Towards high-throughput functional target discovery in angiogenesis research

Trends in Molecular Medicine

Volumn 12, Issue 1, 2006, Pages 44-52

  Van Beijnum, Judy R ^a   Eijgelaar, Wouter J ^a   Griffioen, Arjan W ^a  

^a MAASTRICHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; COMPLEMENTARY DNA;

ANGIOGENESIS; CELL MIGRATION; DOWN REGULATION; ENDOTHELIUM CELL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC SCREENING; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HUMAN; PHENOTYPE; PROTEIN FUNCTION; REVIEW; RNA INTERFERENCE; VALIDATION STUDY;

ANIMALS; GENE EXPRESSION; GENE LIBRARY; GENETIC TECHNIQUES; GENOMICS; HUMANS; NEOVASCULARIZATION, PATHOLOGIC; OLIGONUCLEOTIDES, ANTISENSE; RESEARCH DESIGN; RNA INTERFERENCE; TRANSFECTION;

EID: 30644465701     PISSN: 14714914     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molmed.2005.11.005     Document Type: Review

References (66)

1. A.W. Griffioen, and G. Molema Angiogenesis: potentials for pharmacologic intervention in the treatment of cancer, cardiovascular diseases, and chronic inflammation Pharmacol. Rev. 52 2000 237 268
2. J. Folkman Tumor angiogenesis J.F. Holland Cancer Medicine 5th Edn 2000 B.C. Decker 132 152
3. S.L. Madden Vascular gene expression in nonneoplastic and malignant brain Am. J. Pathol. 165 2004 601 608
4. B.S. Parker Alterations in vascular gene expression in invasive breast carcinoma Cancer Res. 64 2004 7857 7866
5. B. St Croix Genes expressed in human tumor endothelium Science 289 2000 1197 1202
6. J.R. van Beijnum, and A.W. Griffioen In silico analysis of angiogenesis associated gene expression identifies angiogenic stage related profiles Biochim. Biophys. Acta 1755 2005 121 134
7. R. Auerbach Angiogenesis assays: a critical overview Clin. Chem. 49 2003 32 40
8. J. Hasan Quantitative angiogenesis assays in vivo - a review Angiogenesis 7 2004 1 16
9. M. Schena Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
10. J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
11. S.M. Elbashir Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Nature 411 2001 494 498
12. A. Fire Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391 1998 806 811
13. R.H. Plasterk RNA silencing: the genome's immune system Science 296 2002 1263 1265
14. T.R. Brummelkamp A system for stable expression of short interfering RNAs in mammalian cells Science 296 2002 550 553
15. M. Miyagishi, and K. Taira U6 promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells Nat. Biotechnol. 20 2002 497 500
16. P.J. Paddison Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells Genes Dev. 16 2002 948 958
17. N.S. Lee Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells Nat. Biotechnol. 20 2002 500 505
18. B. Luo Small interfering RNA production by enzymatic engineering of DNA (SPEED) Proc. Natl. Acad. Sci. U. S. A. 101 2004 5494 5499
19. G. Sen Restriction enzyme-generated siRNA (REGS) vectors and libraries Nat. Genet. 36 2004 183 189
20. D. Yang Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells Proc. Natl. Acad. Sci. U. S. A. 99 2002 9942 9947
21. R. Kittler An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division Nature 432 2004 1036 1040
22. P.Y. Lu Modulation of angiogenesis with siRNA inhibitors for novel therapeutics Trends Mol. Med. 11 2005 104 113
23. Z. Chen Down-regulation of vascular endothelial cell growth factor-C expression using small interfering RNA vectors in mammary tumors inhibits tumor lymphangiogenesis and spontaneous metastasis and enhances survival Cancer Res. 65 2005 9004 9011
24. P. Dell'Era Gene expression profile in fibroblast growth factor 2-transformed endothelial cells Oncogene 21 2002 2433 2440
25. P. Dell'Era FGF2-induced upregulation of DNA polymerase-δ p12 subunit in endothelial cells Oncogene 24 2005 1117 1121
26. R.M. Schiffelers Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle Nucleic Acids Res. 32 2004 e149
27. P.Y. Lu In vivo application of RNA interference: from functional genomics to therapeutics Adv. Genet. 54 2005 117 142
28. M. Sioud siRNA delivery in vivo Methods Mol. Biol. 309 2005 237 250
29. F. Shi, and D. Hoekstra Effective intracellular delivery of oligonucleotides in order to make sense of antisense J. Control. Release 97 2004 189 209
30. M. Abe, and Y. Sato cDNA microarray analysis of the gene expression profile of VEGF-activated human umbilical vein endothelial cells Angiogenesis 4 2001 289 298
31. M. Iizuka Down syndrome candidate region 1, a downstream target of VEGF, participates in endothelial cell migration and angiogenesis J. Vasc. Res. 41 2004 334 344
32. H.G. Hotz VEGF antisense therapy inhibits tumor growth and improves survival in experimental pancreatic cancer Surgery 137 2005 192 199
33. M.E. Gleave, and B.P. Monia Antisense therapy for cancer Nat. Rev. Cancer 5 2005 468 479
34. V. Zaric Effective polyethylenimine-mediated gene transfer into human endothelial cells J. Gene Med. 6 2004 176 184
35. J.L. Hernandez A highly efficient electroporation method for the transfection of endothelial cells Angiogenesis 7 2004 235 241
36. N. Iversen Electroporation by nucleofector is the best nonviral transfection technique in human endothelial and smooth muscle cells Genet. Vaccines Ther. 3 2005 2
37. N.J. Horwood High-efficiency gene transfer into nontransformed cells: utility for studying gene regulation and analysis of potential therapeutic targets Arthritis Res. 4 Suppl. 3 2002 S215 S225
38. M. Li, and J.J. Rossi Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells Methods Mol. Biol. 309 2005 261 272
39. C. Leimeister Analysis of HeyL expression in wild-type and Notch pathway mutant mouse embryos Mech. Dev. 98 2000 175 178
40. F. Michiels Arrayed adenoviral expression libraries for functional screening Nat. Biotechnol. 20 2002 1154 1157
41. G.J. Arts Adenoviral vectors expressing siRNAs for discovery and validation of gene function Genome Res. 13 2003 2325 2332
42. D.B. Wheeler RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells Nat. Methods 1 2004 127 132
43. J. Ziauddin, and D.M. Sabatini Microarrays of cells expressing defined cDNAs Nature 411 2001 107 110
44. L. Zheng An approach to genome-wide screens of expressed small interfering RNAs in mammalian cells Proc. Natl. Acad. Sci. U. S. A. 101 2004 135 140
45. T. Yoshikawa Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown J. Control. Release 96 2004 227 232
46. J.M. Silva RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells Proc. Natl. Acad. Sci. U. S. A. 101 2004 6548 6552
47. S. Mousses RNAi microarray analysis in cultured mammalian cells Genome Res. 13 2003 2341 2347
48. (2004) Abstracts of the 15th endothelial cell research symposium. Maastricht, the Netherlands, 23 November 2004. In Angiogenesis (Vol. 7), pp. 165-189, Kluwer Academic Publishers
49. J.N. Harada Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis Genome Res. 15 2005 1136 1144
50. C. Conrad Automatic identification of subcellular phenotypes on human cell arrays Genome Res. 14 2004 1130 1136
51. J. Clayton RNA interference: the silent treatment Nature 431 2004 599 605
52. T.R. Brummelkamp Stable suppression of tumorigenicity by virus-mediated RNA interference Cancer Cell 2 2002 243 247
53. H. Mizuguchi, and T. Hayakawa Targeted adenovirus vectors Hum. Gene Ther. 15 2004 1034 1044
54. E. Palmer, and T. Freeman Cell-based microarrays: current progress, future prospects Pharmacogenomics 6 2005 527 534
55. V. Mastyugin A quantitative high-throughput endothelial cell migration assay J. Biomol. Screen. 9 2004 712 718
56. J.C. Yarrow A high-throughput cell migration assay using scratch wound healing, a comparison of image-based readout methods BMC Biotechnol. 4 2004 21
57. J. Song Gene silencing in androgen-responsive prostate cancer cells from the tissue-specific prostate-specific antigen promoter Cancer Res. 64 2004 7661 7663
58. M. van de Wetering Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector EMBO Rep. 4 2003 609 615
59. S. Matsukura Establishment of conditional vectors for hairpin siRNA knockdowns Nucleic Acids Res. 31 2003 e77
60. A. Ventura Cre-lox-regulated conditional RNA interference from transgenes Proc. Natl. Acad. Sci. U. S. A. 101 2004 10380 10385
61. O.V. Matveeva Thermodynamic criteria for high hit rate antisense oligonucleotide design Nucleic Acids Res. 31 2003 4989 4994
62. M.C. Giddings Artificial neural network prediction of antisense oligodeoxynucleotide activity Nucleic Acids Res. 30 2002 4295 4304
63. A.A. Levin A review of the issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides Biochim. Biophys. Acta 1489 1999 69 84
64. A. Ray, and B. Norden Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future FASEB J. 14 2000 1041 1060
65. J.S. Jepsen, and J. Wengel LNA-antisense rivals siRNA for gene silencing Curr. Opin. Drug Discov. Devel. 7 2004 188 194
66. G. Schmajuk Antisense oligonucleotides with different backbones. Modification of splicing pathways and efficacy of uptake J. Biol. Chem. 274 1999 21783 21789