101
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van de Kooij B, Kruswick A, van Attikum H, Yaffe MB. Multi-pathway DNA-repair reporters reveal competition between end-joining, single-strand annealing and homologous recombination at Cas9-induced DNA double-strand breaks. Nat Commun 2022; 13:5295. [PMID: 36075911 PMCID: PMC9458747 DOI: 10.1038/s41467-022-32743-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
DNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to mutagenesis and genomic loss. DSB-repair pathway cross-talk and compensation is incompletely understood, despite its importance for genomic stability, oncogenesis, and genome editing using CRISPR/Cas9. To address this, we constructed and validated three fluorescent Cas9-based reporters, named DSB-Spectrum, that simultaneously quantify the contribution of multiple DNA repair pathways at a DSB. DSB-Spectrum reporters distinguish between DSB-repair by error-free canonical non-homologous end-joining (c-NHEJ) versus homologous recombination (HR; reporter 1), mutagenic repair versus HR (reporter 2), and mutagenic end-joining versus single strand annealing (SSA) versus HR (reporter 3). Using these reporters, we show that inhibiting the c-NHEJ factor DNA-PKcs increases repair by HR, but also substantially increases mutagenic SSA. Our data indicate that SSA-mediated DSB-repair also occurs at endogenous genomic loci, driven by Alu elements or homologous gene regions. Finally, we demonstrate that long-range end-resection factors DNA2 and Exo1 promote SSA and reduce HR, when both pathways compete for the same substrate. These new Cas9-based DSB-Spectrum reporters facilitate the comprehensive analysis of repair pathway crosstalk and DSB-repair outcome.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex Kruswick
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands.
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, MA, USA.
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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102
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Statkute E, Wang ECY, Stanton RJ. An Optimized CRISPR/Cas9 Adenovirus Vector (AdZ-CRISPR) for High-Throughput Cloning of sgRNA, Using Enhanced sgRNA and Cas9 Variants. Hum Gene Ther 2022; 33:990-1001. [PMID: 35196879 DOI: 10.1089/hum.2021.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombinant adenovirus vectors enable highly efficient gene delivery in vitro and in vivo. As a result, they are widely used in gene therapy, vaccination, and anticancer applications. We have previously developed the AdZ vector system, which uses recombineering to permit high-throughput cloning of transgenes into Adenovirus vectors, simplifies alteration of the vector backbone, and enables rapid recovery of infectious virus, even if a transgene is incompatible with vector replication. In this study, we adapt this vector system to enable high-throughput cloning of sequences for CRISPR/Cas9 editing. Vectors were optimized to ensure efficient cloning, and high editing efficiency using spCas9 and single guide RNA (sgRNA) sequences in a single vector. Using a multiplicity of infection of 50, knockout efficiencies of up to 80% could be achieved with a single sgRNA. Vectors were further enhanced by altering the spCas9 sequence to match that of SniperCas9, which has reduced off-target activity, but maintains on-target efficiency, and by applying modifications to the sgRNA sequence that significantly enhance editing efficiency. Thus, the AdZ-CRISPR vectors offer highly efficient knockout, even in hard to transfect cells, and enables large-scale CRISPR/Cas9 projects to be undertaken easily and quickly.
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Affiliation(s)
- Evelina Statkute
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Eddie C Y Wang
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Richard J Stanton
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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103
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Verkuijl SAN, Anderson MAE, Alphey L, Bonsall MB. Daisy-chain gene drives: The role of low cut-rate, resistance mutations, and maternal deposition. PLoS Genet 2022; 18:e1010370. [PMID: 36121880 PMCID: PMC9521892 DOI: 10.1371/journal.pgen.1010370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/29/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
The introgression of genetic traits through gene drive may serve as a powerful and widely applicable method of biological control. However, for many applications, a self-perpetuating gene drive that can spread beyond the specific target population may be undesirable and preclude use. Daisy-chain gene drives have been proposed as a means of tuning the invasiveness of a gene drive, allowing it to spread efficiently into the target population, but be self-limiting beyond that. Daisy-chain gene drives are made up of multiple independent drive elements, where each element, except one, biases the inheritance of another, forming a chain. Under ideal inheritance biasing conditions, the released drive elements remain linked in the same configuration, generating copies of most of their elements except for the last remaining link in the chain. Through mathematical modelling of populations connected by migration, we have evaluated the effect of resistance alleles, different fitness costs, reduction in the cut-rate, and maternal deposition on two alternative daisy-chain gene drive designs. We find that the self-limiting nature of daisy-chain gene drives makes their spread highly dependent on the efficiency and fidelity of the inheritance biasing mechanism. In particular, reductions in the cut-rate and the formation of non-lethal resistance alleles can cause drive elements to lose their linked configuration. This severely reduces the invasiveness of the drives and allows for phantom cutting, where an upstream drive element cuts a downstream target locus despite the corresponding drive element being absent, creating and biasing the inheritance of additional resistance alleles. This phantom cutting can be mitigated by an alternative indirect daisy-chain design. We further find that while dominant fitness costs and maternal deposition reduce daisy-chain invasiveness, if overcome with an increased release frequency, they can reduce the spread of the drive into a neighbouring population.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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104
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Diorio C, Murray R, Naniong M, Barrera L, Camblin A, Chukinas J, Coholan L, Edwards A, Fuller T, Gonzales C, Grupp SA, Ladd A, Le M, Messana A, Musenge F, Newman H, Poh YC, Poulin H, Ryan T, Shraim R, Tasian SK, Vincent T, Young L, Zhang Y, Ciaramella G, Gehrke J, Teachey DT. Cytosine base editing enables quadruple-edited allogeneic CART cells for T-ALL. Blood 2022; 140:619-629. [PMID: 35560156 PMCID: PMC9373016 DOI: 10.1182/blood.2022015825] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Allogeneic chimeric antigen receptor T-cell (CART) therapies require multiple gene edits to be clinically tractable. Most allogeneic CARTs have been created using gene editing techniques that induce DNA double-stranded breaks (DSBs), resulting in unintended on-target editing outcomes with potentially unforeseen consequences. Cytosine base editors (CBEs) install C•G to T•A point mutations in T cells, with between 90% and 99% efficiency to silence gene expression without creating DSBs, greatly reducing or eliminating undesired editing outcomes following multiplexed editing as compared with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). Using CBE, we developed 7CAR8, a CD7-directed allogeneic CART created using 4 simultaneous base edits. We show that CBE, unlike CRISPR-Cas9, does not impact T-cell proliferation, lead to aberrant DNA damage response pathway activation, or result in karyotypic abnormalities following multiplexed editing. We demonstrate 7CAR8 to be highly efficacious against T-cell acute lymphoblastic leukemia (T-ALL) using multiple in vitro and in vivo models. Thus, CBE is a promising technology for applications requiring multiplexed gene editing and can be used to manufacture quadruple-edited 7CAR8 cells, with high potential for clinical translation for relapsed and refractory T-ALL.
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Affiliation(s)
- Caroline Diorio
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
| | | | | | | | | | - John Chukinas
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Tori Fuller
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Stephan A Grupp
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
| | | | | | | | | | - Haley Newman
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
| | | | | | - Theresa Ryan
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Rawan Shraim
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah K Tasian
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
| | - Tiffaney Vincent
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | | | - David T Teachey
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
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105
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Schmidt JK, Reynolds MR, Golos TG, Slukvin II. CRISPR/Cas9 genome editing to create nonhuman primate models for studying stem cell therapies for HIV infection. Retrovirology 2022; 19:17. [PMID: 35948929 PMCID: PMC9363854 DOI: 10.1186/s12977-022-00604-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Nonhuman primates (NHPs) are well-established basic and translational research models for human immunodeficiency virus (HIV) infections and pathophysiology, hematopoietic stem cell (HSC) transplantation, and assisted reproductive technologies. Recent advances in CRISPR/Cas9 gene editing technologies present opportunities to refine NHP HIV models for investigating genetic factors that affect HIV replication and designing cellular therapies that exploit genetic barriers to HIV infections, including engineering mutations into CCR5 and conferring resistance to HIV/simian immunodeficiency virus (SIV) infections. In this report, we provide an overview of recent advances and challenges in gene editing NHP embryos and discuss the value of genetically engineered animal models for developing novel stem cell-based therapies for curing HIV.
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Affiliation(s)
- Jenna Kropp Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R Reynolds
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA.
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106
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Sipe CJ, Kluesner MG, Bingea SP, Lahr WS, Andrew AA, Wang M, DeFeo AP, Hinkel TL, Laoharawee K, Wagner JE, MacMillan ML, Vercellotti GM, Tolar J, Osborn MJ, McIvor RS, Webber BR, Moriarity BS. Correction of Fanconi Anemia Mutations Using Digital Genome Engineering. Int J Mol Sci 2022; 23:8416. [PMID: 35955545 PMCID: PMC9369391 DOI: 10.3390/ijms23158416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease in which genes essential for DNA repair are mutated. Both the interstrand crosslink (ICL) and double-strand break (DSB) repair pathways are disrupted in FA, leading to patient bone marrow failure (BMF) and cancer predisposition. The only curative therapy for the hematological manifestations of FA is an allogeneic hematopoietic cell transplant (HCT); however, many (>70%) patients lack a suitable human leukocyte antigen (HLA)-matched donor, often resulting in increased rates of graft-versus-host disease (GvHD) and, potentially, the exacerbation of cancer risk. Successful engraftment of gene-corrected autologous hematopoietic stem cells (HSC) circumvents the need for an allogeneic HCT and has been achieved in other genetic diseases using targeted nucleases to induce site specific DSBs and the correction of mutated genes through homology-directed repair (HDR). However, this process is extremely inefficient in FA cells, as they are inherently deficient in DNA repair. Here, we demonstrate the correction of FANCA mutations in primary patient cells using ‘digital’ genome editing with the cytosine and adenine base editors (BEs). These Cas9-based tools allow for C:G > T:A or A:T > C:G base transitions without the induction of a toxic DSB or the need for a DNA donor molecule. These genetic corrections or conservative codon substitution strategies lead to phenotypic rescue as illustrated by a resistance to the alkylating crosslinking agent Mitomycin C (MMC). Further, FANCA protein expression was restored, and an intact FA pathway was demonstrated by downstream FANCD2 monoubiquitination induction. This BE digital correction strategy will enable the use of gene-corrected FA patient hematopoietic stem and progenitor cells (HSPCs) for autologous HCT, obviating the risks associated with allogeneic HCT and DSB induction during autologous HSC gene therapy.
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Affiliation(s)
- Christopher J. Sipe
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Samuel P. Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S. Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aneesha A. Andrew
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anthony P. DeFeo
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy L. Hinkel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - John E. Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret L. MacMillan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gregory M. Vercellotti
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark J. Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - R. Scott McIvor
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
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107
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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108
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Zhou H, Wang X, Steer CJ, Song G, Niu J. Efficient silencing of hepatitis B virus S gene through CRISPR-mediated base editing. Hepatol Commun 2022; 6:1652-1663. [PMID: 35338607 PMCID: PMC9234685 DOI: 10.1002/hep4.1933] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 02/06/2022] [Accepted: 02/13/2022] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a major risk factor of liver cirrhosis and hepatocellular carcinoma. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has been used to precisely edit the HBV genome and eliminate HBV through non-homologous end-joining repair of double-stranded break (DSB). However, the CRISPR/Cas9-mediated DSB triggers instability of host genome and exhibits low efficiency to edit genome, limiting its application. CRISPR cytidine base editors (CBEs) could silence genes by generating a premature stop codon. Here we developed a CRISPR base editor approach to precisely edit single nucleotide within the HBV genome to impair HBV gene expression. Specifically, a single-guide RNA (sgRNA) was designed to edit the 30th codon of HBV S gene, which encodes HBV surface antigen (HBsAg), from CAG (glutamine) to stop codon TAG. We next used human hepatoma PLC/PRF/5 cells carrying the HBV genome to establish a cell line that expresses a CBE (PLC/PRF/5-CBE). Lentivirus was used to introduce sgRNA into PLC/PRF/5-CBE cells. Phenotypically, 71% of PLC/PRF/5-CBE cells developed a premature stop codon within the S gene. Levels of HBs messenger RNA were significantly decreased. A 92% reduction of HBsAg secretion was observed in PLC/PRF/5-CBE cells. The intracellular HBsAg was also reduced by 84% after treatment of gRNA_S. Furthermore, no off-target effect was detected in predicted off-target loci within the HBV genome. Sequencing confirmed that 95%, 93%, 93%, 9%, and 72% S gene sequences of HBV genotypes B, C, F, G, and H had the binding site of sgRNA. Conclusion: Our findings indicate that CRISPR-mediated base editing is an efficient approach to silence the HBV S gene, suggesting its therapeutic potential to eliminate HBV.
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Affiliation(s)
- Hao Zhou
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina
- Department of MedicineUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Xiaomei Wang
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina
- Department of MedicineUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Clifford J. Steer
- Department of MedicineUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Guisheng Song
- Department of MedicineUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Junqi Niu
- Department of HepatologyThe First Hospital of Jilin UniversityChangchunChina
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109
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Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun 2022; 13:3685. [PMID: 35760782 PMCID: PMC9237045 DOI: 10.1038/s41467-022-31322-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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110
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Kosicki M, Allen F, Steward F, Tomberg K, Pan Y, Bradley A. Cas9-induced large deletions and small indels are controlled in a convergent fashion. Nat Commun 2022; 13:3422. [PMID: 35701408 PMCID: PMC9197861 DOI: 10.1038/s41467-022-30480-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Repair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation. CRISPR/Cas9 system has revolutionized science and therapy, but DNA damage it causes often goes beyond the desired ’precision editing’. Here, the authors identify general and target specific DNA repair pathways responsible for unwanted mutagenesis.
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Affiliation(s)
| | | | - Frances Steward
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kärt Tomberg
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yangyang Pan
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Allan Bradley
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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111
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Luk K, Liu P, Zeng J, Wang Y, Maitland SA, Idrizi F, Ponnienselvan K, Iyer S, Zhu LJ, Luban J, Bauer DE, Wolfe SA. Optimization of Nuclear Localization Signal Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. GEN BIOTECHNOLOGY 2022; 1:271-284. [PMID: 38405215 PMCID: PMC10887433 DOI: 10.1089/genbio.2022.0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Type V CRISPR-Cas12a systems are an attractive Cas9-alternative nuclease platform for specific genome editing applications. However, previous studies demonstrate that there is a gap in overall activity between Cas12a and Cas9 in primary cells.1 Here we describe optimization to the NLS composition and architecture of Cas12a to facilitate highly efficient targeted mutagenesis in human transformed cell lines (HEK293T, Jurkat, and K562 cells) and primary cells (NK cells and CD34+ HSPCs), regardless of Cas12a ortholog. Our 3xNLS Cas12a architecture resulted in the most robust editing platform. The improved editing activity of Cas12a in both NK cells and CD34+ HSPCs resulted in pronounced phenotypic changes associated with target gene editing. Lastly, we demonstrated that optimization of the NLS composition and architecture of Cas12a did not increase editing at potential off-target sites in HEK293T or CD34+ HSPCs. Our new Cas12a NLS variant provides an improved nuclease platform for therapeutic genome editing.
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Affiliation(s)
- Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute of Harvard and MIT, Harvard Medical School, Boston, MA, USA
| | - Yetao Wang
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Beijing, Beijing, CN
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Feston Idrizi
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sukanya Iyer
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute of Harvard and MIT, Harvard Medical School, Boston, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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112
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Abstract
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
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113
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Jiang H, Jing Q, Yang Q, Qiao C, Liao Y, Liu W, Xing Y. Efficient Simultaneous Introduction of Premature Stop Codons in Three Tumor Suppressor Genes in PFFs via a Cytosine Base Editor. Genes (Basel) 2022; 13:genes13050835. [PMID: 35627220 PMCID: PMC9140995 DOI: 10.3390/genes13050835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
Base editing is an efficient and precise gene-editing technique, by which a single base can be changed without introducing double-strand breaks, and it is currently widely used in studies of various species. In this study, we used hA3A-BE3-Y130F to simultaneously introduce premature stop codons (TAG, TGA, and TAA) into three tumor suppressor genes, TP53, PTEN, and APC, in large white porcine fetal fibroblasts (PFFs). Among the isolated 290 single-cell colonies, 232 (80%) had premature stop codons in all the three genes. C−to−T conversion was found in 98.6%, 92.8%, and 87.2% of these cell colonies for TP53, PTEN, and APC, respectively. High frequencies of bystander C−to−T edits were observed within the editing window (positions 3−8), and there were nine (3.01%) clones with the designed simultaneous three-gene C−to−T conversion without bystander conversion. C−to−T conversion outside the editing window was found in 9.0%, 14.1%, and 26.2% of the 290 cell colonies for TP53, PTEN, and APC, respectively. Low-frequency C−to−G or C−to−A transversion occurred in APC. The mRNA levels of the three genes showed significant declines in triple-gene-mutant (Tri-Mut) cells as expected. No PTEN and a significantly lower (p < 0.05) APC protein expression were detected in Tri-Mut cells. Interestingly, the premature stop codon introduced into the TP53 gene did not eliminate the expression of its full-length protein in the Tri-Mut cells, suggesting that stop codon read-through occurred. Tri-Mut cells showed a significantly higher (p < 0.05) proliferation rate than WT cells. Furthermore, we identified 1418 differentially expressed genes (DEGs) between the Tri-Mut and WT groups, which were mainly involved in functions such as tumor progression, cell cycle, and DNA repair. This study indicates that hA3A-BE3-Y130F can be a powerful tool to create diverse knockout cell models without double-strand breaks (DSBs), with further possibilities to produce porcine models with various purposes.
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114
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Generation of Isogenic hiPSCs with Targeted Edits at Multiple Intronic SNPs to Study the Effects of the Type 2 Diabetes Associated KCNQ1 Locus in American Indians. Cells 2022; 11:cells11091446. [PMID: 35563754 PMCID: PMC9102014 DOI: 10.3390/cells11091446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022] Open
Abstract
The top genetic association signal for type 2 diabetes (T2D) in Southwestern American Indians maps to intron 15 of KCNQ1, an imprinted gene. We aim to understand the biology whereby variation at this locus affects T2D specifically in this genomic background. To do so, we obtained human induced pluripotent stem cells (hiPSC) derived from American Indians. Using these iPSCs, we show that imprinting of KCNQ1 and CDKN1C during pancreatic islet-like cell generation from iPSCs is consistent with known imprinting patterns in fetal pancreas and adult islets and therefore is an ideal model system to study this locus. In this report, we detail the use of allele-specific guide RNAs and CRISPR to generate isogenic hiPSCs that differ only at multiple T2D associated intronic SNPs at this locus which can be used to elucidate their functional effects. Characterization of these isogenic hiPSCs identified a few aberrant cell lines; namely cell lines with large hemizygous deletions in the putative functional region of KCNQ1 and cell lines hypomethylated at the KCNQ1OT1 promoter. Comparison of an isogenic cell line with a hemizygous deletion to the parental cell line identified CDKN1C and H19 as differentially expressed during the endocrine progenitor stage of pancreatic-islet development.
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115
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Simkin D, Papakis V, Bustos BI, Ambrosi CM, Ryan SJ, Baru V, Williams LA, Dempsey GT, McManus OB, Landers JE, Lubbe SJ, George AL, Kiskinis E. Homozygous might be hemizygous: CRISPR/Cas9 editing in iPSCs results in detrimental on-target defects that escape standard quality controls. Stem Cell Reports 2022; 17:993-1008. [PMID: 35276091 PMCID: PMC9023783 DOI: 10.1016/j.stemcr.2022.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to precisely edit the genome of human induced pluripotent stem cell (iPSC) lines using CRISPR/Cas9 has enabled the development of cellular models that can address genotype to phenotype relationships. While genome editing is becoming an essential tool in iPSC-based disease modeling studies, there is no established quality control workflow for edited cells. Moreover, large on-target deletions and insertions that occur through DNA repair mechanisms have recently been uncovered in CRISPR/Cas9-edited loci. Yet the frequency of these events in human iPSCs remains unclear, as they can be difficult to detect. We examined 27 iPSC clones generated after targeting 9 loci and found that 33% had acquired large, on-target genomic defects, including insertions and loss of heterozygosity. Critically, all defects had escaped standard PCR and Sanger sequencing analysis. We describe a cost-efficient quality control strategy that successfully identified all edited clones with detrimental on-target events and could facilitate the integrity of iPSC-based studies.
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Affiliation(s)
- Dina Simkin
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | | | | | | | | | | | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Steven J Lubbe
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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116
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Verkuijl SAN, Ang JXD, Alphey L, Bonsall MB, Anderson MAE. The Challenges in Developing Efficient and Robust Synthetic Homing Endonuclease Gene Drives. Front Bioeng Biotechnol 2022; 10:856981. [PMID: 35419354 PMCID: PMC8996256 DOI: 10.3389/fbioe.2022.856981] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Making discrete and precise genetic changes to wild populations has been proposed as a means of addressing some of the world's most pressing ecological and public health challenges caused by insect pests. Technologies that would allow this, such as synthetic gene drives, have been under development for many decades. Recently, a new generation of programmable nucleases has dramatically accelerated technological development. CRISPR-Cas9 has improved the efficiency of genetic engineering and has been used as the principal effector nuclease in different gene drive inheritance biasing mechanisms. Of these nuclease-based gene drives, homing endonuclease gene drives have been the subject of the bulk of research efforts (particularly in insects), with many different iterations having been developed upon similar core designs. We chart the history of homing gene drive development, highlighting the emergence of challenges such as unintended repair outcomes, "leaky" expression, and parental deposition. We conclude by discussing the progress made in developing strategies to increase the efficiency of homing endonuclease gene drives and mitigate or prevent unintended outcomes.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Joshua X. D. Ang
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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117
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Peterka M, Akrap N, Li S, Wimberger S, Hsieh PP, Degtev D, Bestas B, Barr J, van de Plassche S, Mendoza-Garcia P, Šviković S, Sienski G, Firth M, Maresca M. Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing. Nat Commun 2022; 13:1240. [PMID: 35332138 PMCID: PMC8948305 DOI: 10.1038/s41467-022-28771-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/07/2022] [Indexed: 12/26/2022] Open
Abstract
Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two strategies that install precise genomic insertions using an SpCas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing leads to increased levels of by-products, it can rescue pegRNAs that perform poorly with a nickase-based prime editor. We also present a small molecule approach that yields increased product purity of PEn editing. Next, we develop a homology-independent PEn editing strategy, which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells. Prime editing is a next-generation approach for precision genome engineering. Here the authors design a nuclease-based prime editor that leverages DNA repair pathways for targeted genomic insertions.
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Affiliation(s)
- Martin Peterka
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Nina Akrap
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.,Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pei-Pei Hsieh
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Jack Barr
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Stijn van de Plassche
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Patricia Mendoza-Garcia
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Saša Šviković
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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118
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Böck D, Rothgangl T, Villiger L, Schmidheini L, Matsushita M, Mathis N, Ioannidi E, Rimann N, Grisch-Chan HM, Kreutzer S, Kontarakis Z, Kopf M, Thöny B, Schwank G. In vivo prime editing of a metabolic liver disease in mice. Sci Transl Med 2022; 14:eabl9238. [PMID: 35294257 PMCID: PMC7614134 DOI: 10.1126/scitranslmed.abl9238] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Prime editing is a highly versatile CRISPR-based genome editing technology that works without DNA double-strand break formation. Despite rapid technological advances, in vivo application for the treatment of genetic diseases remains challenging. Here, we developed a size-reduced SpCas9 prime editor (PE) lacking the RNaseH domain (PE2ΔRnH) and an intein-split construct (PE2 p.1153) for adeno-associated virus-mediated delivery into the liver. Editing efficiencies reached 15% at the Dnmt1 locus and were further elevated to 58% by delivering unsplit PE2ΔRnH via human adenoviral vector 5 (AdV). To provide proof of concept for correcting a genetic liver disease, we used the AdV approach for repairing the disease-causing Pahenu2 mutation in a mouse model of phenylketonuria (PKU) via prime editing. Average correction efficiencies of 11.1% (up to 17.4%) in neonates led to therapeutic reduction of blood phenylalanine, without inducing detectable off-target mutations or prolonged liver inflammation. Although the current in vivo prime editing approach for PKU has limitations for clinical application due to the requirement of high vector doses (7 × 1014 vg/kg) and the induction of immune responses to the vector and the PE, further development of the technology may lead to curative therapies for PKU and other genetic liver diseases.
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Affiliation(s)
- Desirée Böck
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Lukas Villiger
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Correspondence to: Lukas Villiger () and Gerald Schwank ()
| | - Lukas Schmidheini
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Mai Matsushita
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Nicolas Mathis
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Eleonora Ioannidi
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicole Rimann
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Hiu Man Grisch-Chan
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Susanne Kreutzer
- Genome Engineering and Measurement Laboratory (GEML), ETH Zurich, 8093 Zurich, Switzerland,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Zacharias Kontarakis
- Genome Engineering and Measurement Laboratory (GEML), ETH Zurich, 8093 Zurich, Switzerland,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat Thöny
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland,Zurich Center for Integrative Human Physiology, 8006 Zurich, Switzerland,Neuroscience Center Zurich, 8057 Zurich, Switzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Correspondence to: Lukas Villiger () and Gerald Schwank ()
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CRISPR-Cas9 gene editing induced complex on-target outcomes in human cells. Exp Hematol 2022; 110:13-19. [PMID: 35304271 DOI: 10.1016/j.exphem.2022.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas9 is a powerful tool to edit the genome and holds great promise for gene therapy applications. Initial concerns of gene engineering focus on off-target effects. However, in addition to short indel mutations (often < 50 bp), an increasing number of studies have revealed complex on-target results after double-strand break repair by CRISPR-Cas9, such as large deletions, gene rearrangement, and loss of heterozygosity. These unintended mutations are potential safety concerns in clinical gene editing. Here, in this review, we summarize the significant findings of CRISPR-Cas9-induced on-target deleterious outcomes and discuss putative ways to achieve safe gene therapy.
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120
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Yin J, Lu R, Xin C, Wang Y, Ling X, Li D, Zhang W, Liu M, Xie W, Kong L, Si W, Wei P, Xiao B, Lee HY, Liu T, Hu J. Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing. Nat Commun 2022; 13:1204. [PMID: 35260581 PMCID: PMC8904484 DOI: 10.1038/s41467-022-28900-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/18/2022] [Indexed: 12/27/2022] Open
Abstract
The mechanism underlying unwanted structural variations induced by CRISPR-Cas9 remains poorly understood, and no effective strategy is available to inhibit the generation of these byproducts. Here we find that the generation of a high level of translocations is dependent on repeated cleavage at the Cas9-targeting sites. Therefore, we employ a strategy in which Cas9 is fused with optimized TREX2 to generate Cas9TX, a Cas9 exo-endonuclease, which prevents perfect DNA repair and thereby avoids repeated cleavage. In comparison with CRISPR-Cas9, CRISPR-Cas9TX greatly suppressed translocation levels and enhanced the editing efficiency of single-site editing. The number of large deletions associated with Cas9TX was also reduced to very low level. The application of CRISPR-Cas9TX for multiplex gene editing in chimeric antigen receptor T cells nearly eliminated deleterious chromosomal translocations. We report the mechanism underlying translocations induced by Cas9, and propose a general strategy for reducing chromosomal abnormalities induced by CRISPR-RNA-guided endonucleases.
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Affiliation(s)
- Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Rusen Lu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Changchang Xin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Yuhong Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191, Beijing, China
| | - Dong Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Mengzhu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Wutao Xie
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Lingyun Kong
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Wen Si
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Ping Wei
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Bingbing Xiao
- Department of Obstetrics and Gynecology, Peking University First Hospital, 100034, Beijing, China
| | - Hsiang-Ying Lee
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191, Beijing, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, 100871, Beijing, China.
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121
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Salas SP. Edición genética humana: análisis de algunos desafíos éticos. REVISTA MÉDICA CLÍNICA LAS CONDES 2022. [DOI: 10.1016/j.rmclc.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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122
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The Utility of Genomic Testing for Hyperphenylalaninemia. J Clin Med 2022; 11:jcm11041061. [PMID: 35207333 PMCID: PMC8879487 DOI: 10.3390/jcm11041061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/16/2022] [Indexed: 12/10/2022] Open
Abstract
Hyperphenylalaninemia (HPA), the most common amino acid metabolism disorder, is caused by defects in enzymes involved in phenylalanine metabolism, with the consequent accumulation of phenylalanine and its secondary metabolites in body fluids and tissues. Clinical manifestations of HPA include mental retardation, and its early diagnosis with timely treatment can improve the prognosis of affected patients. Due to the genetic complexity and heterogeneity of HPA, high-throughput molecular technologies, such as next-generation sequencing (NGS), are becoming indispensable tools to fully characterize the etiology, helping clinicians to promptly identify the exact patients’ genotype and determine the appropriate treatment. In this review, after a brief overview of the key enzymes involved in phenylalanine metabolism, we represent the wide spectrum of genes and their variants associated with HPA and discuss the utility of genomic testing for improved diagnosis and clinical management of HPA.
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123
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Höijer I, Emmanouilidou A, Östlund R, van Schendel R, Bozorgpana S, Tijsterman M, Feuk L, Gyllensten U, den Hoed M, Ameur A. CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations. Nat Commun 2022; 13:627. [PMID: 35110541 PMCID: PMC8810904 DOI: 10.1038/s41467-022-28244-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas9 genome editing has potential to cure diseases without current treatments, but therapies must be safe. Here we show that CRISPR-Cas9 editing can introduce unintended mutations in vivo, which are passed on to the next generation. By editing fertilized zebrafish eggs using four guide RNAs selected for off-target activity in vitro, followed by long-read sequencing of DNA from >1100 larvae, juvenile and adult fish across two generations, we find that structural variants (SVs), i.e., insertions and deletions ≥50 bp, represent 6% of editing outcomes in founder larvae. These SVs occur both at on-target and off-target sites. Our results also illustrate that adult founder zebrafish are mosaic in their germ cells, and that 26% of their offspring carries an off-target mutation and 9% an SV. Hence, pre-testing for off-target activity and SVs using patient material is advisable in clinical applications, to reduce the risk of unanticipated effects with potentially large implications.
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Affiliation(s)
- Ida Höijer
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Anastasia Emmanouilidou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rebecka Östlund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Selma Bozorgpana
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marcel den Hoed
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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124
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Ye ZF, Zhang P, Gai TT, Lou JH, Dai FY, Tong XL. Sob gene is critical to wing development in Bombyx mori and Tribolium castaneum. INSECT SCIENCE 2022; 29:65-77. [PMID: 33822467 DOI: 10.1111/1744-7917.12911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/26/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
The development of insect appendages requires the expression of multiple genes in a strict spatial and temporal order. The odd-skipped family genes are vital transcriptional factors involved in embryonic development. The development and morphogenesis of the insect wing requires multiple transcription factors to regulate the expression of wing patterning genes at the transcriptional level. However, the function of odd-related genes in insect wing morphogenesis and development during postembryonic stages is unclear. We focused on the roles of the sister of odd and bowl (sob) gene, a member of odd-skipped family genes, during the wing morphopoiesis in Bombyx mori using the clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 system and in Tribolium castaneum by RNA interference. The results showed that the wings were significantly smaller and degenerated, and wing veins were indistinct in the sob gene loss-of-function group in both B. mori and T. castaneum. Quantitative real-time polymerase chain reaction revealed that the Tcsob gene regulated the expression of wing development genes, such as the cht 7 and the vg gene. The findings suggest the importance of sob gene in insect wing morphology formation during postembryonic stages.
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Affiliation(s)
- Zhan-Feng Ye
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
| | - Pan Zhang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
| | - Ting-Ting Gai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
| | - Jing-Hou Lou
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
| | - Fang-Yin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
| | - Xiao-Ling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, China
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125
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Page EC, Heatley SL, Eadie LN, McClure BJ, de Bock CE, Omari S, Yeung DT, Hughes TP, Thomas PQ, White DL. HMGN1 plays a significant role in CRLF2 driven Down Syndrome leukemia and provides a potential therapeutic target in this high-risk cohort. Oncogene 2022; 41:797-808. [PMID: 34857887 DOI: 10.1038/s41388-021-02126-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022]
Abstract
The genetic basis of the predisposition for Down Syndrome (DS) patients to develop cytokine receptor-like factor 2 rearranged (CRLF2r) acute lymphoblastic leukemia (ALL) is currently unknown. Genes located on chromosome 21 and expressed in hematopoietic cells are likely candidates for investigation of CRLF2r DS-ALL pathogenesis. We explored the high-mobility group nucleosome-binding protein 1 (HMGN1), located in the DS critical region, in an inducible CRISPR/Cas9 knockout (KO) xenograft model to assess the effect of HMGN1 loss of function on the leukemic burden. We demonstrated HMGN1 KO-mitigated leukemic phenotypes including hepatosplenomegaly, thrombocytopenia, and anemia, commonly observed in leukemia patients, and significantly increased survival in vivo. HMGN1 overexpression in murine stem cells and Ba/F3 cells in vitro, in combination with P2RY8-CRLF2, resulted in cytokine-independent transformation and upregulation of cell signaling pathways associated with leukemic development. Finally, in vitro screening demonstrated successful targeting of P2RY8-CRLF2 and HMGN1 co-expressing cell lines and patient samples with fedratinib (JAK2 inhibitor), and GSK-J4 (demethylase inhibitor) in combination. Together, these data provide critical insight into the development and persistence of CRLF2r DS-ALL and identify HMGN1 as a potential therapeutic target to improve outcomes and reduce toxicity in this high-risk cohort of young patients.
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Affiliation(s)
- Elyse C Page
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Susan L Heatley
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
- Australian and New Zealand Children's Haematology/Oncology Group (ANZCHOG), Sydney, NSW, Australia
| | - Laura N Eadie
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group, Melbourne, VIC, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia
| | - Timothy P Hughes
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group, Melbourne, VIC, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
| | - Paul Q Thomas
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
- Gene Editing Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.
- Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia.
- Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.
- Australian and New Zealand Children's Haematology/Oncology Group (ANZCHOG), Sydney, NSW, Australia.
- Australasian Leukaemia and Lymphoma Group, Melbourne, VIC, Australia.
- Australian Genomic Health Alliance (AGHA), Sydney, NSW, Australia.
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126
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Boutin J, Cappellen D, Rosier J, Amintas S, Dabernat S, Bedel A, Moreau-Gaudry F. ON-target Adverse Events of CRISPR-Cas9 Nuclease: More Chaotic than Expected. CRISPR J 2022; 5:19-30. [DOI: 10.1089/crispr.2021.0120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Julian Boutin
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - David Cappellen
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Tumor Biology and Tumor Bank Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - Juliette Rosier
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
| | - Samuel Amintas
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Tumor Biology and Tumor Bank Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - Sandrine Dabernat
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - Aurélie Bedel
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - François Moreau-Gaudry
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France
- Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
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127
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
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128
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Lansing F, Mukhametzyanova L, Rojo-Romanos T, Iwasawa K, Kimura M, Paszkowski-Rogacz M, Karpinski J, Grass T, Sonntag J, Schneider PM, Günes C, Hoersten J, Schmitt LT, Rodriguez-Muela N, Knöfler R, Takebe T, Buchholz F. Correction of a Factor VIII genomic inversion with designer-recombinases. Nat Commun 2022; 13:422. [PMID: 35058465 PMCID: PMC8776779 DOI: 10.1038/s41467-022-28080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions. Correction of disease-causing large genomic inversions remains challenging. Here, the authors developed a dual designer-recombinase system (RecF8) that efficiently corrects a 140 kb inversion frequently found in patients with severe Hemophilia A.
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129
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Lim K, Cho SI, Kim JS. Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases. Nat Commun 2022; 13:366. [PMID: 35042880 PMCID: PMC8766470 DOI: 10.1038/s41467-022-27962-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
Base editing in nuclear DNA and mitochondrial DNA (mtDNA) is broadly useful for biomedical research, medicine, and biotechnology. Here, we present a base editing platform, termed zinc finger deaminases (ZFDs), composed of custom-designed zinc-finger DNA-binding proteins, the split interbacterial toxin deaminase DddAtox, and a uracil glycosylase inhibitor (UGI), which catalyze targeted C-to-T base conversions without inducing unwanted small insertions and deletions (indels) in human cells. We assemble plasmids encoding ZFDs using publicly available zinc finger resources to achieve base editing at frequencies of up to 60% in nuclear DNA and 30% in mtDNA. Because ZFDs, unlike CRISPR-derived base editors, do not cleave DNA to yield single- or double-strand breaks, no unwanted indels caused by error-prone non-homologous end joining are produced at target sites. Furthermore, recombinant ZFD proteins, expressed in and purified from E. coli, penetrate cultured human cells spontaneously to induce targeted base conversions, demonstrating the proof-of-principle of gene-free gene therapy. Base editing in nuclear DNA and mitochondrial DNA (mtDNA) is broadly useful for biomedical research, medicine, and biotechnology. Here the authors present zinc finger deaminases which catalyze targeted C-to-T base conversions without inducing unwanted indels in human cells.
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Affiliation(s)
- Kayeong Lim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea.
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130
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Mianné J, Nasri A, Van CN, Bourguignon C, Fieldès M, Ahmed E, Duthoit C, Martin N, Parrinello H, Louis A, Iché A, Gayon R, Samain F, Lamouroux L, Bouillé P, Bourdin A, Assou S, De Vos J. CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles. BMC Biol 2022; 20:8. [PMID: 34996449 PMCID: PMC8742436 DOI: 10.1186/s12915-021-01214-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The application of CRISPR/Cas9 technology in human induced pluripotent stem cells (hiPSC) holds tremendous potential for basic research and cell-based gene therapy. However, the fulfillment of these promises relies on the capacity to efficiently deliver exogenous nucleic acids and harness the repair mechanisms induced by the nuclease activity in order to knock-out or repair targeted genes. Moreover, transient delivery should be preferred to avoid persistent nuclease activity and to decrease the risk of off-target events. We recently developed bacteriophage-chimeric retrovirus-like particles that exploit the properties of bacteriophage coat proteins to package exogenous RNA, and the benefits of lentiviral transduction to achieve highly efficient, non-integrative RNA delivery in human cells. Here, we investigated the potential of bacteriophage-chimeric retrovirus-like particles for the non-integrative delivery of RNA molecules in hiPSC for CRISPR/Cas9 applications. RESULTS We found that these particles efficiently convey RNA molecules for transient expression in hiPSC, with minimal toxicity and without affecting the cell pluripotency and subsequent differentiation. We then used this system to transiently deliver in a single step the CRISPR-Cas9 components (Cas9 mRNA and sgRNA) to generate gene knockout with high indel rate (up to 85%) at multiple loci. Strikingly, when using an allele-specific sgRNA at a locus harboring compound heterozygous mutations, the targeted allele was not altered by NHEJ/MMEJ, but was repaired at high frequency using the homologous wild type allele, i.e., by interallelic gene conversion. CONCLUSIONS Our results highlight the potential of bacteriophage-chimeric retrovirus-like particles to efficiently and safely deliver RNA molecules in hiPSC, and describe for the first time genome engineering by gene conversion in hiPSC. Harnessing this DNA repair mechanism could facilitate the therapeutic correction of human genetic disorders in hiPSC.
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Affiliation(s)
- Joffrey Mianné
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Amel Nasri
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Nguyen Van
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Chloé Bourguignon
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Mathieu Fieldès
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - Engi Ahmed
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | | | | | - Hugues Parrinello
- Univ. Montpellier, CNRS, INSERM, Montpellier, France
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Anaïs Louis
- Univ. Montpellier, CNRS, INSERM, Montpellier, France
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | | | | | | | | | | | - Arnaud Bourdin
- PhyMedExp, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Said Assou
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France
| | - John De Vos
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34295, Montpellier, France.
- Department of Cell and Tissue Engineering, Univ Montpellier, CHU Montpellier, Montpellier, France.
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131
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Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
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Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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132
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Yoo KW, Yadav MK, Song Q, Atala A, Lu B. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3944-3957. [PMID: 35323942 PMCID: PMC9023269 DOI: 10.1093/nar/gkac186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kyung W Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Manish Kumar Yadav
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Qianqian Song
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Baisong Lu
- To whom correspondence should be addressed. Tel: +1 336 713 7276; Fax: +1 336 713 7290;
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133
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Kuno A, Ikeda Y, Ayabe S, Kato K, Sakamoto K, Suzuki SR, Morimoto K, Wakimoto A, Mikami N, Ishida M, Iki N, Hamada Y, Takemura M, Daitoku Y, Tanimoto Y, Dinh TTH, Murata K, Hamada M, Muratani M, Yoshiki A, Sugiyama F, Takahashi S, Mizuno S. DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biol 2022; 20:e3001507. [PMID: 35041655 PMCID: PMC8765641 DOI: 10.1371/journal.pbio.3001507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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Affiliation(s)
- Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Ikeda
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Sakamoto
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Sayaka R. Suzuki
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Arata Wakimoto
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Natsuki Mikami
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Natsumi Iki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Megumi Takemura
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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134
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Pavani G, Amendola M. Targeted Gene Delivery: Where to Land. Front Genome Ed 2021; 2:609650. [PMID: 34713234 PMCID: PMC8525409 DOI: 10.3389/fgeed.2020.609650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-editing technologies have the potential to correct most genetic defects involved in blood disorders. In contrast to mutation-specific editing, targeted gene insertion can correct most of the mutations affecting the same gene with a single therapeutic strategy (gene replacement) or provide novel functions to edited cells (gene addition). Targeting a selected genomic harbor can reduce insertional mutagenesis risk, while enabling the exploitation of endogenous promoters, or selected chromatin contexts, to achieve specific transgene expression levels/patterns and the modulation of disease-modifier genes. In this review, we will discuss targeted gene insertion and the advantages and limitations of different genomic harbors currently under investigation for various gene therapy applications.
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Affiliation(s)
- Giulia Pavani
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Univ Paris-Saclay, Evry, France
| | - Mario Amendola
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Univ Paris-Saclay, Evry, France
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135
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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136
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Adikusuma F, Lushington C, Arudkumar J, Godahewa G, Chey YCJ, Gierus L, Piltz S, Geiger A, Jain Y, Reti D, Wilson LOW, Bauer D, Thomas P. Optimized nickase- and nuclease-based prime editing in human and mouse cells. Nucleic Acids Res 2021; 49:10785-10795. [PMID: 34534334 PMCID: PMC8501948 DOI: 10.1093/nar/gkab792] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Precise genomic modification using prime editing (PE) holds enormous potential for research and clinical applications. In this study, we generated all-in-one prime editing (PEA1) constructs that carry all the components required for PE, along with a selection marker. We tested these constructs (with selection) in HEK293T, K562, HeLa and mouse embryonic stem (ES) cells. We discovered that PE efficiency in HEK293T cells was much higher than previously observed, reaching up to 95% (mean 67%). The efficiency in K562 and HeLa cells, however, remained low. To improve PE efficiency in K562 and HeLa, we generated a nuclease prime editor and tested this system in these cell lines as well as mouse ES cells. PE-nuclease greatly increased prime editing initiation, however, installation of the intended edits was often accompanied by extra insertions derived from the repair template. Finally, we show that zygotic injection of the nuclease prime editor can generate correct modifications in mouse fetuses with up to 100% efficiency.
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Affiliation(s)
- Fatwa Adikusuma
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- CSIRO Synthetic Biology Future Science Platform, Australia
| | - Caleb Lushington
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Jayshen Arudkumar
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Gelshan I Godahewa
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Yu C J Chey
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Luke Gierus
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Sandra Piltz
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- South Australian Genome Editing (SAGE), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Ashleigh Geiger
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- CSIRO Synthetic Biology Future Science Platform, Australia
| | - Yatish Jain
- Australian e-Health Research Centre, CSIRO, North Ryde, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Daniel Reti
- Australian e-Health Research Centre, CSIRO, North Ryde, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Laurence O W Wilson
- Australian e-Health Research Centre, CSIRO, North Ryde, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Denis C Bauer
- Australian e-Health Research Centre, CSIRO, North Ryde, Australia
- Department of Biomedical Sciences, Macquarie University, New South Wales, Sydney, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Paul Q Thomas
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- South Australian Genome Editing (SAGE), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
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137
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Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. [PMID: 34615869 PMCID: PMC8494802 DOI: 10.1038/s41467-021-26097-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell L Leibowitz
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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138
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Amendola M, Bedel A, Buj-Bello A, Carrara M, Concordet JP, Frati G, Gilot D, Giovannangeli C, Gutierrez-Guerrero A, Laurent M, Miccio A, Moreau-Gaudry F, Sourd C, Valton J, Verhoeyen E. Recent Progress in Genome Editing for Gene Therapy Applications: The French Perspective. Hum Gene Ther 2021; 32:1059-1075. [PMID: 34494480 DOI: 10.1089/hum.2021.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent advances in genome editing tools, especially novel developments in the clustered regularly interspaced short palindromic repeats associated to Cas9 nucleases (CRISPR/Cas9)-derived editing machinery, have revolutionized not only basic science but, importantly, also the gene therapy field. Their flexibility and ability to introduce precise modifications in the genome to disrupt or correct genes or insert expression cassettes in safe harbors in the genome underline their potential applications as a medicine of the future to cure many genetic diseases. In this review, we give an overview of the recent progress made by French researchers in the field of therapeutic genome editing, while putting their work in the general context of advances made in the field. We focus on recent hematopoietic stem cell gene editing strategies for blood diseases affecting the red blood cells or blood coagulation as well as lysosomal storage diseases. We report on a genome editing-based therapy for muscular dystrophy and the potency of T cell gene editing to increase anticancer activity of chimeric antigen receptor T cells to combat cancer. We will also discuss technical obstacles and side effects such as unwanted editing activity that need to be surmounted on the way toward a clinical implementation of genome editing. We propose here improvements developed today, including by French researchers to overcome the editing-related genotoxicity and improve editing precision by the use of novel recombinant nuclease-based systems such as nickases, base editors, and prime editors. Finally, a solution is proposed to resolve the cellular toxicity induced by the systems employed for gene editing machinery delivery.
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Affiliation(s)
- Mario Amendola
- Genethon, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, Evry, France
| | - Aurélie Bedel
- Bordeaux University, Bordeaux, France.,INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France.,Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - Ana Buj-Bello
- Genethon, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, Evry, France
| | - Mathieu Carrara
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Jean-Paul Concordet
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Giacomo Frati
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris, France.,Université de Paris, Paris, France
| | - David Gilot
- Inserm U1242, Université de Rennes, Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Carine Giovannangeli
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Alejandra Gutierrez-Guerrero
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Marine Laurent
- Genethon, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, Evry, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris, France.,Université de Paris, Paris, France
| | - François Moreau-Gaudry
- Bordeaux University, Bordeaux, France.,INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux, France.,Biochemistry Laboratory, University Hospital Bordeaux, Bordeaux, France
| | - Célia Sourd
- Genethon, Evry, France.,Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, Evry, France
| | | | - Els Verhoeyen
- CIRI-International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France.,Université Côte d'Azur, INSERM, C3M, Nice, France
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139
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Dawes JC, Uren AG. Forward and Reverse Genetics of B Cell Malignancies: From Insertional Mutagenesis to CRISPR-Cas. Front Immunol 2021; 12:670280. [PMID: 34484175 PMCID: PMC8414522 DOI: 10.3389/fimmu.2021.670280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer genome sequencing has identified dozens of mutations with a putative role in lymphomagenesis and leukemogenesis. Validation of driver mutations responsible for B cell neoplasms is complicated by the volume of mutations worthy of investigation and by the complex ways that multiple mutations arising from different stages of B cell development can cooperate. Forward and reverse genetic strategies in mice can provide complementary validation of human driver genes and in some cases comparative genomics of these models with human tumors has directed the identification of new drivers in human malignancies. We review a collection of forward genetic screens performed using insertional mutagenesis, chemical mutagenesis and exome sequencing and discuss how the high coverage of subclonal mutations in insertional mutagenesis screens can identify cooperating mutations at rates not possible using human tumor genomes. We also compare a set of independently conducted screens from Pax5 mutant mice that converge upon a common set of mutations observed in human acute lymphoblastic leukemia (ALL). We also discuss reverse genetic models and screens that use CRISPR-Cas, ORFs and shRNAs to provide high throughput in vivo proof of oncogenic function, with an emphasis on models using adoptive transfer of ex vivo cultured cells. Finally, we summarize mouse models that offer temporal regulation of candidate genes in an in vivo setting to demonstrate the potential of their encoded proteins as therapeutic targets.
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Affiliation(s)
- Joanna C Dawes
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Anthony G Uren
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
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140
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Wen W, Quan ZJ, Li SA, Yang ZX, Fu YW, Zhang F, Li GH, Zhao M, Yin MD, Xu J, Zhang JP, Cheng T, Zhang XB. Effective control of large deletions after double-strand breaks by homology-directed repair and dsODN insertion. Genome Biol 2021; 22:236. [PMID: 34416913 PMCID: PMC8377869 DOI: 10.1186/s13059-021-02462-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/06/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences. RESULTS We show that large deletions are ubiquitous but are dependent on editing sites and cell types. Human primary T cells display more significant deletions than hematopoietic stem and progenitor cells (HSPCs), whereas we observe low levels in induced pluripotent stem cells (iPSCs). We find that the homology-directed repair (HDR) with single-stranded oligodeoxynucleotides (ssODNs) carrying short homology reduces the deletion damage by almost half, while adeno-associated virus (AAV) donors with long homology reduce large deletions by approximately 80%. In the absence of HDR, the insertion of a short double-stranded ODN by NHEJ reduces deletion indexes by about 60%. CONCLUSIONS Timely bridging of broken ends by HDR and NHEJ vastly decreases the unintended consequences of dsDNA cleavage. These strategies can be harnessed in gene editing applications to attenuate unintended outcomes.
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Affiliation(s)
- Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zi-Jun Quan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Ya-Wen Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Guo-Hua Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Meng-Di Yin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jing Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China.
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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141
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Boutin J, Rosier J, Cappellen D, Prat F, Toutain J, Pennamen P, Bouron J, Rooryck C, Merlio JP, Lamrissi-Garcia I, Cullot G, Amintas S, Guyonnet-Duperat V, Ged C, Blouin JM, Richard E, Dabernat S, Moreau-Gaudry F, Bedel A. CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells. Nat Commun 2021; 12:4922. [PMID: 34389729 PMCID: PMC8363739 DOI: 10.1038/s41467-021-25190-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is a promising technology for gene therapy. However, the ON-target genotoxicity of CRISPR-Cas9 nuclease due to DNA double-strand breaks has received little attention and is probably underestimated. Here we report that genome editing targeting globin genes induces megabase-scale losses of heterozygosity (LOH) from the globin CRISPR-Cas9 cut-site to the telomere (5.2 Mb). In established lines, CRISPR-Cas9 nuclease induces frequent terminal chromosome 11p truncations and rare copy-neutral LOH. In primary hematopoietic progenitor/stem cells, we detect 1.1% of clones (7/648) with acquired megabase LOH induced by CRISPR-Cas9. In-depth analysis by SNP-array reveals the presence of copy-neutral LOH. This leads to 11p15.5 partial uniparental disomy, comprising two Chr11p15.5 imprinting centers (H19/IGF2:IG-DMR/IC1 and KCNQ1OT1:TSS-DMR/IC2) and impacting H19 and IGF2 expression. While this genotoxicity is a safety concern for CRISPR clinical trials, it is also an opportunity to model copy-neutral-LOH for genetic diseases and cancers.
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Affiliation(s)
- J Boutin
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - J Rosier
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - D Cappellen
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
- University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory, Bordeaux, France
| | - F Prat
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - J Toutain
- Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - P Pennamen
- Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - J Bouron
- Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - C Rooryck
- Bordeaux University, Bordeaux, France
- Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - J P Merlio
- Bordeaux University, Bordeaux, France
- University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory, Bordeaux, France
- INSERM U1053, Bordeaux Research in Translational Oncology, Bordeaux, France
| | - I Lamrissi-Garcia
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - G Cullot
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - S Amintas
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
- University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory, Bordeaux, France
| | - V Guyonnet-Duperat
- INSERM US 005-CNRS UMS 342-TBM-Core, Bordeaux University, Bordeaux, France
| | - C Ged
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - J M Blouin
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - E Richard
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - S Dabernat
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
| | - F Moreau-Gaudry
- Bordeaux University, Bordeaux, France.
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France.
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France.
- Laboratory of Excellence, Gr-Ex, Bordeaux, France.
- INSERM US 005-CNRS UMS 342-TBM-Core, Bordeaux University, Bordeaux, France.
| | - A Bedel
- Bordeaux University, Bordeaux, France
- INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory disorders and Cancers, Bordeaux, France
- University Hospital Bordeaux, Biochemistry Laboratory, Bordeaux, France
- Laboratory of Excellence, Gr-Ex, Bordeaux, France
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142
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Ferreira da Silva J, Meyenberg M, Loizou JI. Tissue specificity of DNA repair: the CRISPR compass. Trends Genet 2021; 37:958-962. [PMID: 34392967 DOI: 10.1016/j.tig.2021.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9-mediated genome editing holds great promise for the correction of pathogenic variants in humans. However, its therapeutic implementation is hampered due to unwanted editing outcomes. A better understanding of cell type- and tissue-specific DNA repair processes will ultimately enable precise control of editing outcomes for safer and effective therapies.
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Affiliation(s)
- Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mathilde Meyenberg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria.
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143
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Liu M, Zhang W, Xin C, Yin J, Shang Y, Ai C, Li J, Meng FL, Hu J. Global detection of DNA repair outcomes induced by CRISPR-Cas9. Nucleic Acids Res 2021; 49:8732-8742. [PMID: 34365511 PMCID: PMC8421148 DOI: 10.1093/nar/gkab686] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/28/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
CRISPR–Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR–Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR–Cas9 editing, including large deletions, vector integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.
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Affiliation(s)
- Mengzhu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Changchang Xin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Yafang Shang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jiaxin Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
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144
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Zhang C, Lu T, Zhang Y, Li J, Tarique I, Wen F, Chen A, Wang J, Zhang Z, Zhang Y, Shi DL, Shao M. Rapid generation of maternal mutants via oocyte transgenic expression of CRISPR-Cas9 and sgRNAs in zebrafish. SCIENCE ADVANCES 2021; 7:eabg4243. [PMID: 34362733 PMCID: PMC8346210 DOI: 10.1126/sciadv.abg4243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 05/08/2023]
Abstract
Maternal products are exclusive factors to drive oogenesis and early embryonic development. As disrupting maternal gene functions is either time-consuming or technically challenging, early developmental programs regulated by maternal factors remain mostly elusive. We provide a transgenic approach to inactivate maternal genes in zebrafish primary oocytes. By introducing three tandem single guide RNA (sgRNA) expression cassettes and a green fluorescent protein (GFP) reporter into Tg(zpc:zcas9) embryos, we efficiently obtained maternal nanog and ctnnb2 mutants among GFP-positive F1 offspring. Notably, most of these maternal mutants displayed either sgRNA site-spanning genomic deletions or unintended large deletions extending distantly from the sgRNA targets, suggesting a prominent deletion-prone tendency of genome editing in the oocyte. Thus, our method allows maternal gene knockout in the absence of viable and fertile homozygous mutant adults. This approach is particularly time-saving and can be applied for functional screening of maternal factors and generating genomic deletions in zebrafish.
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Affiliation(s)
- Chong Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yizhuang Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaguang Li
- Shandong University Taishan College, Qingdao 266237, China
| | - Imran Tarique
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fenfen Wen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aijun Chen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiasheng Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Zhuoyu Zhang
- Shandong University Taishan College, Qingdao 266237, China
| | - Yanjun Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
- Developmental Biology Laboratory, CNRS-UMR7622, Institut de Biologie Paris-Seine, Sorbonne University, Paris 75005, France
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
- Shandong University Taishan College, Qingdao 266237, China
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145
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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146
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Xu L, Zhang C, Li H, Wang P, Gao Y, Mokadam NA, Ma J, Arnold WD, Han R. Efficient precise in vivo base editing in adult dystrophic mice. Nat Commun 2021; 12:3719. [PMID: 34140489 PMCID: PMC8211797 DOI: 10.1038/s41467-021-23996-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/29/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in base editing have created an exciting opportunity to precisely correct disease-causing mutations. However, the large size of base editors and their inherited off-target activities pose challenges for in vivo base editing. Moreover, the requirement of a protospacer adjacent motif (PAM) nearby the mutation site further limits the targeting feasibility. Here we modify the NG-targeting adenine base editor (iABE-NGA) to overcome these challenges and demonstrate the high efficiency to precisely edit a Duchenne muscular dystrophy (DMD) mutation in adult mice. Systemic delivery of AAV9-iABE-NGA results in dystrophin restoration and functional improvement. At 10 months after AAV9-iABE-NGA treatment, a near complete rescue of dystrophin is measured in mdx4cv mouse hearts with up to 15% rescue in skeletal muscle fibers. The off-target activities remains low and no obvious toxicity is detected. This study highlights the promise of permanent base editing using iABE-NGA for the treatment of monogenic diseases.
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MESH Headings
- Animals
- CRISPR-Cas Systems
- Cell Line
- Dependovirus
- Disease Models, Animal
- Dystrophin/genetics
- Dystrophin/metabolism
- Gene Editing/methods
- Genetic Therapy/methods
- Genetic Vectors
- Humans
- Mice
- Mice, Inbred mdx
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/therapy
- Mutation
- RNA-Seq
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Affiliation(s)
- Li Xu
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Chen Zhang
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Haiwen Li
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Peipei Wang
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yandi Gao
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Nahush A Mokadam
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jianjie Ma
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - W David Arnold
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Renzhi Han
- Division of Cardiac Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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147
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Zhang W, Yin J, Zhang-Ding Z, Xin C, Liu M, Wang Y, Ai C, Hu J. In-depth assessment of the PAM compatibility and editing activities of Cas9 variants. Nucleic Acids Res 2021; 49:8785-8795. [PMID: 34133740 PMCID: PMC8421146 DOI: 10.1093/nar/gkab507] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
A series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR-Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR-Cas9 editing, raising an urgent issue to be addressed.
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Affiliation(s)
- Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Zhengrong Zhang-Ding
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Changchang Xin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Mengzhu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Yuhong Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing 100871, China
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148
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Wilde JJ, Aida T, Del Rosario RCH, Kaiser T, Qi P, Wienisch M, Zhang Q, Colvin S, Feng G. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 2021; 184:3267-3280.e18. [PMID: 34043941 PMCID: PMC8240950 DOI: 10.1016/j.cell.2021.04.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 03/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.
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Affiliation(s)
- Jonathan J Wilde
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Tomomi Aida
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Kaiser
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Peimin Qi
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Martin Wienisch
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Steven Colvin
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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149
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Affiliation(s)
- Stephanie Mack
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
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150
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Leibowitz ML, Papathanasiou S, Doerfler PA, Blaine LJ, Sun L, Yao Y, Zhang CZ, Weiss MJ, Pellman D. Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing. Nat Genet 2021; 53:895-905. [PMID: 33846636 PMCID: PMC8192433 DOI: 10.1038/s41588-021-00838-7] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022]
Abstract
Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of chromosome structural abnormalities. Here, using model cells and single-cell whole-genome sequencing, as well as by editing at a clinically relevant locus in clinically relevant cells, we show that CRISPR-Cas9 editing generates structural defects of the nucleus, micronuclei and chromosome bridges, which initiate a mutational process called chromothripsis. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer. These results demonstrate that chromothripsis is a previously unappreciated on-target consequence of CRISPR-Cas9-generated DSBs. As genome editing is implemented in the clinic, the potential for extensive chromosomal rearrangements should be considered and monitored.
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Affiliation(s)
- Mitchell L Leibowitz
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lili Sun
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - David Pellman
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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