Early days: genomics and human responses to infection

Current Opinion in Microbiology

Volumn 9, Issue 3, 2006, Pages 312-319

  Liu, Minghsun ^a   Popper, Stephen J ^a   Rubins, Kathleen H ^a   Relman, David A ^a,b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

CANCER; CELL HETEROGENEITY; CELL POPULATION; CELL TYPE; DATA ANALYSIS; DNA MICROARRAY; DNA REPLICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; HOST; HOST PATHOGEN INTERACTION; HUMAN; INFECTION; METHODOLOGY; NONHUMAN; PATHOGENESIS; REVIEW; VALIDATION PROCESS;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; INFECTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS;

PRIMATES;

EID: 33744516054     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2006.04.006     Document Type: Review

References (51)

1. Walduck A., Rudel T., and Meyer T.F. Proteomic and gene profiling approaches to study host responses to bacterial infection. Curr Opin Microbiol 7 (2004) 33-38
2. Jenner R.G., and Young R.A. Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol 3 (2005) 281-294. This review provides a meta-analysis of many previous data sets, and reveals the difficulty and challenges at the present time with this potentially valuable approach.
3. Coombes B.K., Hardwidge P.R., and Finlay B.B. Interpreting the host-pathogen dialogue through microarrays. Adv Appl Microbiol 54 (2004) 291-331
4. Motomura K., Toyoda N., Oishi K., Sato H., Nagai S., Hashimoto S., Tugume S.B., Enzama R., Mugewa R., Mutuluuza C.K., et al. Identification of a host gene subset related to disease prognosis of HIV-1 infected individuals. Int Immunopharmacol 4 (2004) 1829-1836
5. Pulliam L., Sun B., and Rempel H. Invasive chronic inflammatory monocyte phenotype in subjects with high HIV-1 viral load. J Neuroimmunol 157 (2004) 93-98
6. Prucha M., Ruryk A., Boriss H., Moller E., Zazula R., Herold I., Claus R.A., Reinhart K.A., Deigner P., and Russwurm S. Expression profiling: toward an application in sepsis diagnostics. Shock 22 (2004) 29-33
7. Lee Y.S., Chen C.H., Chao A., Chen E.S., Wei M.L., Chen L.K., Yang K.D., Lin M.C., Wang Y.H., Liu J.W., et al. Molecular signature of clinical severity in patients infected with severe acute respiratory syndrome coronavirus (SARS-CoV). BMC Genomics 6 (2005) 132
8. Yu S.Y., Hu Y.W., Liu X.Y., Xiong W., Zhou Z.T., and Yuan Z.H. Gene expression profiles in peripheral blood mononuclear cells of SARS patients. World J Gastroenterol 11 (2005) 5037-5043
9. 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. Genomewide analysis of the host response to malaria in Kenyan children. J Infect Dis 191 (2005) 1599-1611. This study explores the complex clinical parameters associated with patterns of gene transcript abundance.
10. Thach D.C., Agan B.K., Olsen C., Diao J., Lin B., Gomez J., Jesse M., Jenkins M., Rowley R., Hanson E., et al. Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes. Genes Immun 6 (2005) 588-595
11. Whitney A.R., Diehn M., Popper S.J., Alizadeh A.A., Boldrick J.C., Relman D.A., and Brown P.O. Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci USA 100 (2003) 1896-1901
12. Deirmengian C., Lonner J.H., and Booth Jr. R.E. The Mark Coventry Award: white blood cell gene expression: a new approach toward the study and diagnosis of infection. Clin Orthop Relat Res 440 (2005) 38-44
13. Cunha-Neto E., Dzau V.J., Allen P.D., Stamatiou D., Benvenutti L., Higuchi M.L., Koyama N.S., Silva J.S., Kalil J., and Liew C.C. Cardiac gene expression profiling provides evidence for cytokinopathy as a molecular mechanism in Chagas' disease cardiomyopathy. Am J Pathol 167 (2005) 305-313
14. Hayashida K., Daiba A., Sakai A., Tanaka T., Kaji K., Inaba N., Ando S., Kajiyama N., Terasaki H., Abe A., et al. Pretreatment prediction of interferon-alfa efficacy in chronic hepatitis C patients. Clin Gastroenterol Hepatol 3 (2005) 1253-1259
15. Smith M.W., Walters K.A., Korth M.J., Fitzgibbon M., Proll S., Thompson J.C., Yeh M.M., Shuhart M.C., Furlong J.C., Cox P.P., et al. Gene expression patterns that correlate with hepatitis C and early progression to fibrosis in liver transplant recipients. Gastroenterology 130 (2006) 179-187
16. Lau D.T., Luxon B.A., Xiao S.Y., Beard M.R., and Lemon S.M. Intrahepatic gene expression profiles and alpha-smooth muscle actin patterns in hepatitis C virus induced fibrosis. Hepatology 42 (2005) 273-281
17. Chen L., Borozan I., Feld J., Sun J., Tannis L.L., Coltescu C., Heathcote J., Edwards A.M., and McGilvray I.D. Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection. Gastroenterology 128 (2005) 1437-1444
18. Shao R.X., Hoshida Y., Otsuka M., Kato N., Tateishi R., Teratani T., Shiina S., Taniguchi H., Moriyama M., Kawabe T., et al. Hepatic gene expression profiles associated with fibrosis progression and hepatocarcinogenesis in hepatitis C patients. World J Gastroenterol 11 (2005) 1995-1999
19. Mannick E.E., Schurr J.R., Zapata A., Lentz J.J., Gastanaduy M., Cote R.L., Delgado A., Correa P., and Correa H. Gene expression in gastric biopsies from patients infected with Helicobacter pylori. Scand J Gastroenterol 39 (2004) 1192-1200
20. Wen S., Felley C.P., Bouzourene H., Reimers M., Michetti P., and Pan-Hammarstrom Q. Inflammatory gene profiles in gastric mucosa during Helicobacter pylori infection in humans. J Immunol 172 (2004) 2595-2606
21. Everall I., Salaria S., Roberts E., Corbeil J., Sasik R., Fox H., Grant I., and Masliah E. Methamphetamine stimulates interferon inducible genes in HIV infected brain. J Neuroimmunol 170 (2005) 158-171
22. Masliah E., Roberts E.S., Langford D., Everall I., Crews L., Adame A., Rockenstein E., and Fox H.S. Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. J Neuroimmunol 157 (2004) 163-175
23. Gelman B.B., Soukup V.M., Schuenke K.W., Keherly M.J., Holzer III C., Richey F.J., and Lahart C.J. Acquired neuronal channelopathies in HIV-associated dementia. J Neuroimmunol 157 (2004) 111-119
24. Li Y., Zhou X., St John M.A., and Wong D.T. RNA profiling of cell-free saliva using microarray technology. J Dent Res 83 (2004) 199-203
25. Calvano S.E., Xiao W., Richards D.R., Felciano R.M., Baker H.V., Cho R.J., Chen R.O., Brownstein B.H., Cobb J.P., Tschoeke S.K., et al. A network-based analysis of systemic inflammation in humans. Nature 437 (2005) 1032-1037. The authors build a knowledge-based network analysis tool for identifying functional groups of genes that are regulated in response to a specific stimulus and apply it to a human model of endotoxin exposure.
26. Prabhakar U., Conway T.M., Murdock P., Mooney J.L., Clark S., Hedge P., Bond B.C., Jazwinska E.C., Barnes M.R., Tobin F., et al. Correlation of protein and gene expression profiles of inflammatory proteins after endotoxin challenge in human subjects. DNA Cell Biol 24 (2005) 410-431
27. National Institutes of Health. NIH Consensus Statement on Management of Hepatitis C: 2002. NIH Consens State Sci Statements 19 (2002) 1-46
28. Morgan K.T., Jayyosi Z., Hower M.A., Pino M.V., Connolly T.M., Kotlenga K., Lin J., Wang M., Schmidts H.L., Bonnefoi M.S., et al. The hepatic transcriptome as a window on whole-body physiology and pathophysiology. Toxicol Pathol 33 (2005) 136-145
29. Bieche I., Asselah T., Laurendeau I., Vidaud D., Degot C., Paradis V., Bedossa P., Valla D.C., Marcellin P., and Vidaud M. Molecular profiling of early stage liver fibrosis in patients with chronic hepatitis C virus infection. Virology 332 (2005) 130-144
30. Cobb J.P., Mindrinos M.N., Miller-Graziano C., Calvano S.E., Baker H.V., Xiao W., Laudanski K., Brownstein B.H., Elson C.M., Hayden D.L., et al. Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci USA 102 (2005) 4801-4806
31. O'Toole M., Janszen D.B., Slonim D.K., Reddy P.S., Ellis D.K., Legault H.M., Hill A.A., Whitley M.Z., Mounts W.M., Zuberek K., et al. Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells. Arch Neurol 62 (2005) 1531-1536. This is an interesting study that suggests the possibility of prognostic biomarkers for evaluation of vaccines.
32. Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7 (2006) 55-65. This is a particularly useful review of a rapidly emerging discipline.
33. Baskin C.R., Garcia-Sastre A., Tumpey T.M., Bielefeldt-Ohmann H., Carter V.S., Nistal-Villan E., and Katze M.G. Integration of clinical data, pathology, and cDNA microarrays in influenza virus-infected pigtailed macaques (Macaca nemestrina). J Virol 78 (2004) 10420-10432
34. McLaren P.J., Mayne M., Rosser S., Moffatt T., Becker K.G., Plummer F.A., and Fowke K.R. Antigen-specific gene expression profiles of peripheral blood mononuclear cells do not reflect those of T-lymphocyte subsets. Clin Diagn Lab Immunol 11 (2004) 977-982
35. Rubins K.H., Hensley L.E., Jahrling P.B., Whitney A.R., Geisbert T.W., Huggins J.W., Owen A., Leduc J.W., Brown P.O., and Relman D.A. The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model. Proc Natl Acad Sci USA 101 (2004) 15190-15195. The authors evaluate multiple sources of variation in gene transcript abundance patterns, and provide new insight into an infectious disease of immense historical importance.
36. 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. This study provides an important example of the benefits of measuring transcript abundance patterns from single cell types.
37. Palmer C, Diehn M, Alizadeh AA, Brown PO: Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 2006, in press.
38. 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
39. Rocca-Serra P., Brazma A., Parkinson H., Sarkans U., Shojatalab M., Contrino S., Vilo J., Abeygunawardena N., Mukherjee G., Hollowayx E., et al. ArrayExpress: a public database of gene expression data at EBI. C R Biol 326 (2003) 1075-1078
40. Edgar R., Domrachev M., and Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30 (2002) 207-210
41. Ikeo K., Ishi-i J., Tamura T., Gojobori T., and Tateno Y. CIBEX: center for information biology gene expression database. C R Biol 326 (2003) 1079-1082
42. Pathan N., Hemingway C.A., Alizadeh A.A., Stephens A.C., Boldrick J.C., Oragui E.E., McCabe C., Welch S.B., Whitney A., O'Gara P., et al. Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock. Lancet 363 (2004) 203-209. The authors pursue leads generated by microarray data with a creative mix of follow-up and functional assays.
43. Liu P.T., Stenger S., Li H., Wenzel L., Tan B.H., Krutzik S.R., Ochoa M.T., Schauber J., Wu K., Meinken C., et al. Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response. Science 311 (2006) 1770-1773
44. Paddison P.J., Silva J.M., Conklin D.S., Schlabach M., Li M., Aruleba S., Balija V., O'Shaughnessy A., Gnoj L., Scobie K., et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428 (2004) 427-431
45. Tibshirani R., Hastie T., Narasimhan B., and Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99 (2002) 6567-6572
46. Zeeberg B.R., Feng W., Wang G., Wang M.D., Fojo A.T., Sunshine M., Narasimhan S., Kane D.W., Reinhold W.C., Lababidi S., et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4 (2003) R28
47. Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4 (2003) R7.1-R7.12
48. Battle A., Segal E., and Koller D. Probabilistic discovery of overlapping cellular processes and their regulation. J Comput Biol 12 (2005) 909-927
49. Segal E., Friedman N., Koller D., and Regev A. A module map showing conditional activity of expression modules in cancer. Nat Genet 36 (2004) 1090-1098. The authors develop a modeling approach for analyzing microarray expression data that reveals functional gene modules and regulatory relationships.
50. Huang S.H., Triche T., and Jong A.Y. Infectomics: genomics and proteomics of microbial infections. Funct Integr Genomics 1 (2002) 331-344
51. 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