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Denes CE, Cole AJ, Tran MTN, Mohd Khalid MKN, Hewitt AW, Hesselson D, Neely GG. The VEGAS Platform Is Unsuitable for Mammalian Directed Evolution. ACS Synth Biol 2022; 11:3544-3549. [PMID: 36219697 DOI: 10.1021/acssynbio.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Directed evolution uses cycles of gene diversification and selection to generate proteins with novel properties. While traditionally directed evolution is performed in prokaryotic systems, recently a mammalian directed evolution system (viral evolution of genetically actuating sequences, or "VEGAS") has been described. Here we report that the VEGAS system has major limitations that preclude its use for directed evolution. The deconstructed Sindbis virus (SINV) genome that comprises the VEGAS system could no longer promote Sindbis structural gene (SSG)-dependent viral replication. Moreover, viral particles generated using the VEGAS system rapidly lost the target directed evolution transgene, and instead, "cheater" particles, primarily containing RNA encoding SINV structural components, arose. By sequencing, we found that this contamination came from RNA provided during initial SINV packaging, not RNA derived from the VEGAS system. Of note, both the structural RNA and target transgenes used in the VEGAS system contain viral packaging sequences. The impact of SINV "cheater" particles could be potentially overcome in the context of a robust VEGAS circuit, but since SSG complementation is also defective in the VEGAS system, selection for authentic evolution products is not currently possible. Similar results have been obtained in independent laboratories. Taken together, these results show that the VEGAS system does not work as described and, without significant redesign, cannot be used for mammalian directed evolution campaigns.
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Affiliation(s)
- Christopher E Denes
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alexander J Cole
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Minh Thuan Nguyen Tran
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania 7000, Australia
| | | | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Daniel Hesselson
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - G Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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2
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Abstract
Base editors mediate the targeted conversion of single nucleobases in a therapeutically relevant manner. Herein, we present a hypothetical taxonomic and phylogenetic framework for the classification of more than 200 different DNA base editors, and we categorize them based on their described properties. Following evaluation of their in situ activity windows, which were derived by cataloguing their activity in published literature, organization is done hierarchically, with specific base editor signatures being subcategorized according to their on-target activity or nonspecific, genome- or transcriptome-wide activity. Based on this categorization, we curate a phylogenetic framework, based on protein homology alignment, and describe a taxonomic structure that clusters base editor variants on their target chemistry, endonuclease component, identity of their deaminase component, and their described properties into discrete taxa. Thus, we establish a hypothetical taxonomic structure that can describe and organize current and potentially future base editing variants into clearly defined groups that are defined by their characteristics. Finally, we summarize our findings into a navigable database (ShinyApp in R) that allows users to select through our repository to nominate ideal base editor candidates as a starting point for further testing in their specific application.
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Affiliation(s)
- Minh Thuan Nguyen Tran
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia
| | - Rajendra Kc
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia.,Centre for Eye Research Australia, The University of Melbourne, Melbourne, Australia
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Stellon D, Tran MTN, Talbot J, Chear S, Khalid MKNM, Pébay A, Vickers JC, King AE, Hewitt AW, Cook AL. CRISPR/Cas-Mediated Knock-in of Genetically Encoded Fluorescent Biosensors into the AAVS1 Locus of Human-Induced Pluripotent Stem Cells. Methods Mol Biol 2021; 2549:379-398. [PMID: 34505269 DOI: 10.1007/7651_2021_422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded fluorescent biosensors (GEFBs) enable researchers to visualize and quantify cellular processes in live cells. Induced pluripotent stem cells (iPSCs) can be genetically engineered to express GEFBs via integration into the Adeno-Associated Virus Integration Site 1 (AAVS1) safe harbor locus. This can be achieved using CRISPR/Cas ribonucleoprotein targeting to cause a double-strand break at the AAVS1 locus, which subsequently undergoes homology-directed repair (HDR) in the presence of a donor plasmid containing the GEFB sequence. We describe an optimized protocol for CRISPR/Cas-mediated knock-in of GEFBs into the AAVS1 locus of human iPSCs that allows puromycin selection and which exhibits negligible off-target editing. The resulting iPSC lines can be differentiated into cells of different lineages while retaining expression of the GEFB, enabling live-cell interrogation of cell pathway activities across a diversity of disease models.
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Affiliation(s)
- David Stellon
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
| | | | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | | | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
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Wang Q, Chear S, Wing K, Stellon D, Nguyen Tran MT, Talbot J, Pébay A, Hewitt AW, Cook AL. Use of CRISPR/Cas ribonucleoproteins for high throughput gene editing of induced pluripotent stem cells. Methods 2021; 194:18-29. [PMID: 33607266 DOI: 10.1016/j.ymeth.2021.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have become widely used for disease modelling, particularly with regard to predisposing genetic risk factors and causal gene variants. Alongside this, technologies such as the CRISPR/Cas system have been adapted to enable programmable gene editing in human cells. When combined, CRISPR/Cas gene editing of donor-specific iPSC to generate isogenic cell lines that differ only at specific gene variants provides a powerful model with which to investigate genetic variants associated with diseases affecting many organs, including the brain and eye. Here we describe our optimized protocol for using CRISPR/Cas ribonucleoproteins to edit disease causing gene variants in human iPSCs. We discuss design of crRNAs and homology-directed repair templates, assembly of CRISPR/Cas ribonucleoproteins, optimization of delivery via nucleofection, and strategies for single cell cloning, efficient clone cryopreservation and genotyping for identifying iPSC clones for further characterization.
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Affiliation(s)
- Qi Wang
- Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Tasmania, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - David Stellon
- Wicking Dementia Research and Education Centre, University of Tasmania, Tasmania, Australia
| | | | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Tasmania, Australia
| | - Alice Pébay
- Department of Anatomy and Neuroscience, the University of Melbourne, Australia; Department of Surgery, the University of Melbourne, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Tasmania, Australia.
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Nguyen Tran MT, Mohd Khalid MKN, Wang Q, Walker JKR, Lidgerwood GE, Dilworth KL, Lisowski L, Pébay A, Hewitt AW. Engineering domain-inlaid SaCas9 adenine base editors with reduced RNA off-targets and increased on-target DNA editing. Nat Commun 2020; 11:4871. [PMID: 32978399 PMCID: PMC7519688 DOI: 10.1038/s41467-020-18715-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
Precision genome engineering has dramatically advanced with the development of CRISPR/Cas base editing systems that include cytosine base editors and adenine base editors (ABEs). Herein, we compare the editing profile of circularly permuted and domain-inlaid Cas9 base editors, and find that on-target editing is largely maintained following their intradomain insertion, but that structural permutation of the ABE can affect differing RNA off-target events. With this insight, structure-guided design was used to engineer an SaCas9 ABE variant (microABE I744) that has dramatically improved on-target editing efficiency and a reduced RNA-off target footprint compared to current N-terminal linked SaCas9 ABE variants. This represents one of the smallest AAV-deliverable Cas9-ABEs available, which has been optimized for robust on-target activity and RNA-fidelity based upon its stereochemistry. Off-target effects and the feasibility for AAV-mediated delivery are the major barriers impeding the clinical in vivo application of base editors. Here, the authors report the small size AAV-deliverable Cas9-ABE variant that has improved on-target editing efficiency and reduced RNA-off target footprint.
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Affiliation(s)
- Minh Thuan Nguyen Tran
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia.
| | | | - Qi Wang
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia
| | - Jacqueline K R Walker
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia
| | - Grace E Lidgerwood
- Department of Surgery, The University of Melbourne, Victoria, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Australia
| | - Kimberley L Dilworth
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
| | - Alice Pébay
- Department of Surgery, The University of Melbourne, Victoria, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia.,Centre for Eye Research Australia, The University of Melbourne, Victoria, Australia
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Li F, Wing K, Wang JH, Luu CD, Bender JA, Chen J, Wang Q, Lu Q, Nguyen Tran MT, Young KM, Wong RCB, Pébay A, Cook AL, Hung SSC, Liu GS, Hewitt AW. Comparison of CRISPR/Cas Endonucleases for in vivo Retinal Gene Editing. Front Cell Neurosci 2020; 14:570917. [PMID: 33132845 PMCID: PMC7511709 DOI: 10.3389/fncel.2020.570917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas has opened the prospect of direct gene correction therapy for some inherited retinal diseases. Previous work has demonstrated the utility of adeno-associated virus (AAV) mediated delivery to retinal cells in vivo; however, with the expanding repertoire of CRISPR/Cas endonucleases, it is not clear which of these are most efficacious for retinal editing in vivo. We sought to compare CRISPR/Cas endonuclease activity using both single and dual AAV delivery strategies for gene editing in retinal cells. Plasmids of a dual vector system with SpCas9, SaCas9, Cas12a, CjCas9 and a sgRNA targeting YFP, as well as a single vector system with SaCas9/YFP sgRNA were generated and validated in YFP-expressing HEK293A cell by flow cytometry and the T7E1 assay. Paired CRISPR/Cas endonuclease and its best performing sgRNA was then packaged into an AAV2 capsid derivative, AAV7m8, and injected intravitreally into CMV-Cre:Rosa26-YFP mice. SpCas9 and Cas12a achieved better knockout efficiency than SaCas9 and CjCas9. Moreover, no significant difference in YFP gene editing was found between single and dual CRISPR/SaCas9 vector systems. With a marked reduction of YFP-positive retinal cells, AAV7m8 delivered SpCas9 was found to have the highest knockout efficacy among all investigated endonucleases. We demonstrate that the AAV7m8-mediated delivery of CRISPR/SpCas9 construct achieves the most efficient gene modification in neurosensory retinal cells in vivo.
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Affiliation(s)
- Fan Li
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou, China
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Chi D Luu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
| | - James A Bender
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Jinying Chen
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qi Wang
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Kaylene M Young
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
| | - Alice Pébay
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Sandy S C Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
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Tran MTN, Khalid MKNM, Pébay A, Cook AL, Liang HH, Wong RCB, Craig JE, Liu GS, Hung SS, Hewitt AW. Screening of CRISPR/Cas base editors to target the AMD high-risk Y402H complement factor H variant. Mol Vis 2019; 25:174-182. [PMID: 30996586 PMCID: PMC6441356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/14/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose To evaluate the efficacy of using a CRISPR/Cas-mediated strategy to correct a common high-risk allele that is associated with age-related macular degeneration (AMD; rs1061170; NM_000186.3:c.1204T>C; NP_000177.2:p.His402Tyr) in the complement factor H (CFH) gene. Methods A human embryonic kidney cell line (HEK293A) was engineered to contain the pathogenic risk variant for AMD (HEK293A-CFH). Several different base editor constructs (BE3, SaBE3, SaKKH-BE3, VQR-BE3, and Target-AID) and their respective single-guide RNA (sgRNA) expression cassettes targeting either the pathogenic risk variant allele in the CFH locus or the LacZ gene, as a negative control, were evaluated head-to-head for the incidence of a cytosine-to-thymine nucleotide correction. The base editor construct that showed appreciable editing activity was selected for further assessment in which the base-edited region was subjected to next-generation deep sequencing to quantify on-target and off-target editing efficacy. Results The tandem use of the Target-AID base editor and its respective sgRNA demonstrated a base editing efficiency of facilitating a cytosine-to-thymine nucleotide correction in 21.5% of the total sequencing reads. Additionally, the incidence of insertions and deletions (indels) was detected in only 0.15% of the sequencing reads with virtually no off-target effects evident across the top 11 predicted off-target sites containing at least one cytosine in the activity window (n = 3, pooled amplicons). Conclusions CRISPR-mediated base editing can be used to facilitate a permanent and stably inherited cytosine-to-thymine nucleotide correction of the rs1061170 SNP in the CFH gene with minimal off-target effects.
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Affiliation(s)
| | | | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Victoria, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Victoria, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Victoria, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Victoria, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Victoria, Australia
| | - Sandy S Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Victoria, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Victoria, Australia
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