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Gapmers pp 3–19Cite as

Invention and Early History of Gapmers

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2176))

Abstract

Gapmers are antisense oligonucleotides composed of a central DNA segment flanked by nucleotides of modified chemistry. Hybridizing with transcripts by sequence complementarity, gapmers recruit ribonuclease H and induce target RNA degradation. Since its concept first emerged in the 1980s, much work has gone into developing gapmers for use in basic research and therapy. These include improvements in gapmer chemistry, delivery, and therapeutic safety. Gapmers have also successfully entered clinical trials for various genetic disorders, with two already approved by the U.S. Food and Drug Administration for the treatment of familial hypercholesterolemia and transthyretin amyloidosis-associated polyneuropathy. Here, we review the events surrounding the early development of gapmers, from conception to their maturity, and briefly conclude with perspectives on their use in therapy.

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References

  1. Prelich G (2012) Gene overexpression: uses, mechanisms, and interpretation. Genetics 190:841–854. https://doi.org/10.1534/genetics.111.136911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Bolognesi B, Lehner B (2018) Protein overexpression: reaching the limit. Elife. https://doi.org/10.7554/eLife.39804

  3. Aguzzi A, O’Connor T (2010) Protein aggregation diseases: pathogenicity and therapeutic perspectives. Nat Rev Drug Discov 9:237–248. https://doi.org/10.1038/nrd3050

    Article  CAS  PubMed  Google Scholar 

  4. Jackson M, Marks L, May GHW, Wilson JB (2018) The genetic basis of disease. Essays Biochem 62:643–723. https://doi.org/10.1042/EBC20170053

    Article  PubMed  PubMed Central  Google Scholar 

  5. Wang LH, Tawil R (2016) Facioscapulohumeral dystrophy. Curr Neurol Neurosci Rep 16:66. https://doi.org/10.1007/s11910-016-0667-0

    Article  CAS  PubMed  Google Scholar 

  6. Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current Progress and future prospects. Chem Biol 19:60–71. https://doi.org/10.1016/j.chembiol.2011.12.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Stephenson ML, Zamecnik PC (1978) Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci U S A 75:285–288. https://doi.org/10.1073/pnas.75.1.285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Zamecnik PC, Stephenson ML (1978) Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc Natl Acad Sci U S A 75:280–284. https://doi.org/10.1073/pnas.75.1.280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Bennett CF, Swayze EE (2010) RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu Rev Pharmacol Toxicol 50:259–293. https://doi.org/10.1146/annurev.pharmtox.010909.105654

    Article  CAS  PubMed  Google Scholar 

  10. Lim KRQ, Yokota T (2018) Invention and early history of exon skipping and splice modulation. In: Yokota T, Maruyama R (eds) Exon Skipp. Incl. Ther. Methods Protoc. Springer, New York, pp 3–30

    Chapter  Google Scholar 

  11. Hair P, Cameron F, McKeage K (2013) Mipomersen sodium: first global approval. Drugs 73:487–493. https://doi.org/10.1007/s40265-013-0042-2

    Article  CAS  PubMed  Google Scholar 

  12. Keam SJ (2018) Inotersen: first global approval. Drugs 78:1371–1376. https://doi.org/10.1007/s40265-018-0968-5

    Article  CAS  PubMed  Google Scholar 

  13. Shen X, Corey DR (2018) Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucleic Acids Res 46:1584–1600. https://doi.org/10.1093/nar/gkx1239

    Article  CAS  PubMed  Google Scholar 

  14. Cerritelli SM, Crouch RJ (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS J 276:1494–1505. https://doi.org/10.1111/j.1742-4658.2009.06908.x

    Article  CAS  PubMed  Google Scholar 

  15. Moelling K, Broecker F, Russo G, Sunagawa S (2017) RNase H as gene modifier, driver of evolution and antiviral defense. Front Microbiol 8:1745. https://doi.org/10.3389/fmicb.2017.01745

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kojima K, Baba M, Tsukiashi M et al (2018) RNA/DNA structures recognized by RNase H2. Brief Funct Genomics 18(3):169–173. https://doi.org/10.1093/bfgp/ely024

    Article  CAS  PubMed  Google Scholar 

  17. Stein H, Hausen P (1969) Enzyme from calf thymus degrading the RNA moiety of DNA-RNA hybrids: effect on DNA-dependent RNA polymerase. Science 166:393–395

    Article  CAS  Google Scholar 

  18. Busen W, Hausen P (1975) Distinct Ribonuclease H activities in calf thymus. Eur J Biochem 52:179–190. https://doi.org/10.1111/j.1432-1033.1975.tb03985.x

    Article  CAS  PubMed  Google Scholar 

  19. Cerritelli SM, Frolova EG, Feng C et al (2003) Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Mol Cell 11:807–815

    Article  CAS  Google Scholar 

  20. Hiller B, Achleitner M, Glage S et al (2012) Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity. J Exp Med 209:1419–1426. https://doi.org/10.1084/jem.20120876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Fazzi E, Cattalini M, Orcesi S et al (2013) Aicardi–Goutieres syndrome, a rare neurological disease in children: a new autoimmune disorder? Autoimmun Rev 12:506–509. https://doi.org/10.1016/j.autrev.2012.08.012

    Article  CAS  PubMed  Google Scholar 

  22. Frank P, Braunshofer-Reiter C, Wintersberger U et al (1998) Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII. Proc Natl Acad Sci 95:12872–12877. https://doi.org/10.1073/pnas.95.22.12872

    Article  CAS  PubMed  Google Scholar 

  23. Eder PS, Walder RY, Walder JA (1993) Substrate specificity of human RNase H1 and its role in excision repair of ribose residues misincorporated in DNA. Biochimie 75:123–126

    Article  CAS  Google Scholar 

  24. Reijns MAM, Bubeck D, Gibson LCD et al (2011) The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease. J Biol Chem 286:10530–10539. https://doi.org/10.1074/jbc.M110.177394

    Article  CAS  PubMed  Google Scholar 

  25. Zamaratski E, Pradeepkumar PI, Chattopadhyaya J (2001) A critical survey of the structure-function of the antisense oligo/RNA heteroduplex as substrate for RNase H. J Biochem Biophys Methods 48:189–208

    Article  CAS  Google Scholar 

  26. Herdewijn P (1999) Conformationally restricted carbohydrate-modified nucleic acids and antisense technology. Biochim Biophys Acta 1489:167–179

    Article  CAS  Google Scholar 

  27. Paterson BM, Roberts BE, Kuff EL (1977) Structural gene identification and mapping by DNA-mRNA hybrid-arrested cell-free translation. Proc Natl Acad Sci U S A 74:4370–4374. https://doi.org/10.1073/pnas.74.10.4370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Donis-Keller H (1979) Site specific enzymatic cleavage of RNA. Nucleic Acids Res 7:179–192. https://doi.org/10.1093/nar/7.1.179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Minshull J, Hunt T (1986) The use of single-stranded DNA and RNase H to promote quantitative “hybrid arrest of translation” of mRNA/DNA hybrids in reticulocyte lysate cell-free translations. Nucleic Acids Res 14:6433–6451. https://doi.org/10.1093/nar/14.16.6433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Walder RY, Walder JA (1988) Role of RNase H in hybrid-arrested translation by antisense oligonucleotides. Proc Natl Acad Sci U S A 85:5011–5015. https://doi.org/10.1073/pnas.85.14.5011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Blake KR, Murakami A, Miller PS (1985) Inhibition of rabbit globin mRNA translation by sequence-specific oligodeoxyribonucleotides. Biochemistry 24:6132–6138

    Article  CAS  Google Scholar 

  32. Cazenave C, Loreau N, Toulmé JJ, Hélène C (1986) Anti-messenger oligodeoxynucleotides: specific inhibition of rabbit beta-globin synthesis in wheat germ extracts and Xenopus oocytes. Biochimie 68:1063–1069

    Article  CAS  Google Scholar 

  33. Cazenave C, Loreau N, Thuong NT et al (1987) Enzymatic amplification of translation inhibition of rabbit β-globin mRNA mediated by anti-messenger oligodeoxynucleotides covalently linked to intercalating agents. Nucleic Acids Res 15:4717–4736. https://doi.org/10.1093/nar/15.12.4717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lawson TG, Ray BK, Dodds JT et al (1986) Influence of 5′ proximal secondary structure on the translational efficiency of eukaryotic mRNAs and on their interaction with initiation factors. J Biol Chem 261:13979–13989

    CAS  PubMed  Google Scholar 

  35. Kawasaki ES (1985) Quantitative hybridization-arrest of mRNA in Xenopus oocytes using single-stranded complementary DNA or oligonucleotide probes. Nucleic Acids Res 13:4991–5004. https://doi.org/10.1093/nar/13.13.4991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dash P, Lotan I, Knapp M et al (1987) Selective elimination of mRNAs in vivo: complementary oligodeoxynucleotides promote RNA degradation by an RNase H-like activity. Proc Natl Acad Sci U S A 84:7896–7900. https://doi.org/10.1073/pnas.84.22.7896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Zamecnik PC, Goodchild J, Taguchi Y, Sarin PS (1986) Inhibition of replication and expression of human T-cell lymphotropic virus type III in cultured cells by exogenous synthetic oligonucleotides complementary to viral RNA. Proc Natl Acad Sci 83:4143–4146. https://doi.org/10.1073/pnas.83.12.4143

    Article  CAS  PubMed  Google Scholar 

  38. Smith CC, Aurelian L, Reddy MP et al (1986) Antiviral effect of an oligo(nucleoside methylphosphonate) complementary to the splice junction of herpes simplex virus type 1 immediate early pre-mRNAs 4 and 5. Proc Natl Acad Sci 83:2787–2791. https://doi.org/10.1073/pnas.83.9.2787

    Article  CAS  PubMed  Google Scholar 

  39. Gupta KC (1987) Antisense oligodeoxynucleotides provide insight into mechanism of translation initiation of two Sendai virus mRNAs. J Biol Chem 262:7492–7496

    CAS  PubMed  Google Scholar 

  40. Cornelissen AWCA, Verspieren MP, Toulmé J-J et al (1986) The common 5′ terminal sequence on trypanosome mRNAs: a target for anti-messenger oligodeoxynucleotides. Nucleic Acids Res 14:5605–5614. https://doi.org/10.1093/nar/14.14.5605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Walder J, Eder P, Engman D et al (1986) The 35-nucleotide spliced leader sequence is common to all trypanosome messenger RNA’s. Science 233:569–571. https://doi.org/10.1126/science.3523758

    Article  CAS  PubMed  Google Scholar 

  42. Verspieren P, Cornelissen AW, Thuong NT et al (1987) An acridine-linked oligodeoxynucleotide targeted to the common 5′ end of trypanosome mRNAs kills cultured parasites. Gene 61:307–315

    Article  CAS  Google Scholar 

  43. Rebagliati MR, Melton DA (1987) Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity. Cell 48:599–605

    Article  CAS  Google Scholar 

  44. Wickstrom E (1986) Oligodeoxynucleotide stability in subcellular extracts and culture media. J Biochem Biophys Methods 13:97–102. https://doi.org/10.1016/0165-022X(86)90021-7

    Article  CAS  PubMed  Google Scholar 

  45. Oberemok V, Laikova K, Repetskaya A et al (2018) A half-century history of applications of antisense oligonucleotides in medicine, agriculture and forestry: we should continue the journey. Molecules 23:1302. https://doi.org/10.3390/molecules23061302

    Article  CAS  PubMed Central  Google Scholar 

  46. Khvorova A, Watts JK (2017) The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 35:238–248. https://doi.org/10.1038/nbt.3765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Lundin KE, Gissberg O, Smith CIE (2015) Oligonucleotide therapies: the past and the present. Hum Gene Ther 26:475–485. https://doi.org/10.1089/hum.2015.070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Miller PS, Yano J, Yano E et al (1979) Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry 18:5134–5143

    Article  CAS  Google Scholar 

  49. Eckstein F (1966) Nucleoside Phosphorothioates. J Am Chem Soc 88:4292–4294. https://doi.org/10.1021/ja00970a054

    Article  CAS  Google Scholar 

  50. Bobst AM, Cerutti PA, Rottman F (1969) Structure of poly(2’-O-methyladenylic acid) at acidic and neutral pH. J Am Chem Soc 91:1246–1248. https://doi.org/10.1021/ja01033a054

    Article  CAS  Google Scholar 

  51. Blake KR, Murakami A, Spitz SA et al (1985) Hybridization arrest of globin synthesis in rabbit reticulocyte lysates and cells by oligodeoxyribonucleoside methylphosphonates. Biochemistry 24:6139–6145

    Article  CAS  Google Scholar 

  52. Maher LJ, Dolnick BJ (1988) Comparative hybrid arrest by tandem antisense oligodeoxyribonucleotides or oligodeoxyribonucleoside methylpbosphonates in a cell-free system. Nucleic Acids Res 16:3341–3358. https://doi.org/10.1093/nar/16.8.3341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Akhtar S, Kole R, Juliano RL (1991) Stability of antisense DNA oligodeoxynucleotide analogs in cellular extracts and sera. Life Sci 49:1793–1801

    Article  CAS  Google Scholar 

  54. Inoue H, Hayase Y, Iwai S, Ohtsuka E (1987) Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H. FEBS Lett 215:327–330

    Article  CAS  Google Scholar 

  55. Campbell JM, Bacon TA, Wickstrom E (1990) Oligodeoxynucleoside phosphorothioate stability in subcellular extracts, culture media, sera and cerebrospinal fluid. J Biochem Biophys Methods 20:259–267. https://doi.org/10.1016/0165-022X(90)90084-P

    Article  CAS  PubMed  Google Scholar 

  56. Reed JC, Stein C, Subasinghe C et al (1990) Antisense-mediated inhibition of BCL2 protooncogene expression and leukemic cell growth and survival: comparisons of phosphodiester and phosphorothioate oligodeoxynucleotides. Cancer Res 50:6565–6570

    CAS  PubMed  Google Scholar 

  57. Baker C, Holland D, Edge M, Colman A (1990) Effects of oligo sequence and chemistry on the efficiency of oligodeoxyribonucleotide-mediated mRNA cleavage. Nucleic Acids Res 18:3537–3543. https://doi.org/10.1093/nar/18.12.3537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Walder J, Walder R (1995) Nucleic acid hybridization and amplification method for detection of specific sequences in which a complementary labeled nucleic acid probe is cleaved. US Patent US5403711A, 4 April 1995

    Google Scholar 

  59. Quartin RS, Brakel CL, Wetmur G (1989) Number and distribution of methyiphosphonate linkages in oligodeoxynucleotides affect exo- and endonuclease sensitivity and ability to form RNase H substrates. Nucleic Acids Res 17:7253–7262. https://doi.org/10.1093/nar/17.18.7253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Furdon PJ, Dominski Z, Kole R (1989) RNase H cleavage of RNA hybridized to oligonucleotides containing methylphosphonate, phosphorothioate and phosphodiester bonds. Nucleic Acids Res 17:9193–9204. https://doi.org/10.1093/nar/17.22.9193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Hayase Y, Inoue H, Ohtsuka E (1990) Secondary structure in formylmethionine tRNA influences the site-directed cleavage of ribonuclease H using chimeric 2′-O-methyl oligodeoxyribonucleotides. Biochemistry 29:8793–8797

    Article  CAS  Google Scholar 

  62. Agrawal S, Mayrand SH, Zamecnik PC, Pederson T (1990) Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides. Proc Natl Acad Sci U S A 87:1401–1405. https://doi.org/10.1073/pnas.87.4.1401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Dagle JM, Walder JA, Weeks DL (1990) Targeted degradation of mRNA in Xenopus oocytes and embryos directed by modified oligonucleotides: studies of An2 and cyclin in embryogenesis. Nucleic Acids Res 18:4751–4757. https://doi.org/10.1093/nar/18.16.4751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Potts JD, Dagle JM, Walder JA et al (1991) Epithelial-mesenchymal transformation of embryonic cardiac endothelial cells is inhibited by a modified antisense oligodeoxynucleotide to transforming growth factor beta 3. Proc Natl Acad Sci 88:1516–1520. https://doi.org/10.1073/pnas.88.4.1516

    Article  CAS  PubMed  Google Scholar 

  65. Heikkila R, Schwab G, Wickstrom E et al (1987) A c-myc antisense oligodeoxynucleotide inhibits entry into S phase but not progress from G0 to G1. Nature 328:445–449. https://doi.org/10.1038/328445a0

    Article  CAS  PubMed  Google Scholar 

  66. Loke SL, Stein C, Zhang X et al (1988) Delivery of c-myc antisense phosphorothioate oligodeoxynucleotides to hematopoietic cells in culture by liposome fusion: specific reduction in c-myc protein expression correlates with inhibition of cell growth and DNA synthesis. Curr Top Microbiol Immunol 141:282–289

    CAS  PubMed  Google Scholar 

  67. Tidd DM, Warenius HM (1989) Partial protection of oncogene, anti-sense oligodeoxynucleotides against serum nuclease degradation using terminal methylphosphonate groups. Br J Cancer 60:343–350. https://doi.org/10.1038/bjc.1989.283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Tidd DM, Hawley P, Warenius HM, Gibson I (1988) Evaluation of N-ras oncogene anti-sense, sense and nonsense sequence methylphosphonate oligonucleotide analogues. Anticancer Drug Des 3:117–127

    CAS  PubMed  Google Scholar 

  69. Giles RV, Tidd DM (1992) Enhanced RNase H activity with methylphosphonodiester/phosphodiester chimeric antisense oligodeoxynucleotides. Anticancer Drug Des 7:37–48

    CAS  PubMed  Google Scholar 

  70. Monia BP, Lesnik EA, Gonzalez C et al (1993) Evaluation of 2′-modified oligonucleotides containing 2′-deoxy gaps as antisense inhibitors of gene expression. J Biol Chem 268:14514–14522

    CAS  PubMed  Google Scholar 

  71. Giles RV, Tidd DM (1992) Increased specificity for antisense oligodeoxynucleotide targeting of RNA cleavage by RNase H using chimeric methylphosphonodiester/phosphodiester structures. Nucleic Acids Res 20:763–770. https://doi.org/10.1093/nar/20.4.763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Crooke ST, Lemonidis KM, Neilson L et al (1995) Kinetic characteristics of Escherichia coli RNase H1: cleavage of various antisense oligonucleotide-RNA duplexes. Biochem J 312:599–608. https://doi.org/10.1042/bj3120599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 8:1–7

    Article  CAS  Google Scholar 

  74. Obika S, Nanbu D, Hari Y et al (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O,4′-C-methyleneribonucleosides. Tetrahedron Lett 39:5401–5404. https://doi.org/10.1016/S0040-4039(98)01084-3

    Article  CAS  Google Scholar 

  75. Koshkin AA, Singh SK, Nielsen P et al (1998) LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54:3607–3630. https://doi.org/10.1016/S0040-4020(98)00094-5

    Article  CAS  Google Scholar 

  76. Wahlestedt C, Salmi P, Good L et al (2000) Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc Natl Acad Sci U S A 97:5633–5638. https://doi.org/10.1073/pnas.97.10.5633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Kasuya T, Hori S, Watanabe A et al (2016) Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides. Sci Rep 6:30377. https://doi.org/10.1038/srep30377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Swayze EE, Siwkowski AM, Wancewicz EV et al (2007) Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals. Nucleic Acids Res 35:687–700. https://doi.org/10.1093/nar/gkl1071

    Article  CAS  PubMed  Google Scholar 

  79. Kakiuchi-Kiyota S, Koza-Taylor PH, Mantena SR et al (2014) Comparison of hepatic transcription profiles of locked ribonucleic acid antisense oligonucleotides: evidence of distinct pathways contributing to non-target mediated toxicity in mice. Toxicol Sci 138:234–248. https://doi.org/10.1093/toxsci/kft278

    Article  CAS  PubMed  Google Scholar 

  80. Burel SA, Hart CE, Cauntay P et al (2016) Hepatotoxicity of high affinity gapmer antisense oligonucleotides is mediated by RNase H1 dependent promiscuous reduction of very long pre-mRNA transcripts. Nucleic Acids Res 44:2093–2109. https://doi.org/10.1093/nar/gkv1210

    Article  CAS  PubMed  Google Scholar 

  81. Martin P (1995) Ein neuer Zugang zu 2’-O-Alkylribonucleosiden und Eigenschaften deren Oligonucleotide. Helv Chim Acta 78:486–504. https://doi.org/10.1002/hlca.19950780219

    Article  CAS  Google Scholar 

  82. Garay M, Gaarde W, Monia BP et al (2000) Inhibition of hypoxia/reoxygenation-induced apoptosis by an antisense oligonucleotide targeted to JNK1 in human kidney cells. Biochem Pharmacol 59:1033–1043. https://doi.org/10.1016/S0006-2952(99)00412-8

    Article  CAS  PubMed  Google Scholar 

  83. Levesque L, Dean NM, Sasmor H, Crooke ST (1997) Antisense oligonucleotides targeting human protein kinase C-alpha inhibit phorbol ester-induced reduction of bradykinin-evoked calcium mobilization in A549 cells. Mol Pharmacol 51:209–216

    Article  CAS  Google Scholar 

  84. Moreno PMD, Pêgo AP (2014) Therapeutic antisense oligonucleotides against cancer: hurdling to the clinic. Front Chem 2:87. https://doi.org/10.3389/fchem.2014.00087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Jauvin D, Chrétien J, Pandey SK et al (2017) Targeting DMPK with antisense oligonucleotide improves muscle strength in Myotonic dystrophy type 1 mice. Mol Ther Nucleic Acids 7:465–474. https://doi.org/10.1016/j.omtn.2017.05.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Yamamoto T, Wada F, Harada-Shiba M (2016) Development of antisense drugs for dyslipidemia. J Atheroscler Thromb 23:1011–1025. https://doi.org/10.5551/jat.RV16001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Lucas T, Bonauer A, Dimmeler S (2018) RNA therapeutics in cardiovascular disease. Circ Res 123:205–220. https://doi.org/10.1161/CIRCRESAHA.117.311311

    Article  CAS  PubMed  Google Scholar 

  88. Amodio N, Stamato MA, Juli G et al (2018) Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity. Leukemia 32:1948–1957. https://doi.org/10.1038/s41375-018-0067-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Salehi M, Sharifi M, Bagheri M (2019) Knockdown of long noncoding RNA Plasmacytoma variant translocation 1 with antisense locked nucleic acid GapmeRs exerts tumor-suppressive functions in human acute Erythroleukemia cells through Downregulation of C-MYC expression. Cancer Biother Radiopharm 34(6):371–379. https://doi.org/10.1089/cbr.2018.2510

    Article  CAS  PubMed  Google Scholar 

  90. Mirtschink P, Bischof C, Pham M-D et al (2019) Inhibition of the HIF1α-induced Cardiospecific HERNA1 eRNA protects from heart disease. Circulation 139(24):2778–2792. https://doi.org/10.1161/CIRCULATIONAHA.118.036769

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Yu RZ, Kim T-W, Hong A et al (2006) Cross-species pharmacokinetic comparison from mouse to man of a second-generation antisense oligonucleotide, ISIS 301012, targeting human Apolipoprotein B-100. Drug Metab Dispos 35:460–468. https://doi.org/10.1124/dmd.106.012401

    Article  CAS  PubMed  Google Scholar 

  92. Seth PP, Siwkowski A, Allerson CR et al (2008) Design, synthesis and evaluation of constrained methoxyethyl (cMOE) and constrained ethyl (cEt) nucleoside analogs. Nucleic Acids Symp Ser (Oxf) 52:553–554. https://doi.org/10.1093/nass/nrn280

    Article  CAS  Google Scholar 

  93. Shen W, De Hoyos CL, Migawa MT et al (2019) Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index. Nat Biotechnol 37(6):640–650. https://doi.org/10.1038/s41587-019-0106-2

    Article  CAS  PubMed  Google Scholar 

  94. Hagedorn PH, Yakimov V, Ottosen S et al (2013) Hepatotoxic potential of therapeutic oligonucleotides can be predicted from their sequence and modification pattern. Nucleic Acid Ther 23:302–310. https://doi.org/10.1089/nat.2013.0436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Burdick AD, Sciabola S, Mantena SR et al (2014) Sequence motifs associated with hepatotoxicity of locked nucleic acid—modified antisense oligonucleotides. Nucleic Acids Res 42:4882–4891. https://doi.org/10.1093/nar/gku142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Kasuya T, Kugimiya A (2018) Role of computationally evaluated target specificity in the hepatotoxicity of Gapmer antisense oligonucleotides. Nucleic Acid Ther 28:312–317. https://doi.org/10.1089/nat.2018.0724

    Article  CAS  PubMed  Google Scholar 

  97. Uppuladinne MVN, Sonavane UB, Deka RC, Joshi RR (2019) Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations. J Biomol Struct Dyn 37:2823–2836. https://doi.org/10.1080/07391102.2018.1498390

    Article  CAS  PubMed  Google Scholar 

  98. Fazil MHUT, Ong ST, Chalasani MLS et al (2016) GapmeR cellular internalization by macropinocytosis induces sequence-specific gene silencing in human primary T-cells. Sci Rep 6:37721. https://doi.org/10.1038/srep37721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hvam ML, Cai Y, Dagnæs-Hansen F et al (2017) Fatty acid-modified Gapmer antisense oligonucleotide and serum albumin constructs for pharmacokinetic modulation. Mol Ther 25:1710–1717. https://doi.org/10.1016/j.ymthe.2017.05.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Crooke ST, Wang S, Vickers TA et al (2017) Cellular uptake and trafficking of antisense oligonucleotides. Nat Biotechnol 35:230–237. https://doi.org/10.1038/nbt.3779

    Article  CAS  PubMed  Google Scholar 

  101. Liang X-H, Sun H, Nichols JG, Crooke ST (2017) RNase H1-dependent antisense oligonucleotides are robustly active in directing RNA cleavage in both the cytoplasm and the nucleus. Mol Ther 25:2075–2092. https://doi.org/10.1016/j.ymthe.2017.06.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Cheng X, Liu Q, Li H et al (2017) Lipid nanoparticles loaded with an antisense oligonucleotide Gapmer against Bcl-2 for treatment of lung cancer. Pharm Res 34:310–320

    Article  CAS  Google Scholar 

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Correspondence to Toshifumi Yokota .

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Lim, K.R.Q., Yokota, T. (2020). Invention and Early History of Gapmers. In: Yokota, T., Maruyama, R. (eds) Gapmers. Methods in Molecular Biology, vol 2176. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0771-8_1

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  • DOI: https://doi.org/10.1007/978-1-0716-0771-8_1

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