Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications

Nature Reviews Genetics

Volumn 10, Issue 8, 2009, Pages 578-585

  Brown, Brian D ^a   Naldini, Luigi ^b  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VACCINE; MICRORNA; ONCOLYTIC VIRUS; POLIOMYELITIS VACCINE; RIBONUCLEOPROTEIN; VIRUS VACCINE; VIRUS VECTOR;

CANCER GENETICS; GENE EXPRESSION REGULATION; GENE THERAPY; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; STEM CELL GENE THERAPY; STEM CELL TRANSPLANTATION; SUICIDE GENE THERAPY; TRANSGENICS; VIRAL GENE DELIVERY SYSTEM;

ANIMALS; GENE THERAPY; HUMANS; MICRORNAS; NEOPLASMS;

ANIMALIA;

EID: 67651087321     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2628     Document Type: Review

References (67)

1. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233 (2009).
2. Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414 (2007).
3. Griffiths-Jones, S., Saini, H. K., van Dongen, S. & Enright, A. J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154-D158 (2008).
4. Brown, B. D., Venneri, M. A., Zingale, A., Sergi Sergi, L. & Naldini, L. Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer. Nature Med. 12, 585-591 (2006).
5. Brown, B. D. et al. Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state. Nature Biotechnol. 25, 1457-1467 (2007).
6. Barnes, D., Kunitomi, M., Vignuzzi, M., Saksela, K. & Andino, R. Harnessing endogenous miRNAs to control virus tissue tropism as a strategy for developing attenuated virus vaccines. Cell Host Microbe 4, 239-248 (2008).
7. Kelly, E. J., Hadac, E. M., Greiner, S. & Russell, S. J. Engineering microRNA responsiveness to decrease virus pathogenicity. Nature Med. 14, 1278-1283 (2008).
8. Papapetrou, E. P., Kovalovsky, D., Beloeil, L., Sant'angelo, D. & Sadelain, M. Harnessing endogenous miR-181a to segregate transgenic antigen receptor expression in developing versus post-thymic T cells in murine hematopoietic chimeras. J. Clin. Invest. 119, 157-168 (2008).
9. Edge, R. E. et al. A let-7 microRNA-sensitive vesicular stomatitis virus demonstrates tumor-specific replication. Mol. Ther. 16, 1437-1443 (2008).
10. Suzuki, T. et al. miR-122a-regulated expression of a suicide gene prevents hepatotoxicity without altering antitumor effects in suicide gene therapy. Mol. Ther. 16, 1719-1726 (2008).
11. Ylosmaki, E. et al. Generation of a conditionally replicating adenovirus based on targeted destruction of E1A mRNA by a cell type-specific microRNA. J. Virol. 82, 11009-11015 (2008).
12. Cawood, R. et al. Use of tissue-specific microRNA to control pathology of wild-type adenovirus without attenuation of its ability to kill cancer cells. PLoS Pathog. 5, e1000440 (2009).
13. Baek, D. et al. The impact of microRNAs on protein output. Nature 455, 64-71 (2008).
14. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63 (2008).
15. Mansfield, J. H. et al. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genet. 36, 1079-1083 (2004).
16. Brown, B. D. et al. A microRNA-regulated lentiviral vector mediates stable correction of hemophilia B mice. Blood 110, 4144-4152 (2007).
17. Care, A. et al. MicroRNA-133 controls cardiac hypertrophy. Nature Med. 13, 613-618 (2007).
18. Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nature Methods 4, 721-726 (2007).
19. Scherr, M. et al. Lentivirus-mediated antagomir expression for specific inhibition of miRNA function. Nucleic Acids Res. 35, e149 (2007).
20. Bonci, D. et al. The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nature Med. 14, 1271-1277 (2008).
21. Gentner, B. et al. Stable knockdown of microRNA in vivo by lentiviral vectors. Nature Methods 6, 63-66 (2009).
22. Kumar, M. S. et al. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc. Natl. Acad. Sci. USA 105, 3903-3908 (2008).
23. Sayed, D. et al. MicroRNA-21 targets Sprouty2 and promotes cellular outgrowths. Mol. Biol. Cell 19, 3272-3282 (2008).
24. Valastyan, S. et al. A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell 137, 1032-1046 (2009).
25. Kelly, E. J. & Russell, S. J. MicroRNAs and the regulation of vector tropism. Mol. Ther. 17, 409-416 (2008).
26. Waehler, R., Russell, S. J. & Curiel, D. T. Engineering targeted viral vectors for gene therapy. Nature Rev. Genet. 8, 573-587 (2007).
27. Schmidt-Supprian, M. & Rajewsky, K. Vagaries of conditional gene targeting. Nature Immunol. 8, 665-668 (2007).
28. De Palma, M. et al. Promoter trapping reveals significant differences in integration site selection between MLV and HIV vectors in primary hematopoietic cells. Blood 105, 2307-2315 (2005).
29. Brown, B. D. & Lillicrap, D. Dangerous liaisons: the role of 'danger' signals in the immune response to gene therapy. Blood 100, 1133-1140 (2002).
30. Cao, O., Furlan-Freguia, C., Arruda, V. R. & Herzog, R. W. Emerging role of regulatory T cells in gene transfer. Curr. Gene Ther. 7, 381-390 (2007).
31. Wolff, L. J., Wolff, J. A. & Sebestyen, M. G. Effect of tissue-specific promoters and microRNA recognition elements on stability of transgene expression after hydrodynamic naked plasmid DNA delivery. Hum. Gene Ther. 20, 374-388 (2009).
32. Neilson, J. R., Zheng, G. X., Burge, C. B. & Sharp, P. A. Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21, 578-589 (2007).
33. Colin, A. et al. Engineered lentiviral vector targeting astrocytes in vivo. Glia 57, 667-679 (2009).
34. Perez, J. T. et al. MicroRNA-mediated species-specific attenuation of influenza A virus. Nature Biotechnol. 27, 572-576 (2009).
35. Haasnoot, J., Westerhout, E. M. & Berkhout, B. RNA interference against viruses: strike and counterstrike. Nature Biotechnol. 25, 1435-1443 (2007).
36. Boden, D., Pusch, O., Lee, F., Tucker, L. & Ramratnam, B. Human immunodeficiency virus type 1 escape from RNA interference. J. Virol. 77, 11531-11535 (2003).
37. Gitlin, L., Karelsky, S. & Andino, R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 418, 430-434 (2002).
38. Gitlin, L., Stone, J. K. & Andino, R. Poliovirus escape from RNA interference: short interfering RNA-target recognition and implications for therapeutic approaches. J. Virol. 79, 1027-1035 (2005).
39. Vignuzzi, M., Wendt, E. & Andino, R. Engineering attenuated virus vaccines by controlling replication fidelity. Nature Med. 14, 154-161 (2008).
40. Arai, F. et al. Tie2/angiopoietin-1 signaling regulates hematopoietic stem cell quiescence in the bone marrow niche. Cell 118, 149-161 (2004).
41. De Palma, M., Venneri, M. A., Roca, C. & Naldini, L. Targeting exogenous genes to tumor angiogenesis by transplantation of genetically modified hematopoietic stem cells. Nature Med. 9, 789-795 (2003).
42. Constien, R. et al. Characterization of a novel EGFP reporter mouse to monitor Cre recombination as demonstrated by a Tie2 Cre mouse line. Genesis 30, 36-44 (2001).
43. Pucci, F. et al. A distinguishing gene signature shared by tumor-infiltrating Tie2-expressing monocytes (TEMs), blood 'resident' monocytes and embryonic macrophages suggests common functions and developmental relationships. Blood 21 Apr 2009 (doi:10.1182/blood-2009-01-200931).
44. Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438-442 (2003).
45. Haraguchi, T., Ozaki, Y. & Iba, H. Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells. Nucleic Acids Res. 37, e43 (2009).
46. Kim, V. N., Han, J. & Siomi, M. C. Biogenesis of small RNAs in animals. Nature Rev. Mol. Cell Biol. 10, 126-139 (2009).
47. Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature 438, 685-689 (2005).
48. Horwich, M. D. & Zamore, P. D. Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells. Nature Protoc. 3, 1537-1549 (2008).
49. Kloosterman, W. P. & Plasterk, R. H. The diverse functions of microRNAs in animal development and disease. Dev. Cell 11, 441-450 (2006).
50. Johnnidis, J. B. et al. Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451, 1125-1129 (2008).
51. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005).
52. Landthaler, M. et al. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 14, 2580-2596 (2008).
53. Schmitter, D. et al. Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res. 34, 4801-4815 (2006).
54. Xiao, C. et al. MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 131, 146-159 (2007).
55. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105 (2007).
56. Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511 (2004).
57. Seitz, H. Redefining microRNA targets. Curr. Biol. 19, 870-873 (2009).
58. Forstemann, K., Horwich, M. D., Wee, L., Tomari, Y. & Zamore, P. D. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130, 287-297 (2007).
59. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005).
60. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437-1441 (2004).
61. Hutvagner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056-2060 (2002).
62. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102-114 (2008).
63. Behm-Ansmant, I. et al. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 20, 1885-1898 (2006).
64. Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854 (1993).
65. Ameres, S. L., Martinez, J. & Schroeder, R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130, 101-112 (2007).
66. Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214-220 (2005).
67. Kedde, M. et al. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 131, 1273-1286 (2007).