MicroRNAs in genetic disease: Rethinking the dosage

Current Gene Therapy

Volumn 12, Issue 4, 2012, Pages 292-300

  Henrion Caude, Alexandra ^a   Girard, Muriel ^a   Amiel, Jeanne ^a  

^a IMAGINE INSTITUTE   (France)

Author keywords

Anti miRs; Disease; Dosage; Genetics; Genotype; MicroRNA; Mimics

Indexed keywords

CELL PENETRATING PEPTIDE; LOCKED NUCLEIC ACID; MICRORNA; MICRORNA 34A; OLIGONUCLEOTIDE;

ARTICLE; BIOGENESIS; DRUG CONJUGATION; DRUG DELIVERY SYSTEM; EMULSION; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENE SWITCHING; GENE TARGETING; GENETIC DISORDER; GENETIC EPISTASIS; GENOMICS; HEPATITIS C; HUMAN; LUNG NON SMALL CELL CANCER; NONHUMAN; PHENOTYPE;

EPIGENESIS, GENETIC; GENE DOSAGE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC DISEASES, INBORN; GENETIC THERAPY; HUMANS; MICRORNAS; MOLECULAR TARGETED THERAPY; MUTATION;

EID: 84864562306     PISSN: 15665232     EISSN: 18755631     Source Type: Journal    
DOI: 10.2174/156652312802083602     Document Type: Article

References (101)

1. Rother S, Meister G. Small RNAs derived from longer non-coding RNAs. Biochimie. 2011 Nov;93(11):1905-15.
2. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004 Jan 23;116(2):281-97.
3. Griffiths-Jones S. miRBase: microRNA sequences and annotation. Curr Protoc Bioinformatics. 2010 Mar;Chapter 12:Unit 12 9 1-0.
4. Saini HK, Griffiths-Jones S, Enright AJ. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17719-24.
5. Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 2005 Mar;11(3):241-7.
6. Morlando M, Ballarino M, Gromak N, Pagano F, Bozzoni I, Proudfoot NJ. Primary microRNA transcripts are processed cotranscriptionally. Nat Struct Mol Biol. 2008 Sep;15(9):902-9.
7. Kim YK, Kim VN. Processing of intronic microRNAs. EMBO J. 2007 Feb 7;26(3):775-83.
8. He C, Li Z, Chen P, Huang H, Hurst LD, Chen J. Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution. Nucleic Acids Res. May 1;40(9):4002-12.
9. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8.
10. Olena AF, Patton JG. Genomic organization of microRNAs. J Cell Physiol. 2010 Mar;222(3):540-5.
11. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2999-3004.
12. Lee R, Feinbaum R, Ambros V. A short history of a short RNA. Cell. 2004 Jan 23;116(2 Suppl):S89-92, 1 p following S6.
13. Schanen BC, Li X. Transcriptional regulation of mammalian miRNA genes. Genomics. 2011 Jan;97(1):1-6.
14. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003 Sep 25;425(6956):415-9.
15. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 2003 Dec 15;17(24):3011-6.
16. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature. 2005 Aug 4;436(7051):740-4.
17. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicerindependent miRNA biogenesis pathway that requires Ago catalysis. Nature. 2010 Jun 3;465(7298):584-9.
18. Gregory RI, Shiekhattar R. MicroRNA biogenesis and cancer. Cancer Res. 2005 May 1;65(9):3509-12.
19. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003 Oct 17;115(2):199-208.
20. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, et al. Widespread regulatory activity of vertebrate microRNA* species. RNA. 2011 Feb;17(2):312-26.
21. Packer AN, Xing Y, Harper SQ, Jones L, Davidson BL. The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington's disease. J Neurosci. 2008 Dec 31;28(53):14341-6.
22. Yoo AS, Staahl BT, Chen L, Crabtree GR. MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature. 2009 Jul 30;460(7255):642-6.
23. Kim S, Lee UJ, Kim MN, Lee EJ, Kim JY, Lee MY, et al. MicroRNA miR-199a* regulates the MET proto-oncogene and the downstream extracellular signal-regulated kinase 2 (ERK2). J Biol Chem. 2008 Jun 27;283(26):18158-66.
24. Lee YB, Bantounas I, Lee DY, Phylactou L, Caldwell MA, Uney JB. Twist-1 regulates the miR-199a/214 cluster during development. Nucleic Acids Res. 2009 Jan;37(1):123-8.
25. Lin EA, Kong L, Bai XH, Luan Y, Liu CJ. miR-199a, a bone morphogenic protein 2-responsive MicroRNA, regulates chondrogenesis via direct targeting to Smad1. J Biol Chem. 2009 Apr 24;284(17):11326-35.
26. Ro S, Park C, Young D, Sanders KM, Yan W. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res. 2007;35(17):5944-53.
27. Tsang WP, Kwok TT. The miR-18a* microRNA functions as a potential tumor suppressor by targeting on K-Ras. Carcinogenesis. 2009 Jun;30(6):953-9.
28. Biasiolo M, Sales G, Lionetti M, Agnelli L, Todoerti K, Bisognin A, et al. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One. 2011;6(8):e23854.
29. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, et al. Widespread regulatory activity of vertebrate microRNA* species. RNA. 2011 Feb;17(2):312-26.
30. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009 Jan 23;136(2):215-33.
31. Bandiera S, Hatem E, Lyonnet S, Henrion-Caude A. microRNAs in diseases: from candidate to modifier genes. Clin Genet. 2010 Apr;77(4):306-13.
32. Weiler J, Hunziker J, Hall J. Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease? Gene Ther. 2006 Mar;13(6):496-502.
33. Lennox KA, Behlke MA. Chemical modification and design of anti-miRNA oligonucleotides. Gene Ther. 2011 Dec;18(12):1111-20.
34. Moulton JD. Using morpholinos to control gene expression. Curr Protoc Nucleic Acid Chem. 2007 Jan;Chapter 4:Unit 4 30.
35. Cheng CJ, Saltzman WM. Polymer Nanoparticle-Mediated Delivery of MicroRNA Inhibition and Alternative Splicing. Mol Pharm. 2012 May 7;9(5):1481-8.
36. Tivnan A, Orr WS, Gubala V, Nooney R, Williams DE, McDonagh C, et al. Inhibition of Neuroblastoma Tumor Growth by Targeted Delivery of MicroRNA-34a Using Anti-Disialoganglioside GD(2) Coated Nanoparticles. PLoS One. 2012;7(5):e38129.
37. Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME, et al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science. 2010 Jan 8;327(5962):198-201.
38. Kairouz V, Lipskaia L, Hajjar RJ, Chemaly ER. Molecular targets in heart failure gene therapy: current controversies and translational perspectives. Ann N Y Acad Sci. 2012 Apr;1254(1):42-50.
39. van Rooij E, Purcell AL, Levin AA. Developing microRNA therapeutics. Circ Res. 2012 Feb 3;110(3):496-507.
40. Thum T, Gross C, Fiedler J, Fischer T, Kissler S, Bussen M, et al. MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature. 2008 Dec 18;456(7224):980-4.
41. Patrick DM, Zhang CC, Tao Y, Yao H, Qi X, Schwartz RJ, et al. Defective erythroid differentiation in miR-451 mutant mice mediated by 14-3-3zeta. Genes Dev. 2010 Aug 1;24(15):1614-9.
42. Trang P, Wiggins JF, Daige CL, Cho C, Omotola M, Brown D, et al. Systemic delivery of tumor suppressor microRNA mimics using a neutral lipid emulsion inhibits lung tumors in mice. Mol Ther. 2011 Jun;19(6):1116-22.
43. Craig VJ, Tzankov A, Flori M, Schmid CA, Bader AG, Muller A. Systemic microRNA-34a delivery induces apoptosis and abrogates growth of diffuse large B-cell lymphoma in vivo. Leukemia. 2012 Apr 23.
44. Kumar MS, Erkeland SJ, Pester RE, Chen CY, Ebert MS, Sharp PA, et al. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3903-8.
45. Cai C, Ashktorab H, Pang X, Zhao Y, Sha W, Liu Y, et al. MicroRNA-211 expression promotes colorectal cancer cell growth in vitro and in vivo by targeting tumor suppressor CHD5. PLoS One. 2012;7(1):e29750.
46. Kasar S, Salerno E, Yuan Y, Underbayev C, Vollenweider D, Laurindo MF, et al. Systemic in vivo lentiviral delivery of miR-15a/16 reduces malignancy in the NZB de novo mouse model of chronic lymphocytic leukemia. Genes Immun. 2012 Feb;13(2):109-19.
47. McBride JL, Boudreau RL, Harper SQ, Staber PD, Monteys AM, Martins I, et al. Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: implications for the therapeutic development of RNAi. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5868-73.
48. Grimm D, Streetz KL, Jopling CL, Storm TA, Pandey K, Davis CR, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature. 2006 May 25;441(7092):537-41.
49. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993 Dec 3;75(5):843-54.
50. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000 Feb 24;403(6772):901-6.
51. Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell. 2009 May 15;137(4):647-58.
52. Georgantas RW, 3rd, Hildreth R, Morisot S, Alder J, Liu CG, Heimfeld S, et al. CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control. Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2750-5.
53. Cheng LC, Pastrana E, Tavazoie M, Doetsch F. miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci. 2009 Apr;12(4):399-408.
54. Wang Y, Baskerville S, Shenoy A, Babiarz JE, Baehner L, Blelloch R. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet. 2008 Dec;40(12):1478-83.
55. Melton C, Judson RL, Blelloch R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature. 2010 Feb 4;463(7281):621-6.
56. Yu Z, Wang C, Wang M, Li Z, Casimiro MC, Liu M, et al. A cyclin D1/microRNA 17/20 regulatory feedback loop in control of breast cancer cell proliferation. J Cell Biol. 2008 Aug 11;182(3):509-17.
57. Le MT, Shyh-Chang N, Khaw SL, Chin L, Teh C, Tay J, et al. Conserved regulation of p53 network dosage by microRNA-125b occurs through evolving miRNA-target gene pairs. PLoS Genet. 2011 Sep;7(9):e1002242.
58. Smith P, Al Hashimi A, Girard J, Delay C, Hebert SS. In vivo regulation of amyloid precursor protein neuronal splicing by microRNAs. J Neurochem. 2010 Jan;116(2):240-7.
59. McCoy CE, Sheedy FJ, Qualls JE, Doyle SL, Quinn SR, Murray PJ, et al. IL-10 inhibits miR-155 induction by toll-like receptors. J Biol Chem. 2010 Jul 2;285(27):20492-8.
60. Sheedy FJ, Palsson-McDermott E, Hennessy EJ, Martin C, O'Leary JJ, Ruan Q, et al. Negative regulation of TLR4 via targeting of the proinflammatory tumor suppressor PDCD4 by the microRNA miR-21. Nat Immunol. 2009 Feb;11(2):141-7.
61. van der Maarel SM, Tawil R, Tapscott SJ. Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence. Trends Mol Med. 2011 May;17(5):252-8.
62. Lemmers RJ, van der Vliet PJ, Klooster R, Sacconi S, Camano P, Dauwerse JG, et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010 Sep 24;329(5999):1650-3.
63. Wallace LM, Liu J, Domire JS, Garwick-Coppens SE, Guckes SM, Mendell JR, et al. RNA Interference Inhibits DUX4-induced Muscle Toxicity In Vivo: Implications for a Targeted FSHD Therapy. Mol Ther. 2012 Apr 17.
64. 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. 2009 Apr;37(6):e43.
65. Kluiver J, Gibcus JH, Hettinga C, Adema A, Richter MK, Halsema N, et al. Rapid generation of microRNA sponges for microRNA inhibition. PLoS One. 2012;7(1):e29275.
66. Mockenhaupt S, Schurmann N, Grimm D. When cellular networks run out of control: global dysregulation of the RNAi machinery in human pathology and therapy. Prog Mol Biol Transl Sci. 2011;102:165-242.
67. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, Li MZ, et al. Dicer is essential for mouse development. Nat Genet. 2003 Nov;35(3):215-7.
68. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science. 2005 May 6;308(5723):833-8.
69. Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, et al. Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1949-54.
70. Morita S, Horii T, Kimura M, Goto Y, Ochiya T, Hatada I. One Argonaute family member, Eif2c2 (Ago2), is essential for development and appears not to be involved in DNA methylation. Genomics. 2007 Jun;89(6):687-96.
71. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, et al. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9136-41.
72. Hill DA, Ivanovich J, Priest JR, Gurnett CA, Dehner LP, Desruisseau D, et al. DICER1 mutations in familial pleuropulmonary blastoma. Science. 2009 Aug 21;325(5943):965.
73. Caudy AA, Myers M, Hannon GJ, Hammond SM. Fragile Xrelated protein and VIG associate with the RNA interference machinery. Genes Dev. 2002 Oct 1;16(19):2491-6.
74. Stark KL, Xu B, Bagchi A, Lai WS, Liu H, Hsu R, et al. Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat Genet. 2008 Jun;40(6):751-60.
75. Drake KM, Ruteshouser EC, Natrajan R, Harbor P, Wegert J, Gessler M, et al. Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562. Clin Cancer Res. 2009 Oct 1;15(19):5985-92.
76. Astuti D, Morris MR, Cooper WN, Staals RH, Wake NC, Fews GA, et al. Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility. Nat Genet. 2012 Mar;44(3):277-84.
77. Ota A, Tagawa H, Karnan S, Tsuzuki S, Karpas A, Kira S, et al. Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res. 2004 May 1;64(9):3087-95.
78. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, et al. A microRNA polycistron as a potential human oncogene. Nature. 2005 Jun 9;435(7043):828-33.
79. van Bokhoven H, Celli J, van Reeuwijk J, Rinne T, Glaudemans B, van Beusekom E, et al. MYCN haploinsufficiency is associated with reduced brain size and intestinal atresias in Feingold syndrome. Nat Genet. 2005 May;37(5):465-7.
80. de Pontual L, Yao E, Callier P, Faivre L, Drouin V, Cariou S, et al. Germline deletion of the miR-17-92 cluster causes skeletal and growth defects in humans. Nat Genet. 2011 Oct;43(10):1026-30.
81. Mendell JT. miRiad roles for the miR-17-92 cluster in development and disease. Cell. 2008 Apr 18;133(2):217-22.
82. Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, et al. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science. 2005 Oct 14;310(5746):317-20.
83. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet. 2006 Jul;38(7):813-8.
84. Landi D, Gemignani F, Barale R, Landi S. A catalog of polymorphisms falling in microRNA-binding regions of cancer genes. DNA Cell Biol. 2008 Jan;27(1):35-43.
85. Saunders MA, Liang H, Li WH. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3300-5.
86. Sethupathy P, Collins FS. MicroRNA target site polymorphisms and human disease. Trends Genet. 2008 Oct;24(10):489-97.
87. Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat Genet. 2011 Mar;43(3):242-5.
88. Mencia A, Modamio-Hoybjor S, Redshaw N, Morin M, Mayo-Merino F, Olavarrieta L, et al. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet. 2009 May;41(5):609-13.
89. Solda G, Robusto M, Primignani P, Castorina P, Benzoni E, Cesarani A, et al. A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing. Hum Mol Genet. 2012 Feb 1;21(3):577-85.
90. Hughes AE, Bradley DT, Campbell M, Lechner J, Dash DP, Simpson DA, et al. Mutation altering the miR-184 seed region causes familial keratoconus with cataract. Am J Hum Genet. 2011 Nov 11;89(5):628-33.
91. Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 2010 79:351-79.
92. Hwang HW, Wentzel EA, Mendell JT. A hexanucleotide element directs microRNA nuclear import. Science. 2007 Jan 5;315(5808):97-100.
93. Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, et al. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One. 2010;5(5):e10563.
94. Jeffries CD, Fried HM, Perkins DO. Nuclear and cytoplasmic localization of neural stem cell microRNAs. RNA. 2011 Apr;17(4):675-86.
95. Gibbings DJ, Ciaudo C, Erhardt M, Voinnet O. Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol. 2009 Sep;11(9):1143-9.
96. Lee YS, Pressman S, Andress AP, Kim K, White JL, Cassidy JJ, et al. Silencing by small RNAs is linked to endosomal trafficking. Nat Cell Biol. 2009 Sep;11(9):1150-6.
97. Bandiera S, Hanein S, Lyonnet S, Henrion-Caude A. Mitochondria as novel players of the cellular RNA interference. J Biol Chem. 2011 Sep 23;286(38):le19.
98. Fichtlscherer S, Zeiher AM, Dimmeler S. Circulating microRNAs: biomarkers or mediators of cardiovascular diseases? Arterioscler Thromb Vasc Biol. 2011 Nov;31(11):2383-90.
99. Cortez MA, Bueso-Ramos C, Ferdin J, Lopez-Berestein G, Sood AK, Calin GA. MicroRNAs in body fluids--the mix of hormones and biomarkers. Nat Rev Clin Oncol. 2011 Aug;8(8):467-77.
100. Papapetrou EP, Korkola JE, Sadelain M. A genetic strategy for single and combinatorial analysis of miRNA function in mammalian hematopoietic stem cells. Stem Cells. 2010 Feb;28(2):287-96.
101. Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, et al. An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet. 2009 May;41(5):614-8.