RNA editing: Expanding the potential of RNA therapeutics
Open accessAbstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
RNA editing is generally considered safer than DNA-targeted options as unwanted editing is not permanently retained in the host.
“While RNA editing is generally considered safer than DNA-targeted options as unwanted editing is not permanently retained in the host (47)”
From Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina (2024) · cites this paper as [47]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis
Gillmore, J. D., Gane, E., Taubel, J., Kao, J., Fontana, M., Maitland, M. L., Seitzer, J., O’Connell, D., Walsh, K. R., Wood, K., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2107454 · Cited by 1,766 · cited 1× · see citing works
“Despite the potential and early clinical success of CRISPR-Cas DNA-editing technologies, 135 safety concerns persist.”
Identification of preexisting adaptive immunity to Cas9 proteins in humans
Charlesworth, C. T., Deshpande, P. S., Dever, D. P., Camarena, J., Lemgart, V. T., Cromer, M. K., Vakulskas, C. A., Collingwood, M. A., Zhang, L., Bode, N. M., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0326-x · Cited by 1,093 · see citing works
Directed evolution of adeno-associated virus yields enhanced gene delivery vectors
Maheshri, N., Koerber, J. T., Kaspar, B. K., & Schaffer, D. V. (2006) · Nature Biotechnology · doi:10.1038/nbt1182 · Cited by 538 · see citing works
Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing
Yin, H., Song, C.-Q., Suresh, S., Wu, Q., Walsh, S., Rhym, L. H., Mintzer, E., Bolukbasi, M. F., Zhu, L. J., Kauffman, K., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.4005 · Cited by 499 · see citing works
High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population
Wagner, D. L., Amini, L., Wendering, D. J., Burkhardt, L.-M., Akyüz, L., Reinke, P., Volk, H.-D., & Schmueck-Henneresse, M. (2019) · Nature Medicine · doi:10.1038/s41591-018-0204-6 · Cited by 399 · see citing works
Manufacturing challenges and rational formulation development for AAV viral vectors
Srivastava, A., Mallela, K. M. G., Deorkar, N., & Brophy, G. (2021) · Journal of Pharmaceutical Sciences · doi:10.1016/j.xphs.2021.03.024 · Cited by 269 · see citing works
Kluesner, M. G., Lahr, W. S., Lonetree, C.-L., Smeester, B. A., Qiu, X., Slipek, N. J., Claudio Vázquez, P. N., Pitzen, S. P., Pomeroy, E. J., Vignes, M. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22009-2 · Cited by 121 · see citing works
Flagged first, then by citations
Research works printed but not linked: 145
- [1]Consortium G.T. The genotype-tissue expression (GTEx) project Nat. Genet. 45 2013 580 585 23715323 PMC4010069
- [2]Karczewski K.J. Francioli L.C. Tiao G. Cummings B.B. Alföldi J. Wang Q. Collins R.L. Laricchia K.M. Ganna A. Birnbaum D.P. The mutational constraint spectrum quantified from variation in 141,456 humans Nature 581 2020 434 443 32461654 PMC7334197
- [3]Bass B.L. Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate Cell 55 1988 1089 1098 3203381
- [4]Bass B.L. Weintraub H. A developmentally regulated activity that unwinds RNA duplexes Cell 48 1987 607 613 2434241
- [5]Woolf T.M. Chase J.M. Stinchcomb D.T. Toward the therapeutic editing of mutated RNA sequences Proc. Natl. Acad. Sci. USA 92 1995 8298 8302 7545300 PMC41144
- [6]Merkle T. Merz S. Reautschnig P. Blaha A. Li Q. Vogel P. Wettengel J. Li J.B. Stafforst T. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides Nat. Biotechnol. 37 2019 133 138 30692694
- [7]Reautschnig P. Wahn N. Wettengel J. Schulz A.E. Latifi N. Vogel P. Kang T.W. Pfeiffer L.S. Zarges C. Naumann U. CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo Nat. Biotechnol. 40 2022 759 768 34980913
- [8]Katrekar D. Yen J. Xiang Y. Saha A. Meluzzi D. Savva Y. Mali P. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs Nat. Biotechnol. 40 2022 938 945 35145312 PMC9232839
- [9]Katrekar D. Chen G. Meluzzi D. Ganesh A. Worlikar A. Shih Y.R. Varghese S. Mali P. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases Nat. Methods 16 2019 239 242 30737497 PMC6395520
- [10]Qu L. Yi Z. Zhu S. Wang C. Cao Z. Zhou Z. Yuan P. Yu Y. Tian F. Liu Z. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs Nat. Biotechnol. 37 2019 1059 1069 31308540
- [11]Yi Z. Qu L. Tang H. Liu Z. Liu Y. Tian F. Wang C. Zhang X. Feng Z. Yu Y. Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo Nat. Biotechnol. 40 2022 946 955 35145313
- [12]Monian P. Shivalila C. Lu G. Shimizu M. Boulay D. Bussow K. Byrne M. Bezigian A. Chatterjee A. Chew D. Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides Nat. Biotechnol. 40 2022 1093 1102 35256816
- [13]Doherty E.E. Wilcox X.E. van Sint Fiet L. Kemmel C. Turunen J.J. Klein B. Tantillo D.J. Fisher A.J. Beal P.A. Rational design of RNA editing guide strands: cytidine analogs at the orphan position J. Am. Chem. Soc. 143 2021 6865 6876 33939417 PMC8608393
- [14]Nose K. Hidaka K. Yano T. Tomita Y. Fukuda M. Short-chain guide RNA for site-directed A-to-I RNA editing Nucleic Acid Ther. 31 2021 58 67 33170095
- [15]Cox D.B.T. Gootenberg J.S. Abudayyeh O.O. Franklin B. Kellner M.J. Joung J. Zhang F. RNA editing with CRISPR-Cas13 Science 358 2017 1019 1027 29070703 PMC5793859
- [16]Rauch S. He E. Srienc M. Zhou H. Zhang Z. Dickinson B.C. Programmable RNA-guided RNA effector proteins built from human parts Cell 178 2019 122 134.e12 31230714 PMC6657360
- [17]Li J.B. Levanon E.Y. Yoon J.K. Aach J. Xie B. Leproust E. Zhang K. Gao Y. Church G.M. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing Science 324 2009 1210 1213 19478186
- [18]Pinto Y. Cohen H.Y. Levanon E.Y. Mammalian conserved ADAR targets comprise only a small fragment of the human editosome Genome Biol. 15 2014 R5 24393560 PMC4053846
- [19]Sinnamon J.R. Kim S.Y. Corson G.M. Song Z. Nakai H. Adelman J.P. Mandel G. Site-directed RNA repair of endogenous Mecp2 RNA in neurons Proc. Natl. Acad. Sci. USA 114 2017 E9395 E9402 29078406 PMC5676935
- [20]Sinnamon J.R. Jacobson M.E. Yung J.F. Fisk J.R. Jeng S. McWeeney S.K. Parmelee L.K. Chan C.N. Yee S.P. Mandel G. Targeted RNA editing in brainstem alleviates respiratory dysfunction in a mouse model of Rett syndrome Proc. Natl. Acad. Sci. USA 119 2022 e2206053119 PMC9388114 35939700
- [21]Geary R.S. Norris D. Yu R. Bennett C.F. Pharmacokinetics, biodistribution and cell uptake of antisense oligonucleotides Adv. Drug Deliv. Rev. 87 2015 46 51 25666165
- [22]Gerber A. O'Connell M.A. Keller W. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette RNA 3 1997 453 463 9149227 PMC1369496
- [23]Chen C.X. Cho D.S. Wang Q. Lai F. Carter K.C. Nishikura K. A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains RNA 6 2000 755 767 10836796 PMC1369955
- [24]Oakes E. Anderson A. Cohen-Gadol A. Hundley H.A. Adenosine deaminase that acts on RNA 3 (ADAR3) binding to glutamate receptor subunit B pre-mRNA inhibits RNA editing in glioblastoma J. Biol. Chem. 292 2017 4326 4335 28167531 PMC5354488
- [25]Raghava Kurup R. Oakes E.K. Manning A.C. Mukherjee P. Vadlamani P. Hundley H.A. RNA binding by ADAR3 inhibits adenosine-to-inosine editing and promotes expression of immune response protein MAVS J. Biol. Chem. 298 2022 102267 35850307 PMC9418441
- [26]Masliah G. Barraud P. Allain F.H.T. RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence Cell. Mol. Life Sci. 70 2013 1875 1895 22918483 PMC3724394
- [27]Stephens O.M. Haudenschild B.L. Beal P.A. The binding selectivity of ADAR2's dsRBMs contributes to RNA-editing selectivity Chem. Biol. 11 2004 1239 1250 15380184
- [28]Liu Y. Lei M. Samuel C.E. Chimeric double-stranded RNA-specific adenosine deaminase ADAR1 proteins reveal functional selectivity of double-stranded RNA-binding domains from ADAR1 and protein kinase PKR Proc. Natl. Acad. Sci. USA 97 2000 12541 12546 11070079 PMC18800
- [29]Källman A.M. Sahlin M. Öhman M. ADAR2 A→I editing: site selectivity and editing efficiency are separate events Nucleic Acids Res. 31 2003 4874 4881 12907730 PMC169957
- [30]Stefl R. Oberstrass F.C. Hood J.L. Jourdan M. Zimmermann M. Skrisovska L. Maris C. Peng L. Hofr C. Emeson R.B. Allain F.H.T. The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove Cell 143 2010 225 237 20946981 PMC2956598
- [31]Matthews M.M. Thomas J.M. Zheng Y. Tran K. Phelps K.J. Scott A.I. Havel J. Fisher A.J. Beal P.A. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity Nat. Struct. Mol. Biol. 23 2016 426 433 27065196 PMC4918759
- [32]Park S. Doherty E.E. Xie Y. Padyana A.K. Fang F. Zhang Y. Karki A. Lebrilla C.B. Siegel J.B. Beal P.A. High-throughput mutagenesis reveals unique structural features of human ADAR1 Nat. Commun. 11 2020 5130 33046702 PMC7550611
- [33]Brooks S.C. Adhikary S. Rubinson E.H. Eichman B.F. Recent advances in the structural mechanisms of DNA glycosylases Biochim. Biophys. Acta 1834 2013 247 271 23076011 PMC3530658
- [34]Kuttan A. Bass B.L. Mechanistic insights into editing-site specificity of ADARs Proc. Natl. Acad. Sci. USA 109 2012 E3295 E3304 23129636 PMC3511710
- [35]Doherty E.E. Karki A. Wilcox X.E. Mendoza H.G. Manjunath A. Matos V.J. Fisher A.J. Beal P.A. ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site Nucleic Acids Res. 50 2022 10857 10868 36243986 PMC9638939
- [36]Schneider M.F. Wettengel J. Hoffmann P.C. Stafforst T. Optimal guideRNAs for re-directing deaminase activity of hADAR1 and hADAR2 in trans Nucleic Acids Res. 42 2014 e87 24744243 PMC4041445
- [37]Thuy-Boun A.S. Thomas J.M. Grajo H.L. Palumbo C.M. Park S. Nguyen L.T. Fisher A.J. Beal P.A. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition Nucleic Acids Res. 48 2020 7958 7972 32597966 PMC7641318
- [38]Poulsen H. Jorgensen R. Heding A. Nielsen F.C. Bonven B. Egebjerg J. Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain RNA 12 2006 1350 1360 16682559 PMC1484439
- [39]Bazak L. Haviv A. Barak M. Jacob-Hirsch J. Deng P. Zhang R. Isaacs F.J. Rechavi G. Li J.B. Eisenberg E. Levanon E.Y. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes Genome Res. 24 2014 365 376 24347612 PMC3941102
- [40]Tan M.H. Li Q. Shanmugam R. Piskol R. Kohler J. Young A.N. Liu K.I. Zhang R. Ramaswami G. Ariyoshi K. Dynamic landscape and regulation of RNA editing in mammals Nature 550 2017 249 254 29022589 PMC5723435
- [41]Liddicoat B.J. Piskol R. Chalk A.M. Ramaswami G. Higuchi M. Hartner J.C. Li J.B. Seeburg P.H. Walkley C.R. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself Science 349 2015 1115 1120 26275108 PMC5444807
- [42]Rice G.I. Kasher P.R. Forte G.M.A. Mannion N.M. Greenwood S.M. Szynkiewicz M. Dickerson J.E. Bhaskar S.S. Zampini M. Briggs T.A. Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature Nat. Genet. 44 2012 1243 1248 23001123 PMC4154508
- [43]Lamers M.M. van den Hoogen B.G. Haagmans B.L. ADAR1: “Editor-in-Chief” of cytoplasmic innate immunity Front. Immunol. 10 2019 1763 31404141 PMC6669771
- [44]Wang Q. Miyakoda M. Yang W. Khillan J. Stachura D.L. Weiss M.J. Nishikura K. Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene J. Biol. Chem. 279 2004 4952 4961 14613934
- [45]Baker A.R. Slack F.J. ADAR1 and its implications in cancer development and treatment Trends Genet. 38 2022 821 830 35459560 PMC9283316
- [46]Gannon H.S. Zou T. Kiessling M.K. Gao G.F. Cai D. Choi P.S. Ivan A.P. Buchumenski I. Berger A.C. Goldstein J.T. Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells Nat. Commun. 9 2018 5450 30575730 PMC6303303
- [47]George C.X. Samuel C.E. Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible Proc. Natl. Acad. Sci. USA 96 1999 4621 4626 10200312 PMC16382
- [48]Kleinova R. Leuchtenberger A.F. Giudice C.L. Tanzer A. Derdak S. Picardi E. Jantsch M.F. The ADAR1 editome reveals drivers of editing-specificity for ADAR1-isoforms Preprint at bioRxiv 2021 10.1101/2021.11.24.469911 PMC10201426 37026479 · DOI
- [49]Pfaller C.K. George C.X. Samuel C.E. Adenosine deaminases acting on RNA (ADARs) and viral infections Annu. Rev. Virol. 8 2021 239 264 33882257 PMC12925331
- [50]Jain M. Mann T.D. Stulić M. Rao S.P. Kirsch A. Pullirsch D. Strobl X. Rath C. Reissig L. Moreth K. RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure EMBO J. 37 2018 e94813 30087110 PMC6166124
- [51]Roth S.H. Levanon E.Y. Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity Nat. Methods 16 2019 1131 1138 31636457
- [52]Higuchi M. Maas S. Single F.N. Hartner J. Rozov A. Burnashev N. Feldmeyer D. Sprengel R. Seeburg P.H. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2 Nature 406 2000 78 81 10894545
- [53]Melcher T. Maas S. Herb A. Sprengel R. Higuchi M. Seeburg P.H. RED2, a brain-specific member of the RNA-specific adenosine deaminase family J. Biol. Chem. 271 1996 31795 31798 8943218
- [54]Mladenova D. Barry G. Konen L.M. Pineda S.S. Guennewig B. Avesson L. Zinn R. Schonrock N. Bitar M. Jonkhout N. Adar3 is involved in learning and memory in mice Front. Neurosci. 12 2018 243 29719497 PMC5914295
- [55]Maas S. Gommans W.M. Identification of a selective nuclear import signal in adenosine deaminases acting on RNA Nucleic Acids Res. 37 2009 5822 5829 19617375 PMC2761270
- [56]Licht K. Kapoor U. Amman F. Picardi E. Martin D. Bajad P. Jantsch M.F. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing Genome Res. 29 2019 1453 1463 31427386 PMC6724681
- [57]Desterro J.M.P. Keegan L.P. Lafarga M. Berciano M.T. O'Connell M. Carmo-Fonseca M. Dynamic association of RNA-editing enzymes with the nucleolus J. Cell Sci. 116 2003 1805 1818 12665561
- [58]Barraud P. Banerjee S. Mohamed W.I. Jantsch M.F. Allain F.H.T. A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1 Proc. Natl. Acad. Sci. USA 111 2014 E1852 E1861 24753571 PMC4020056
- [59]Freund E.C. Sapiro A.L. Li Q. Linder S. Moresco J.J. Yates J.R. 3rd Li J.B. Unbiased identification of trans regulators of ADAR and A-to-I RNA editing Cell Rep. 31 2020 107656 32433965 PMC7306178
- [60]Nourreddine S. Lavoie G. Paradis J. Ben El Kadhi K. Méant A. Aubert L. Grondin B. Gendron P. Chabot B. Bouvier M. NF45 and NF90 regulate mitotic gene expression by competing with staufen-mediated mRNA decay Cell Rep. 31 2020 107660 32433969
- [61]Pfaller C.K. Li Z. George C.X. Samuel C.E. Protein kinase PKR and RNA adenosine deaminase ADAR1: new roles for old players as modulators of the interferon response Curr. Opin. Immunol. 23 2011 573 582 21924887 PMC3190076
- [62]Wang Y. Park S. Beal P.A. Selective recognition of RNA substrates by ADAR deaminase domains Biochemistry 57 2018 1640 1651 29457714 PMC5898644
- [63]Schaffer A.A. Kopel E. Hendel A. Picardi E. Levanon E.Y. Eisenberg E. The cell line A-to-I RNA editing catalogue Nucleic Acids Res. 48 2020 5849 5858 32383740 PMC7293008
- [64]Brown C.R. Gupta S. Qin J. Racie T. He G. Lentini S. Malone R. Yu M. Matsuda S. Shulga-Morskaya S. Investigating the pharmacodynamic durability of GalNAc-siRNA conjugates Nucleic Acids Res. 48 2020 11827 11844 32808038 PMC7708070
- [65]Fukuda M. Umeno H. Nose K. Nishitarumizu A. Noguchi R. Nakagawa H. Construction of a guide-RNA for site-directed RNA mutagenesis utilising intracellular A-to-I RNA editing Sci. Rep. 7 2017 41478 28148949 PMC5288656
- [66]Stafforst T. Schneider M.F. An RNA-deaminase conjugate selectively repairs point mutations Angew. Chem. Int. Ed. Engl. 51 2012 11166 11169 23038402
- [67]Montiel-Gonzalez M.F. Vallecillo-Viejo I. Yudowski G.A. Rosenthal J.J.C. Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing Proc. Natl. Acad. Sci. USA 110 2013 18285 18290 24108353 PMC3831439
- [68]Wettengel J. Reautschnig P. Geisler S. Kahle P.J. Stafforst T. Harnessing human ADAR2 for RNA repair - recoding a PINK1 mutation rescues mitophagy Nucleic Acids Res. 45 2017 2797 2808 27907896 PMC5389476
- [69]Monteleone L.R. Matthews M.M. Palumbo C.M. Thomas J.M. Zheng Y. Chiang Y. Fisher A.J. Beal P.A. A bump-hole approach for directed RNA editing Cell Chem. Biol. 26 2019 269 277.e5 30581135 PMC6386613
- [70]Sinnamon J.R. Kim S.Y. Fisk J.R. Song Z. Nakai H. Jeng S. McWeeney S.K. Mandel G. In vivo repair of a protein underlying a neurological disorder by programmable RNA editing Cell Rep. 32 2020 107878 32668243 PMC7449137
- [71]Vallecillo-Viejo I.C. Liscovitch-Brauer N. Montiel-Gonzalez M.F. Eisenberg E. Rosenthal J.J.C. Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme RNA Biol. 15 2018 104 114 29099293 PMC5786015
- [72]Katrekar D. Xiang Y. Palmer N. Saha A. Meluzzi D. Mali P. Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA editing activity and specificity Elife 11 2022 e75555 35044296 PMC8809894
- [73]Katrekar D. Yen J. Xiang Y. Saha A. Meluzzi D. Savva Y. Mali P. Robust RNA Editing via Recruitment of Endogenous ADARs Using Circular Guide RNAs Preprint at bioRxiv 2021 10.1101/2021.01.12.426286 PMC9232839 35145312 · DOI
- [74]Litke J.L. Jaffrey S.R. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts Nat. Biotechnol. 37 2019 667 675 30962542 PMC6554452
- [75]Zhao M. Woodside M.T. Mechanical strength of RNA knot in Zika virus protects against cellular defenses Nat. Chem. Biol. 17 2021 975 981 34253909
- [76]MacFadden A. O'Donoghue Z. Silva P.A.G.C. Chapman E.G. Olsthoorn R.C. Sterken M.G. Pijlman G.P. Bredenbeek P.J. Kieft J.S. Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs Nat. Commun. 9 2018 119 29317714 PMC5760640
- [77]Zhang G. Liu Y. Huang S. Qu S. Cheng D. Yao Y. Ji Q. Wang X. Huang X. Liu J. Enhancement of prime editing via xrRNA motif-joined pegRNA Nat. Commun. 13 2022 1856 35387980 PMC8986804
- [78]Nelson J.W. Randolph P.B. Shen S.P. Everette K.A. Chen P.J. Anzalone A.V. An M. Newby G.A. Chen J.C. Hsu A. Liu D.R. Engineered pegRNAs improve prime editing efficiency Nat. Biotechnol. 40 2022 402 410 34608327 PMC8930418
- [79]Paul C.P. Good P.D. Winer I. Engelke D.R. Effective expression of small interfering RNA in human cells Nat. Biotechnol. 20 2002 505 508 11981566
- [80]Disney M.D. Targeting RNA with small molecules to capture opportunities at the intersection of chemistry, biology, and medicine J. Am. Chem. Soc. 141 2019 6776 6790 30896935 PMC6541398
- [81]Pennacchio L.A. Loots G.G. Nobrega M.A. Ovcharenko I. Predicting tissue-specific enhancers in the human genome Genome Res. 17 2007 201 211 17210927 PMC1781352
- [82]Uzonyi A. Nir R. Shliefer O. Stern-Ginossar N. Antebi Y. Stelzer Y. Levanon E.Y. Schwartz S. Deciphering the principles of the RNA editing code via large-scale systematic probing Mol. Cell 81 2021 2374 2387.e3 33905683
- [83]Kim D.D.Y. Kim T.T.Y. Walsh T. Kobayashi Y. Matise T.C. Buyske S. Gabriel A. Widespread RNA editing of embedded alu elements in the human transcriptome Genome Res. 14 2004 1719 1725 15342557 PMC515317
- [84]Athanasiadis A. Rich A. Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome Plos Biol. 2 2004 e391 15534692 PMC526178
- [85]Egebjerg J. Kukekov V. Heinemann S.F. Intron sequence directs RNA editing of the glutamate receptor subunit GluR2 coding sequence Proc. Natl. Acad. Sci. USA 91 1994 10270 10274 7937939 PMC45001
- [86]Yeo J. Goodman R.A. Schirle N.T. David S.S. Beal P.A. RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1 Proc. Natl. Acad. Sci. USA 107 2010 20715 20719 21068368 PMC2996456
- [87]Niswender C.M. Sanders-Bush E. Emeson R.B. Identification and characterization of RNA editing events within the 5-HT2C receptora Ann. N. Y. Acad. Sci. 861 1998 38 48 9928237
- [88]Lehmann K.A. Bass B.L. The importance of internal loops within RNA substrates of ADAR111Edited by D. E. Draper J. Mol. Biol. 291 1999 1 13 10438602
- [89]Liu X. Sun T. Shcherbina A. Li Q. Jarmoskaite I. Kappel K. Ramaswami G. Das R. Kundaje A. Li J.B. Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis Nat. Commun. 12 2021 2165 33846332 PMC8041805
- [90]Song Y. Yang W. Fu Q. Wu L. Zhao X. Zhang Y. Zhang R. irCLASH reveals RNA substrates recognized by human ADARs Nat. Struct. Mol. Biol. 27 2020 351 362 32203492
- [91]Brown D. Altermatt M. Dobreva T. Chen S. Wang A. Thomson M. Gradinaru V. Deep parallel characterization of AAV tropism and AAV-mediated transcriptional changes via single-cell RNA sequencing Front. Immunol. 12 2021 730825 34759919 PMC8574206
- [93]Li W. Zhang L. Johnson J.S. Zhijian W. Grieger J.C. Ping-Jie X. Drouin L.M. Agbandje-McKenna M. Pickles R.J. Samulski R.J. Generation of novel AAV variants by directed evolution for improved CFTR delivery to human ciliated airway epithelium Mol. Ther. 17 2009 2067 2077 19603002 PMC2801879
- [94]Chan K.Y. Jang M.J. Yoo B.B. Greenbaum A. Ravi N. Wu W.L. Sánchez-Guardado L. Lois C. Mazmanian S.K. Deverman B.E. Gradinaru V. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems Nat. Neurosci. 20 2017 1172 1179 28671695 PMC5529245
- [95]Tabebordbar M. Lagerborg K.A. Stanton A. King E.M. Ye S. Tellez L. Krunnfusz A. Tavakoli S. Widrick J.J. Messemer K.A. Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species Cell 184 2021 4919 4938.e22 34506722 PMC9344975
- [96]Becker J. Fakhiri J. Grimm D. Fantastic AAV gene therapy vectors and how to find them-random diversification, rational design and machine learning Pathogens 11 2022 PMC9318892 35890005
- [97]Agrawal S. The evolution of antisense oligonucleotide chemistry-A personal journey Biomedicines 9 2021 503 34063675 PMC8147625
- [98]Alhamadani F. Zhang K. Parikh R. Wu H. Rasmussen T.P. Bahal R. Zhong X.B. Manautou J.E. Adverse drug reactions and toxicity of the food and drug administration-approved antisense oligonucleotide drugs Drug Metab. Dispos. 50 2022 879 887 35221289 PMC11022857
- [99]Zhu Y. Zhu L. Wang X. Jin H. RNA-based therapeutics: an overview and prospectus Cell Death Dis. 13 2022 644 35871216 PMC9308039
- [101]Karaki S. Paris C. Rocchi P. Antisense oligonucleotides, A novel developing targeting therapy Sharad S. Kapur S. Antisense Therapy 2019 10.5772/intechopen.82105 · DOI
- [102]Zeng Y. Cullen B.R. RNA interference in human cells is restricted to the cytoplasm RNA 8 2002 855 860 12166640 PMC1370302
- [103]Rodriguez J. Menet J.S. Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila Mol. Cell 47 2012 27 37 22658416 PMC3409466
- [105]Ryan D.E. Taussig D. Steinfeld I. Phadnis S.M. Lunstad B.D. Singh M. Vuong X. Okochi K.D. McCaffrey R. Olesiak M. Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs Nucleic Acids Res. 46 2018 792 803 29216382 PMC5778453
- [106]Schubert M.S. Cedrone E. Neun B. Behlke M.A. Dobrovolskaia M.A. Chemical modification of CRISPR gRNAs eliminate type I interferon responses in human peripheral blood mononuclear cells J. Cytokine Biol. 3 2018 121 30225466 PMC6138052
- [107]O'Shea J.J. Schwartz D.M. Villarino A.V. Gadina M. McInnes I.B. Laurence A. The JAK-STAT pathway: impact on human disease and therapeutic intervention Annu. Rev. Med. 66 2015 311 328 25587654 PMC5634336
- [108]Greene C.M. Marciniak S.J. Teckman J. Ferrarotti I. Brantly M.L. Lomas D.A. Stoller J.K. McElvaney N.G. alpha1-Antitrypsin deficiency Nat. Rev. Dis. Primers 2 2016 16051 27465791
- [109]Frazier K.S. Antisense oligonucleotide therapies: the promise and the challenges from a toxicologic pathologist's perspective Toxicol. Pathol. 43 2015 78 89 25385330
- [110]Malik T.N. Doherty E.E. Gaded V.M. Hill T.M. Beal P.A. Emeson R.B. Regulation of RNA editing by intracellular acidification Nucleic Acids Res. 49 2021 4020 4036 33721028 PMC8053123
- [111]Rueter S.M. Dawson T.R. Emeson R.B. Regulation of alternative splicing by RNA editing Nature 399 1999 75 80 10331393
- [113]Long C. Li H. Tiburcy M. Rodriguez-Caycedo C. Kyrychenko V. Zhou H. Zhang Y. Min Y.L. Shelton J.M. Mammen P.P.A. Correction of diverse muscular dystrophy mutations in human engineered heart muscle by single-site genome editing Sci. Adv. 4 2018 eaap9004 29404407 PMC5796795
- [114]García-Tuñón I. Alonso-Pérez V. Vuelta E. Pérez-Ramos S. Herrero M. Méndez L. Hernández-Sánchez J.M. Martín-Izquierdo M. Saldaña R. Sevilla J. Splice donor site sgRNAs enhance CRISPR/Cas9-mediated knockout efficiency PLoS One 14 2019 e0216674 31071190 PMC6508695
- [115]Havens M.A. Hastings M.L. Splice-switching antisense oligonucleotides as therapeutic drugs Nucleic Acids Res. 44 2016 6549 6563 27288447 PMC5001604
- [116]Marsollier A.C. Joubert R. Mariot V. Dumonceaux J. Targeting the polyadenylation signal of pre-mRNA: a new gene silencing approach for facioscapulohumeral dystrophy Int. J. Mol. Sci. 19 2018 1347 29751519 PMC5983732
- [117]Vickers T.A. Wyatt J.R. Burckin T. Bennett C.F. Freier S.M. Fully modified 2' MOE oligonucleotides redirect polyadenylation Nucleic Acids Res. 29 2001 1293 1299 11238995 PMC29745
- [118]Marsollier A.C. Ciszewski L. Mariot V. Popplewell L. Voit T. Dickson G. Dumonceaux J. Antisense targeting of 3' end elements involved in DUX4 mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: a new gene-silencing approach Hum. Mol. Genet. 25 2016 1468 1478 26787513
- [119]Boiziau C. Kurfurst R. Cazenave C. Roig V. Thuong N.T. Toulmé J.J. Inhibition of translation initiation by antisense oligonucleotides via an RNase-H independent mechanism Nucleic Acids Res. 19 1991 1113 1119 1850511 PMC333789
- [120]Liang X.H. Sun H. Shen W. Wang S. Yao J. Migawa M.T. Bui H.H. Damle S.S. Riney S. Graham M.J. Antisense oligonucleotides targeting translation inhibitory elements in 5' UTRs can selectively increase protein levels Nucleic Acids Res. 45 2017 9528 9546 28934489 PMC5766168
- [121]Wang Z. The principles of MiRNA-masking antisense oligonucleotides technology Methods Mol. Biol. 676 2011 43 49 20931388
- [122]Chen S. Xie W. Liu Z. Shan H. Chen M. Song Y. Yu H. Lai L. Li Z. CRISPR start-loss: a novel and practical alternative for gene silencing through base-editing-induced start codon mutations Mol. Ther. Nucleic Acids 21 2020 1062 1073 32854061 PMC7452150
- [123]Winter J. Luu A. Gapinske M. Manandhar S. Shirguppe S. Woods W.S. Song J.S. Perez-Pinera P. Targeted exon skipping with AAV-mediated split adenine base editors Cell Discov. 5 2019 41 31636954 PMC6796986
- [124]Šikrová D. Cadar V.A. Ariyurek Y. Laros J.F.J. Balog J. van der Maarel S.M. Adenine base editing of the DUX4 polyadenylation signal for targeted genetic therapy in facioscapulohumeral muscular dystrophy Mol. Ther. Nucleic Acids 25 2021 342 354 34484861 PMC8399085
- [125]Köhler G. Milstein C. Continuous cultures of fused cells secreting antibody of predefined specificity Nature 256 1975 495 497 1172191
- [126]Mitoma H. Horiuchi T. Tsukamoto H. Ueda N. Molecular mechanisms of action of anti-TNF-alpha agents - comparison among therapeutic TNF-alpha antagonists Cytokine 101 2018 56 63 27567553
- [127]Costa R.L.B. Czerniecki B.J. Clinical development of immunotherapies for HER2(+) breast cancer: a review of HER2-directed monoclonal antibodies and beyond NPJ Breast Cancer 6 2020 10 32195333 PMC7067811
- [128]Zhang X. Song W. The role of APP and BACE1 trafficking in APP processing and amyloid-beta generation Alzheimers Res. Ther. 5 2013 46 24103387 PMC3978418
- [129]Tan B.Z. Huang H. Lam R. Soong T.W. Dynamic regulation of RNA editing of ion channels and receptors in the mammalian nervous system Mol. Brain 2 2009 13 19480689 PMC2694175
- [130]King G.F. Vetter I. No gain, no pain: NaV1.7 as an analgesic target ACS Chem. Neurosci. 5 2014 749 751 25111714
- [131]Moreno A.M. Alemán F. Catroli G.F. Hunt M. Hu M. Dailamy A. Pla A. Woller S.A. Palmer N. Parekh U. Long-lasting analgesia via targeted in situ repression of NaV1.7 in mice Sci. Transl. Med. 13 2021 eaay9056 33692134 PMC8830379
- [132]Riemondy K.A. Gillen A.E. White E.A. Bogren L.K. Hesselberth J.R. Martin S.L. Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation RNA 24 2018 1481 1495 30065024 PMC6191720
- [133]Garrett S. Rosenthal J.J.C. RNA editing underlies temperature adaptation in K+ channels from polar octopuses Science 335 2012 848 851 22223739 PMC4219319
- [134]Palavicini J.P. Correa-Rojas R.A. Rosenthal J.J.C. Extra double-stranded RNA binding domain (dsRBD) in a squid RNA editing enzyme confers resistance to high salt environment J. Biol. Chem. 287 2012 17754 17764 22457361 PMC3366847
- [136]Leibowitz M.L. Papathanasiou S. Doerfler P.A. Blaine L.J. Sun L. Yao Y. Zhang C.Z. Weiss M.J. Pellman D. Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing Nat. Genet. 53 2021 895 905 33846636 PMC8192433
- [139]Bhakta S. Sakari M. Tsukahara T. RNA editing of BFP, a point mutant of GFP, using artificial APOBEC1 deaminase to restore the genetic code Sci. Rep. 10 2020 17304 33057101 PMC7560856
- [140]Jiang K. Koob J. Chen X.D. Krajeski R.N. Zhang Y. Volf V. Zhou W. Sgrizzi S.R. Villiger L. Gootenberg J.S. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR Nat. Biotechnol. 2022 10.1038/s41587-022-01534-5 online ahead of print 36302988 · DOI
- [141]Kaseniit K.E. Katz N. Kolber N.S. Call C.C. Wengier D.L. Cody W.B. Sattely E.S. Gao X.J. Modular, programmable RNA sensing using ADAR editing in living cells Nat. Biotechnol. 2022 online ahead of print PMC12516989 36198772
- [142]Qian Y. Li J. Zhao S. Matthews E.A. Adoff M. Zhong W. An X. Yeo M. Park C. Yang X. Programmable RNA sensing for cell monitoring and manipulation Nature 610 2022 713 721 36198803 PMC10348343
- [154]Lo Giudice C. Silvestris D.A. Roth S.H. Eisenberg E. Pesole G. Gallo A. Picardi E. Quantifying RNA editing in deep transcriptome datasets Front. Genet. 11 2020 194 32211029 PMC7069340
- [155]Maeder M.L. Stefanidakis M. Wilson C.J. Baral R. Barrera L.A. Bounoutas G.S. Bumcrot D. Chao H. Ciulla D.M. DaSilva J.A. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10 Nat. Med. 25 2019 229 233 30664785
- [156]Reich D.P. Bass B.L. Mapping the dsRNA world Cold Spring Harb. Perspect. Biol. 11 2019 a035352 30824577 PMC6396333
- [157]Licht K. Hartl M. Amman F. Anrather D. Janisiw M.P. Jantsch M.F. Inosine induces context-dependent recoding and translational stalling Nucleic Acids Res. 47 2019 3 14 30462291 PMC6326813
- [158]Crooke S.T. Baker B.F. Crooke R.M. Liang X.H. Antisense technology: an overview and prospectus Nat. Rev. Drug Discov. 20 2021 427 453 33762737
- [160]Korneyenkov M.A. Zamyatnin A.A. Jr. Next step in gene delivery: modern approaches and further perspectives of AAV tropism modification Pharmaceutics 13 2021 750 34069541 PMC8160765
- [162]Colella P. Ronzitti G. Mingozzi F. Emerging issues in AAV-mediated in vivo gene therapy Mol. Ther. Methods Clin. Dev. 8 2018 87 104 29326962 PMC5758940
- [163]Mingozzi F. High K.A. Immune responses to AAV vectors: overcoming barriers to successful gene therapy Blood 122 2013 23 36 23596044 PMC3701904
- [164]Moreno A.M. Palmer N. Alemán F. Chen G. Pla A. Jiang N. Leong Chew W. Law M. Mali P. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy Nat. Biomed. Eng. 3 2019 806 816 31332341 PMC6783354
- [165]Kim J. Hu C. Moufawad El Achkar C. Black L.E. Douville J. Larson A. Pendergast M.K. Goldkind S.F. Lee E.A. Kuniholm A. Patient-customized oligonucleotide therapy for a rare genetic disease N. Engl. J. Med. 381 2019 1644 1652 31597037 PMC6961983
Cited by
Sorted by citations
Past, present, and future of CRISPR genome editing technologies
Pacesa, M., Pelea, O., & Jinek, M. (2024) · Cell · doi:10.1016/j.cell.2024.01.042 · Cited by 609 · see citing works
Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina
Kumar, S., Hsiao, Y.-W., Wong, V. H. Y., Aubin, D., Wang, J.-H., Lisowski, L., Rakoczy, E. P., Li, F., Alarcon-Martinez, L., Gonzalez-Cordero, A., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2408345121 · Cited by 19 · see citing works
- Authors
- Booth, B. J., Nourreddine, S., Katrekar, D., Savva, Y., Bose, D., Long, T. J., Huss, D. J., & Mali, P.
- Affiliations
- University of California San Diego (US)
- Corresponding author
- Huss, David J.
- Mali, Prashant
- Venue
- Molecular Therapy
- Publisher
- Elsevier BV
- Published
- 2023-06
- Volume
- 31
- Issue
- 6
- Pages
- 1533-1549
- ISSN
- 1525-0016 (ISSN-L)
- PMC
- PMC9824937
- OpenAlex
- W4313680674
- Cited by
- 171
- References
- 7
- Citations by year
- 2026: 42 · 2025: 61 · 2024: 57 · 2023: 11
- FWCI
- 4.54
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Therapy (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- Funders
- California Institute for Regenerative Medicine (EDUC4-12804)
- DOD (W81XWH-22-1-0401)
- NIH (OT2OD032742, R01GM123313)
- University of California, San Diego
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- RNA editing, A-to-I RNA editing, ADAR, RNA therapeutics, mRNA vaccines, pre-mRNA splicing, mRNA knockdown, protein function modulation
- MeSH terms
- COVID-19, Adenosine Deaminase, Humans, RNA, RNA-Binding Proteins, RNA Editing, Pandemics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review