Quantifying CRISPR off-target effects

Emerging topics in life sciences - Tập 3 Số 3 - Trang 327-334 - 2019
Soragia Athina Gkazi1
1Molecular and Cellular Immunology, University College London, Great Ormond Street Institute of Child Health, London, U.K.

Tóm tắt

Abstract Recent advances in the era of genetic engineering have significantly improved our ability to make precise changes in the genomes of human cells. Throughout the years, clinical trials based on gene therapies have led to the cure of diseases such as X-linked severe combined immunodeficiency (SCID-X1), adenosine deaminase deficiency (ADA-SCID) and Wiskott–Aldrich syndrome. Despite the success gene therapy has had, there is still the risk of genotoxicity due to the potential oncogenesis introduced by utilising viral vectors. Research has focused on alternative strategies like genome editing without viral vectors as a means to reduce genotoxicity introduced by the viral vectors. Although there is an extensive use of RNA-guided genome editing via the clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein-9 (Cas9) technology for biomedical research, its genome-wide target specificity and its genotoxic side effects remain controversial. There have been reports of on- and off-target effects created by CRISPR–Cas9 that can include small and large indels and inversions, highlighting the potential risk of insertional mutagenesis. In the last few years, a plethora of in silico, in vitro and in vivo genome-wide assays have been introduced with the sole purpose of profiling these effects. Here, we are going to discuss the genotoxic obstacles in gene therapies and give an up-to-date overview of methodologies for quantifying CRISPR–Cas9 effects.

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Tài liệu tham khảo

2017, Viral vectors: the road to reducing genotoxicity, Toxicol. Sci., 155, 315, 10.1093/toxsci/kfw220

2016, Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles, Proc. Natl Acad. Sci. U.S.A., 113, 2868, 10.1073/pnas.1520244113

2016, Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo, Nat. Biotechnol., 34, 328, 10.1038/nbt.3471

2015, Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo, Nat. Biotechnol., 33, 73, 10.1038/nbt.3081

2011, Structural basis for CRISPR RNA-guided DNA recognition by Cascade, Nat. Struct. Mol. Biol., 18, 529, 10.1038/nsmb.2019

2009, Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense, Structure, 17, 904, 10.1016/j.str.2009.03.019

2013, Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease, Nat. Biotechnol., 31, 230, 10.1038/nbt.2507

2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143

2013, RNA-programmed genome editing in human cells, eLife, 2, e00471, 10.7554/eLife.00471

2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033

2013, CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity, Nucleic Acids Res., 41, 9584, 10.1093/nar/gkt714

2013, High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nat. Biotechnol., 31, 822, 10.1038/nbt.2623

2014, Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease, Nat. Biotechnol., 32, 677, 10.1038/nbt.2916

2017, Optimizing the DNA donor template for homology-directed repair of double-strand breaks, Mol. Ther.-Nucleic Acids, 7, 53, 10.1016/j.omtn.2017.02.006

2017, In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting, Nat. Commun., 8, 657, 10.1038/s41467-017-00687-1

2018, Precise and efficient nucleotide substitution near genomic nick via noncanonical homology-directed repair, Genome. Res., 28, 223, 10.1101/gr.226027.117

2016, Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA, Nat. Biotechnol., 34, 339, 10.1038/nbt.3481

2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647

2014, E-CRISP: fast CRISPR target site identification, Nat. Methods, 11, 122, 10.1038/nmeth.2812

2014, Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases, Bioinformatics, 30, 1473, 10.1093/bioinformatics/btu048

2014, COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites, Mol. Ther.-Nucleic Acids, 3, 10.1038/mtna.2014.64

2016, Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes, Nucleic Acids Res., 44, W267, 10.1093/nar/gkw407

2017, A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action, PLoS Comput. Biol., 13, e1005807, 10.1371/journal.pcbi.1005807

2018, DeepCRISPR: optimized CRISPR guide RNA design by deep learning, Genome Biol., 19, 80, 10.1186/s13059-018-1459-4

2018, Off-target predictions in CRISPR-Cas9 gene editing using deep learning, Bioinformatics, 34, 656, 10.1093/bioinformatics/bty554

2011, Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes, Cell, 147, 95, 10.1016/j.cell.2011.07.048

2013, 53BP1 alters the landscape of DNA rearrangements and suppresses AID-induced B cell lymphoma, Mol. Cell, 49, 623, 10.1016/j.molcel.2012.11.029

2014, Noncoding RNA transcription targets AID to divergently transcribed loci in B cells, Nature, 514, 389, 10.1038/nature13580

2015, Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells, Nat. Methods, 12, 237, 10.1038/nmeth.3284

2016, Recent progress in CRISPR/Cas9 technology, J. Genet. Genomics, 43, 63, 10.1016/j.jgg.2016.01.001

2016, Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing, Nat. Protoc., 11, 853, 10.1038/nprot.2016.043

2018, DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA, Genome Res., 28, 1894, 10.1101/gr.236620.118

2019, Improving CRISPR-Cas9 genome editing efficiency by fusion with chromatin-modulating peptides, CRISPR J., 2, 51, 10.1089/crispr.2018.0036

2017, Mapping the genomic landscape of CRISPR-Cas9 cleavage, Nat. Methods, 14, 600, 10.1038/nmeth.4284

2017, SITE-Seq: A Genome-Wide Method to Measure Cas9 Cleavage

2018, Corrigendum: CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets, Nat. Methods, 15, 394, 10.1038/nmeth0518-394c

2018, Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq, Nat. Protoc., 13, 2615, 10.1038/s41596-018-0055-0

2007, High-resolution profiling of histone methylations in the human genome, Cell, 129, 823, 10.1016/j.cell.2007.05.009

2007, Genome-wide mapping of in vivo protein-DNA interactions, Science, 316, 1497, 10.1126/science.1141319

2007, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, 448, 553, 10.1038/nature06008

2012, ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions, Nat. Rev. Genet., 13, 840, 10.1038/nrg3306

2012, ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia, Genome Res., 22, 1813, 10.1101/gr.136184.111

2013, Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing, Nat. Methods, 10, 361, 10.1038/nmeth.2408

2015, In vivo genome editing using Staphylococcus aureus Cas9, Nature, 520, 186, 10.1038/nature14299

2015, GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases, Nat. Biotechnol., 33, 187, 10.1038/nbt.3117

2011, Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells, Cell, 147, 1640, 10.1016/j.cell.2011.12.009

2015, Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases, Nat. Biotechnol., 33, 179, 10.1038/nbt.3101

2011, An unbiased genome-wide analysis of zinc-finger nuclease specificity, Nat. Biotechnol., 29, 816, 10.1038/nbt.1948

2015, Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors, Nat. Biotechnol., 33, 175, 10.1038/nbt.3127

2014, Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases, Genome Res., 24, 132, 10.1101/gr.162339.113

2016, A self-restricted CRISPR system to reduce off-target effects, Mol. Ther., 24, 2132, 10.1038/mt.2016.198

2013, Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity, Cell, 155, 479, 10.1016/j.cell.2013.09.040

2014, Dimeric CRISPR/Cas-based nucleases for high-precision genome editing in human cells, Human Gene Therapy, 25, A120, 10.1038/nbt.2908

2016, High-fidelity CRISPR-Cas9 nucleases with No detectable genome-wide off-target effects, Mol. Ther., 24, S288, 10.1016/S1525-0016(16)33539-0

2016, Rationally engineered Cas9 nucleases with improved specificity, Science, 351, 84, 10.1126/science.aad5227

2018, Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements, Nat. Biotechnol., 36, 899, 10.1038/nbt0918-899c

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Emerging topics in life sciences

Tập 3 Số 3

327-334

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