CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery.

Genome editing offers promising solutions to genetic disorders by editing DNA sequences or modulating gene expression. The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) technology can be used to edit single or multiple genes in a wide variety of cell types and organisms in vitro and in vivo. Herein, we review the rapidly developing CRISPR/Cas9-based technologies for disease modeling and gene correction and recent progress toward Cas9/guide RNA (gRNA) delivery based on viral and nonviral vectors. We discuss the relative merits of delivering the genome editing elements in the form of DNA, mRNA, or protein, and the opportunities of combining viral delivery of a transgene encoding Cas9 with nonviral delivery of gRNA. We highlight the lessons learned from nonviral gene delivery in the past three decades and consider their applicability for CRISPR/Cas9 delivery. We also include a discussion of bioinformatics tools for gRNA design and chemical modifications of gRNA. Finally, we consider the extracellular and intracellular barriers to nonviral CRISPR/Cas9 delivery and propose strategies that may overcome these barriers to realize the clinical potential of CRISPR/Cas9-based genome editing.

[1]  D. Wells,et al.  Gene Therapy Progress and Prospects: Electroporation and other physical methods , 2004, Gene Therapy.

[2]  David R. Liu,et al.  Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases. , 2016, Cell chemical biology.

[3]  M. Garber,et al.  DNA-binding domain fusions enhance the targeting range and precision of Cas9 , 2015, Nature Methods.

[4]  Christopher M. Vockley,et al.  Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers , 2015, Nature Biotechnology.

[5]  K. Leong,et al.  Tuning physical properties of nanocomplexes through microfluidics-assisted confinement. , 2011, Nano letters.

[6]  M. Capecchi,et al.  Altering the genome by homologous recombination. , 1989, Science.

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

[8]  V. Iyer,et al.  Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects , 2014, Nature Methods.

[9]  M. Jinek,et al.  Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. , 2016, Molecular cell.

[10]  Zhongda Liu,et al.  SNS01-T Modulation of eIF5A Inhibits B-cell Cancer Progression and Synergizes With Bortezomib and Lenalidomide , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[11]  Morgan L. Maeder,et al.  Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications , 2015, Genome Biology.

[12]  Yi-Wei Lee,et al.  Direct Cytosolic Delivery of CRISPR/Cas9-Ribonucleoprotein for Efficient Gene Editing. , 2017, ACS nano.

[13]  S. Beer-Hammer,et al.  In vivo genome editing using nuclease-encoding mRNA corrects SP-B deficiency , 2015, Nature Biotechnology.

[14]  Jennifer A. Doudna,et al.  Conformational control of DNA target cleavage by CRISPR–Cas9 , 2015, Nature.

[15]  Tobias Schmidt,et al.  A ligation-independent cloning technique for high-throughput assembly of transcription activator–like effector genes , 2012, Nature Biotechnology.

[16]  R. Kontermann,et al.  Strategies for extended serum half-life of protein therapeutics. , 2011, Current opinion in biotechnology.

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

[18]  K. Leong,et al.  The effect of the degree of chitosan deacetylation on the efficiency of gene transfection. , 2004, Biomaterials.

[19]  Soon Il Kwon,et al.  DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins , 2015, Nature Biotechnology.

[20]  Joseph M. DeSimone,et al.  Reductively labile PRINT particles for the delivery of doxorubicin to HeLa cells. , 2008, Journal of the American Chemical Society.

[21]  K. Leong,et al.  MicroRNA delivery for regenerative medicine. , 2015, Advanced drug delivery reviews.

[22]  Vincent M Rotello,et al.  Gold nanoparticles in delivery applications. , 2008, Advanced drug delivery reviews.

[23]  Matthew Meyerson,et al.  Targeted genomic rearrangements using CRISPR/Cas technology , 2014, Nature Communications.

[24]  Chad A. Cowan,et al.  Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. , 2014, Cell stem cell.

[25]  L. Zhu,et al.  CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems , 2014, PloS one.

[26]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[27]  A. Mikos,et al.  Size matters: molecular weight affects the efficiency of poly(ethylenimine) as a gene delivery vehicle. , 1999, Journal of biomedical materials research.

[28]  Kostas Kostarelos,et al.  Carbon nanotubes as vectors for gene therapy: past achievements, present challenges and future goals. , 2013, Advanced drug delivery reviews.

[29]  Robert Langer,et al.  A vector-free microfluidic platform for intracellular delivery , 2013, Proceedings of the National Academy of Sciences.

[30]  S. L. Hyatt,et al.  Plasmid size up to 20 kbp does not limit effective in vivo lung gene transfer using compacted DNA nanoparticles , 2006, Gene Therapy.

[31]  David Putnam,et al.  Polymers for gene delivery across length scales , 2006, Nature materials.

[32]  Randall J. Platt,et al.  Therapeutic genome editing: prospects and challenges , 2015, Nature Medicine.

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

[34]  Yong-Hee Kim,et al.  Current and future delivery systems for engineered nucleases: ZFN, TALEN and RGEN. , 2015, Journal of controlled release : official journal of the Controlled Release Society.

[35]  Xingxu Huang,et al.  sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites , 2014, PloS one.

[36]  M. Bentley,et al.  Chemistry for peptide and protein PEGylation. , 2002, Advanced drug delivery reviews.

[37]  Osamu Nureki,et al.  Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. , 2016, Molecular cell.

[38]  S. L. Hyatt,et al.  Compacted DNA nanoparticles administered to the nasal mucosa of cystic fibrosis subjects are safe and demonstrate partial to complete cystic fibrosis transmembrane regulator reconstitution. , 2004, Human gene therapy.

[39]  Z. Glass,et al.  Non-viral delivery of genome-editing nucleases for gene therapy , 2016, Gene Therapy.

[40]  F. Gleason,et al.  Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA , 2014 .

[41]  David A. Scott,et al.  Rationally engineered Cas9 nucleases with improved specificity , 2015, Science.

[42]  G. Church,et al.  Cas9 gRNA engineering for genome editing, activation and repression , 2015, Nature Methods.

[43]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[44]  I. Kwon,et al.  Structural characteristics of size-controlled self-aggregates of deoxycholic acid-modified chitosan and their application as a DNA delivery carrier. , 2001, Bioconjugate chemistry.

[45]  M. Uesaka,et al.  Accumulation of sub-100 nm polymeric micelles in poorly permeable tumours depends on size. , 2011, Nature nanotechnology.

[46]  Mario R. Capecchi,et al.  High efficiency transformation by direct microinjection of DNA into cultured mammalian cells , 1980, Cell.

[47]  Sunil Singh,et al.  Antisense oligonucleotides: modifications and clinical trials , 2014 .

[48]  Yong Ren,et al.  Recent advances in nanoparticle-mediated siRNA delivery. , 2014, Annual review of biomedical engineering.

[49]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[50]  T. Schlake,et al.  A novel, disruptive vaccination technology , 2013, Human vaccines & immunotherapeutics.

[51]  Daniel W. Pack,et al.  Design and development of polymers for gene delivery , 2005, Nature Reviews Drug Discovery.

[52]  S. Cho,et al.  Heritable gene knockout in C. elegans by direct injection of Cas9-sgRNA ribonucleoproteins , 2013 .

[53]  M. Caruthers,et al.  Solid-phase chemical synthesis of phosphonoacetate and thiophosphonoacetate oligodeoxynucleotides. , 2003, Journal of the American Chemical Society.

[54]  Jennifer A. Doudna,et al.  Generation of knock-in primary human T cells using Cas9 ribonucleoproteins , 2015, Proceedings of the National Academy of Sciences.

[55]  Andrew W. Folkmann,et al.  1 High efficiency , homology-directed genome editing in C . elegans using CRISPR / Cas 9 ribonucleoprotein complexes , 2015 .

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

[57]  Feng Zhang,et al.  An RNA-aptamer-based two-color CRISPR labeling system , 2016, Scientific Reports.

[58]  Asher Mullard,et al.  Novartis secures first CRISPR pharma collaborations , 2015, Nature Reviews Drug Discovery.

[59]  K. Dawson,et al.  Observation of a rectangular columnar phase in a DNA-calcium-zwitterionic lipid complex. , 2004, Journal of the American Chemical Society.

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

[61]  T. Cathomen,et al.  Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells , 2012, Nucleic acids research.

[62]  G. Church,et al.  Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach , 2015, Nature Methods.

[63]  Robert Langer,et al.  Microfluidic technologies for accelerating the clinical translation of nanoparticles. , 2012, Nature nanotechnology.

[64]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[65]  Hakho Lee,et al.  Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis , 2015, Cell.

[66]  Daniel Anderson,et al.  Delivery materials for siRNA therapeutics. , 2013, Nature materials.

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

[68]  Lars J. Brandén,et al.  A peptide nucleic acid–nuclear localization signal fusion that mediates nuclear transport of DNA , 1999, Nature Biotechnology.

[69]  J. Joung,et al.  Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases , 2016, Nature Reviews Genetics.

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

[71]  Zhen Gu,et al.  Stimuli-responsive nanomaterials for therapeutic protein delivery. , 2014, Journal of controlled release : official journal of the Controlled Release Society.

[72]  Jin-Soo Kim,et al.  Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases , 2014, Bioinform..

[73]  Stuart S Dunn,et al.  Reductively responsive siRNA-conjugated hydrogel nanoparticles for gene silencing. , 2012, Journal of the American Chemical Society.

[74]  N. Bavarsad,et al.  mRNA transfection of cervical carcinoma and mesenchymal stem cells mediated by cationic carriers. , 2010, Journal of controlled release : official journal of the Controlled Release Society.

[75]  M. Kay State-of-the-art gene-based therapies: the road ahead , 2011, Nature Reviews Genetics.

[76]  D. Corey,et al.  Stepping toward therapeutic CRISPR , 2015, Proceedings of the National Academy of Sciences.

[77]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[78]  K. Leong,et al.  Aptamer nanomedicine for cancer therapeutics: barriers and potential for translation. , 2015, ACS nano.

[79]  J. Kjems,et al.  A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity , 2009, Nucleic acids research.

[80]  David Cyranoski,et al.  Chinese scientists to pioneer first human CRISPR trial , 2016, Nature.

[81]  K. Leong,et al.  Transfection efficiency and transgene expression kinetics of mRNA delivered in naked and nanoparticle format. , 2013, Journal of controlled release : official journal of the Controlled Release Society.

[82]  Eric S. Lander,et al.  C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector , 2016, Science.

[83]  Feng Zhang,et al.  A split-Cas9 architecture for inducible genome editing and transcription modulation , 2015, Nature Biotechnology.

[84]  Wei Tang,et al.  Correction of a genetic disease in mouse via use of CRISPR-Cas9. , 2013, Cell stem cell.

[85]  Z. Cai,et al.  Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells , 2014, Nature Communications.

[86]  E. Wagner Biomaterials in RNAi therapeutics: quo vadis? , 2013, Biomaterials science.

[87]  T Nakamura,et al.  A multifunctional envelope-type nanodevice for use in nanomedicine: concept and applications. , 2012, Accounts of chemical research.

[88]  J. Rosenecker,et al.  PEGylation Improves Nanoparticle Formation and Transfection Efficiency of Messenger RNA , 2011, Pharmaceutical Research.

[89]  Charles A. Gersbach,et al.  A CRISPR/Cas9-Based System for Reprogramming Cell Lineage Specification , 2014, Stem cell reports.

[90]  J. Keith Joung,et al.  Improving CRISPR-Cas nuclease specificity using truncated guide RNAs , 2014, Nature Biotechnology.

[91]  J. Rosenecker,et al.  Expression of therapeutic proteins after delivery of chemically modified mRNA in mice , 2011, Nature Biotechnology.

[92]  Jin-Soo Kim,et al.  Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases , 2014, Genome research.

[93]  M. Rowicka,et al.  Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing , 2013, Nature Methods.

[94]  G. Vanham,et al.  Type I IFN counteracts the induction of antigen-specific immune responses by lipid-based delivery of mRNA vaccines. , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[95]  Luke A. Gilbert,et al.  Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds , 2015, Cell.

[96]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[97]  M. Fotin‐Mleczek,et al.  Messenger RNA-based Vaccines With Dual Activity Induce Balanced TLR-7 Dependent Adaptive Immune Responses and Provide Antitumor Activity , 2011, Journal of immunotherapy.

[98]  Benjamin L. Oakes,et al.  Programmable RNA recognition and cleavage by CRISPR/Cas9 , 2014, Nature.

[99]  Fabien Zoulim,et al.  Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases , 2013, Nature Reviews Drug Discovery.

[100]  C. Burrows,et al.  Chemical modification of siRNA bases to probe and enhance RNA interference. , 2011, The Journal of organic chemistry.

[101]  S. Benner,et al.  Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. , 2012, Accounts of chemical research.

[102]  Gang Bao,et al.  Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection , 2014, Proceedings of the National Academy of Sciences.

[103]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[104]  E. Lander,et al.  Genetic Screens in Human Cells Using the CRISPR-Cas9 System , 2013, Science.

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

[106]  Shiroh Futaki,et al.  Development of a non-viral multifunctional envelope-type nano device by a novel lipid film hydration method. , 2004, Journal of controlled release : official journal of the Controlled Release Society.

[107]  Daniel F. Voytas,et al.  Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool , 2007, Nucleic Acids Res..

[108]  Yarden Katz,et al.  Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system , 2013, Cell Research.

[109]  J. L. Mateo,et al.  CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool , 2015, PloS one.

[110]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[111]  Feng Zhang,et al.  In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9 , 2014, Nature Biotechnology.

[112]  Mary E Napier,et al.  PRINT: a novel platform toward shape and size specific nanoparticle theranostics. , 2011, Accounts of chemical research.

[113]  L. Tesson,et al.  Efficient Generation of Myostatin Knock-Out Sheep Using CRISPR/Cas9 Technology and Microinjection into Zygotes , 2015, PloS one.

[114]  T. Schlake,et al.  Sequence-engineered mRNA Without Chemical Nucleoside Modifications Enables an Effective Protein Therapy in Large Animals , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[115]  J. Kent,et al.  Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR , 2016, Genome Biology.

[116]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[117]  Feng Chen,et al.  Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. , 2014, Cell stem cell.

[118]  Zhijian Wu,et al.  Effect of genome size on AAV vector packaging. , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

[119]  H. Smyth,et al.  Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9. , 2015, International journal of pharmaceutics.

[120]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

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

[122]  Jianglin Fan,et al.  Effective gene targeting in rabbits using RNA-guided Cas9 nucleases. , 2014, Journal of molecular cell biology.

[123]  B. Dujon,et al.  Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes. , 1992, Nucleic acids research.

[124]  Jeffry D. Sander,et al.  Efficient In Vivo Genome Editing Using RNA-Guided Nucleases , 2013, Nature Biotechnology.

[125]  Lei Wang,et al.  Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos , 2014, Cell.

[126]  Janka Mátrai,et al.  Recent advances in lentiviral vector development and applications. , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

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

[128]  Dennis E Discher,et al.  Minimal " Self " Peptides That Inhibit Phagocytic Clearance and Enhance Delivery of Nanoparticles References and Notes , 2022 .

[129]  S. Wise Nanocarriers as an emerging platform for cancer therapy , 2007 .

[130]  G. Osorio-Revilla,et al.  Microencapsulation of insulin using a W/O/W double emulsion followed by complex coacervation to provide protection in the gastrointestinal tract , 2015, Journal of microencapsulation.

[131]  A. Baas,et al.  FDA-approved poly(ethylene glycol)–protein conjugate drugs , 2011 .

[132]  David V Schaffer,et al.  Viral Vectors for Gene Therapy: Translational and Clinical Outlook. , 2015, Annual review of biomedical engineering.

[133]  P. Barbry,et al.  FibromiRs: translating molecular discoveries into new anti-fibrotic drugs. , 2014, Trends in pharmacological sciences.

[134]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[135]  Namritha Ravinder,et al.  Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. , 2015, Journal of biotechnology.

[136]  C. Rubinstein,et al.  Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila , 2014, Genetics.

[137]  Kun Zhang,et al.  Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. , 2014, Cell stem cell.

[138]  Zhen Gu,et al.  Tailoring Nanocarriers for Intracellular Protein Delivery , 2011 .

[139]  Y Kopelman,et al.  Phase 1/2a, dose-escalation, safety, pharmacokinetic and preliminary efficacy study of intratumoral administration of BC-819 in patients with unresectable pancreatic cancer , 2012, Cancer Gene Therapy.

[140]  David A. Scott,et al.  Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.

[141]  B. Stoddard,et al.  Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. , 2011, Structure.

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

[143]  Tao Wang,et al.  Design of multifunctional non-viral gene vectors to overcome physiological barriers: dilemmas and strategies. , 2012, International journal of pharmaceutics.

[144]  Hao Yin,et al.  CRISPR-mediated direct mutation of cancer genes in the mouse liver , 2014, Nature.

[145]  H. Rammensee,et al.  Direct Injection of Protamine-protected mRNA: Results of a Phase 1/2 Vaccination Trial in Metastatic Melanoma Patients , 2009, Journal of immunotherapy.

[146]  Suresh Ramakrishna,et al.  Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA , 2014, Genome research.

[147]  Hao Zhu,et al.  Non-Viral CRISPR/Cas Gene Editing In Vitro and In Vivo Enabled by Synthetic Nanoparticle Co-Delivery of Cas9 mRNA and sgRNA. , 2017, Angewandte Chemie.

[148]  H. Gendelman,et al.  Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study , 2016, Gene Therapy.

[149]  J. Joung,et al.  Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition , 2015, Nature Biotechnology.

[150]  C. Fong,et al.  Transfection efficiency of chitosan vectors: effect of polymer molecular weight and degree of deacetylation. , 2005, Journal of controlled release : official journal of the Controlled Release Society.

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

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

[153]  Ning Wang,et al.  Artificial Virus Delivers CRISPR-Cas9 System for Genome Editing of Cells in Mice. , 2017, ACS nano.

[154]  Karsten König,et al.  Cell biology: Targeted transfection by femtosecond laser , 2002, Nature.

[155]  David V. Schaffer,et al.  Engineering adeno-associated viruses for clinical gene therapy , 2014, Nature Reviews Genetics.

[156]  Ulrich S Schubert,et al.  Inkjet printing as a deposition and patterning tool for polymers and inorganic particles. , 2008, Soft matter.

[157]  P. Duchateau,et al.  A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences , 2006, Nucleic acids research.

[158]  Eric M. Walters,et al.  Use of the CRISPR/Cas9 System to Produce Genetically Engineered Pigs from In Vitro-Derived Oocytes and Embryos1 , 2014, Biology of reproduction.

[159]  Henriette O'Geen,et al.  A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture , 2014, bioRxiv.

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

[161]  Gang Bao,et al.  CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences , 2014, Nucleic acids research.

[162]  D. Weissman,et al.  Increased Erythropoiesis in Mice Injected With Submicrogram Quantities of Pseudouridine-containing mRNA Encoding Erythropoietin , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

[163]  Daesik Kim,et al.  Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins , 2014, Genome research.

[164]  Meredith A Mintzer,et al.  Nonviral vectors for gene delivery. , 2009, Chemical reviews.

[165]  Lianfeng Zhang,et al.  Heritable Multiplex Genetic Engineering in Rats Using CRISPR/Cas9 , 2014, PloS one.

[166]  Timothy L. Bailey,et al.  GT-Scan: identifying unique genomic targets , 2014, Bioinform..

[167]  S. Schneider,et al.  CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering. , 2015, Angewandte Chemie.

[168]  Sheng Huang,et al.  TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain , 2010, Nucleic Acids Res..

[169]  J. Karn,et al.  Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing , 2015, Scientific Reports.

[170]  Gang Wang,et al.  Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells , 2014, Nature Communications.

[171]  Ding-Shinn Chen,et al.  The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo , 2014, Molecular therapy. Nucleic acids.

[172]  Clifford A. Meyer,et al.  Sequence determinants of improved CRISPR sgRNA design , 2015, Genome research.

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

[174]  Samuel T. Edwards,et al.  Mutations altering the cleavage specificity of a homing endonuclease. , 2002, Nucleic acids research.

[175]  Daniel G. Anderson,et al.  Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo , 2016, Nature Biotechnology.

[176]  Yilong Li,et al.  Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library , 2013, Nature Biotechnology.

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

[178]  Luke A. Gilbert,et al.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.

[179]  David R Corey,et al.  RNA interference in mammalian cells by chemically-modified RNA. , 2003, Biochemistry.

[180]  Ping Zhu,et al.  Correction of a genetic disease by CRISPR-Cas9-mediated gene editing in mouse spermatogonial stem cells , 2014, Cell Research.

[181]  Xiaowei Wang,et al.  WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system , 2015, Genome Biology.

[182]  G. Deleavey,et al.  Designing chemically modified oligonucleotides for targeted gene silencing. , 2012, Chemistry & biology.

[183]  E. Rebar,et al.  Genome editing with engineered zinc finger nucleases , 2010, Nature Reviews Genetics.

[184]  W. Mark Saltzman,et al.  Enhancement of transfection by physical concentration of DNA at the cell surface , 2000, Nature Biotechnology.

[185]  J. Joung,et al.  High-fidelity CRISPR-Cas9 variants with undetectable genome-wide off-targets , 2015, Nature.

[186]  Emily Kang,et al.  Cancer-Associated Protein Kinase C Mutations Reveal Kinase’s Role as Tumor Suppressor , 2015, Cell.

[187]  Simon C Watkins,et al.  Dynamic changes in the characteristics of cationic lipidic vectors after exposure to mouse serum: implications for intravenous lipofection , 1999, Gene Therapy.

[188]  Eugene V Koonin,et al.  Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. , 2015, Molecular cell.

[189]  Aviv Regev,et al.  Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing , 2014, Nature Biotechnology.

[190]  P. Linsley,et al.  Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application , 2010, Nature Reviews Drug Discovery.

[191]  R. Samulski,et al.  Integration of adeno-associated virus (AAV) and recombinant AAV vectors. , 2004, Annual review of genetics.

[192]  H. Rakowski,et al.  The use of cationic microbubbles to improve ultrasound-targeted gene delivery to the ischemic myocardium. , 2013, Biomaterials.

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

[194]  Amrita Singh,et al.  CRISPR/Cas9: a historical and chemical biology perspective of targeted genome engineering. , 2016, Chemical Society reviews.

[195]  D. Lauffenburger,et al.  Vector unpacking as a potential barrier for receptor-mediated polyplex gene delivery. , 2000, Biotechnology and bioengineering.

[196]  J. Rolland,et al.  Delivery of multiple siRNAs using lipid-coated PLGA nanoparticles for treatment of prostate cancer. , 2012, Nano letters.

[197]  David R. Liu,et al.  Small Molecule-Triggered Cas9 Protein with Improved Genome-Editing Specificity , 2015, Nature chemical biology.

[198]  Mark E. Davis The first targeted delivery of siRNA in humans via a self-assembling, cyclodextrin polymer-based nanoparticle: from concept to clinic. , 2009, Molecular pharmaceutics.

[199]  A. Graessmann,et al.  Microinjection of tissue culture cells. , 1983, Methods in enzymology.

[200]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[201]  Mazhar Adli,et al.  Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease , 2014, Nature Biotechnology.

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

[203]  Gene W. Yeo,et al.  Applications of Cas 9 as an RNA-programmed RNA-binding protein , 2015 .

[204]  J. Keith Joung,et al.  High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells , 2013, Nature Biotechnology.

[205]  Zhonghan Li,et al.  Therapeutic targeting of microRNAs: current status and future challenges , 2014, Nature Reviews Drug Discovery.

[206]  Hans Clevers,et al.  Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. , 2013, Cell stem cell.

[207]  Feng Zhang,et al.  Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system , 2013, Nucleic acids research.

[208]  Prashant Mali,et al.  A multifunctional AAV–CRISPR–Cas9 and its host response , 2016, Nature Methods.

[209]  Thomas Krucker,et al.  Nonviral delivery of self-amplifying RNA vaccines , 2012, Proceedings of the National Academy of Sciences.

[210]  Charles E. Vejnar,et al.  CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo , 2015, Nature Methods.

[211]  C. Bennett,et al.  Synthetic CRISPR RNA-Cas9–guided genome editing in human cells , 2015, Proceedings of the National Academy of Sciences.

[212]  S. Akira,et al.  A Toll-like receptor recognizes bacterial DNA , 2000, Nature.

[213]  Chunsheng Dong,et al.  Targeting hepatitis B virus cccDNA by CRISPR/Cas9 nuclease efficiently inhibits viral replication. , 2015, Antiviral research.

[214]  Randall J. Platt,et al.  Optical Control of Mammalian Endogenous Transcription and Epigenetic States , 2013, Nature.

[215]  M. Isalan Zinc-finger nucleases: how to play two good hands , 2011, Nature Methods.

[216]  G. Gasiunas,et al.  Rewiring Cas9 to Target New PAM Sequences. , 2016, Molecular cell.

[217]  David S. Weiss,et al.  Cas9-mediated targeting of viral RNA in eukaryotic cells , 2015, Proceedings of the National Academy of Sciences.

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

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

[220]  Jong-il Kim,et al.  Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells , 2015, Nature Methods.

[221]  U. Schubert,et al.  Poly(ethylene glycol) in Drug Delivery: Pros and Cons as Well as Potential Alternatives. , 2011 .

[222]  Mazhar Adli,et al.  Cas9-chromatin binding information enables more accurate CRISPR off-target prediction , 2015, Nucleic acids research.

[223]  Federica Chiellini,et al.  Chitosan—A versatile semi-synthetic polymer in biomedical applications , 2011 .

[224]  S. Quake,et al.  RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection , 2014, Proceedings of the National Academy of Sciences.

[225]  Daniel G. Anderson,et al.  Optimization of Lipid Nanoparticle Formulations for mRNA Delivery in Vivo with Fractional Factorial and Definitive Screening Designs. , 2015, Nano letters.

[226]  William C. Skarnes,et al.  WGE: a CRISPR database for genome engineering , 2015, Bioinform..

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

[228]  J. Wower,et al.  Therapeutic RNA aptamers in clinical trials. , 2013, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[229]  Thomas A. Campbell,et al.  3D printing of multifunctional nanocomposites , 2013 .

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

[231]  Neville E. Sanjana,et al.  Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells , 2014, Science.

[232]  Wolfgang Wurst,et al.  Development of an intein-mediated split–Cas9 system for gene therapy , 2015, Nucleic acids research.

[233]  Hong Wang,et al.  Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. , 2015, Human molecular genetics.

[234]  K. Khalili,et al.  Inhibition of HSV-1 Replication by Gene Editing Strategy , 2016, Scientific Reports.

[235]  J. Keith Joung,et al.  Efficient Delivery of Genome-Editing Proteins In Vitro and In Vivo , 2014, Nature Biotechnology.

[236]  George M. Church,et al.  CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing , 2014, Nucleic Acids Res..

[237]  Irene Georgakoudi,et al.  Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles , 2016, Proceedings of the National Academy of Sciences.

[238]  L. Zentilin,et al.  A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9 , 2015, Proceedings of the National Academy of Sciences.

[239]  S. Carotta,et al.  Different behavior of branched and linear polyethylenimine for gene delivery in vitro and in vivo , 2001, The journal of gene medicine.

[240]  Michael B Lawrence,et al.  Ultrasound-based molecular imaging and specific gene delivery to mesenteric vasculature by endothelial adhesion molecule targeted microbubbles in a mouse model of Crohn's disease. , 2013, Journal of controlled release : official journal of the Controlled Release Society.

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

[242]  Daniel G. Anderson,et al.  Non-viral vectors for gene-based therapy , 2014, Nature Reviews Genetics.

[243]  Morgan L. Maeder,et al.  Delivery and Specificity of CRISPR-Cas9 Genome Editing Technologies for Human Gene Therapy. , 2015, Human gene therapy.

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

[245]  Tza-Huei Wang,et al.  The convergence of quantum-dot-mediated fluorescence resonance energy transfer and microfluidics for monitoring DNA polyplex self-assembly in real time , 2009, Nanotechnology.

[246]  M. Behlke,et al.  Chemical modification and design of anti-miRNA oligonucleotides , 2011, Gene Therapy.

[247]  Hans Clevers,et al.  Efficient Intracellular Delivery of Native Proteins , 2015, Cell.

[248]  M. Gonçalves,et al.  Engineered Viruses as Genome Editing Devices , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[249]  Sita J. Saunders,et al.  An updated evolutionary classification of CRISPR–Cas systems , 2015, Nature Reviews Microbiology.

[250]  Ying Li,et al.  CRISPR-Cas9 delivery to hard-to-transfect cells via membrane deformation , 2015, Science Advances.

[251]  J. Isner,et al.  Transcutaneous ultrasound augments naked DNA transfection of skeletal muscle. , 2002, Molecular therapy : the journal of the American Society of Gene Therapy.

[252]  G. Owens,et al.  RNA replicon delivery via lipid-complexed PRINT protein particles. , 2013, Molecular pharmaceutics.

[253]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[254]  Robert Langer,et al.  CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling , 2014, Cell.

[255]  Yoshio Koyanagi,et al.  Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus , 2013, Scientific Reports.

[256]  John M. Shelton,et al.  Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy , 2016, Science.

[257]  Marc Tessier-Lavigne,et al.  Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9 , 2016, Nature.

[258]  M. Kimura,et al.  Generation of an ICF Syndrome Model by Efficient Genome Editing of Human Induced Pluripotent Stem Cells Using the CRISPR System , 2013, International journal of molecular sciences.

[259]  Yukiko Kimura,et al.  Efficient generation of knock-in transgenic zebrafish carrying reporter/driver genes by CRISPR/Cas9-mediated genome engineering , 2014, Scientific Reports.

[260]  Yi-Ping Ho,et al.  Three-dimensional hydrodynamic focusing method for polyplex synthesis. , 2014, ACS nano.

[261]  D. de Semir,et al.  Comparative transfection of DNA into primary and transformed mammalian cells from different lineages , 2010, BMC biotechnology.

[262]  Leaf Huang,et al.  Nonviral vectors: we have come a long way. , 2014, Advances in genetics.

[263]  Xiaoling Wang,et al.  Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors , 2015, Nature Biotechnology.

[264]  Bryan R. Cullen,et al.  Inactivation of the Human Papillomavirus E6 or E7 Gene in Cervical Carcinoma Cells by Using a Bacterial CRISPR/Cas RNA-Guided Endonuclease , 2014, Journal of Virology.

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

[266]  S. Déjean,et al.  First-in-man phase 1 clinical trial of gene therapy for advanced pancreatic cancer: safety, biodistribution, and preliminary clinical findings. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[267]  P. Cullis,et al.  Liposomal drug delivery systems: from concept to clinical applications. , 2013, Advanced drug delivery reviews.

[268]  Barry L. Stoddard,et al.  Homing endonuclease I-CreI derivatives with novel DNA target specificities , 2006, Nucleic acids research.

[269]  Takanori Kanai,et al.  Modeling colorectal cancer using CRISPR-Cas9–mediated engineering of human intestinal organoids , 2015, Nature Medicine.

[270]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[271]  R. Scheule,et al.  Basis of pulmonary toxicity associated with cationic lipid-mediated gene transfer to the mammalian lung. , 1997, Human gene therapy.

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

[273]  M. Spector,et al.  Plasmid size influences chitosan nanoparticle mediated gene transfer to chondrocytes. , 2008, Journal of biomedical materials research. Part A.

[274]  J. Fu,et al.  Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus , 2015, Gene Therapy.

[275]  Zhiping Weng,et al.  Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses. , 2015, Human gene therapy.

[276]  Matthias John,et al.  RNAi-mediated gene silencing in non-human primates , 2006, Nature.

[277]  E. Wisse,et al.  The size of endothelial fenestrae in human liver sinusoids: implications for hepatocyte-directed gene transfer , 2008, Gene Therapy.

[278]  Isaac B. Hilton,et al.  Editing the epigenome: technologies for programmable transcription and epigenetic modulation , 2016, Nature Methods.

[279]  Chih-Kuang Yeh,et al.  Focused ultrasound-induced blood-brain barrier opening for non-viral, non-invasive, and targeted gene delivery. , 2015, Journal of controlled release : official journal of the Controlled Release Society.

[280]  M. Boutros,et al.  E-CRISP: fast CRISPR target site identification , 2014, Nature Methods.

[281]  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.

[282]  Volker Hovestadt,et al.  Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling , 2015, Nature Communications.

[283]  Gene W. Yeo,et al.  Applications of Cas9 as an RNA-programmed RNA-binding protein. , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[284]  K. Chayama,et al.  Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system , 2014, Scientific Reports.

[285]  Morgan L. Maeder,et al.  CRISPR RNA-guided activation of endogenous human genes , 2013, Nature Methods.

[286]  George M. Church,et al.  In vivo gene editing in dystrophic mouse muscle and muscle stem cells , 2016, Science.

[287]  Alexander Bolotin,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.

[288]  Christopher M. Vockley,et al.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors , 2013, Nature Methods.

[289]  D. Chung,et al.  Enhancement of chitosan-mediated gene delivery through combination with phiC31 integrase. , 2015, Acta biomaterialia.

[290]  David A. Scott,et al.  Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells , 2014, Nature Biotechnology.

[291]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[292]  B. Sullenger,et al.  RNA aptamers as reversible antagonists of coagulation factor IXa , 2002, Nature.

[293]  Dongsheng Duan,et al.  In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy , 2016, Science.

[294]  David S. Weiss,et al.  A CRISPR-CAS System Mediates Bacterial Innate Immune Evasion and Virulence , 2013, Nature.

[295]  K. Makino,et al.  Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product , 1987, Journal of bacteriology.

[296]  R. Jaenisch,et al.  One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[297]  Zhan Yuin Ong,et al.  Polymer- and lipid-based nanoparticle therapeutics for the treatment of liver diseases , 2010 .

[298]  Yi-Ping Ho,et al.  Microfluidic Preparation of Polymer-Nucleic Acid Nanocomplexes Improves Nonviral Gene Transfer , 2013, Scientific Reports.