Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy

Virology Journal

Volumn 10, Issue , 2013, Pages

  Wu, Jing Qin ^a   Sassé, Tara Ruth ^b   Saksena, Monica Miranda ^b   Saksena, Nitin K ^b  

^a UNIVERSITY OF NEWCASTLE   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Antigen presentation; HAART; HIV; Monocyte; Transcriptome; Virological failure

Indexed keywords

TRANSCRIPTOME;

ADAPTIVE IMMUNITY; ANTIGEN PRESENTATION; ARTICLE; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DISEASE COURSE; GENE EXPRESSION; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MONOCYTE; PHAGOCYTOSIS; POLYMERASE CHAIN REACTION; VALIDATION STUDY; VIREMIA;

ADULT; ANTI-RETROVIRAL AGENTS; CELLS, CULTURED; FEMALE; GENE EXPRESSION PROFILING; HIV INFECTIONS; HUMANS; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; MONOCYTES; TREATMENT OUTCOME;

EID: 84890985394     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-10-361     Document Type: Article

References (61)

1. Differentiation of phagocytic monocytes into lymph node dendritic cells in vivo. Randolph GJ, Inaba K, Robbiani DF, Steinman RM, Muller WA, Immunity 1999 11 753 761 10.1016/S1074-7613(00)80149-1 10626897
2. The origin of dendritic cells. Geissmann F, Nat Immunol 2007 8 558 560 10.1038/ni0607-558 17514208
3. Monocytes and their role in human immunodeficiency virus pathogenesis. Sasse TR, Wu JQ, Li Z, Saksena NK, Am J Infect Dis 2012 8 92 105 10.3844/ajidsp.2012.92.105
4. Mononuclear phagocytes of blood and bone marrow: comparative roles as viral reservoirs in human immunodeficiency virus type 1 infections. McElrath MJ, Pruett JE, Cohn ZA, Proc Natl Acad Sci USA 1989 86 675 679 10.1073/pnas.86.2. 675 2492110
5. HIV-1 DNA and mRNA concentrations are similar in peripheral blood monocytes and alveolar macrophages in HIV-1-infected individuals. Lewin SR, Kirihara J, Sonza S, Irving L, Mills J, Crowe SM, AIDS 1998 12 719 727 10.1097/00002030-199807000-00008 9619803
6. Efficient isolation and propagation of human immunodeficiency virus on recombinant colony-stimulating factor 1-treated monocytes. Gendelman HE, Orenstein JM, Martin MA, Ferrua C, Mitra R, Phipps T, Wahl LA, Lane HC, Fauci AS, Burke DS, et al. J Exp Med 1988 167 1428 1441 10.1084/jem.167.4.1428 3258626
7. Infection of monocyte-derived macrophages with human immunodeficiency virus type 1 (HIV-1). Monocyte-tropic and lymphocyte-tropic strains of HIV-1 show distinctive patterns of replication in a panel of cell types. Collman R, Hassan NF, Walker R, Godfrey B, Cutilli J, Hastings JC, Friedman H, Douglas SD, Nathanson N, J Exp Med 1989 170 1149 1163 10.1084/jem.170.4.1149 2571666
8. HIV-1 can be recovered from a variety of cells including peripheral blood monocytes of patients receiving highly active antiretroviral therapy: a further obstacle to eradication. Crowe SM, Sonza S, J Leukoc Biol 2000 68 345 350 10985250
9. Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection. Fulcher JA, Hwangbo Y, Zioni R, Nickle D, Lin X, Heath L, Mullins JI, Corey L, Zhu T, J Virol 2004 78 7883 7893 10.1128/JVI.78.15.7883-7893.2004 15254161
10. HIV-1 in peripheral blood monocytes: an underrated viral source. Zhu T, J Antimicrob Chemother 2002 50 309 311 10.1093/jac/dkf143 12205054
11. HIV-1 infection of bone marrow hematopoietic progenitor cells and their role in trafficking and viral dissemination. Alexaki A, Wigdahl B, PLoS Pathog 2008 4 1000215 10.1371/journal.ppat.1000215 19112504
12. Cellular reservoirs of HIV-1 and their role in viral persistence. Alexaki A, Liu Y, Wigdahl B, Curr HIV Res 2008 6 388 400 10.2174/157016208785861195 18855649
13. Microarray data on gene modulation by HIV-1 in immune cells: 2000-2006. Giri MS, Nebozhyn M, Showe L, Montaner LJ, J Leukoc Biol 2006 80 1031 1043 10.1189/jlb.0306157 16940334
14. HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages. Izmailova E, Bertley FM, Huang Q, Makori N, Miller CJ, Young RA, Aldovini A, Nat Med 2003 9 191 197 10.1038/nm822 12539042
15. Impact on genetic networks in human macrophages by a CCR5 strain of human immunodeficiency virus type 1. Coberley CR, Kohler JJ, Brown JN, Oshier JT, Baker HV, Popp MP, Sleasman JW, Goodenow MM, J Virol 2004 78 11477 11486 10.1128/JVI.78.21.11477-11486.2004 15479790
16. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Cicala C, Arthos J, Selig SM, Dennis G Jr, Hosack DA, Van Ryk D, Spangler ML, Steenbeke TD, Khazanie P, Gupta N, et al. Proc Natl Acad Sci USA 2002 99 9380 9385 10.1073/pnas.142287999 12089333
17. Regulation of HIV-1 transcription in cells of the monocyte-macrophage lineage. Kilareski EM, Shah S, Nonnemacher MR, Wigdahl B, Retrovirology 2009 6 118 10.1186/1742-4690-6-118 20030845
18. Macrophage signaling in HIV-1 infection. Herbein G, Gras G, Khan KA, Abbas W, Retrovirology 2010 7 34 10.1186/1742-4690-7-34 20380698
19. Circulating monocytes in HIV-1-infected viremic subjects exhibit an antiapoptosis gene signature and virus- and host-mediated apoptosis resistance. Giri MS, Nebozyhn M, Raymond A, Gekonge B, Hancock A, Creer S, Nicols C, Yousef M, Foulkes AS, Mounzer K, et al. J Immunol 2009 182 4459 4470 10.4049/jimmunol.0801450 19299747
20. Invasive chronic inflammatory monocyte phenotype in subjects with high HIV-1 viral load. Pulliam L, Sun B, Rempel H, J Neuroimmunol 2004 157 93 98 10.1016/j.jneuroim.2004.08.039 15579285
21. Diminished production of monocyte proinflammatory cytokines during human immunodeficiency virus viremia is mediated by type I interferons. Tilton JC, Johnson AJ, Luskin MR, Manion MM, Yang J, Adelsberger JW, Lempicki RA, Hallahan CW, McLaughlin M, Mican JM, et al. J Virol 2006 80 11486 11497 10.1128/JVI.00324-06 17005663
22. Transcriptome analysis of monocyte-HIV interactions. Van den Bergh R, Florence E, Vlieghe E, Boonefaes T, Grooten J, Houthuys E, Tran HT, Gali Y, De Baetselier P, Vanham G, Raes G, Retrovirology 2010 7 53 10.1186/1742-4690-7-53 20546557
23. Transcriptome analysis of primary monocytes shows global down-regulation of genetic networks in HIV viremic patients versus long-term non-progressors. Wu JQ, Sasse TR, Wolkenstein G, Conceicao V, Saksena MM, Soedjono M, Perera SS, Wang B, Dwyer DE, Saksena NK, Virology 2013 435 308 319 10.1016/j.virol.2012.10. 026 23158100
24. Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease. Wu JQ, Dwyer DE, Dyer WB, Yang YH, Wang B, Saksena NK, Retrovirology 2011 8 18 10.1186/1742-4690-8-18 21410942
25. Immuno-virologic outcomes and immuno-virologic discordance among adults alive and on anti-retroviral therapy at 12 months in Nigeria. Anude CJ, Eze E, Onyegbutulem HC, Charurat M, Etiebet MA, Ajayi S, Dakum P, Akinwande O, Beyrer C, Abimiku A, Blattner W, BMC Infect Dis 2013 13 113 10.1186/1471-2334-13-113 23452915
26. British HIV Association (BHIVA) national cohort outcomes audit of patients commencing antiretrovirals from naive. Street E, Curtis H, Sabin CA, Monteiro EF, Johnson MA, HIV Med 2009 10 337 342 10.1111/j.1468-1293.2009.00692. x 19490183
27. Constitutive gene expression in monocytes from chronic HIV-1 infection overlaps with acute Toll-like receptor induced monocyte activation profiles. Gekonge B, Giri MS, Kossenkov AV, Nebozyhn M, Yousef M, Mounzer K, Showe L, Montaner LJ, PLoS ONE 2012 7 41153 10.1371/journal.pone.0041153 22815948
28. Human immunodeficiency virus type 1-induced macrophage gene expression includes the p21 gene, a target for viral regulation. Vazquez N, Greenwell-Wild T, Marinos NJ, Swaim WD, Nares S, Ott DE, Schubert U, Henklein P, Orenstein JM, Sporn MB, Wahl SM, J Virol 2005 79 4479 4491 10.1128/JVI.79.7.4479-4491.2005 15767448
29. HIV-1 infection initiates changes in the expression of a wide array of genes in U937 promonocytes and HUT78 T cells. Wen W, Chen S, Cao Y, Zhu Y, Yamamoto Y, Virus Res 2005 113 26 35 10.1016/j.virusres.2005.04.002 15885842
30. Interferon gene expression following HIV type 1 infection of monocyte-derived macrophages. Woelk CH, Ottones F, Plotkin CR, Du P, Royer CD, Rought SE, Lozach J, Sasik R, Kornbluth RS, Richman DD, Corbeil J, AIDS Res Hum Retroviruses 2004 20 1210 1222 10.1089/aid.2004.20.1210 15588343
31. PAGE: parametric analysis of gene set enrichment. Kim SY, Volsky DJ, BMC Bioinforma 2005 6 144 10.1186/1471-2105-6-144
32. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP, Proc Natl Acad Sci USA 2005 102 15545 15550 10.1073/pnas.0506580102 16199517
33. TRANSFAC: transcriptional regulation, from patterns to profiles. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al. Nucleic Acids Res 2003 31 374 378 10.1093/nar/gkg108 12520026
34. Heterogeneity of peripheral blood monocyte populations in human immunodeficiency virus-1 seropositive patients. Abel PM, McSharry C, Galloway E, Ross C, Severn A, Toner G, Gruer L, Wilkinson PC, FEMS Microbiol Immunol 1992 5 317 323 1466904
35. Increased density of HLA-DR antigen on monocytes of patients infected with the human immunodeficiency virus. Koethe SM, Carrigan DR, Turner PA, J Med Virol 1989 29 82 87 10.1002/jmv.1890290203 2600592
36. Expression patterns of Fc gamma receptors, HLA-DR and selected adhesion molecules on monocytes from normal and HIV-infected individuals. Locher C, Vanham G, Kestens L, Kruger M, Ceuppens JL, Vingerhoets J, Gigase P, Clin Exp Immunol 1994 98 115 122 7923868
37. Heat shock protein 90AB1 and hyperthermia rescue infectivity of HIV with defective cores. Joshi P, Sloan B, Torbett BE, Stoddart CA, Virology 2013 436 162 172 10.1016/j.virol.2012.11.005 23200770
38. The RTP site shared by the HIV-1 Tat protein and the 11S regulator subunit alpha is crucial for their effects on proteasome function including antigen processing. Huang X, Seifert U, Salzmann U, Henklein P, Preissner R, Henke W, Sijts AJ, Kloetzel PM, Dubiel W, J Mol Biol 2002 323 771 782 10.1016/S0022-2836(02)00998-1 12419264
39. Influence of HLA-C expression level on HIV control. Apps R, Qi Y, Carlson JM, Chen H, Gao X, Thomas R, Yuki Y, Del Prete GQ, Goulder P, Brumme ZL, et al. Science 2013 340 87 91 10.1126/science.1232685 23559252
40. HIV disease progression correlates with the generation of dysfunctional naive CD8(low) T cells. Favre D, Stoddart CA, Emu B, Hoh R, Martin JN, Hecht FM, Deeks SG, McCune JM, Blood 2011 117 2189 2199 10.1182/blood-2010-06-288035 21200021
41. Modulation of the complement system in monocytes contributes to tuberculosis-associated immune reconstitution inflammatory syndrome. Tran HT, Van den Bergh R, Loembe MM, Worodria W, Mayanja-Kizza H, Colebunders R, Mascart F, Stordeur P, Kestens L, De Baetselier P, Raes G, AIDS 2013 27 1725 1734 10.1097/QAD.0b013e328361648b 23807270
42. The complement system in regulation of adaptive immunity. Carroll MC, Nat Immunol 2004 5 981 986 10.1038/ni1113 15454921
43. Human immunodeficiency virus causes mononuclear phagocyte dysfunction. Baldwin GC, Fleischmann J, Chung Y, Koyanagi Y, Chen IS, Golde DW, Proc Natl Acad Sci USA 1990 87 3933 3937 10.1073/pnas.87.10.3933 2187195
44. Monocyte and macrophage dysfunction as a cause of HIV-1 induced dysfunction of innate immunity. Collini P, Noursadeghi M, Sabroe I, Miller RF, Dockrell DH, Curr Mol Med 2010 10 727 740 10.2174/156652410793384141 20937022
45. Impaired phagocytosis among patients infected by the human immunodeficiency virus: implication for a role of highly active anti-retroviral therapy. Michailidis C, Giannopoulos G, Vigklis V, Armenis K, Tsakris A, Gargalianos P, Clin Exp Immunol 2012 167 499 504 10.1111/j.1365-2249.2011.04526. x 22288593
46. Decreased Fc receptor expression on innate immune cells is associated with impaired antibody-mediated cellular phagocytic activity in chronically HIV-1 infected individuals. Dugast AS, Tonelli A, Berger CT, Ackerman ME, Sciaranghella G, Liu Q, Sips M, Toth I, Piechocka-Trocha A, Ghebremichael M, Alter G, Virology 2011 415 160 167 10.1016/j.virol.2011.03.012 21565376
47. HIV-1 inhibits autophagy in bystander macrophage/monocytic cells through Src-Akt and STAT3. Van Grol J, Subauste C, Andrade RM, Fujinaga K, Nelson J, Subauste CS, PLoS ONE 2010 5 11733 10.1371/journal.pone.0011733 20661303
48. Akt inhibitors as an HIV-1 infected macrophage-specific anti-viral therapy. Chugh P, Bradel-Tretheway B, Monteiro-Filho CM, Planelles V, Maggirwar SB, Dewhurst S, Kim B, Retrovirology 2008 5 11 10.1186/1742-4690-5-11 18237430
49. R5 and ×4 HIV viruses differentially modulate host gene expression in resting CD4+ T cells. Sirois M, Robitaille L, Sasik R, Estaquier J, Fortin J, Corbeil J, AIDS Res Hum Retroviruses 2008 24 485 493 10.1089/aid.2007.0120 18327980
50. Inhibiting the Arp2/3 complex limits infection of both intracellular mature vaccinia virus and primate lentiviruses. Komano J, Miyauchi K, Matsuda Z, Yamamoto N, Mol Biol Cell 2004 15 5197 5207 10.1091/mbc.E04-04-0279 15385624
51. The HIV-1 Nef protein and phagocyte NADPH oxidase activation. Vilhardt F, Plastre O, Sawada M, Suzuki K, Wiznerowicz M, Kiyokawa E, Trono D, Krause KH, J Biol Chem 2002 277 42136 42143 10.1074/jbc.M200862200 12207012
52. LIM kinase 1-dependent cofilin 1 pathway and actin dynamics mediate nuclear retinoid receptor function in T lymphocytes. Ishaq M, Lin BR, Bosche M, Zheng X, Yang J, Huang D, Lempicki RA, Natarajan V, BMC Mol Biol 2011 12 41 10.1186/1471-2199-12-41 21923909
53. Divergent regulation of HIV-1 replication in PBMC of infected individuals by CC chemokines: suppression by RANTES, MIP-1alpha, and MCP-3, and enhancement by MCP-1. Vicenzi E, Alfano M, Ghezzi S, Gatti A, Veglia F, Lazzarin A, Sozzani S, Mantovani A, Poli G, J Leukoc Biol 2000 68 405 412 10985258
54. Molecular mechanisms involving sigma receptor-mediated induction of MCP-1: implication for increased monocyte transmigration. Yao H, Yang Y, Kim KJ, Bethel-Brown C, Gong N, Funa K, Gendelman HE, Su TP, Wang JQ, Buch S, Blood 2010 115 4951 4962 10.1182/blood-2010-01-266221 20354174
55. Microarray analysis of human leucocyte subsets: the advantages of positive selection and rapid purification. Lyons PA, Koukoulaki M, Hatton A, Doggett K, Woffendin HB, Chaudhry AN, Smith KG, BMC Genomics 2007 8 64 10.1186/1471-2164-8-64 17338817
56. lumi: a pipeline for processing Illumina microarray. Du P, Kibbe WA, Lin SM, Bioinformatics 2008 24 1547 1548 10.1093/bioinformatics/btn224 18467348
57. Model-based variance-stabilizing transformation for Illumina microarray data. Lin SM, Du P, Huber W, Kibbe WA, Nucleic Acids Res 2008 36 11 18178591
58. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Smyth GK, Stat Appl Genet Mol Biol 2004 3 rticle3 16646809
59. DAVID: database for annotation, visualization, and integrated discovery. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA, Genome Biol 2003 4 3 10.1186/gb-2003-4-5-p3 12734009
60. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG, Nucleic Acids Res 2009 37 417 D422 10.1093/nar/gkn708 18927109
61. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M, Nature 2005 434 338 345 10.1038/nature03441 15735639