MicroRNA: an Emerging Therapeutic Target and Intervention Tool

MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression patterns of miRNAs to a variety of diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases and viral infections. MiRNAs provide its particular layer of network for gene regulation, thus possessing the great potential both as a novel class of therapeutic targets and as a powerful intervention tool. In this regard, synthetic RNAs that contain the binding sites of miRNA have been shown to work as a “decoy” or “miRNA sponge” to inhibit the function of specific miRNAs. On the other hand, miRNA expression vectors have been used to restore or overexpress specific miRNAs to achieve a long-term effect. Further, double-stranded miRNA mimetics for transient replacement have been experimentally validated. Endogenous precursor miRNAs have also been used as scaffolds for the induction of RNA interference. This article reviews the recent progress on this emerging technology as a powerful tool for gene regulation studies and particularly as a rationale strategy for design of therapeutics.

[1]  Baohong Zhang,et al.  Plant microRNA: a small regulatory molecule with big impact. , 2006, Developmental biology.

[2]  Jerry Pelletier,et al.  Short RNAs repress translation after initiation in mammalian cells. , 2006, Molecular cell.

[3]  Anton P. McCaffrey,et al.  Advances in microRNAs: implications for gene therapists. , 2008, Human gene therapy.

[4]  S. Hammond,et al.  An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells , 2000, Nature.

[5]  U. Kutay,et al.  Nuclear Export of MicroRNA Precursors , 2004, Science.

[6]  Sek Won Kong,et al.  Altered microRNA expression in human heart disease. , 2007, Physiological genomics.

[7]  L. Miraglia,et al.  Characterization of a Potent and Specific Class of Antisense Oligonucleotide Inhibitor of Human Protein Kinase C-α Expression* , 1999, The Journal of Biological Chemistry.

[8]  T. Golub,et al.  Impaired microRNA processing enhances cellular transformation and tumorigenesis , 2007, Nature Genetics.

[9]  S. Murray,et al.  Spinal distribution and metabolism of 2′-O-(2-methoxyethyl)-modified oligonucleotides after intrathecal administration in rats , 2005, Neuroscience.

[10]  K. Esser,et al.  MicroRNA-1 and microRNA-133a expression are decreased during skeletal muscle hypertrophy. , 2007, Journal of applied physiology.

[11]  Tammy Chang,et al.  Inhibition of HIV-1 replication with designed miRNAs expressed from RNA polymerase II promoters , 2007, Gene Therapy.

[12]  Anastasia Khvorova,et al.  Corrigendum: 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets , 2007, Nature Methods.

[13]  M. Simon,et al.  A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs , 2007, BMC Molecular Biology.

[14]  A. Bradley,et al.  Identification of mammalian microRNA host genes and transcription units. , 2004, Genome research.

[15]  Z. Mourelatos,et al.  A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. , 2005, Genes & development.

[16]  R. Hartmann,et al.  Locked nucleic acid oligonucleotides: the next generation of antisense agents? , 2007, BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy.

[17]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[18]  A. Klippel,et al.  Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. , 2003, Nucleic acids research.

[19]  K. Czaplinski,et al.  Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. , 2004, RNA.

[20]  Bing Yu,et al.  Construction and identification of a human liver specific microRNA eukaryotic expression vector. , 2007, Cellular & molecular immunology.

[21]  B. Davidson,et al.  RNA polymerase III transcribes human microRNAs , 2006, Nature Structural &Molecular Biology.

[22]  Stefano Volinia,et al.  Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Byoung-Tak Zhang,et al.  Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex , 2006, Cell.

[24]  V. Kim,et al.  The role of PACT in the RNA silencing pathway , 2006, The EMBO journal.

[25]  N. Rajewsky,et al.  Silencing of microRNAs in vivo with ‘antagomirs’ , 2005, Nature.

[26]  V. Scaria,et al.  microRNA: an Emerging Therapeutic , 2007, ChemMedChem.

[27]  R. Stephens,et al.  Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. , 2006, Cancer cell.

[28]  T. Okanoue,et al.  Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues , 2006, Oncogene.

[29]  R. Russell,et al.  Principles of MicroRNA–Target Recognition , 2005, PLoS biology.

[30]  M. Gleave,et al.  Antitumor activity of antisense clusterin oligonucleotides is improved in vitro and in vivo by incorporation of 2'-O-(2-methoxy)ethyl chemistry. , 2001, The Journal of pharmacology and experimental therapeutics.

[31]  James M. Pipas,et al.  SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells , 2005, Nature.

[32]  R. Shiekhattar,et al.  TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing , 2005, Nature.

[33]  J. Keller,et al.  RNA in Brain Disease: No Longer Just "The Messenger in the Middle" , 2007, Journal of neuropathology and experimental neurology.

[34]  T. Rana,et al.  siRNA function in RNAi: a chemical modification analysis. , 2003, RNA.

[35]  M. Eccles,et al.  Conjugate for efficient delivery of short interfering RNA (siRNA) into mammalian cells , 2004, FEBS letters.

[36]  Theresa A. Storm,et al.  Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways , 2006, Nature.

[37]  Phillip A Sharp,et al.  siRNAs can function as miRNAs , 2003 .

[38]  B. Cullen,et al.  MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Wayne Tam,et al.  Accumulation of miR-155 and BIC RNA in human B cell lymphomas. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  C. Croce,et al.  MicroRNA-133 controls cardiac hypertrophy , 2007, Nature Medicine.

[41]  Martin Tabler,et al.  Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes. , 2003, Nucleic acids research.

[42]  Yanjie Lu,et al.  Retracted: Novel approaches for gene‐specific interference via manipulating actions of microRNAs: Examination on the pacemaker channel genes HCN2 and HCN4 , 2007, Journal of cellular physiology.

[43]  Baohong Zhang,et al.  Translational Medicine: microRNAs: a new emerging class of players for disease diagnostics and gene therapy , 2008 .

[44]  Matthias John,et al.  Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs , 2004, Nature.

[45]  Guihua Sun,et al.  A facile lentiviral vector system for expression of doxycycline-inducible shRNAs: knockdown of the pre-miRNA processing enzyme Drosha. , 2007, Molecular therapy : the journal of the American Society of Gene Therapy.

[46]  F. Orge,et al.  Intravitreous anti-raf-1 kinase antisense oligonucleotide as an angioinhibitory agent in porcine preretinal neovascularization , 2003, Current eye research.

[47]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[48]  W. Paschen,et al.  Conditional gene silencing in mammalian cells mediated by a stress-inducible promoter. , 2008, Biochemical and biophysical research communications.

[49]  G. Hutvagner,et al.  A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.

[50]  V. Ambros,et al.  The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. , 1999, Developmental biology.

[51]  P. Sarnow,et al.  Modulation of Hepatitis C Virus RNA Abundance by a Liver-Specific MicroRNA , 2005, Science.

[52]  L. Lim,et al.  Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. , 2006, RNA.

[53]  K. Morris,et al.  Lentivirus-mediated RNA interference therapy for human immunodeficiency virus type 1 infection. , 2006, Human gene therapy.

[54]  M. Manoharan,et al.  Modulation of plasma protein binding and in vivo liver cell uptake of phosphorothioate oligodeoxynucleotides by cholesterol conjugation. , 2000, Nucleic acids research.

[55]  D. Leake,et al.  Double-stranded regions are essential design components of potent inhibitors of RISC function. , 2007, RNA.

[56]  M. Stoffel,et al.  MicroRNAs: a new class of regulatory genes affecting metabolism. , 2006, Cell metabolism.

[57]  Patrick J. Paddison,et al.  Second-generation shRNA libraries covering the mouse and human genomes , 2005, Nature Genetics.

[58]  S. Freier,et al.  Improved targeting of miRNA with antisense oligonucleotides , 2006, Nucleic acids research.

[59]  C. Croce,et al.  The role of microRNA genes in papillary thyroid carcinoma. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60]  J. Mattes,et al.  Discovery, biology and therapeutic potential of RNA interference, microRNA and antagomirs. , 2008, Pharmacology & therapeutics.

[61]  C. Sander,et al.  Identification of microRNAs of the herpesvirus family , 2005, Nature Methods.

[62]  B. Cullen,et al.  Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. , 2003, Genes & development.

[63]  Masahiro Sato,et al.  The expression profile of microRNAs in mouse embryos , 2006, Nucleic acids research.

[64]  Thomas Tuschl,et al.  Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. , 2004, RNA.

[65]  Tara L. Naylor,et al.  microRNAs exhibit high frequency genomic alterations in human cancer. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Peter Beighton,et al.  de la Chapelle, A. , 1997 .

[67]  Danish Sayed,et al.  MicroRNAs Play an Essential Role in the Development of Cardiac Hypertrophy , 2007, Circulation research.

[68]  Robert H. Silverman,et al.  Activation of the interferon system by short-interfering RNAs , 2003, Nature Cell Biology.

[69]  C. Sander,et al.  miR-122, a Mammalian Liver-Specific microRNA, is Processed from hcr mRNA and MayDownregulate the High Affinity Cationic Amino Acid Transporter CAT-1 , 2004, RNA biology.

[70]  Ola Snøve,et al.  Conserved microRNA characteristics in mammals. , 2006, Oligonucleotides.

[71]  Zuoshang Xu,et al.  An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi , 2005, Nucleic acids research.

[72]  H. Soifer,et al.  MicroRNAs in disease and potential therapeutic applications. , 2007, Molecular therapy : the journal of the American Society of Gene Therapy.

[73]  Margaret S. Ebert,et al.  MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells , 2007, Nature Methods.

[74]  R. Iggo,et al.  Induction of an interferon response by RNAi vectors in mammalian cells , 2003, Nature Genetics.

[75]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[76]  B. Cullen Transcription and processing of human microRNA precursors. , 2004, Molecular cell.

[77]  E. Bertrand,et al.  Human let-7 stem-loop precursors harbor features of RNase III cleavage products. , 2003, Nucleic acids research.

[78]  Stefano Volinia,et al.  MicroRNA expression abnormalities in pancreatic endocrine and acinar tumors are associated with distinctive pathologic features and clinical behavior. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[79]  Phillip D Zamore,et al.  Sequence-Specific Inhibition of Small RNA Function , 2004, PLoS biology.

[80]  M. Samols,et al.  Cloning and Identification of a MicroRNA Cluster within the Latency-Associated Region of Kaposi's Sarcoma-Associated Herpesvirus , 2005, Journal of Virology.

[81]  Detlef Weigel,et al.  Gene silencing in plants using artificial microRNAs and other small RNAs. , 2008, The Plant journal : for cell and molecular biology.

[82]  Thomas Thum,et al.  MicroRNAs in the Human Heart: A Clue to Fetal Gene Reprogramming in Heart Failure , 2007, Circulation.

[83]  C. Croce,et al.  MicroRNA gene expression deregulation in human breast cancer. , 2005, Cancer research.

[84]  Brian L. Gilmore,et al.  Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi , 2008, Proceedings of the National Academy of Sciences.

[85]  Arndt Borkhardt,et al.  High expression of precursor microRNA‐155/BIC RNA in children with Burkitt lymphoma , 2004, Genes, chromosomes & cancer.

[86]  J. Steitz,et al.  Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR , 2007, Proceedings of the National Academy of Sciences.

[87]  Michaela Scherr,et al.  Expression of the miR-17-92 polycistron in chronic myeloid leukemia (CML) CD34+ cells. , 2007, Blood.

[88]  B. Cullen,et al.  Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.

[89]  Detlef Weigel,et al.  Highly Specific Gene Silencing by Artificial miRNAs in Rice , 2008, PloS one.

[90]  Judy Lieberman,et al.  Running interference: prospects and obstacles to using small interfering RNAs as small molecule drugs. , 2006, Annual review of biomedical engineering.

[91]  Mark Graham,et al.  miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. , 2006, Cell metabolism.

[92]  K. Taira,et al.  Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells. , 2003, Nucleic acids research.

[93]  R. Griffey,et al.  Positional effect of chemical modifications on short interference RNA activity in mammalian cells. , 2005, Journal of Medicinal Chemistry.

[94]  S. Orkin,et al.  Site-directed, virus-free, and inducible RNAi in embryonic stem cells , 2007, Proceedings of the National Academy of Sciences.

[95]  Jing Qu,et al.  Artificial MicroRNA-Mediated Virus Resistance in Plants , 2007, Journal of Virology.

[96]  S. Elledge,et al.  A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[97]  A. Annoni,et al.  A microRNA-regulated lentiviral vector mediates stable correction of hemophilia B mice. , 2007, Blood.

[98]  Kwang-Soo Kim,et al.  Depletion of Human Micro-RNA miR-125b Reveals That It Is Critical for the Proliferation of Differentiated Cells but Not for the Down-regulation of Putative Targets during Differentiation* , 2005, Journal of Biological Chemistry.

[99]  W. Filipowicz,et al.  Repression of protein synthesis by miRNAs: how many mechanisms? , 2007, Trends in cell biology.

[100]  M. Stoffel,et al.  Specificity, duplex degradation and subcellular localization of antagomirs , 2007, Nucleic acids research.

[101]  S. Lowe,et al.  Tissue-specific and reversible RNA interference in transgenic mice , 2007, Nature Genetics.

[102]  C. Croce,et al.  miR-15 and miR-16 induce apoptosis by targeting BCL2. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[103]  R. Bernards,et al.  A System for Stable Expression of Short Interfering RNAs in Mammalian Cells , 2002, Science.

[104]  Gerhardt Attard,et al.  Making sense of antisense. , 2005, European journal of cancer.

[105]  Matthias John,et al.  RNAi-mediated gene silencing in non-human primates , 2006, Nature.

[106]  K. Morris,et al.  Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells , 2004, Science.

[107]  V. Velculescu,et al.  Implications of micro-RNA profiling for cancer diagnosis , 2006, Oncogene.

[108]  C. Burge,et al.  The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution , 2005, Science.

[109]  Anastasia Khvorova,et al.  Off-target effects by siRNA can induce toxic phenotype. , 2006, RNA.

[110]  T. Wurdinger,et al.  Molecular therapy in the microRNA era , 2007, The Pharmacogenomics Journal.

[111]  C. Croce,et al.  Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[112]  Muller Fabbri,et al.  A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. , 2005, The New England journal of medicine.

[113]  V. Kim,et al.  The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.

[114]  T. Rana,et al.  Specific and potent RNAi in the nucleus of human cells , 2005, Nature Structural &Molecular Biology.

[115]  Michael T. McManus,et al.  Gene silencing using micro-RNA designed hairpins. , 2002, RNA.

[116]  L. Naldini,et al.  Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer , 2006, Nature Medicine.

[117]  Debora S. Marks,et al.  Antisense-Mediated Depletion Reveals Essential and Specific Functions of MicroRNAs in Drosophila Development , 2005, Cell.

[118]  Chang-Zheng Chen,et al.  MicroRNAs as oncogenes and tumor suppressors. , 2005, The New England journal of medicine.

[119]  Jennifer Taylor,et al.  Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155 , 2006, Nucleic acids research.

[120]  Eric J Wagner,et al.  Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. , 2002, Molecular cell.

[121]  S. O’Brien,et al.  Dispersion of the ras family of transforming genes to four different chromosomes in man , 1983, Nature.

[122]  B. Cullen,et al.  Use of RNA polymerase II to transcribe artificial microRNAs. , 2005, Methods in enzymology.

[123]  Mark A. Kay,et al.  Progress and problems with the use of viral vectors for gene therapy , 2003, Nature Reviews Genetics.

[124]  B. Monia,et al.  Therapeutic potential for microRNAs. , 2007, Advanced drug delivery reviews.

[125]  P. Zamore,et al.  Thirty-three years later, a glimpse at the ribonuclease III active site. , 2001, Molecular cell.

[126]  Anne Gatignol,et al.  Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC , 2007, Nucleic acids research.

[127]  Anastasia Khvorova,et al.  3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets , 2006, Nature Methods.

[128]  Y. Yatabe,et al.  A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. , 2005, Cancer research.

[129]  S. Kauppinen,et al.  LNA-modified oligonucleotides mediate specific inhibition of microRNA function. , 2006, Gene.

[130]  H. Shim,et al.  Blockade of invasion and metastasis of breast cancer cells via targeting CXCR4 with an artificial microRNA. , 2007, Biochemical and biophysical research communications.

[131]  B. Ramratnam,et al.  Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. , 2004, Nucleic acids research.

[132]  V. Kim MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

[133]  A. Saïb,et al.  A Cellular MicroRNA Mediates Antiviral Defense in Human Cells , 2005, Science.

[134]  D. Collen,et al.  Humoral immune response in mice against a circulating antigen induced by adenoviral transfer is strictly dependent on expression in antigen-presenting cells. , 2003, Blood.

[135]  K. Taira,et al.  U6 promoter–driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells , 2002, Nature Biotechnology.

[136]  A. Silahtaroglu,et al.  Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver , 2007, Nucleic acids research.

[137]  E. Wiemer The role of microRNAs in cancer: no small matter. , 2007, European journal of cancer.

[138]  C. Croce,et al.  MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[139]  H. H. Choo,et al.  Inhaled p38alpha mitogen-activated protein kinase antisense oligonucleotide attenuates asthma in mice. , 2005, American journal of respiratory and critical care medicine.

[140]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[141]  Peixuan Guo,et al.  Specific delivery of therapeutic RNAs to cancer cells via the dimerization mechanism of phi29 motor pRNA. , 2005, Human gene therapy.

[142]  Ben Berkhout,et al.  Suppression of RNA Interference by Adenovirus Virus-Associated RNA , 2005, Journal of Virology.