Advertisement

The New Massive Data: miRnomics and Its Application to Therapeutics

  • Mohammad Ahmed Khan
  • Maryam Mahfooz
  • Ghufrana Abdus Sami
  • Hashim AlSalmi
  • Abdullah E. A. Mathkoor
  • Ghazi A. Damanhauri
  • Mahmood Rasool
  • Mohammad Sarwar Jamal
Chapter

Abstract

Genomic medicine is highly dependent on understanding the biological processes regulating gene expression. In this reference, the discovery of phenomena of RNA interference in 1998 served as turning point for the field of genomic medicine. It was observed that the double stranded RNA (dsRNA) is capable of silencing specific genes in Caenorhabditis elegans [12]. Later, studies on RNA interference have revealed that RNA interference operates in many species and serves in silencing genes. In C. elegans, the inhibitory potential of RNA was induced by introducing endogeneous long dsRNA’s while in mammalian cells, the introduction of small 21 nt RNA’s could induce RNAi. [10].

Keywords

Generation AMOs Lock Nucleic Acid Genomic Medicine miRNA Inhibition miRNA Sponge 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Barbato C, Pezzola S, Caggiano C, Antonelli M, Frisone P, Ciotti MT, Ruberti F (2014) A lentiviral sponge for miR-101 regulates RanBP9 expression and amyloid precursor protein metabolism in hippocampal neurons. Front Cell Neurosci 8:37CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Boutla A, Delidakis C, Tabler M (2003) Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes. Nucleic Acids Res 31:4973–4980CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Boyerinas B, Park SM, Hau A, Murmann AE, Peter ME (2010) The role of let-7 in cell differentiation and cancer. Endocr Relat Cancer 17(1):F19–F36CrossRefPubMedGoogle Scholar
  4. 4.
    Bravo-Egana V, Rosero S, Klein D, Jiang Z, Vargas N, Tsinoremas N et al (2012) Inflammation-mediated regulation of MicroRNA expression in transplanted pancreatic islets. J transplant 2012:723614CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Connelly CM, Deiters A (2014) Identification of inhibitors of microRNA function from small molecule screens. Methods Mol Biol 1095:147–156CrossRefPubMedGoogle Scholar
  6. 6.
    Craig VJ, Cogliatti SB, Imig J, Renner C, Neuenschwander S, Rehrauer H, Schlapbach R, Dirnhofer S, Tzankov A, Müller A (2011) Myc-mediated repression of microRNA-34a promotes high-grade transformation of B-cell lymphoma by dysregulation of FoxP1. Blood 117(23):6227–6236CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Devi GR, Beer TM, Corless CL, Arora V, Weller DL, Iversen PL (2005) In vivo bioavailability and pharmacokinetics of a c-MYC antisense phosphorodiamidate morpholino oligomer, AVI-4126, in solid tumors. Clin Cancer Res 11:3930–3938CrossRefPubMedGoogle Scholar
  8. 8.
    Ebert MS, Neilson JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4(9):721–726CrossRefPubMedGoogle Scholar
  9. 9.
    Ebert MS, Sharp PA (2010) MicroRNA sponges: progress and possibilities. RNA 16(11):2043–2050CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498CrossRefPubMedGoogle Scholar
  11. 11.
    Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9(2):102–114CrossRefPubMedGoogle Scholar
  12. 12.
    Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811CrossRefPubMedGoogle Scholar
  13. 13.
    Grueter CE, van Rooij E, Johnson BA, DeLeon SM, Sutherland LB, Qi X, Gautron L, Elmquist JK, Bassel-Duby R, Olson EN (2012) A cardiac microRNA governs systemic energy homeostasis by regulation of MED13. Cell 149(3):671–683CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Guessous F, Zhang Y, Kofman A, Catania A, Li Y, Schiff D, Purow B, Abounader R (2010) MicroRNA-34a is tumor suppressive in brain tumors and glioma stem cells. Cell Cycle 9(6):1031–1036CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Gumireddy K, Young DD, Xiong X, Hogenesch JB, Huang Q, Deiters A (2008) Small-molecule inhibitors of microrna miR-21 function. Angew Chem Int Ed Engl 47(39):7482–7484CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Henry SP, Geary RS, Yu R, Levin AA (2001) Drug properties of second-generation antisense oligonucleotides: how do they measure up to their predecessors? Curr Opin Investig Drugs 2:1444–1449PubMedGoogle Scholar
  17. 17.
    Janet B, Amir H (2008) Therapy analysis-microRNA; update analysis. Pharmaproject, 29Google Scholar
  18. 18.
    Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309(5740):1577–1581CrossRefPubMedGoogle Scholar
  19. 19.
    Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME, Kauppinen S, Ørum H (2010) Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 327(5962):198–201CrossRefPubMedGoogle Scholar
  20. 20.
    Lennox KA, Behlke MA (2010) A direct comparison of anti-microRNA oligonucleotide potency. Pharm Res 27(9):1788–1799CrossRefPubMedGoogle Scholar
  21. 21.
    Lennox KA, Behlke MA (2011) Chemical modification and design of anti-miRNA oligonucleotides. Gene Ther 18(12):1111–1120CrossRefPubMedGoogle Scholar
  22. 22.
    Li Z, Rana TM (2014) Therapeutic targeting of microRNAs: current status and future challenges. Nat Rev Drug Discov 13(8):622–638CrossRefPubMedGoogle Scholar
  23. 23.
    Liu Y, Cui H, Wang W, Li L, Wang Z, Yang S, Zhang X (2013) Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. Int J Biochem Cell Biol 45(11):2643–2650CrossRefPubMedGoogle Scholar
  24. 24.
    Long J, Wang Y, Wang W, Chang BH, Danesh FR (2011) MicroRNA-29c is a signature microRNA under high glucose conditions that targets Sprouty homolog 1, and its in vivo knockdown prevents progression of diabetic nephropathy. J Biol Chem 286:11837–11848CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Lynn FC, Skewes-Cox P, Kosaka Y, McManus MT, Harfe BD, German MS (2007) MicroRNA expression is required for pancreatic islet cell genesis in the mouse. Diabetes 56:2938–2945CrossRefPubMedGoogle Scholar
  26. 26.
    Ma J, Wu Q, Zhang Y, Li J, Yu Y, Pan Q, Sun F (2014) MicroRNA sponge blocks the tumor-suppressing functions of microRNA-122 in human hepatoma and osteosarcoma cells. Oncol Rep 32(6):2744–2752PubMedGoogle Scholar
  27. 27.
    Mack GS (2007) MicroRNA gets down to business. Nat Biotechnol 25(6):631–638CrossRefPubMedGoogle Scholar
  28. 28.
    Mani S, Goel S, Nesterova M, Martin RM, Grindel JM, Rothenberg ML et al (2003) Clinical studies in patients with solid tumors using a second-generation antisense oligonucleotide (GEM 231) targeted against protein kinase A type I. Ann N Y Acad Sci 1002:252–262CrossRefPubMedGoogle Scholar
  29. 29.
    Melo S, Villanueva A, Moutinho C, Davalos V, Spizzo R, Ivan C, Rossi S, Setien F, Casanovas O, Simo-Riudalbas L, Carmona J, Carrere J, Vidal A, Aytes A, Puertas S, Ropero S, Kalluri R, Croce CM, Calin GA, Esteller M (2011) Small molecule enoxacin is a cancer-specific growth inhibitor that acts by enhancing TAR RNA-binding protein 2-mediated microRNA processing. Proc Natl Acad Sci U S A 108:4394–4399CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Montgomery RL, Hullinger TG, Semus HM, Dickinson BA, Seto AG, Lynch JM, Stack C, Latimer PA, Olson EN, van Rooij E (2011) Therapeutic inhibition of miR-208a improves cardiac function and survival during heart failure. Circulation 124(14):1537–1547CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Ohlsson Teague EM, Van der Hoek KH, Van der Hoek MB, Perry N, Wagaarachchi P, Robertson SA, Print CG, Hull LM (2009) MicroRNA-regulated pathways associated with endometriosis. Mol Endocrinol 23(2):265–275CrossRefPubMedGoogle Scholar
  32. 32.
    Pullen TJ, da Silva Xavier G, Kelsey G, Rutter GA (2011) miR-29a and miR-29b contribute to pancreatic beta-cell-specific silencing of monocarboxylate transporter 1 (Mct1). Mol Cell Biol 31:3182–3194CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Raver-Shapira N, Marciano E, Meiri E, Spector Y, Rosenfeld N, Moskovits N, Bentwich Z, Oren M (2007) Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Mol Cell 26(5):731–743CrossRefPubMedGoogle Scholar
  34. 34.
    Roush S, Slack FJ (2008) The let–7 family of microRNAs. Trends Cell Biol 18:505–516CrossRefPubMedGoogle Scholar
  35. 35.
    Scott GK, Mattie MD, Berger CE, Benz SC, Benz CC (2006) Rapid alteration of microRNA levels by histone deacetylase inhibition. Cancer Res 66:1277–1281CrossRefPubMedGoogle Scholar
  36. 36.
    Sicard F, Gayral M, Lulka H, Buscail L, Cordelier P (2013) Targeting miR-21 for the therapy of pancreatic cancer. Mol Ther 21(5):986–994CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Simonson B, Das S (2015) MicroRNA therapeutics: the next magic bullet? Mini Rev Med Chem 15(6):467–474CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Swayze EE, Siwkowski AM, Wancewicz EV, Migawa MT, Wyrzykiewicz TK, Hung G, Monia BP, Bennett CF (2007) Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals. Nucleic Acids Res 35(2):687–700CrossRefPubMedGoogle Scholar
  39. 39.
    Glaser V (2008) Tapping miRNA-regulated pathways. Genet Eng Biotechnol News 28(5)Google Scholar
  40. 40.
    Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F, Lieberman J, Rigoutsos I, Pandolfi PP (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147(2):344–357CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Ucar A, Gupta SK, Fiedler J, Erikci E, Kardasinski M, Batkai S, Dangwal S, Kumarswamy R, Bang C, Holzmann A, Remke J, Caprio M, Jentzsch C, Engelhardt S, Geisendorf S, Glas C, Hofmann TG, Nessling M, Richter K, Schiffer M, Carrier L, Napp LC, Bauersachs J, Chowdhury K, Thum T (2012) The miRNA-212/132 family regulates both cardiac hypertrophy and cardiomyocyte autophagy. Nat Commun 3:1078CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    van der Ree MH, van der Meer AJ, de Bruijne J, Maan R, van Vliet A, Welzel TM, Zeuzem S, Lawitz EJ, Rodriguez-Torres M, Kupcova V, Wiercinska-Drapalo A, Hodges MR, Janssen HL, Reesink HW (2014) Long-term safety and efficacy of microRNA-targeted therapy in chronic hepatitis C patients. Antivir Res 111:53–59CrossRefPubMedGoogle Scholar
  43. 43.
    van Rooij E, Purcell AL, Levin AA (2012) Developing microRNA therapeutics. Circ Res 110(3):496–507CrossRefPubMedGoogle Scholar
  44. 44.
    van Rooij E, Quiat D, Johnson BA, Sutherland LB, Qi X, Richardson JA, Kelm RJ Jr, Olson EN (2009) A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Dev Cell 17(5):662–673CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, Rigoutsos I, Nelson PT (2008) The expression of microRNA miR-107 decreases early in Alzheimer’s disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci 28(5):1213–1223CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Wang Z (2011) The concept of multiple-target anti-miRNA antisense oligonucleotide technology. Methods Mol Biol 676:51–57CrossRefPubMedGoogle Scholar
  47. 47.
    Weiler J, Hunziker J, Hall J (2006) Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease? Gene Ther 13(6):496–502CrossRefPubMedGoogle Scholar
  48. 48.
    Yan LX, Wu QN, Zhang Y, Li YY, Liao DZ, Hou JH, Fu J, Zeng MS, Yun JP, Wu QL, Zeng YX, Shao JY (2011) Knockdown of miR-21 in human breast cancer cell lines inhibits proliferation, in vitro migration and in vivo tumor growth. Breast Cancer Res 13(1):R2CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Zhang C (2008) MicroRNomics: a newly emerging approach for disease biology. Physiol Genomics 33(2):139–147CrossRefPubMedGoogle Scholar
  50. 50.
    Zhang S, Chen L, Jung EJ, Calin GA (2010) Targeting microRNAs with small molecules: from dream to reality. Clin Pharmacol Ther 87:754–758CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer India 2016

Authors and Affiliations

  • Mohammad Ahmed Khan
    • 1
  • Maryam Mahfooz
    • 2
  • Ghufrana Abdus Sami
    • 3
  • Hashim AlSalmi
    • 4
  • Abdullah E. A. Mathkoor
    • 3
  • Ghazi A. Damanhauri
    • 4
  • Mahmood Rasool
    • 5
  • Mohammad Sarwar Jamal
    • 4
  1. 1.National Institute of BiologicalsNoidaIndia
  2. 2.Department of Computer ScienceJamia Millia IslamiaNew DelhiIndia
  3. 3.Department of BiotechnologyJamia Millia IslamiaNew DelhiIndia
  4. 4.King Fahd Medical Research Center (KFMRC)King Abdulaziz UniversityJeddahSaudi Arabia
  5. 5.Center of Excellence in Genomic Medicine Research (CEGMR)King Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations