Genome Editing: A New Approach to Human Therapeutics.

The ability to manipulate the genome with precise spatial and nucleotide resolution (genome editing) has been a powerful research tool. In the past decade, the tools and expertise for using genome editing in human somatic cells and pluripotent cells have increased to such an extent that the approach is now being developed widely as a strategy to treat human disease. The fundamental process depends on creating a site-specific DNA double-strand break (DSB) in the genome and then allowing the cell's endogenous DSB repair machinery to fix the break such that precise nucleotide changes are made to the DNA sequence. With the development and discovery of several different nuclease platforms and increasing knowledge of the parameters affecting different genome editing outcomes, genome editing frequencies now reach therapeutic relevance for a wide variety of diseases. Moreover, there is a series of complementary approaches to assessing the safety and toxicity of any genome editing process, irrespective of the underlying nuclease used. Finally, the development of genome editing has raised the issue of whether it should be used to engineer the human germline. Although such an approach could clearly prevent the birth of people with devastating and destructive genetic diseases, questions remain about whether human society is morally responsible enough to use this tool.

[1]  B. Vogelstein,et al.  Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, Science.

[2]  Fyodor D Urnov,et al.  Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases , 2007, Proceedings of the National Academy of Sciences.

[3]  Ying Sun,et al.  CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes , 2015, Protein & Cell.

[4]  Alexander Pertsemlidis,et al.  Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9 , 2005, Nature Genetics.

[5]  B. Vogelstein,et al.  Cancer risk: Role of environment—Response , 2015, Science.

[6]  Shondra M. Pruett-Miller,et al.  Nuclease-mediated gene editing by homologous recombination of the human globin locus , 2013, Nucleic acids research.

[7]  Luigi Naldini,et al.  A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-antigen-receptor and eliminate expression of endogenous TCR. , 2012, Blood.

[8]  E. Haddad,et al.  Targeted gene addition to human mesenchymal stromal cells as a cell-based plasma-soluble protein delivery platform. , 2010, Cytotherapy.

[9]  Eunji Kim,et al.  Targeted chromosomal deletions in human cells using zinc finger nucleases. , 2010, Genome research.

[10]  D. Russell,et al.  Human gene targeting by viral vectors , 1998, Nature Genetics.

[11]  M H Porteus,et al.  Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs , 2012, Gene Therapy.

[12]  Peng Qiu,et al.  COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites , 2014, Molecular therapy. Nucleic acids.

[13]  J. Hauber,et al.  mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5 , 2015, Nucleic acids research.

[14]  P. Renz,et al.  CRISPR-mediated genotypic and phenotypic correction of a chronic granulomatous disease mutation in human iPS cells , 2015, Experimental hematology.

[15]  P. Gregory,et al.  Genomic Editing of the HIV-1 Coreceptor CCR5 in Adult Hematopoietic Stem and Progenitor Cells Using Zinc Finger Nucleases , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[16]  Erin L. Doyle,et al.  Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting , 2011, Nucleic acids research.

[17]  David R. Liu,et al.  Revealing Off-Target Cleavage Specificities of Zinc Finger Nucleases by In Vitro Selection , 2011, Nature Methods.

[18]  Michel Sadelain,et al.  Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells , 2011, Nature Biotechnology.

[19]  Claudio Mussolino,et al.  TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity , 2014, Nucleic acids research.

[20]  Adrian P Gee,et al.  Inducible apoptosis as a safety switch for adoptive cell therapy. , 2011, The New England journal of medicine.

[21]  Carl O. Pabo,et al.  A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites , 1997, Science.

[22]  M. Porteus Seeing the light: integrating genome engineering with double-strand break repair , 2011, Nature Methods.

[23]  David Baltimore,et al.  Chimeric Nucleases Stimulate Gene Targeting in Human Cells , 2003, Science.

[24]  B. Stoddard,et al.  Homing endonucleases: structure, function and evolution , 1999, Cellular and Molecular Life Sciences CMLS.

[25]  M. Porteus,et al.  Mammalian gene targeting with designed zinc finger nucleases. , 2006, Molecular therapy : the journal of the American Society of Gene Therapy.

[26]  B. Dujon,et al.  Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[27]  J. Haber,et al.  Multiple Pathways of Recombination Induced by Double-Strand Breaks in Saccharomyces cerevisiae , 1999, Microbiology and Molecular Biology Reviews.

[28]  Y. Doyon,et al.  Robust ZFN-mediated genome editing in adult hemophilic mice. , 2013, Blood.

[29]  Martin J. Aryee,et al.  Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing , 2014, Nature Biotechnology.

[30]  Marius Wernig,et al.  Treatment of Sickle Cell Anemia Mouse Model with iPS Cells Generated from Autologous Skin , 2007, Science.

[31]  R. Krance,et al.  Inducible caspase-9 suicide gene controls adverse effects from alloreplete T cells after haploidentical stem cell transplantation. , 2015, Blood.

[32]  M. van der Burg,et al.  Targeted Genome Editing in Human Repopulating Hematopoietic Stem Cells , 2014, Nature.

[33]  T. Doetschman,et al.  Targeted mutation of the Hprt gene in mouse embryonic stem cells. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[35]  Thuy D. Vo,et al.  Transient cold shock enhances zinc-finger nuclease–mediated gene disruption , 2010, Nature Methods.

[36]  V. Wahn,et al.  Diversity, functionality, and stability of the T cell repertoire derived in vivo from a single human T cell precursor. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Morgan L. Maeder,et al.  Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[38]  H. Miller Germline gene therapy: We're ready. , 2015, Science.

[39]  Christine Richardson,et al.  Frequent chromosomal translocations induced by DNA double-strand breaks , 2000, Nature.

[40]  Israel Steinfeld,et al.  Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells , 2015, Nature Biotechnology.

[41]  Wei-Ting Hwang,et al.  Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. , 2014, The New England journal of medicine.

[42]  Dana Carroll,et al.  Genome engineering with targetable nucleases. , 2014, Annual review of biochemistry.

[43]  Hao Yin,et al.  Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype , 2014, Nature Biotechnology.

[44]  J. Orange,et al.  Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases , 2008, Nature Biotechnology.

[45]  G. Church,et al.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering , 2013, Nature Biotechnology.

[46]  Shondra M. Pruett-Miller,et al.  Attenuation of Zinc Finger Nuclease Toxicity by Small-Molecule Regulation of Protein Levels , 2009, PLoS genetics.

[47]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[48]  A. Waldman,et al.  Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA. , 2001, Nucleic acids research.

[49]  Jeffrey C. Miller,et al.  An unbiased genome-wide analysis of zinc-finger nuclease specificity , 2011, Nature Biotechnology.

[50]  C. Case,et al.  Validated Zinc Finger Protein Designs for All 16 GNN DNA Triplet Targets* , 2002, The Journal of Biological Chemistry.

[51]  J. Vogel,et al.  CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III , 2011, Nature.

[52]  Gang Bao,et al.  CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity , 2013, Nucleic acids research.

[53]  David A. Scott,et al.  In vivo genome editing using Staphylococcus aureus Cas9 , 2015, Nature.

[54]  Toni Cathomen,et al.  Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases , 2007, Nature Biotechnology.

[55]  Vanessa Taupin,et al.  Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo , 2010, Nature Biotechnology.

[56]  Shingo Suzuki,et al.  Nuclease-mediated double-strand break (DSB) enhancement of small fragment homologous recombination (SFHR) gene modification in human-induced pluripotent stem cells (hiPSCs). , 2014, Methods in molecular biology.

[57]  David Bryder,et al.  Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. , 2014, Cell stem cell.

[58]  Shondra M Pruett-Miller,et al.  High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases , 2011, Nature Methods.

[59]  E. Hendrickson,et al.  Ku70, an essential gene, modulates the frequency of rAAV-mediated gene targeting in human somatic cells , 2008, Proceedings of the National Academy of Sciences.

[60]  Keiichiro Suzuki,et al.  Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells , 2015, Nature Communications.

[61]  M. Porteus,et al.  Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double‐strand breaks , 2006, The EMBO journal.

[62]  M. Porteus,et al.  Genome Editing in Mouse Spermatogonial Stem/Progenitor Cells Using Engineered Nucleases , 2014, PloS one.

[63]  William H. Majoros,et al.  Multiplex CRISPR/Cas9-Based Genome Editing for Correction of Dystrophin Mutations that Cause Duchenne Muscular Dystrophy , 2015, Nature Communications.

[64]  Gang Bao,et al.  Quantifying on- and off-target genome editing. , 2015, Trends in biotechnology.

[65]  S. Holland,et al.  An AAVS1-targeted minigene platform for correction of iPSCs from all five types of chronic granulomatous disease. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[66]  M. del Río,et al.  Targeted gene addition in human epithelial stem cells by zinc-finger nuclease-mediated homologous recombination. , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[67]  P. Mali,et al.  Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. , 2011, Blood.

[68]  E. Thiel,et al.  Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. , 2009, The New England journal of medicine.

[69]  Hojun Li,et al.  In vivo genome editing restores hemostasis in a mouse model of hemophilia , 2011, Nature.

[70]  E. Lanphier,et al.  Don’t edit the human germ line , 2015, Nature.

[71]  David R. Liu,et al.  Determining the specificities of TALENs, Cas9, and other genome-editing enzymes. , 2014, Methods in enzymology.

[72]  Charles A Gersbach,et al.  Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[73]  A. Waldman,et al.  Capture of DNA sequences at double-strand breaks in mammalian chromosomes. , 2001, Genetics.

[74]  P. Rouet,et al.  Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. , 1995, Nucleic acids research.

[75]  Jacqueline Corrigan-Curay,et al.  Genome Editing Technologies: Defining a Path to Clinic: Genomic Editing: Establishing Preclinical Toxicology Standards, Bethesda, Maryland 10 June 2014. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[76]  William H. Majoros,et al.  Correction of Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients Through Genomic Excision of Exon 51 by Zinc Finger Nucleases , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[77]  J. Haber,et al.  Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences , 1988, Molecular and cellular biology.

[78]  S Chandrasegaran,et al.  Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. , 2000, Nucleic acids research.

[79]  David Mittelman,et al.  Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo , 2014, Genome Biology.

[80]  Christof von Kalle,et al.  TALEN-based gene correction for epidermolysis bullosa. , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[81]  M. Jasin,et al.  Homologous integration in mammalian cells without target gene selection. , 1988, Genes & development.

[82]  M. Grez,et al.  An improved bicistronic CD20/tCD34 vector for efficient purification and in vivo depletion of gene-modified T cells for adoptive immunotherapy. , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

[83]  Sarah K. Baxter,et al.  Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases , 2007, Nucleic acids research.

[84]  David W. Melton,et al.  Targetted correction of a mutant HPRT gene in mouse embryonic stem cells , 1987, Nature.

[85]  M. Brodsky,et al.  A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors , 2005, Nature Biotechnology.

[86]  S Chandrasegaran,et al.  Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[87]  Benjamin L. Oakes,et al.  Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets , 2013, Nucleic acids research.

[88]  M. Kay,et al.  Human COL7A1-corrected induced pluripotent stem cells for the treatment of recessive dystrophic epidermolysis bullosa , 2014, Science Translational Medicine.

[89]  C. Pabo,et al.  Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. , 1994, Science.

[90]  M. Porteus,et al.  Gene therapy for primary immunodeficiencies , 2012, Current opinion in pediatrics.

[91]  D. Atanackovic,et al.  TALEN-mediated editing of endogenous T-cell receptors facilitates efficient reprogramming of T lymphocytes by lentiviral gene transfer , 2014, Gene Therapy.

[92]  Jennifer A. Doudna,et al.  A prudent path forward for genomic engineering and germline gene modification , 2015, Science.

[93]  A. Bogdanove,et al.  TAL Effectors: Customizable Proteins for DNA Targeting , 2011, Science.

[94]  M. Napierala,et al.  Excision of Expanded GAA Repeats Alleviates the Molecular Phenotype of Friedreich's Ataxia. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[95]  M. Capecchi,et al.  Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells , 1987, Cell.

[96]  Jeremy M. Stark,et al.  Double-strand breaks and tumorigenesis. , 2001, Trends in cell biology.

[97]  Richard L. Frock,et al.  Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases , 2014, Nature Biotechnology.

[98]  M. Porteus,et al.  Genome editing of the germline: broadening the discussion. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[99]  J. Hoeijmakers,et al.  Molecular mechanisms of DNA double strand break repair. , 1998, Trends in cell biology.

[100]  Jack W. Szostak,et al.  The double-strand-break repair model for recombination , 1983, Cell.

[101]  Dana Carroll,et al.  Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases , 2001, Molecular and Cellular Biology.

[102]  Eunji Kim,et al.  Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. , 2012, Genome research.

[103]  David R. Liu,et al.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity , 2013, Nature Biotechnology.

[104]  Morgan L. Maeder,et al.  In Situ Genetic Correction of the Sickle Cell Anemia Mutation in Human Induced Pluripotent Stem Cells Using Engineered Zinc Finger Nucleases , 2011, Stem cells.

[105]  Jeffry D Sander,et al.  FLAsH assembly of TALeNs for high-throughput genome editing , 2022 .

[106]  J. C. Belmonte,et al.  Selective Elimination of Mitochondrial Mutations in the Germline by Genome Editing , 2015, Cell.

[107]  Lei Zhang,et al.  Editing T cell specificity towards leukemia by zinc finger nucleases and lentiviral gene transfer , 2012, Nature Medicine.

[108]  D J Segal,et al.  Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins. , 2001, Current opinion in biotechnology.

[109]  H. Blum,et al.  Clinical Interpretation and Implications of Whole Genome Sequencing , 2014 .

[110]  Kyle A. Barlow,et al.  Improved specificity of TALE-based genome editing using an expanded RVD repertoire , 2015, Nature Methods.

[111]  H. Kiem,et al.  Efficient and stable MGMT-mediated selection of long-term repopulating stem cells in nonhuman primates. , 2010, The Journal of clinical investigation.

[112]  Linzhao Cheng,et al.  Oxidase-deficient neutrophils from X-linked chronic granulomatous disease iPS cells: functional correction by zinc finger nuclease-mediated safe harbor targeting. , 2011, Blood.

[113]  A. Hagenbeek,et al.  Safety of retroviral gene marking with a truncated NGF receptor , 2003, Nature Medicine.

[114]  D. Weinstock,et al.  Modeling oncogenic translocations: distinct roles for double-strand break repair pathways in translocation formation in mammalian cells. , 2006, DNA repair.

[115]  Dana Carroll,et al.  Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. , 2002, Genetics.

[116]  Jonathan C. Cohen,et al.  Molecular characterization of loss-of-function mutations in PCSK9 and identification of a compound heterozygote. , 2006, American journal of human genetics.

[117]  C. Desmaze,et al.  Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. , 2004, Molecular cell.

[118]  J W Szostak,et al.  Genetic applications of yeast transformation with linear and gapped plasmids. , 1983, Methods in enzymology.

[119]  Joshua T. Schiffer,et al.  Targeted DNA Mutagenesis for the Cure of Chronic Viral Infections , 2012, Journal of Virology.

[120]  Stefano Monti,et al.  Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells , 2011, Cell.

[121]  Stephen C. West,et al.  Molecular views of recombination proteins and their control , 2003, Nature Reviews Molecular Cell Biology.

[122]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[123]  M. Capecchi,et al.  Introduction of homologous DNA sequences into mammalian cells induces mutations in the cognate gene , 1986, Nature.

[124]  Larry N. Singh,et al.  Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. , 2015, American journal of human genetics.

[125]  Adam James Waite,et al.  An improved zinc-finger nuclease architecture for highly specific genome editing , 2007, Nature Biotechnology.

[126]  J. Keith Joung,et al.  FLASH Assembly of TALENs Enables High-Throughput Genome Editing , 2012, Nature Biotechnology.

[127]  Gang Bao,et al.  An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage , 2013, Nucleic acids research.

[128]  M. Brenneman,et al.  Repair of site-specific double-strand breaks in a mammalian chromosome by homologous and illegitimate recombination , 1997, Molecular and cellular biology.

[129]  Gang Bao,et al.  Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. , 2014, Cell reports.

[130]  A. Zanghellini,et al.  A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. , 2003, Nucleic acids research.

[131]  Lei S. Qi,et al.  Small molecules enhance CRISPR genome editing in pluripotent stem cells. , 2015, Cell stem cell.

[132]  Daniel J. Rader,et al.  Permanent Alteration of PCSK9 With In Vivo CRISPR-Cas9 Genome Editing , 2014, Circulation research.

[133]  R. Beerli,et al.  Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.

[134]  Jeffrey C. Miller,et al.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.

[135]  R. Samulski,et al.  Self-complementary AAV mediates gene targeting and enhances endonuclease delivery for double-strand break repair , 2010, Gene Therapy.

[136]  Ioannis Papaioannou,et al.  Oligonucleotide-directed gene-editing technology: mechanisms and future prospects , 2012, Expert opinion on biological therapy.

[137]  M. Porteus,et al.  Genome Editing of Mouse Fibroblasts by Homologous Recombination for Sustained Secretion of PDGF-B and Augmentation of Wound Healing , 2014, Plastic and reconstructive surgery.

[138]  Matthew J. Moscou,et al.  A Simple Cipher Governs DNA Recognition by TAL Effectors , 2009, Science.

[139]  S Chandrasegaran,et al.  Chimeric restriction endonuclease. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[140]  Rafael J. Yáñez-Muñoz,et al.  Gene correction of a duchenne muscular dystrophy mutation by meganuclease-enhanced exon knock-in. , 2013, Human gene therapy.

[141]  Hidde L Ploegh,et al.  Inhibition of non-homologous end joining increases the efficiency of CRISPR/Cas9-mediated precise [TM: inserted] genome editing , 2015, Nature Biotechnology.

[142]  J. Keith Joung,et al.  Broad Specificity Profiling of TALENs Results in Engineered Nucleases With Improved DNA Cleavage Specificity , 2014, Nature Methods.

[143]  G. Lucarelli,et al.  Allogeneic cellular gene therapy for hemoglobinopathies. , 2010, Hematology/oncology clinics of North America.

[144]  H. Stefánsson,et al.  Identification of a large set of rare complete human knockouts , 2015, Nature Genetics.

[145]  Matthew C. Canver,et al.  An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level , 2013, Science.

[146]  처치 죠지엠.,et al.  Orthogonal cas9 proteins for rna-guided gene regulation and editing , 2014 .

[147]  Dana Carroll,et al.  Gene targeting using zinc finger nucleases , 2005, Nature Biotechnology.

[148]  Hui Zhang,et al.  Transcription Activator-like Effector Nuclease (TALEN)-mediated Gene Correction in Integration-free β-Thalassemia Induced Pluripotent Stem Cells* , 2013, The Journal of Biological Chemistry.

[149]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[150]  E. Bouhassira,et al.  Zinc-finger nuclease-mediated correction of α-thalassemia in iPS cells. , 2012, Blood.

[151]  David J. Rawlings,et al.  Tracking genome engineering outcome at individual DNA breakpoints , 2011, Nature Methods.

[152]  Daniel G. Miller,et al.  Adeno-associated virus vectors integrate at chromosome breakage sites , 2004, Nature Genetics.

[153]  Dana Carroll,et al.  Enhancing Gene Targeting with Designed Zinc Finger Nucleases , 2003, Science.

[154]  A. Klug,et al.  A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter , 2001, Nature Biotechnology.

[155]  P. Rouet,et al.  Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. , 1994, Molecular and cellular biology.

[156]  S. Riddell,et al.  A transgene-encoded cell surface polypeptide for selection, in vivo tracking, and ablation of engineered cells. , 2011, Blood.

[157]  P. Rouet,et al.  Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[158]  M. Porteus,et al.  Generation of an HIV resistant T-cell line by targeted "stacking" of restriction factors. , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[159]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[160]  F. Daboussi,et al.  Targeted Gene Therapy of Xeroderma Pigmentosum Cells Using Meganuclease and TALEN™ , 2013, PloS one.

[161]  Ronnie J Winfrey,et al.  Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. , 2008, Molecular cell.

[162]  Erin L. Doyle,et al.  Targeting DNA Double-Strand Breaks with TAL Effector Nucleases , 2010, Genetics.

[163]  Barry L. Stoddard,et al.  High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display , 2009, Nucleic acids research.

[164]  K. Morris,et al.  The therapeutic application of CRISPR/Cas9 technologies for HIV , 2015, Expert opinion on biological therapy.

[165]  Michel Sadelain,et al.  Safe harbours for the integration of new DNA in the human genome , 2011, Nature Reviews Cancer.

[166]  Martin J. Aryee,et al.  Engineered CRISPR-Cas9 nucleases with altered PAM specificities , 2015, Nature.

[167]  Sarah K. Baxter,et al.  Coupling endonucleases with DNA end–processing enzymes to drive gene disruption , 2012, Nature Methods.

[168]  E. Charpentier CRISPR-Cas9: how research on a bacterial RNA-guided mechanism opened new perspectives in biotechnology and biomedicine , 2015, EMBO molecular medicine.

[169]  J. Nickoloff,et al.  Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells , 1997, Molecular and cellular biology.

[170]  Jonathan C. Cohen,et al.  Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. , 2006, The New England journal of medicine.

[171]  T. Tada,et al.  Genome editing in induced pluripotent stem cells , 2012, Genes to cells : devoted to molecular & cellular mechanisms.

[172]  Margherita Neri,et al.  Site-specific integration and tailoring of cassette design for sustainable gene transfer , 2011, Nature Methods.

[173]  N. Maizels,et al.  Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair , 2014, Proceedings of the National Academy of Sciences.

[174]  Summer B. Thyme,et al.  Exploitation of binding energy for catalysis and design , 2009, Nature.

[175]  Benjamin L. Oakes,et al.  A systematic survey of the Cys2His2 zinc finger DNA-binding landscape , 2015, Nucleic acids research.

[176]  Christof von Kalle,et al.  Fanconi anemia gene editing by the CRISPR/Cas9 system. , 2015, Human gene therapy.

[177]  Jin-Soo Kim,et al.  Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs , 2014, Proceedings of the National Academy of Sciences.

[178]  Anton P. McCaffrey,et al.  Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs. , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

[179]  R. Kucherlapati,et al.  Insertion of DNA sequences into the human chromosomal β-globin locus by homologous recombination , 1985, Nature.

[180]  M. Gonçalves,et al.  Genome editing at the crossroads of delivery, specificity, and fidelity. , 2015, Trends in biotechnology.

[181]  David R. Liu,et al.  Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification , 2014, Nature Biotechnology.

[182]  M. Weitzman,et al.  Efficient Gene Targeting Mediated by Adeno-Associated Virus and DNA Double-Strand Breaks , 2003, Molecular and Cellular Biology.

[183]  Yong Huang,et al.  Promoterless gene targeting without nucleases ameliorates haemophilia B in mice , 2014, Nature.

[184]  Thuy D Vo,et al.  Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures , 2011, Nature Methods.

[185]  Lei Zhang,et al.  Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. , 2010, Genome research.

[186]  Claudio Mussolino,et al.  A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity , 2011, Nucleic acids research.

[187]  Claudio Mussolino,et al.  Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects , 2012, Nucleic acids research.

[188]  David Baker,et al.  megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering , 2013, Nucleic acids research.

[189]  B. Stoddard,et al.  Design, activity, and structure of a highly specific artificial endonuclease. , 2002, Molecular cell.

[190]  K. Khanna,et al.  DNA double-strand breaks: signaling, repair and the cancer connection , 2001, Nature Genetics.

[191]  P. Hasty,et al.  A mutation in mouse rad51 results in an early embryonic lethal that is suppressed by a mutation in p53 , 1996, Molecular and cellular biology.

[192]  P. Gregory,et al.  Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery , 2007, Nature Biotechnology.

[193]  Elo Leung,et al.  A TALE nuclease architecture for efficient genome editing , 2011, Nature Biotechnology.

[194]  P. Duchateau,et al.  Meganucleases and Other Tools for Targeted Genome Engineering: Perspectives and Challenges for Gene Therapy , 2011, Current gene therapy.

[195]  J. Keith Joung,et al.  TALENs: a widely applicable technology for targeted genome editing , 2012, Nature Reviews Molecular Cell Biology.

[196]  Martin J. Aryee,et al.  GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases , 2014, Nature Biotechnology.

[197]  S Chandrasegaran,et al.  A detailed study of the substrate specificity of a chimeric restriction enzyme. , 1999, Nucleic acids research.

[198]  Daniel G. Miller,et al.  Human Gene Targeting by Adeno-Associated Virus Vectors Is Enhanced by DNA Double-Strand Breaks , 2003, Molecular and Cellular Biology.

[199]  Mario R. Capecchi,et al.  Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes , 1988, Nature.