How the host 'sees' pathogens: Global gene expression responses to infection

Current Opinion in Immunology

Volumn 12, Issue 2, 2000, Pages 215-218

  Manger, Ian D ^a,b   Relman, David A ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b VA PALO ALTO HEALTH CARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA;

DATA ANALYSIS; DNA DETERMINATION; GENE EXPRESSION; HOST PARASITE INTERACTION; IMMUNE RESPONSE; IMMUNOSTIMULATION; INFECTION; RECOMBINANT DNA TECHNOLOGY; SHORT SURVEY;

EID: 0034107833     PISSN: 09527915     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0952-7915(99)00077-1     Document Type: Review

References (32)

1. Lueking A., Horn M., Eickhoff H., Bussow K., Lehrach H., Walter G. Protein microarrays for gene expression and antibody screening. Anal Biochem. 270:1999;103-111.
2. Saunders N.J., Moxon E.R. Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr Opin Biotechnol. 9:1998;618-623.
3. de Saizieu A., Certa U., Warrington J., Gray C., Keck W., Mous J. Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays. Nat Biotechnol. 16:1998;45-48.
4. Wilson M., DeRisi J., Kristensen H.H., Imboden P., Rane S., Brown P.O., Schoolnik G.K. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci USA. 96:1999;12833-12838.
5. Gingeras T.R., Ghandour G., Wang E., Berno A., Small P.M., Drobniewski F., Alland D., Desmond E., Holodniy M., Drenkow J. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res. 8:1998;435-448.
6. Behr M.A., Wilson M.A., Gill W.P., Salamon H., Schoolnik G.K., Rane S., Small P.M. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science. 284:1999;1520-1523.
7. Bowtell D.D. Options available - from start to finish - for obtaining expression data by microarray. Nat Genet. 21:1999;25-32. [Published erratum appears in Nat Genet 1999, 21:241.].
8. Cheung V.G., Morley M., Aguilar F., Massimi A., Kucherlapati R., Childs G. Making and reading microarrays. Nat Genet. 21:1999;15-19.
9. Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J.M. Expression profiling using cDNA microarrays. Nat Genet. 21:1999;10-14.
10. Eisen M.B., Brown P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303:1999;179-205. A useful set of procedures for widespread use.
11. Gerhold D., Rushmore T., Caskey C.T. DNA chips: promising toys have become powerful tools. Trends Biochem Sci. 24:1999;168-173.
12. Lipshutz R.J., Fodor S.P., Gingeras T.R., Lockhart D.J. High density synthetic oligonucleotide arrays. Nat Genet. 21:1999;20-24.
13. Der S.D., Zhou A., Williams B.R., Silverman R.H. Identification of genes differentially regulated by interferon alpha, beta, or gamma using oligonucleotide arrays. Proc Natl Acad Sci USA. 95:1998;15623-15628.
14. Alizadeh A., Eisen M., Botstein D., Brown P.O., Staudt L.M. Probing lymphocyte biology by genomic-scale gene expression analysis. J Clin Immunol. 18:1998;373-379.
15. Schena M., Shalon D., Heller R., Chai A., Brown P.O., Davis R.W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 93:1996;10614-10619.
16. 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. 95:1998;14470-14475. This analysis reveals several insights into CMV pathogenesis.
17. Saederup N., Lin Y.C., Dairaghi D.J., Schall T.J., Mocarski E.S. Cytomegalovirus-encoded beta chemokine promotes monocyte-associated viremia in the host. Proc Natl Acad Sci USA. 96:1999;10881-10886.
18. Penfold M.E., Dairaghi D.J., Duke G.M., Saederup N., Mocarski E.S., Kemble G.W., Schall T.J. Cytomegalovirus encodes a potent alpha chemokine. Proc Natl Acad Sci USA. 96:1999;9839-9844.
19. Baize S., Leroy E.M., Georges-Courbot M.C., Capron M., Lansoud-Soukate J., Debre P., Fisher-Hoch S.P., McCormick J.B., Georges A.J. Defective humoral responses and extensive intravascular apoptosis are associated with fatal outcome in Ebola virus-infected patients. Nat Med. 5:1999;423-426.
20. Nabel G.J. Surviving Ebola virus infection. Nat Med. 5:1999;373-374.
21. Xiang C., Young H., Alterson H., Reynolds D., Bittner M., Chen Y., Gooden G., Jiang Y., Meltzer P., Trent J.et al. Comparison of cellular gene expression in Ebola-Zaire and Ebola-Reston virus-infected primary human monocytes. Nat Genet. 23:1999;82.
22. Wallace D.M., Clayton C.L., Cox J.M., Falciani F., Trower M., Robinson P.A., Crabtree J.E. Identification of Helicobacter pylori epithelial cell response genes by screening high-density cDNA arrays. Nat Genet. 23:1999;80.
23. Bassett D.E. Jr., Eisen M.B., Boguski M.S. Gene expression informatics - it's all in your mine. Nat Genet. 21:1999;51-55.
24. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 95:1998;14863-14868. Hierarchical clustering provides a means for organizing genome-wide data in a useful visual format and tends to group genes according to similar function.
25. Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., Lander E.S., Golub T.R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA. 96:1999;2907-2912. An alternative method for gene clustering (see [22]) that might be combined with a hierarchical method for optimal association of genes with like function.
26. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., Levine A.J. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA. 96:1999;6745-6750.
27. Perou C.M., Jeffrey S.S., van de Rijn M., Rees C.A., Eisen M.B., Ross D.T., Pergamenschikov A., Williams C.F., Zhu S.X., Lee J.C.et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA. 96:1999;9212-9217. Breast cancer can be distinguished from other disturbances in mammary epithelial cells using expression microarray analysis and the relative contribution of stromal and inflammatory cells to overall breast cancer expression profiles can be deduced.
28. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A.et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 286:1999;531-537. Acute leukemia subtypes are accurately classified and novel subtypes predicted using the expression response profiles from classes of host genes.
29. Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., Boldrick J.C., Sabet H., Tran T., Yu X.et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:2000;503-511. Expression profile analysis reveals two distinct, previously unrecognized types of diffuse large-B-cell lymphoma with different clinical courses.
30. Brown P.O., Hartwell L. Genomics and human disease - variations on variation. Nat Genet. 18:1998;91-93.
31. Relman D.A. Detection and identification of previously unrecognized microbial pathogens. Emerg Infect Dis. 4:1998;382-389.
32. Relman D.A. The search for unrecognized pathogens. Science. 284:1999;1308-1310.