNA as the most up-regulated gene in HCC. This gene was also cloned from different monkeys and characterized by quantitative RT-PCR, Northern blot analysis and in situ hybridization. Structural and functional studies included comparative sequence and protein expression analyses, quantitative RT-PCR of polysomal preparations, and siRNA-mediated knockdown experiments. Results: The most up-regulated gene in HCC named highly up-regulated in liver cancer (HULC) was characterized as a novel mRNA-like ncRNA. HULC RNA is spliced and polyadenlyated, and resembles the mammalian LTR transposon 1A. It does not contain substantial open reading frames, and no native translation product was detected. HULC is present in the cytoplasm, where it copurifies with ribosomes. siRNA-mediated knockdown of HULC RNA in 2 HCC cell lines altered the expression of several genes, 5 of which were known to be affected in HCC, suggesting a role for HULC in post-transcriptional modulation of gene expression. Conclusions: HULC is the first ncRNA with highly specific up-regulation in HCC. Because HULC was detected in blood of HCC patients, a potential use as novel biomarker can be envisaged.

Section snippets

Human Tissues

Human tissue samples were retrieved from the biobank at the Institute of Pathology, Medical University of Graz, Austria. Tissues obtained from surgically resected tumors and adjacent non-neoplastic tissue or from explanted livers were either snap frozen in methyl butane precooled with liquid nitrogen within 20 minutes after operation or fixed in phosphate-buffered (pH 7.4) 4% formaldehyde solution and embedded in paraffin. The study was approved by the ethics committee of the Medical University

HULC Is Specifically Expressed in Hepatocytes and Highly Up-regulated in HCC

For a genome-wide gene expression profiling approach, we generated HCC-specific cDNA libraries by subtractive suppressive hybridization.21 Clones from the HCC cDNA library in conjunction with well-known cancer-related and control genes were used for the production of an HCC-specific cDNA microarray containing a total of 6912 cDNA clones. Tissue samples of 46 HCCs, 4 FNHs, 7 cirrhoses, and 2 non-neoplastic livers were compared with a pool of non-neoplastic liver samples (Figure 1A; full dataset

Discussion

Using an HCC-specific cDNA microarray platform, we identified HULC, a novel mRNA-like ncRNA, as 1 of the most up-regulated genes in HCC. The levels of HULC RNA expression and up-regulation exceeded well-established, cancer-related genes analyzed in our study as well as those identified in other gene expression profiling studies.30, 31, 32 Examples of such genes are the E2F targets proliferating cell nuclear antigen and histone 1, the proliferation-associated genes cyclin D1, and c-jun, the

References (41)

  • C. Jopling et al.

    Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA

    Science

    (2005)
  • V.A. Erdmann et al.

    Collection of mRNA-like non-coding RNAs

    Nucleic Acids Res

    (1999)
  • W. Tam et al.

    Bic, a novel gene activated by proviral insertions in avian leukosis virus-induced lymphomas, is likely to function through its non-coding RNA

    Mol Cell Biol

    (1997)
  • P. Ji et al.

    MALAT-1, a novel non-coding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer

    Oncogene

    (2003)
  • W. Chen et al.

    Expression of neural BC200 RNA in human tumours

    J Pathol

    (1997)
  • J. Li et al.

    Expression of the putative proto-oncogene His-1 in normal and neoplastic tissues

    Am J Pathol

    (1997)
  • V. Srikantan et al.

    PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer

    Proc Natl Acad Sci U S A

    (2000)
  • M.J. Bussemakers et al.

    DD3: a new prostate-specific gene, highly overexpressed in prostate cancer

    Cancer Res

    (1999)
  • G. Petrovics et al.

    Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients

    Oncogene

    (2004)
  • A. Iacoangeli et al.

    BC200 RNA in invasive and preinvasive breast cancer

    Carcinogenesis

    (2004)
  • Cited by (0)

    Supported by the Austrian Science Fund (FWF) grant #S7401-MOB, the Austrian Industrial Research Promotion Fund (FFF) grant #804714, the Austrian Genome Program GEN-AU, and the Lore Saldow Fund.

    1

    K.P. and M.M.O.T. contributed equally to this work.

    2

    Current address for Christian Guelly, Tarek, Moustafa, Martin Stradner, and Heimo M. Strohmaier: Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.

    3

    Current address for Charles R. Buck: Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907.

    View full text