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Adlat S, Vázquez Salgado AM, Lee M, Yin D, Wangensteen KJ. Emerging and potential use of CRISPR in human liver disease. Hepatology 2023:01515467-990000000-00538. [PMID: 37607734 PMCID: PMC10881897 DOI: 10.1097/hep.0000000000000578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
CRISPR is a gene editing tool adapted from naturally occurring defense systems from bacteria. It is a technology that is revolutionizing the interrogation of gene functions in driving liver disease, especially through genetic screens and by facilitating animal knockout and knockin models. It is being used in models of liver disease to identify which genes are critical for liver pathology, especially in genetic liver disease, hepatitis, and in cancer initiation and progression. It holds tremendous promise in treating human diseases directly by editing DNA. It could disable gene function in the case of expression of a maladaptive protein, such as blocking transthyretin as a therapy for amyloidosis, or to correct gene defects, such as restoring the normal functions of liver enzymes fumarylacetoacetate hydrolase or alpha-1 antitrypsin. It is also being studied for treatment of hepatitis B infection. CRISPR is an exciting, evolving technology that is facilitating gene characterization and discovery in liver disease and holds the potential to treat liver diseases safely and permanently.
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Affiliation(s)
- Salah Adlat
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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52
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Su L, Gong X, Zhou J, Li H. An efficient and recyclable electroeluter: from homemade to modular design for potential mass production. LAB ON A CHIP 2023; 23:3874-3881. [PMID: 37539696 DOI: 10.1039/d3lc00428g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Electrophoresis is one of the most powerful techniques to separate nucleic acids or protein molecules. The recovery of purified components from the gel is key to downstream analysis or function study. Here, we provide a cost-effective electroeluter in both homemade and module-assembled versions. The recovery yield can reach as high as >90% for single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and protein in practical testing, which outperforms a commercial kit as well as a purchased electroeluter. It fully addresses the existing concerns in this field. First of all, for almost all kits, there remains ambiguity in recovering ssDNA to satisfy specific demands, which is generally ignored. Secondly, the recovery of dsDNA from agarose gel with consumables is vulnerable to a lot of factors and involves chemicals/materials that are not friendly to the environment and operating personnel. Thirdly, recovery from polyacrylamide matrices is very difficult, and the most exploited diffusion method through crush-and-soak suffers from low yield even after a long-time diffusion. Lastly, there is a universal problem in scaling up, especially for commercial electroeluters. The present electroelution method addresses the above issues, and it is believed that it will facilitate associated research and find widespread application.
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Affiliation(s)
- Linhan Su
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Xueting Gong
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Ju Zhou
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Hailong Li
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
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53
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Chen H, Liu X, Li L, Tan Q, Li S, Li L, Li C, Fu J, Lu Y, Wang Y, Sun Y, Luo ZG, Lu Z, Sun Q, Liu Z. CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression. Genome Biol 2023; 24:146. [PMID: 37353834 PMCID: PMC10288798 DOI: 10.1186/s13059-023-02987-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substantial proportion of DNA repair during CRISPR-mediated gene editing. Using CasRx to downregulate a key MMEJ factor, Polymerase Q (Polq), we improve the targeted integration efficiency of linearized DNA fragments and single-strand oligonucleotides (ssODN) in mouse embryos and offspring. CasRX-assisted targeted integration (CATI) also leads to substantial improvements in HDR efficiency during the CRISPR/Cas9 editing of monkey embryos. We present a promising tool for generating monkey models and developing gene therapies for clinical trials.
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Affiliation(s)
- Hongyu Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xingchen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Lanxin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qingtong Tan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Shiyan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Li Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Chunyang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yong Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yidi Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zongyang Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
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54
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McBeath E, Fujiwara K, Hofmann MC. Evidence-Based Guide to Using Artificial Introns for Tissue-Specific Knockout in Mice. Int J Mol Sci 2023; 24:10258. [PMID: 37373404 PMCID: PMC10299402 DOI: 10.3390/ijms241210258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Up until recently, methods for generating floxed mice either conventionally or by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 (CRISPR-associated protein 9) editing have been technically challenging, expensive and error-prone, or time-consuming. To circumvent these issues, several labs have started successfully using a small artificial intron to conditionally knockout (KO) a gene of interest in mice. However, many other labs are having difficulty getting the technique to work. The key problem appears to be either a failure in achieving correct splicing after the introduction of the artificial intron into the gene or, just as crucial, insufficient functional KO of the gene's protein after Cre-induced removal of the intron's branchpoint. Presented here is a guide on how to choose an appropriate exon and where to place the recombinase-regulated artificial intron (rAI) in that exon to prevent disrupting normal gene splicing while maximizing mRNA degradation after recombinase treatment. The reasoning behind each step in the guide is also discussed. Following these recommendations should increase the success rate of this easy, new, and alternative technique for producing tissue-specific KO mice.
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Affiliation(s)
- Elena McBeath
- Department of Endocrine Neoplasia & Hormonal Disorders, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Keigi Fujiwara
- National Coalition of Independent Scholars, Brattleboro, VT 05301, USA;
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia & Hormonal Disorders, MD Anderson Cancer Center, Houston, TX 77030, USA;
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55
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3403. [PMID: 37296101 PMCID: PMC10256788 DOI: 10.1038/s41467-023-39040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.
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Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | | | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Nadine Girard
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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56
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Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
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57
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Mabuchi A, Hata S, Genova M, Tei C, Ito KK, Hirota M, Komori T, Fukuyama M, Chinen T, Toyoda A, Kitagawa D. ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid RPE1 and HCT116 cells. BMC Genomics 2023; 24:289. [PMID: 37248464 DOI: 10.1186/s12864-023-09377-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/14/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Recent advances in CRISPR technology have enabled us to perform gene knock-in in various species and cell lines. CRISPR-mediated knock-in requires donor DNA which serves as a template for homology-directed repair (HDR). For knock-in of short sequences or base substitutions, ssDNA donors are frequently used among various other forms of HDR donors, such as linear dsDNA. However, partly due to the complexity of long ssDNA preparation, it remains unclear whether ssDNA is the optimal type of HDR donors for insertion of long transgenes such as fluorescent reporters in human cells. RESULTS In this study, we established a nuclease-based simple method for the preparation of long ssDNA with high yield and purity, and comprehensively compared the performance of ssDNA and dsDNA donors with 90 bases of homology arms for endogenous gene tagging with long transgenes in human diploid RPE1 and HCT116 cells. Quantification using flow cytometry revealed lower efficiency of endogenous fluorescent tagging with ssDNA donors than with dsDNA. By analyzing knock-in outcomes using long-read amplicon sequencing and a classification framework, a variety of mis-integration events were detected regardless of the donor type. Importantly, the ratio of precise insertion was lower with ssDNA donors than with dsDNA. Moreover, in off-target integration analyses using donors without homology arms, ssDNA and dsDNA were comparably prone to non-homologous integration. CONCLUSIONS These results indicate that ssDNA is not superior to dsDNA as long HDR donors with relatively short homology arms for gene knock-in in human RPE1 and HCT116 cells.
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Affiliation(s)
- Akira Mabuchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama, Japan.
| | - Mariya Genova
- Zentrum Für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Chiharu Tei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kei K Ito
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masayasu Hirota
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory and Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
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58
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Tompkins J, Lizhar E, Shokrani A, Wu X, Berley J, Kamali D, Hussey D, Cerneckis J, Kang TH, Wang J, Tsark W, Zeng D, Godatha S, Natarajan R, Riggs A. Engineering CpG island DNA methylation in pluripotent cells through synthetic CpG-free ssDNA insertion. CELL REPORTS METHODS 2023; 3:100465. [PMID: 37323577 PMCID: PMC10261899 DOI: 10.1016/j.crmeth.2023.100465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/14/2023] [Accepted: 04/12/2023] [Indexed: 06/17/2023]
Abstract
Cellular differentiation requires global changes to DNA methylation (DNAme), where it functions to regulate transcription factor, chromatin remodeling activity, and genome interpretation. Here, we describe a simple DNAme engineering approach in pluripotent stem cells (PSCs) that stably extends DNAme across target CpG islands (CGIs). Integration of synthetic CpG-free single-stranded DNA (ssDNA) induces a target CpG island methylation response (CIMR) in multiple PSC lines, Nt2d1 embryonal carcinoma cells, and mouse PSCs but not in highly methylated CpG island hypermethylator phenotype (CIMP)+ cancer lines. MLH1 CIMR DNAme spanned the CGI, was precisely maintained through cellular differentiation, suppressed MLH1 expression, and sensitized derived cardiomyocytes and thymic epithelial cells to cisplatin. Guidelines for CIMR editing are provided, and initial CIMR DNAme is characterized at TP53 and ONECUT1 CGIs. Collectively, this resource facilitates CpG island DNAme engineering in pluripotency and the genesis of novel epigenetic models of development and disease.
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Affiliation(s)
- Joshua Tompkins
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Elizabeth Lizhar
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Alireza Shokrani
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Jordan Berley
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Diba Kamali
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Deborah Hussey
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Jonas Cerneckis
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Tae Hyuk Kang
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Walter Tsark
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Defu Zeng
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Swetha Godatha
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Arthur Riggs
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
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59
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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60
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Grzelka K, Wilhelms H, Dodt S, Dreisow ML, Madara JC, Walker SJ, Wu C, Wang D, Lowell BB, Fenselau H. A synaptic amplifier of hunger for regaining body weight in the hypothalamus. Cell Metab 2023; 35:770-785.e5. [PMID: 36965483 PMCID: PMC10160008 DOI: 10.1016/j.cmet.2023.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 12/15/2022] [Accepted: 03/01/2023] [Indexed: 03/27/2023]
Abstract
Restricting caloric intake effectively reduces body weight, but most dieters fail long-term adherence to caloric deficit and eventually regain lost weight. Hypothalamic circuits that control hunger drive critically determine body weight; yet, how weight loss sculpts these circuits to motivate food consumption until lost weight is regained remains unclear. Here, we probe the contribution of synaptic plasticity in discrete excitatory afferents on hunger-promoting AgRP neurons. We reveal a crucial role for activity-dependent, remarkably long-lasting amplification of synaptic activity originating from paraventricular hypothalamus thyrotropin-releasing (PVHTRH) neurons in long-term body weight control. Silencing PVHTRH neurons inhibits the potentiation of excitatory input to AgRP neurons and diminishes concomitant regain of lost weight. Brief stimulation of the pathway is sufficient to enduringly potentiate this glutamatergic hunger synapse and triggers an NMDAR-dependent gaining of body weight that enduringly persists. Identification of this activity-dependent synaptic amplifier provides a previously unrecognized target to combat regain of lost weight.
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Affiliation(s)
- Katarzyna Grzelka
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
| | - Hannah Wilhelms
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
| | - Stephan Dodt
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Marie-Luise Dreisow
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
| | - Joseph C Madara
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Samuel J Walker
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chen Wu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daqing Wang
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Bradford B Lowell
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02215, USA.
| | - Henning Fenselau
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Straße 26, Cologne 50931, Germany.
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61
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Oh W, Kim AMJ, Dhawan D, Kirkham PM, Ostafe R, Franco J, Aryal UK, Carnahan RH, Patsekin V, Robinson JP, Knapp DW, Lim SO. Development of an Anti-canine PD-L1 Antibody and Caninized PD-L1 Mouse Model as Translational Research Tools for the Study of Immunotherapy in Humans. CANCER RESEARCH COMMUNICATIONS 2023; 3:860-873. [PMID: 37377896 PMCID: PMC10184575 DOI: 10.1158/2767-9764.crc-22-0468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 06/29/2023]
Abstract
Immune checkpoint blockade therapy, one of the most promising cancer immunotherapies, has shown remarkable clinical impact in multiple cancer types. Despite the recent success of immune checkpoint blockade therapy, however, the response rates in patients with cancer are limited (∼20%-40%). To improve the success of immune checkpoint blockade therapy, relevant preclinical animal models are essential for the development and testing of multiple combination approaches and strategies. Companion dogs naturally develop several types of cancer that in many respects resemble clinical cancer in human patients. Therefore, the canine studies of immuno-oncology drugs can generate knowledge that informs and prioritizes new immuno-oncology therapy in humans. The challenge has been, however, that immunotherapeutic antibodies targeting canine immune checkpoint molecules such as canine PD-L1 (cPD-L1) have not been commercially available. Here, we developed a new cPD-L1 antibody as an immuno-oncology drug and characterized its functional and biological properties in multiple assays. We also evaluated the therapeutic efficacy of cPD-L1 antibodies in our unique caninized PD-L1 mice. Together, these in vitro and in vivo data, which include an initial safety profile in laboratory dogs, support development of this cPD-L1 antibody as an immune checkpoint inhibitor for studies in dogs with naturally occurring cancer for translational research. Our new therapeutic antibody and caninized PD-L1 mouse model will be essential translational research tools in raising the success rate of immunotherapy in both dogs and humans. Significance Our cPD-L1 antibody and unique caninized mouse model will be critical research tools to improve the efficacy of immune checkpoint blockade therapy in both dogs and humans. Furthermore, these tools will open new perspectives for immunotherapy applications in cancer as well as other autoimmune diseases that could benefit a diverse and broader patient population.
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Affiliation(s)
- Wonkyung Oh
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Alyssa Min Jung Kim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Deepika Dhawan
- Department of Veterinary Clinical Science, Purdue University, West Lafayette, Indiana
| | - Perry M. Kirkham
- Office of the Executive Vice President for Research and Partnerships, Purdue University, West Lafayette, Indiana
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production, Purdue Institute for Inflammation Immunology and Infection Diseases, Purdue University, West Lafayette, Indiana
| | - Jackeline Franco
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Valery Patsekin
- Department of Basic Medical Sciences, Purdue University, West Lafayette, Indiana
| | - J. Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, Indiana
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Deborah W. Knapp
- Department of Veterinary Clinical Science, Purdue University, West Lafayette, Indiana
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana
| | - Seung-Oe Lim
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana
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62
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Konturek-Ciesla A, Dhapola P, Zhang Q, Säwén P, Wan H, Karlsson G, Bryder D. Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age. Cell Rep 2023; 42:112304. [PMID: 36961818 DOI: 10.1016/j.celrep.2023.112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Aging negatively affects hematopoiesis, with consequences for immunity and acquired blood cell disorders. Although impairments in hematopoietic stem cell (HSC) function contribute to this, the in vivo dynamics of such changes remain obscure. Here, we integrate extensive longitudinal functional assessments of HSC-specific lineage tracing with single-cell transcriptome and epitope profiling. In contrast to recent suggestions from single-cell RNA sequencing alone, our data favor a defined structure of HSC/progenitor differentiation that deviates substantially from HSC-derived hematopoiesis following transplantation. Native age-dependent attrition in HSC differentiation manifests as drastically reduced lymphoid output through an early lymphoid-primed progenitor (MPP Ly-I). While in vitro activation fails to rescue lymphoid differentiation from most aged HSCs, robust lymphopoiesis can be achieved by culturing elevated numbers of candidate HSCs. Therefore, our data position rare chronologically aged HSC clones, fully competent at producing lymphoid offspring, as a prime target for approaches aimed to improve lymphopoiesis in the elderly.
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Affiliation(s)
- Anna Konturek-Ciesla
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Parashar Dhapola
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Qinyu Zhang
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Petter Säwén
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Haixia Wan
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Göran Karlsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden.
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63
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Schiepers A, van 't Wout MFL, Greaney AJ, Zang T, Muramatsu H, Lin PJC, Tam YK, Mesin L, Starr TN, Bieniasz PD, Pardi N, Bloom JD, Victora GD. Molecular fate-mapping of serum antibody responses to repeat immunization. Nature 2023; 615:482-489. [PMID: 36646114 PMCID: PMC10023323 DOI: 10.1038/s41586-023-05715-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023]
Abstract
The protective efficacy of serum antibodies results from the interplay of antigen-specific B cell clones of different affinities and specificities. These cellular dynamics underlie serum-level phenomena such as original antigenic sin (OAS)-a proposed propensity of the immune system to rely repeatedly on the first cohort of B cells engaged by an antigenic stimulus when encountering related antigens, in detriment to the induction of de novo responses1-5. OAS-type suppression of new, variant-specific antibodies may pose a barrier to vaccination against rapidly evolving viruses such as influenza and SARS-CoV-26,7. Precise measurement of OAS-type suppression is challenging because cellular and temporal origins cannot readily be ascribed to antibodies in circulation; its effect on subsequent antibody responses therefore remains unclear5,8. Here we introduce a molecular fate-mapping approach with which serum antibodies derived from specific cohorts of B cells can be differentially detected. We show that serum responses to sequential homologous boosting derive overwhelmingly from primary cohort B cells, while later induction of new antibody responses from naive B cells is strongly suppressed. Such 'primary addiction' decreases sharply as a function of antigenic distance, allowing reimmunization with divergent viral glycoproteins to produce de novo antibody responses targeting epitopes that are absent from the priming variant. Our findings have implications for the understanding of OAS and for the design and testing of vaccines against evolving pathogens.
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Affiliation(s)
- Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | | | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Trinity Zang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paulo J C Lin
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Ying K Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
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64
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Nong Y, Stoppel DC, Johnson MA, Boillot M, Todorovic J, Shen J, Zhou X, Nadler MJ, Rodriguez C, Huo Y, Nagakura I, Kasper EM, Anderson MP. UBE3A and transsynaptic complex NRXN1-CBLN1-GluD1 in a hypothalamic VMHvl-arcuate feedback circuit regulates aggression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530462. [PMID: 36909588 PMCID: PMC10002692 DOI: 10.1101/2023.02.28.530462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
The circuit origins of aggression in autism spectrum disorder remain undefined. Here we report Tac1-expressing glutamatergic neurons in ventrolateral division of ventromedial hypothalamus (VMHvl) drive intermale aggression. Aggression is increased due to increases of Ube3a gene dosage in the VMHvl neurons when modeling autism due to maternal 15q11-13 triplication. Targeted deletion of increased Ube3a copies in VMHvl reverses the elevated aggression adult mice. VMHvl neurons form excitatory synapses onto hypothalamic arcuate nucleus AgRP/NPY neurons through a NRXN1-CBLN1-GluD1 transsynaptic complex and UBE3A impairs this synapse by decreasing Cbln1 gene expression. Exciting AgRP/NPY arcuate neurons leads to feedback inhibition of VMHvl neurons and inhibits aggression. Asymptomatic increases of UBE3A synergize with a heterozygous deficiency of presynaptic Nrxn1 or postsynaptic Grid1 (both ASD genes) to increase aggression. Targeted deletions of Grid1 in arcuate AgRP neurons impairs the VMHvl to AgRP/NPY neuron excitatory synapses while increasing aggression. Chemogenetic/optogenetic activation of arcuate AgRP/NPY neurons inhibits VMHvl neurons and represses aggression. These data reveal that multiple autism genes converge to regulate the VMHvl-arcuate AgRP/NPY glutamatergic synapse. The hypothalamic circuitry implicated by these data suggest impaired excitation of AgRP/NPY feedback inhibitory neurons may explain the increased aggression behavior found in genetic forms of autism.
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Affiliation(s)
- Yi Nong
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
| | - David C. Stoppel
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mark A. Johnson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Morgane Boillot
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Jelena Todorovic
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Jason Shen
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Xinyu Zhou
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Monica J.S. Nadler
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Carrie Rodriguez
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Yuda Huo
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
| | - Ikue Nagakura
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Ekkehard M. Kasper
- Department of Surgery, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
| | - Matthew P. Anderson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02115, USA
- Boston Children’s Hospital Intellectual and Developmental Disabilities Research Center, 300 Longwood Avenue, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
- Regeneron 777 Old Saw Mill River Road Tarrytown, NY 10591, USA
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65
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Niemi NM, Serrano LR, Muehlbauer LK, Balnis C, Kozul KL, Rashan EH, Shishkova E, Schueler KL, Keller MP, Attie AD, Pagan J, Coon JJ, Pagliarini DJ. Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530351. [PMID: 36909604 PMCID: PMC10002655 DOI: 10.1101/2023.02.28.530351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Pptc7 is a resident mitochondrial phosphatase essential for maintaining proper mitochondrial content and function. Newborn mice lacking Pptc7 exhibit aberrant mitochondrial protein phosphorylation, suffer from a range of metabolic defects, and fail to survive beyond one day after birth. Using an inducible knockout model, we reveal that loss of Pptc7 in adult mice causes marked reduction in mitochondrial mass concomitant with elevation of the mitophagy receptors Bnip3 and Nix. Consistently, Pptc7-/- mouse embryonic fibroblasts (MEFs) exhibit a major increase in mitophagy that is reversed upon deletion of these receptors. Our phosphoproteomics analyses reveal a common set of elevated phosphosites between perinatal tissues, adult liver, and MEFs-including multiple sites on Bnip3 and Nix. These data suggest that Pptc7 deletion causes mitochondrial dysfunction via dysregulation of several metabolic pathways and that Pptc7 may directly regulate mitophagy receptor function or stability. Overall, our work reveals a significant role for Pptc7 in the mitophagic response and furthers the growing notion that management of mitochondrial protein phosphorylation is essential for ensuring proper organelle content and function.
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Affiliation(s)
- Natalie M. Niemi
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lia R. Serrano
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Catie Balnis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Keri-Lyn Kozul
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Julia Pagan
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Joshua J. Coon
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - David J. Pagliarini
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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66
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Bhatia R, Siddiqui JA, Ganguly K, Thompson CM, Cannon A, Aithal A, Perumal N, Maurya SK, Li X, Cox JL, Gurumurthy CB, Rachagani S, Jain M, Nasser MW, Batra SK, Kumar S. Muc4 loss mitigates epidermal growth factor receptor activity essential for PDAC tumorigenesis. Oncogene 2023; 42:759-770. [PMID: 36624189 PMCID: PMC10198580 DOI: 10.1038/s41388-022-02587-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023]
Abstract
Mucin4 (MUC4) appears early during pancreatic intraepithelial neoplasia-1 (PanIN1), coinciding with the expression of epidermal growth factor receptor-1 (EGFR). The EGFR signaling is required for the onset of Kras-driven pancreatic ductal adenocarcinoma (PDAC); however, the players and mechanisms involved in sustained EGFR signaling in early PanIN lesions remain elusive. We generated a unique Esai-CRISPR-based Muc4 conditional knockout murine model to evaluate its effect on PDAC pathology. The Muc4 depletion in the autochthonous murine model carrying K-ras and p53 mutations (K-rasG12D; TP53R172H; Pdx-1cre, KPC) to generate the KPCM4-/- murine model showed a significant delay in the PanIN lesion formation with a significant reduction (p < 0.01) in EGFR (Y1068) and ERK1/2 (T202/Y204) phosphorylation. Further, a significant decrease (p < 0.01) in Sox9 expression in PanIN lesions of KPCM4-/- mice suggested the impairment of acinar-to-ductal metaplasia in Muc4-depleted cells. The biochemical analyses demonstrated that MUC4, through its juxtamembrane EGF-like domains, interacts with the EGFR ectodomain, and its cytoplasmic tail prevents EGFR ubiquitination and subsequent proteasomal degradation upon ligand stimulation, leading to sustained downstream oncogenic signaling. Targeting the MUC4 and EGFR interacting interface provides a promising strategy to improve the efficacy of EGFR-targeted therapies in PDAC and other MUC4-expressing malignancies.
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Affiliation(s)
- Rakesh Bhatia
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christopher M Thompson
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andrew Cannon
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Abhijit Aithal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Naveenkumar Perumal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shailendra K Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Xiaoqi Li
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jesse L Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
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67
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Du W, Ergin V, Loeb C, Huang M, Silver S, Armstrong AM, Huang Z, Gurumurthy CB, Staecker H, Liu X, Chen ZY. Rescue of Auditory Function by a Single Administration of AAV- TMPRSS3 Gene Therapy in Aged Mice of Human Recessive Deafness DFNB8. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530035. [PMID: 36865298 PMCID: PMC9980176 DOI: 10.1101/2023.02.25.530035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Patients with mutations in the TMPRSS3 gene suffer from recessive deafness DFNB8/DFNB10 for whom cochlear implantation is the only treatment option. Poor cochlear implantation outcomes are seen in some patients. To develop biological treatment for TMPRSS3 patients, we generated a knock-in mouse model with a frequent human DFNB8 TMPRSS3 mutation. The Tmprss3 A306T/A306T homozygous mice display delayed onset progressive hearing loss similar to human DFNB8 patients. Using AAV2 as a vector to carry a human TMPRSS3 gene, AAV2-h TMPRSS3 injection in the adult knock-in mouse inner ears results in TMPRSS3 expression in the hair cells and the spiral ganglion neurons. A single AAV2-h TMPRSS3 injection in aged Tmprss3 A306T/A306T mice leads to sustained rescue of the auditory function, to a level similar to the wildtype mice. AAV2-h TMPRSS3 delivery rescues the hair cells and the spiral ganglions. This is the first study to demonstrate successful gene therapy in an aged mouse model of human genetic deafness. This study lays the foundation to develop AAV2-h TMPRSS3 gene therapy to treat DFNB8 patients, as a standalone therapy or in combination with cochlear implantation.
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68
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Medert R, Thumberger T, Tavhelidse-Suck T, Hub T, Kellner T, Oguchi Y, Dlugosz S, Zimmermann F, Wittbrodt J, Freichel M. Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice. Nucleic Acids Res 2023; 51:e14. [PMID: 36533445 PMCID: PMC10021492 DOI: 10.1093/nar/gkac1150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 09/22/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging given that donor constructs preferentially integrate as concatemers. Here, we showed that injecting 5' biotinylated donor DNA into mouse embryos at the two-cell stage led to efficient single-copy HDR (scHDR) allele generation. Our dedicated genotyping strategy showed that these alleles occurred with frequencies of 19%, 20%, and 26% at three independent gene loci, indicating that scHDR was dramatically increased by 5' biotinylation. Thus, we suggest that the combination of a 5' biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins in the mouse genome.
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Affiliation(s)
- Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Tobias Hub
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yoko Oguchi
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Sascha Dlugosz
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Frank Zimmermann
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
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69
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Giandomenico SL, Schuman EM. Genetic manipulation and targeted protein degradation in mammalian systems: practical considerations, tips and tricks for discovery research. FEBS Open Bio 2023. [PMID: 36815235 DOI: 10.1002/2211-5463.13581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Gaining a mechanistic understanding of the molecular pathways underpinning cellular and organismal physiology invariably relies on the perturbation of an experimental system to infer causality. This can be achieved either by genetic manipulation or by pharmacological treatment. Generally, the former approach is applicable to a wider range of targets, is more precise, and can address more nuanced functional aspects. Despite such apparent advantages, genetic manipulation (i.e., knock-down, knock-out, mutation, and tagging) in mammalian systems can be challenging due to problems with delivery, low rates of homologous recombination, and epigenetic silencing. The advent of CRISPR-Cas9 in combination with the development of robust differentiation protocols that can efficiently generate a variety of different cell types in vitro has accelerated our ability to probe gene function in a more physiological setting. Often, the main obstacle in this path of enquiry is to achieve the desired genetic modification. In this short review, we will focus on gene perturbation in mammalian cells and how editing and differentiation of pluripotent stem cells can complement more traditional approaches. Additionally, we introduce novel targeted protein degradation approaches as an alternative to DNA/RNA-based manipulation. Our aim is to present a broad overview of recent approaches and in vitro systems to study mammalian cell biology. Due to space limitations, we limit ourselves to providing the inexperienced reader with a conceptual framework on how to use these tools, and for more in-depth information, we will provide specific references throughout.
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Affiliation(s)
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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70
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Phan HTL, Kim K, Lee H, Seong JK. Progress in and Prospects of Genome Editing Tools for Human Disease Model Development and Therapeutic Applications. Genes (Basel) 2023; 14:483. [PMID: 36833410 PMCID: PMC9957140 DOI: 10.3390/genes14020483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Programmable nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas, are widely accepted because of their diversity and enormous potential for targeted genomic modifications in eukaryotes and other animals. Moreover, rapid advances in genome editing tools have accelerated the ability to produce various genetically modified animal models for studying human diseases. Given the advances in gene editing tools, these animal models are gradually evolving toward mimicking human diseases through the introduction of human pathogenic mutations in their genome rather than the conventional gene knockout. In the present review, we summarize the current progress in and discuss the prospects for developing mouse models of human diseases and their therapeutic applications based on advances in the study of programmable nucleases.
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Affiliation(s)
- Hong Thi Lam Phan
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, Republic of Korea
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71
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Kobayashi R, Horii T, Hatada I. Efficient Detection of Flox Mice Using In Vitro Cre Recombination. Methods Mol Biol 2023; 2637:149-159. [PMID: 36773145 DOI: 10.1007/978-1-0716-3016-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Advances in CRISPR/Cas9 genome editing technologies have allowed for the rapid generation of Cre-loxP conditional knockout mice. However, current strategies for genotyping flox mice, typically based on Sanger sequencing following cloning of target sequences from dozens of pups, are time-consuming. Here, we describe a rapid screening method for flox mice, using in vitro Cre recombination that can be performed using simple enzymatic reactions and enables detection of functional flox mouse within 1 day. In addition, we introduce an efficient strategy for subsequent sequence analysis by cloning of floxed regions using the In-Fusion system. Our genotyping pipeline reduces laborious tasks and thus contributes to the rapid selection of accurately edited flox mice.
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Affiliation(s)
- Ryosuke Kobayashi
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
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72
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Watson ET, Pauers MM, Seibert MJ, Vevea JD, Chapman ER. Synaptic vesicle proteins are selectively delivered to axons in mammalian neurons. eLife 2023; 12:e82568. [PMID: 36729040 PMCID: PMC9894587 DOI: 10.7554/elife.82568] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Neurotransmitter-filled synaptic vesicles (SVs) mediate synaptic transmission and are a hallmark specialization in neuronal axons. Yet, how SV proteins are sorted to presynaptic nerve terminals remains the subject of debate. The leading model posits that these proteins are randomly trafficked throughout neurons and are selectively retained in presynaptic boutons. Here, we used the RUSH (retention using selective hooks) system, in conjunction with HaloTag labeling approaches, to study the egress of two distinct transmembrane SV proteins, synaptotagmin 1 and synaptobrevin 2, from the soma of mature cultured rat and mouse neurons. For these studies, the SV reporter constructs were expressed at carefully controlled, very low levels. In sharp contrast to the selective retention model, both proteins selectively and specifically entered axons with minimal entry into dendrites. However, even moderate overexpression resulted in the spillover of SV proteins into dendrites, potentially explaining the origin of previous non-polarized transport models, revealing the limited, saturable nature of the direct axonal trafficking pathway. Moreover, we observed that SV constituents were first delivered to the presynaptic plasma membrane before incorporation into SVs. These experiments reveal a new-found membrane trafficking pathway, for SV proteins, in classically polarized mammalian neurons and provide a glimpse at the first steps of SV biogenesis.
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Affiliation(s)
- Emma T Watson
- Department of Neuroscience, University of Wisconsin-MadisonMadisonUnited States
- Howard Hughes Medical InstituteMadisonUnited States
| | - Michaela M Pauers
- Department of Neuroscience, University of Wisconsin-MadisonMadisonUnited States
- Howard Hughes Medical InstituteMadisonUnited States
| | - Michael J Seibert
- Department of Neuroscience, University of Wisconsin-MadisonMadisonUnited States
- Howard Hughes Medical InstituteMadisonUnited States
| | - Jason D Vevea
- Department of Neuroscience, University of Wisconsin-MadisonMadisonUnited States
- Howard Hughes Medical InstituteMadisonUnited States
| | - Edwin R Chapman
- Department of Neuroscience, University of Wisconsin-MadisonMadisonUnited States
- Howard Hughes Medical InstituteMadisonUnited States
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73
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Crichton JH, Dunce JM, Dunne OM, Salmon LJ, Devenney PS, Lawson J, Adams IR, Davies OR. Structural maturation of SYCP1-mediated meiotic chromosome synapsis by SYCE3. Nat Struct Mol Biol 2023; 30:188-199. [PMID: 36635604 PMCID: PMC7614228 DOI: 10.1038/s41594-022-00909-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/06/2022] [Indexed: 01/13/2023]
Abstract
In meiosis, a supramolecular protein structure, the synaptonemal complex (SC), assembles between homologous chromosomes to facilitate their recombination. Mammalian SC formation is thought to involve hierarchical zipper-like assembly of an SYCP1 protein lattice that recruits stabilizing central element (CE) proteins as it extends. Here we combine biochemical approaches with separation-of-function mutagenesis in mice to show that, rather than stabilizing the SYCP1 lattice, the CE protein SYCE3 actively remodels this structure during synapsis. We find that SYCP1 tetramers undergo conformational change into 2:1 heterotrimers on SYCE3 binding, removing their assembly interfaces and disrupting the SYCP1 lattice. SYCE3 then establishes a new lattice by its self-assembly mimicking the role of the disrupted interface in tethering together SYCP1 dimers. SYCE3 also interacts with CE complexes SYCE1-SIX6OS1 and SYCE2-TEX12, providing a mechanism for their recruitment. Thus, SYCE3 remodels the SYCP1 lattice into a CE-binding integrated SYCP1-SYCE3 lattice to achieve long-range synapsis by a mature SC.
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Affiliation(s)
- James H Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James M Dunce
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Orla M Dunne
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - Lucy J Salmon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul S Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jennifer Lawson
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Owen R Davies
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK.
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Ohtsuka M, Imafuku J, Hori S, Kurosaki A, Nakamura A, Nakahara T, Yahata T, Bhat K, Papastefan ST, Nakagawa S, Quadros RM, Miura H, Gurumurthy CB. Delivering mRNAs to mouse tissues using the SEND system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.28.522652. [PMID: 36747769 PMCID: PMC9900891 DOI: 10.1101/2023.01.28.522652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
mRNAs produced in a cell are almost always translated within the same cell. Some mRNAs are transported to other cells of the organism through processes involving membrane nanotubes or extracellular vesicles. A recent report describes a surprising new phenomenon of encapsulating mRNAs inside virus-like particles (VLPs) to deliver them to other cells in a process that was named SEND (Selective Endogenous eNcapsidation for cellular Delivery). Although the seminal work demonstrates the SEND process in cultured cells, it is unknown whether this phenomenon occurs in vivo . Here, we demonstrate the SEND process in living organisms using specially designed genetically engineered mouse models. Our proof of principle study lays a foundation for the SEND-VLP system to potentially be used as a gene therapy tool to deliver therapeutically important mRNAs to tissues.
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75
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Villar-Pazos S, Thomas L, Yang Y, Chen K, Lyles JB, Deitch BJ, Ochaba J, Ling K, Powers B, Gingras S, Kordasiewicz HB, Grubisha MJ, Huang YH, Thomas G. RNA-targeted therapy corrects neuronal deficits in PACS1 syndrome mice. RESEARCH SQUARE 2023:rs.3.rs-2440581. [PMID: 36747781 PMCID: PMC9901029 DOI: 10.21203/rs.3.rs-2440581/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Neurodevelopmental disorders (NDDs) are frequently associated with dendritic abnormalities in pyramidal neurons that affect arbor complexity, spine density, and synaptic communication 1,2. The underlying genetic causes are often complex, obscuring the molecular pathways that drive these disorders 3. Next-generation sequencing has identified recurrent de novo missense mutations in a handful of genes associated with NDDs, offering a unique opportunity to decipher the molecular pathways 4. One such gene is PACS1, which encodes the multi-functional trafficking protein PACS1 (or PACS-1); a single recurrent de novo missense mutation, c607C>T (PACS1R203W), causes developmental delay and intellectual disability (ID) 5,6. The processes by which PACS1R203W causes PACS1 syndrome are unknown, and there is no curative treatment. We show that PACS1R203W increases the interaction between PACS1 and the α-tubulin deacetylase HDAC6, elevating enzyme activity and appropriating control of its posttranscriptional regulation. Consequently, PACS1R203W reduces acetylation of α-tubulin and cortactin, causing the Golgi to fragment and enter developing neurites, leading to increased dendrite arborization. The dendrites, however, are beset with diminished spine density and fewer functional synapses, characteristic of ID pathology. Treatment of PACS1 syndrome mice with PACS1- or HDAC6-targeting antisense oligonucleotides restores neuronal structure and synaptic transmission, suggesting PACS1R203W/HDAC6 may be targeted for treating PACS1 syndrome neuropathology.
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Affiliation(s)
- Sabrina Villar-Pazos
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Laurel Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yunhan Yang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kun Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jenea B. Lyles
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Bradley J. Deitch
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Karen Ling
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | - Sebastien Gingras
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | | | - Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yanhua H. Huang
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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76
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Strategies for generation of mice via CRISPR/HDR-mediated knock-in. Mol Biol Rep 2023; 50:3189-3204. [PMID: 36701041 DOI: 10.1007/s11033-023-08278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023]
Abstract
CRISPR/Cas9 framework is generally used to generate genetically modified mouse models. The clustered regularly interspaced short palindromic repeat gene editing technique, can efficiently generate knock-outs using the non-homologous end-joining repair pathway. Small knock-ins also work precisely using a repair template with help of homology-directed-repair (HDR) mechanism. However, when the fragment size is larger than 4-5 kb, the knock-in tends to be error prone and the efficiency decreases. Certain types of modifications, in particular insertions of very large DNA fragments (10-100 kb) or entire gene replacements, are still difficult. The HDR process needs further streamlining and improvement. Here in this review, we describe methods to enhance the efficiency of the knock-in through checking each step from the guide design to the microinjection and choice of the oocyte donors. This helps in understanding the parameters that can be modified to get improved knock-in efficiency via CRISPR targeting.
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77
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Wallace M, White JM, Kouranova E, Wang ZT, Cui X. Floxing by Electroporating Single-Cell Embryos with Two CRISPR RNPs and Two ssODNs. Methods Mol Biol 2023; 2631:231-252. [PMID: 36995670 DOI: 10.1007/978-1-0716-2990-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Floxed alleles and Cre drivers are two components of most conditional knockout mouse models, which are not only important for studying a given gene in a tissue-specific manner, but also useful for functional analysis of various sized genomic regions. With the increased demand for floxed mouse models in biomedical research, reliable and economical creation of floxed alleles is clearly highly valuable yet remains challenging. Here we provide technical details on the method consisting of electroporating single-cell embryos with CRISPR RNPs and ssODNs, next-generation sequencing (NGS)-based genotyping, an in vitro Cre assay (recombination followed by PCR) for loxP phasing determination, and optional second round targeting of an indel in cis with one loxP insertion in embryos obtained via in vitro fertilization (IVF). As importantly, we present protocols for validation of gRNAs and ssODNs before electroporation of embryos, to confirm phasing of loxP and the indel to be retargeted in individual blastocysts and an alternative strategy to insert loxP sites sequentially. Together, we hope to help researchers reliably obtain floxed alleles in a predictable and timely manner.
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Affiliation(s)
- Mia Wallace
- Mouse Genetics Core, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - J Michael White
- Transgenic, Knockout and Microinjection Core, Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Evgenea Kouranova
- Genome Engineering & Stem Cell Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Zi Teng Wang
- Genome Engineering & Stem Cell Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Xiaoxia Cui
- Genome Engineering & Stem Cell Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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78
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Singh S, Chaudhary R, Deshmukh R, Tiwari S. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. PLANT MOLECULAR BIOLOGY 2023; 111:1-20. [PMID: 36315306 DOI: 10.1007/s11103-022-01321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.
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Affiliation(s)
- Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | | | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India.
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79
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Huang Z, Liu G. Current advancement in the application of prime editing. Front Bioeng Biotechnol 2023; 11:1039315. [PMID: 36873365 PMCID: PMC9978821 DOI: 10.3389/fbioe.2023.1039315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Prime editing (PE) is a precise genome manipulation technology based on the "search and replace" approach of the CRISPR-Cas9 system, while it does not require the exogenous donor DNA and the DNA double-strand breaks (DSBs). Comparing the base editing technology, the editing scope of prime editing has been widely expanded. Prime editing has been successfully applied in a variety of plant cells, animal cells and the model microorganism Escherichia coli so far, and it has shown a good application potential in breeding and genomic functional study of animals and plants, disease treatment, and modification of the microbial strains. In this paper, the basic strategies of prime editing are briefly described, and its research progress is summarized and prospected from the application of multiple species. In addition, a variety of optimization strategies for improving its efficiency and specificity of prime editing are outlined.
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Affiliation(s)
- Zhangrao Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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80
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Lintott LG, Nutter LMJ. Genetic and Molecular Quality Control of Genetically Engineered Mice. Methods Mol Biol 2023; 2631:53-101. [PMID: 36995664 DOI: 10.1007/978-1-0716-2990-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genetically engineered mice are used as avatars to understand mammalian gene function and develop therapies for human disease. During genetic modification, unintended changes can occur, and these changes may result in misassigned gene-phenotype relationships leading to incorrect or incomplete experimental interpretations. The types of unintended changes that may occur depend on the allele type being made and the genetic engineering approach used. Here we broadly categorize allele types as deletions, insertions, base changes, and transgenes derived from engineered embryonic stem (ES) cells or edited mouse embryos. However, the methods we describe can be adapted to other allele types and engineering strategies. We describe the sources and consequ ences of common unintended changes and best practices for detecting both intended and unintended changes by screening and genetic and molecular quality control (QC) of chimeras, founders, and their progeny. Employing these practices, along with careful allele design and good colony management, will increase the chance that investigations using genetically engineered mice will produce high-quality reproducible results, to enable a robust understanding of gene function, human disease etiology, and therapeutic development.
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Affiliation(s)
- Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada.
- The Hospital for Sick Children, Toronto, ON, Canada.
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81
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Shakirova A, Karpov T, Komarova Y, Lepik K. In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization. Front Genome Ed 2023; 5:1068637. [PMID: 36911237 PMCID: PMC9992834 DOI: 10.3389/fgeed.2023.1068637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Gene therapy is a fast developing field of medicine with hundreds of ongoing early-stage clinical trials and numerous preclinical studies. Genome editing (GE) now is an increasingly important technology for achieving stable therapeutic effect in gene correction, with hematopoietic cells representing a key target cell population for developing novel treatments for a number of hereditary diseases, infections and cancer. By introducing a double strand break (DSB) in the defined locus of genomic DNA, GE tools allow to knockout the desired gene or to knock-in the therapeutic gene if provided with an appropriate repair template. Currently, the efficiency of methods for GE-mediated knock-in is limited. Significant efforts were focused on improving the parameters and interaction of GE nuclease proteins. However, emerging data suggests that optimal characteristics of repair templates may play an important role in the knock-in mechanisms. While viral vectors with notable example of AAVs as a donor template carrier remain the mainstay in many preclinical trials, non-viral templates, including plasmid and linear dsDNA, long ssDNA templates, single and double-stranded ODNs, represent a promising alternative. Furthermore, tuning of editing conditions for the chosen template as well as its structure, length, sequence optimization, homology arm (HA) modifications may have paramount importance for achieving highly efficient knock-in with favorable safety profile. This review outlines the current developments in optimization of templates for the GE mediated therapeutic gene correction.
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Affiliation(s)
- Alena Shakirova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Timofey Karpov
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Yaroslava Komarova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
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82
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Sato M, Nakamura A, Sekiguchi M, Matsuwaki T, Miura H, Gurumurthy CB, Kakuta S, Ohtsuka M. Improved Genome Editing via Oviductal Nucleic Acids Delivery (i-GONAD): Protocol Steps and Additional Notes. Methods Mol Biol 2023; 2631:325-340. [PMID: 36995675 DOI: 10.1007/978-1-0716-2990-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology has made it possible to produce genome-edited (GE) animals more easily and rapidly than before. In most cases, GE mice are produced by microinjection (MI) or by in vitro electroporation (EP) of CRISPR reagents into fertilized eggs (zygotes). Both of these approaches require ex vivo handling of isolated embryos and their subsequent transfer into another set of mice (called recipient or pseudopregnant mice). Such experiments are performed by highly skilled technicians (especially for MI). We recently developed a novel genome editing method, called "GONAD (Genome-editing via Oviductal Nucleic Acids Delivery)," which can completely eliminate the ex vivo handling of embryos. We also made improvements to the GONAD method, termed "improved-GONAD (i-GONAD)." The i-GONAD method involves injection of CRISPR reagents into the oviduct of an anesthetized pregnant female using a mouthpiece-controlled glass micropipette under a dissecting microscope, followed by EP of the entire oviduct allowing the CRISPR reagents to enter into the zygotes present inside the oviduct, in situ. After the i-GONAD procedure, the mouse recovered from anesthesia is allowed to continue the pregnancy to full term to deliver its pups. The i-GONAD method does not require pseudopregnant female animals for embryo transfer, unlike the methods relying on ex vivo handling of zygotes. Therefore, the i-GONAD method can reduce the number of animals used, compared to the traditional methods. In this chapter, we describe some newer technical tips about the i-GONAD method. Additionally, even though the detailed protocols of GONAD and i-GONAD have been published elsewhere (Gurumurthy et al., Curr Protoc Hum Genet 88:15.8.1-15.8.12, 2016 Nat Protoc 14:2452-2482, 2019), we provide all the protocol steps of i-GONAD in this chapter so that the reader can find most of the information, needed for performing i-GONAD experiments, in one place.
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Affiliation(s)
- Masahiro Sato
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan.
| | - Ayaka Nakamura
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Marie Sekiguchi
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Matsuwaki
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shigeru Kakuta
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan.
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan.
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83
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Wefers B, Wurst W, Kühn R. Gene Editing in Mouse Zygotes Using the CRISPR/Cas9 System. Methods Mol Biol 2023; 2631:207-230. [PMID: 36995669 DOI: 10.1007/978-1-0716-2990-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Engineering of the mouse germline is a key technology in biomedical research for studying the function of genes in health and disease. Since the first knockout mouse was described in 1989, gene targeting was based on recombination of vector encoded sequences in mouse embryonic stem cell lines and their introduction into preimplantation embryos to obtain germline chimeric mice. This approach has been replaced in 2013 by the application of the RNA-guided CRISPR/Cas9 nuclease system, which is introduced into zygotes and directly creates targeted modifications in the mouse genome. Upon the introduction of Cas9 nuclease and guide RNAs into one-cell embryos, sequence-specific double-strand breaks are created that are highly recombinogenic and processed by DNA repair enzymes. Gene editing commonly refers to the diversity of DSB repair products that include imprecise deletions or precise sequence modifications copied from repair template molecules. Since gene editing can now be easily applied directly in mouse zygotes, it has rapidly become the standard procedure for generating genetically engineered mice. This article covers the design of guide RNAs, knockout and knockin alleles, options for donor delivery, preparation of reagents, microinjection or electroporation of zygotes, and the genotyping of pups derived from gene editing projects.
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Affiliation(s)
- Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany.
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany
- Technische Universität München-Weihenstephan, Chair of Developmental Genetics, c/o Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
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84
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Liao J, Wu Y. Gene Editing in Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:177-199. [PMID: 38228965 DOI: 10.1007/978-981-99-7471-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) can be isolated and collected from the body, genetically modified, and expanded ex vivo. The invention of innovative and powerful gene editing tools has provided researchers with great convenience in genetically modifying a wide range of cells, including hematopoietic stem and progenitor cells (HSPCs). In addition to being used to modify genes to study the functional role that specific genes play in the hematopoietic system, the application of gene editing platforms in HSCs is largely focused on the development of cell-based gene editing therapies to treat diseases such as immune deficiency disorders and inherited blood disorders. Here, we review the application of gene editing tools in HSPCs. In particular, we provide a broad overview of the development of gene editing tools, multiple strategies for the application of gene editing tools in HSPCs, and exciting clinical advances in HSPC gene editing therapies. We also outline the various challenges integral to clinical translation of HSPC gene editing and provide the possible corresponding solutions.
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Affiliation(s)
- Jiaoyang Liao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuxuan Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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85
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Yunaini L, Ari Pujianto D. Various gene modification techniques to discover molecular targets for nonhormonal male contraceptives: A review. Int J Reprod Biomed 2023; 21:17-32. [PMID: 36875503 PMCID: PMC9982321 DOI: 10.18502/ijrm.v21i1.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 06/07/2022] [Accepted: 11/20/2022] [Indexed: 02/11/2023] Open
Abstract
The identification and characterization of relevant targets are necessary for developing nonhormonal male contraceptives. The molecules must demonstrate that they are necessary for reproduction. As a result, a sophisticated technique is required to identify the molecular targets for nonhormonal male contraceptives. Genetic modification (GM) techniques are one method that can be applied. This technique has been widely used to study gene function that effected male fertility and has resulted in the discovery of numerous nonhormonal male contraceptive target molecules. We examined GM techniques and approaches used to investigate genes involved in male fertility as potential targets for nonhormonal contraceptives. The discovery of nonhormonal contraceptive candidate molecules was increased by using GM techniques, especially the Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 method. The discovery of candidate nonhormonal contraceptive molecules can be a wide-open research for the development of nonhormonal male contraceptives. Therefore, we are believing that one day nonhormonal male contraceptives will be released.
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Affiliation(s)
- Luluk Yunaini
- Doctoral Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta Pusat, Indonesia.,Department of Medicine Biology, Faculty of Medicine, Universitas Indonesia, Jakarta Pusat, Indonesia
| | - Dwi Ari Pujianto
- Department of Medicine Biology, Faculty of Medicine, Universitas Indonesia, Jakarta Pusat, Indonesia
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86
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Cassidy AM, Thomas DB, Kuliyev E, Chen H, Pelletier S. One-step generation of a conditional allele in mice using a short artificial intron. Heliyon 2022; 8:e12630. [PMID: 36619446 PMCID: PMC9816766 DOI: 10.1016/j.heliyon.2022.e12630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 12/19/2022] [Indexed: 12/26/2022] Open
Abstract
Despite tremendous advances in genome editing technologies, generation of conditional alleles in mice has remained challenging. Recent studies in cells have successfully made use of short artificial introns to engineer conditional alleles. The approach consists of inserting a small cassette within an exon of a gene using CRISPR-Cas9 technology. The cassette, referred to as Artificial Intron version 4 (AIv4), contains sequences encoding a splice donor, essential intronic sequences flanked by loxP sites and a splice acceptor site. Under normal conditions, the artificial intron is removed by the splicing machinery, allowing for proper expression of the gene product. Following Cre-mediated recombination of the two loxP sites, the intron is disabled, and splicing can no longer occur. The remaining intronic sequences create a frameshift and early translation termination. Here we describe the application of this technology to engineer a conditional allele in mice using Scyl1 as a model gene. Insertion of the cassette occurred in 17% of edited mice obtained from pronuclear stage zygote microinjection. Mice homozygous for the insertion expressed SCYL1 at levels comparable to wild-type mice and showed no overt abnormalities associated with the loss of Scyl1 function, indicating the proper removal of the artificial intron. Inactivation of the cassette via Cre-mediated recombination in vivo occurred at high frequency, abrogated SCYL1 protein expression, and resulted in loss-of-function phenotypes. Our results broaden the applicability of this approach to engineering conditional alleles in mice.
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Affiliation(s)
- Annelise M. Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University—Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Destinée B. Thomas
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University—Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Emin Kuliyev
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hanying Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University—Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University—Purdue University Indianapolis, Indianapolis, IN, 46202, USA,Corresponding author.
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87
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Ozawa M, Taguchi J, Katsuma K, Ishikawa-Yamauchi Y, Kikuchi M, Sakamoto R, Yamada Y, Ikawa M. Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice. Sci Rep 2022; 12:21558. [PMID: 36513736 PMCID: PMC9748034 DOI: 10.1038/s41598-022-26107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Gene targeting of embryonic stem (ES) cells followed by chimera production has been conventionally used for developing gene-manipulated mice. Although direct knock-in (KI) using murine zygote via CRISPR/Cas9-mediated genome editing has been reported, ES cell targeting still has merits, e.g., high throughput work can be performed in vitro. In this study, we first compared the KI efficiency of mouse ES cells with CRISPR/Cas9 expression vector and ribonucleoprotein (RNP), and confirmed that KI efficiency was significantly increased by using RNP. Using CRISPR/Cas9 RNP and circular plasmid with homologous arms as a targeting vector, knock-in within ES cell clones could be obtained efficiently without drug selection, thus potentially shortening the vector construction or cell culture period. Moreover, by incorporating a drug-resistant cassette into the targeting vectors, double DNA KI can be simultaneously achieved at high efficiency by a single electroporation. This technique will help to facilitate the production of genetically modified mouse models that are fundamental for exploring topics related to human and mammalian biology.
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Affiliation(s)
- Manabu Ozawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Jumpei Taguchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Kento Katsuma
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yu Ishikawa-Yamauchi
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Mio Kikuchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Reiko Sakamoto
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yasuhiro Yamada
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Masahito Ikawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan ,grid.136593.b0000 0004 0373 3971Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
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88
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SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection. Exp Mol Med 2022; 54:2188-2199. [PMID: 36494589 PMCID: PMC9794761 DOI: 10.1038/s12276-022-00891-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 12/14/2022] Open
Abstract
The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables the rapid generation of conditional alleles via one-step zygote injection. In this study, a total of 13 SCON mouse lines were successfully generated by 2 different laboratories. SCON has conditional intronic functions in various vertebrate species, and its target insertion is as simple as CRISPR/Cas9-mediated gene tagging.
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89
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Fu H, Siggs OM, Knight LS, Staffieri SE, Ruddle JB, Birsner AE, Collantes ER, Craig JE, Wiggs JL, D’Amato RJ. Thrombospondin 1 missense alleles induce extracellular matrix protein aggregation and TM dysfunction in congenital glaucoma. J Clin Invest 2022; 132:e156967. [PMID: 36453543 PMCID: PMC9711877 DOI: 10.1172/jci156967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/11/2022] [Indexed: 12/03/2022] Open
Abstract
Glaucoma is a highly heritable disease that is a leading cause of blindness worldwide. Here, we identified heterozygous thrombospondin 1 (THBS1) missense alleles altering p.Arg1034, a highly evolutionarily conserved amino acid, in 3 unrelated and ethnically diverse families affected by congenital glaucoma, a severe form of glaucoma affecting children. Thbs1R1034C-mutant mice had elevated intraocular pressure (IOP), reduced ocular fluid outflow, and retinal ganglion cell loss. Histology revealed an abundant, abnormal extracellular accumulation of THBS1 with abnormal morphology of juxtacanalicular trabecular meshwork (TM), an ocular tissue critical for aqueous fluid outflow. Functional characterization showed that the THBS1 missense alleles found in affected individuals destabilized the THBS1 C-terminus, causing protein misfolding and extracellular aggregation. Analysis using a range of amino acid substitutions at position R1034 showed that the extent of aggregation was correlated with the change in protein-folding free energy caused by variations in amino acid structure. Extracellular matrix (ECM) proteins, especially fibronectin, which bind to THBS1, also accumulated within THBS1 deposits. These results show that missense variants altering THBS1 p.Arg1034 can cause elevated IOP through a mechanism involving impaired TM fluid outflow in association with accumulation of aggregated THBS1 in the ECM of juxtacanalicular meshwork with altered morphology.
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Affiliation(s)
- Haojie Fu
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Owen M. Siggs
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Lachlan S.W. Knight
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Sandra E. Staffieri
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Department of Ophthalmology, University of Melbourne, Department of Surgery, Parkville, Victoria, Australia
- Department of Ophthalmology, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Jonathan B. Ruddle
- Department of Ophthalmology, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Amy E. Birsner
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Robert J. D’Amato
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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90
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Cao C, Fleming MD. Loss of the placental iron exporter ferroportin 1 causes embryonic demise in late-gestation mouse pregnancy. Development 2022; 149:285826. [PMID: 36398730 DOI: 10.1242/dev.201160] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Fetal development relies on adequate iron supply by the placenta. The placental syncytiotrophoblasts (SCTB) express high levels of iron transporters, including ferroportin1 (Fpn1). Whether they are essential in the placenta has not been tested directly, mainly due to the lack of gene manipulation tools in SCTB. Here, we aimed to generate a SCTB-specific Cre mouse and use it to determine the role of placental Fpn1. Using CRISPR/Cas9 technology, we created a syncytin b (Synb) Cre line (SynbCre) targeting the fetal-facing SCTB layer in mouse placental labyrinth. SynbCre deleted Fpn1 in late gestation mouse placentas reliably with high efficiency. Embryos without placental Fpn1 were pale and runted, and died before birth. Fpn1 null placentas had reduced transferrin receptor expression, increased oxidative stress and detoxification responses, and accumulated ferritin in the SCTB instead of the fetal endothelium. In summary, we demonstrate that SynbCre is an effective and specific tool to investigate placental gene function in vivo. The loss of Fpn1 in late gestation mouse placenta is embryonically lethal, providing direct evidence for an essential role of Fpn1 in placental iron transport.
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Affiliation(s)
- Chang Cao
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
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91
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Mesnard CS, Hays CL, Barta CL, Sladek AL, Grassmeyer JJ, Hinz KK, Quadros RM, Gurumurthy CB, Thoreson WB. Synaptotagmins 1 and 7 in vesicle release from rods of mouse retina. Exp Eye Res 2022; 225:109279. [PMID: 36280223 PMCID: PMC9830644 DOI: 10.1016/j.exer.2022.109279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/14/2022] [Accepted: 10/10/2022] [Indexed: 01/13/2023]
Abstract
Synaptotagmins are the primary Ca2+ sensors for synaptic exocytosis. Previous work suggested synaptotagmin-1 (Syt1) mediates evoked vesicle release from cone photoreceptor cells in the vertebrate retina whereas release from rods may involve another sensor in addition to Syt1. We found immunohistochemical evidence for syntaptotagmin-7 (Syt7) in mouse rod terminals and so performed electroretinograms (ERG) and single-cell recordings using mice in which Syt1 and/or Syt7 were conditionally removed from rods and/or cones. Synaptic release was measured in mouse rods by recording presynaptic anion currents activated during glutamate re-uptake and from exocytotic membrane capacitance changes. Deleting Syt1 from rods reduced glutamate release evoked by short depolarizing steps but not long steps whereas deleting Syt7 from rods reduced release evoked by long but not short steps. Deleting both sensors completely abolished depolarization-evoked release from rods. Effects of various intracellular Ca2+ buffers showed that Syt1-mediated release from rods involves vesicles close to ribbon-associated Ca2+ channels whereas Syt7-mediated release evoked by longer steps involves more distant release sites. Spontaneous release from rods was unaffected by eliminating Syt7. While whole animal knockout of Syt7 slightly reduced ERG b-waves and oscillatory potentials, selective elimination of Syt7 from rods had no effect on ERGs. Furthermore, eliminating Syt1 from rods and cones abolished ERG b-waves and additional elimination of Syt7 had no further effect. These results show that while Syt7 contributes to slow non-ribbon release from rods, Syt1 is the principal sensor shaping rod and cone inputs to bipolar cells in response to light flashes.
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Affiliation(s)
- C S Mesnard
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA; Pharmacology and Experimental Neuroscience, USA
| | - C L Hays
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA
| | - C L Barta
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA
| | - A L Sladek
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA
| | - J J Grassmeyer
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA; Pharmacology and Experimental Neuroscience, USA
| | - K K Hinz
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA
| | - R M Quadros
- Pharmacology and Experimental Neuroscience, USA; Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68106, USA
| | - C B Gurumurthy
- Pharmacology and Experimental Neuroscience, USA; Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68106, USA
| | - W B Thoreson
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, USA; Pharmacology and Experimental Neuroscience, USA.
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92
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Miyata M, Yoshida J, Takagishi I, Horie K. Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells. DNA Res 2022; 30:6854440. [PMID: 36448318 PMCID: PMC9847339 DOI: 10.1093/dnares/dsac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters and topologically associating domains. To analyse these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster in mouse embryonic stem cells using CRISPR-Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN); and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. Inversion was also detected at similar efficiency. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31-63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.
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Affiliation(s)
- Masayuki Miyata
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Junko Yoshida
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Itsuki Takagishi
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Kyoji Horie
- To whom correspondence should be addressed. Tel: +81 744 23 4696. Fax: +81 744 23 4696.
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93
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Yoshida M, Saito T, Takayanagi Y, Totsuka Y, Onaka T. Necessity of integrated genomic analysis to establish a designed knock-in mouse from CRISPR-Cas9-induced mutants. Sci Rep 2022; 12:20390. [PMID: 36437283 PMCID: PMC9701781 DOI: 10.1038/s41598-022-24810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The CRISPR-Cas9 method for generation of knock-in mutations in rodent embryos yields many F0 generation candidates that may have the designed mutations. The first task for selection of promising F0 generations is to analyze genomic DNA which likely contains a mixture of designed and unexpected mutations. In our study, while generating Prlhr-Venus knock-in reporter mice, we found that genomic rearrangements near the targeted knock-in allele, tandem multicopies at a target allele locus, and mosaic genotypes for two different knock-in alleles occurred in addition to the designed knock-in mutation in the F0 generation. Conventional PCR and genomic sequencing were not able to detect mosaicism nor discriminate between the designed one-copy knock-in mutant and a multicopy-inserted mutant. However, by using a combination of Southern blotting and the next-generation sequencing-based RAISING method, these mutants were successfully detected in the F0 generation. In the F1 and F2 generations, droplet digital PCR assisted in establishing the strain, although a multicopy was falsely detected as one copy by analysis of the F0 generation. Thus, the combination of these methods allowed us to select promising F0 generations and facilitated establishment of the designed strain. We emphasize that focusing only on positive evidence of knock-in can lead to erroneous selection of undesirable strains.
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Affiliation(s)
- Masahide Yoshida
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Tomoko Saito
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Yuki Takayanagi
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yoshikazu Totsuka
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Tatsushi Onaka
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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94
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Zhang CH, Gao Y, Hung HH, Zhuo Z, Grodzinsky AJ, Lassar AB. Creb5 coordinates synovial joint formation with the genesis of articular cartilage. Nat Commun 2022; 13:7295. [PMID: 36435829 PMCID: PMC9701237 DOI: 10.1038/s41467-022-35010-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of signaling molecules that block a Wnt5a autoregulatory loop in the perichondrium. Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression in the articular cartilage; and a non-cell autonomous up-regulation of Ctgf. Our findings indicate that Creb5 promotes joint formation and the subsequent development of articular chondrocytes by driving the expression of signaling molecules that both specify the joint interzone and simultaneously inhibit a Wnt5a positive-feedback loop in the perichondrium.
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Affiliation(s)
- Cheng-Hai Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
| | - Yao Gao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Han-Hwa Hung
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zhu Zhuo
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Alan J Grodzinsky
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Andrew B Lassar
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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95
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Suzuki T, Kamiya H. Easily-controllable, helper phage-free single-stranded phagemid production system. Genes Environ 2022; 44:25. [DOI: 10.1186/s41021-022-00254-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Single-stranded (ss) DNAs are utilized in various molecular biological and biotechnological applications including the construction of double-stranded DNAs with a DNA lesion, and are commonly prepared by using chimeric phage-plasmids (phagemids) plus M13-derived helper phages. However, the yields of ss DNA with these methods are poorly reproducible, and multiple factors must be optimized.
Results
In this report, we describe a new arabinose-inducible ss phagemid production method without helper phage infection. The newly exploited DNA derived from VCSM13 expresses the pII protein, which initiates ss DNA synthesis, under the control of the araBAD promoter. In addition, the packaging signal is deleted in the DNA to reduce the contamination of the phage-derived ss DNA. The phagemid DNA of interest, carrying the M13 origin of replication and the packaging signal, was introduced into bacterial cells maintaining the modified VCSM13 DNA as a plasmid, and the ss phagemid DNA production was induced by arabinose. The DNA recovered from the phage particles had less contamination from VCSM13 DNA, as compared to the conventional method. Moreover, we extended the method to purify the ss DNAs by using an anion-exchange column, to avoid the use of hazardous chemicals.
Conclusion
Using this combination of methods, large quantities of phagemid ss DNAs of interest can be consistently obtained.
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96
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JADE2 Is Essential for Hippocampal Synaptic Plasticity and Cognitive Functions in Mice. Biol Psychiatry 2022; 92:800-814. [PMID: 36008159 DOI: 10.1016/j.biopsych.2022.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/20/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Impairment of synaptic plasticity is closely correlated with a range of pathological conditions, such as cognitive deficits. However, how synaptic efficacy is regulated remains incompletely understood. Here, we report that the epigenetic factor JADE2 was indispensable for the maintenance of hippocampal synaptic plasticity and cognitive functions in mice. METHODS We used the Morris water maze and the fear conditioning test to examine learning-related behaviors. In addition, Western blotting, viral-mediated JADE2 manipulations, RNA sequencing, and electrophysiological recordings were used to address our questions. RESULTS JADE2 expression is increased upon enhanced neuronal activity in vitro and in vivo. Knockdown or genetic deletion of Jade2 in hippocampal CA1 results in impaired structural and functional synaptic plasticity, leading to memory impairment, whereas overexpression of JADE2 in CA1 neurons facilitates hippocampal-dependent learning and memory. Mechanistically, our data show that JADE2 modulates synaptic functions mainly by transcriptional activation of cytoskeletal regulator Rac1, and this activity is dependent on its interaction with histone acetyltransferase HBO1. Finally, we demonstrate that restoring RAC1 expression in Jade2 knockout mice could rescue the deficits in synaptic plasticity and learning-related behaviors. CONCLUSIONS Our findings reveal that JADE2 plays a critical role in regulating synaptic plasticity and memory formation, suggesting that activity-dependent epigenetic regulation is an important molecular mechanism in controlling synaptic plasticity.
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97
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Catecholaminergic cell type-specific expression of Cre recombinase in knock-in transgenic rats generated by the Combi-CRISPR technology. J Neurosci Methods 2022; 381:109707. [PMID: 36089167 DOI: 10.1016/j.jneumeth.2022.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cell groups containing catecholamines provide a useful model to study the molecular and cellular mechanisms underlying the morphogenesis, physiology, and pathology of the central nervous system. For this purpose, it is necessary to establish a system to induce catecholaminergic group-specific expression of Cre recombinase. Recently, we introduced a gene cassette encoding 2A peptide fused to Cre recombinase into the site between the C-terminus and translational termination codons of the rat tyrosine hydroxylase (TH) open reading frame by the Combi-CRISPR technology, which is a genomic editing method to enable an efficient knock-in (KI) of long DNA sequence into a target site. However, the expression patterns of the transgene and its function as well as the effect of the mutation on the biochemical and behavioral phenotypes in the KI strains have not been characterized yet. NEW METHOD We aimed to evaluate the usefulness of TH-Cre KI rats as an experimental model for investigating the structure and function of catecholaminergic neurons in the brain. RESULTS We detected cell type-specific expression of Cre recombinase and site-specific recombination activity in the representative catecholaminergic groups in the TH-Cre KI rat strains. In addition, we measured TH protein levels and catecholamine accumulation in the brain regions, as well as motor, reward-related, and anxiety-like behaviors, indicating that catecholamine metabolism and general behavior are apparently normal in these KI rats. CONCLUSIONS TH-Cre KI rat strains produced by the Combi-CRISPR system offer a beneficial model to study the molecular and cellular mechanics for the morphogenesis, physiology, and pathology of catecholamine-containing neurons in the brain.
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98
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Balog M, Anderson A, Gurumurthy CB, Quadros RM, Korade Z, Mirnics K. Knock-in mouse models for studying somatostatin and cholecystokinin expressing cells. J Neurosci Methods 2022; 381:109704. [PMID: 36070817 DOI: 10.1016/j.jneumeth.2022.109704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Somatostatin (SST) and cholecystokinin (CCK) are peptide hormones that regulate the endocrine system, cell proliferation and neurotransmission. NEW METHOD We utilized the novel Easi-CRISPR system to generate two knock-in mouse strains with Cre recombinase in SST- and CCK-expressing cells and validated their utility in the developing and adult brain tissues. RESULTS The full nomenclature for the newly generated strains are C57BL/6-Sstem1(P2A-iCre-T2A-mCherry)Mirn and C57BL/6-Cckem1(iCre-T2A-mCherry-P2A)Mirn. For the Sst locus, a P2A-iCre-T2A-mCherry cassette was inserted immediately upstream of the stop codon (C terminus fusion). For the Cck locus, iCre-P2A-mCherry-T2A cassette was inserted at the start codon (N terminus fusion). Knock-in mice were generated using the Easi-CRISPR method. Developmental and adult SST and CCK expressions were preserved and showed an appropriate expression pattern in both models, with an active fluorescent tag in both animal lines. COMPARISON WITH EXISTING METHODS Knock-in mouse models to study cell types that produce these critically important molecules are limited to date. The knock-in mice we generated can be used as reporters to study development, physiology, or pathophysiology of SST and CCK expressing cells - without interference with native expression of SST and CCK. In addition, they can be used as Cre driver models to conditionally delete floxed genes in SST and CCK expressing cells across various tissues. CONCLUSIONS These two mouse models serve as valuable tools for in vitro and in vivo research studies related to SST and CCK biology across the lifespan and across different tissue types.
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Affiliation(s)
- Marta Balog
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center Omaha, NE, USA; Department of Medical Biology and Genetics, Faculty of Medicine, University of Osijek, Osijek, Croatia
| | - Allison Anderson
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center Omaha, NE, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA; Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
| | - Zeljka Korade
- Department of Pediatrics, University of Nebraska Medical Center Omaha, NE, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center Omaha, NE, USA; Child Health Research Institute, University of Nebraska Medical Center Omaha, NE, USA.
| | - Karoly Mirnics
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center Omaha, NE, USA; Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA; Department of Pediatrics, University of Nebraska Medical Center Omaha, NE, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center Omaha, NE, USA; Child Health Research Institute, University of Nebraska Medical Center Omaha, NE, USA.
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99
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Tanaka M, Yokoyama K, Hayashi H, Isaki S, Kitatani K, Wang T, Kawata H, Matsuzawa H, Gurumurthy CB, Miura H, Ohtsuka M. CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice. Genome Biol 2022; 23:228. [PMID: 36284311 PMCID: PMC9594901 DOI: 10.1186/s13059-022-02779-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesions or random insertions of donor DNAs. Simpler methods to identify off-target lesions and random insertions, using tail or earpiece DNA, are unavailable. We develop CRISPR-KRISPR (CRISPR-Knock-ins and Random Inserts Searching PRotocol), a method to identify both off-target lesions and random insertions. CRISPR-KRISPR uses as little as 3.4 μg of genomic DNA; thus, it can be easily incorporated as an additional step to genotype founder animals for further breeding.
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Affiliation(s)
- Masayuki Tanaka
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Keiko Yokoyama
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideki Hayashi
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Sanae Isaki
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Kanae Kitatani
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Ting Wang
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hisako Kawata
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideyuki Matsuzawa
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Channabasavaiah B. Gurumurthy
- grid.266813.80000 0001 0666 4105Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Genome Editing and Education Center Nebraska (GEEC-Nebraska), College of Medicine, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Hiromi Miura
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Masato Ohtsuka
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan ,grid.265061.60000 0001 1516 6626The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193 Japan
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100
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Development of an in vivo cleavable donor plasmid for targeted transgene integration by CRISPR-Cas9 and CRISPR-Cas12a. Sci Rep 2022; 12:17775. [PMID: 36272994 PMCID: PMC9588054 DOI: 10.1038/s41598-022-22639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
The CRISPR-Cas system is widely used for genome editing of cultured cells and organisms. The discovery of a new single RNA-guided endonuclease, CRISPR-Cas12a, in addition to the conventional CRISPR-Cas9 has broadened the number of editable target sites on the genome. Here, we developed an in vivo cleavable donor plasmid for precise targeted knock-in of external DNA by both Cas9 and Cas12a. This plasmid, named pCriMGET_9-12a (plasmid of synthetic CRISPR-coded RNA target sequence-equipped donor plasmid-mediated gene targeting via Cas9 and Cas12a), comprises the protospacer-adjacent motif sequences of Cas9 and Cas12a at the side of an off-target free synthetic CRISPR-coded RNA target sequence and a multiple cloning site for donor cassette insertion. pCriMGET_9-12a generates a linearized donor cassette in vivo by both CRISPR-Cas9 and CRISPR-Cas12a, which resulted in increased knock-in efficiency in culture cells. This method also achieved > 25% targeted knock-in of long external DNA (> 4 kb) in mice by both CRISPR-Cas9 and CRISPR-Cas12a. The pCriMGET_9-12a system expands the genomic target space for transgene knock-in and provides a versatile, low-cost, and high-performance CRISPR genome editing tool.
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