Refining strategies to translate genome editing to the clinic

Recent progress in developing programmable nucleases, such as zinc-finger nucleases, transcription activator–like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)–Cas nucleases, have paved the way for gene editing to enter clinical practice. This translation is a result of combining high nuclease activity with high specificity and successfully applying this technology in various preclinical disease models, including infectious disease, primary immunodeficiencies, hemoglobinopathies, hemophilia and muscular dystrophy. Several clinical gene-editing trials, both ex vivo and in vivo, have been initiated in the past 2 years, including studies that aim to knockout genes as well as to add therapeutic transgenes. Here we discuss the advances made in the gene-editing field in recent years, and specify priorities that need to be addressed to expand therapeutic genome editing to further disease entities.

[1]  David R. Liu,et al.  Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage , 2016, Nature.

[2]  Matthew C. Canver,et al.  BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis , 2015, Nature.

[3]  J. Keith Joung,et al.  731. High-Fidelity CRISPR-Cas9 Nucleases with No Detectable Genome-Wide Off-Target Effects , 2016 .

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

[5]  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.

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

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

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

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

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

[11]  David A. Williams,et al.  Concise Review: Lessons Learned From Clinical Trials of Gene Therapy in Monogenic Immunodeficiency Diseases , 2014, Stem cells translational medicine.

[12]  R. Hardison,et al.  A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition , 2016, Nature Medicine.

[13]  Y. Doyon,et al.  In vivo genome editing of the albumin locus as a platform for protein replacement therapy. , 2015, Blood.

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

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

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

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

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

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

[20]  Pavel Sumazin,et al.  Reprogramming metabolic pathways in vivo with CRISPR/Cas9 genome editing to treat hereditary tyrosinaemia , 2016, Nature Communications.

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

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

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

[24]  T. Cathomen,et al.  Inactivation of Hepatitis B Virus Replication in Cultured Cells and In Vivo with Engineered Transcription Activator-Like Effector Nucleases , 2013, Molecular therapy : the journal of the American Society of Gene Therapy.

[25]  Aaron R Cooper,et al.  CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells. , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[26]  Kezhen Li,et al.  Zinc Finger Nucleases Targeting the Human Papillomavirus E7 Oncogene Induce E7 Disruption and a Transformed Phenotype in HPV16/18-Positive Cervical Cancer Cells , 2014, Clinical Cancer Research.

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

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

[29]  Yang Yang,et al.  A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice , 2016, Nature Biotechnology.

[30]  Castle Raley,et al.  Targeted Gene Addition to a Safe Harbor locus in human CD34+ Hematopoietic Stem Cells for Correction of X-linked Chronic Granulomatous Disease , 2016, Nature Biotechnology.

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

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

[33]  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.

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

[35]  Davide Cittaro,et al.  Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing , 2016, Cell.

[36]  A. Rodríguez-Gascón,et al.  Treatment of ocular disorders by gene therapy. , 2015, European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V.

[37]  Jennifer Doudna,et al.  RNA-programmed genome editing in human cells , 2013, eLife.

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

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

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

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

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

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

[44]  Gang Bao,et al.  The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[45]  D. Carroll Genome Engineering With Zinc-Finger Nucleases , 2011, Genetics.

[46]  Yongyan Wu,et al.  Generation of TALE nickase-mediated gene-targeted cows expressing human serum albumin in mammary glands , 2016, Scientific Reports.

[47]  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.

[48]  Edward M. Callaway,et al.  In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration , 2016, Nature.

[49]  Luigi Naldini,et al.  Gene therapy returns to centre stage , 2015, Nature.

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

[51]  J F Glenn,et al.  Prospects and challenges. , 1967, The Journal of urology.

[52]  F. Daboussi,et al.  Optimized tuning of TALEN specificity using non-conventional RVDs , 2015, Scientific Reports.

[53]  Y. E. Chen,et al.  RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency , 2016, Nature Communications.

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

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

[56]  Martin J. Aryee,et al.  Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells , 2016, Nature Biotechnology.

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

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

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

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

[61]  V. Poli,et al.  STAT1 and STAT3 in tumorigenesis , 2012, JAK-STAT.

[62]  H. Ochs,et al.  Targeted gene editing restores regulated CD40L function in X-linked hyper-IgM syndrome. , 2016, Blood.

[63]  Lei Zhang,et al.  Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells. , 2015, Blood.

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

[65]  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.

[66]  V. Hornung,et al.  Intracellular DNA recognition , 2010, Nature Reviews Immunology.

[67]  A. Schambach,et al.  Gene therapy on the move , 2013, EMBO molecular medicine.

[68]  Toni Cathomen,et al.  Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion , 2010, Nucleic acids research.

[69]  A. Schambach,et al.  Successful RAG1-SCID gene therapy depends on the level of RAG1 expression. , 2014, The Journal of allergy and clinical immunology.

[70]  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.

[71]  G. Church,et al.  Cas9 as a versatile tool for engineering biology , 2013, Nature Methods.

[72]  Ciaran M Lee,et al.  Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[73]  Jin-Soo Kim,et al.  Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells , 2016, Nature Biotechnology.

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

[75]  David A. Williams,et al.  Chance or necessity? Insertional mutagenesis in gene therapy and its consequences. , 2003, Molecular therapy : the journal of the American Society of Gene Therapy.

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

[77]  Sruthi Mantri,et al.  CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells , 2016, Nature.

[78]  R. Barrangou,et al.  Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria , 2012, Proceedings of the National Academy of Sciences.

[79]  Baorui Liu,et al.  CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients , 2016, Scientific Reports.

[80]  Seung Woo Cho,et al.  Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[81]  A. Scharenberg,et al.  Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template , 2015, Science Translational Medicine.

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

[83]  P. Gregory,et al.  Homology-driven genome editing in hematopoietic stem and progenitor cells using zinc finger nuclease mRNA and AAV6 donors , 2015, Nature Biotechnology.

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

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

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

[87]  C. Hogan A matter of balance. , 1995, Australian family physician.

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

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

[90]  Maximilian Müller,et al.  Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome. , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

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

[92]  A. R. Gascón,et al.  Multicomponent nanoparticles as nonviral vectors for the treatment of Fabry disease by gene therapy , 2012, Drug design, development and therapy.

[93]  C. Dunbar,et al.  Gene Editing of Human Hematopoietic Stem and Progenitor Cells: Promise and Potential Hurdles. , 2016, Human gene therapy.

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

[95]  Aymeric Duclert,et al.  Multiplex Genome-Edited T-cell Manufacturing Platform for "Off-the-Shelf" Adoptive T-cell Immunotherapies. , 2015, Cancer research.

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

[97]  Adrian J. Thrasher,et al.  Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells , 2017, Science Translational Medicine.