151
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Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the –123 region. Base editing at –123 and –124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of –123T > C and –124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Beeke Wienert
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anila George
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Kirti Prasad
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | | | - Vignesh Rajendiran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Nazar Syedbasha
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Japan, Tokyo, Japan
| | | | | | | | - Srujan Marepally
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Mark A DeWitt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland
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152
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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: 60] [Impact Index Per Article: 30.0] [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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153
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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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154
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Abstract
Genome editing by programmable RNA-dependent Cas endonucleases has revolutionised the field of genome engineering, achieving targeted genomic change at unprecedented efficiencies with considerable application in laboratory animal research. Despite its ease of use and wide application, there remain concerns about the precision of this technology and a number of unpredictable consequences have been reported, mostly resulting from the DNA double-strand break (DSB) that conventional CRISPR editing induces. In order to improve editing precision, several iterations of the technology been developed over the years. Base editing is one of most successful developments, allowing for single base conversions but without the need for a DSB. Cytosine and adenine base editing are now established as reliable methods to achieve precise genome editing in animal research studies. Both cytosine and adenine base editors have been applied successfully to the editing of zygotes, resulting in the generation of animal models. Similarly, both base editors have achieved precise editing of point mutations in somatic cells, facilitating the development of gene therapy approaches. Despite rapid progress in optimising these tools, base editing can address only a subset of possible base conversions within a relatively narrow window and larger genomic manipulations are not possible. The recent development of prime editing, originally defined as a simple 'search and replace' editing tool, may help address these limitations and could widen the range of genome manipulations possible. Preliminary reports of prime editing in animals are being published, and this new technology may allow significant advancements for laboratory animal research.
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Affiliation(s)
- Federico Caso
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, UK
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155
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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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156
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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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157
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Zhou H, Xu L, Li F, Li Y. Transcriptional regulation by CRISPR/dCas9 in common wheat. Gene 2022; 807:145919. [PMID: 34454034 DOI: 10.1016/j.gene.2021.145919] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/04/2022]
Abstract
The application of CRISPR/Cas9 system for gene editing, as a technical coup for biotechnology, is worldwide and encompasses multiple of species. The inactivation of catalytical site in Cas9 (dCas9) has been reprogrammed as an effective approach to regulate the transcriptional level of target genes, especially for the functionally essential genes and redundant genes. Here, we exploited the CRISPR/dCas9 system to manipulate the transcriptional level of target genes in common wheat. To improve target gene's expression, we generated transcriptional activator by fusing 6×TAL-VP128 activation domain to the C-terminus of dCas9 in frame. For target gene's repressing expression transcriptionally, 3×SRDX repression domain was conjugated to the C-terminus of dCas9 in frame. Our results showed that dCas9 fused activation or repression domain could increase or decrease the transcriptional level of target gene effectively in stable transgenic lines of wheat. The study on the tRNA-processing system in CRISPR/dCas9 based transcriptional regulation system demonstrated that this robust multiplex targeted tool can be incorporated to the CRISPR/dCas9 system to facilitate the target regulation of several genes' transcriptional level. Our data broaden the application of CRISPR/dCas9 based transcriptional regulation and provide great opportunities to investigate the function of essential genes in common wheat.
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Affiliation(s)
- Huajie Zhou
- College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Lixia District, Jinan 250014, Shandong, China
| | - Lei Xu
- College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Lixia District, Jinan 250014, Shandong, China
| | - Feng Li
- Shandong Shunfeng Biotechnology Co. Ltd., 11 Floor, Main Building, QiLu Innovalley Incubator, High-tech Industry Development Zone, Jinan 250000, Shandong, China
| | - Yansha Li
- Shandong Shunfeng Biotechnology Co. Ltd., 11 Floor, Main Building, QiLu Innovalley Incubator, High-tech Industry Development Zone, Jinan 250000, Shandong, China.
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158
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Alhawaj AF. Stem cell-based therapy for hirschsprung disease, do we have the guts to treat? Gene Ther 2022; 29:578-587. [PMID: 34121091 PMCID: PMC9684071 DOI: 10.1038/s41434-021-00268-4] [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: 04/23/2020] [Revised: 04/26/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital anomaly of the colon that results from failure of enteric nervous system formation, leading to a constricted dysfunctional segment of the colon with variable lengths, and necessitating surgical intervention. The underlying pathophysiology includes a defect in neural crest cells migration, proliferation and differentiation, which are partially explained by identified genetic and epigenetic alterations. Despite the high success rate of the curative surgeries, they are associated with significant adverse outcomes such as enterocolitis, fecal soiling, and chronic constipation. In addition, some patients suffer from extensive lethal variants of the disease, all of which justify the need for an alternative cure. During the last 5 years, there has been considerable progress in HSCR stem cell-based therapy research. However, many major issues remain unsolved. This review will provide concise background information on HSCR, outline the future approaches of stem cell-based HSCR therapy, review recent key publications, discuss technical and ethical challenges the field faces prior to clinical translation, and tackle such challenges by proposing solutions and evaluating existing approaches to progress further.
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Affiliation(s)
- Ali Fouad Alhawaj
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6DD, United Kingdom. .,Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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159
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Li C, Liu Z, Zhang X, Wang H, Friedman GK, Ding Q, Zhao X, Li H, Kim K, Yu X, Burt Nabors L, Han X, Zhao R. Generation of chromosome 1p/19q co-deletion by CRISPR/Cas9-guided genomic editing. Neurooncol Adv 2022; 4:vdac131. [PMID: 36225650 PMCID: PMC9547542 DOI: 10.1093/noajnl/vdac131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background Chromosomal translocation has been detected in many human cancers including gliomas and is considered a driving force in tumorigenesis. Co-deletion of chromosome arms 1p and 19q is a hallmark for oligodendrogliomas. On the molecular level, 1p/19q co-deletion results from t(1;19)(q10;p10), which leads to the concomitant formation of a hybrid chromosome containing the 1q and 19p arms. A method to generate 1p/19q co-deletion is lacking, which hinders the investigation of how 1p/19q co-deletion contributes to gliomagenesis. Methods We hypothesized that chromosomal translocation, such as t(1;19)(q10;p10) resulting in the 1p/19q co-deletion, may be induced by simultaneously introducing DNA double-strand breaks (DSBs) into chromosomes 1p and 19q using CRISPR/Cas9. We developed a CRISPR/Cas9-based strategy to induce t(1;19)(q10;p10) and droplet digital PCR (ddPCR) assays to detect the hybrid 1q/19p and 1p/19q chromosomes. Results After translocation induction, we detected both 1p/19q and 1q/19p hybrid chromosomes by PCR amplification of the junction regions in HEK 293T, and U-251 and LN-229 glioblastoma cells. Sequencing analyses of the PCR products confirmed DNA sequences matching both chromosomes 1 and 19. Furthermore, the 1p/19q hybrid chromosome was rapidly lost in all tested cell lines. The 1q/19p hybrid chromosome also become undetectable over time likely due to cell survival disadvantage. Conclusion We demonstrated that t(1;19)(q10;p10) may be induced by CRISPR/Cas9-mediated genomic editing. This method represents an important step toward engineering the 1p/19q co-deletion to model oligodendrogliomas. This method may also be generalizable to engineering other cancer-relevant translocations, which may facilitate the understanding of translocation roles in cancer progression.
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Affiliation(s)
- Chao Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
| | - Zhong Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
| | - Xiaoxia Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, AL 35294, USA
| | - Huafeng Wang
- Department of Neurology, University of Alabama at Birmingham, AL 35294, USA
| | - Gregory K Friedman
- Department of Pediatrics, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Qiang Ding
- Department of Anesthesiology and Perioperative Medicine & Molecular and Translational Biomedicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xinyang Zhao
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55904, USA
| | - Kitai Kim
- Human Stem Cell & Genome Engineering Center and Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Xi Yu
- Clinical Oncology Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - L Burt Nabors
- Department of Neurology, University of Alabama at Birmingham, AL 35294, USA
| | - Xiaosi Han
- Department of Neurology, University of Alabama at Birmingham, AL 35294, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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160
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Xiong X, Li Z, Liang J, Liu K, Li C, Li JF. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3565-3580. [PMID: 35286371 PMCID: PMC8989527 DOI: 10.1093/nar/gkac166] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.
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Affiliation(s)
| | - Zhenxiang Li
- Correspondence may also be addressed to Zhenxiang Li.
| | - Jieping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kehui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenlong Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- To whom correspondence should be addressed. Tel: +86 20 39943513; Fax: +86 20 39943513;
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161
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Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Mol Cell 2021; 82:333-347. [PMID: 34968414 DOI: 10.1016/j.molcel.2021.12.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023]
Abstract
The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.
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Affiliation(s)
- Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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162
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Evaluation of two in vitro assays for tumorigenicity assessment of CRISPR-Cas9 genome-edited cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:241-253. [PMID: 34703845 PMCID: PMC8505356 DOI: 10.1016/j.omtm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/03/2021] [Indexed: 12/26/2022]
Abstract
Off-target editing is one of the main safety concerns for the use of CRISPR-Cas9 genome editing in gene therapy. These unwanted modifications could lead to malignant transformation, which renders tumorigenicity assessment of gene therapy products indispensable. In this study, we established two in vitro transformation assays, the soft agar colony-forming assay (SACF) and the growth in low attachment assay (GILA) as alternative methods for tumorigenicity evaluation of genome-edited cells. Using a CRISPR-Cas9-based approach to transform immortalized MCF10A cells, we identified PTPN12, a known tumor suppressor, as a valid positive control in GILA and SACF. Next, we measured the limit of detection for both assays and proved that SACF is more sensitive than GILA (0.8% versus 3.1% transformed cells). We further validated SACF and GILA by identifying a set of positive and negative controls and by testing the suitability of another cell line (THLE-2). Moreover, in contrast to SACF and GILA, an in vivo tumorigenicity study failed to detect the known tumorigenic potential of PTPN12 deletion, demonstrating the relevance of GILA and SACF in tumorigenicity testing. In conclusion, SACF and GILA are both attractive and valuable additions to preclinical safety assessment of gene therapy products.
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163
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Zhao X, Fu X, Yin C, Lu F. Wheat speciation and adaptation: perspectives from reticulate evolution. ABIOTECH 2021; 2:386-402. [PMID: 36311810 PMCID: PMC9590565 DOI: 10.1007/s42994-021-00047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
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Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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164
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Kostyushev D, Kostyusheva A, Ponomareva N, Brezgin S, Chulanov V. CRISPR/Cas and Hepatitis B Therapy: Technological Advances and Practical Barriers. Nucleic Acid Ther 2021; 32:14-28. [PMID: 34797701 DOI: 10.1089/nat.2021.0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
After almost a decade of using CRISPR/Cas9 systems to edit target genes, CRISPR/Cas9 and related technologies are rapidly moving to clinical trials. Hepatitis B virus (HBV), which causes severe liver disease, cannot be cleared by modern antivirals, but represents an ideal target for CRISPR/Cas9 systems. Early studies demonstrated very high antiviral potency of CRISPR/Cas9 and supported its use for developing a cure against chronic HBV infection. This review discusses the key issues that must be solved to make CRISPR/Cas9 an anti-HBV therapy.
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Affiliation(s)
- Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
| | - Natalia Ponomareva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.,Department of Infectious Diseases, Sechenov University, Moscow, Russia
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.,Department of Infectious Diseases, Sechenov University, Moscow, Russia
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165
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Lea RA, McCarthy A, Boeing S, Fallesen T, Elder K, Snell P, Christie L, Adkins S, Shaikly V, Taranissi M, Niakan KK. KLF17 promotes human naïve pluripotency but is not required for its establishment. Development 2021; 148:272511. [PMID: 34661235 PMCID: PMC8645209 DOI: 10.1242/dev.199378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of interspecies conservation observed. Single-cell transcriptomics analysis of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve human embryonic stem cells (hESCs). Here, we show that KLF17 is expressed coincident with the known pluripotency-associated factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisition in vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling pathways following KLF17 loss of function, and possible redundancy with other KLF paralogues. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the given in vitro conditions. Summary: Given that KLF17 was shown to be sufficient, but not necessary, to establish naïve pluripotent hESCs, KLF17 might function as a peripheral regulator of human pluripotent stem cells.
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Affiliation(s)
- Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Todd Fallesen
- Crick Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Sarah Adkins
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | - Valerie Shaikly
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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166
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A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing. Nat Commun 2021; 12:6512. [PMID: 34764240 PMCID: PMC8586238 DOI: 10.1038/s41467-021-26788-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/23/2021] [Indexed: 12/20/2022] Open
Abstract
Recent studies have reported that genome editing by CRISPR–Cas9 induces a DNA damage response mediated by p53 in primary cells hampering their growth. This could lead to a selection of cells with pre-existing p53 mutations. In this study, employing an integrated computational and experimental framework, we systematically investigated the possibility of selection of additional cancer driver mutations during CRISPR-Cas9 gene editing. We first confirm the previous findings of the selection for pre-existing p53 mutations by CRISPR-Cas9. We next demonstrate that similar to p53, wildtype KRAS may also hamper the growth of Cas9-edited cells, potentially conferring a selective advantage to pre-existing KRAS-mutant cells. These selective effects are widespread, extending across cell-types and methods of CRISPR-Cas9 delivery and the strength of selection depends on the sgRNA sequence and the gene being edited. The selection for pre-existing p53 or KRAS mutations may confound CRISPR-Cas9 screens in cancer cells and more importantly, calls for monitoring patients undergoing CRISPR-Cas9-based editing for clinical therapeutics for pre-existing p53 and KRAS mutations. CRISPR-Cas9 gene editing can induce a p53 mediated damage response. Here the authors investigate the possibility of selection of pre-existing cancer driver mutations during CRISPR-Cas9 knockout based gene editing and identify KRAS mutants that may confer a selected advantage to edited cells.
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167
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Rees HA, Minella AC, Burnett CA, Komor AC, Gaudelli NM. CRISPR-derived genome editing therapies: Progress from bench to bedside. Mol Ther 2021; 29:3125-3139. [PMID: 34619370 PMCID: PMC8572140 DOI: 10.1016/j.ymthe.2021.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
The development of CRISPR-derived genome editing technologies has enabled the precise manipulation of DNA sequences within the human genome. In this review, we discuss the initial development and cellular mechanism of action of CRISPR nucleases and DNA base editors. We then describe factors that must be taken into consideration when developing these tools into therapeutic agents, including the potential for unintended and off-target edits when using these genome editing tools, and methods to characterize these types of edits. We finish by considering specific challenges associated with bringing a CRISPR-based therapy to the clinic, including manufacturing, regulatory oversight, and considerations for clinical trials that involve genome editing agents.
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168
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BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors. Nat Commun 2021; 12:6353. [PMID: 34732717 PMCID: PMC8566456 DOI: 10.1038/s41467-021-26461-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Adenine and cytosine base editors (ABE, CBE) allow for precision genome engineering. Here, Base Editor Activity Reporter (BEAR), a plasmid-based fluorescent tool is introduced, which can be applied to report on ABE and CBE editing in a virtually unrestricted sequence context or to label base edited cells for enrichment. Using BEAR-enrichment, we increase the yield of base editing performed by nuclease inactive base editors to the level of the nickase versions while maintaining significantly lower indel background. Furthermore, by exploiting the semi-high-throughput potential of BEAR, we examine whether increased fidelity SpCas9 variants can be used to decrease SpCas9-dependent off-target effects of ABE and CBE. Comparing them on the same target sets reveals that CBE remains active on sequences, where increased fidelity mutations and/or mismatches decrease the activity of ABE. Our results suggest that the deaminase domain of ABE is less effective to act on rather transiently separated target DNA strands, than that of CBE explaining its lower mismatch tolerance.
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169
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Wardyn JD, Chan ASY, Jeyasekharan AD. A Robust Protocol for CRISPR-Cas9 Gene Editing in Human Suspension Cell Lines. Curr Protoc 2021; 1:e286. [PMID: 34748280 DOI: 10.1002/cpz1.286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The implementation of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 systems in mammalian cells has sparked an exciting new era in targeted gene editing. CRISPR-Cas9 technologies allow gene function to be interrogated by gene deletions, mutations, and truncations, and by epitope tagging and promoter activity modulation. Many robust protocols have been published to date on CRISPR-Cas9 techniques, however, most of these focus on adherent cell lines. Suspension cell lines, typically of hematolymphoid origin, such as Jurkat, Daudi, and TOLEDO, pose unique challenges to the setup of CRISPR experiments. Here, using B cell lymphoma cells as a primary model, we describe a comprehensive protocol for targeted gene manipulations using the CRISPR-Cas9 system in suspension cells. We also highlight necessary optimization steps to make this approach universal to other suspension cell lines. We first describe a detailed protocol for transient expression of the Cas9 nuclease and guide RNAs. We then suggest workflows for obtaining single-cell clones and for screening for successful homozygous knockout (KO) clones in suspension lines. This protocol aims to serve as a comprehensive resource to facilitate gene editing experiments for users starting CRISPR-Cas9 gene editing protocols on suspension cell lines or those looking to optimize their current workflows. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by NeonTM electroporation Support Protocol 1: Designing and preparing gene-specific gRNA Support Protocol 2: Preparation of conditioned medium and culture vessels for single-cell FACS Alternate Protocol 1: Transient CRISPR Cas9-gRNA delivery for gene knockout by Nepagene electroporator Basic Protocol 2: FACS and single-cell clone generation Alternate Protocol 2: Manual cell dilution to obtain single-cell clones Basic Protocol 3: Confirming indels status in single-cell clones by PCR on genomic DNA and Sanger sequencing.
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Affiliation(s)
- Joanna D Wardyn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- MSD Singapore, Quantitative Biosciences, MSD, Singapore
| | - Allison S Y Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore
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170
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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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171
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Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, Liu X, Lv Z, Yang P, Xu W, Gao W, Wu Y. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol Cancer 2021; 20:126. [PMID: 34598686 PMCID: PMC8484294 DOI: 10.1186/s12943-021-01431-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.
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Affiliation(s)
- Huimin Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Chunhong Qin
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Changming An
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Shuxin Wen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Wenjie Chen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Xianfang Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Zhenghua Lv
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Pingchang Yang
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, 518055, Guangdong, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, 518055, Guangdong, China
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China. .,Department of Cell biology and Genetics, Basic Medical School of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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172
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Mettananda S. Genetic and Epigenetic Therapies for β-Thalassaemia by Altering the Expression of α-Globin Gene. Front Genome Ed 2021; 3:752278. [PMID: 34713267 PMCID: PMC8525347 DOI: 10.3389/fgeed.2021.752278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 01/19/2023] Open
Abstract
β-Thalassaemia is caused by over 300 mutations in and around the β-globin gene that lead to impaired synthesis of β-globin. The expression of α-globin continues normally, resulting in an excess of α-globin chains within red blood cells and their precursors. These unpaired α-globin chains form unstable α-hemichromes that trigger cascades of events to generate reactive oxygen species, leading to ineffective erythropoiesis and haemolysis in patients with β-thalassaemia. The clinical genetic data reported over several decades have demonstrated how the coinheritance of α-thalassaemia ameliorates the disease phenotype of β-thalassaemia. Thus, it is evident that down-regulation of the α-globin gene expression in patients with β-thalassaemia could ameliorate or even cure β-thalassaemia. Over the last few years, significant progress has been made in utilising this pathway to devise a cure for β-thalassaemia. Most research has been done to alter the epigenetic landscape of the α-globin locus or the well-characterised distant enhancers of α-globin. In vitro, pre-clinical studies on primary human erythroid cells have unveiled inhibition of histone lysine demethylation and histone deacetylation as potential targets to achieve selective downregulation of α-globin through epigenetic drug targeting. CRISPR based genome editing has been successfully used in vitro to mutate α-globin genes or enhancers of α-goblin to achieve clinically significant knockdowns of α-globin to the levels beneficial for patients with β-thalassaemia. This review summarises the current knowledge on the regulation of human α-globin genes and the clinical genetic data supporting the pathway of targeting α-globin as a treatment for β-thalassaemia. It also presents the progress of epigenetic drug and genome editing approaches currently in development to treat β-thalassaemia.
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Affiliation(s)
- Sachith Mettananda
- Department of Paediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
- University Paediatrics Unit, Colombo North Teaching Hospital, Ragama, Sri Lanka
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173
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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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174
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Aquino-Jarquin G. Current advances in overcoming obstacles of CRISPR/Cas9 off-target genome editing. Mol Genet Metab 2021; 134:77-86. [PMID: 34391646 DOI: 10.1016/j.ymgme.2021.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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175
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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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176
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Rappaport Y, Achache H, Falk R, Murik O, Ram O, Tzur YB. Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans. Nat Commun 2021; 12:4802. [PMID: 34376665 PMCID: PMC8355143 DOI: 10.1038/s41467-021-24815-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
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Affiliation(s)
- Yisrael Rappaport
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanna Achache
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roni Falk
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Murik
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Oren Ram
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonatan B Tzur
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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177
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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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178
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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179
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Eleveld TF, Bakali C, Eijk PP, Stathi P, Vriend LE, Poddighe PJ, Ylstra B. Engineering large-scale chromosomal deletions by CRISPR-Cas9. Nucleic Acids Res 2021; 49:12007-12016. [PMID: 34230973 PMCID: PMC8643637 DOI: 10.1093/nar/gkab557] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 01/06/2023] Open
Abstract
Large-scale chromosomal deletions are a prevalent and defining feature of cancer. A high degree of tumor-type and subtype specific recurrencies suggest a selective oncogenic advantage. However, due to their large size it has been difficult to pinpoint the oncogenic drivers that confer this advantage. Suitable functional genomics approaches to study the oncogenic driving capacity of large-scale deletions are limited. Here, we present an effective technique to engineer large-scale deletions by CRISPR-Cas9 and create isogenic cell line models. We simultaneously induce double-strand breaks (DSBs) at two ends of a chromosomal arm and select the cells that have lost the intermittent region. Using this technique, we induced large-scale deletions on chromosome 11q (65 Mb) and chromosome 6q (53 Mb) in neuroblastoma cell lines. A high frequency of successful deletions (up to 30% of selected clones) and increased colony forming capacity in the 11q deleted lines suggest an oncogenic advantage of these deletions. Such isogenic models enable further research on the role of large-scale deletions in tumor development and growth, and their possible therapeutic potential.
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Affiliation(s)
- Thomas F Eleveld
- Department of Pathology, Cancer CenterAmsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Chaimaa Bakali
- Department of Pathology, Cancer CenterAmsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Paul P Eijk
- Department of Pathology, Cancer CenterAmsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Phylicia Stathi
- Department of Pathology, Cancer CenterAmsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Lianne E Vriend
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Pino J Poddighe
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer CenterAmsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
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180
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Baxter J. When is it Safe to Edit the Human Germline? SCIENCE AND ENGINEERING ETHICS 2021; 27:43. [PMID: 34231047 DOI: 10.1007/s11948-021-00320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
In the fall of 2018 Jiankui He shocked the international community with the following announcement: two female babies, "Lulu" and "Nana," whose germlines had been modified by the cutting edge, yet profoundly unsafe CRISPR-Cas9 technology had been born. This event galvanized policy makers and scientists to advocate for more explicit and firm regulation of human germline gene editing (GGE). Recent policy proposals attempt to integrate safety considerations and public input to identify specific types of diseases that may be safe targets for human GGE (Sarkar forthcoming; Guttinger. 2019. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy; Lander et al., 2019). This paper argues these policy proposals are inadequate in different ways. While Sarkar (forthcoming) intends to incorporate input from the disability community for the purpose of deciding the value of human GGE, I argue that his strategy for doing so is inadequate. I'll argue that an iterative, deliberative process is a more appropriate framework for allowing the disability community to inform policy on human GGE. Further policy proposals have been framed in terms of monogenetic or single-gene diseases (Guttinger. 2019. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy. "Editing the Reactive Genome: Towards Postgenomic Ethics of Germline Editing." Journal of Applied Philosophy; Lander et al., 2019). I argue that this way of conceptualizing disease is not what matters for deciding which disorders are viable candidates for human GGE. Instead, what matters is that (1) the disease in question must have (among its set of causes) genes that have a high degree of causal control with respect to the disease and (2) alternative nucleic acid sequences variants that are likely to produce traits deemed desirable must be identified. Previous policy proposals leave (2) unspecified. What conditions must be met for satisfying condition (2) should not be left to individual scientists to decide for themselves. The present proposal offers some guidance on this issue.
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Affiliation(s)
- Janella Baxter
- Department of Philosophy, Washington University, Campus Box 1073 One Brookings Drive, St. Louis, MO, US.
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181
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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: 120] [Impact Index Per Article: 40.0] [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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182
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Sledzinski P, Dabrowska M, Nowaczyk M, Olejniczak M. Paving the way towards precise and safe CRISPR genome editing. Biotechnol Adv 2021; 49:107737. [PMID: 33785374 DOI: 10.1016/j.biotechadv.2021.107737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
As the possibilities of CRISPR-Cas9 technology have been revealed, we have entered a new era of research aimed at increasing its specificity and safety. This stage of technology development is necessary not only for its wider application in the clinic but also in basic research to better control the process of genome editing. Research during the past eight years has identified some factors influencing editing outcomes and led to the development of highly specific endonucleases, modified guide RNAs and computational tools supporting experiments. More recently, large-scale experiments revealed a previously overlooked feature: Cas9 can generate reproducible mutation patterns. As a result, it has become apparent that Cas9-induced double-strand break (DSB) repair is nonrandom and can be predicted to some extent. Here, we review the present state of knowledge regarding the specificity and safety of CRISPR-Cas9 technology to define gRNA, protein and target-related problems and solutions. These issues include sequence-specific off-target effects, immune responses, genetic variation and chromatin accessibility. We present new insights into the role of DNA repair in genome editing and define factors influencing editing outcomes. In addition, we propose practical guidelines for increasing the specificity of editing and discuss novel perspectives in improvement of this technology.
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Affiliation(s)
- Pawel Sledzinski
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Mateusz Nowaczyk
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland.
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183
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Zeballos C MA, Gaj T. Next-Generation CRISPR Technologies and Their Applications in Gene and Cell Therapy. Trends Biotechnol 2021; 39:692-705. [PMID: 33277043 DOI: 10.1016/j.tibtech.2020.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022]
Abstract
The emergence of clustered regularly interspaced short palindromic repeat (CRISPR) nucleases has transformed biotechnology by providing an easy, efficient, and versatile platform for editing DNA. However, traditional CRISPR-based technologies initiate editing by activating DNA double-strand break (DSB) repair pathways, which can cause adverse effects in cells and restrict certain therapeutic applications of the technology. To this end, several new CRISPR-based modalities have been developed that are capable of catalyzing editing without the requirement for a DSB. Here, we review three of these technologies: base editors, prime editors, and RNA-targeting CRISPR-associated protein (Cas)13 effectors. We discuss their strengths compared to traditional gene-modifying systems, we highlight their emerging therapeutic applications, and we examine challenges facing their safe and effective clinical implementation.
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Affiliation(s)
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.
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184
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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: 30] [Impact Index Per Article: 10.0] [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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185
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Balderston S, Clouse G, Ripoll JJ, Pratt GK, Gasiunas G, Bock JO, Bennett EP, Aran K. Diversification of the CRISPR Toolbox: Applications of CRISPR-Cas Systems Beyond Genome Editing. CRISPR J 2021; 4:400-415. [PMID: 34152221 PMCID: PMC8418451 DOI: 10.1089/crispr.2020.0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The discovery of CRISPR has revolutionized the field of genome engineering, but the potential of this technology is far from reaching its limits. In this review, we explore the broad range of applications of CRISPR technology to highlight the rapid expansion of the field beyond gene editing alone. It has been demonstrated that CRISPR technology can control gene expression, spatiotemporally image the genome in vivo, and detect specific nucleic acid sequences for diagnostics. In addition, new technologies are under development to improve CRISPR quality controls for gene editing, thereby improving the reliability of these technologies for therapeutics and beyond. These are just some of the many CRISPR tools that have been developed in recent years, and the toolbox continues to diversify.
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Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabrielle Clouse
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juan-José Ripoll
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Grace K. Pratt
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giedrius Gasiunas
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- CasZyme, Vilnius, Lithuania; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens-Ole Bock
- Cobo Technologies ApS, Maaloev, Denmark; and Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Paul Bennett
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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186
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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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187
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Epstein LR, Lee SS, Miller MF, Lombardi HA. CRISPR, animals, and FDA oversight: Building a path to success. Proc Natl Acad Sci U S A 2021; 118:e2004831117. [PMID: 34050010 PMCID: PMC8179205 DOI: 10.1073/pnas.2004831117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Technological advances, such as genome editing and specifically CRISPR, offer exciting promise for the creation of products that address public health concerns, such as disease transmission and a sustainable food supply and enable production of human therapeutics, such as organs and tissues for xenotransplantation or recombinant human proteins to treat disease. The Food and Drug Administration recognizes the need for such innovative solutions and plays a key role in bringing safe and effective animal biotechnology products to the marketplace. In this article, we (the Food and Drug Administration/Center for Veterinary Medicine) describe the current state of the science, including advances in technology as well as scientific limitations and considerations for how researchers and commercial developers working to create intentional genomic alterations in animals can work within these limitations. We also describe our risk-based approach and how it strikes a balance between our regulatory responsibilities and the need to get innovative products to market efficiently. We continue to seek input from our stakeholders and hope to use this feedback to improve the transparency, predictability, and efficiency of our process. We think that working together, using appropriate science- and risk-based oversight, is the foundation to a successful path forward.
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Affiliation(s)
- Laura R Epstein
- Office of the Director, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Stella S Lee
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855
| | - Mayumi F Miller
- Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD 20708
| | - Heather A Lombardi
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD 20855;
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188
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Correction of β-thalassemia by CRISPR/Cas9 editing of the α-globin locus in human hematopoietic stem cells. Blood Adv 2021; 5:1137-1153. [PMID: 33635334 DOI: 10.1182/bloodadvances.2020001996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
β-thalassemias (β-thal) are a group of blood disorders caused by mutations in the β-globin gene (HBB) cluster. β-globin associates with α-globin to form adult hemoglobin (HbA, α2β2), the main oxygen-carrier in erythrocytes. When β-globin chains are absent or limiting, free α-globins precipitate and damage cell membranes, causing hemolysis and ineffective erythropoiesis. Clinical data show that severity of β-thal correlates with the number of inherited α-globin genes (HBA1 and HBA2), with α-globin gene deletions having a beneficial effect for patients. Here, we describe a novel strategy to treat β-thal based on genome editing of the α-globin locus in human hematopoietic stem/progenitor cells (HSPCs). Using CRISPR/Cas9, we combined 2 therapeutic approaches: (1) α-globin downregulation, by deleting the HBA2 gene to recreate an α-thalassemia trait, and (2) β-globin expression, by targeted integration of a β-globin transgene downstream the HBA2 promoter. First, we optimized the CRISPR/Cas9 strategy and corrected the pathological phenotype in a cellular model of β-thalassemia (human erythroid progenitor cell [HUDEP-2] β0). Then, we edited healthy donor HSPCs and demonstrated that they maintained long-term repopulation capacity and multipotency in xenotransplanted mice. To assess the clinical potential of this approach, we next edited β-thal HSPCs and achieved correction of α/β globin imbalance in HSPC-derived erythroblasts. As a safer option for clinical translation, we performed editing in HSPCs using Cas9 nickase showing precise editing with no InDels. Overall, we described an innovative CRISPR/Cas9 approach to improve α/β globin imbalance in thalassemic HSPCs, paving the way for novel therapeutic strategies for β-thal.
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189
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Xiang X, Corsi GI, Anthon C, Qu K, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y. Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning. Nat Commun 2021; 12:3238. [PMID: 34050182 PMCID: PMC8163799 DOI: 10.1038/s41467-021-23576-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, we train a deep learning model, CRISPRon, on 23,902 gRNAs. Compared to existing tools, CRISPRon exhibits significantly higher prediction performances on four test datasets not overlapping with training data used for the development of these tools. Furthermore, we present an interactive gRNA design webserver based on the CRISPRon standalone software, both available via https://rth.dk/resources/crispr/ . CRISPRon advances CRISPR applications by providing more accurate gRNA efficiency predictions than the existing tools.
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Affiliation(s)
- Xi Xiang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Giulia I Corsi
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Lijun Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | | | - Tao Ma
- MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Lin Lin
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University, Aarhus, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.
- BGI-Shenzhen, Shenzhen, China.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Steno Diabetes Center Aarhus, Aarhus University, Aarhus, Denmark.
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190
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High level of fetal-globin reactivation by designed transcriptional activator-like effector. Blood Adv 2021; 4:687-695. [PMID: 32084259 DOI: 10.1182/bloodadvances.2019000482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/27/2020] [Indexed: 12/15/2022] Open
Abstract
The fetal-to-adult hemoglobin switch has been a focus of a long-standing effort to potentially treat sickle cell disease and β thalassemia by induction of fetal hemoglobin. In a continuation of this effort, we designed specific transcriptional activator-like effectors (TALEs) to target both the Gγ and Aγ-globin promoters. We fused the TALEs to a LIM domain binding protein (Ldb1) dimerization domain, followed by a T2A green fluorescent protein (GFP) cassette, which were assembled into a lentiviral vector. To prevent deletions caused by the repeats of TALEs during the lentivirus packing process, we changed the TALE encoding DNA by codon optimization. Intriguingly, 5 of 14 TALEs showed forced reactivation of fetal-globin expression in human umbilical cord blood-derived erythroid progenitor (HUDEP-2) cells, with a significant increase in the γ-globin mRNA level by more than 70-fold. We also observed a more than 50% reduction of β-globin mRNA. High-performance liquid chromatography analysis revealed more than 30% fetal globin in TALE-induced cells compared with the control of 2%. Among several promoters studied, the β-globin gene promoter with the locus control region (LCR) enhancer showed the highest TALE expression during CD34 erythroid differentiation. At day 19 of differentiation, 2 TALEs increased fetal-globin expression more than 40-fold in the mRNA level and up to 70% of the total globin protein. These TALEs have potential for clinical translation.
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191
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Hendriks D, Clevers H, Artegiani B. CRISPR-Cas Tools and Their Application in Genetic Engineering of Human Stem Cells and Organoids. Cell Stem Cell 2021; 27:705-731. [PMID: 33157047 DOI: 10.1016/j.stem.2020.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas technology has revolutionized biological research and holds great therapeutic potential. Here, we review CRISPR-Cas systems and their latest developments with an emphasis on application to human cells. We also discuss how different CRISPR-based strategies can be used to accomplish a particular genome engineering goal. We then review how different CRISPR tools have been used in genome engineering of human stem cells in vitro, covering both the pluripotent (iPSC/ESC) and somatic adult stem cell fields and, in particular, 3D organoid cultures. Finally, we discuss the progress and challenges associated with CRISPR-based genome editing of human stem cells for therapeutic use.
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Affiliation(s)
- Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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192
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Kluesner MG, Lahr WS, Lonetree CL, Smeester BA, Qiu X, Slipek NJ, Claudio Vázquez PN, Pitzen SP, Pomeroy EJ, Vignes MJ, Lee SC, Bingea SP, Andrew AA, Webber BR, Moriarity BS. CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells. Nat Commun 2021; 12:2437. [PMID: 33893286 PMCID: PMC8065034 DOI: 10.1038/s41467-021-22009-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas9 cytidine and adenosine base editors (CBEs and ABEs) can disrupt genes without introducing double-stranded breaks by inactivating splice sites (BE-splice) or by introducing premature stop (pmSTOP) codons. However, no in-depth comparison of these methods or a modular tool for designing BE-splice sgRNAs exists. To address these needs, we develop SpliceR ( http://z.umn.edu/spliceR ) to design and rank BE-splice sgRNAs for any Ensembl annotated genome, and compared disruption approaches in T cells using a screen against the TCR-CD3 MHC Class I immune synapse. Among the targeted genes, we find that targeting splice-donors is the most reliable disruption method, followed by targeting splice-acceptors, and introducing pmSTOPs. Further, the CBE BE4 is more effective for disruption than the ABE ABE7.10, however this disparity is eliminated by employing ABE8e. Collectively, we demonstrate a robust method for gene disruption, accompanied by a modular design tool that is of use to basic and translational researchers alike.
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Affiliation(s)
- Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Xiaohong Qiu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patricia N Claudio Vázquez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Pitzen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Madison J Vignes
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samantha C Lee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Aneesha A Andrew
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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193
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Piergentili R, Del Rio A, Signore F, Umani Ronchi F, Marinelli E, Zaami S. CRISPR-Cas and Its Wide-Ranging Applications: From Human Genome Editing to Environmental Implications, Technical Limitations, Hazards and Bioethical Issues. Cells 2021; 10:cells10050969. [PMID: 33919194 PMCID: PMC8143109 DOI: 10.3390/cells10050969] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
The CRISPR-Cas system is a powerful tool for in vivo editing the genome of most organisms, including man. During the years this technique has been applied in several fields, such as agriculture for crop upgrade and breeding including the creation of allergy-free foods, for eradicating pests, for the improvement of animal breeds, in the industry of bio-fuels and it can even be used as a basis for a cell-based recording apparatus. Possible applications in human health include the making of new medicines through the creation of genetically modified organisms, the treatment of viral infections, the control of pathogens, applications in clinical diagnostics and the cure of human genetic diseases, either caused by somatic (e.g., cancer) or inherited (mendelian disorders) mutations. One of the most divisive, possible uses of this system is the modification of human embryos, for the purpose of preventing or curing a human being before birth. However, the technology in this field is evolving faster than regulations and several concerns are raised by its enormous yet controversial potential. In this scenario, appropriate laws need to be issued and ethical guidelines must be developed, in order to properly assess advantages as well as risks of this approach. In this review, we summarize the potential of these genome editing techniques and their applications in human embryo treatment. We will analyze CRISPR-Cas limitations and the possible genome damage caused in the treated embryo. Finally, we will discuss how all this impacts the law, ethics and common sense.
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Affiliation(s)
- Roberto Piergentili
- Institute of Molecular Biology and Pathology, Italian National Research Council (CNR-IBPM), 00185 Rome, Italy;
| | - Alessandro Del Rio
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
- Correspondence: or
| | - Fabrizio Signore
- Obstetrics and Gynecology Department, USL Roma2, Sant’Eugenio Hospital, 00144 Rome, Italy;
| | - Federica Umani Ronchi
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
| | - Enrico Marinelli
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
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194
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Frequent loss of heterozygosity in CRISPR-Cas9-edited early human embryos. Proc Natl Acad Sci U S A 2021; 118:2004832117. [PMID: 34050011 DOI: 10.1073/pnas.2004832117] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germ line. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism, and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss of heterozygosity in edited cells that spanned regions beyond the POU5F1 on-target locus, as well as segmental loss and gain of chromosome 6, on which the POU5F1 gene is located. Unintended genome editing outcomes were present in ∼16% of the human embryo cells analyzed and spanned 4-20 kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology.
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Noé V, Ciudad CJ. Polypurine Reverse-Hoogsteen Hairpins as a Tool for Exon Skipping at the Genomic Level in Mammalian Cells. Int J Mol Sci 2021; 22:3784. [PMID: 33917446 PMCID: PMC8038689 DOI: 10.3390/ijms22073784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 01/15/2023] Open
Abstract
Therapeutic strategies for rare diseases based on exon skipping are aimed at mediating the elimination of mutated exons and restoring the reading frame of the affected protein. We explored the capability of polypurine reverse-Hoogsteen hairpins (PPRHs) to cause exon skipping in NB6 cells carrying a duplication of exon 2 of the DHFR gene that causes a frameshift abolishing DHFR activity. METHODS Different editing PPRHs were designed and transfected in NB6 cells followed by incubation in a DHFR-selective medium lacking hypoxanthine and thymidine. Surviving colonies were analyzed by DNA sequencing, RT-PCR, Western blotting and DHFR enzymatic activity. RESULTS Transfection of editing PPRHs originated colonies in the DHFR-selective medium. DNA sequencing results proved that the DHFR sequence in all these colonies corresponded to the wildtype sequence with just one copy of exon 2. In the edited colonies, the skipping of the additional exon was confirmed at the mRNA level, the DHFR protein was restored, and it showed high levels of DHFR activity. CONCLUSIONS Editing-PPRHs are able to cause exon skipping at the DNA level and could be applied as a possible therapeutic tool for rare diseases.
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Affiliation(s)
- Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences & IN2UB, University of Barcelona, 08028 Barcelona, Spain;
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Yang Y, Xu J, Ge S, Lai L. CRISPR/Cas: Advances, Limitations, and Applications for Precision Cancer Research. Front Med (Lausanne) 2021; 8:649896. [PMID: 33748164 PMCID: PMC7965951 DOI: 10.3389/fmed.2021.649896] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer is one of the most leading causes of mortalities worldwide. It is caused by the accumulation of genetic and epigenetic alterations in 2 types of genes: tumor suppressor genes (TSGs) and proto-oncogenes. In recent years, development of the clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized genome engineering for different cancer research ranging for research ranging from fundamental science to translational medicine and precise cancer treatment. The CRISPR/CRISPR associated proteins (CRISPR/Cas) are prokaryote-derived genome editing systems that have enabled researchers to detect, image, manipulate and annotate specific DNA and RNA sequences in various types of living cells. The CRISPR/Cas systems have significant contributions to discovery of proto-oncogenes and TSGs, tumor cell epigenome normalization, targeted delivery, identification of drug resistance mechanisms, development of high-throughput genetic screening, tumor models establishment, and cancer immunotherapy and gene therapy in clinics. Robust technical improvements in CRISPR/Cas systems have shown a considerable degree of efficacy, specificity, and flexibility to target the specific locus in the genome for the desired applications. Recent developments in CRISPRs technology offers a significant hope of medical cure against cancer and other deadly diseases. Despite significant improvements in this field, several technical challenges need to be addressed, such as off-target activity, insufficient indel or low homology-directed repair (HDR) efficiency, in vivo delivery of the Cas system components, and immune responses. This study aims to overview the recent technological advancements, preclinical and perspectives on clinical applications of CRISPR along with their advantages and limitations. Moreover, the potential applications of CRISPR/Cas in precise cancer tumor research, genetic, and other precise cancer treatments discussed.
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Affiliation(s)
- Yue Yang
- Department of Pathology, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Jin Xu
- Department of Otolaryngology, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Shuyu Ge
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Liqin Lai
- Department of Pathology, Tongde Hospital of Zhejiang Province, Hangzhou, China
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Weisheit I, Kroeger JA, Malik R, Wefers B, Lichtner P, Wurst W, Dichgans M, Paquet D. Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping. Nat Protoc 2021; 16:1714-1739. [PMID: 33597771 DOI: 10.1038/s41596-020-00481-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023]
Abstract
The recent CRISPR revolution has provided researchers with powerful tools to perform genome editing in a variety of organisms. However, recent reports indicate widespread occurrence of unintended CRISPR-induced on-target effects (OnTEs) at the edited site in mice and human induced pluripotent stem cells (iPSCs) that escape standard quality controls. By altering gene expression of targeted or neighbouring genes, OnTEs can severely affect phenotypes of CRISPR-edited cells and organisms and thus lead to data misinterpretation, which can undermine the reliability of CRISPR-based studies. Here we describe a broadly applicable framework for detecting OnTEs in genome-edited cells and organisms after non-homologous end joining-mediated and homology-directed repair-mediated editing. Our protocol enables identification of OnTEs such as large deletions, large insertions, rearrangements or loss of heterozygosity (LOH). This is achieved by subjecting genomic DNA first to quantitative genotyping PCR (qgPCR), which determines the number of intact alleles at the target site using the same PCR amplicon that has been optimized for genotyping. This combination of genotyping and quantitation makes it possible to exclude clones with monoallelic OnTEs and hemizygous editing, which are often mischaracterized as correctly edited in standard Sanger sequencing. Second, occurrence of LOH around the edited locus is detected by genotyping neighbouring single-nucleotide polymorphisms (SNPs), using either a Sanger sequencing-based method or SNP microarrays. All steps are optimized to maximize simplicity and minimize cost to promote wide dissemination and applicability across the field. The entire protocol from genomic DNA extraction to OnTE exclusion can be performed in 6-9 d.
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Affiliation(s)
- Isabel Weisheit
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany
| | - Joseph A Kroeger
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Institute of Developmental Genetics (IDG), HelmholtzZentrum München, Neuherberg, Germany
| | - Peter Lichtner
- Core Facility NGS, HelmholtzZentrum München, Neuherberg, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Institute of Developmental Genetics (IDG), HelmholtzZentrum München, Neuherberg, Germany
- Technische Universität München-Weihenstephan, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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Pal M, Herold MJ. CRISPR base editing applications for identifying cancer-driving mutations. Biochem Soc Trans 2021; 49:269-280. [PMID: 33449100 PMCID: PMC7925010 DOI: 10.1042/bst20200550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
CRISPR base editing technology is a promising genome editing tool as (i) it does not require a DNA template to introduce mutations and (ii) it avoids creating DNA double-strand breaks, which can lead to unintended chromosomal alterations or elicit an unwanted DNA damage response. Given many cancers originate from point mutations in cancer-driving genes, the application of base editing for either modelling tumour development, therapeutic editing, or functional screening is of great promise. In this review, we summarise current DNA base editing technologies and will discuss recent advancements and existing hurdles for its usage in cancer research.
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Affiliation(s)
- Martin Pal
- WEHI (Walter and Eliza Hall Institute of Melbourne), Melbourne, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Marco J. Herold
- WEHI (Walter and Eliza Hall Institute of Melbourne), Melbourne, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3052, Australia
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Amini L, Greig J, Schmueck-Henneresse M, Volk HD, Bézie S, Reinke P, Guillonneau C, Wagner DL, Anegon I. Super-Treg: Toward a New Era of Adoptive Treg Therapy Enabled by Genetic Modifications. Front Immunol 2021; 11:611638. [PMID: 33717052 PMCID: PMC7945682 DOI: 10.3389/fimmu.2020.611638] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022] Open
Abstract
Regulatory Tcells (Treg) are essential components of peripheral immune homeostasis. Adoptive Treg cell therapy has shown efficacy in a variety of immune-mediated diseases in preclinical studies and is now moving from phase I/IIa to larger phase II studies aiming to demonstrate efficacy. However, hurdles such as in vivo stability and efficacy remain to be addressed. Nevertheless, preclinical models have shown that Treg function and specificity can be increased by pharmacological substances or gene modifications, and even that conventional T cells can be converted to Treg potentially providing new sources of Treg and facilitating Treg cell therapy. The exponential growth in genetic engineering techniques and their application to T cells coupled to a large body of knowledge on Treg open numerous opportunities to generate Treg with "superpowers". This review summarizes the genetic engineering techniques available and their applications for the next-generation of Super-Treg with increased function, stability, redirected specificity and survival.
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Affiliation(s)
- Leila Amini
- BIH Center for Regenerative Therapies (BCRT) and Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Jenny Greig
- INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT) and Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT) and Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Séverine Bézie
- INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Petra Reinke
- BIH Center for Regenerative Therapies (BCRT) and Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Carole Guillonneau
- INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Dimitrios L. Wagner
- BIH Center for Regenerative Therapies (BCRT) and Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Ignacio Anegon
- INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
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