CRISPR genome engineering and viral gene delivery: A case of mutual attraction

The adaptation of the CRISPR/Cas9 DNA engineering machinery for mammalian cells has revolutionized our approaches to low‐ or high‐throughput genome annotation and paved the way for conceptually novel therapeutic strategies. A large part of the attraction of CRISPR stems from the small size of its two core components – Cas9 and gRNA – and hence its compatibility with virtually any available viral vector delivery system. As a result, over the past two years, four major classes of viral vectors have already been engineered and applied as CRISPR delivery tools – retroviruses, lentiviruses, adenoviruses, and adeno‐associated viruses (AAVs). The juxtaposition of these two technologies reflects a case of tremendous mutual attraction and holds unprecedented promises for biology and medicine. Here, we provide an overview of the state‐of‐the‐art of this rapidly emerging field, from a comparative description of the principal vector designs, to a synopsis of some of the most exciting applications that were reported to date, including the use of viral CRISPR vectors for genome‐wide loss‐of‐function screens, multiplexed gene editing or disease modeling in animals. Once specificity and safety have been improved further, viral vector‐mediated in vitro/in vivo CRISPR delivery and expression promise to radically transform basic and applied biomedical research.

[1]  M. Kay,et al.  Therapeutic application of RNAi: is mRNA targeting finally ready for prime time? , 2007, The Journal of clinical investigation.

[2]  D. Trono,et al.  Dual-regulated lentiviral vector for gene therapy of X-linked chronic granulomatosis. , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[3]  M. Ehlers,et al.  Optimizing promoters for recombinant adeno-associated virus-mediated gene expression in the peripheral and central nervous system using self-complementary vectors. , 2011, Human gene therapy.

[4]  D. Bouard,et al.  Viral vectors: from virology to transgene expression , 2009, British journal of pharmacology.

[5]  Shiyou Zhu,et al.  High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells , 2014, Nature.

[6]  Joana A. Vidigal,et al.  In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system , 2014, Nature.

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

[8]  Pumin Zhang,et al.  Efficient gene editing in adult mouse livers via adenoviral delivery of CRISPR/Cas9 , 2014, FEBS letters.

[9]  Charles A. Gersbach,et al.  Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector , 2014, Nucleic acids research.

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

[11]  L. Nissim,et al.  Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. , 2014, Molecular cell.

[12]  T. Kinsella,et al.  DNA mismatch repair (MMR) mediates 6-thioguanine genotoxicity by introducing single-strand breaks to signal a G2-M arrest in MMR-proficient RKO cells. , 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

[13]  Claudio Mussolino,et al.  TALE nucleases: tailored genome engineering made easy. , 2012, Current opinion in biotechnology.

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

[15]  Theresa A. Storm,et al.  In Vitro and In Vivo Gene Therapy Vector Evolution via Multispecies Interbreeding and Retargeting of Adeno-Associated Viruses , 2008, Journal of Virology.

[16]  Dirk Grimm,et al.  The dose can make the poison: lessons learned from adverse in vivo toxicities caused by RNAi overexpression , 2011, Silence.

[17]  Elizabeth Pennisi,et al.  The CRISPR craze. , 2013, Science.

[18]  A. Annoni,et al.  A microRNA-regulated lentiviral vector mediates stable correction of hemophilia B mice. , 2007, Blood.

[19]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[20]  Jennifer A. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas 9 GENOME , 2014 .

[21]  Dominik Niopek,et al.  CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. , 2014, Biotechnology journal.

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

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

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

[25]  M. Gonçalves,et al.  Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells , 2014, Scientific Reports.

[26]  D. Grimm Production methods for gene transfer vectors based on adeno-associated virus serotypes. , 2002, Methods.

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

[28]  J. Cigudosa,et al.  Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR–Cas9 system , 2014, Nature Communications.

[29]  Theresa A. Storm,et al.  Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways , 2006, Nature.

[30]  Juan Li,et al.  Liver-specific microRNA-122 target sequences incorporated in AAV vectors efficiently inhibits transgene expression in the liver , 2010, Gene Therapy.

[31]  Luigi Naldini,et al.  Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications , 2009, Nature Reviews Genetics.

[32]  D. McCarty,et al.  Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis , 2001, Gene Therapy.

[33]  John J. Rossi,et al.  Strategies for silencing human disease using RNA interference , 2007, Nature Reviews Genetics.

[34]  M. Porteus,et al.  Development of nuclease-mediated site-specific genome modification. , 2012, Current opinion in immunology.

[35]  Toni Cathomen,et al.  Adenoviral vector DNA for accurate genome editing with engineered nucleases , 2014, Nature Methods.

[36]  M. Kay,et al.  From virus evolution to vector revolution: use of naturally occurring serotypes of adeno-associated virus (AAV) as novel vectors for human gene therapy. , 2003, Current gene therapy.

[37]  D. Lillicrap,et al.  Current status of haemophilia gene therapy , 2014, Haemophilia : the official journal of the World Federation of Hemophilia.

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

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

[40]  Elif Karaca,et al.  Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. , 2014, Cell reports.

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

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

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

[44]  R. Eils,et al.  Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells , 2014, Nature Communications.

[45]  L. Medina-Kauwe,et al.  Effective high-capacity gutless adenoviral vectors mediate transgene expression in human glioma cells. , 2006, Molecular therapy : the journal of the American Society of Gene Therapy.

[46]  D. Grimm,et al.  Engineering and evolution of synthetic adeno-associated virus (AAV) gene therapy vectors via DNA family shuffling. , 2012, Journal of visualized experiments : JoVE.

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

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

[49]  D. Trono Lentiviral vectors: turning a deadly foe into a therapeutic agent , 2000, Gene Therapy.

[50]  Wadih Arap,et al.  Random peptide libraries displayed on adeno-associated virus to select for targeted gene therapy vectors , 2003, Nature Biotechnology.

[51]  James M. Wilson,et al.  New recombinant serotypes of AAV vectors. , 2005, Current gene therapy.

[52]  H. Nakai,et al.  Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing , 2014, Nature Communications.

[53]  D. Schaffer,et al.  DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

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

[55]  Mark A. Kay,et al.  Progress and problems with the use of viral vectors for gene therapy , 2003, Nature Reviews Genetics.

[56]  Inder M. Verma,et al.  Gene therapy: trials and tribulations , 2000, Nature Reviews Genetics.

[57]  C. Sheridan,et al.  Gene therapy finds its niche , 2011, Nature Biotechnology.

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

[59]  N. Sharpless,et al.  Engineering and Selection of Shuffled AAV Genomes: A New Strategy for Producing Targeted Biological Nanoparticles. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[60]  L. Naldini,et al.  Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer , 2006, Nature Medicine.

[61]  R. Samulski,et al.  Directed evolution of a novel adeno-associated virus (AAV) vector that crosses the seizure-compromised blood-brain barrier (BBB). , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

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

[63]  D. Trono,et al.  A Third-Generation Lentivirus Vector with a Conditional Packaging System , 1998, Journal of Virology.

[64]  L. Biasco,et al.  Retroviral Integrations in Gene Therapy Trials , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

[65]  M. Hallek,et al.  Genetic modifications of the adeno-associated virus type 2 capsid reduce the affinity and the neutralizing effects of human serum antibodies , 2003, Gene Therapy.

[66]  Josée Dostie,et al.  Repurposing CRISPR/Cas9 for in situ functional assays , 2013, Genes & development.

[67]  Knut Stieger,et al.  In vivo gene regulation using tetracycline-regulatable systems , 2009, Advanced Drug Delivery Reviews.

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

[69]  R. Kontermann,et al.  Tropism Modification of Adenovirus Vectors by Peptide Ligand Insertion into Various Positions of the Adenovirus Serotype 41 Short-Fiber Knob Domain , 2006, Journal of Virology.

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

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

[72]  C. von Kalle,et al.  Uncovering and dissecting the genotoxicity of self-inactivating lentiviral vectors in vivo. , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[73]  R. Herzog,et al.  Long-term correction of inhibitor-prone hemophilia B dogs treated with liver-directed AAV2-mediated factor IX gene therapy. , 2009, Blood.

[74]  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.

[75]  David T. Curiel,et al.  Engineering targeted viral vectors for gene therapy , 2007, Nature Reviews Genetics.