Antiretroviral therapy down-regulates innate antiviral response genes in patients with AIDS in sub-Saharan Africa

Journal of Acquired Immune Deficiency Syndromes

Volumn 55, Issue 4, 2010, Pages 428-438

  Boulware, David R ^a,b   Meya, David B ^c   Bergemann, Tracy L ^d   Williams, Darlisha ^a,b   Vlasova St Louis, Irina A ^b   Rhein, Josh ^a,b   Staddon, Jack ^a,b   Kambugu, Andrew ^c   Janoff, Edward N ^e   Bohjanen, Paul R ^a,b  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c MAKERERE UNIVERSITY   (Uganda)

^d UNIVERSITY OF MINNESOTA   (United States)

^e UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

adult; AIDS; gene expression profiling BL; HAART; HIV; oligonucleotide array sequence analysis

Indexed keywords

ANTIRETROVIRUS AGENT; INTERFERON; MESSENGER RNA; PATTERN RECOGNITION RECEPTOR;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADULT; AFRICA; APOPTOSIS; ARTICLE; BLOOD; CELL PROLIFERATION; CLINICAL ARTICLE; DOWN REGULATION; FEMALE; GENE EXPRESSION; HUMAN; INNATE IMMUNITY; MALE; PRIORITY JOURNAL; T LYMPHOCYTE ACTIVATION; UPREGULATION; VIRUS GENE;

ACQUIRED IMMUNODEFICIENCY SYNDROME; ADULT; ANTI-RETROVIRAL AGENTS; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; DOWN-REGULATION; FEMALE; HIV-1; HUMANS; IMMUNITY, INNATE; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; PROSPECTIVE STUDIES; UGANDA;

EID: 78650244230     PISSN: 15254135     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAI.0b013e3181ef4963     Document Type: Article

References (61)

1. Schacker TW, Nguyen PL, Beilman GJ, et al. Collagen deposition in HIV-1 infected lymphatic tissues and T cell homeostasis. J Clin Invest. 2002;110: 1133-1139.
2. Li Q, Schacker T, Carlis J, et al. Functional genomic analysis of the response of HIV-1-infected lymphatic tissue to antiretroviral therapy. J Infect Dis. 2004;189:572-582.
3. Vahey MT, Ockenhouse CF, Wang Z, et al. Impact of antiretroviral treatment on gene expression in peripheral blood mononuclear cells from SIVmac251-infected macaques. J Infect Dis. 2007;196:384-393.
4. Moir S, Malaspina A, Pickeral OK, et al. Decreased survival of B cells of HIV-viremic patients mediated by altered expression of receptors of the TNF superfamily. J Exp Med. 2004;200:587-599.
5. Montano M, Rarick M, Sebastiani P, et al. Gene-expression profiling of HIV-1 infection and perinatal transmission in Botswana. Genes Immun. 2006;7:298-309.
6. Rotger M, Dang KK, Fellay J, et al. Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog. 2010;6:el000781.
7. Giri MS, Nebozhyn M, Showe L, et al. Microarray data on gene modulation by HIV-1 in immune cells: 2000-2006. J Leukoc Biol. 2006; 80:1031-1043.
8. Guadalupe M, Reay E, Sankaran S, et al. Severe CD4+ T-cell depletion in gut lymphoid tissue during primary human immunodeficiency virus type 1 infection and substantial delay in restoration following highly active antiretroviral therapy. J Virol. 2003;77:11708-11717.
9. Li Q, Smith AJ, Schacker TW, et al. Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. J Immunol. 2009;183:1975-1982.
10. Jacquelin B, Mayau V, Targat B, et al. Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type IIFN response. J Clin Invest. 2009;119:3544-3555.
11. Consortium M, Shi L, Reid LH, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006;24:1151-1161.
12. Chen JJ, Hsueh HM, Delongchamp RR, et al. Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics. 2007;8:412.
13. Spanish Society of Infectious Diseases and Clinical Microbiology, Orta Mira N, Guna Serrano Mdel R, Latorre Martínez JC, et al. Analysis of the results of the SEIMC External Quality Control Program for HIV-1 and HCV viral loads, 2007 [in Spanish]. Enferm Infecc Microbiol Clin. 2008; 26(Suppl 13): 8-13.
14. Brambilla D, Jennings C, Aldrovandi G, et al. Multicenter evaluation of use of dried blood and plasma spot specimens in quantitative assays for human immunodeficiency virus RNA: measurement, precision, and RNA stability. J Clin Microbiol. 2003;41:1888-1893.
15. Baechler EC, Batliwalla FM, Karypis G, et al. Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation. Genes Immun. 2004;5:347-353.
16. Debey S, Schoenbeck U, Hellmich M, et al. Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J. 2004;4:193-207.
17. Feezor RJ, Baker HV, Mindrinos M, et al. Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics. 2004;19: 247-254.
18. Chai V, Vassilakos A, Lee Y, et al. Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples. J Clin Lab Anal. 2005;19:182-188.
19. Bolstad BM, Irizarry RA, Astrand M, et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185-193.
20. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57: 289-300.
21. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
22. Raghavan A, Dhalla M, Bakheet T, et al. Patterns of coordinate down-regulation of ARE-containing transcripts following immune cell activation. Genomics. 2004;84:1002-1013.
23. Huthoff H, Towers GJ. Restriction of retroviral replication by APOBEC3 G/F and TRIM5alpha. Trends Microbiol. 2008;16:612-619.
24. Langelier CR, Sandrin V, Eckert DM, et al. Biochemical characterization of a recombinant TRIM5alpha protein that restricts human immunodeficiency virus type 1 replication. J Virol. 2008;82:11682-11694.
25. Glickman MH, Ciechanover A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev. 2002;82: 373-428.
26. Imbeault M, Ouellet M, Tremblay MJ. Microarray study reveals that HIV-1 induces rapid type-I interferon-dependent p53 mRNA up-regulation in human primary CD4+ T cells. Retrovirology. 2009;6:5.
27. Rempel H, Calosing C, Sun B, et al. Sialoadhesin expressed on IFN-induced monocytes binds HIV-1 and enhances infectivity. PLoS ONE. 2008;3:el967.
28. van der Kuyl AC, van den Burg R, Zorgdrager F, et al. Sialoadhesin (CD169) expression in CD14+ cells is upregulated early after HIV-1 infection and increases during disease progression. PLoS ONE. 2007;2:e257.
29. Silverman RH, Sengupta DN. Translational regulation by HIV leader RNA, TAT, and interferon-inducible enzymes. J Exp Pathol. 1990;5:69-77.
30. Vollbrecht T, Brackmann H, Henrich N, et al. Impact of changes in antigen level on CD38/PD-1 co-expression on HlV-specific CD8 T cells in chronic, untreated HIV-1 infection. J Med Virol. 2010;82:358-370.
31. Coetzee LM, Tay SS, Lawrie D, et al. From research tool to routine test: CD38 monitoring in HIV patients. Cytometry B Clin Cytom. 2009;76: 375-384.
32. Tuaillon E, Al Tabaa Y, Baillat V, et al. Close association of CD8+/CD38 bright with HIV-1 replication and complex relationship with CD4+ T-cell count. Cytometry B Clin Cytom. 2009;76B:249-260.
33. Cocude C, Truong MJ, Billaut-Mulot O, et al. A novel cellular RNA helicase, RH116, differentially regulates cell growth, programmed cell death and human immunodeficiency virus type 1 replication. J Gen Virol. 2003;84(Pt 12):3215-3225.
34. Kalia V, Sarkar S, Gupta P, et al. Rational site-directed mutations of the LLP-1 and LLP-2 lentivirus lytic peptide domains in the intracytoplasmic tail of human immunodeficiency virus type 1 gp41 indicate common functions in cell-cell fusion but distinct roles in virion envelope incorporation. J Virol. 2003;77:3634-3646.
35. Kreuzer KA, Dayer JM, Rockstroh JK, et al. The IL-1 system in HIV infection: peripheral concentrations of IL-1 beta, IL-1 receptor antagonist and soluble IL-1 receptor type II. Clin Exp Immunol. 1997;109:54-58.
36. Yadav A, Fitzgerald P, Sajadi MM, et al. Increased expression of suppressor of cytokine signaling-1 (SOCS-1): a mechanism for dysregulated T helper-1 responses in HIV-1 disease. Virology. 2009; 385:126-133.
37. Yan N, Cherepanov P, Daigle JE, et al. The SET complex acts as a barrier to autointegration of HIV-1. PLoS Pathog. 2009;5:el000327.
38. Zauli G, Milani D, Mirandola P, et al. HIV-1 Tat protein down-regulates CREB transcription factor expression in PC12 neuronal cells through a phosphatidylinositol 3-kinase/AKT/cyclic nucleoside phosphodiester-ase pathway. FASEB J. 2001;15:483-491.
39. Mangeat B, Turelli P, Caron G, et al. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature. 2003;424:99-103.
40. Goila-Gaur R, Khan M, Miyagi E, et al. Targeting APOBEC3A to the viral nucleoprotein complex confers antiviral activity. Retrovirology. 2007;4:61.
41. Yu X, Yu Y, Liu B, et al. Induction of APOBEC3G Ubiquitination and Degradation by an HIV-1 Vif-Cul5-SCF Complex. Science. 2003;302: 1056-1060.
42. Mehle A, Goncalves J, Santa-Marta M, et al. Phosphorylation of a novel SOCS-box regulates assembly of the HIV-1 Vif-Cul5 complex that promotes APOBEC3G degradation. Genes Dev. 2004;18:2861-2866.
43. Xiao Z, Ehrlich E, Yu Y, et al. Assembly of HIV-1 Vif-Cul5 E3 ubiquitin ligase through a novel zinc-binding domain-stabilized hydrophobic interface in Vif. Virology. 2006;349:290-299.
44. Ockenhouse CF, Bernstein WB, Wang Z, et al. Functional genomic relationships in HIV-1 disease revealed by gene-expression profiling of primary human peripheral blood mononuclear cells. J Infect Dis. 2005; 191:2064-2074.
45. Zhang W, Chen G, Niewiadomska AM, et al. Distinct determinants in HIV-1 Vif and human APOBEC3 proteins are required for the suppression of diverse host anti-viral proteins. PLoS ONE. 2008;3:e3963.
46. Sawyer SL, Emerman M, Malik HS. Discordant evolution of the adjacent antiretro viral genes TRIM22 and TRIM5 in mammals. PLoS Pathog. 2007;3:el97.
47. Kaiser SM, Malik HS, Emerman M. Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein. Science. 2007;316:1756-1758.
48. Stremlau M, Owens CM, Perron MJ, et al. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature. 2004;427:848-853.
49. Barr SD, Smiley JR, Bushman FD. The Interferon Response Inhibits HIV Particle Production by Induction of TRIM22. PLoS Pathog. 2008;4: el000007.
50. Morrissey LM, Kirkegaard K. Regulation of a double-stranded RNA modification activity in human cells. Mol Cell Biol. 1991;11:3719-3725.
51. Phuphuakrat A, Kraiwong R, Boonarkart C, et al. Double-stranded RNA adenosine deaminases enhance expression of human immunodeficiency virus type 1 proteins. J Virol. 2008;82:10864-10872.
52. Harenberg A, Guillaume F, Ryan EJ, et al. Gene profiling analysis of ALVAC infected human monocyte derived dendritic cells. Vaccine. 2008; 26:5004-5013.
53. Gack MU, Shin YC, Joo CH, et al. TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature. 2007;446: 916-920.
54. Biacchesi S, LeBerre M, Lamoureux A, et al. MAVS plays a major role in induction of the fish innate immune response against RNA and DNA viruses. J. V i ro l . 2009:83;7815-7827.
55. Espert L, Degols G, Lin YL, et al. Interferon-induced exonuclease ISG20 exhibits an antiviral activity against human immunodeficiency virus type 1. J Gen Virol. 2005;86(Pt 8):2221-2229.
56. Okumura A, Lu G, Pitha-Rowe I, et al. Innate antiviral response targets HIV-1 release by the induction of ubiquitin-like protein ISG15. Proc Natl Acad Sci USA. 2006;103:1440-1445.
57. Harty RN, Pitha PM, Okumura A. Antiviral activity of innate immune protein ISG15. J Innate Immun. 2009;l:397-404.
58. Chen H, Dziuba N, Friedrich B, et al. A critical role for CD63 in HIV replication and infection of macrophages and cell lines. Virology. 2008;379:191-196.
59. Kaufmann GR, Zaunders JJ, Cunningham P, et al. Rapid restoration of CD4 T cell subsets in subjects receiving antiretroviral therapy during primary HIV-1 infection. AIDS. 2000;14:2643-2651.
60. Bren GD, Trushin SA, Whitman J, et al. HIV gpl20 induces, NF-kappaB dependent, HIV replication that requires procaspase 8. PLoS ONE. 2009; 4:e4875.
61. Micali OC, Cheung HH, Plenchette S, et al. Silencing of the XAF1 gene by promoter hypermethylation in cancer cells and reactivation to TRAIL-sensitization by IFN-beta. BMC Cancer. 2007;7:52.