Cited by 1,185CRISPR and Genetic EngineeringRNA Interference and Gene DeliveryVirus-based gene therapy research

The DOI matches its Crossref record; 229 of the 233 references it cites were found in a registry or an index; 38 of the 138 sources its claims cite were checked for support.

Delivering CRISPR: a review of the challenges and approaches

Open access

Abstract

Gene therapy has long held promise to correct a variety of human diseases and defects. Discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR), the mechanism of the CRISPR-based prokaryotic adaptive immune system (CRISPR-associated system, Cas), and its repurposing into a potent gene editing tool has revolutionized the field of molecular biology and generated excitement for new and improved gene therapies. Additionally, the simplicity and flexibility of the CRISPR/Cas9 site-specific nuclease system has led to its widespread use in many biological research areas including development of model cell lines, discovering mechanisms of disease, identifying disease targets, development of transgene animals and plants, and transcriptional modulation. In this review, we present the brief history and basic mechanisms of the CRISPR/Cas9 system and its predecessors (ZFNs and TALENs), lessons learned from past human gene therapy efforts, and recent modifications of CRISPR/Cas9 to provide functions beyond gene editing. We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized. The focus then turns to the most difficult barrier to potential in vivo use of CRISPR/Cas9, delivery. We detail the various cargos and delivery vehicles reported for CRISPR/Cas9, including physical delivery methods (e.g. microinjection; electroporation), viral delivery methods (e.g. adeno-associated virus (AAV); full-sized adenovirus and lentivirus), and non-viral delivery methods (e.g. liposomes; polyplexes; gold particles), and discuss their relative merits. We also examine several technologies that, while not currently reported for CRISPR/Cas9 delivery, appear to have promise in this field. The therapeutic potential of CRISPR/Cas9 is vast and will only increase as the technology and its delivery improves.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

This review summarizes CRISPR/Cas9 biology, modifications beyond gene editing, factors affecting efficacy, and delivery vehicles for in vivo gene therapy, concluding that delivery is the greatest obstacle. It surveys physical, viral, non-viral, and emerging delivery approaches and their relative merits.

Key findings

  • CRISPR/Cas9 is a two-component RNA-guided nuclease that has been repurposed beyond editing, including CRISPRi, CRISPRa, base editing of A•T to G•C at ~50% efficiency with few undesired mutations in human cells, epigenetic modulation, inducible systems, CASFISH, and RNA targeting.
  • Delivery remains the greatest obstacle; cargo options are DNA plasmid, Cas9 mRNA plus sgRNA, or Cas9:sgRNA ribonucleoprotein (RNP), with RNP generally giving the best editing and minimal off-target effects. Reported efficiencies include microinjection approaching 100%, DNA nanoclew ~36% versus 5% for bare Cas9:sgRNA plus PEI, gold nanoparticles ~30%, iTOP ~70% knockout, and lipid nanoparticles ~70% in vitro after lipid screening.
  • Viral vector capacities differ: AAV ~4.5–5 kb, adenovirus 8 kb, and lentivirus ~10 kb up to 18 kb; AAV is ~20 nm while lentivirus/adenovirus are ~80–100 nm. Viral vectors are common for in vivo work but carry immunogenicity and integration risks.
  • Efficacy factors include HDR versus NHEJ repair (in mice, HDR 0.5–20% and NHEJ 20–60%), Scr7 increasing HDR up to 19-fold, low Cas9 turnover of ~0.3–1.0 min−1, and persistent off-target cutting. Early gene therapy tragedies were delivery-related: in the SCID-X1 trial 17 were cured, five developed T-cell leukemia, and one died; an OTC patient died from an adenovirus vector inflammatory response.

Methods

  • Narrative review with no primary experiments; it synthesizes published literature on CRISPR/Cas9 history, mechanism, modifications, efficacy factors, and delivery.
  • Includes Table 1 comparing delivery vehicles by composition, common cargo, capacity, advantages, limitations, ease of use, and references, and discusses selected preclinical studies.
  • Main analysis is qualitative synthesis; no systematic search, meta-analysis, or new data are reported.

Limitations

  • Stated: delivery remains the greatest obstacle and no all-purpose method has emerged; off-target effects and poor understanding of them remain; safety and long-term toxicity of nanoparticle components have limited information; many emerging technologies are not yet proven with CRISPR.
  • Stated: some methods are in vitro/ex vivo only (microinjection and electroporation generally; hydrodynamic delivery is not being considered clinically due to trauma; CPPs are not generally used in vivo); viral vectors elicit immune responses and cannot completely eliminate integration risk.
  • Evident: as a narrative review, it lacks systematic search/meta-analysis and primary data; Table 1 ease-of-use is explicitly described as subjective.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1080/10717544.2018.1474964

Cites

229 of 229 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Figures

Figure 1. Following formation of a double stranded break (DSB), endogenous DNA repair can occur by (A) non-homologous end joining (NHEJ) resulting in random indels, or by (B) homology-directed repair (HDR) which uses a template DNA strand for precise repair.
Figure 1. Following formation of a double stranded break (DSB), endogenous DNA repair can occur by (A) non-homologous end joining (NHEJ) resulting in random indels, or by (B) homology-directed repair (HDR) which uses a template DNA strand for precise repair.CC BY · PubMed Central
Figure 2. Products of site-specific nuclease-based gene editing: (A) gene knockout, (B) gene deletion, (C) gene correction, and (D) gene addition.
Figure 2. Products of site-specific nuclease-based gene editing: (A) gene knockout, (B) gene deletion, (C) gene correction, and (D) gene addition.CC BY · PubMed Central
Figure 3. Site-specific endonucleases with programable DNA-binding protein domains: (A) zinc finger nucleases (ZFNs) and (B) transcription activator-like effector nucleases (TALENs).
Figure 3. Site-specific endonucleases with programable DNA-binding protein domains: (A) zinc finger nucleases (ZFNs) and (B) transcription activator-like effector nucleases (TALENs).CC BY · PubMed Central
Figure 4. Biology of the type II CRISPR/Cas system. (A) Genomic representation of CRISPR/Cas9 along with relevant transcription/translation products. (B) Engineered CRISPR/Cas9 for site-specific gene editing (sgRNA:Cas9). Grey arrows indicate sites of single-stranded nucleotide breaks.
Figure 4. Biology of the type II CRISPR/Cas system. (A) Genomic representation of CRISPR/Cas9 along with relevant transcription/translation products. (B) Engineered CRISPR/Cas9 for site-specific gene editing (sgRNA:Cas9). Grey arrows indicate sites of single-stranded nucleotide breaks.CC BY · PubMed Central
Figure 5. Physical methods for delivery of CRISPR. (A) Microinjection disrupting two genes (Ppar-γ and Rag1) in Cynomolgus monkeys from a single injection into one-cell-stage embryos. Photographs of Founder Monkeys A and B, PCR products of the targeted loci from genomic DNA of A and B, and a control wild-type Cynomolgus monkey (Con). Adapted with permission from Nui et al. (2014). Copyright 2014 Elsevier Inc. (B) Electroporation delivery of CRISPR RNP targeting genes impacting mice coat color (Tyr) followed by transfer to pseudopregnant mothers. Bar plot quantifies coat color phenotypes generated from microinjection and electroporation at 1 ms pulse length and 3 ms pulse length. Adapted with permission from Chen et al. (2016). Copyright 2016 American Society for Biochemistry and Molecular Biology. (C) Hydrodynamic injection of CRISPR into mice results in liver-specific targeting (see bioluminescence image of hydrodynamically injected luciferase plasmid), generating indel mutation of two tumor suppressor genes and oncogenes. The development of liver tumors can be seen in the hematoxylin and eosin (H&E) and cytokeratin 19 (Ck19)-stained micrographs. Adapted with permission from Xue et al. (2014). Copyright 2014 Macmillan Publishers Ltd: Nature.
Figure 5. Physical methods for delivery of CRISPR. (A) Microinjection disrupting two genes (Ppar-γ and Rag1) in Cynomolgus monkeys from a single injection into one-cell-stage embryos. Photographs of Founder Monkeys A and B, PCR products of the targeted loci from genomic DNA of A and B, and a control wild-type Cynomolgus monkey (Con). Adapted with permission from Nui et al. (2014). Copyright 2014 Elsevier Inc. (B) Electroporation delivery of CRISPR RNP targeting genes impacting mice coat color (Tyr) followed by transfer to pseudopregnant mothers. Bar plot quantifies coat color phenotypes generated from microinjection and electroporation at 1 ms pulse length and 3 ms pulse length. Adapted with permission from Chen et al. (2016). Copyright 2016 American Society for Biochemistry and Molecular Biology. (C) Hydrodynamic injection of CRISPR into mice results in liver-specific targeting (see bioluminescence image of hydrodynamically injected luciferase plasmid), generating indel mutation of two tumor suppressor genes and oncogenes. The development of liver tumors can be seen in the hematoxylin and eosin (H&E) and cytokeratin 19 (Ck19)-stained micrographs. Adapted with permission from Xue et al. (2014). Copyright 2014 Macmillan Publishers Ltd: Nature.CC BY · PubMed Central
Figure 6. Viral vector methods for delivery of CRISPR. (A) AAV delivery of Cas9 and sgRNAs disrupting mutations in the Dmd gene in adult mdx mice, resulting in improvement of muscle biochemistry and function. Adapted with permission from Long et al. (2016). Copyright 2016 American Association for the Advancement of Science. (B) AAV intratracheal instillation delivery of sgRNAs in Cre-dependent Cas9 knock-in mice, resulting in lung adenocarcinoma (EGFP-positive tumors). Adapted with permission from Platt et al. (2016). Copyright 2014 Elsevier Inc. (C) A split Cas9 system in which the Cas9 C-terminal is packaged into one AAV vector and the Cas9 N-terminal is packaged into a second AAV vector. Reconstitution results in a fully functioning Cas9. Reprinted from Truong et al. (2015). Copyright 2014 The Authors (CC BY license). (D) AdV delivery of Cas9 and sgRNA targeting the Pten gene in mouse liver resulting in Pten mutation (see arrows by gel), and massive hepatomegaly and features of NASH in infected livers. Immunohistochemistry shows loss of Pten staining (arrows) one month after AdV infection; H&E stained micrographs show sections of steatosis (lipid accumulation, arrows) four months post infection. Adapted with permission from Wang et al., 2015. Copyright 2015 Mary Ann Liebert, Inc. Publishers. (E) Schematic of a lentivirus and CRISPR-based gene library functional screen used to identify the genes essential for West-Nile-virus-induced cell death. Reprinted from Ma et al. (2015). Copyright 2015 The Authors (CC BY license).
Figure 6. Viral vector methods for delivery of CRISPR. (A) AAV delivery of Cas9 and sgRNAs disrupting mutations in the Dmd gene in adult mdx mice, resulting in improvement of muscle biochemistry and function. Adapted with permission from Long et al. (2016). Copyright 2016 American Association for the Advancement of Science. (B) AAV intratracheal instillation delivery of sgRNAs in Cre-dependent Cas9 knock-in mice, resulting in lung adenocarcinoma (EGFP-positive tumors). Adapted with permission from Platt et al. (2016). Copyright 2014 Elsevier Inc. (C) A split Cas9 system in which the Cas9 C-terminal is packaged into one AAV vector and the Cas9 N-terminal is packaged into a second AAV vector. Reconstitution results in a fully functioning Cas9. Reprinted from Truong et al. (2015). Copyright 2014 The Authors (CC BY license). (D) AdV delivery of Cas9 and sgRNA targeting the Pten gene in mouse liver resulting in Pten mutation (see arrows by gel), and massive hepatomegaly and features of NASH in infected livers. Immunohistochemistry shows loss of Pten staining (arrows) one month after AdV infection; H&E stained micrographs show sections of steatosis (lipid accumulation, arrows) four months post infection. Adapted with permission from Wang et al., 2015. Copyright 2015 Mary Ann Liebert, Inc. Publishers. (E) Schematic of a lentivirus and CRISPR-based gene library functional screen used to identify the genes essential for West-Nile-virus-induced cell death. Reprinted from Ma et al. (2015). Copyright 2015 The Authors (CC BY license).CC BY · PubMed Central
Figure 7. Lipid nanoparticle and polyplex delivery of CRISPR. (A) Combining bioreducible lipid nanoparticles and anionic Cas9:sgRNA complexes drives the electrostatic self-assembly of nanoparticles (see TEM micrograph of 3-O14B/Cas9:sgRNA nanoparticles) for potent protein delivery and genome editing. Adapted with permission from Wang et al. (2016). Copyright 2017 National Academy of Sciences. (B) Microinjection of PEI with Cas9- and sgRNA-encoding plasmid DNA into mouse brain directed against the Ptch1 locus to generate a malignant brain tumor model. Compare the wild type and Trp53± H&E stained micrographs (arrows indicate small lesions encompassing only one cerebellar folium) with the tumor from the Trp53−/− condition (MB = medulloblastoma). Adapted from Zuckermann et al. (2015). Copyright 2015 The Authors (CC BY license).
Figure 7. Lipid nanoparticle and polyplex delivery of CRISPR. (A) Combining bioreducible lipid nanoparticles and anionic Cas9:sgRNA complexes drives the electrostatic self-assembly of nanoparticles (see TEM micrograph of 3-O14B/Cas9:sgRNA nanoparticles) for potent protein delivery and genome editing. Adapted with permission from Wang et al. (2016). Copyright 2017 National Academy of Sciences. (B) Microinjection of PEI with Cas9- and sgRNA-encoding plasmid DNA into mouse brain directed against the Ptch1 locus to generate a malignant brain tumor model. Compare the wild type and Trp53± H&E stained micrographs (arrows indicate small lesions encompassing only one cerebellar folium) with the tumor from the Trp53−/− condition (MB = medulloblastoma). Adapted from Zuckermann et al. (2015). Copyright 2015 The Authors (CC BY license).CC BY · PubMed Central
Figure 8. Nanomaterial delivery vehicles for CRISPR delivery. (A) DNA ‘nanoclew’ loaded with Cas9:sgRNA RNP via Watson-Crick base pairing, followed by coating with PEI to improve endosomal escape. Reprinted with permission from Sun et al. (2015). Copyright 2015 John Wiley & Sons. (B) Arginine-modified gold nanoparticles (ArgNPs, positively charged) interact with multiple Cas9:sgRNA RNPs engineered with an E-tag to form a local negatively charged region, forming a nanoassembly that delivers Cas9 via membrane fusion. Reprinted with permission from Mout et al. (2017). Copyright 2017 American Chemical Society. (C) Synthesis of AuNPs engineered to complex with multiple Cas9:sgRNA RNPs, followed by coating in silica and the endosomal disruptive polymer PASp(DET). Adapted with permission from Lee et al. (2017). Copyright 2017 Macmillan Publishers Ltd: Nature Biomedical Engineering.
Figure 8. Nanomaterial delivery vehicles for CRISPR delivery. (A) DNA ‘nanoclew’ loaded with Cas9:sgRNA RNP via Watson-Crick base pairing, followed by coating with PEI to improve endosomal escape. Reprinted with permission from Sun et al. (2015). Copyright 2015 John Wiley & Sons. (B) Arginine-modified gold nanoparticles (ArgNPs, positively charged) interact with multiple Cas9:sgRNA RNPs engineered with an E-tag to form a local negatively charged region, forming a nanoassembly that delivers Cas9 via membrane fusion. Reprinted with permission from Mout et al. (2017). Copyright 2017 American Chemical Society. (C) Synthesis of AuNPs engineered to complex with multiple Cas9:sgRNA RNPs, followed by coating in silica and the endosomal disruptive polymer PASp(DET). Adapted with permission from Lee et al. (2017). Copyright 2017 Macmillan Publishers Ltd: Nature Biomedical Engineering.CC BY · PubMed Central

Verification

Claims the paper makes

54 Not checked yet · 42 No basis given · 35 Own interpretation · 19 Supported · 15 Partly supported · 8 Sources not found · 8 No full text of the sources · accuracy not yet measured

Verify all 72 references — free account

Show all 92 claims

  • It may state two separate claims as one. 65
  • Probably not a substantial claim. 30
89 of 89
  • The paper relies on this without support.

    Effective in vivo human gene therapy with CRISPR/Cas9 is achievable once the factors influencing efficacy and delivery are addressed.

    “We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized.”
  • The paper relies on this without support.

    In eukaryotic cells, Cas9 must translocate into the nucleus.

    “For gene editing in eukaryotic cells, Cas9 must translocate into the nucleus.”
  • The paper relies on this without support.

    Blood is incompressible.

    “As blood is incompressible, the large bolus of liquid results in an increase in hydrodynamic pressure that temporarily enhances permeability into endothelial and parenchymal cells, allowing for cargo not normally capable of crossing a cellular membrane to pass into cells.”
  • The paper relies on this without support.

    AAV is not known to cause or relate with any diseases in humans.

    “AAV is not known to cause or relate with any diseases in humans.”
  • The paper relies on this without support.

    Hydrodynamic delivery is not currently being considered for clinical applications.

    “Despite these successes, hydrodynamic delivery is not currently being considered for clinical applications.”
  • The paper relies on this without support.

    Nucleic acids are typically unstable outside of cells and, owing to their highly anionic nature, do not easily pass through the cell membrane.

    “Nucleic acids are typically unstable outside of cells, and owing to their highly anionic nature, they do not easily pass through the cell membrane.”
  • The paper relies on this without support.

    Branched PEI is cytotoxic.

    “However, branched PEI is cytotoxic.”
  • The paper relies on this without support.

    CPPs typically show low efficiency of the desired targeted mutation in cells, usually around 10–20%.

    “Typically, CPPs show low efficiency of the desired targeted mutation in cells – usually around 10–20%.”
  • The paper relies on this without support.

    Naked plasmids can achieve tangible long-term effects with an efficiency rate of just 0.4%.

    “As shown above, however, naked plasmids can achieve tangible long-term effects with an efficiency rate of just 0.4%.”
  • The paper relies on this without support.

    CRISPR/Cas9 components, whether in an RNP complex, as mRNA, or as DNA plasmids, are larger than other components that have been reported to load within lipid-coated mesoporous silica particles.

    “CRISPR/Cas9 components, whether in an RNP complex, as mRNA, or as DNA plasmids, are larger than other components that have been reported to load within the particles.”
  • The paper relies on this without support.

    The number of peer-reviewed scientific papers with the term CRISPR in the title or abstract has increased by 1,453% since 2011.

    “Importantly, the CRISPR field is evolving at an incredible pace, with the number of peer-reviewed scientific papers with the term CRISPR in the title or abstract increasing by 1,453% since 2011.”
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Citations

Cites

Show all 233 references

Research works printed but not linked: 3

  1. Deyle DR, 2009, Curr Opin Mol Ther, 11, 442
  2. Garrett RA, 2015, Life (Basel, Switzerland), 5, 783
  3. Tomkinson AE, 2013, Translational Cancer Res, 2, 1219

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Metadata

Authors
Lino, C. A., Harper, J. C., Carney, J. P., & Timlin, J. A.
Affiliations
Sandia National Laboratories (US)
Corresponding author
Timlin, Jerilyn A.
Venue
Drug Delivery
Published
2018-01-01
Volume
25
Issue
1
Pages
1234-1257
ISSN
  • 1071-7544 (ISSN-L)
  • 1521-0464
OpenAlex
W2804566227
Cited by
1,185
References
233
Citations by year
2026: 101 · 2025: 127 · 2024: 151 · 2023: 171 · 2022: 183 · 2021: 177 · 2020: 198 · 2019: 63 · 2018: 10
FWCI
10.99
Type
journal article
Language
en
Open access
Locations
  • Drug Delivery (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • Sandia National Laboratories
  • US Department of Energy's National Nuclear Security Administration (DE-NA0003525)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
Keywords
CRISPR/Cas9, gene therapy, genome editing, CRISPR/Cas9 delivery, adeno-associated virus vectors, adenoviral vector, lentiviral vectors, liposomes, polyplexes, gold nanoparticles, electroporation, microinjection, zinc finger nucleases, TALEN, in vivo gene therapy
MeSH terms
Gene Editing, Animals, Humans, Genetic Therapy, Gene Transfer Techniques, Clustered Regularly Interspaced Short Palindromic Repeats

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