Correction of the aprt Gene Using Repair-Polypurine Reverse Hoogsteen Hairpins in Mammalian Cells

Alex J. Félix1,2, Carlos J. Ciudad1,2, Véronique Noé1,2
1Institute for Nanoscience and Nanotechnology IN2UB, University of Barcelona, 08028 Barcelona, Spain
2Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain

Tóm tắt

Từ khóa


Tài liệu tham khảo

(1996). Control of hereditary diseases. Report of a WHO Scientific Group. World Health Organ. Tech. Rep. Ser. 865, 1–84.

Urnov, 2005, Highly efficient endogenous human gene correction using designed zinc-finger nucleases, Nature, 435, 646, 10.1038/nature03556

Yusa, 2011, Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells, Nature, 478, 391, 10.1038/nature10424

Chen, 2011, High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases, Nat. Methods, 8, 753, 10.1038/nmeth.1653

Mori, 2014, Sandwiched zinc-finger nucleases demonstrating higher homologous recombination rates than conventional zinc-finger nucleases in mammalian cells, Bioorg. Med. Chem. Lett., 24, 813, 10.1016/j.bmcl.2013.12.096

Ding, 2013, A TALEN genome-editing system for generating human stem cell-based disease models, Cell Stem Cell, 12, 238, 10.1016/j.stem.2012.11.011

Mosbach, 2018, TALEN-induced double-strand break repair of CTG trinucleotide repeats, Cell Rep., 22, 2146, 10.1016/j.celrep.2018.01.083

Yahata, 2017, TALEN-mediated shift of mitochondrial DNA heteroplasmy in MELAS-iPSCs with m.13513G>A mutation, Sci. Rep., 7, 15557, 10.1038/s41598-017-15871-y

Bedell, 2012, In vivo genome editing using a high-efficiency TALEN system, Nature, 491, 114, 10.1038/nature11537

Low, 2014, Correction of the Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair, Invest. Ophthalmol. Vis. Sci., 55, 387, 10.1167/iovs.13-13278

Jain, 2017, CRISPR-Cas9-based treatment of myocilin-associated glaucoma, Proc. Natl. Acad. Sci. USA, 114, 11199, 10.1073/pnas.1706193114

Park, 2019, In vivo neuronal gene editing via CRISPR-Cas9 amphiphilic nanocomplexes alleviates deficits in mouse models of Alzheimer’s disease, Nat. Neurosci., 22, 524, 10.1038/s41593-019-0352-0

Amoasii, 2018, Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy, Science, 362, 86, 10.1126/science.aau1549

Ousterout, 2015, Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy, Nat. Commun., 6, 6244, 10.1038/ncomms7244

Ruan, 2019, Efficient gene editing at major CFTR mutation loci, Mol. Ther. Nucleic Acids, 16, 73, 10.1016/j.omtn.2019.02.006

Komor, 2016, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature, 533, 420, 10.1038/nature17946

Gaudelli, 2017, Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage, Nature, 551, 464, 10.1038/nature24644

Komor, 2018, Editing the genome without double-stranded DNA breaks, ACS Chem. Biol., 13, 383, 10.1021/acschembio.7b00710

Anzalone, 2019, Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, 576, 149, 10.1038/s41586-019-1711-4

Zhang, 2015, Off-target effects in CRISPR/Cas9-mediated genome engineering, Mol. Ther. Nucleic Acids, 4, e264, 10.1038/mtna.2015.37

Shin, 2017, CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome, Nat. Commun., 8, 15464, 10.1038/ncomms15464

van Ravesteyn, 2016, LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells, Proc. Natl. Acad. Sci. USA, 113, 4122, 10.1073/pnas.1513315113

Igoucheva, 2001, Targeted gene correction by small single-stranded oligonucleotides in mammalian cells, Gene Ther., 8, 391, 10.1038/sj.gt.3301414

Ellis, 2001, High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides, Proc. Natl. Acad. Sci. USA, 98, 6742, 10.1073/pnas.121164898

McLachlan, 2009, Specific targeted gene repair using single-stranded DNA oligonucleotides at an endogenous locus in mammalian cells uses homologous recombination, DNA Repair (Amst.), 8, 1424, 10.1016/j.dnarep.2009.09.014

Chin, 2008, Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids, Proc. Natl. Acad. Sci. USA, 105, 13514, 10.1073/pnas.0711793105

Lonkar, 2009, Targeted correction of a thalassemia-associated β-globin mutation induced by pseudo-complementary peptide nucleic acids, Nucleic Acids Res., 37, 3635, 10.1093/nar/gkp217

Bahal, 2016, In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery, Nat. Commun., 7, 13304, 10.1038/ncomms13304

Ricciardi, 2018, In utero nanoparticle delivery for site-specific genome editing, Nat. Commun., 9, 2481, 10.1038/s41467-018-04894-2

McNeer, 2015, Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium, Nat. Commun., 6, 6952, 10.1038/ncomms7952

de Almagro, 2009, Polypurine hairpins directed against the template strand of DNA knock down the expression of mammalian genes, J. Biol. Chem., 284, 11579, 10.1074/jbc.M900981200

Ciudad, 2017, Polypurine reverse Hoogsteen hairpins as a gene silencing tool for cancer, Curr. Med. Chem., 24, 2809, 10.2174/0929867324666170301114127

Mencia, 2011, Underexpression of miR-224 in methotrexate resistant human colon cancer cells, Biochem. Pharmacol., 82, 1572, 10.1016/j.bcp.2011.08.009

Rodríguez, 2013, Polypurine reverse Hoogsteen hairpins as a gene therapy tool against survivin in human prostate cancer PC3 cells in vitro and in vivo, Biochem. Pharmacol., 86, 1541, 10.1016/j.bcp.2013.09.013

Oleaga, 2012, Identification of novel Sp1 targets involved in proliferation and cancer by functional genomics, Biochem. Pharmacol., 84, 1581, 10.1016/j.bcp.2012.09.014

Villalobos, 2015, Effect of polypurine reverse Hoogsteen hairpins on relevant cancer target genes in different human cell lines, Nucleic Acid Ther., 25, 198, 10.1089/nat.2015.0531

de Almagro, 2011, Coding polypurine hairpins cause target-induced cell death in breast cancer cells, Hum. Gene Ther., 22, 451, 10.1089/hum.2010.102

Bener, 2016, Silencing of CD47 and SIRPα by polypurine reverse Hoogsteen hairpins to promote MCF-7 breast cancer cells death by PMA-differentiated THP-1 cells, BMC Immunol., 17, 32, 10.1186/s12865-016-0170-z

Medina Enríquez, 2018, Cancer immunotherapy using Polypurine reverse Hoogsteen hairpins targeting the PD-1/PD-L1 pathway in human tumor cells, PLoS One, 13, e0206818, 10.1371/journal.pone.0206818

Ciudad, 2019, Silencing PD-1 and PD-L1: the potential of PolyPurine Reverse Hoogsteen hairpins for the elimination of tumor cells, Immunotherapy, 11, 369, 10.2217/imt-2018-0215

Félix, 2018, Functional pharmacogenomics and toxicity of PolyPurine Reverse Hoogsteen hairpins directed against survivin in human cells, Biochem. Pharmacol., 155, 8, 10.1016/j.bcp.2018.06.020

Solé, 2014, Repair of single-point mutations by polypurine reverse Hoogsteen hairpins, Hum. Gene Ther. Methods, 25, 288, 10.1089/hgtb.2014.049

Solé, 2016, Correction of point mutations at the endogenous locus of the dihydrofolate reductase gene using repair-PolyPurine Reverse Hoogsteen hairpins in mammalian cells, Biochem. Pharmacol., 110–111, 16, 10.1016/j.bcp.2016.04.002

Edvardsson, 2019

Bollée, 2012, Adenine phosphoribosyltransferase deficiency, Clin. J. Am. Soc. Nephrol., 7, 1521, 10.2215/CJN.02320312

Goñi, 2004, Triplex-forming oligonucleotide target sequences in the human genome, Nucleic Acids Res., 32, 354, 10.1093/nar/gkh188

Brachman, 2005, Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks, DNA Repair (Amst.), 4, 445, 10.1016/j.dnarep.2004.11.007

Majumdar, 2003, Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide, J. Biol. Chem., 278, 11072, 10.1074/jbc.M211837200

Olsen, 2005, Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides, Gene Ther., 12, 546, 10.1038/sj.gt.3302454

Cradick, 2013, CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity, Nucleic Acids Res., 41, 9584, 10.1093/nar/gkt714

Allen, 2018, Predicting the mutations generated by repair of Cas9-induced double-strand breaks, Nat. Biotechnol., 37, 64, 10.1038/nbt.4317

Anderson, 2018, CRISPR off-target analysis in genetically engineered rats and mice, Nat. Methods, 15, 512, 10.1038/s41592-018-0011-5

Lin, 2014, CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences, Nucleic Acids Res., 42, 7473, 10.1093/nar/gku402

Schaefer, 2017, Unexpected mutations after CRISPR-Cas9 editing in vivo, Nat. Methods, 14, 547, 10.1038/nmeth.4293

Haapaniemi, 2018, CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response, Nat. Med., 24, 927, 10.1038/s41591-018-0049-z

Kosicki, 2018, Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements, Nat. Biotechnol., 36, 765, 10.1038/nbt.4192

Cullot, 2019, CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations, Nat. Commun., 10, 1136, 10.1038/s41467-019-09006-2

Wagner, 2019, High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population, Nat. Med., 25, 242, 10.1038/s41591-018-0204-6

Charlesworth, 2019, Identification of preexisting adaptive immunity to Cas9 proteins in humans, Nat. Med., 25, 249, 10.1038/s41591-018-0326-x

Villalobos, 2014, Stability and immunogenicity properties of the gene-silencing polypurine reverse Hoogsteen hairpins, Mol. Pharm., 11, 254, 10.1021/mp400431f

Berman, 2016, OSWG recommendations for genotoxicity testing of novel oligonucleotide-based therapeutics, Nucleic Acid Ther., 26, 73, 10.1089/nat.2015.0534

2005

Henry, 2002, Assessment of the genotoxic potential of ISIS 2302: a phosphorothioate oligodeoxynucleotide, Mutagenesis, 17, 201, 10.1093/mutage/17.3.201

Sazani, 2010, Safety pharmacology and genotoxicity evaluation of AVI-4658, Int. J. Toxicol., 29, 143, 10.1177/1091581809359206

Guérard, 2017, Locked nucleic acid (LNA): based single-stranded oligonucleotides are not genotoxic, Environ. Mol. Mutagen., 58, 112, 10.1002/em.22076

Knauert, 2006, Triplex-stimulated intermolecular recombination at a single-copy genomic target, Mol. Ther., 14, 392, 10.1016/j.ymthe.2006.03.020

Datta, 2001, Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51, J. Biol. Chem., 276, 18018, 10.1074/jbc.M011646200

Rogers, 2002, Site-directed recombination via bifunctional PNA-DNA conjugates, Proc. Natl. Acad. Sci. USA, 99, 16695, 10.1073/pnas.262556899

Faruqi, 2000, Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway, Mol. Cell. Biol., 20, 990, 10.1128/MCB.20.3.990-1000.2000

Papaioannou, 2012, Oligonucleotide-directed gene-editing technology: mechanisms and future prospects, Expert Opin. Biol. Ther., 12, 329, 10.1517/14712598.2012.660522

Gupta, 1997, Activities of human recombination protein Rad51, Proc. Natl. Acad. Sci. USA, 94, 463, 10.1073/pnas.94.2.463

Krejci, 2012, Homologous recombination and its regulation, Nucleic Acids Res., 40, 5795, 10.1093/nar/gks270

Vasquez, 2002, Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions, Proc. Natl. Acad. Sci. USA, 99, 5848, 10.1073/pnas.082193799

Phear, 1989, Molecular basis of spontaneous mutation at the aprt locus of hamster cells, J. Mol. Biol., 209, 577, 10.1016/0022-2836(89)90595-0

Simon, 1982, Model involving gene inactivation in the generation of autosomal recessive mutants in mammalian cells in culture, Mol. Cell. Biol., 2, 1126

Wigler, 1979, DNA-mediated transfer of the adenine phosphoribosyltransferase locus into mammalian cells, Proc. Natl. Acad. Sci. USA, 76, 1373, 10.1073/pnas.76.3.1373

Johnson, 1977, Adenine phosphoribosyltransferase: a simple spectrophotometric assay and the incidence of mutation in the normal population, Biochem. Genet., 15, 265, 10.1007/BF00484458

Marco-Sola, 2012, The GEM mapper: fast, accurate and versatile alignment by filtration, Nat. Methods, 9, 1185, 10.1038/nmeth.2221

McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2