Progress and challenges towards CRISPR/Cas clinical translation.

CRISPR/Cas systems (clustered regularly interspaced short palindromic repeats) have emerged as powerful tools to manipulate the genome for both research and therapeutic purposes. However, the clinical use of this system is hindered by multiple challenges, such as the rate of off-target effects, editing efficiency, the efficacy of HDR, immunogenicity, as well as development of efficient and safe delivery vehicles that can carry these compounds. Tremendous efforts are being conducted to overcome these challenges, including the discovery and engineering of more precise and efficacious Cas nucleases. Moreover, in recent years multiple viral and non-viral delivery approaches have been explored for in vivo delivery of CRISPR components. Here, we summarize the available CRISPR/Cas toolbox for genome editing as well as the recently developed in vivo delivery vehicles for CRISPR/Cas system. Furthermore, we discuss the remaining challenges for successful clinical translation of this system and highlight the current clinical applications.

[1]  Bin Zhang,et al.  CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia. , 2019, The New England journal of medicine.

[2]  Adrian Pickar-Oliver,et al.  The next generation of CRISPR–Cas technologies and applications , 2019, Nature Reviews Molecular Cell Biology.

[3]  Yuan He,et al.  CRISPR/Cas9-Mediated CCR5 Ablation in Human Hematopoietic Stem/Progenitor Cells Confers HIV-1 Resistance In Vivo. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[4]  Jun Li,et al.  Targeted genome modification of crop plants using a CRISPR-Cas system , 2013, Nature Biotechnology.

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

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

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

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

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

[10]  W. Harrington,et al.  A Single Administration of CRISPR/Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing. , 2018, Cell reports.

[11]  Namritha Ravinder,et al.  Enhanced CRISPR/Cas9-mediated precise genome editing by improved design and delivery of gRNA, Cas9 nuclease, and donor DNA. , 2017, Journal of biotechnology.

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

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

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

[15]  Zhen Gu,et al.  Rational designs of in vivo CRISPR-Cas delivery systems. , 2019, Advanced drug delivery reviews.

[16]  Dana V. Foss,et al.  Clinical applications of CRISPR‐based genome editing and diagnostics , 2019, Transfusion.

[17]  D. Peer,et al.  A Combinatorial Library of Lipid Nanoparticles for RNA Delivery to Leukocytes , 2020, Advanced materials.

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

[19]  Melissa M. Harrison,et al.  Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease , 2013, Genetics.

[20]  Max J. Kellner,et al.  RNA editing with CRISPR-Cas13 , 2017, Science.

[21]  J. Bungert,et al.  Genome Editing for Sickle Cell Disease: A Little BCL11A Goes a Long Way. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[22]  D. Peer,et al.  Targeted lipid nanoparticles for RNA therapeutics and immunomodulation in leukocytes. , 2020, Advanced drug delivery reviews.

[23]  Y. Kan,et al.  Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac , 2014, Genome research.

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

[25]  Xiaoyuan Chen,et al.  Non-viral delivery systems for CRISPR/Cas9-based genome editing: Challenges and opportunities. , 2018, Biomaterials.

[26]  Kira S. Makarova,et al.  Diversity and evolution of class 2 CRISPR–Cas systems , 2017, Nature Reviews Microbiology.

[27]  Minjung Song The CRISPR/Cas9 system: Their delivery, in vivo and ex vivo applications and clinical development by startups , 2017, Biotechnology progress.

[28]  CRISPR/Cas9 system targeting regulatory genes of HIV-1 inhibits viral replication in infected T-cell cultures , 2018, Scientific Reports.

[29]  R. Rad,et al.  Engineering CRISPR mouse models of cancer. , 2019, Current opinion in genetics & development.

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

[31]  E. M. DeGennaro,et al.  Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array , 2016, Nature Biotechnology.

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

[33]  Jiaqiang Zhang,et al.  CRISPR-Cas12 and Cas13: the lesser known siblings of CRISPR-Cas9 , 2019, Cell Biology and Toxicology.

[34]  S. Konermann,et al.  Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors , 2018, Cell.

[35]  Mithat Gönen,et al.  Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection , 2017, Nature.

[36]  E. Nowak,et al.  5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes. , 2018, Journal of the American Chemical Society.

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

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

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

[40]  Sheridan M. Hoy Patisiran: First Global Approval , 2018, Drugs.

[41]  E. Olson,et al.  CRISPR-Cas9 corrects Duchenne muscular dystrophy exon 44 deletion mutations in mice and human cells , 2019, Science Advances.

[42]  Wei Li,et al.  Repurposing CRISPR-Cas12b for mammalian genome engineering , 2018, Cell Discovery.

[43]  M. Porteus,et al.  Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements. , 2019, Molecular therapy : the journal of the American Society of Gene Therapy.

[44]  Haiyan Jiang,et al.  Prevalence of Pre-existing Antibodies to CRISPR-Associated Nuclease Cas9 in the USA Population , 2018, Molecular therapy. Methods & clinical development.

[45]  Daniel G Anderson,et al.  Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery. , 2019, Molecular therapy : the journal of the American Society of Gene Therapy.

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

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

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

[49]  Baohui Chen,et al.  Recent advances in CRISPR research , 2020, Protein & Cell.

[50]  F. Zhang,et al.  Development of CRISPR-Cas systems for genome editing and beyond , 2019, Quarterly Reviews of Biophysics.

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

[52]  Yunmei Ma,et al.  Mechanism and regulation of human non-homologous DNA end-joining , 2003, Nature Reviews Molecular Cell Biology.

[53]  Haiyan Jiang,et al.  Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10 , 2019, Nature Medicine.

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

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

[56]  Vijender Chaitankar,et al.  Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice , 2017, Nature Communications.

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

[58]  Marilyn Fisher,et al.  Simple and efficient CRISPR/Cas9‐mediated targeted mutagenesis in Xenopus tropicalis , 2013, Genesis.

[59]  George M. Church,et al.  Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems , 2013, Nucleic acids research.

[60]  Yanhua Cui,et al.  Analysis of CRISPR-Cas System in Streptococcus thermophilus and Its Application , 2018, Front. Microbiol..

[61]  R. Bak,et al.  CRISPR-Mediated Integration of Large Gene Cassettes Using AAV Donor Vectors. , 2017, Cell reports.

[62]  Kira S. Makarova,et al.  Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL domain-containing accessory protein , 2018, Molecular cell.

[63]  M. Hope,et al.  Pieter Cullis’ quest for a lipid-based, fusogenic delivery system for nucleic acid therapeutics: success with siRNA so what about mRNA? , 2016, Journal of drug targeting.

[64]  P. Duchateau,et al.  ‘Off-the-shelf’ allogeneic CAR T cells: development and challenges , 2020, Nature Reviews Drug Discovery.

[65]  J. Neefjes,et al.  Towards a systems understanding of MHC class I and MHC class II antigen presentation , 2011, Nature Reviews Immunology.

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

[67]  J. Christensen,et al.  Adaptive Immunity against Streptococcus pyogenes in Adults Involves Increased IFN-γ and IgG3 Responses Compared with Children , 2015, The Journal of Immunology.

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

[69]  Daniel G. Anderson,et al.  Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing , 2017, Nature Biotechnology.

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

[71]  Bruno Laugel,et al.  Beyond the Antigen Receptor: Editing the Genome of T-Cells for Cancer Adoptive Cellular Therapies , 2013, Front. Immunol..

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

[73]  Yuquan Wei,et al.  A phase I trial of PD-1 deficient engineered T cells with CRISPR/Cas9 in patients with advanced non-small cell lung cancer. , 2018 .

[74]  Beum-Chang Kang,et al.  CRISPR/Cpf1-mediated DNA-free plant genome editing , 2017, Nature Communications.

[75]  David C. Smith,et al.  Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. , 2012, The New England journal of medicine.

[76]  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.

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

[78]  J. Tisdale,et al.  Gene therapy for sickle cell disease: An update. , 2018, Cytotherapy.

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

[80]  Sergey A. Shmakov,et al.  Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28 , 2016, bioRxiv.

[81]  O. Merkel,et al.  Immunogenicity of Cas9 Protein. , 2020, Journal of pharmaceutical sciences.

[82]  Jacob E Corn,et al.  Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA , 2016, Nature Biotechnology.

[83]  Antonio J Giraldez,et al.  CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing , 2017, bioRxiv.

[84]  George M. Church,et al.  Heritable genome editing in C. elegans via a CRISPR-Cas9 system , 2013, Nature Methods.

[85]  P. Cullis,et al.  Lipid Nanoparticle Systems for Enabling Gene Therapies. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[86]  Ping Wang,et al.  In Vivo Ovarian Cancer Gene Therapy Using CRISPR-Cas9. , 2018, Human gene therapy.

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

[88]  D. Vanrompay,et al.  mRNA therapeutics deliver a hopeful message , 2018, Nano Today.

[89]  K. Heuner,et al.  First indication for a functional CRISPR/Cas system in Francisella tularensis. , 2013, International journal of medical microbiology : IJMM.

[90]  S. Sarcar,et al.  Efficient In Vivo Liver-Directed Gene Editing Using CRISPR/Cas9 , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[91]  F. Lowy Staphylococcus aureus infections. , 2009, The New England journal of medicine.

[92]  George M. Church,et al.  Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9 , 2013, Nature Biotechnology.

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

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

[95]  Gerald Schwank,et al.  Advances in therapeutic CRISPR/Cas9 genome editing. , 2016, Translational research : the journal of laboratory and clinical medicine.

[96]  Daniel G. Anderson,et al.  Engineering circular RNA for potent and stable translation in eukaryotic cells , 2018, Nature Communications.

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

[98]  Dan Peer,et al.  Progress and challenges towards targeted delivery of cancer therapeutics , 2018, Nature Communications.

[99]  Chen Li,et al.  A clinically meaningful fetal hemoglobin threshold for children with sickle cell anemia during hydroxyurea therapy , 2017, American journal of hematology.

[100]  Jennifer A. Doudna,et al.  Programmed DNA destruction by miniature CRISPR-Cas14 enzymes , 2018, Science.

[101]  J. Kinney,et al.  Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization , 2017, Nature Communications.

[102]  Benjamin L. Oakes,et al.  CRISPR-CasX is an RNA-dominated enzyme active for human genome editing , 2019, Nature.

[103]  Yi-Wei Lee,et al.  In Vivo Delivery of CRISPR/Cas9 for Therapeutic Gene Editing: Progress and Challenges. , 2017, Bioconjugate chemistry.

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

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

[106]  Venkata R. Krishnamurthy,et al.  Recent advances in polymeric materials for the delivery of RNA therapeutics , 2019, Expert opinion on drug delivery.

[107]  Yang Liu,et al.  Systemic delivery of CRISPR/Cas9 with PEG-PLGA nanoparticles for chronic myeloid leukemia targeted therapy. , 2018, Biomaterials science.

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

[109]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[110]  Theresa A. Storm,et al.  Comparison of adenoviral and adeno-associated viral vectors for pancreatic gene delivery in vivo. , 2004, Human gene therapy.

[111]  H. Wasan,et al.  Clinical efficacy and safety of anti-PD-1/PD-L1 inhibitors for the treatment of advanced or metastatic cancer: a systematic review and meta-analysis , 2020, Scientific Reports.

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

[113]  Enrico Mastrobattista,et al.  Delivery Aspects of CRISPR/Cas for in Vivo Genome Editing , 2019, Accounts of chemical research.

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

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

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

[117]  Shiraz A Shah,et al.  CRISPR adaptive immune systems of Archaea , 2014, RNA biology.

[118]  Robert Brenner,et al.  Nanoparticle delivery of CRISPR into the brain rescues a mouse model of fragile X syndrome from exaggerated repetitive behaviours , 2018, Nature Biomedical Engineering.

[119]  Yan Zhang,et al.  DNase H Activity of Neisseria meningitidis Cas9. , 2015, Molecular cell.

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

[121]  D. Peer,et al.  Delivering the right message: Challenges and opportunities in lipid nanoparticles-mediated modified mRNA therapeutics-An innate immune system standpoint. , 2017, Seminars in immunology.

[122]  Eugene V Koonin,et al.  RNA-guided DNA insertion with CRISPR-associated transposases , 2019, Science.

[123]  Gang Bao,et al.  A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human haematopoietic stem and progenitor cells , 2018, Nature Medicine.

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

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

[126]  E. Fuchs,et al.  Allogeneic stem cell transplantation for sickle cell disease , 2016, Current opinion in hematology.

[127]  Y. Yamaguchi-Iwai,et al.  Homologous recombination and non‐homologous end‐joining pathways of DNA double‐strand break repair have overlapping roles in the maintenance of chromosomal integrity in vertebrate cells , 1998, The EMBO journal.

[128]  Jennifer A. Doudna,et al.  New CRISPR-Cas systems from uncultivated microbes , 2016, Nature.