RNA profiling in host-pathogen interactions

Current Opinion in Microbiology

Volumn 10, Issue 3, 2007, Pages 297-302

  Waddell, Simon J ^a   Butcher, Philip D ^a   Stoker, Neil G ^b  

^a ST GEORGE'S UNIVERSITY OF LONDON   (United Kingdom)

^b ROYAL VETERINARY COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

BACTERIAL METABOLISM; BACTERIAL SURVIVAL; BACTERIAL VIRULENCE; CELL ADHESION; CELL INVASION; GENE EXPRESSION; HOST PATHOGEN INTERACTION; IMMUNE RESPONSE; NONHUMAN; REVIEW;

ANIMALS; BACTERIA; BACTERIAL INFECTIONS; GENE EXPRESSION PROFILING; HUMANS; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL;

BACTERIA (MICROORGANISMS);

EID: 34250737962     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2007.05.013     Document Type: Review

References (57)

1. Jansen A., and Yu J. Differential gene expression of pathogens inside infected hosts. Curr Opin Microbiol 9 (2006) 138-142
2. Staudinger B.J., Oberdoerster M.A., Lewis P.J., and Rosen H. mRNA expression profiles for Escherichia coli ingested by normal and phagocyte oxidase-deficient human neutrophils. J Clin Invest 110 (2002) 1151-1163
3. Schnappinger D., Ehrt S., Voskuil M.I., Liu Y., Mangan J.A., Monahan I.M., Dolganov G., Efron B., Butcher P.D., Nathan C., and Schoolnik G.K. Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Exp Med 198 (2003) 693-704. A differential lysis method of RNA extraction was used to define the metabolic and respiratory state of M. tuberculosis after murine macrophage infection and demonstrated a nitric oxide-dependent transcriptome in IFN-γ stimulated macrophages. The pathogen profile was used as a bioprobe for the intracellular environment.
4. Grifantini R., Bartolini E., Muzzi A., Draghi M., Frigimelica E., Berger J., Ratti G., Petracca R., Galli G., Agnusdei M., et al. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 20 (2002) 914-921
5. Liu M., Popper S.J., Rubins K.H., and Relman D.A. Early days: genomics and human responses to infection. Curr Opin Microbiol 9 (2006) 312-319
6. Jenner R.G., and Young R.A. Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol 3 (2005) 281-294. A detailed review comparing of the global transcriptional responses of host cells to infection.
7. Kato-Maeda M., Gao Q., and Small P.M. Microarray analysis of pathogens and their interaction with hosts. Cell Microbiol 3 (2007) 713-719
8. Bryant P., Venter D., Robins-Browne R., and Curtis N. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4 (2004) 100-111
9. Mangan J.A., Sole K.M., Mitchison D.A., and Butcher P.D. An effective method of RNA extraction from bacteria refractory to disruption, including mycobacteria. Nucleic Acids Res 25 (1997) 675-676
10. Li M.S., Monahan I.M., Waddell S.J., Mangan J.A., Martin S.L., Everett M.J., and Butcher P.D. cDNA-RNA subtractive hybridization reveals increased expression of mycocerosic acid synthase in intracellular Mycobacterium bovis BCG. Microbiol 147 (2001) 2293-2305
11. Li M.S., Waddell S.J., Monahan I.M., Mangan J.A., Martin S.L., Everett M.J., and Butcher P.D. Increased transcription of a potential sigma factor regulatory gene Rv1364c in Mycobacterium bovis BCG while residing in macrophages indicates use of alternative promoters. FEMS Microbiol Lett 233 (2004) 333-339
12. Eriksson S., Lucchini S., Thompson A., Rhen M., and Hinton J.C. Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol 47 (2003) 103-118. The first paper to define the intracellular transcriptome of a bacterial pathogen. It showed the intracellular compartment to be different from that predicted for other intracellular bacteria.
13. Hinton J.C., Hautefort I., Eriksson S., Thompson A., and Rhen M. Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr Opin Microbiol 7 (2004) 277-282
14. Belland R.J., Nelson D.E., Virok D., Crane D.D., Hogan D., Sturdevant D., Beatty W.L., and Caldwell H.D. Transcriptome analysis of chlamydial growth during IFN-gamma-mediated persistence and reactivation. Proc Natl Acad Sci USA 100 (2003) 15971-15976
15. Faucher S.P., Porwollik S., Dozois C.M., McClelland M., and Daigle F. Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences. Proc Natl Acad Sci USA 103 (2006) 1906-1911
16. Motley S.T., Morrow B.J., Liu X., Dodge I.L., Vitiello A., Ward C.K., and Shaw K.J. Simultaneous analysis of host and pathogen interactions during an in vivo infection reveals local induction of host acute phase response proteins, a novel bacterial stress response, and evidence of a host-imposed metal ion limited environment. Cell Microbiol 6 (2004) 849-865. RNA amplification was used to investigate host and pathogen transcriptional profiles from the same RNA extraction in an E. coli murine infection model.
17. Lucchini S., Liu H., Jin Q., Hinton J.C., and Yu J. Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen. Infect Immun 73 (2005) 88-102. The transcriptional profile of S. flexneri was compared after infection of two different cell types.
18. Sauvonnet N., Pradet-Balade B., Garcia-Sanz J.A., and Cornelis G.R. Regulation of mRNA expression in macrophages after Yersinia enterocolitica infection. Role of different Yop effectors. J Biol Chem 277 (2002) 25133-25142
19. McMorran B., Town L., Costelloe E., Palmer J., Engel J., Hume D., and Wainwright B. Effector ExoU from the type III secretion system is an important modulator of gene expression in lung epithelial cells in response to Pseudomonas aeruginosa infection. Infect Immun 71 (2003) 6035-6044
20. Guillemin K., Salama N.R., Tompkins L.S., and Falkow S. Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. Proc Natl Acad Sci USA 99 (2002) 15136-15141
21. Shi S., Blumenthal A., Hickey C.M., Gandotra S., Levy D., and Ehrt S. Expression of many immunologically important genes in Mycobacterium tuberculosis-infected macrophages is independent of both TLR2 and TLR4 but dependent on IFN-alphabeta receptor and STAT1. J Immunol 175 (2005) 3318-3328
22. Chatterjee S.S., Hossain H., Otten S., Kuenne C., Kuchmina K., Machata S., Domann E., Chakraborty T., and Hain T. Intracellular gene expression profile of Listeria monocytogenes. Infect Immun 74 (2006) 1323-1338
23. Joseph B., Przybilla K., Stuhler C., Schauer K., Slaghuis J., Fuchs T.M., and Goebel W. Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening. J Bacteriol 188 (2006) 556-568
24. McCaffrey R.L., Fawcett P., O'Riordan M., Lee K.D., Havell E.A., Brown P.O., and Portnoy D.A. A specific gene expression program triggered by Gram-positive bacteria in the cytosol. Proc Natl Acad Sci USA 101 (2004) 11386-11391
25. Dietrich G., Kurz S., Hubner C., Aepinus C., Theiss S., Guckenberger M., Panzner U., Weber J., and Frosch M. Transcriptome analysis of Neisseria meningitidis during infection. J Bacteriol 185 (2003) 155-164
26. Jain S.K., Paul-Satyaseela M., Lamichhane G., Kim K.S., and Bishai W.R. Mycobacterium tuberculosis invasion and traversal across an in vitro human blood-brain barrier as a pathogenic mechanism for central nervous system tuberculosis. J Infect Dis 193 (2006) 1287-1295
27. Pedron T., Thibault C., and Sansonetti P.J. The invasive phenotype of Shigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2. J Biol Chem 278 (2003) 33878-33886. Comparison of the host response to invasive and non-invasive S. flexneri strains was used to define invasion-responsive genes in epithelial cells.
28. Voyich J.M., Braughton K.R., Sturdevant D.E., Whitney A.R., Said-Salim B., Porcella S.F., Long R.D., Dorward D.W., Gardner D.J., Kreiswirth B.N., et al. Insights into mechanisms used by Staphylococcus aureus to avoid destruction by human neutrophils. J Immunol 175 (2005) 3907-3919
29. Huang Q., Liu D., Majewski P., Schulte L.C., Korn J.M., Young R.A., Lander E.S., and Hacohen N. The plasticity of dendritic cell responses to pathogens and their components. Science 294 (2001) 870-875
30. Boldrick J.C., Alizadeh A.A., Diehn M., Dudoit S., Liu C.L., Belcher C.E., Botstein D., Staudt L.M., Brown P.O., and Relman D.A. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci USA 99 (2002) 972-977
31. Kobayashi S.D., Braughton K.R., Whitney A.R., Voyich J.M., Schwan T.G., Musser J.M., and DeLeo F.R. Bacterial pathogens modulate an apoptosis differentiation program in human neutrophils. Proc Natl Acad Sci USA 100 (2003) 10948-10953
32. Feezor R.J., Oberholzer C., Baker H.V., Novick D., Rubinstein M., Moldawer L.L., Pribble J., Souza S., Dinarello C.A., Ertel W., and Oberholzer A. Molecular characterization of the acute inflammatory response to infections with gram-negative versus gram-positive bacteria. Infect Immun 71 (2003) 5803-5813
33. Nau G.J., Richmond J.F., Schlesinger A., Jennings E.G., Lander E.S., and Young R.A. Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci USA 99 (2002) 1503-1508
34. Chaussabel D., Semnani R.T., McDowell M.A., Sacks D., Sher A., and Nutman T.B. Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood 102 (2003) 672-681
35. Granucci F., Vizzardelli C., Pavelka N., Feau S., Persico M., Virzi E., Rescigno M., Moro G., and Ricciardi-Castagnoli P. Inducible IL-2 production by dendritic cells revealed by global gene expression analysis. Nat Immunol 2 (2001) 882-888
36. Xu Q., Dziejman M., and Mekalanos J.J. Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro. Proc Natl Acad Sci USA 100 (2003) 1286-1291
37. Stintzi A., Marlow D., Palyada K., Naikare H., Panciera R., Whitworth L., and Clarke C. Use of genome-wide expression profiling and mutagenesis to study the intestinal lifestyle of Campylobacter jejuni. Infect Immun 73 (2005) 1797-1810. The combination of transcriptional analysis and knockout mutants was used to define gene function in C. jejuni.
38. Huff J.L., Hansen L.M., and Solnick J.V. Gastric transcription profile of Helicobacter pylori infection in the rhesus macaque. Infect Immun 72 (2004) 5216-5226
39. Mueller A., Merrell D.S., Grimm J., and Falkow S. Profiling of microdissected gastric epithelial cells reveals a cell type-specific response to Helicobacter pylori infection. Gastroenterology 127 (2004) 1446-1462
40. Smajs D., McKevitt M., Howell J.K., Norris S.J., Cai W.W., Palzkill T., and Weinstock G.M. Transcriptome of Treponema pallidum: gene expression profile during experimental rabbit infection. J Bacteriol 187 (2005) 1866-1874
41. Sebbane F., Lemaitre N., Sturdevant D.E., Rebeil R., Virtaneva K., Porcella S.F., and Hinnebusch B.J. Adaptive response of Yersinia pestis to extracellular effectors of innate immunity during bubonic plague. Proc Natl Acad Sci USA 103 (2006) 11766-11771
42. Lathem W.W., Crosby S.D., Miller V.L., and Goldman W.E. Progression of primary pneumonic plague: a mouse model of infection, pathology, and bacterial transcriptional activity. Proc Natl Acad Sci USA 102 (2005) 17786-17791
43. Talaat A.M., Lyons R., Howard S.T., and Johnston S.A. The temporal expression profile of Mycobacterium tuberculosis infection in mice. Proc Natl Acad Sci USA 101 (2004) 4602-4607
44. Liang F.T., Nelson F.K., and Fikrig E. Molecular adaptation of Borrelia burgdorferi in the murine host. J Exp Med 196 (2002) 275-280
45. Orihuela C.J., Radin J.N., Sublett J.E., Gao G., Kaushal D., and Tuomanen E.I. Microarray analysis of pneumococcal gene expression during invasive disease. Infect Immun 72 (2004) 5582-5596
46. Virtaneva K., Porcella S.F., Graham M.R., Ireland R.M., Johnson C.A., Ricklefs S.M., Babar I., Parkins L.D., Romero R.A., Corn G.J., et al. Longitudinal analysis of the group A Streptococcus transcriptome in experimental pharyngitis in cynomolgus macaques. Proc Natl Acad Sci USA 102 (2005) 9014-9019. Bacterial transcriptional patterns were correlated with clinical parameters through the course of infection.
47. Yarwood J.M., McCormick J.K., Paustian M.L., Kapur V., and Schlievert P.M. Repression of the Staphylococcus aureus accessory gene regulator in serum and in vivo. J Bacteriol 184 (2002) 1095-1101
48. Karakousis P.C., Yoshimatsu T., Lamichhane G., Woolwine S.C., Nuermberger E.L., Grosset J., and Bishai W.R. Dormancy phenotype displayed by extracellular Mycobacterium tuberculosis within artificial granulomas in mice. J Exp Med 200 (2004) 647-657
49. Revel A.T., Talaat A.M., and Norgard M.V. DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete. Proc Natl Acad Sci USA 99 (2002) 1562-1567
50. Rachman H., Strong M., Ulrichs T., Grode L., Schuchhardt J., Mollenkopf H., Kosmiadi G.A., Eisenberg D., and Kaufmann S.H. Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect Immun 74 (2006) 1233-1242. The gene expression profiles of M. tuberculosis in different human lung tissues extracted after surgery were compared.
51. Merrell D.S., Butler S.M., Qadri F., Dolganov N.A., Alam A., Cohen M.B., Calderwood S.B., Schoolnik G.K., and Camilli A. Host-induced epidemic spread of the cholera bacterium. Nature 417 (2002) 642-645
52. Larocque R.C., Harris J.B., Dziejman M., Li X., Khan A.I., Faruque A.S., Faruque S.M., Nair G.B., Ryan E.T., Qadri F., et al. Transcriptional profiling of Vibrio cholerae recovered directly from patient specimens during early and late stages of human infection. Infect Immun 73 (2005) 4488-4493
53. Resnick M.B., Sabo E., Meitner P.A., Kim S.S., Cho Y., Kim H.K., Tavares R., and Moss S.F. Global analysis of the human gastric epithelial transcriptome altered by Helicobacter pylori eradication in vivo. Gut 55 (2006) 1717-1724. Laser capture dissection was used to profile distinct cell types from human biopsies before and after H. pylori infection in the same patient.
54. Griffiths M.J., Shafi M.J., Popper S.J., Hemingway C.A., Kortok M.M., Wathen A., Rockett K.A., Mott R., Levin M., Newton C.R., et al. Genome-wide analysis of the host response to malaria in Kenyan children. J Infect Dis 191 (2005) 1599-1611
55. Li Y., Zhou X., St J.M., and Wong D.T. RNA profiling of cell-free saliva using microarray technology. J Dent Res 83 (2004) 199-203
56. Ramilo O., Allman W., Chung W., Mejias A., Ardura M., Glaser C., Wittkowski K.M., Piqueras B., Banchereau J., Palucka A.K., and Chaussabel D. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 109 (2007) 2066-2077. Gene expression signatures were identified in human patient leukocytes that were able to discriminate between bacterial infections.
57. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29 (2001) 365-371