Use of DNA microarrays to monitor host response to virus and virus-derived gene therapy vectors

American Journal of PharmacoGenomics

Volumn 4, Issue 6, 2004, Pages 345-356

  Piersanti, Stefania ^a,b   Martina, Yuri ^a,c   Cherubini, Gioia ^a,b   Avitabile, Daniele ^a,d   Saggio, Isabella ^a,b,e  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Parco Scientifico Biomedico San Raffaele   (Italy)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d LABORATORIO DI PATOLOGIA VASCOLARE   (Italy)

^e CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS VECTOR; CHEMOKINE LIGAND 2; COMPLEMENTARY DNA; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; GENE PRODUCT; HEAT SHOCK PROTEIN 70; INTERLEUKIN 8; LENTIVIRUS VECTOR; MONOKINE; ONYX 015; PLATELET DERIVED GROWTH FACTOR RECEPTOR; TRANSACTIVATOR PROTEIN; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; VIRUS VECTOR;

ADENOVIRUS; ADENOVIRUS 5; ANTINEOPLASTIC ACTIVITY; BIK GENE; CXCL9 GENE; DNA MICROARRAY; GENE; GENE EXPRESSION; GENE INDUCTION; GENE REPRESSION; GENE TARGETING; GENETIC TRANSDUCTION; HEPATITIS C VIRUS; HERPES SIMPLEX VIRUS 1; HUMAN; HUMAN CYTOMEGALOVIRUS; IMMUNE RESPONSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; REVIEW; SIMIAN IMMUNODEFICIENCY VIRUS; VIRAL GENE DELIVERY SYSTEM; VIRAL GENE THERAPY; VIRUS CELL INTERACTION; VIRUS ENVELOPE; VIRUS GENE; VIRUS INFECTION;

ANIMALS; DNA, VIRAL; GENE THERAPY; GENE TRANSFER TECHNIQUES; GENETIC VECTORS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VIRUS DISEASES; VIRUSES;

ADENO-ASSOCIATED VIRUS; ADENOVIRIDAE; CYTOMEGALOVIRUS; HEPATITIS C VIRUS; HUMAN ADENOVIRUS TYPE 5; HUMAN HERPESVIRUS 1; HUMAN HERPESVIRUS 5; LENTIVIRUS; SIMIAE; SIMIAN IMMUNODEFICIENCY VIRUS; SIMPLEXVIRUS;

EID: 11144241331     PISSN: 11752203     EISSN: None     Source Type: Journal    
DOI: 10.2165/00129785-200404060-00002     Document Type: Review

References (55)

1. Raper SE, Yudkoff M, Chirmule N, et al. A pilot study of in vivo liver-directed gene transfer with an adenoviral vector in partial ornithine transcarbamylase deficiency. Hum Gene Ther 2002; 13 (1): 163-75
2. Ries S, Korn WM. ONYX-015: mechanisms of action and clinical potential of a replication-selective adenovirus. Br J Cancer 2002; 86 (1): 5-11
3. Brown P, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet 1999; 21: 33-7
4. Bryant PA, Venter D, Robins-Browne R, et al. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 2004; 4 (2): 100-11
5. Hardiman G. Microarray technologies 2003: an overview. Pharmacogenomics 2003; 4 (3): 251-6
6. Leung YF, Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet 2003; 19(11): 649-59
7. Sevenet N, Cussenot O. DNA microarrays in clinical practice: past, present, and future. Clin Exp Med 2003; 3 (1): 1-3
8. Duggan DJ, Bittner M, Chen Y, et al. Expression profiling using cDNA microarrays. Nat Genet 1999; 21 (1 Suppl): 10-4
9. Lipshutz RJ, Fodor SP, Gingeras TR, et al. High density synthetic oligonucleotide arrays. Nat Genet 1999; 21 (1 Suppl.): 20-4
10. Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol 1999; 303: 179-205
11. Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996; 14 (13): 1675-80
12. Chambers J, Angulo A, Amaratunga D, et al. DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J Virol 1999; 73: 5757-66
13. Stingley SW, Ramirez JJ, Aguilar SA, et al. Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray. J Virol 2000; 74 (21): 9916-27
14. Ghedin E, Pumfery A, De La Fuente C, et al. Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChiP-chip analysis. Retrovirology 2004; 1 (1): 10
15. Wang D, Coscoy L, Zylberberg M, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 2002; 99 (24): 15687-92
16. Di Pasquale G, Davidson BL, Stein CS, et al. Identification of PDGFR as a receptor for AAV-5 transduction. Nat Med 2003; 9 (10): 1306-12
17. Zhao H, Granberg F, Elfineh L, et al. Strategic attack on host cell gene expression during adenovirus infection. J Virol 2003; 77 (20): 11006-15
18. Natarajan K, Shepard LA, Chodosh J. The use of DNA array technology in studies of ocular viral pathogenesis. DNA Cell Biol 2002; 21 (5-6): 483-90
19. Stilwell JL, McCarty DM, Negishi A, et al. Development and characterization of novel empty adenovirus capsids and their impact on cellular gene expression. J Virol 2003; 77 (23): 12881-5
20. Stilwell JL, Samulski RJ. Role of viral vectors and virion shells in cellular gene expression. Mol Ther 2004; 9 (3): 337-46
21. Haberberger T, Kupfer K, Murphy J. Profiling of genes which are differentially expressed in mouse liver in response to adenoviral vectors and delivered genes. Gene Ther 2000; 7: 903-9
22. Geimonen E, Neff S, Raymond T, et al. Pathogenic and nonpathogenic hantaviruses differentially regulate endothelial cell responses. Proc Natl Acad Sci U S A 2002; 99 (21): 13837-42
23. Simmen KA, Singh J, Luukkonen BG, et al. Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B. Proc Natl Acad Sci U S A 2001; 98 (13): 7140-5
24. Browne EP, Wing B, Coleman D, et al. Altered cellular mRNA levels in human cytomegalovirus-infected fibroblasts: viral block to the accumulation of antiviral mRNAs. J Virol 2001; 75 (24): 12319-30
25. Bigger CB, Brasky KM, Lanford RE. DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J Virol 2001; 75 (15): 7059-66
26. Su AI, Pezacki JP, Wodicka L, et al. Genomic analysis of the host response to hepatitis C virus infection. Proc Natl Acad Sci U S A 2002; 99 (24): 15669-74
27. Geiss G, Buragarner R, An M, et al. Large-scale monitoring of host-cell gene expression uring HIV-1 infection using cDNA microarrays. Virology 2000; 266: 8-16
28. Izmailova E, Bertley FM, Huang Q, et al. HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages. Nat Med 2003; 9 (2): 191-7
29. Mitchell R, Chiang CY, Berry C, et al. Global analysis of cellular transcription following infection with an HIV-based vector. Mol Ther 2003; 8 (4): 674-87
30. Taddeo B, Esclatine A, Roizman B. The patterns of accumulation of cellular RNAs in cells infected with a wild-type and a mutant herpes simplex virus 1 lacking the virion host shutoff gene. Proc Natl Acad Sci U S A 2002; 99 (26): 17031-6
31. Jenner RG, Alba MM, Boshoff C, et al. Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays. J Virol 2001; 75 (2): 891-902
32. Geiss GK, An MC, Bumgarner RE, et al. Global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events. J Virol 2001; 75 (9): 4321-31
33. Poggioli GJ, DeBiasi RL, Bickel R, et al. Reovirus-induced alterations in gene expression related to cell cycle regulation. J Virol 2002; 76 (6): 2585-94
34. Cuadras M, Feigelstock D, An S, et al. Gene expression pattern in Caco-2 cells following Rotavirus infection. J Virol 2002; 76: 4467-82
35. George MD, Sankaran S, Reay E, et al. High-throughput gene expression profiling indicates dysregulation of intestinal cell cycle mediators and growth factors during primary simian immunodeficiency virus infection. Virology 2003; 312 (1): 84-94
36. Jones JO, Arvin AM. 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 2003; 77 (2): 1268-80
37. Blankestein T. Gene therapy: principles and applications. Basel: Birkhauser Verlag, 1999
38. Curiel D, Douglas J. Adenoviral vectors for gene therapy. San Diego (CA): Elsevier Science, 2002
39. Monahan PE, Samulski RJ. AAV vectors: is clinical success on the horizon? Gene Ther 2000; 7 (1): 24-30
40. Naldini L, Blomer U, Gallay P, et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 1996; 272 (5259): 263-7
41. Hamaguchi I, Woods NB, Panagopoulos I, et al. Lentivirus vector gene expression during ES cell-derived hematopoietic development in vitro. J Virol 2000; 74 (22): 10778-84
42. Zufferey R, Dull T, Mandel RJ, et al. Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J Virol 1998; 72 (12): 9873-80
43. Kremer E, Perricaudet M. Adenovirus and adeno-associated virus mediated gene tansfer. Br Med Bull 1995; 51 (1): 31-44
44. Gene therapy clinical trials worldwide [online]. The Journal of Gene Medicine. Available from URL: http://www.wiley.co.uk/genmed/clinical/ [Accessed 2004 Sep 28]
45. Kochaneck S, Clemens PR, Mitani K, et al. A new adenoviral vector: replacement of all viral coding sequences with 28 kb of DNA indipendently expressing both full length dystrophoin and beta-galctosidase. Proc Natl Acad Sci USA 1996; 93: 5731-6
46. Liu Q, Muruve D. Molecular basis of the inflammatory response to adenovirus vectors. Gene Ther 2003; 10: 935-40
47. Morral N, O'Neal W, Rice K, et al. Administration of helper-dependent adenoviral vectors and sequential delivery of different vector serotype for long-term liver-directed gene transfer in baboons. Proc Natl Acad Sci U S A 1999; 96 (22): 12816-21
48. Qin L, Ding Y, Pahud DR, et al. Adenovirus-mediated gene transfer of viral interleukin-10 inhibits the immune response to both alloantigen and adenoviral antigen. Hum Gene Ther 1997; 8: 1365-74
49. Lieber A, He CY, Meuse L, et al. Inhibition of NF-kappaB activation in combination with bcl-2 expression allows for persistence of first-generation adenovirus vectors in the mouse liver. J Virol 1998; 72 (11): 9267-77
50. Schaack J, Bennett ML, Colbert JD, et al. E1A and E1B proteins inhibit inflammation induced by adenovirus. Proc Natl Acad Sci U S A 2004; 101 (9): 3124-9
51. Schowalter DB, Tubb JC, Liu M, et al. Heterologous expression of adenovirus E3-gpl9k in an E1a-deleted adenovirus vector inhibits MHC I expression in vitro, but does not prolong transgene espression in vivo. Gene Ther 1997; 4: 351-60
52. Dedieu J-F, Vigne E, Torrent C, et al. Long-term gene delivery into the livers of immunocompetent mice with E1/E4-defective adenoviruses. J Virol 1997; 71: 4626-37
53. Lee MG, Abina MA, Haddada H, et al. The constitutive expression of the immunomodulatory gp19k protein in E1-, E3-adenoviral vectors strongly reduces the host cytotoxic T cell response against the vector. Gene Ther 1995; 2: 1-7
54. Rothmann T, Hengstermann A, Whitaker NJ, et al. Replication of ONYX-015, a potential anticancer adenovirus, is independent of p53 status in tumor cells. J Virol 1998; 72 (12): 9470-8
55. Edwards SJ, Dix BR, Myers CJ, et al. Evidence that replication of the antitumor adenovirus ONYX-015 is not controlled by the p53 and p 14 (ARF) tumor suppressor genes. J Virol 2002; 76 (24): 12483-90