When the human viral infectome and diseasome networks collide: Towards a systems biology platform for the aetiology of human diseases

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Navratil, Vincent ^a,b,e   de Chassey, Benoit ^a,c   Combe, Chantal R ^a,c   Lotteau, Vincent ^a,c,d  

^a UNIVERSITÉ DE LYON   (France)

^b UMR 754   (France)

^c INSERM   (France)

^d CROIX ROUSSE HOSPITAL   (France)

^e UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS C VIRUS;

PROTEOME;

ARTICLE; COMMUNICABLE DISEASE; GENETICS; HEPATITIS C VIRUS; HOST PARASITE INTERACTION; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; SYSTEMS BIOLOGY; VIROLOGY;

COMMUNICABLE DISEASES; DIABETES MELLITUS, TYPE 1; HEPACIVIRUS; HOST-PARASITE INTERACTIONS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; PROTEOME; SYSTEMS BIOLOGY;

EID: 78651526843     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-13     Document Type: Article

References (42)

1. Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, et al. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci USA 2007, 104:7606-7611. 10.1073/pnas.0702332104, 1863443, 17446270.
2. de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, et al. Hepatitis C virus infection protein network. Mol Syst Biol 2008, 4:230. 10.1038/msb.2008.66, 2600670, 18985028.
3. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ. Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008, 319:921-926. 10.1126/science.1152725, 18187620.
4. Hao L, Sakurai A, Watanabe T, Sorensen E, Nidom CA, Newton MA, Ahlquist P, Kawaoka Y. Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 2008, 454:890-893. 10.1038/nature07151, 2574945, 18615016.
5. Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, Brass AL, Adametz R, Tsui M, Qian F, et al. RNA interference screen for human genes associated with West Nile virus infection. Nature 2008, 455:242-245. 10.1038/nature07207, 18690214.
6. Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008, 135:49-60. 10.1016/j.cell.2008.07.032, 2628946, 18854154.
7. Zhou H, Xu M, Huang Q, Gates AT, Zhang XD, Castle JC, Stec E, Ferrer M, Strulovici B, Hazuda DJ, Espeseth AS. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 2008, 4:495-504. 10.1016/j.chom.2008.10.004, 18976975.
8. Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, Andre P, Lotteau V, Rabourdin-Combe C. VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res 2009, 37:D661-668. 10.1093/nar/gkn794, 2686459, 18984613.
9. Walker L, Levine H, Jucker M. Koch's postulates and infectious proteins. Acta Neuropathol 2006, 112:1-4. 10.1007/s00401-006-0072-x, 16703338.
10. Navratil V, de Chassey B, Meyniel L, Pradezynski F, Andre P, Rabourdin-Combe C, Lotteau V. System-level comparison of protein-protein interactions between viruses and the human type I interferon system network. J Proteome Res 2010, 9:3527-3536. 10.1021/pr100326j, 20459142.
11. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc Natl Acad Sci USA 2007, 104:8685-8690. 10.1073/pnas.0701361104, 1885563, 17502601.
12. Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabasi AL. The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci USA 2008, 105:9880-9885. 10.1073/pnas.0802208105, 2481357, 18599447.
13. Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, et al. Literature-curated protein interaction datasets. Nat Methods 2009, 6:39-46. 10.1038/nmeth.1284, 2683745, 19116613.
14. Dyer MD, Murali TM, Sobral BW. The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 2008, 4:e32. 10.1371/journal.ppat.0040032, 2242834, 18282095.
15. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93. 10.1038/nature02555, 15190252.
16. Palla G, Derenyi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818. 10.1038/nature03607, 15944704.
17. Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT. A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 2009, 5:298-307. 10.1016/j.chom.2009.02.001, 2756022, 19286138.
18. Deng M, Tu Z, Sun F, Chen T. Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics 2004, 20:895-902. 10.1093/bioinformatics/btg500, 14751964.
19. Hamosh A, Scott AF, Amberger J, Valle D, McKusick VA. Online Mendelian Inheritance in Man (OMIM). Hum Mutat 2000, 15:57-61. 10.1002/(SICI)1098-1004(200001)15:1<57::AID-HUMU12>3.0.CO;2-G, 10612823.
20. Moriya K, Fujie H, Shintani Y, Yotsuyanagi H, Tsutsumi T, Ishibashi K, Matsuura Y, Kimura S, Miyamura T, Koike K. The core protein of hepatitis C virus induces hepatocellular carcinoma in transgenic mice. Nat Med 1998, 4:1065-1067. 10.1038/2053, 9734402.
21. Kivity S, Agmon-Levin N, Blank M, Shoenfeld Y. Infections and autoimmunity--friends or foes?. Trends Immunol 2009, 30:409-414. 10.1016/j.it.2009.05.005, 19643667.
22. Fairweather D, Rose NR. Type 1 diabetes: virus infection or autoimmune disease?. Nat Immunol 2002, 3:338-340. 10.1038/ni0402-338, 11919574.
23. Zipris D. Epidemiology of type 1 diabetes and what animal models teach us about the role of viruses in disease mechanisms. Clin Immunol 2009, 131:11-23. 10.1016/j.clim.2008.12.011, 19185542.
24. Wolter TR, Wong R, Sarkar SA, Zipris D. DNA microarray analysis for the identification of innate immune pathways implicated in virus-induced autoimmune diabetes. Clin Immunol 2009, 132:103-115. 10.1016/j.clim.2009.02.007, 19328037.
25. Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ. EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res 2007, 35:D751-755. 10.1093/nar/gkl748, 1781120, 17071715.
26. Smink LJ, Helton EM, Healy BC, Cavnor CC, Lam AC, Flamez D, Burren OS, Wang Y, Dolman GE, Burdick DB, et al. T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res 2005, 33:D544-549. 10.1093/nar/gki095, 540049, 15608258.
27. Wallis RH, Wang K, Marandi L, Hsieh E, Ning T, Chao GY, Sarmiento J, Paterson AD, Poussier P. Type 1 diabetes in the BB rat: a polygenic disease. Diabetes 2009, 58:1007-1017. 10.2337/db08-1215, 2661594, 19168599.
28. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3:e59. 10.1371/journal.pcbi.0030059, 1853125, 17447836.
29. Spiro Z, Kovacs IA, Csermely P. Drug-therapy networks and the prediction of novel drug targets. J Biol 2008, 7:20. 10.1186/jbiol81, 2776392, 18710588.
30. Faustino RS, Terzic A. Bioinformatic networks: molecular reticles for pinpointing pharmacological target selection. Clin Pharmacol Ther 2008, 84:543-545. 10.1038/clpt.2008.181, 18941454.
31. Falkow S. Molecular Koch's postulates applied to microbial pathogenicity. Rev Infect Dis 1988, 10(Suppl 2):S274-276.
32. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 2006, 38:617-619. 10.1038/ng1800, 16699517.
33. Liu S, Wang H, Jin Y, Podolsky R, Reddy MV, Pedersen J, Bode B, Reed J, Steed D, Anderson S, et al. IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells. Hum Mol Genet 2009, 18:358-365. 10.1093/hmg/ddn342, 2638779, 18927125.
34. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009, 324:387-389. 10.1126/science.1167728, 2707798, 19264985.
35. Pelegrin M, Devedjian JC, Costa C, Visa J, Solanes G, Pujol A, Asins G, Valera A, Bosch F. Evidence from transgenic mice that interferon-beta may be involved in the onset of diabetes mellitus. J Biol Chem 1998, 273:12332-12340. 10.1074/jbc.273.20.12332, 9575186.
36. Filippi CM, Estes EA, Oldham JE, von Herrath MG. Immunoregulatory mechanisms triggered by viral infections protect from type 1 diabetes in mice. J Clin Invest 2009, 119:1515-1523. 2689128, 19478458.
37. Taguchi T, Nagano-Fujii M, Akutsu M, Kadoya H, Ohgimoto S, Ishido S, Hotta H. Hepatitis C virus NS5A protein interacts with 2',5'-oligoadenylate synthetase and inhibits antiviral activity of IFN in an IFN sensitivity-determining region-independent manner. J Gen Virol 2004, 85:959-969. 10.1099/vir.0.19513-0, 15039538.
38. Tessier MC, Qu HQ, Frechette R, Bacot F, Grabs R, Taback SP, Lawson ML, Kirsch SE, Hudson TJ, Polychronakos C. Type 1 diabetes and the OAS gene cluster: association with splicing polymorphism or haplotype?. J Med Genet 2006, 43:129-132. 10.1136/jmg.2005.035212, 2564627, 16014697.
39. Andrejeva J, Childs KS, Young DF, Carlos TS, Stock N, Goodbourn S, Randall RE. The V proteins of paramyxoviruses bind the IFN-inducible RNA helicase, mda-5, and inhibit its activation of the IFN-beta promoter. Proc Natl Acad Sci USA 2004, 101:17264-17269. 10.1073/pnas.0407639101, 535396, 15563593.
40. Childs K, Stock N, Ross C, Andrejeva J, Hilton L, Skinner M, Randall R, Goodbourn S. mda-5, but not RIG-I, is a common target for paramyxovirus V proteins. Virology 2007, 359:190-200. 10.1016/j.virol.2006.09.023, 17049367.
41. Hwang WC, YR C, A Z, Ramanathan M. Bridging Centrality: Identiffying Briding Nodes In Scale-free Networks. KDD'06 August 20-23 2006, Philadelphia, PA, USA.
42. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.