SMALL NONCODING RNA AS PERSPECTIVE BIOMARKERS: BIOGENESIS AND THERAPEUTIC STRATIGIES
https://doi.org/10.20538/1682-0363-2016-2-112-126
Abstract
The review presents the opening story, biogenesis and functions of basic groups of human’s small noncoding RNA: microRNA and short interfering RNA. These RNA molecules inhibit gene expression during translation by RNA interference. It was found that microRNA and short interfering RNA circulate in bioliquids and can serve as biomarkers of different human diseases because of its conservative sequences, tissue specificity and resistance to environment factors. The paper considers techniques to study noncoding RNA (cloning, bioinformatics analysis and hybridization methods: northern-blotting, RT-PCR, in situ hybridization, microarray analysis, reporter analysis). Possible noncoding RNA-targeted therapy can suggest delivery microRNA, anti-microRNA, antagomirs, microRNAsponges to target tissue by virus molecules, liposomes or nanoparticles.
About the Authors
V. V. Tiguntsev
Siberian State Medical University, Tomsk;
Mental Health Research Institute, Tomsk
Russian Federation
Russian Federation
S. A. Ivanova
Mental Health Research Institute, Tomsk
Russian Federation
Russian Federation
V. Yu. Serebrov
Siberian State Medical University, Tomsk
Russian Federation
Russian Federation
M. B. Buhareva
National Research Tomsk Polytechnic University, Tomsk
Russian Federation
Russian Federation
References
1. Boehm M.., Slack F. A Developmental Timing MicroRNA and Its Target Regulate Life Span in C. elegans // // Science. 2005. V. 310, № 5756. P. 1954–1957.
2. Sood P., Krek A., Zavolan M. et al. Cell-type-specific signature of microRNAs on target mRNA expression // PNAS USA. 2006. V. 103, № 8. P. 2746–2751.
3. Li M., Li J., Ding X. et al. MicroRNA and cancer // AAPS J. 2010. V. 12, № 3. P. 309–317. Science. 2005. V. 310, № 5756. P. 1954–1957.
4. Ghildiyal M., Zamore P.D. Small silencing RNAs: an expanding universe // Nat. Rev. Genet. 2009. V. 10, № 2. P. 94–108.
5. Choudhuri S. Small Noncoding RNAs: Biogenesis, Function, and Emerging Significance in Toxicology // J. Biochem. Molecular Toxicology. 2010. V. 24, № 3. P. 195– 216.
6. Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans // The Plant Cell. 1990. V.2, № 4. P. 279–289.
7. van der Krol A.R., Mur L.A., Beld M. et al. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression // The Plant Cell 1990. V. 2, № 4. P. 291–299.
8. Cogoni C., Macino G. Post-transcriptional gene silencing across kingdoms // Curr. Opin. Genet. Dev. 2000. V. 10, № 6. P. 638–643.
9. 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. 1993. V. 75, № 5. P. 843–854.
10. Fire A., Xu S., Montgomery M.K. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans // Nature. 1998. V. 391, № 6669. P. 806–811.
11. Reinhart B.J., Slack F.J., Basson M. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans // Nature. 2000. V. 403, № 6772. P. 901–906.
12. Pasquinelli A.E., Reinhart B.J., Slack F. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA // Nature. 2000. V. 408, № 6808. P. 86–89.
13. Lau N.C., Lim L.P.,Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans // Science. 2001.V. 294, № 5543. P. 858–862.
14. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs // Science. 2001. V. 294, № 5543. P. 853–858.
15. Lee R.C, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans // Science. 2001. V. 294, № 5543. P. 862–864.
16. Hammond S.M., Bernstein E., Beach D., Hannon G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells // Nature. 2000. V. 404, № 6775. P. 293–296.
17. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference // Nature. 2001. V. 409, № 6818. P. 363–366.
18. Grishok A., Pasquinelli A.E., Conte D. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell. 2001. V. 106, № 1. P. 23–34.
19. Hutvґagner G., McLachlan J., Pasquinelli A.E. et al. A cellular function for the RNA interference enzyme Dicer in the maturation of the let-7 small temporal RNA // Science. 2001. V. 293, № 5589. P. 834–838.
20. Lee Y., Kim M., Han J. et al. MicroRNA genes are transcribed by RNA polymerase II // EMBO J. 2004. V. 23, № 20. P. 4051–4060.
21. Schwarz D., Zamore P. Why do miRNAs live in the miRNP? // Genes and Dev. 2002. V. 16. P. 1025–1031.
22. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias // Cell. 2003. V. 115, № 2. P. 209–216.
23. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function // Cell. 2004. V. 116, № 2. P. 281–297.
24. Kim V.N., Nam J.W. Genomics of microRNA // Trends Genet. 2006. V. 22, № 3. P. 165–173.
25. Zeng Y., Wagner E., Cullen B. Both natural and designed microRNAs can inhibit the expression of cognate mRNAs when expressed in human cells // Mol. Cell. 2002. V. 9, № 6. P. 1327–1333.
26. Mourelatos Z., Dostie J., Paushkin S. et al. miRNPs: A novel class of ribonucleoproteines containing numerous microRNAs // Genes and Dev. 2002. V. 16. P. 720–728.
27. Hutvagner G., Zamore P.D. A miRNA in a multiple-turnover RNAi enzyme complex // Science. 2002. V. 297. P. 2056–2060.
28. Carmell M.A., Xuan Zh., Zhand M.Q., Hannon G.J. The argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis // Genes and Dev. 2002. V. 16, № 21. P. 2733–2742.
29. Babushkina N.P., Kucher A.N. Geneticheskaya osnova funktsionirovaniya malyih regulyatornyih RNK u cheloveka [Genetic base of functioning of human small regulatory RNA]. Genetika cheloveka i patologiya: sbornik Sb. nauch. trudov / pod red. V. P. Puzyireva, Vyip. 8. Tomsk: Izd-vo «Pechatnaya manufaktura» Publ., 2007, pp. 219–228 (in Russian).
30. Doench J.G., Petersen Ch.P., Sharp Ph.A. siRNAs can function as miRNAs // Genes and Dev. 2003. V. 17, № 4. P. 438–442.
31. Lim L.P., Glasner M.E., Yekta S. et al. Vertebrate microRNA genes // Science. 2003. V. 299, № 5612. P. 1540.
32. Ruby J.G., Jan C.H., Bartel D.P. Intronic microRNA precursors that bypass Drosha processing // Nature. 2007. V. 448, № 7149. P. 83–86.
33. Berezikov E., Chung W.J., Willis J. et al. Mammalian mirtron genes // Mol. Cell. 2007. V. 28, № 2. P. 328–336.
34. Okamura K., Hagen J.W., Duan H. et al. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila // Cell. 2007. V. 130, № 1. P. 89–100.
35. Griffiths-Jones S., Grocock R.J., van Dongen S. et al. MiRBase: microRNA sequences, targets and gene nomenclature // Nucleic Acids Res. 2006. № 34. P. D140–D144.
36. Kennerdell J.R., Carthew R.W. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and friz zled 2 act in the wingless pathway // Cell. 1998. V. 95, № 7. P. 1017–1026.
37. Tuschl T., Zamore P.D., Lehmann R. et al. Targeted mRNA degradation by double-stranded RNA in vitro // Genes Dev. 1999. V. 13, № 24. P. 3191–3197.
38. Zamore P.D., Tuschl T., Sharp P.A., Bartel D.P. RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals // Cell. 2000. V. 101, № 1. P. 25–33.
39. Tomari Y., Zamore P.D. Perspective: machines for RNAi // Genes Dev. 2005. V. 19, № 5. P. 517–529.
40. Liu Y., Ye X., Jiang F. et al. C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation // Science. 2009. V. 325, № 5941. P. 750–753.
41. Pena J.T.G., Lee C.S., Rouhanifard S.H. et al. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues // Nature Methods. 2009. V. 6, № 2. P. 139–141.
42. Aravin A., Tuschl T. Identification and characterization of small RNAs involved in RNA silencing // FEBS Lett. 2005. V. 579, № 26. P. 5830–5840.
43. Lim L.P., Lau N.C., Garrett-Engele A. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs // Nature. 2005. V. 433, № 7027. P. 769–773.
44. Poy M.N., Eliasson L., Krutzfeldt J. et al. A pancreatic islet-specific microRNA regulates insulin secretion // Nature. 2004. V. 432, № 7014. P. 226–230.
45. Esau C., Davis S., Murray S.F., et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting // Cell Metab. 2006. V. 3, № 2. P. 87–98.
46. Khalaj M., Tavakkoli M., Stranahan A.W., Park C.Y. Pathogenic microRNA’s in myeloid malignancies // Front Genet. 2014. V. 5, № 361. P.
47. Simone N.L., Soule B.P., Ly D. et al. Ionizing radiationinduced oxidative stress alters miRNA expression. PLoS One. 2009. 4 (7): e6377. DOI: 10.1371/journal. pone.0006377.
48. Wang K., Zhang S., Weber J. et al. Export of microRNAs and microRNA-protective protein by mammalian cells // Nucleic Acids Research. 2010. V. 38, № 20. P. 7248–7259.
49. Arroyo J.D., Chevillet J.R., Kroh E.M. et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma // PNAS USA. 2011. V. 108, № 12. P. 5003–5008.
50. Hunter M.P., Ismail N., Zhang X. Detection of microRNA expression in human peripheral blood microvesicles // PLoS ONE. 2008. 3 (11): e3694. DOI: 10.1371/journal. pone.0003694. PMCID: PMC2577891.
51. Gallo A., Tandon M., Alevizos I., Illei G.G. The majority of microRNAs detectable in serum and saliva is concentrated in exosomes // PLoS ONE. 2012. 7 (3): e30679. DOI: 10.1371/journal.pone.0030679.
52. Valadi H., Ekstrom K., Bossios A. et al. Exosomemediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells // Nature Cell Biology. 2007. V. 9, № 6. P. 654–659.
53. Wagner J., Riwanto M., Besler C. Characterization of levels and cellular transfer of circulating lipoprotein_bound microRNAs // Arteriosclerosis, Thrombosis, and Vascular Biology. 2013. V. 33, № 6. P. 1392–1400.
54. Tiguntsev V.V., Ivanova S.A., Serebrov V.Yu., Buhareva M.B. Cirkuliruyushchie mikroRNK otkryvayut novyj podhod k diagnostike i prognozirovaniyu psihicheskih zabolevanij [Circulating microRNA open a new technic to diagnose and to predict mental diseases]. Innovations and Science, 2015, vol . 4, no. 1, pp. 127–129 (in Russian).
55. Chen X., Ba Y., Ma L. et al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases // Cell. 2008. № 18, № 10. P. 997–1006.
56. Mitchell P.S., Parkin R.K., Kroh E.M. et al. Circulating microRNAs as stable blood-based markers for cancer detection // PNAS USA. 2008. V. 105, № 30. P. 10513– 10518.
57. Tiguntsev V.V., Ivanova S.A., Serebrov V.Yu., Buhareva M.B. Dostoinstva i nedostatki opredeleniya mikroRNK kak potentsialnyih diagnosticheskih biomarkyorov [Advantages and disadvantages of the definition of microRNAs as potential diagnostic biomarkers]. Innovations and Science, 2015, vol . 4, no. 1, pp. 126–129 (in Russian).
58. Jiang J., Zheng X., Xu X. et al. Prognostic significance of miR-181b and miR-21 in gastric cancer patients treated with S-1/Oxaliplatin or Doxifluridine/Oxaliplatin // PLoS One. 2011. 6 (8): e23271. DOI: 10.1371/journal. pone.0023271.
59. Stegmeier F., Hu G., Rickles R.J. et al. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells // PNAS USA. 2005. V. 102, № 37. P. 13212–13217.
60. Chung K.H., Hart C.C., Al-Bassam S. et al. Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155 // Nucleic Acids Res. 2006. V. 34 (7): e53.
61. Chehonin V.P., Tsibulkina E.A., Ryabinina A.E. i soavt. Immunoliposomalnyie konteyneryi kak sistemyi napravlennogo transporta malyih interferiruyuschih RNK v shvannovskie kletki [Immunoliposomal containers as systems of forwarded transport of short interfering RNA to Schwann cells]. Byulleten eksperimentalnoy biologii i meditsinyi – Bulletin of Experimental Biology and Medicine, 2008, T. 146, no 10, pp. 431–434 (in Russian).
62. Young L.S., Searle P.F., Onion D., Mautner V. Viral gene therapy strategies: from basic science to clinical application // J. Pathol. 2006. V. 208, № 2. P. 299–318.
63. Borisenko A.S., Svitich O.A., Krivtsov G.G. i soavt. Effektivnost polikationnyih nanochastits polietilenimin-poligidrozid-hitozana (PEI-PG-OHG) v kachestve vektora dlya korotkih interferiruyuschih RNK, napravlennyih na podavlenie replikatsii virusa prostogo gerpesa 2 tipa [Efficiency of polycationic polyethilenimin-polyhydrazide-chitosan nanoparticles (PEI-PG-OHG) as vector for short interfering RNA to suppress replication of herpes simplex virus type 2]. Zhurn. Mikrobiol. – Microbiology, Zhurn. Mikrobiol.-Microbiology, 2015, no 3, pp. 31–37. (in Russian).
64. Kota J., Chivukula R.R., O’Donnell K.A. et al. Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model // Cell. 2009. V. 137, № 6. P. 1005–1017.
65. Shirshova A.N., Smetanina M.A., Aushev V.N., Filipenko M.L., Kushlinskiy N.E. MikroRNK – novyie perspektivnyie biomarkyoryi opuholey i misheni himioterapii. Chast 3. Terapevticheskoe primenenie mikroRNK. Metodyi kolichestvennogo opredeleniya [MicroRNA – new perspective tumor biomarkers and chemotherapy targets. Part 3. Therapeutic using of microRNA. Quantitative methods.]. Voprosyi biologicheskoy, meditsinskoy i farmatsevticheskoy himii – Problems of Biological, Medical and Pharmaceutical Chemistry, 2015, no. 4. pp. 31–39. (in Russian).
66. Wang Z. miRNA mimic technology. miRNA interference technologies // Springer: Berlin, Heidelberg, 2009. P. 93– 100.
67. Doxakis E. Post-transcriptional regulation of alphasynuclein expression by mir-7 and mir-153 // J. Biol. Chem. 2010. V. 285, № 17. P. 12726–12734.
68. Cho H.J., Liu G., Jin S.M. et al. MicroRNA-205 regulates the expression of Parkinson’s disease-related leucine-rich repeat kinase 2 protein // Hum. Mol. Genet. 2014. V. 22, № 3. P. 608–620.
69. Boutla A., Delidakis C., Tabler M. Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes // Nucleic Acids Res. 2003 V. 31, № 17. P. 4973– 4980.
70. Hutvagner G., Simard M.J., Mello C.C., Zamore P.D. Sequence-specific inhibition of small RNA function // PLoS Biol. 2004. 2 (4): E98.
71. Vester B., Wengel J. LNA (locked nucleic acid): highaffinity targeting of complementary RNA and DNA // Biochemistry. 2004. V. 43, № 42. P. 13233–13241.
72. Si M.L., Zhu S., Wu H. et al. miR-21-mediated tumor growth // Oncogene. 2007. V. 26, № 19. P. 2799 –2803.
73. Weiler J., Hunziker J., Hall J. Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease? // Gene Ther. 2006. V. 13, № 6. P. 496 –502.
74. Krьtzfeld J., Rajewsky N., Braich R. et al. Silencing of microRNAs in vivo with ‘antagomirs’ // Nature. 2005. V. 438, № 7068. P. 685–689.
75. Lindow M., Kauppinen S. Discovering the first microRNA-targeted drug // J. Cell Biol. 2012. V. 199, № 3. P. 407–412.
76. Ebert M.S., Neilson J.R., Sharp P.A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells // Nat. Methods. 2007. V. 4, № 9. P. 721–726.
77. Xiao J., Yang B., Lin H. et al. Novel approaches for gene-specific interference via manipulating actions of microRNAs: examination of the pacemaker channel genes HCN2 and HCN4 // J. Cell Physiol. 2007. V. 212, № 2. P. 285–292.
78. Tan H., Poidevin M., Li H. et al. MicroRNA-277 modulates the neurodegeneration caused by Fragile X permutation rCGG repeats // PLoS Genet. 2012. 8 (5): e1002681. DOI: 10.1371/journal.pgen.1002681. PMCID: PMC3343002.
79. Fedorov Y., Anderson E.M., Birmingham A. et al. Off-target effects by siRNA can induce toxic phenotype // RNA. 2006. V. 12, № 7. P. 1188–1196.
80. Calin G.A., Cimmino A., Fabbri M. et al. MiR-15a and miR-16–1 cluster functions in human leukemia // PNAS USA. 2008. V. 105, № 13. P. 5166–5171.
81. Grimm D., Streetz K.L., Jopling C.L. et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways // Nature. 2006. V. 441, № 7092. P. 537–541.
82. Koval E.D., Shaner C., Zhang P. et al. Method for widespread microRNA-155 inhibition prolongs survival in ALS-model mice // Hum. Mol. Genet. 2013. V. 22, № 20. P. 4127–4135.
83. Miller T.M., Pestronk A., David W. et al. An antisense oligonucleotide against SOD1 delivered intrathecally for patients with SOD1 familial amyotrophic lateral sclerosis: a phase 1, randomized, first-in-man study // Lancet Neurol. 2013. V. 12, № 5. P. 435–442.
Review
For citations:
Tiguntsev V.V., Ivanova S.A., Serebrov V.Yu., Buhareva M.B. SMALL NONCODING RNA AS PERSPECTIVE BIOMARKERS: BIOGENESIS AND THERAPEUTIC STRATIGIES. Bulletin of Siberian Medicine. 2016;15(2):112-126. (In Russ.) https://doi.org/10.20538/1682-0363-2016-2-112-126
Views:
1473
Email this article 