Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Zheng, Siyuan ^a   Tansey, William P ^b,c,d   Hiebert, Scott W ^b,c   Zhao, Zhongming ^a,b,c  

^a VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c VANDERBILT INGRAM CANCER CENTER   (United States)

^d NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADVANCED CANCER; ARTICLE; CANCER GROWTH; CARCINOGENESIS; CONTROLLED STUDY; CYCLIN DEPENDENT KINASE 1 GENE; DYSPLASIA; EARLY CANCER; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ASSOCIATION; HEPATITIS C VIRUS; HUMAN; HUMAN TISSUE; LIVER CELL CARCINOMA; LIVER CIRRHOSIS; LYMPHOCYTE SPECIFIC PROTEIN TYROSINE KINASE GENE; MATRIX METALLOPROTEINASE GENE; ONCOGENE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TISSUE INHIBITOR OF METALLOPROTEINASE GENE; DISEASE COURSE; GENE REGULATORY NETWORK; GENETICS; LIVER TUMOR; PATHOLOGY; VIROLOGY;

HEPATITIS C VIRUS;

CARCINOMA, HEPATOCELLULAR; DISEASE PROGRESSION; GENE REGULATORY NETWORKS; HEPACIVIRUS; HUMANS; LIVER NEOPLASMS;

EID: 79961125191     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-62     Document Type: Article

References (51)

1. Hepatocellular carcinoma - epidemiological trends and risk factors. Schutte K, Bornschein J, Malfertheiner P, Dig Dis 2009 27 80 92 19546545
2. The past incidence of hepatitis C virus infection: implications for the future burden of chronic liver disease in the United States. Armstrong GL, Alter MJ, McQuillan GM, Margolis HS, Hepatology 2000 31 777 782 10.1002/hep.510310332 10706572 (Pubitemid 30118650)
3. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Wurmbach E, Chen YB, Khitrov G, Zhang W, Roayaie S, Schwartz M, Fiel I, Thung S, Mazzaferro V, Bruix J, et al. Hepatology 2007 45 938 947 10.1002/hep.21622 17393520 (Pubitemid 46646500)
4. Peginterferon alfa-2b and ribavirin for the treatment of chronic hepatitis C in blacks and non-Hispanic whites. Muir AJ, Bornstein JD, Killenberg PG, N Engl J Med 2004 350 2265 2271 10.1056/NEJMoa032502 15163776 (Pubitemid 38669209)
5. Epidemiology of hepatocellular carcinoma. Kew MC, Toxicology 2002 181-182 35 38 12505281 (Pubitemid 36015669)
6. The continuing increase in the incidence of hepatocellular carcinoma in the United States: an update. El-Serag HB, Davila JA, Petersen NJ, McGlynn KA, Ann Intern Med 2003 139 817 823 14623619
7. Molecular pathogenesis of human hepatocellular carcinoma. Thorgeirsson SS, Grisham JW, Nat Genet 2002 31 339 346 10.1038/ng0802-339 12149612 (Pubitemid 35154440)
8. Hepatitis C virus expression suppresses interferon signaling by degrading STAT1. Lin W, Choe WH, Hiasa Y, Kamegaya Y, Blackard JT, Schmidt EV, Chung RT, Gastroenterology 2005 128 1034 1041 10.1053/j.gastro.2005.02.006 15825084 (Pubitemid 40523553)
9. c-Jun mediates hepatitis C virus hepatocarcinogenesis through signal transducer and activator of transcription 3 and nitric oxide-dependent impairment of oxidative DNA repair. Machida K, Tsukamoto H, Liu JC, Han YP, Govindarajan S, Lai MM, Akira S, Ou JH, Hepatology 2010 52 480 492 10.1002/hep.23697 20683948
10. CD4+ T-lymphocyte telomere length is related to fibrosis stage, clinical outcome and treatment response in chronic hepatitis C virus infection. Hoare M, Gelson WT, Das A, Fletcher JM, Davies SE, Curran MD, Vowler SL, Maini MK, Akbar AN, Alexander GJ, J Hepatol 2010 53 252 260 10.1016/j.jhep.2010.03.005 20462651
11. Significance of serum matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 in chronic hepatitis C patients. Badra G, Lotfy M, El-Refaie A, Obada M, Abdelmonem E, Kandeel S, Fathy A, Acta Microbiol Immunol Hung 2010 57 29 42 10.1556/AMicr.57.2010.1.3 20350877
12. Integrative analysis of the melanoma transcriptome. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, et al. Genome Res 2010 20 413 427 10.1101/gr.103697.109 20179022
13. Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, Monighetti CK, Stanley SJ, Olsen KD, Kasperbauer JL, Moore EJ, et al. PLoS One 2010 5 9317 10.1371/journal.pone.0009317 20174472
14. Molecular changes from dysplastic nodule to hepatocellular carcinoma through gene expression profiling. Nam SW, Park JY, Ramasamy A, Shevade S, Islam A, Long PM, Park CK, Park SE, Kim SY, Lee SH, et al. Hepatology 2005 42 809 818 10.1002/hep.20878 16175600 (Pubitemid 41401118)
15. Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma. Mas VR, Maluf DG, Archer KJ, Yanek K, Kong X, Kulik L, Freise CE, Olthoff KM, Ghobrial RM, McIver P, Fisher R, Mol Med 2009 15 85 94 19098997
16. Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. Archer KJ, Zhao Z, Guennel T, Maluf DG, Fisher RA, Mas VR, Int J Comput Biol Drug Des 2010 3 52 67 10.1504/IJCBDD.2010.034499 20693610
17. Hdac3 is essential for the maintenance of chromatin structure and genome stability. Bhaskara S, Knutson SK, Jiang G, Chandrasekharan MB, Wilson AJ, Zheng S, Yenamandra A, Locke K, Yuan J-l, Bonine-Summers AR, et al. Cancer Cell 2010 18 436 447 10.1016/j.ccr.2010.10.022 21075309
18. NCBI GEO: archive for high-throughput functional genomic data. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. Nucleic Acids Res 2009 37 885 890 10.1093/nar/gkn764 18940857
19. Integrated network analysis platform for protein-protein interactions. Wu J, Vallenius T, Ovaska K, Westermarck J, Makela TP, Hautaniemi S, Nat Methods 2009 6 75 77 10.1038/nmeth.1282 19079255
20. Hepatitis C Virus Protein Interaction Database. http://cbrc.kaust.edu.sa/ hcvpro/
21. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Jia P, Zheng S, Long J, Zheng W, Zhao Z, Bioinformatics 2011 27 95 102 10.1093/bioinformatics/btq615 21045073
22. Network-based classification of breast cancer metastasis. Chuang HY, Lee E, Liu YT, Lee D, Ideker T, Mol Syst Biol 2007 3 140 17940530
23. On random graphs. Erdos P, Renyi A, Publicationes Mathematicae 1959 6 290 297
24. Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. Sun J, Jia P, Fanous AH, van den Oord E, Chen X, Riley BP, Amdur RL, Kendler KS, Zhao Z, PLoS One 2010 5 11351 10.1371/journal.pone.0011351 20613869
25. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Nat Genet 2000 25 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
26. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Jiang C, Han L, Su B, Li WH, Zhao Z, Mol Biol Evol 2007 24 1991 2000 10.1093/molbev/msm128 17591602 (Pubitemid 47357614)
27. MPSQ: a web tool for protein-state searching. Zheng S, Sheng J, Wang C, Wang X, Yu Y, Li Y, Michie A, Dai J, Zhong Y, Hao P, et al. Bioinformatics 2008 24 2412 2413 10.1093/bioinformatics/btn427 18697766
28. Protein complexes and functional modules in molecular networks. Spirin V, Mirny LA, Proc Natl Acad Sci USA 2003 100 12123 12128 10.1073/pnas.2032324100 14517352 (Pubitemid 37271525)
29. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. Pang PS, Jankowsky E, Planet PJ, Pyle AM, EMBO J 2002 21 1168 1176 10.1093/emboj/21.5.1168 11867545 (Pubitemid 34206190)
30. Hepatitis C Virus NS3 Protein Can Activate the Notch-Signaling Pathway through Binding to a Transcription Factor, SRCAP. Iwai A, Takegami T, Shiozaki T, Miyazaki T, PLoS One 2011 6 20718 10.1371/journal.pone.0020718 21673954
31. The NS3 protein of hepatitis C virus induces caspase-8-mediated apoptosis independent of its protease or helicase activities. Prikhod'ko EA, Prikhod'ko GG, Siegel RM, Thompson P, Major ME, Cohen JI, Virology 2004 329 53 67 10.1016/j.virol.2004.08.012 15476874 (Pubitemid 39346028)
32. The Hepatitis C virus NS5A protein activates a phosphoinositide 3-kinase-dependent survival signaling cascade. Street A, Macdonald A, Crowder K, Harris M, J Biol Chem 2004 279 12232 12241 14709551 (Pubitemid 38445788)
33. Systematic identification of hepatocellular proteins interacting with NS5A of the hepatitis C virus. Ahn J, Chung KS, Kim DU, Won M, Kim L, Kim KS, Nam M, Choi SJ, Kim HC, Yoon M, et al. J Biochem Mol Biol 2004 37 741 748 10.5483/BMBRep.2004.37.6.741 15607035 (Pubitemid 40221537)
34. Hepatitis C virus infection protein network. de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, et al. Mol Syst Biol 2008 4 230 18985028
35. Cell adhesion molecules: role and clinical significance in cancer. Makrilia N, Kollias A, Manolopoulos L, Syrigos K, Cancer Invest 2009 27 1023 1037 10.3109/07357900902769749 19909018
36. Growth suppression by acute promyelocytic leukemia-associated protein PLZF is mediated by repression of c-myc expression. McConnell MJ, Chevallier N, Berkofsky-Fessler W, Giltnane JM, Malani RB, Staudt LM, Licht JD, Mol Cell Biol 2003 23 9375 9388 10.1128/MCB.23.24.9375-9388.2003 14645547 (Pubitemid 37499823)
37. Role of PLZF in melanoma progression. Felicetti F, Bottero L, Felli N, Mattia G, Labbaye C, Alvino E, Peschle C, Colombo MP, Care A, Oncogene 2004 23 4567 4576 10.1038/sj.onc.1207597 15077196 (Pubitemid 38850404)
38. Antigen processing via autophagy - not only for MHC class II presentation anymore? Munz C, Curr Opin Immunol 2010 22 89 93 10.1016/j.coi.2010.01.016 20149615
39. Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation. Palacios EH, Weiss A, Oncogene 2004 23 7990 8000 10.1038/sj.onc.1208074 15489916 (Pubitemid 39468856)
40. Lck protein tyrosine kinase is a key regulator of T-cell activation and a target for signal intervention by Herpesvirus saimiri and other viral gene products. Isakov N, Biesinger B, Eur J Biochem 2000 267 3413 3421 10848956 (Pubitemid 30423000)
41. Unscrambling hepatitis C virus-host interactions. Chisari FV, Nature 2005 436 930 932 10.1038/nature04076 16107831 (Pubitemid 41191667)
42. Hypoxia and transforming growth factor-beta 1 act independently to increase extracellular matrix production by placental fibroblasts. Chen CP, Yang YC, Su TH, Chen CY, Aplin JD, J Clin Endocrinol Metab 2005 90 1083 1090 15522940 (Pubitemid 40279238)
43. Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. Mendez J, Stillman B, Mol Cell Biol 2000 20 8602 8612 10.1128/MCB.20.22.8602-8612.2000 11046155
44. Cdk1, Plks, Auroras, and Neks: the mitotic bodyguards. Salaun P, Rannou Y, Prigent C, Adv Exp Med Biol 2008 617 41 56 10.1007/978-0-387-69080-3-4 18497029
45. Polo-like kinase (Plk) 1: a novel target for the treatment of prostate cancer. Ahmad N, Faseb J 2004 18 5 7 10.1096/fj.03-0848hyp 14718382 (Pubitemid 38076461)
46. Identification of human polo-like kinase 1 as a potential therapeutic target in pancreatic cancer. Gray PJ, Bearss DJ, Han H, Nagle R, Tsao MS, Dean N, Von Hoff DD, Mol Cancer Ther 2004 3 641 646 10.4161/cbt.3.7.918 15141022 (Pubitemid 39193743)
47. Role of p38 MAPK and RNA-dependent protein kinase (PKR) in hepatitis C virus core-dependent nuclear delocalization of cyclin B1. Spaziani A, Alisi A, Sanna D, Balsano C, J Biol Chem 2006 281 10983 10989 10.1074/jbc.M512536200 16446363 (Pubitemid 43855521)
48. Drug discovery: a historical perspective. Drews J, Science 2000 287 1960 1964 10.1126/science.287.5460.1960 10720314 (Pubitemid 30158662)
49. Protein kinases - the major drug targets of the twenty-first century? Cohen P, Nat Rev Drug Discov 2002 1 309 315 10.1038/nrd773 12120282 (Pubitemid 37361447)
50. Inhibition of CDK1 as a potential therapy for tumors over-expressing MYC. Goga A, Yang D, Tward AD, Morgan DO, Bishop JM, Nat Med 2007 13 820 827 10.1038/nm1606 17589519 (Pubitemid 47038193)
51. KEGG: kyoto encyclopedia of genes and genomes. Kanehisa M, Goto S, Nucleic Acids Res 2000 28 27 30 10.1093/nar/28.1.27 10592173 (Pubitemid 30047706)