Insights into host responses against pathogens from transcriptional profiling

Nature Reviews Microbiology

Volumn 3, Issue 4, 2005, Pages 281-294

  Jenner, Richard G ^a   Young, R A ^a,b,c  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CHEMOKINE; CYTOKINE; INTERFERON; TOLL LIKE RECEPTOR; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 3; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR 7; VIRUS PROTEIN;

CARCINOGENESIS; CELL FUNCTION; COMPARATIVE STUDY; DATA ANALYSIS; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INDUCTION; GENE REPRESSION; GENETIC TRANSCRIPTION; HOST PATHOGEN INTERACTION; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE RESPONSE; IMMUNOCOMPETENT CELL; IMMUNOMODULATION; IN VIVO STUDY; INFLAMMATION; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PUBLICATION; REVIEW; SIGNAL TRANSDUCTION; VIRUS INHIBITION;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BACTERIA; BACTERIAL INFECTIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; IMMUNITY; MEMBRANE GLYCOPROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECEPTORS, CELL SURFACE; TOLL-LIKE RECEPTORS; TRANSCRIPTION, GENETIC; VIRUS DISEASES; VIRUSES;

BACTERIA (MICROORGANISMS); HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 15944395145     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro1126     Document Type: Review

References (91)

1. Der, S. D., Zhou, A., Williams, B. R. & Silverman, R. H. Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95 15623-15628 (1998).
2. Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T. & Shenk, T. Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 14470-14475 (1998).
3. Boldrick, J. C. et al. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl Acad. Sci. USA 99, 972-977 (2002).
4. Nau, G. J. et al. Human macrophage activation programs induced by bacterial pathogens. Proc. Natl Acad. Sci. USA 99, 1503-1508 (2002).
5. Kobayashi, S. D. et al. Bacterial pathogens modulate an apoptosis differentiation program in human neutrophils. Proc. Natl Acad. Sci. USA 100, 10948-10953 (2003).
6. Huang, Q. et al. The plasticity of dendritic cell responses to pathogens and their components. Science 294, 870-875 (2001).
7. Izmailova, E. et al. HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages. Nature Med. 9, 191-197 (2003).
8. Hertzog, P. J., O'Neill, L. A. & Hamilton, J. A. The interferon in TLR signaling: more than just antiviral. Trends Immunol. 24, 534-539 (2003).
9. Hooper, L. V. et al. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881-884 (2001).
10. Chaussabel, D. et al. Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood 102, 672-681 (2003).
11. Beutler, B. Inferences, questions and possibilities in Toll-like receptor signalling. Nature 430, 257-263 (2004).
12. Doyle, S. et al. IRF3 mediates a TLR3/TLR4-specific antiviral gene program. Immunity 17, 251-263 (2002).
13. Taniguchi, T. & Takaoka, A. The interferon-α/β system in antiviral responses: a multimodal machinery of gene regulation by the IRF family of transcription factors. Curr. Opin. Immunol. 14, 111-116 (2002).
14. Geiss, G. et al. A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling. J. Biol. Chem. 276, 30178-30182 (2001).
15. Rosenberger, C. M., Scott, M. G., Gold, M. R., Hancock, R. E. & Finlay, B. B. Salmonella typhimurium infection and lipopolysaccharide stimulation induce similar changes in macrophage gene expression. J. Immunol. 164, 5894-5904 (2000).
16. Poltorak, A. et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science 282 2085-2088 (1998).
17. + T cell differentiation in response to a recombinant heat shock fusion protein. J. Immunol. 172, 2885-2893 (2004).
18. Weighardt, H. et al. Identification of a TLR4- and TRIF-dependent activation program of dendritic cells. Eur. J. Immunol. 34, 558-564 (2004).
19. Rogers, P. D. et al. Pneumolysin-dependent and -independent gene expression identified by cDNA microarray analysis of THP-1 human mononuclear cells stimulated by Streptococcus pneumoniae. Infect. Immun. 71, 2087-2094 (2003).
20. Malley, R. et al. Recognition of pneumolysin by Toll-like receptor 4 confers resistance to pneumococcal infection. Proc. Natl Acad. Sci. USA 100, 1966-1971 (2003).
21. Kurt-Jones, E. A. et al. Pattern recognition receptors TLR4 and CD14 mediate response to respiratory syncytial virus. Nature Immunol. 1, 398-401 (2000).
22. Hayashi, F. et al. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410, 1099-1103 (2001).
23. Zeng, H. et al. Flagellin is the major proinflammatory determinant of enteropathogenic Salmonella. J. Immunol. 171, 3668-3674 (2003).
24. Nau, G. J., Schlesinger, A., Richmond, J. F. & Young, R. A. Cumulative Toll-like receptor activation in human macrophages treated with whole bacteria. J. Immunol. 170, 5203-5209 (2003).
25. Toshchakov, V. et al. TLR4, but not TLR2, mediates IFN-β-induced STAT1α/β-dependent gene expression in macrophages. Nature Immunol. 3, 392-398 (2002).
26. Lund, J. M. et al. Recognition of single-stranded RNA viruses by Toll-like receptor 7. Proc. Natl Acad. Sci. USA 101 5598-5603 (2004).
27. Underhill, D. M. & Ozinsky, A. Toll-like receptors: key mediators of microbe detection. Curr. Opin. Immunol. 14, 103-110 (2002).
28. Simmen, K. A. et al. Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B. Proc. Natl Acad. Sci. USA 98, 7140-7145 (2001).
29. Boehme, K. W., Singh, J., Perry, S. T. & Compton, T. Human cytomegalovirus elicits a coordinated cellular antiviral response via envelope glycoprotein B. J. Virol. 78, 1202-1211 (2004).
30. Compton, T. et al. Human cytomegalovirus activates inflammatory cytokine responses via CD14 and Toll-like receptor 2. J. Virol. 77, 4588-4596 (2003).
31. Wang, X., Huong, S. M., Chiu, M. L., Raab-Traub, N. & Huang, E. S. Epidermal growth factor receptor is a cellular receptor for human cytomegalovirus. Nature 424, 456-461 (2003).
32. Mossman, K. L. et al. Herpes simplex virus triggers and then disarms a host antiviral response. J. Virol. 75, 750-758 (2001).
33. Browne, E. P., Wing, B., Coleman, D. & Shenk, T. Altered cellular mRNA levels in human cytomegalovirus-infected fibroblasts: viral block to the accumulation of antiviral mRNAs. J. Virol. 75, 12319-12330 (2001).
34. Browne, E. P. & Shenk, T. Human cytomegalovirus UL83-coded pp65 virion protein inhibits antiviral gene expression in infected cells. Proc. Natl Acad. Sci. USA 100, 11439-11444 (2003).
35. Chang, Y. E. & Laimins, L. A. Microarray analysis identifies interferon-inducible genes and Stat-1 as major transcriptional targets of human papillomavirus type 31. J. Virol. 74, 4174-4182 (2000).
36. Nees, M. et al. Papillomavirus type 16 oncogenes downregulate expression of interferon-responsive genes and upregulate proliferation-associated and NF-κB-responsive genes in cervical keratinocytes. J. Virol. 75, 4283-4296 (2001).
37. Simmons, A., Aluvihare, V. & McMichael, A. Nef triggers a transcriptional program in T cells imitating single-signal T cell activation and inducing HIV virulence mediators. Immunity 14, 763-777 (2001).
38. Corbeil, J. et al. Temporal gene regulation during HIV-1 infection of human CD4+ T cells. Genome Res. 11, 1198-11204 (2001).
39. +-T-cell lines. J. Virol. 77, 1392-1402 (2003).
40. Ehrt, S. et al. Reprogramming of the macrophage transcriptome in response to interferon-γ and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase. J. Exp. Med. 194, 1123-1140 (2001).
41. Sauvonnet, N., Pradet-Balade, B., Garcia-Sanz, J. A. & Cornelis, G. R. Regulation of mRNA expression in macrophages after Yersinia enterocolitica infection. Role of different Yop effectors. J. Biol. Chem. 277, 25133-25142 (2002).
42. Bohn, E. et al. Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica. Cell. Microbiol. 6, 129-141 (2004).
43. Geiss, G. K. et al. Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc. Natl Acad. Sci. USA 99, 10736-10741 (2002).
44. Girard, S. et al. An altered cellular response to interferon and up-regulation of interleukn-8 induced by the hepatitis C viral protein NS5A uncovered by microarray analysis. Virology 295, 272-283 (2002).
45. Geiss, G. K. et al. Gene expression profiling of the cellular transcriptional network regulated by α/β interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J. Virol. 77, 6367-6375 (2003).
46. Polyak, S. J., Khabar, K. S., Rezeiq, M. & Gretch, D. R. Elevated levels of interleukn-8 in serum are associated with hepatitis C virus infection and resistance to interferon therapy. J. Virol. 75, 6209-6211 (2001).
47. Geimonen, E. et al. Pathogenic and nonpathogenic hantaviruses differentially regulate endothelial cell responses. Proc. Natl Acad. Sci. USA 99, 13837-13842 (2002).
48. Guerra, S. et al. Cellular gene expression survey of vaccinia virus infection of human HeLa cells. J. Virol. 77, 6493-6506 (2003).
49. Guerra, S. et al. Microarray analysis reveals characteristic changes of host cell gene expression in response to attenuated modified vaccinia virus Ankara infection of human HeLa cells. J. Virol. 78, 5820-5834 (2004).
50. Ichikawa, J. K. et al. Interaction of Pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs. Proc. Natl Acad. Sci. USA 97, 9659-9664 (2000).
51. Detweiler, C. S., Cunanan, D. B. & Falkow, S. Host microarray analysis reveals a role for the Salmonella response regulator phoP in human macrophage cell death. Proc. Natl Acad. Sci. USA 98, 5850-5855 (2001).
52. Pathan, N. et al. Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock. Lancet 363, 203-209 (2004).
53. Taylor, L. A. et al. Host gene regulation during coxsackievirus B3 infection in mice: assessment by microarrays. Circ. Res. 87, 328-334 (2000).
54. Sui, Y. et al. Microarray analysis of cytokine and chemokine genes in the brains of macaques with SHIV-encephalitis. J. Med. Primatol. 32, 229-239 (2003).
55. Roberts, E. S. et al. Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am. J. Pathol. 162, 2041-2057 (2003).
56. Domachowske, J. B., Bonville, C. A., Easton, A. J. & Rosenberg, H. F. Differential expression of proinflammatory cytokine genes in vivo in response to pathogenic and nonpathogenic pneumovirus infections. J. Infect. Dis. 186, 8-14 (2002).
57. Johnston, C., Jiang, W., Chu, T. & Levine, B. Identification of genes involved in the host response to neurovirulent alphavirus infection. J. Virol. 75, 10431-10445 (2001).
58. Bigger, C. B., Brasky, K. M. & Lanford, R. E. DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J. Virol. 75, 7059-7066 (2001).
59. George, M. D., Sankaran, S., Reay, E., Gelli, A. C. & Dandekar, S. High-throughput gene expression profiling indicates dysregulation of intestinal cell cycle mediators and growth factors during primary simian immunodeficiency virus infection. Virology 312, 84-94 (2003).
60. Guadalupe, M. 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. 77, 11708-11717 (2003).
61. Chun, T. W. et al. Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc. Natl Acad. Sci. USA 100, 1908-1913 (2003).
62. Mueller, A. et al. Protective immunity against Helicobacter is characterized by a unique transcriptional signature. Proc. Natl Acad. Sci. USA 100, 12289-12294 (2003).
63. Wu, C. G. et al. Distinctive gene expression profiles associated with Hepatitis B virus x protein. Oncogene 20, 3674-3682 (2001).
64. Xu, X. R. et al. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc. Natl Acad. Sci. USA 98, 15080-15094 (2001).
65. Okabe, H. et al. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res. 61, 2129-2137 (2001).
66. Iizuka, N. et al. Comparison of gene expression profiles between hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on the basis of a supervised learning method. Cancer Res. 62, 3939-3944 (2002).
67. Wang, H. W. et al. Kaposi sarcoma herpesvirus-induced cellular reprogramming contributes to the lymphatic endothelial gene expression in Kaposi sarcoma. Nature Genet. 36, 687-693 (2004).
68. Hong, Y. K. et al. Lymphatic reprogramming of blood vascular endothelium by Kaposi sarcoma-associated herpesvirus. Nature Genet. 36, 683-685 (2004).
69. Jenner, R. G. et al. Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile. Proc. Natl Acad. Sci. USA 100, 10399-10404 (2003).
70. Klein, U. et al. Gene expression profile analysis of AIDS-related primary effusion lymphoma (PEL) suggests a plasmablastic derivation and identifies PEL-specific transcripts. Blood 101 4115-4121 (2003).
71. Moses, A. V. et al. Kaposi's sarcoma-associated herpesvirus-induced upregulation of the c-kit proto-oncogene, as identified by gene expression profiling, is essential for the transformation of endothelial cells. J. Virol. 76, 8383-8399 (2002).
72. Casadevall, A. & Pirofski, L. A. The damage-response framework of microbial pathogenesis. Nature Rev. Microbiol. 1 17-24 (2003).
73. Schnappinger, D. et al. Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J. Exp. Med. 198, 693-704 (2003).
74. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
75. Odom, D. T. et al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378-1381 (2004).
76. Rodriguez, N. E., Chang, H. K. & Wilson, M. E. Novel program of macrophage gene expression induced by phagocytosis of Leishmania chagasi. Infect. Immun. 72, 2111-2122 (2004).
77. Dietz, A. B., Bulur, P. A., Knutson, G. J., Matasic, R. & Vuk-Pavlovic, S. Maturation of human monocyte-derived dendritic cells studied by microarray hybridization. Biochem. Biophys. Res. Commun. 275, 731-738 (2000).
78. Feezor, R. J. et al. Molecular characterization of the acute inflammatory response to infections with gram-negative versus gram-positive bacteria. Infect. Immun. 71, 5803-5813 (2003).
79. Jones, J. O. & Arvin, A. M. Microarray analysis of host cell gene transcription in response to varicella-zoster virus infection of human T cells and fibroblasts in vitro and SCIDhu skin xenografts in vivo. J. Virol. 77, 1268-1280 (2003).
80. Iizuka, N. et al. Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocellular carcinoma after curative resection. Lancet 361, 923-929 (2003).
81. Kramer, M. F. et al. Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression. J. Virol. 77, 9533-9541 (2003).
82. Radhakrishnan, S. et al. JC virus-induced changes in cellular gene expression in primary human astrocytes. J. Virol. 77, 10638-10644 (2003).
83. Warke, R. V. et al. Dengue virus induces novel changes in gene expression of human umbilical vein endothelial cells. J. Virol. 77, 11822-11832 (2003).
84. Belcher, C. E. et al. The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proc. Natl Acad. Sci. USA 97, 13847-13852 (2000).
85. Zhang, Y. et al. Expression of respiratory syncytial virus-induced chemokine gene networks in lower airway epithelial cells revealed by cDNA microarrays. J. Virol. 75, 9044-9058 (2001).
86. Tian, B. et al. Identification of NF-κB-dependent gene networks in respiratory syncytial virus-infected cells. J. Virol. 76, 6800-6814 (2002).
87. Zhang, Y. et al. Ribavirin treatment up-regulates antiviral gene expression via the interferon-stimulated response element in respiratory syncytial virus-infected epithelial cells. J. Virol. 77, 5933-5947 (2003).
88. Cuadras, M. A., Feigelstock, D. A., An, S. & Greenberg, H. B. Gene expression pattern in Caco-2 cells following rotavirus infection. J. Virol. 76, 4467-4482 (2002).
89. Wells, S. I. et al. Transcriptome signature of irreversible senescence in human papillomavirus-positive cervical cancer cells. Proc. Natl Acad. Sci. USA 100, 7093-7098 (2003).
90. Guillemin, K., Salama, N. R., Tompkins, L. S. & Falkow, S. Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. Proc. Natl Acad. Sci. USA 99, 15136-15141 (2002).
91. Mueller, A. et al. Distinct gene expression profiles characterize the histopathological stages of disease in Helicobacter induced mucosa-associated lymphoid tissue lymphoma. Proc. Natl Acad. Sci. USA 100, 1292-1297 (2003).