DNA microarrays in vaccine research

Current Opinion in Molecular Therapeutics

Volumn 5, Issue 6, 2003, Pages 575-583

  Dietrich, Guido ^a  

^a Berna Biotech AG   (Switzerland)

Author keywords

Antigen identification; DNA microarrays; Vaccine candidates

Indexed keywords

BACTERIAL VACCINE; BCG VACCINE; BRCA1 PROTEIN; CANCER VACCINE; CHOLERA VACCINE; DNA; DNA VACCINE; EPIDERMAL GROWTH FACTOR RECEPTOR 2; HELICOBACTER PYLORI VACCINE; HEPATITIS C VACCINE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; KEYHOLE LIMPET HEMOCYANIN; LEISHMANIA VACCINE; LIVE VACCINE; MALARIA VACCINE; MELANOMA ANTIGEN 1; MUCIN 1; POLYSACCHARIDE VACCINE; PROTOZOAL VACCINE; SALMONELLOSIS VACCINE; SHIGELLA VACCINE; THERATOPE; TOXOPLASMA GONDII VACCINE; TYPHOID VACCINE; VIRUS VACCINE;

ANALYTIC METHOD; ARTICLE; BACTERIAL GENETICS; BACTERIAL INFECTION; BACTERIAL MENINGITIS; BACTERIAL VIRULENCE; BIOMEDICINE; BIOTECHNOLOGY; BREAST CANCER; CARCINOGENESIS; CHOLERA; DNA MICROARRAY; DNA PROBE; DNA SEQUENCE; DRUG RESEARCH; GENE MUTATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HELICOBACTER INFECTION; HELICOBACTER PYLORI; HEPATITIS C; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LEISHMANIA; LEISHMANIASIS; LISTERIA MONOCYTOGENES; LISTERIOSIS; MALARIA FALCIPARUM; MALIGNANT NEOPLASTIC DISEASE; MYCOBACTERIUM TUBERCULOSIS; NEISSERIA MENINGITIDIS; NUCLEIC ACID HYBRIDIZATION; OPEN READING FRAME; PLASMODIUM FALCIPARUM; PROTOZOAL INFECTION; SALMONELLA TYPHI; SALMONELLOSIS; SHIGELLOSIS; TOXOPLASMA GONDII; TOXOPLASMOSIS; TUBERCULOSIS; TYPHOID FEVER;

BACTERIAL VACCINES; CANCER VACCINES; GENE EXPRESSION PROFILING; GENES, PROTOZOAN; GENOME, BACTERIAL; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VIRAL VACCINES;

BACTERIA (MICROORGANISMS); HELICOBACTER; HELICOBACTER PYLORI; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; LISTERIA; LISTERIA MONOCYTOGENES; MYCOBACTERIUM; MYCOBACTERIUM BOVIS BCG; MYCOBACTERIUM TUBERCULOSIS; NEGIBACTERIA; NEISSERIA; NEISSERIA MENINGITIDIS; PLASMODIUM FALCIPARUM; POSIBACTERIA; SALMONELLA; SALMONELLA TYPHI; SHIGELLA; TOXOPLASMA GONDII;

EID: 0346458899     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (45)

1. The chipping forecast. Nature Genetics (2002) 32(4 Suppl):461-552.
2. Dietrich G, Viret JF, Hess J: Mycobecterium bovis BCG-based vaccines against tuberculosis: Novel developments. Vaccine (2003) 21(7-8):667-670.
3. Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, Rane S, Small PM: Comparative genomics of BCG vaccines by wholegenome DNA microarray. Science (1999) 284(5419):1520-1523.
4. Kamath AT, Feng CG, Macdonald M, Briscoe H, Britton WJ: Differential protective efficacy of DNA vaccines expressing secreted proteins of Mycobacterium tuberculosis. Infect Immun (1999) 67(4):1702-1707.
5. Brandt L, Elhay M, Rosenkrands I, Lindblad EB, Andersen P: ESAT-6 subunit vaccination against Mycobacterium tuberculosis. Infect Immun (2000) 68(2):791-795.
6. Pym AS, Brodin P, Majlessi L, Brosch R, Demangel C, Williams A, Griffiths KE, Marchal G, Leclerc C, Cole ST: Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat Med (2003) 9(5):533-539.
7. Lewis KN, Liao R, Guinn KM, Hickey MJ, Smith S, Behr MA, Sherman DR: Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guérin attenuation. J Infect Dis (2003) 187(1):117-123.
8. Behr MA: Correlation between BCG genomics and protective efficacy. Scand J Infect Dis (2001) 33(4):249-252.
9. Kato-Maeda M, Rhee JT, Gingeras TR, Salamon H, Drenkow J, Smittipat N, Small PM: Comparing genomes within the species Mycobacterium tuberculosis. Genome Res (2001) 11(4):547-554.
10. Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Young DB, Butcher PD: Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology (2002) 148(Pt 10):3129-3138.
11. Fisher MA, Plikaytis BB, Shinnick TM: Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes. J Bacteriol (2002) 184(14):4025-4032.
12. Mangan JA, Monahan IM, Wilson MA, Schnappinger D, Schoolnik GK, Butcher PD: The expression profile of Mycobacterfurn tuberculosis infecting the human monocytic cell line THP-1 using whole genome microarray analysis. Nat Genet (1999) 23:61.
13. Sassetti CM, Boyd DH, Rubin EJ: Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci USA (2001) 98(22):12712-12717.
14. Vermont CL, van den Dobbelsteen GP, de Groot R: Recent developments in vaccines to prevent meningococcal serogroup B infections. Curr Opin Mol Ther (2003) 5(1):33-38.
15. Dietrich G, Kurz S, Hübner C, Aepinus C, Theiss S, Guckenberger M, Panzner U, Weber J, Frosch M: Transcriptome analysis of Neisseria meningitidis during infection. J Bacteriol (2003) 185(1):155-164.
16. Kurz S, Hübner C, Aepinus C, Theiss S, Guckenberger M, Panzner U, Weber J, Frosch M, Dietrich G: Transcriptome-based antigen identification for Neisseria meningitidis. Vaccine (2003) 21(7-8):768-775.
17. Grifantini R, Bartoloni E, Muzzi A, Draghi M, Frigimelica E, Berger J, Ratti G, Petracca R, Galli G, Agnusdei M, Giuliani MM et at. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol (2002) 20(9):914-921.
18. Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger J, Randazzo F, Grandi G: Gene expression profile in Neisseria meningitidis and Neisseria lactamica upon host-cell contact: From basic research to vaccine development. Ann NY Acad Sci (2002) 975:202-216.
19. Perrin A, Bonacorsi S, Carbonnelle E, Talibi D, Dessen P, Nassif X, Tinsley C: Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. Infect Immun (2002) 70(12):7063-7072.
20. Guckenberger M, Kurz S, Aepinus C, Theiss S, Haller S, Leimbach T, Panzner U, Weber J, Paul H, Unkmeir A, Frosch M, Dietrich G: Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays. J Bacteriol (2002) 184(9):2546-2551.
21. Dietrich G, Griot-Wenk M, Metcalfe IC, Lang AB, Viret JF: Experience with registered mucosal vaccines. Vaccine (2003) 21(7-8):678-683.
22. Xu Q, Dziejman M, Mekalanos JJ: Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro. Proc Natl Acad Sci USA (2003) 100(3):1286-1291.
23. Ehksson S, Lucchini S, Thompson A, Rhen M, Hinton JCD: Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol (2003) 47(1):103-118.
24. Milohanic E, Glaser P, Coppee JY, Frangeul L, Vega Y, Vazquez-Boland A Kunst F, Cossart P, Buchrieser C: Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differentially regulated by PrfA. Mol Microbiol (2003) 47(6):1613-1625.
25. Nau GJ, Richmond JFL, Schlesinger A, Jennings EG, Lander ES, Young RA: Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci USA (2002) 99(3):1503-1508.
26. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S: A whole-genome microarray reveals genetic diversity among Helicobacter pylod strains. Proc Natl Acad Sci USA (2000) 97(26):14668-14673.
27. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol (2003) 4(2): R9.
28. Le Roch KG, Zhou Y, Batalov S, Winzeler EA: Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. Am J Trop Med Hyg (2002) 67(3):233-243.
29. Almeida R, Norrish A, Levick M, Vetrie D, Freeman T, Vilo J, Ivens A, Lange U, Stober C, McCann S, Blackwell JM: From genomes to vaccines: Leishmania as a model. Philos Trans R Soc Lond B Biol Sci (2002) 357(1417):5-11.
30. Chaussabel D, Semnani RT, McDowell MA, Sacks D, Sher A, Nutman TB: Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood (2003) 102(2):672-681.
31. Diehl S, Diehl F, El-Sayed NM, Clayton C, Hoheisel JD: Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA microarray. Mol Biochem Parasitol (2002) 123(2):115-123.
32. Hoffmann KF, Johnston DA, Dunne DW: Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling. Genome Biol (2002) 3(8):RESEARCH0041.1-0041.12.
33. Cleary MD, Singh U, Blader IJ, Brewer JL, Boothroyd JC: Toxoplasma gondii asexual development: Identification of developmentally regulated genes and distinct patterns of gene expression. Eukaryot Cell (2002) 1(3):329-340.
34. Walker BD, Korber BT: Immune control of HIV: The obstacles of HLA and viral diversity. Nat Immunol (2001) 2(6):473-475.
35. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR: Extensive polymorphisms observed in HIV-1 clade B protease gone using high density oligonucleotide arrays. Nat Med (1996) 2(7):753-759.
36. Zhao W, Liu W, Liu Q, Zhang L, Zhou Z, Liu X, Zhang H: Genotyping of hepatitis C virus by hepatitis gene diagnosis microarray. Zhonghua Yi Xue Za Zhi (2002) 82(18):1249-1253.
37. Chizhikov V, Wagner M, Ivshina A, Hoshino Y, Kapikian AZ, Chumakov K: Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J Clin Microbiol (2002) 40(7):2398-2407.
38. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL: Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA (2002) 99(24):15687-15692.
39. Izmailova E, Bertley FM, Huang Q, Makori N, Miller CJ, Young RA, Aldovini A: HIV-1 Tat reprograms immature dendritic cells to express chemoattractants; for activated T cells and macrophages. Nat Med (2003) 9(2):191-197.
40. Chambers J, Angulo A, Amaratunga D, Guo H, Jiang Y, Wan JS, Bittner A, Frueh K, Jackson MR, Peterson PA, Erlander MG, Ghazal P: DNA microarrays of the complex human cytomegalovirus genome: Profiling kinetic class with drug sensitivity of viral gene expression. J Virol (1999) 73(7):5757-5766.
41. Welcsh PL, Lee MK, Gonzalez-Hernandez RM, Black DJ, Mahadevappa M, Swisher EM, Warrington JA, King MC: BRCA1 transcriptionally regulates genes involved in breast tumorigenesis. Proc Natl Acad Sci USA (2002) 99(11):7560-7565,
42. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ et al: Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 415(6871):530-536.
43. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO: Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA (2002) 99(20):12963-12968.
44. Aoyagi K, Tatsuta T, Nishigaki M, Akimoto S, Tanabe C, Omoto Y, Hayashi S, Sakamoto H, Sakamoto M, Yoshida T, Terada M et at. A faithful method for PCR-medlated global mRNA amplification and its integration into microarray analysis on laser-captured cells. Biochem Biophys Res Commun (2003) 300(4):915-920.
45. Amexis G, Rubin S, Chizhikov V, Pelloquin F, Carbone K, Chumakov K: Sequence diversity of Jerryl Lynn strain of mumps virus: Quantitative mutant analysis for vaccine quality control. Virology (2002) 300(2):171-179.