Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma

A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a dynamic cascaded method to reconstruct dynamic gene networks from sample-based transcriptional data. Our method is based on two biologically plausible assumptions, which can characterise the dynamic and continuous nature of gene transcription. Our approach was successfully applied to reconstruct the dynamic gene networks of hepatocellular carcinoma (HCC) progression. The derived HCC networks were verified by functional analysis and network enrichment analysis.

[1]  Fabrizio Dal Piaz,et al.  Human hepatocellular carcinoma expresses specific PCNA isoforms: an in vivo and in vitro evaluation , 2008, Laboratory Investigation.

[2]  A. Roberts,et al.  Transforming growth factor-beta is a potent immunosuppressive agent that inhibits IL-1-dependent lymphocyte proliferation. , 1988, Journal of immunology.

[3]  Qing Yang,et al.  ITFP: an integrated platform of mammalian transcription factors , 2008, Bioinform..

[4]  Thorsten Maass,et al.  Liver-specific Ldb1 deletion results in enhanced liver cancer development. , 2010, Journal of hepatology.

[5]  J. Trent,et al.  WAF1, a potential mediator of p53 tumor suppression , 1993, Cell.

[6]  A. Hagemeijer,et al.  Sequence conservation of the rad21 Schizosaccharomyces pombe DNA double-strand break repair gene in human and mouse. , 1996, Genomics.

[7]  J. Bergelson,et al.  Virus-Induced Abl and Fyn Kinase Signals Permit Coxsackievirus Entry through Epithelial Tight Junctions , 2006, Cell.

[8]  Jacques Ferlay,et al.  Estimating the world cancer burden: Globocan 2000 , 2001, International journal of cancer.

[9]  Jianmin Wu,et al.  PINA v2.0: mining interactome modules , 2011, Nucleic Acids Res..

[10]  R. Derynck,et al.  Smad-dependent and Smad-independent pathways in TGF-beta family signalling. , 2003, Nature.

[11]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[12]  Hiroyoshi Taniguchi,et al.  Hepatitis C virus core protein upregulates transforming growth factor-beta 1 transcription. , 2004, Journal of medical virology.

[13]  Michael Hecker,et al.  Gene regulatory network inference: Data integration in dynamic models - A review , 2009, Biosyst..

[14]  A. Chung,et al.  MicroRNA‐224 is up‐regulated in hepatocellular carcinoma through epigenetic mechanisms , 2012, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[15]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[16]  M. Newman,et al.  Random graphs with arbitrary degree distributions and their applications. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[17]  松尾 拓哉.  Control mechanism of the circadian clock for timing of cell division in vivo , 2004 .

[18]  J. Weinstein,et al.  A novel mammalian protein, p55CDC, present in dividing cells is associated with protein kinase activity and has homology to the Saccharomyces cerevisiae cell division cycle proteins Cdc20 and Cdc4 , 1994, Molecular and cellular biology.

[19]  V. Mazzaferro,et al.  Genome‐wide molecular profiles of HCV‐induced dysplasia and hepatocellular carcinoma , 2007, Hepatology.

[20]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[21]  W. Marsden.  I and J , 2012 .

[22]  Johan Garssen,et al.  Transforming growth factor-beta inhibits human antigen-specific CD4+ T cell proliferation without modulating the cytokine response. , 2003, International immunology.

[23]  R. Chung,et al.  Viral hepatocarcinogenesis , 2010, Oncogene.

[24]  Luonan Chen,et al.  Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma. , 2012, Journal of molecular cell biology.

[25]  Kazuyuki Aihara,et al.  Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers , 2012, Scientific Reports.

[26]  J Weinstein,et al.  Cell Cycle-regulated Expression, Phosphorylation, and Degradation of p55Cdc , 1997, The Journal of Biological Chemistry.

[27]  Yutaka Hoshikawa,et al.  Activation of the CKI-CDK-Rb-E2F Pathway in Full Genome Hepatitis C Virus-expressing Cells* , 2004, Journal of Biological Chemistry.

[28]  J. Massagué,et al.  A Smad Transcriptional Corepressor , 1999, Cell.

[29]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[30]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[31]  Hiroyoshi Taniguchi,et al.  Hepatitis C virus core protein upregulates transforming growth factor‐β1 transcription , 2004 .

[32]  Min Wu,et al.  Expression of cell cycle/growth regulator genes in human hepatocellular carcinoma and adjacent normal liver tissues. , 2003, Oncology reports.