'Omics investigations of HIV and SIV pathogenesis and innate immunity

Current Topics in Microbiology and Immunology

Volumn 363, Issue , 2012, Pages 87-116

  Palermo, Robert E ^a,b   Fuller, Deborah H ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Washington National Primate Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA INTERFERON; DNA DIRECTED RNA POLYMERASE III; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; RETINOIC ACID INDUCIBLE PROTEIN I; TOLL LIKE RECEPTOR 3; TOLL LIKE RECEPTOR 7; TOLL LIKE RECEPTOR 9; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTION FACTOR RELB; UNTRANSLATED RNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADAPTIVE IMMUNITY; ANTIGEN PRESENTATION; ANTIGEN PRESENTING CELL; ARTICLE; B LYMPHOCYTE; DENDRITIC CELL; DOWN REGULATION; EPIDEMIC; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HUMORAL IMMUNITY; IN VITRO STUDY; INNATE IMMUNITY; MICROARRAY ANALYSIS; NONHUMAN; PATHOGENESIS; PRIMARY CELL CULTURE; PRIORITY JOURNAL; PROTEOMICS; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY; T LYMPHOCYTE; UPREGULATION; VIRUS CELL INTERACTION; VIRUS REPLICATION;

ACQUIRED IMMUNODEFICIENCY SYNDROME; ANIMALS; GENOMICS; HIV; HUMANS; IMMUNITY, INNATE; PROTEOMICS; SIMIAN IMMUNODEFICIENCY VIRUS; SYSTEMS BIOLOGY;

EID: 84874916618     PISSN: 0070217X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/82-2012-255     Document Type: Article

References (91)

1. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S., Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG (2011) A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. mBio 2: e00325-10
2. Agy MB, Wambach M, Foy K, Katze MG (1990) Expression of cellular genes in CD4 positive lymphoid cells infected by the human immunodeficiency virus, HIV-1: evidence for a host protein synthesis shut-off induced by cellular mRNA degradation. Virology 177: 251-8
3. Agy MB, Frumkin LR, Corey L, Coombs RW, Wolinsky SM, Koehler J, Morton WR, Katze MG (1992) Infection of Macaca nemestrina by human immunodeficiency virus type-1. Science 257: 103-6
4. Apetrei C, Sumpter B, Souquiere S, Chahroudi A, Makuwa M, Reed P, Ribeiro RM, Pandrea I, Roques P, Silvestri G (2011) Immunovirological analyses of chronically simian immunodeficiency virus SIVmnd-1-and SIVmnd-2-infected mandrills (Mandrillus sphinx). J Virol 85: 13077-87
5. Arhel N (2010) Revisiting HIV-1 uncoating. Retrovirology 7: 96
6. Barnett SW, Burke B, Sun Y, Kan E, Legg H, Lian Y, Bost K, Zhou F, Goodsell A, Zur Megede J, Polo J, Donnelly J, Ulmer J, Otten GR, Miller CJ, Vajdy M, Srivastava IK (2010) Antibody-mediated protection against mucosal simian-human immunodeficiency virus challenge of macaques immunized with alphavirus replicon particles and boosted with trimeric envelope glycoprotein in MF59 adjuvant. J Virol 84: 5975-85
7. Barouch DH, Liu J, Li H, Maxfield LF, Abbink P, Lynch DM, Iampietro MJ, SanMiguel A, Seaman MS, Ferrari G, Forthal DN, Ourmanov I, Hirsch VM, Carville A, Mansfield KG, Stablein D, Pau MG, Schuitemaker H, Sadoff JC, Billings EA, Rao M, Robb ML, Kim JH, Marovich MA, Goudsmit J, Michael NL (2012) Vaccine protection against acquisition of neutralization-resistant SIV challenges in rhesus monkeys. Nature 482: 89-93
8. Baskin CR, Bielefeldt-Ohmann H,Garcia-Sastre A,Tumpey TM, Van HN, Carter VS, Thomas MJ, Proll S, Solorzano A, Billharz R, Fornek JL, Thomas S, Chen CH, Clark EA, Murali-Krishna K, Katze MG (2007) Functional genomic and serological analysis of the protective immune response resulting from vaccination of macaques with an NS1-truncated influenza virus. J Virol 81: 11817-11827
9. Batten CJ, De Rose R, Wilson KM, Agy MB, Chea S, Stratov I, Montefiori DC, Kent SJ (2006) Comparative evaluation of simian, simian-human, and human immunodeficiency virus infections in the pigtail macaque (Macaca nemestrina) model. AIDS Res Hum Retroviruses 22: 580-8
10. Belyakov IM, Hel Z, Kelsall B, Kuznetsov VA, Ahlers JD, Nacsa J, Watkins DI, Allen TM, Sette A, Altman J, Woodward R, Markham PD, Clements JD, Franchini G, Strober W, Berzofsky JA (2001) Mucosal AIDS vaccine reduces disease and viral load in gut reservoir and blood after mucosal infection of macaques. Nat Med 7: 1320-6
11. Bosinger SE, Li Q, Gordon SN, Klatt NR, Duan L, Xu L, Francella N, Sidahmed A, Smith AJ, Cramer EM, Zeng M, Masopust D, Carlis JV, Ran L, Vanderford TH, Paiardini M, Isett RB, Baldwin DA, Else JG, Staprans SI, Silvestri G, Haase AT, Kelvin DJ (2009) Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. J Clin Invest 119: 3556-72
12. Brugger B, Krautkramer E, Tibroni N, Munte CE, Rauch S,Leibrecht I, Glass B, Breuer S, Geyer M, Krausslich HG, Kalbitzer HR, Wieland FT, Fackler OT (2007) Human immunodeficiency virus type 1 Nef protein modulates the lipid composition of virions and host cell membrane microdomains. Retrovirology 4: 70
13. Chahroudi A, Bosinger SE, Vanderford TH, Paiardini M, Silvestri G (2012) Natural SIV hosts: showing AIDS the door. Science 335: 1188-93
14. Chan EY, Qian WJ, Diamond DL, Liu T, Gritsenko MA, Monroe ME, Camp DG 2nd, Smith RD, Katze MG (2007) Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production. J Virol 81: 7571-83
15. Chan EY, Sutton JN, Jacobs JM, Bondarenko A, Smith RD, Katze MG (2009) Dynamic host energetics and cytoskeletal proteomes in human immunodeficiency virus type 1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry. J Virol 83: 9283-95
16. Chang ST, Sova P, Peng X et al (2011) Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and regulation of noncoding RNA expression in a CD4 ? T Cell line. mBio 2(5): doi: 10.1128/mBio.00134-11
17. Chiu YH, Macmillan JB, Chen ZJ (2009) RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell 138: 576-91
18. Cilloniz C, Shinya K, Peng X, Korth MJ, Proll SC, Aicher LD, Carter VS, Chang JH, Kobasa D, Feldmann F, Strong JE, Feldmann H, Kawaoka Y, Katze MG (2009) Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes. PLoS Pathog 5: e1000604
19. Cilloniz C, Ebihara H, Ni C, Neumann G, Korth MJ, Kelly SM, KawaokaY,FeldmannH,Katze MG (2011) Functional genomics reveals the induction of inflammatory response and metallopro-teinase gene expression during lethal Ebola virus infection. J Virol 85: 9060-8
20. Corbeil J, Sheeter D, Genini D, Rought S, Leoni L, Du P, Ferguson M, Masys DR, Welsh JB, Fink JL, Sasik R, Huang D, Drenkow J, Richman DD, Gingeras T (2001) Temporal gene regulation during HIV-1 infection of human CD4+ T cells. Genome Res 11: 1198-1204
21. Daniel MD, Kirchhoff F, Czajak SC, Sehgal PK, Desrosiers RC (1992) Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene. Science 258: 1938-41
22. de Lang A, Baas T, Teal T, Leijten LM, Rain B, Osterhaus AD, Haagmans BL, Katze MG (2007) Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques. PLoS Pathog 3: e112
23. Deeks SG, Walker BD (2007) Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. Immunity 27: 406-16
24. Diop OM, Gueye A, Dias-Tavares M, Kornfeld C, Faye A, Ave P, Huerre M, Corbet S, Barre-Sinoussi F, Muller-Trutwin MC (2000) High levels of viral replication during primary simian immunodeficiency virus SIVagm infection are rapidly and strongly controlled in African green monkeys. J Virol 74: 7538-47
25. Diop OM, Ploquin MJ, Mortara L, Faye A, Jacquelin B, Kunkel D, Lebon P, Butor C, Hosmalin A, Barre-Sinoussi F, Muller-Trutwin MC (2008) Plasmacytoid dendritic cell dynamics and alpha interferon production during Simian immunodeficiency virus infection with a nonpathogenic outcome. J Virol 82: 5145-52
26. Favre D, Lederer S, Kanwar B, Ma ZM, Proll S, Kasakow Z, Mold J, Swainson L, Barbour JD, Baskin CR, Palermo R, Pandrea I, Miller CJ, Katze MG, McCune JM (2009) Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection. PLoS Pathog 5: e1000295
27. Frumkin LR, Agy MB, Coombs RW, Panther L, Morton WR, Koehler J, Florey MJ, Dragavon J, Schmidt A, Katze MG et al (1993) Acute infection of Macaca nemestrina by human immunodeficiency virus type 1. Virology 195: 422-31
28. Fuller DH, Rajakumar PA, Wilson LA, Trichel AM, Fuller JT, Shipley T, Wu MS, Weis K, Rinaldo CR, Haynes JR, Murphey-Corb M (2002) Induction of mucosal protection against primary, heterologous simian immunodeficiency virus by a DNA vaccine. J Virol 76: 3309-17
29. Fuller DH, Rajakumar P, Che JW, Narendran A, Nyaundi J, Michael H, Yager EJ, Stagnar C, Wahlberg B, Taber R, Haynes JR, Cook FC, Ertl P, Tite J, Amedee AM, Murphey-Corb M (2012) Therapeutic DNA vaccine induces broad T cell responses in the gut and sustained protection from viral rebound and AIDS in SIV-infected rhesus macaques. PLoS One 7: e33715
30. Gale M Jr, Katze MG (1998) Molecular mechanisms of interferon resistance mediated by viral-directed inhibition of PKR, the interferon-induced protein kinase. Pharmacol Ther 78: 29-46
31. Gaucher D, Therrien R, Kettaf N, Angermann BR, Boucher G, Filali-Mouhim A, Moser JM, Mehta RS, DrakeDR 3rd, CastroE,AkondyR,RinfretA,Yassine-DiabB,Said EA, Chouikh Y, CameronMJ, ClumR,KelvinD,SomogyiR,GrellerLD, BalderasRS, WilkinsonP,Pantaleo G, Tartaglia J,Haddad EK, Sekaly RP (2008) Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 205: 3119-31
32. Geiss GK, Bumgarner RE, An MC, Agy MB, van 't Wout AB, Hammersmark E, Carter VS, Upchurch D, Mullins JI, Katze MG (2000) Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology 266: 8-16
33. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, MinxP,Nelson JO, Pepin KH, QinX,Sutton GG, VenterE,Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, GlasscockJ,Harris RA, HavlakP,Jackson AR, JiangH etal (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234
34. Goldstein S, Ourmanov I, Brown CR, Plishka R, Buckler-White A, Byrum R, Hirsch VM (2005) Plateau levels of viremia correlate with the degree of CD4+-T-cell loss in simian immunodeficiency virus SIVagm-infected pigtailed macaques: variable pathogenicity of natural SIVagm isolates. J Virol 79: 5153-62
35. Gupta A, Nagilla P, Le HS, Bunney C, Zych C, Thalamuthu A, Bar-Joseph Z, Mathavan S, Ayyavoo V (2011) Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). PLoS One 6: e22730
36. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-7
37. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 19: 1720-1730
38. Henriet S, Mercenne G, Bernacchi S, Paillart JC, Marquet R (2009) Tumultuous relationship between the human immunodeficiency virus type 1 viral infectivity factor (Vif) and the human APOBEC-3G and APOBEC-3F restriction factors. Microbiol Mol Biol Rev 73: 211-32
39. Imbeault M, Ouellet M, Tremblay MJ (2009) Microarray study reveals that HIV-1 induces rapid type-I interferon-dependent p53 mRNA up-regulation in human primary CD4+ T cells. Retrovirology 6: 5
40. Jacquelin B, Mayau V, Targat B, Liovat AS, Kunkel D, Petitjean G, Dillies MA, Roques P, Butor C, Silvestri G, Giavedoni LD, Lebon P, Barre-Sinoussi F, Benecke A, Muller-Trutwin MC (2009) Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response. J Clin Invest 119: 3544-55
41. Katze MG (1995) Regulation of the interferon-induced PKR: can viruses cope? Trends Microbiol 3: 75-8
42. Katze MG (2002) Interferon, PKR, virology, and genomics: what is past and what is next in the new millennium? J Interferon Cytokine Res 22: 283-6
43. Katze MG, Agy MB (1990) Regulation of viral and cellular RNA turnover in cells infected by eukaryotic viruses including HIV-1. Enzyme 44: 332-46
44. Katze MG, He Y, Gale M Jr (2002) Viruses and interferon: a fight for supremacy. Nat Rev Immunol 2: 675-87
45. Kawai T, Akira S (2010) The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat Immunol 11: 373-84
46. Kobasa D, Jones SM, Shinya K, Kash JC, Copps J, Ebihara H, Hatta Y, Kim JH, Halfmann P, Hatta M, Feldmann F, Alimonti JB, Fernando L, Li Y, Katze MG, Feldmann H, Kawaoka Y (2007) Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 445: 319-23
47. Korth MJ, Kash JC, Furlong JC, Katze MG (2005) Virus infection and the interferon response: a global view through functional genomics. Methods Mol Med 116: 37-55
48. Lai L, Kwa S, Kozlowski PA, Montefiori DC, Ferrari G, Johnson WE, Hirsch V, Villinger F, Chennareddi L, Earl PL, Moss B, Amara RR, Robinson HL (2011) Prevention of infection by a granulocyte-macrophage colony-stimulating factor co-expressing DNA/modified vaccinia Ankara simian immunodeficiency virus vaccine. J Infect Dis 204: 164-73
49. Lederer S, Favre D, Walters KA, Proll S, Kanwar B, Kasakow Z, Baskin CR, Palermo R, McCune JM, Katze MG (2009) Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization. PLoS Pathog 5: e1000296, 10.1371/journal.ppat. 1000296
50. Li Y, Chan EY, Katze MG (2007) Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus. Virology 366: 137-49
51. Loudon PT, Yager EJ, Lynch DT, Narendran A, Stagnar C, Franchini AM, Fuller JT, White PA, Nyuandi J, Wiley CA, Murphey-Corb M, Fuller DH (2010) GM-CSF increases mucosal and systemic immunogenicity of an H1N1 influenza DNA vaccine administered into the epidermis of non-human primates. PloS one 5: e11021
52. Magness CL, Fellin PC, Thomas MJ, Korth MJ, Agy MB, Proll SC, Fitzgibbon M, Scherer CA, Miner DG, Katze MG, Iadonato SP (2005) Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. Genome Biol 6: R60
53. Manrique M, Kozlowski PA, Cobo-Molinos A, Wang SW, Wilson RL, Montefiori DC, Mansfield KG, Carville A, Aldovini A (2011) Long-term control of simian immunodeficiency Virus mac251 viremia to undetectable levels in half of infected female rhesus macaques nasally vaccinated with simian immunodeficiency virus DNA/recombinant modified vaccinia virus Ankara. J Immunol 186: 3581-93
54. McDermott JE, Shankaran H, Eisfeld AJ, Belisle SE, Neuman G, Li C, McWeeney S, Sabourin C, Kawaoka Y, Katze MG, Waters KM (2011) Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems. BMC Syst Biol 5: 190
55. Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10: 155-9
56. Mir KD, Bosinger SE, Gasper M, Ho O, Else JG, Brenchley JM, Kelvin DJ, Silvestri G, Hu SL, Sodora DL (2012) SIV-induced alterations in monocyte TNF-alpha production contribute to reduced immune activation in sooty mangabeys. J Virol 86: 7605-7615
57. Moresco EM, LaVine D, Beutler B (2011) Toll-like receptors. Curr Biol 21: R488-93
58. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-8
59. Nakaya HI,WrammertJ,LeeEK, RacioppiL,Marie-KunzeS,HainingWN,Means AR,Kasturi SP, Khan N, Li GM, McCausland M, Kanchan V, Kokko KE, Li S, Elbein R, Mehta AK, Aderem A, Subbarao K, Ahmed R, Pulendran B (2011) Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 12: 786-95
60. Napolitani G, Rinaldi A, Bertoni F, Sallusto F, Lanzavecchia A (2005) Selected Toll-like receptor agonist combinations synergistically trigger a T helper type 1-polarizing program in dendritic cells. Nat Immunol 6: 769-76
61. Navare AT, SovaP,PurdyDE, Weiss JM, Wolf-YadlinA,Korth MJ,Chang ST, Proll SC,JahanTA, Krasnoselsky AL, Palermo RE, Katze MG (2012) Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation. Virology 429: 37-46
62. Palermo RE, Patterson LJ, Aicher LD, Korth MJ, Robert-Guroff M, Katze MG (2011) Genomic analysis reveals pre-and postchallenge differences in a rhesus macaque AIDS vaccine trial: insights into mechanisms of vaccine efficacy. J Virol 85: 1099-116
63. Pandrea I, Apetrei C, Dufour J, Dillon N, Barbercheck J, Metzger M, Jacquelin B, Bohm R, Marx PA, Barre-Sinoussi F, Hirsch VM, Muller-Trutwin MC, Lackner AA, Veazey RS (2006) Simian immunodeficiency virus SIVagm.sab infection of Caribbean African green monkeys: a new model for the study of SIV pathogenesis in natural hosts. J Virol 80: 4858-67
64. Pandrea IV, Gautam R, Ribeiro RM, Brenchley JM, Butler IF, Pattison M, Rasmussen T, Marx PA, Silvestri G, Lackner AA, Perelson AS, Douek DC, Veazey RS, Apetrei C (2007) Acute loss of intestinal CD4+ T cells is not predictive of simian immunodeficiency virus virulence. J Immunol 179: 3035-3046
65. Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS (2009) Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 182: 7738-48
66. Patterson LJ, Malkevitch N, Venzon D, Pinczewski J, Gomez-Roman VR, Wang L, Kalyanaraman VS, Markham PD, Robey FA, Robert-Guroff M (2004) Protection against mucosal simian immunodeficiency virus SIV(mac251) challenge by using replicating adenovirus-SIV multigene vaccine priming and subunit boosting. J Virol 78: 2212-2221
67. Peng X, Gralinski L, Armour CD, Ferris MT, Thomas MJ, Proll S, Bradel-Tretheway BG, Korth MJ, Castle JC, Biery MC, Bouzek HK, Haynor DR, Frieman MB, HeiseM,Raymond CK, Baric RS, Katze MG(2010) Unique signatures oflong noncoding RNA expression in response to virus infection and altered innate immune signaling. MBio 1: e00206-10
68. Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, Kennedy K, Wu H, Bennouna S, Oluoch H, Miller J, Vencio RZ, Mulligan M, Aderem A, Ahmed R, Pulendran B (2009) Systems biology approach predicts immunoge-nicity of the yellow fever vaccine in humans. Nat Immunol 10: 116-25
69. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Chiu J, Paris R, Premsri N, Namwat C, de Souza M, Adams E, Benenson M, Gurunathan S, Tartaglia J, McNeil JG, Francis DP, Stablein D, Birx DL, Chunsuttiwat S, Khamboonruang C, Thongcharoen P, Robb ML, Michael NL, Kunasol P, Kim JH (2009) Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med 361: 2209-20
70. Safronetz D, Rockx B, Feldmann F, Belisle SE, Palermo RE, Brining D, Gardner D, Proll SC, Marzi A, Tsuda Y, Lacasse RA, Kercher L, York A, Korth MJ, Long D, Rosenke R, Shupert WL, Aranda CA, Mattoon JS, KobasaD, KobingerG, Li Y,Taubenberger JK, Richt JA, Parnell M, Ebihara H, Kawaoka Y, Katze MG, Feldmann H (2011) Pandemic swine-origin H1N1 influenzaA virus isolates show heterogeneous virulence in macaques.J Virol 85: 1214-23
71. Sheehy AM, Gaddis NC, Choi JD, Malim MH (2002) Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418: 646-50
72. Silvestri G, Sodora DL, Koup RA, Paiardini M, O'Neil SP, McClure HM, Staprans SI, Feinberg MB (2003) Nonpathogenic SIV infection of sooty mangabeys is characterized by limited bystander immunopathology despite chronic high-level viremia. Immunity 18: 441-52
73. Staprans SI, Barry AP, Silvestri G, Safrit JT, Kozyr N, Sumpter B, Nguyen H, McClure H, Montefiori D, Cohen JI, Feinberg MB (2004) Enhanced SIV replication and accelerated progression to AIDS in macaques primed to mount a CD4 T cell response to the SIV envelope protein. Proc. Natl. Acad. Sci. U.S.A. 101: 13026-13031
74. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-60
75. Szabo G, Dolganiuc A (2008) The role of plasmacytoid dendritic cell-derived IFN alpha in antiviral immunity. Crit Rev Immunol 28: 61-94
76. Taylor HE, Linde ME, Khatua AK, Popik W, Hildreth JE (2011) Sterol regulatory element-binding protein 2 couples HIV-1 transcription to cholesterol homeostasis and T cell activation. J Virol 85: 7699-709
77. Thomas MJ, Agy MB, Proll SC, Paeper BW, Li Y, Jensen KL, Korth MJ, Katze MG (2006) Functional gene analysis of individual response to challenge of SIVmac239 in M. mulatta PBMC culture. Virology 348: 242-252
78. Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE (2004) Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics 3: 960-969
79. Tisoncik JR, Belisle SE, Diamond DL, Korth MJ, Katze MG (2009) Is systems biology the key to preventing the next pandemic? Future Virol 4: 553-561
80. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-5
81. Turville SG, Santos JJ, Frank I, Cameron PU, Wilkinson J, Miranda-Saksena M, Dable J, Stossel H, Romani N, Piatak M Jr, Lifson JD, Pope M, Cunningham AL (2004) Immunodeficiency virus uptake, turnover, and 2-phase transfer in human dendritic cells. Blood 103: 2170-9
82. Vahey MT, Nau ME, Jagodzinski LL, Yalley-Ogunro J, Taubman M, Michael NL, Lewis MG (2002) Impact of viral infection on the gene expression profiles of proliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RF. AIDS Res Hum. Retroviruses 18: 179-192
83. van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI (2003) Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. J Virol 77: 1392-402
84. van 't Wout AB, Swain JV, Schindler M, Rao U, Pathmajeyan MS, Mullins JI, Kirchhoff F (2005) Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells. J Virol 79: 10053-10058
85. Vazquez N, Greenwell-Wild T, Marinos NJ, Swaim WD, Nares S, Ott DE, Schubert U, Henklein P, Orenstein JM, Sporn MB, Wahl SM (2005) Human immunodeficiency virus type 1-induced macrophage gene expression includes the p21 gene, a target for viral regulation. J Virol 79: 4479-91
86. Venkatachari NJ, Buchanan WG, Ayyavoo V (2008) Human immunodeficiency virus (HIV-1) infection selectively downregulates PD-1 expression in infected cells and protects the cells from early apoptosis in vitro and in vivo. Virology 376: 140-53
87. Wallace JC, Korth MJ, Paeper B, Proll SC, Thomas MJ, Magness CL, Iadonato SP, Nelson C, Katze MG (2007) High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. BMC Genomics 8: 28
88. Wilkinson J, Cunningham AL (2006) Mucosal transmission of HIV-1: first stop dendritic cells. Curr Drug Targets 7: 1563-9
89. Woelk CH, Ottones F, Plotkin CR, Du P, Royer CD, Rought SE, Lozach J, Sasik R, Kornbluth RS, Richman DD, Corbeil J (2004) Interferon gene expression following HIV type 1 infection of monocyte-derived macrophages. AIDS Res Hum Retroviruses 20: 1210-22
90. Yin J, Chen MF, Finkel TH (2004) Differential gene expression during HIV-1 infection analyzed by suppression subtractive hybridization. AIDS 18: 587-96
91. Yoneyama M, Fujita T (2009) RNA recognition and signal transduction by RIG-I-like receptors. Immunol Rev 227: 54-65