CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy
Abstract
:1. Introduction
1.1. The Development of CRISPR-Cas System
1.1.1. Canonical CRISPR-SpCas9
1.1.2. CRISPR Interference (CRISPRi)
1.1.3. CRISPR Activation (CRISPRa)
1.1.4. Non Canonical CRISPR-Cas System-SaCas9, Cpf1, FnCas9, C2c1/2/3 and CRISPR-Cas13
SaCas9
Cpf1
FnCas9
Class 2 Candidate 1/2/3 (C2c1/2/3)
CRISPR-Cas13
1.2. Virus-Host Interactions and Strategies Blocking Virus Infection
1.3. CRISPR-Cas System and Human Virus Restriction
1.3.1. Human Immunodeficiency Virus (HIV)
CRISPR-SpCas9 Targeting Host Factors and HIV-1 Genome
CRISPR-SaCas9 Targeting Host Factors and HIV-1 Genome
CRISPRa Targeting HIV-1 LTR and Host Factors
1.3.2. Hepatitis B Virus (HBV)
1.3.3. Human Papillomavirus (HPV)
1.3.4. Epstein–Barr Virus (EBV)
1.4. CRISPR and Human RNA Viruses
1.4.1. Hepatitis C Virus (HCV)
1.4.2. Other RNA Virus: Dengue Virus (DENV) and Zika Virus (ZIKV), West Nile Virus (WNV), Influenza Virus, Ebola Virus (EBOV), SARS-CoV, MERS-CoV
1.5. CRISPR and Plant Viruses
2. Challenge of Using CRISPR-Cas System Targets Host Factors to Protest against Virus Infection in Humans
2.1. Virus Mutation and Host Immune System
2.2. Off Target and Side Effect
2.3. Delivery Method
2.4. Clinical Trials
3. Conclusions and Future Directions
Acknowledgments
Conflicts of Interest
References
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CRISPR-Cas | DNA Cassette: Size | PAMs | Function | Targeting Virus | Virus Related Host Factor | Delivery Vehicle | Pros/Cons | |
---|---|---|---|---|---|---|---|---|
CRISPR-SpCas9 | Sp-Cas9-Flag-T2A-Puro:4641 bp | 5′-NGG-3′ | single-RNA-mediated DNA endonuclease | HIV, HBV, HPV, EBV, ZIKV, DENV | CCR5, CXCR4, LEDGF, TNPO3, BART, EBNA1, CLDN1, OCLN, CD81, AXL, EMC |
| Frequently used/Large protein size | |
CRISPRi | Flag-NLS-dCas9-NLS-KRAB-T2A-Puro:5145 bp | 5′-NGG-3′ | single-RNA-mediated inhibition of mRNA transcription | - | - |
| Multiplex gene transcription inhibition/Large protein size, less application | |
CRISPRa | dCas9-VP64 and MS2–p65–HSF1 | dCas9-VP64-Blast:4872 bp MS2-p65-HSF1-Hygro:2520 bp | 5′-NGG-3′ | single-RNA-mediated activation of mRNA transcription | HIV | IFNγ, APOBEC3G (A3G), APOBEC3G (A3G) |
| Multiplex gene activation/Relative low efficiency, Large protein size, less application |
scFv-GCN4-sfGFP-VP64 and dCas9-24xGCN4-v4 | scFv-GCN4-sfGFP-VP64-GB1-NLS:2031 bp NLS-dCas9-24xGCN4_v4-NLS-P2A-BFP:6906 bp | Single-molecule imaging, transcriptional activation/Super large in size, less application | ||||||
CRISPR-SaCas9 | NLS-SaCas9-NLS-3xHA:3411 bp | 5′-NNGRRT-3′ | single-RNA-mediated DNA endonuclease | HIV | CCR5, CXCR4 |
| Small in size/Relatively strict PAM, less application | |
Cpf1 | AsCpf1:4056 bp LbCpf1:3819 bp FnCpf1:3900 bp | 5′-TTTN-3′ | single-crRNA-mediated DNA Endonuclease/RNase activity | - | - |
| a single and short crRNA, cohesive ends, Multiplex gene editing with tandemly arrayed crRNA/less application in cells | |
FnCas9 | FnCas9:4887 bp | 5′-NGG-3′ | single-RNA-mediated PAM-independent inhibiting of translation of target RNA | HCV | - |
| RNA targeting, Less restrictive PAM/Large in size, less application | |
C2c1/3 | AacC2c1:3387 bp | 5′-TTN-3′ | dual-RNA-guided DNA endonuclease | - | - |
| Small in size/requires a 111-nt sgRNA containing crRNA and tracrRNA, lower cleavage activity, no application in cells | |
C2c2/Cas13 | LwCas13a-msfGFP-2A-Blast:4869 bp | depends on a non-G 3′ protospacer-flanking site (PFS) | single-effector endoRNase mediating ssRNA cleavage with a single crRNA guide | ZIKV, DENV | - |
| RNA targeting, nucleic acid detection/Large in size, less application |
Virus | Genome | CRISPR-Cas for Genetic Targeting | Dependent or Positive Regulators | Restriction Factors |
---|---|---|---|---|
HIV | +ssRNA | CRISPR-SpCas9, CRISPRa CRISPR-SaCas9 (Cpf1, FnCas9, C2c1/3, C2c2/Cas13) | CCR5, CXCR4, LEDGF/p75, TNPO3 (PSIP1, Nup358, CPSF6, ALCAM) | APOBEC3G, APOBEC3B, IFNγ (TRIM5α, BST-2/Tetherin, SAMHD-1, Mx2, Serinc3/5) |
HBV | relaxed circular (RC) DNA | CRISPR-SpCas9 (CRISPR-SaCas9, Cpf1, FnCas9, C2c1/3, C2c2/Cas13) | (NTCP, Hsc70, Hsp90, TDP2, γ2-adaptin) | IFNγ (BST-2/tetherin) |
HPV | dsDNA | CRISPR-SpCas9 (CRISPR-SaCas9, Cpf1, FnCas9, C2c1/3, C2c2/Cas13) | (SIRT1, Brd4, CXCR4, KLF4/13, ORC2) | (Sp100, miR-145, p56, IFI16, C/EBPβ, p53, EVERs, APOBEC, FANCD2) |
EBV | dsDNA | CRISPR-SpCas9 (CRISPR-SaCas9, Cpf1, FnCas9, C2c1/3, C2c2/Cas13) | IKKβ, HOIP, p52, RBP-Jκ, WDR48, MDM2/4, CTBP1, BCL6,SYK,BTK,BLNK,PTEN, CD19/81, TNFRSF1A, BATF, IRF4, IRF2 | (c-CBL) |
HCV | +ssRNA | FnCas9 (C2c2/Cas13) | DGCR8, CLDN1, OCLN, CD81 | (NLRX1, SMYD3, VAP-C) |
ZIKV | +ssRNA | C2c2/Cas13 (FnCas9) | (OST, AXL, RAB5C, RABGEF, NDST1, EXT1, EMC) | - |
DENV | +ssRNA | C2c2/Cas13 (FnCas9) | (OST, RAB5C, RABGEF, NDST1, EXT1, EMC) | - |
WNV | +ssRNA | (FnCas9, C2c2/Cas13) | (SPCS, EMC2, EMC3, SEL1L, DERL2, UBE2G2, UBE2J1, HRD1) | (HSP70) |
IAV | −ssRNA | (FnCas9, C2c2/Cas13) | (IFITM, B4GALNT2, α2,3 linked sialic acid receptor) | (DcR3) |
EBOV | +ssRNA | (FnCas9, C2c2/Cas13) | (NPC1, Tim-1) | - |
SARS-CoV | +ssRNA | (FnCas9, C2c2/Cas13) | (ACE2, IFITM) | - |
MERS-CoV | +ssRNA | (FnCas9, C2c2/Cas13) | (CD26/DDP4, CD9) | - |
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Chen, S.; Yu, X.; Guo, D. CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy. Viruses 2018, 10, 40. https://doi.org/10.3390/v10010040
Chen S, Yu X, Guo D. CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy. Viruses. 2018; 10(1):40. https://doi.org/10.3390/v10010040
Chicago/Turabian StyleChen, Shuliang, Xiao Yu, and Deyin Guo. 2018. "CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy" Viruses 10, no. 1: 40. https://doi.org/10.3390/v10010040