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Long Noncoding RNAs as Therapeutic Targets

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Long Noncoding RNA

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1363))

Abstract

Long noncoding RNAs (lncRNAs) have emerged as critical regulators of cellular functions including maintenance of cellular homeostasis as well as the onset and progression of disease. LncRNAs often exhibit cell-, tissue-, and disease-specific expression patterns, making them desirable therapeutic targets. LncRNAs are commonly targeted using oligonucleotide therapeutics, and advances in oligonucleotide chemistry including C2 ribose sugar modifications such as 2′-fluoro, 2′-O-methyl, and 2-O-methoxyethyl modifications; 2′4′-constrained nucleotides such as locked nucleic acids and constrained 2′-O-ethyl (cEt) nucleotides; and phosphorothioate bonds have dramatically improved efficacy of oligonucleotide therapies. Novel delivery platforms such as viral vectors and nanoparticles have also improved pharmacokinetic properties of oligonucleotides targeting lncRNAs. Accumulating pre-clinical studies have utilized these strategies to therapeutically target lncRNAs and alter progression of many different disease states including Snhg12 and Chast in cardiovascular disease, Mirt2 and HOTTIP in sepsis and autoimmune disease, and Malat1 and HOXB-AS3 in cancer. Emerging oligonucleotide conjugation methods including the use of peptide nucleic acids hold promise to facilitate targeting to specific tissue types. Here, we review recent advances in lncRNA therapeutics and provide examples of how lncRNAs have been successfully targeted in pre-clinical models of disease. Finally, we detail remaining challenges facing the lncRNA field and how advances in delivery platforms and oligonucleotide chemistry might help overcome these barriers to catalyze the translation of pre-clinical studies to successful pharmaceutical development.

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References

  1. Pierce JB, Feinberg MW (2009) Long noncoding RNAs in atherosclerosis and vascular injury: pathobiology, biomarkers, and targets for therapy. Arterioscler Thromb Vasc Biol 40:2002–2017

    Article  Google Scholar 

  2. Lu D, Thum T (2019) RNA-based diagnostic and therapeutic strategies for cardiovascular disease. Nat Rev Cardiol 16(11):661–674

    Article  PubMed  Google Scholar 

  3. Wu G-C, Pan H-F, Leng R-X et al (2015) Emerging role of long noncoding RNAs in autoimmune diseases. Autoimmun Rev 14(9):798–805

    Article  CAS  PubMed  Google Scholar 

  4. Arun G, Diermeier SD, Spector DL (2018) Therapeutic targeting of long non-coding RNAs in cancer. Trends Mol Med 24(3):257–277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. van Haasteren J, Li J, Scheideler OJ, Murthy N, Schaffer DV (2020) The delivery challenge: fulfilling the promise of therapeutic genome editing. Nat Biotechnol:1–11

    Google Scholar 

  6. Wold SMW, Toth K (2013) Adenovirus vectors for gene therapy, vaccination and cancer gene therapy. Curr Gene Ther 13(6):421–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Shaw AR, Suzuki M (2019) Immunology of adenoviral vectors in cancer therapy. Mol Ther Methods Clin Dev 15:418–429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kotterman MA, Schaffer DV (2014) Engineering adeno-associated viruses for clinical gene therapy. Nat Rev Genet 15(7):445–451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mendell JR, Al-Zaidy S, Shell R et al (2017) Single-dose gene-replacement therapy for spinal muscular atrophy. N Engl J Med 377(18):1713–1722

    Article  CAS  PubMed  Google Scholar 

  10. Ferreira V, Twisk J, Kwikkers K et al (2014) Immune responses to intramuscular administration of alipogene tiparvovec (AAV1-LPLS447X) in a phase II clinical trial of lipoprotein lipase deficiency gene therapy. Hum Gene Ther 25(3):180–188

    Article  CAS  PubMed  Google Scholar 

  11. Calcedo R, Vandenberghe LH, Gao G, Lin J, Wilson JM (2009) Worldwide epidemiology of neutralizing antibodies to adeno-associated viruses. J Infect Dis 199(3):381–390

    Article  PubMed  Google Scholar 

  12. Tse LV, Klinc KA, Madigan VJ et al (2017) Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion. Proc Natl Acad Sci 114(24):E4812–E4821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Maheshri N, Koerber JT, Kaspar BK, Schaffer DV (2006) Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat Biotechnol 24(2):198–204

    Article  CAS  PubMed  Google Scholar 

  14. Milone MC, O’Doherty U (2018) Clinical use of lentiviral vectors. Leukemia 32(7):1529–1541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Neelapu SS, Locke FL, Bartlett NL et al (2017) Axicabtagene ciloleucel CAR T-cell therapy in refractory large B-cell lymphoma. N Engl J Med 377(26):2531–2544

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Waehler R, Russell SJ, Curiel DT (2007) Engineering targeted viral vectors for gene therapy. Nat Rev Genet 8(8):573–587

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Mallick S, Choi JS (2014) Liposomes: versatile and biocompatible nanovesicles for efficient biomolecules delivery. J Nanosci Nanotechnol 14(1):755–765

    Article  CAS  PubMed  Google Scholar 

  18. Antimisiaris S, Mourtas S, Papadia K (2017) Targeted si-RNA with liposomes and exosomes (extracellular vesicles): how to unlock the potential. Int J Pharm 525(2):293–312

    Article  CAS  PubMed  Google Scholar 

  19. Li S-D, Huang L (2010) Stealth nanoparticles: high density but sheddable PEG is a key for tumor targeting. J Control Release 145(3):178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Xia Y, Tian J, Chen X (2016) Effect of surface properties on liposomal siRNA delivery. Biomaterials 79:56–68

    Article  CAS  PubMed  Google Scholar 

  21. Wang Y, Miao L, Satterlee A, Huang L (2015) Delivery of oligonucleotides with lipid nanoparticles. Adv Drug Deliv Rev 87:68–80

    Article  PubMed  PubMed Central  Google Scholar 

  22. Kapadia CH, Melamed JR, Day ES (2018) Spherical nucleic acid nanoparticles: therapeutic potential. BioDrugs 32(4):297–309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Gong N, Teng X, Li J, Liang X-J (2018) Antisense oligonucleotide-conjugated nanostructure-targeting lncRNA MALAT1 inhibits cancer metastasis. ACS Appl Mater Interfaces 11(1):37–42

    Article  PubMed  Google Scholar 

  24. Haemmig S, Yang D, Sun X et al (2020) Long noncoding RNA SNHG12 integrates a DNA-PK-mediated DNA damage response and vascular senescence. Sci Transl Med 12:eaaw1868

    Article  CAS  PubMed  Google Scholar 

  25. Dowdy SF (2017) Overcoming cellular barriers for RNA therapeutics. Nat Biotechnol 35(3):222

    Article  CAS  PubMed  Google Scholar 

  26. Ray KK, Landmesser U, Leiter LA et al (2017) Inclisiran in patients at high cardiovascular risk with elevated LDL cholesterol. N Engl J Med 376(15):1430–1440

    Article  CAS  PubMed  Google Scholar 

  27. Ray KK, Stoekenbroek RM, Kallend D et al (2019) Effect of 1 or 2 doses of inclisiran on low-density lipoprotein cholesterol levels: one-year follow-up of the ORION-1 randomized clinical trial. JAMA Cardiol 4(11):1067–1075

    Article  PubMed  PubMed Central  Google Scholar 

  28. Graham MJ, Lee RG, Brandt TA et al (2017) Cardiovascular and metabolic effects of ANGPTL3 antisense oligonucleotides. N Engl J Med 377(3):222–232

    Article  CAS  PubMed  Google Scholar 

  29. 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(2):687–700

    Article  CAS  PubMed  Google Scholar 

  30. 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(8):4882–4891

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. 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

    Article  CAS  PubMed  Google Scholar 

  32. Migawa MT, Shen W, Wan WB et al (2019) Site-specific replacement of phosphorothioate with alkyl phosphonate linkages enhances the therapeutic profile of gapmer ASOs by modulating interactions with cellular proteins. Nucleic Acids Res 47(11):5465–5479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Bianchini D, Omlin A, Pezaro C et al (2013) First-in-human phase I study of EZN-4176, a locked nucleic acid antisense oligonucleotide to exon 4 of the androgen receptor mRNA in patients with castration-resistant prostate cancer. Br J Cancer 109(10):2579–2586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Iannitti T, Cesar Morales-Medina J, Palmieri B (2014) Phosphorothioate oligonucleotides: effectiveness and toxicity. Curr Drug Targets 15(7):663–673

    Article  CAS  PubMed  Google Scholar 

  35. Seth PP, Vasquez G, Allerson CA et al (2010) Synthesis and biophysical evaluation of 2′, 4′-constrained 2′ O-methoxyethyl and 2′, 4′-constrained 2′ O-ethyl nucleic acid analogues. J Org Chem 75(5):1569–1581

    Article  CAS  PubMed  Google Scholar 

  36. Seth PP, Siwkowski A, Allerson CR et al (2009) Short antisense oligonucleotides with novel 2′− 4′ conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem 52(1):10–13

    Article  CAS  PubMed  Google Scholar 

  37. Nielsen PE, Egholm M (1999) An introduction to peptide nucleic acid. Curr Issues Mol Biol 1(1–2):89–104

    CAS  PubMed  Google Scholar 

  38. Gupta A, Mishra A, Puri N (2017) Peptide nucleic acids: advanced tools for biomedical applications. J Biotechnol 259:148–159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cheng CJ, Bahal R, Babar IA et al (2015) MicroRNA silencing for cancer therapy targeted to the tumour microenvironment. Nature 518(7537):107–110

    Article  CAS  PubMed  Google Scholar 

  40. Montagner G, Bezzerri V, Cabrini G et al (2017) An antisense peptide nucleic acid against Pseudomonas aeruginosa inhibiting bacterial-induced inflammatory responses in the cystic fibrosis IB3-1 cellular model system. Int J Biol Macromol 99:492–498

    Article  CAS  PubMed  Google Scholar 

  41. Wancewicz EV, Maier MA, Siwkowski AM et al (2010) Peptide nucleic acids conjugated to short basic peptides show improved pharmacokinetics and antisense activity in adipose tissue. J Med Chem 53(10):3919–3926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Viereck J, Kumarswamy R, Foinquinos A et al (2016) Long noncoding RNA Chast promotes cardiac remodeling. Sci Transl Med 8(326):326ra322

    Article  Google Scholar 

  43. Micheletti R, Plaisance I, Abraham BJ et al (2017) The long noncoding RNA Wisper controls cardiac fibrosis and remodeling. Sci Transl Med 9(395):eaai9118

    Article  PubMed  PubMed Central  Google Scholar 

  44. Zhang J, Yu L, Xu Y et al (2018) Long noncoding RNA upregulated in hypothermia treated cardiomyocytes protects against myocardial infarction through improving mitochondrial function. Int J Cardiol 266:213–217

    Article  PubMed  Google Scholar 

  45. Hawiger J (2018) Heartfelt sepsis: microvascular injury due to genomic storm. Kardiol Pol 76(8):1203–1216

    Article  PubMed  Google Scholar 

  46. Kishimoto K, Matsumoto K, Ninomiya-Tsuji J (2000) TAK1 mitogen-activated protein kinase kinase kinase is activated by autophosphorylation within its activation loop. J Biol Chem 275(10):7359–7364

    Article  CAS  PubMed  Google Scholar 

  47. Lamothe B, Besse A, Campos AD, Webster WK, Wu H, Darnay BG (2007) Site-specific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of I kappa B kinase activation. J Biol Chem 282(6):4102–4112

    Article  CAS  PubMed  Google Scholar 

  48. Du M, Yuan L, Tan X et al (2017) The LPS-inducible lncRNA Mirt2 is a negative regulator of inflammation. Nat Commun 8(1):2049

    Article  PubMed  PubMed Central  Google Scholar 

  49. Sun F, Yuan W, Wu H et al (2020) LncRNA KCNQ1OT1 attenuates sepsis-induced myocardial injury via regulating miR-192-5p/XIAP axis. Exp Biol Med (Maywood):1535370220908041

    Google Scholar 

  50. Yong H, Wu G, Chen J et al (2020) lncRNA MALAT1 accelerates skeletal muscle cell apoptosis and inflammatory response in sepsis by decreasing BRCA1 expression by recruiting EZH2. Mol Ther Nucleic Acids 19:97–108

    Article  CAS  PubMed  Google Scholar 

  51. Teoh H, Quan A, Creighton AK et al (2013) BRCA1 gene therapy reduces systemic inflammatory response and multiple organ failure and improves survival in experimental sepsis. Gene Ther 20(1):51–61

    Article  CAS  PubMed  Google Scholar 

  52. Zhang P, Cao L, Zhou R, Yang X, Wu M (2019) The lncRNA Neat1 promotes activation of inflammasomes in macrophages. Nat Commun 10(1):1495

    Article  PubMed  PubMed Central  Google Scholar 

  53. Zhou H, Wang X, Zhang B (2020) Depression of lncRNA NEAT1 antagonizes LPS-evoked acute injury and inflammatory response in alveolar epithelial cells via HMGB1-RAGE signaling. Mediat Inflamm 2020:8019467

    Article  Google Scholar 

  54. Helmick CG, Felson DT, Lawrence RC et al (2008) Estimates of the prevalence of arthritis and other rheumatic conditions in the United States. Part I. Arthritis Rheum 58(1):15–25

    Article  PubMed  Google Scholar 

  55. McInnes IB, Schett G (2011) The pathogenesis of rheumatoid arthritis. N Engl J Med 365:2205–2219

    Article  CAS  PubMed  Google Scholar 

  56. Bottini N, Firestein GS (2013) Duality of fibroblast-like synoviocytes in RA: passive responders and imprinted aggressors. Nat Rev Rheumatol 9(1):24–33

    Article  CAS  PubMed  Google Scholar 

  57. Mor A, Abramson SB, Pillinger MH (2005) The fibroblast-like synovial cell in rheumatoid arthritis: a key player in inflammation and joint destruction. Clin Immunol 115(2):118–128

    Article  CAS  PubMed  Google Scholar 

  58. Gjertsson I, Laurie KL, Devitt J et al (2009) Tolerance induction using lentiviral gene delivery delays onset and severity of collagen II arthritis. Mol Ther 17(4):632–640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hu X, Tang J, Hu X et al (2020) Silencing of long non-coding RNA HOTTIP reduces inflammation in rheumatoid arthritis by demethylation of SFRP1. Mol Ther Nucleic Acids 19:468–481

    Article  CAS  PubMed  Google Scholar 

  60. Zhang CW, Wu X, Liu D et al (2019) Long non-coding RNA PVT1 knockdown suppresses fibroblast-like synoviocyte inflammation and induces apoptosis in rheumatoid arthritis through demethylation of sirt6. J Biol Eng 13:60

    Article  PubMed  PubMed Central  Google Scholar 

  61. Adán N, Guzmán-Morales J, Ledesma-Colunga MG et al (2013) Prolactin promotes cartilage survival and attenuates inflammation in inflammatory arthritis. J Clin Invest 123(9):3902–3913

    Article  PubMed  PubMed Central  Google Scholar 

  62. Tseng CC, Chen YJ, Chang WA et al (2020) Dual role of chondrocytes in rheumatoid arthritis: the chicken and the egg. Int J Mol Sci 21(3):1071

    Article  CAS  PubMed Central  Google Scholar 

  63. Li G, Liu Y, Meng F et al (2019) LncRNA MEG3 inhibits rheumatoid arthritis through miR-141 and inactivation of AKT/mTOR signalling pathway. J Cell Mol Med 23(10):7116–7120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Zhang HJ, Wei QF, Wang SJ et al (2017) LncRNA HOTAIR alleviates rheumatoid arthritis by targeting miR-138 and inactivating NF-kappaB pathway. Int Immunopharmacol 50:283–290

    Article  CAS  PubMed  Google Scholar 

  65. Arun G, Diermeier S, Akerman M et al (2016) Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 30(1):34–51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Huang L, Damle SS, Booten S et al (2015) Partial hepatectomy induced long noncoding RNA inhibits hepatocyte proliferation during liver regeneration. PLoS One 10(7):e0132798

    Article  PubMed  PubMed Central  Google Scholar 

  67. Papaioannou D, Petri A, Dovey OM et al (2019) The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia. Nat Commun 10(1):1–15

    Article  Google Scholar 

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Correspondence to Mark W. Feinberg .

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Pierce, J.B., Zhou, H., Simion, V., Feinberg, M.W. (2022). Long Noncoding RNAs as Therapeutic Targets. In: Carpenter, S. (eds) Long Noncoding RNA. Advances in Experimental Medicine and Biology, vol 1363. Springer, Cham. https://doi.org/10.1007/978-3-030-92034-0_9

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