Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies
Abstract
:1. Introduction
2. The CRISPR Toolkit—Initial Steps
3. Cellular Models
3.1. Cell Lines
3.2. Induced Pluripotent Stem Cells
3.3. Retinal Organoids
4. Animal Models
4.1. Caenorhabditis elegans
4.2. Drosophila melanogaster
4.3. Xenopus
4.4. Zebrafish
4.5. Rodents
4.6. Pig
4.7. Macaque
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Model | Phenotype | Gene | Genomic Target | Aim | Delivery Method | Nuclease | Reference |
---|---|---|---|---|---|---|---|
H HeLa | adRP | RHO | p.Pro23His | KO | Lipofection (plasmid) | SpCas9 | [34] |
H HEK293FT | LCA | CEP290 | p.Cys998* | KI | Lipofection (plasmid) | SpCas9 | [35] |
H HEK293 | USH2/arRP | USH2A | p.Glu767Serfs*21 | KI | Lipofection (plasmid) | SpCas9 | [36] |
p.Cys759Phe | |||||||
M 661W | adRP | Rp9 | Exon 5 | KO | Fugene HD (plasmid) | SpCas9 | [37] |
p.His137Leu | KI | ||||||
H hTERT-RPE1 | xlRP | RP2 | Exon 2 | KO | Fugene HD (plasmid) | nCas9 pairs | [38] |
RPGR | Exons 2 and 4 | KO | Undetermined | uCas9 | [39] | ||
sarRP | PDE6D | Exon 2 | |||||
INPP5E | Exon 1 | ||||||
arCORD | RPGRIP1L | Exon 3 | |||||
M NSC | arRP | Pde6b | p.Arg560Cys | C KI | Nucleofection (plasmid) | SpCas9 | [40] |
rd12 MEFs | LCA | Rpe65 | p.Arg44* | C KI | Electroporation (RNPs) | SpCas9 | [41] |
PD-Fibroblasts | USH2/arRP | USH2A | p.Glu767Serfs*21 | C KI | Nucleofection (RNPs) | SpCas9 | [36] |
PD-Keratinocytes | SHRF | EXOSC2 | Exon 1 and 4 | KO | Lentiviral transduction | SpCas9 | [42] |
PD-iPSCs | arRP | MAK | c.1513ins353 | C KI | Nucleofection (plasmid) | SpCas9 | [43] |
LCA | CEP290 | p.Cys998* | KO | ||||
KO | Electroporation (plasmid) | SaCas9 | |||||
C KI | |||||||
adRP | RHO | p.Pro23His | KO | ||||
C KI | Undetermined (plasmid) | SpCas9 | |||||
PRPF31 | p.Arg372Glnfs*99 | C KI | Lipofection (plasmid) | SpCas9 | [44] | ||
Exon 7 | KO | Nucleofection (plasmid) | SpCas9 | [45] | |||
PRPF8 | p.Pro2301Ser | C KI | Electroporation (gRNA-plasmid and Cas9 mRNA) | Cas9-Gem | [46] | ||
xlRP | RPGR | p.His562Argfs*20 | KI | Electroporation (plasmid) | SpCas9 | [47] | |
ESCS | NR2E3 | p.Val41Alafs*23 | KI | Lipofection (plasmid) | SpCas9 | [48] | |
p.Arg73Ser | KI | Electroporation (plasmid) | |||||
USH2/arRP | USH2A | p.Glu767Serfs*21 p.Cys759Phe | KI | Nucleofection (plasmid) | eSpCas9 | [49] | |
XLRS | RS1 | p.Arg209Cys | KI | Nanodiamonds (linear DNA) | SpCas9 | [50] | |
Caenorhabditis elegans (nematode) | adRP | prp-8 | p.Arg2310Gly | KI | Injection (RNPs) | SpCas9 | [51] |
p.His2309del | |||||||
snrp-200 | p.Val683Leu | ||||||
p.Ser1087Leu | |||||||
Danio rerio (zebrafish) | arRP | eys | p.Gly1163Valfs*14 | KO | Embryo injection (RNPs) | SpCas9 | [52] |
pcare | p.Gly8Glu*19 | KO | Embryo injection (RNPs) | SpCas9 | [53] | ||
adRP | rho | p.Cys322Argfs*116 | KO | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [54] | |
LCA | cct2 | p.Leu394His-7del | KO | Embryo injection (RNPs) | SpCas9 | [55] | |
USH2/arRP | ush2a | p.Cys780Glnfs*32 | KO | Embryo injection (Cas9 mRNA and gRNAs) | uCas9 | [56] | |
p.Ala5174* | |||||||
p.Lys2532Thrfs*56 | KI | Embryo injection (RNPs) | SpCas9 | [57] | |||
ESCS | nr2e3 | p.Leu162Glnfs*30 | KO | Embryo injection (Cas9 mRNA and gRNAs) | uCas9 | [58] | |
arCD | cacna2d4 | Undetermined | KO | Embryo injection (RNPs) | SpCas9 | [59] | |
adFEVR | znf408 | p.His455Tyr | KI | Embryo injection (RNPs) | uCas9 | [60] | |
Mus musculus (mouse) | Undetermined | Blimp1 | B108 cis-regulatory module | KO | Electroporation—subretinal injection (plasmid) | SpCas9 | [61] |
LCA | Cep290 | p.Cys998* | KO | AAV transduction (subretinal injection) | SpCas9 | [35] | |
Exon 3 | KO | AAV transduction (subretinal injection) | SpCas9 | [62] | |||
Rpe65 | p.Asp477Gly | KI | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [63] | ||
p.Arg44* | C KI | AAV transduction (subretinal injection) | SpCas9 | [41] | |||
Kcnj13 | Exon 2 | KO | Zygote injection (Cas9 mRNA and gRNAs) | SpCas9 | [64] | ||
OCA1 | Tyr | 5’ region | KO | Zygote injection (Cas9 mRNA and gRNAs) | SpCas9 | [65] | |
Thy1-YFP | YFP | 5’ region | KO | AAV transduction (intravitreal injection) | SpCas9 | [66] | |
arRP | Pde6b | p.Arg560Cys | KI | Electroporation—subretinal injection (plasmid) | SpCas9 | [40] | |
p.Tyr347Ter | C KI | Embryo injection (gRNA-plasmid and Cas9 protein) | SpCas9 | [67] | |||
Reep6 | p.Leu135Pro | KI | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [68] | ||
Exon 4 | KO | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [69] | |||
Arl2bp | Exon 2 | KO | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [70] | ||
Hkdc1 | Exon 2 | KO | Undetermined (plasmid) | uCas9 | [71] | ||
adRP | RHO | p.Pro23His | KO | Electroporation (plasmid) | SpCas9 | [34] | |
Electroporation (plasmid) and AAV transduction (intravitreal injection) | SaCas9 and SaCas9-KKH | [72] | |||||
Rho/RHO | Exon 1 | KO | AAV transduction (subretinal injection) | SpCas9 | [73] | ||
arRP/sarRP | Cwc27 | p.Lys338Glyfs*25 | KO | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [74] | |
arRP/adRP | Nrl | Undetermined | KO | AAV transduction (subretinal injection) | SpCas9 | [75] | |
[76] | |||||||
RD | Slc9a8 | Promoter | KO | AAV transduction (subretinal injection) | nmCas9 | [77] | |
Usp45 | Exon 14 | KO | Embryo injection (Cas9 mRNA and gRNAs) | uCas9 | [78] | ||
adCORD | Gucy2e | Exon 2 and 4 | KO | AAV transduction (subretinal injection) | SaCas9 | [79] | |
Thy1-YFP | YFP | Undetermined | KO | AAV transduction (subretinal injection | SpCas9 | [80] | |
XLRS | Rs1 | p.Arg209Cys | KI | Nanodiamonds—intravitreal injection (linear DNA) | SpCas9 | [50] | |
Rattus norvegicus (rat) | OCA1 | Tyr | Exon 2 | KO | Embryo injection (Cas9 mRNA and gRNAs) | uCas9 | [81] |
p.Arg299His | KI | ||||||
adRP | Rho | p.Ser334Ter | KO | Electroporation—subretinal injection (plasmid) | SpCas9 | [82] | |
Xenopus laevis (frog) | adRP | rho | Exon1 | KO | Embryo injection (Cas9 mRNA and gRNAs) | SpCas9 | [83] |
Exon 5 | KI | ||||||
Drosophila melanogaster (fly) | SHRF | rrp4 | Exon 1 and 4 | KO | Embryo injection (gRNA-plasmid into Cas9-expressing strain) | SpCas9 | [42] |
Sus scrofa domesticus (pig) | adRP | RHO | p.Pro23His | KO | AAV transduction (subretinal injection) | SaCas9 | [43] |
Macaca fascicularis (macaque) | adCORD | GUCY2D | Exon 2 and 4 | KO | AAV transduction (subretinal injection) | saCas9 | [79] |
Method | Advantages | Disadvantages |
---|---|---|
Microinjection | Liberated right into the cell High efficacy | Time-consuming Technique expertise |
Electroporation | Normalized open-access protocols High effectiveness with plasmids | In vitro and ex vivo cell restriction Cell cytotoxicity Not all cells are susceptible |
Lipofection | Works in many cell types Easy manipulation Inexpensive Reduced off-targets | Exclusive for cell culture Lysosome degradation |
Nanodiamonds | Highly efficient delivery High biocompatibility Water solubility Fully accessible surface Inexpensive | Genotoxicity High pressure and temperature for synthesis Tissue distribution problems |
AAVs | Low immunogenicity and cytotoxicity Reduced off-targets High efficacy Low immune response detected Infect both dividing and non-dividing cells | Limited cargo capacity (3.5–4 kb) High cost Technique expertise Safety obstacle Not easy to scale-up |
Lentivirus | Expression stability Can be applied in a broad range of cell types Higher efficacy if constructs are shortened Low immune response detected Infect both dividing and non-dividing cells | Limited cargo capacity (8–9 kb) Arbitrary integration Technique expertise Safety obstacle Not easy to scale-up |
Microinjection delivery is based on the use of a 0.5–5.0 µm diameter needle to deliver components into a cell or intercellular space, in this case the Cas9 protein and sgRNAs in any form. The electroporation method requires high voltage currents with the purpose of opening nanopores in the cellular membrane to inlet the CRISPR components resuspended in a specific buffer. Nucleofection is a specific electroporation-based method that allows the direct entry of the components into the nucleus. Lipofection consists in the introduction of the DNA components via a liposome-based transfection, in which synthetic cationic lipids aggregate around the negatively-charged DNA molecules. Cellular uptake is based on the fusion of these liposome-like structures with the phospholipidic membrane. Nanodiamonds are carbon nanomaterials which are suspended in a colloidal solution that allow the binding with or coating of biological material for cell transfection, mainly penetrating by the clathrin-mediated endocytosis pathway. The viral transduction method leverages the natural potential of viruses to infect cells, where the vectors have been deprived of the essential pathogenic genes in their replication. The most commonly used are AAVs and lentivirus. AAVs, which consist of single-stranded DNA, present several serotype versions (allowing tissue-specific transduction) and are considered a safe option, given that they are not associated to human diseases showing low immunogenicity and entailing low cellular toxicity (as they do not integrate into the host genome). Lentiviruses are retroviruses derived from a provirus of HIV that proffer stable expression in both dividing and post-mitotic cells due to their host genome integration, and that additionally accommodate cargos up to 5–6 kb in size. |
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Fuster-García, C.; García-Bohórquez, B.; Rodríguez-Muñoz, A.; Millán, J.M.; García-García, G. Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies. Genes 2020, 11, 473. https://doi.org/10.3390/genes11050473
Fuster-García C, García-Bohórquez B, Rodríguez-Muñoz A, Millán JM, García-García G. Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies. Genes. 2020; 11(5):473. https://doi.org/10.3390/genes11050473
Chicago/Turabian StyleFuster-García, Carla, Belén García-Bohórquez, Ana Rodríguez-Muñoz, José M. Millán, and Gema García-García. 2020. "Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies" Genes 11, no. 5: 473. https://doi.org/10.3390/genes11050473
APA StyleFuster-García, C., García-Bohórquez, B., Rodríguez-Muñoz, A., Millán, J. M., & García-García, G. (2020). Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies. Genes, 11(5), 473. https://doi.org/10.3390/genes11050473