Inference of surface membrane factors of HIV-1 infection through functional interaction networks

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Jaeger, Samira ^a,b   Ertaylan, Gokhan ^c   van Dijk, David ^c   Leser, Ulf ^a   Sloot, Peter ^c  

^a HUMBOLDT UNIVERSITY   (Germany)

^b CWI   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CD2 ANTIGEN; CD97 ANTIGEN; CELL SURFACE PROTEIN; CHEMOKINE BINDING PROTEIN 2; CHEMOKINE RECEPTOR; CHEMOKINE RECEPTOR CCR1; COLONY STIMULATING FACTOR RECEPTOR; COLONY STIMULATING FACTOR RECEPTOR 3; DUFFY ANTIGEN CHEMOKINE RECEPTOR; GLYCOPROTEIN GP 130; HUMAN IMMUNODEFICIENCY VIRUS PROTEIN; LYMPHOTOXIN BETA RECEPTOR; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 3; UNCLASSIFIED DRUG; VIRUS RECEPTOR; MEMBRANE PROTEIN;

ARTICLE; FUNCTIONAL PROTEOMICS; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS; VALIDATION PROCESS; VIRUS CELL INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METABOLISM; PHYSIOLOGY; PROTEIN BINDING; VALIDATION STUDY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

HIV INFECTIONS; HUMANS; MEMBRANE PROTEINS; PROTEIN BINDING;

EID: 78149435935     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013139     Document Type: Article

References (87)

1. Cook JA, August A, Henderson AJ (2002) Recruitment of phosphatidylinositol 3- kinase to CD28 inhibits HIV transcription by a Tat-dependent mechanism. J Immunol 169: 254-260.
2. Piguet V, Trono D (1999) The Nef protein of primate lentiviruses. Rev Med Virol 9: 111-120.
3. Yang B, Akhter S, Chaudhuri A, Kanmogne GD (2009) HIV-1 gp120 induces cytokine expression, leukocyte adhesion, and transmigration across the bloodbrain barrier: modulatory effects of STAT1 signaling. Microvasc Res 77: 212-219.
4. van 't Wout AB, Schuitemaker H, Kootstra NA (2008) Isolation and propagation of HIV-1 on peripheral blood mononuclear cells. Nat Protoc 3: 363-370.
5. Edwards CTT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, et al. (2006) Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol Biol 6: 28.
6. Geijtenbeek TB, Kwon DS, Torensma R, van Vliet SJ, van Duijnhoven GC, et al. (2000) DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell 100: 587-597.
7. Kawamura T, Gulden FO, Sugaya M, McNamara DT, Borris DL, et al. (2003) R5 HIV productively infects Langerhans cells, and infection levels are regulated by compound CCR5 polymorphisms. Proc Natl Acad Sci U S A 100: 8401-8406.
8. Becker Y (2006) Respiratory syncytial virus (RSV) evades the human adaptive immune system by skewing the Th1/Th2 cytokine balance toward increased levels of Th2 cytokines and IgE, markers of allergy-a review. Virus Genes 33: 235-252.
9. Blaak H, Boers PHM, Gruters RA, Schuitemaker H, van der Ende ME, et al. (2005) CCR5, GPR15, and CXCR6 are major coreceptors of human immunodeficiency virus type 2 variants isolated from individuals with and without plasma viremia. J Virol 79: 1686-1700.
10. Liu Y, Liu H, Kim BO, Gattone VH, Li J, et al. (2004) CD4-independent infection of astrocytes by human immunodeficiency virus type 1: requirement for the human mannose receptor. J Virol 78: 4120-4133.
11. Chaipan C, Soilleux EJ, Simpson P, Hofmann H, Gramberg T, et al. (2006) DC-SIGN and CLEC-2 mediate human immunodeficiency virus type 1 capture by platelets. J Virol 80: 8951-8960.
12. Alexaki A, Liu Y, Wigdahl B (2008) Cellular reservoirs of HIV-1 and their role in viral persistence. Curr HIV Res 6: 388-400.
13. Gorry PR, Dunfee RL, Mefford ME, Kunstman K, Morgan T, et al. (2007) Changes in the V3 region of gp120 contribute to unusually broad coreceptor usage of an HIV-1 isolate from a CCR5 Delta32 heterozygote. Virology 362: 163-178.
14. Dong C, Janas AM, Wang JH, Olson WJ, Wu L (2007) Characterization of human immunodeficiency virus type 1 replication in immature and mature dendritic cells reveals dissociable cis- and trans-infection. J Virol 81: 11352-11362.
15. Romani B, Engelbrecht S, Glashoff RH (2010) Functions of Tat: the versatile protein of human immunodeficiency virus type 1. J Gen Virol 91: 1-12.
16. Sloot PM, Coveney PV, Ertaylan G, Müller V, Boucher CA, et al. (2009) HIV decision support: from molecule to man. Philos Transact A Math Phys Eng Sci 367: 2691-2703.
17. Fang CT, Chang YY, Hsu HM, Twu SJ, Chen KT, et al. (2007) Life expectancy of patients with newly-diagnosed HIV infection in the era of highly active antiretroviral therapy. QJM 100: 97-105.
18. Ozgür A, Vu T, Erkan G, Radev DR (2008) Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 24: i277-i285.
19. Chen J, Aronow BJ, Jegga AG (2009) Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10: 73.
20. Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, et al. (2009) Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 37: D417-D422.
21. Shimizu N, Tanaka A, Oue A, Mori T, Ohtsuki T, et al. (2009) Broad usage spectrum of G protein-coupled receptors as coreceptors by primary isolates of HIV. AIDS 27: 761-769.
22. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-D451.
23. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35: D561-D565.
24. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 33: D418-D424.
25. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21: 832-834.
26. Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-D772.
27. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, et al. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35: D572-D574.
28. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 36: D637-D640.
29. UniProt Consortium (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37: D169-D174.
30. Maglott D, Ostell J, Pruitt KD, Tatusova T (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35: D26-D31.
31. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33: D201-D205.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
33. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
34. Couto FM, Silva MJ, Pedro Coutinho PM (2007) Measuring semantic similarity between Gene Ontology terms. Data Knowl Eng 61: 137-152.
35. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
36. Jaeger S, Leser U (2007) High-Precision Function Prediction using Conserved Interactions. In: Falter C, Schliep A, Selbig J, Vingron M, Walther D, eds. Proceedings of the German Conference on Bioinformatics, GCB 2007, September 26-28, 2007, Potsdam, Germany. GI, volume 115 of LNI. pp 146-162.
37. Koschützki D, Schreiber F (2008) Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio 2: 193-201.
38. Brin S, Page L (1998) The anatomy of a large-scale hypertextual Web search engine. Computer Networks and ISDN Systems 30: 107-117.
39. Csardi G, Nepusz T (2006) The igraph software package for complex network research. Inter Journal Complex Systems. pp 1695.
40. van Dijk D, Ertaylan G, Boucher CA, Sloot PM (2010) Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Syst Biol 4: 96.
41. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-D360.
42. Zhang S, Chen H, Liu K, Sun Z (2009) Inferring protein function by domain context similarities in protein-protein interaction networks. BMC Bioinformatics 10: 395.
43. Broder CC, Collman RG (1997) Chemokine receptors and HIV. J Leukoc Biol 62: 20-29.
44. Maho A, Bensimon A, Vassart G, Parmentier M (1999) Mapping of the CCXCR1, CX3CR1, CCBP2 and CCR9 genes to the CCR cluster within the 3p21.3 region of the human genome. Cytogenet Cell Genet 87: 265-268.
45. Zhou H, Xu M, Huang Q, Gates AT, Zhang XD, et al. (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4: 495-504.
46. Dunn SJ, Khan IH, Chan UA, Scearce RL, Melara CL, et al. (2004) Identification of cell surface targets for HIV-1 therapeutics using genetic screens. Virology 321: 260-273.
47. Utaipat U, Duerr A, Rudolph DL, Yang C, Butera ST, et al. (2002) Coreceptor utilization of HIV type 1 subtype E viral isolates from Thai men with HIV type 1-infected and uninfected wives. AIDS Res Hum Retroviruses 18: 1-11.
48. Neil SJD, Aasa-Chapman MMI, Clapham PR, Nibbs RJ, McKnight A, et al. (2005) The promiscuous CC chemokine receptor D6 is a functional coreceptor for primary isolates of human immunodeficiency virus type 1 (HIV-1) and HIV-2 on astrocytes. J Virol 79: 9618-9624.
49. Walton RT, Rowland-Jones SL (2008) HIV and chemokine binding to red blood cells-DARC matters. Cell Host Microbe 4: 3-5.
50. He W, Neil S, Kulkarni H, Wright E, Agan BK, et al. (2008) Duffy antigen receptor for chemokines mediates trans-infection of HIV-1 from red blood cells to target cells and affects HIV-AIDS susceptibility. Cell Host Microbe 4: 52-62.
51. Winkler CA, An P, Johnson R, Nelson GW, Kirk G (2009) Expression of Duffy Antigen Receptor for Chemokines (DARC) Has No Effect on HIV-1 Acquisition or Progression to AIDS in African Americans. Cell Host Microbe 5: 411-413.
52. Horne KC, Li X, Jacobson LP, Palella F, Jamieson BD, et al. (2009) Duffy Antigen Polymorphisms Do Not Alter Progression of HIV in African Americans in the MACS Cohort. Cell Host Microbe 5: 415-417.
53. Julg B, Reddy S, van der Stok M, Kulkarni S, Qi Y, et al. (2009) Lack of Duffy antigen receptor for chemokines: no influence on HIV disease progression in an African treatment-naive population. Cell Host Microbe 5: 413-415.
54. Walley NM, Julg B, Dickson SP, Fellay J, Ge D, et al. (2009) The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression. Cell Host Microbe 5: 408-10; author reply 418-9.
55. Kop EN, Matmati M, Pouwels W, Leclercq G, Tak PP, et al. (2009) Differential expression of CD97 on human lymphocyte subsets and limited effect of CD97 antibodies on allogeneic T-cell stimulation. Immunol Lett 123: 160-168.
56. Morikawa K, Morikawa S, Nakamura M, Miyawaki T (2002) Characterization of granulocyte colony-stimulating factor receptor expressed on human lymphocytes. Br J Haematol 118: 296-304.
57. Baillou C, Simon A, Leclercq V, Azar N, Rosenzwajg M, et al. (2003) Highly active antiretroviral therapy corrects hematopoiesis in HIV-1 infected patients: interest for peripheral blood stem cell-based gene therapy. AIDS 17: 563-574.
58. Rapaport R, McLean C, Campbell T (2004) Filgrastim stimulates hiv-1 replication in monocytoid cells. In: Program Abstr Conf Retrovir Oppor Infect 11th 2004 San Franc Calif.
59. Beel K, Vandenberghe P (2009) G-CSF receptor (CSF3R) mutations in X-linked neutropenia evolving to acute myeloid leukemia or myelodysplasia. Haematologica 94: 1449-1452.
60. Reich D, Nalls MA, Kao WHL, Akylbekova EL, Tandon A, et al. (2009) Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene. PLoS Genet 5: e1000360.
61. Li C, Norris PS, Ni CZ, Havert ML, Chiong EM, et al. (2003) Structurally distinct recognition motifs in lymphotoxin-beta receptor and CD40 for tumor necrosis factor receptor-associated factor (TRAF)-mediated signaling. J Biol Chem 278: 50523-50529.
62. Coleman CM, Wu L (2009) HIV interactions with monocytes and dendritic cells: viral latency and reservoirs. Retrovirology 6: 51.
63. Marshall WL, Brinkman BM, Ambrose CM, Pesavento PA, Uglialoro AM, et al. (1999) Signaling through the lymphotoxin-beta receptor stimulates HIV-1 replication alone and in cooperation with soluble or membrane-bound TNFalpha. J Immunol 162: 6016-6023.
64. Foy TM, Shepherd DM, Durie FH, Aruffo A, Ledbetter JA, et al. (1993) In vivo CD40-gp39 interactions are essential for thymus-dependent humoral immunity. II. Prolonged suppression of the humoral immune response by an antibody to the ligand for CD40, gp39. J Exp Med 178: 1567-1575.
65. Vanham G, Penne L, Devalck J, Kestens L, Colebunders R, et al. (1999) Decreased CD40 ligand induction in CD4 T cells and dysregulated IL-12 production during HIV infection. Clin Exp Immunol 117: 335-342.
66. Martin G, Roy J, Barat C, Ouellet M, Gilbert C, et al. (2007) Human immunodeficiency virus type 1-associated CD40 ligand transactivates B lymphocytes and promotes infection of CD4+ T cells. J Virol 81: 5872-5881.
67. Shen A, Yang HC, Zhou Y, Chase AJ, Boyer JD, et al. (2007) Novel pathway for induction of latent virus from resting CD4(+) T cells in the simian immunodeficiency virus/macaque model of human immunodeficiency virus type 1 latency. J Virol 81: 1660-1670.
68. Bressler P, Pantaleo G, Demaria A, Fauci AS (1991) Anti-CD2 receptor antibodies activate the HIV long terminal repeat in T lymphocytes. J Immunol 147: 2290-2294.
69. Wu JQ, Dyer WB, Chrisp J, Belov L, Wang B, et al. (2008) Longitudinal microarray analysis of cell surface antigens on peripheral blood mononuclear cells from HIV+ individuals on highly active antiretroviral therapy. Retrovirology 5: 24.
70. Fasnacht N, Müller W (2008) Conditional gp130 deficient mouse mutants. Semin Cell Dev Biol 19: 379-384.
71. Patterson BK, Behbahani H, Kabat WJ, Sullivan Y, O'Gorman MR, et al. (2001) Leukemia inhibitory factor inhibits HIV-1 replication and is upregulated in placentae from nontransmitting women. J Clin Invest 107: 287-294.
72. Tjernlund A, Fleener Z, Behbahani H, Connick E, Sönnerborg A, et al. (2003) Suppression of leukemia inhibitor factor in lymphoid tissue in primary HIV infection: absence of HIV replication in gp130-positive cells. AIDS 17: 1303-1310.
73. Tjernlund A, Barqasho B, Nowak P, Kinloch S, Thorborn D, et al. (2006) Early induction of leukemia inhibitor factor (LIF) in acute HIV-1 infection. AIDS 20: 11-19.
74. Favre D, Lederer S, Kanwar B, Ma ZM, Proll S, et al. (2009) Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection. PLoS Pathog 5: e1000295.
75. Macal M, Sankaran S, Chun TW, Reay E, Flamm J, et al. (2008) Effective CD4+ T-cell restoration in gut-associated lymphoid tissue of HIV-infected patients is associated with enhanced Th17 cells and polyfunctional HIV-specific T-cell responses. Mucosal Immunol 1: 475-488.
76. Chu PG, Arber DA (2001) CD79: a review. Appl Immunohistochem Mol Morphol 9: 97-106.
77. Dobbs AK, Yang T, Farmer D, Kager L, Parolini O, et al. (2007) Cutting edge: a hypomorphic mutation in Igbeta (CD79b) in a patient with immunodeficiency and a leaky defect in B cell development. J Immunol 179: 2055-2059.
78. Patke CL, Shearer WT (2000) gp120- and TNF-alpha-induced modulation of human B cell function: proliferation, cyclic AMP generation, Ig production, and B-cell receptor expression. J Allergy Clin Immunol 105: 975-982.
79. Nance CL, Shearer WT (2002) SDF-1alpha regulates HIV-1-gp120-induced changes in CD79b surface expression and Ig production in activated human B cells. Clin Immunol 105: 208-214.
80. Shimizu N, Tanaka A, Mori T, Ohtsuki T, Hoque A, et al. (2008) A formylpeptide receptor, FPRL1, acts as an efficient coreceptor for primary isolates of human immunodeficiency virus. Retrovirology 5: 52.
81. Hadjkacem B, Elleuch H, Gargouri J, Gargouri A (2009) Bernard-Soulier syndrome: novel nonsense mutation in GPIbbeta gene affecting GPIb-IX complex expression. Ann Hematol 88: 465-472.
82. Filonzi M, Cardoso LC, Pimenta MT, Queiroz DBC, Avellar MCW, et al. (2007) Relaxin family peptide receptors Rxfp1 and Rxfp2: mapping of the mRNA and protein distribution in the reproductive tract of the male rat. Reprod Biol Endocrinol 5: 29.
83. Gianesello L, Ferlin A, Menegazzo M, Pepe A, Foresta C (2009) RXFP1 is expressed on the sperm acrosome, and relaxin stimulates the acrosomal reaction of human spermatozoa. Ann N Y Acad Sci 1160: 192-193.
84. Ghosn J, Viard JP, Katlama C, de Almeida M, Tubiana R, et al. (2004) Evidence of genotypic resistance diversity of archived and circulating viral strains in blood and semen of pre-treated HIV-infected men. AIDS 18: 447-457.
85. Kern A, Bryant-Greenwood GD (2009) Mechanisms of relaxin receptor (LGR7/ RXFP1) expression and function. Ann N Y Acad Sci 1160: 60-66.
86. Passam AM, Sourvinos G, Krambovitis E, Miyakis S, Stavrianeas N, et al. (2007) Polymorphisms of Cx(3)CR1 and CXCR6 receptors in relation to HAART therapy of HIV type 1 patients. AIDS Res Hum Retroviruses 23: 1026-1032.
87. Singh P, Kaur G, Sharma G, Mehra NK (2008) Immunogenetic basis of HIV-1 infection, transmission and disease progression. Vaccine 26: 2966-2980.