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Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling MC, Adams DJ, Bradley A, Braun RE, Brown SD, Caulder A, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Duddy G, Gertsenstein M, Goodwin LO, Hérault Y, Lintott LG, Lloyd KCK, Lorenzo I, Mackenzie M, Mallon AM, McKerlie C, Parkinson H, Ramirez-Solis R, Seavitt JR, Sedlacek R, Skarnes WC, Smedley D, Wells S, White JK, Wood JA, Murray SA, Heaney JD, Nutter LMJ. Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines. Sci Rep 2024; 14:22626. [PMID: 39349521 PMCID: PMC11443006 DOI: 10.1038/s41598-024-72418-8] [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: 04/03/2024] [Accepted: 09/06/2024] [Indexed: 10/02/2024] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps - generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease.
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Affiliation(s)
- Hillary Elrick
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | | | - Brandon J Willis
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
| | - Denise G Lanza
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elif F Acar
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Statistics, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- LGC Assure, Fordham, CB7 5WW, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marie-Christine Birling
- CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Allan Bradley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Trinity Lane, Cambridge, CB2 1TN, UK
| | | | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | - Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Francesco J DeMayo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Reproductive and Developmental Biology Laboratory, NIEHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brendan Doe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | | | - Yann Hérault
- CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
- Department of Surgery, School of Medicine, University of California Davis, Davis, CA, 95618, USA
| | - Isabel Lorenzo
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew Mackenzie
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | | | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ramiro Ramirez-Solis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- UT Health San Antonio, San Antonio, TX, 78229, USA
| | - John R Seavitt
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - William C Skarnes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Damien Smedley
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | | | - Joshua A Wood
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
| | | | - Jason D Heaney
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
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2
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Adkins-Threats M, Arimura S, Huang YZ, Divenko M, To S, Mao H, Zeng Y, Hwang JY, Burclaff JR, Jain S, Mills JC. Metabolic regulator ERRγ governs gastric stem cell differentiation into acid-secreting parietal cells. Cell Stem Cell 2024; 31:886-903.e8. [PMID: 38733994 PMCID: PMC11162331 DOI: 10.1016/j.stem.2024.04.016] [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: 06/06/2023] [Revised: 02/26/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Parietal cells (PCs) produce gastric acid to kill pathogens and aid digestion. Dysregulated PC census is common in disease, yet how PCs differentiate is unclear. Here, we identify the PC progenitors arising from isthmal stem cells, using mouse models and human gastric cells, and show that they preferentially express cell-metabolism regulator and orphan nuclear receptor Estrogen-related receptor gamma (Esrrg, encoding ERRγ). Esrrg expression facilitated the tracking of stepwise molecular, cellular, and ultrastructural stages of PC differentiation. EsrrgP2ACreERT2 lineage tracing revealed that Esrrg expression commits progenitors to differentiate into mature PCs. scRNA-seq indicated the earliest Esrrg+ PC progenitors preferentially express SMAD4 and SP1 transcriptional targets and the GTPases regulating acid-secretion signal transduction. As progenitors matured, ERRγ-dependent metabolic transcripts predominated. Organoid and mouse studies validated the requirement of ERRγ for PC differentiation. Our work chronicles stem cell differentiation along a single lineage in vivo and suggests ERRγ as a therapeutic target for PC-related disorders.
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Affiliation(s)
- Mahliyah Adkins-Threats
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Division of Biomedical and Biological Sciences, Washington University, St. Louis, MO 63130, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sumimasa Arimura
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang-Zhe Huang
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margarita Divenko
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah To
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heather Mao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongji Zeng
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jenie Y Hwang
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, TX 78249, USA
| | - Joseph R Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Shilpa Jain
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason C Mills
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Nieto-Romero V, García-Torralba A, Molinos-Vicente A, Moya FJ, Rodríguez-Perales S, García-Escudero R, Salido E, Segovia JC, García-Bravo M. Restored glyoxylate metabolism after AGXT gene correction and direct reprogramming of primary hyperoxaluria type 1 fibroblasts. iScience 2024; 27:109530. [PMID: 38577102 PMCID: PMC10993186 DOI: 10.1016/j.isci.2024.109530] [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: 04/03/2023] [Revised: 01/18/2024] [Accepted: 03/16/2024] [Indexed: 04/06/2024] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare inherited metabolic disorder characterized by oxalate overproduction in the liver, resulting in renal damage. It is caused by mutations in the AGXT gene. Combined liver and kidney transplantation is currently the only permanent curative treatment. We combined locus-specific gene correction and hepatic direct cell reprogramming to generate autologous healthy induced hepatocytes (iHeps) from PH1 patient-derived fibroblasts. First, site-specific AGXT corrected cells were obtained by homology directed repair (HDR) assisted by CRISPR-Cas9, following two different strategies: accurate point mutation (c.731T>C) correction or knockin of an enhanced version of AGXT cDNA. Then, iHeps were generated, by overexpression of hepatic transcription factors. Generated AGXT-corrected iHeps showed hepatic gene expression profile and exhibited in vitro reversion of oxalate accumulation compared to non-edited PH1-derived iHeps. This strategy set up a potential alternative cellular source for liver cell replacement therapy and a personalized PH1 in vitro disease model.
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Affiliation(s)
- Virginia Nieto-Romero
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Aida García-Torralba
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Andrea Molinos-Vicente
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Francisco José Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)-ISCIII, Research Institute Hospital 12 de Octubre (imas12)-University Hospital 12 de Octubre, 28040 Madrid, Spain
| | - Eduardo Salido
- Pathology Department, Hospital Universitario de Canarias, Universidad La Laguna, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 38320 Tenerife, Spain
| | - José-Carlos Segovia
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - María García-Bravo
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
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4
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Capin J, Harrison A, Raele RA, Yadav SKN, Baiwir D, Mazzucchelli G, Quinton L, Satchwell T, Toye A, Schaffitzel C, Berger I, Aulicino F. An engineered baculoviral protein and DNA co-delivery system for CRISPR-based mammalian genome editing. Nucleic Acids Res 2024; 52:3450-3468. [PMID: 38412306 PMCID: PMC11014373 DOI: 10.1093/nar/gkae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
CRISPR-based DNA editing technologies enable rapid and accessible genome engineering of eukaryotic cells. However, the delivery of genetically encoded CRISPR components remains challenging and sustained Cas9 expression correlates with higher off-target activities, which can be reduced via Cas9-protein delivery. Here we demonstrate that baculovirus, alongside its DNA cargo, can be used to package and deliver proteins to human cells. Using protein-loaded baculovirus (pBV), we demonstrate delivery of Cas9 or base editors proteins, leading to efficient genome and base editing in human cells. By implementing a reversible, chemically inducible heterodimerization system, we show that protein cargoes can selectively and more efficiently be loaded into pBVs (spBVs). Using spBVs we achieved high levels of multiplexed genome editing in a panel of human cell lines. Importantly, spBVs maintain high editing efficiencies in absence of detectable off-targets events. Finally, by exploiting Cas9 protein and template DNA co-delivery, we demonstrate up to 5% site-specific targeted integration of a 1.8 kb heterologous DNA payload using a single spBV in a panel of human cell lines. In summary, we demonstrate that spBVs represent a versatile, efficient and potentially safer alternative for CRISPR applications requiring co-delivery of DNA and protein cargoes.
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Affiliation(s)
- Julien Capin
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Alexandra Harrison
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Renata A Raele
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Sathish K N Yadav
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, B-4000 Liege, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Loic Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Timothy J Satchwell
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | - Ashley M Toye
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
| | | | - Imre Berger
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Francesco Aulicino
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK
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5
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Couasnay G, Garcia H, Elefteriou F. A comparative analysis of TonEBP conditional knockout mouse models reveals inter-dependency between compartments of the intervertebral disc. Development 2024; 151:dev202354. [PMID: 38421307 PMCID: PMC11006390 DOI: 10.1242/dev.202354] [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: 09/13/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Interactions between notochord and sclerotome are required for normal embryonic spine patterning, but whether the postnatal derivatives of these tissues also require interactions for postnatal intervertebral disc (IVD) growth and maintenance is less established. We report here the comparative analysis of four conditional knockout mice deficient for TonEBP, a transcription factor known to allow cells to adapt to changes in extracellular osmotic pressure, in specific compartments of the IVD. We show that TonEBP deletion in nucleus pulposus (NP) cells does not affect their survival or aggrecan expression, but promoted cell proliferation in the NP and in adjacent vertebral growth plates (GPs). In cartilage end plates/GPs, TonEBP deletion induced cell death, but also structural alterations in the adjacent NP cells and vertebral bodies. Embryonic or postnatal TonEBP loss generated similar IVD changes. In addition to demonstrating the requirement of TonEBP in the different compartments of the IVD, this comparative analysis uncovers the in vivo interdependency of the different IVD compartments during the growth of the postnatal IVD-vertebral units.
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Affiliation(s)
- Greig Couasnay
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haley Garcia
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Florent Elefteriou
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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6
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McCabe CV, Price PD, Codner GF, Allan AJ, Caulder A, Christou S, Loeffler J, Mackenzie M, Malzer E, Mianné J, Nowicki KJ, O’Neill EJ, Pike FJ, Hutchison M, Petit-Demoulière B, Stewart ME, Gates H, Wells S, Sanderson ND, Teboul L. Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods. PLoS Genet 2024; 20:e1011187. [PMID: 38457464 PMCID: PMC10954187 DOI: 10.1371/journal.pgen.1011187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/20/2024] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Recent developments in CRISPR/Cas9 genome-editing tools have facilitated the introduction of precise alleles, including genetic intervals spanning several kilobases, directly into the embryo. However, the introduction of donor templates, via homology directed repair, can be erroneous or incomplete and these techniques often produce mosaic founder animals. Thus, newly generated alleles must be verified at the sequence level across the targeted locus. Screening for the presence of the desired mutant allele using traditional sequencing methods can be challenging due to the size of the interval to be sequenced, together with the mosaic nature of founders. METHODOLOGY/PRINCIPAL FINDINGS In order to help disentangle the genetic complexity of these animals, we tested the application of Oxford Nanopore Technologies long-read sequencing at the targeted locus and found that the achievable depth of sequencing is sufficient to offset the sequencing error rate associated with the technology used to validate targeted regions of interest. We have assembled an analysis workflow that facilitates interrogating the entire length of a targeted segment in a single read, to confirm that the intended mutant sequence is present in both heterozygous animals and mosaic founders. We used this workflow to compare the output of PCR-based and Cas9 capture-based targeted sequencing for validation of edited alleles. CONCLUSION Targeted long-read sequencing supports in-depth characterisation of all experimental models that aim to produce knock-in or conditional alleles, including those that contain a mix of genome-edited alleles. PCR- or Cas9 capture-based modalities bring different advantages to the analysis.
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Affiliation(s)
| | - Peter D. Price
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Gemma F. Codner
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Elke Malzer
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | | | - Fran J. Pike
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Benoit Petit-Demoulière
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, Illkirch, France
| | | | - Hilary Gates
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
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7
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Perez GA, Park KW, Lanza D, Cicardo J, Danish Uddin M, Jankowsky JL. Generation of a Dcx-CreER T2 knock-in mouse for genetic manipulation of newborn neurons. Genesis 2024; 62:e23584. [PMID: 38102875 PMCID: PMC11021165 DOI: 10.1002/dvg.23584] [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: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
A wide variety of CreERT2 driver lines are available for genetic manipulation of adult-born neurons in the mouse brain. These tools have been instrumental in studying fate potential, migration, circuit integration, and morphology of the stem cells supporting lifelong neurogenesis. Despite a wealth of tools, genetic manipulation of adult-born neurons for circuit and behavioral studies has been limited by poor specificity of many driver lines targeting early progenitor cells and by the inaccessibility of lines selective for later stages of neuronal maturation. We sought to address these limitations by creating a new CreERT2 driver line targeted to the endogenous mouse doublecortin locus as a marker of fate-specified neuroblasts and immature neurons. Our new model places a T2A-CreERT2 cassette immediately downstream of the Dcx coding sequence on the X chromosome, allowing expression of both Dcx and CreERT2 proteins in the endogenous spatiotemporal pattern for this gene. We demonstrate that the new mouse line drives expression of a Cre-dependent reporter throughout the brain in neonatal mice and in known neurogenic niches of adult animals. The line has been deposited with the Jackson Laboratory and should provide an accessible tool for studies targeting fate-restricted neuronal precursors.
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Affiliation(s)
- Gabriella A. Perez
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Kyung-Won Park
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Denise Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Jenna Cicardo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - M. Danish Uddin
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Joanna L. Jankowsky
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Departments of Neurology, Neurosurgery, and Molecular and Cellular Biology, Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
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8
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Felix JB, Saha PK, de Groot E, Tan L, Sharp R, Anaya ES, Li Y, Quang H, Saidi N, Abushamat L, Ballantyne CM, Amos CI, Lorenzi PL, Klein S, Gao X, Hartig SM. N-acetylaspartate from fat cells regulates postprandial body temperature. RESEARCH SQUARE 2024:rs.3.rs-3835159. [PMID: 38260478 PMCID: PMC10802732 DOI: 10.21203/rs.3.rs-3835159/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
N-acetylaspartate (NAA), the brain's second most abundant metabolite, provides essential substrates for myelination through its hydrolysis. However, activities and physiological roles of NAA in other tissues remain unknown. Here, we show aspartoacylase (ASPA) expression in white adipose tissue (WAT) governs systemic NAA levels for postprandial body temperature regulation. Proteomics and mass spectrometry revealed NAA accumulation in WAT of Aspa knockout mice stimulated the pentose phosphate pathway and pyrimidine production. Stable isotope tracing confirmed higher incorporation of glucose-derived carbon into pyrimidine metabolites in Aspa knockout cells. Additionally, serum NAA positively correlates with the pyrimidine intermediate orotidine and this relationship predicted lower body mass index in humans. Using whole-body and tissue-specific knockout mouse models, we demonstrate that fat cells provided plasma NAA and suppressed postprandial body temperature elevation. Furthermore, exogenous NAA supplementation reduced body temperature. Our study unveils WAT-derived NAA as an endocrine regulator of postprandial body temperature and physiological homeostasis.
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Affiliation(s)
- Jessica B. Felix
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Pradip K. Saha
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Evelyn de Groot
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Cancer and Cellular Biology Program, Baylor College of Medicine, Houston, TX
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Robert Sharp
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Elizabeth S. Anaya
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Cancer and Cellular Biology Program, Baylor College of Medicine, Houston, TX
| | - Yafang Li
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Holly Quang
- Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine
| | - Nooshin Saidi
- Data Sciences Program, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD
| | - Layla Abushamat
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Christie M. Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Christopher I. Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO
| | - Xia Gao
- Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine
| | - Sean M. Hartig
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
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9
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Lancaster MS, Kim B, Doud EH, Tate MD, Sharify AD, Gao H, Chen D, Simpson E, Gillespie P, Chu X, Miller MJ, Wang Y, Liu Y, Mosley AL, Kim J, Graham BH. Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism. Cell Rep 2023; 42:113241. [PMID: 37819759 PMCID: PMC10683835 DOI: 10.1016/j.celrep.2023.113241] [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: 08/08/2022] [Revised: 08/24/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Lysine succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the tricarboxylic acid cycle. Deficiency of succinyl-CoA synthetase (SCS), the tricarboxylic acid cycle enzyme catalyzing the interconversion of succinyl-CoA to succinate, results in mitochondrial encephalomyopathy in humans. This report presents a conditional forebrain-specific knockout (KO) mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that accumulation of succinyl-CoA in the absence of SCS leads to hypersuccinylation within the murine cerebral cortex. Specifically, increased succinylation is associated with functionally significant reduced activity of respiratory chain complex I and widescale alterations in chromatin landscape and gene expression. Integrative analysis of the transcriptomic data also reveals perturbations in regulatory networks of neuronal transcription in the KO forebrain. Together, these findings provide evidence that protein succinylation plays a significant role in the pathogenesis of SCS deficiency.
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Affiliation(s)
- Makayla S Lancaster
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Byungwook Kim
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mason D Tate
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ahmad D Sharify
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ed Simpson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Patrick Gillespie
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiaona Chu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jungsu Kim
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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10
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Lee CS, Jung SY, Yee RSZ, Agha NH, Hong J, Chang T, Babcock LW, Fleischman JD, Clayton B, Hanna AD, Ward CS, Lanza D, Hurley AE, Zhang P, Wehrens XHT, Lagor WR, Rodney GG, Hamilton SL. Speg interactions that regulate the stability of excitation-contraction coupling protein complexes in triads and dyads. Commun Biol 2023; 6:942. [PMID: 37709832 PMCID: PMC10502019 DOI: 10.1038/s42003-023-05330-y] [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: 04/03/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023] Open
Abstract
Here we show that striated muscle preferentially expressed protein kinase α (Spegα) maintains cardiac function in hearts with Spegβ deficiency. Speg is required for stability of excitation-contraction coupling (ECC) complexes and interacts with esterase D (Esd), Cardiomyopathy-Associated Protein 5 (Cmya5), and Fibronectin Type III and SPRY Domain Containing 2 (Fsd2) in cardiac and skeletal muscle. Mice with a sequence encoding a V5/HA tag inserted into the first exon of the Speg gene (HA-Speg mice) display a >90% decrease in Spegβ but Spegα is expressed at ~50% of normal levels. Mice deficient in both Spegα and Speg β (Speg KO mice) develop a severe dilated cardiomyopathy and muscle weakness and atrophy, but HA-Speg mice display mild muscle weakness with no cardiac involvement. Spegα in HA-Speg mice suppresses Ca2+ leak, proteolytic cleavage of Jph2, and disruption of transverse tubules. Despite it's low levels, HA-Spegβ immunoprecipitation identified Esd, Cmya5 and Fsd2 as Spegβ binding partners that localize to triads and dyads to stabilize ECC complexes. This study suggests that Spegα and Spegβ display functional redundancy, identifies Esd, Cmya5 and Fsd2 as components of both cardiac dyads and skeletal muscle triads and lays the groundwork for the identification of new therapeutic targets for centronuclear myopathy.
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Affiliation(s)
- Chang Seok Lee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Rachel Sue Zhen Yee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Nadia H Agha
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Jin Hong
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Ting Chang
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Lyle W Babcock
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Jorie D Fleischman
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Benjamin Clayton
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Amy D Hanna
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Christopher S Ward
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Denise Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Ayrea E Hurley
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Pumin Zhang
- The First Affiliated Hospital, Zhejiang University Medical School, Hangzhou, China
| | - Xander H T Wehrens
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - William R Lagor
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - George G Rodney
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Susan L Hamilton
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77096, USA.
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11
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Wang M, Chen Q, Wang S, Xie H, Liu J, Huang R, Xiang Y, Jiang Y, Tian D, Bian E. Super-enhancers complexes zoom in transcription in cancer. J Exp Clin Cancer Res 2023; 42:183. [PMID: 37501079 PMCID: PMC10375641 DOI: 10.1186/s13046-023-02763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.
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Affiliation(s)
- MengTing Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - QingYang Chen
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - ShuJie Wang
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - RuiXiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YuFei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YanYi Jiang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - DaSheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - ErBao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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12
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Maurya VK, Ying Y, Lanza DG, Heaney JD, Lydon JP. A CRISPR/Cas9-engineered mouse carrying a conditional knockout allele for the early growth response-1 transcription factor. Genesis 2023; 61:e23515. [PMID: 36949241 PMCID: PMC10514223 DOI: 10.1002/dvg.23515] [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: 01/11/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/24/2023]
Abstract
Early growth response 1 (EGR1) mediates transcriptional programs that are indispensable for cell division, differentiation, and apoptosis in numerous physiologies and pathophysiologies. Whole-body EGR1 knockouts in mice (Egr1KO ) have advanced our understanding of EGR1 function in an in vivo context. To extend the utility of the mouse to investigate EGR1 responses in a tissue- and/or cell-type-specific manner, we generated a mouse model in which exon 2 of the mouse Egr1 gene is floxed by CRISPR/Cas9 engineering. The floxed Egr1 alleles (Egr1f/f ) are designed to enable spatiotemporal control of Cre-mediated EGR1 ablation in the mouse. To confirm that the Egr1f/f alleles can be abrogated using a Cre driver, we crossed the Egr1f/f mouse with a global Cre driver to generate the Egr1 conditional knockout (Egr1d/d ) mouse in which EGR1 expression is ablated in all tissues. Genetic and protein analysis confirmed the absence of exon 2 and loss of EGR1 expression in the Egr1d/d mouse, respectively. Moreover, the Egr1d/d female exhibits overt reproductive phenotypes previously reported for the Egr1KO mouse. Therefore, studies described in this short technical report underscore the potential utility of the murine Egr1 floxed allele to further resolve EGR1 function at a tissue- and/or cell-type-specific level.
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Affiliation(s)
- Vineet K. Maurya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Yan Ying
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Denise G. Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
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13
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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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14
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Cassidy A, Pelletier S. CRISPR-Cas9-mediated insertion of a short artificial intron for the generation of conditional alleles in mice. STAR Protoc 2023; 4:102116. [PMID: 36853660 PMCID: PMC9943854 DOI: 10.1016/j.xpro.2023.102116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/11/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
In this protocol, we describe the generation of conditional alleles in mice using the DECAI (DEgradation based on Cre-regulated Artificial Intron) approach. We detail steps for the CRISPR-mediated insertion of the short DECAI cassette within exon 3 of Scyl1 and the functional validation of alleles at genomic, transcriptomic, and protein levels. This strategy simplifies the process of generating mice with conditional alleles. For complete details on the use and execution of this protocol, please refer to Cassidy et al. (2022).1.
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Affiliation(s)
- Annelise Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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15
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Qin X, Xie C, Hakenjos JM, MacKenzie KR, Boyd SR, Barzi M, Bissig KD, Young DW, Li F. The roles of Cyp1a2 and Cyp2d in pharmacokinetic profiles of serotonin and norepinephrine reuptake inhibitor duloxetine and its metabolites in mice. Eur J Pharm Sci 2023; 181:106358. [PMID: 36513193 PMCID: PMC10395004 DOI: 10.1016/j.ejps.2022.106358] [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: 09/20/2022] [Revised: 11/03/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Duloxetine (DLX) is widely used to treat major depressive disorder. Little is known about the mechanistic basis for DLX-related adverse effects (e.g., liver injury). Human CYP1A2 and CYP2D6 mainly contributes to DLX metabolism, which was proposed to be involved in its adverse effects. Here, we investigated the roles of Cyp1a2 and Cyp2d on DLX pharmacokinetic profile and tissue distribution using a Cyp1a2 knockout (Cyp1a2-KO) mouse model together with a Cyp2d inhibitor (propranolol). Cyp1a2-KO has the few effects on the systematic exposure (area under the plasma concentration-time curve, AUC) and tissue disposition of DLX and its primary metabolites. Propranolol dramatically increased the AUCs of DLX by 3 folds and 1.5 folds in WT and Cyp1a2-KO mice, respectively. Meanwhile, Cyp2d inhibitor decreased the AUC of Cyp2d-involved DLX metabolites (e.g., M16). Mouse tissue distribution revealed that DLX and its major metabolites were the most abundant in kidney, followed by liver and lung with/without Cyp2d inhibitor. Cyp2d inhibitor significantly increased DLX levels in tissues (e.g., liver) in WT and KO mice and decreases the levels of M3, M15, M16 and M17, while it increased the levels of M4, M28 and M29 in tissues. Our findings indicated that Cyp2d play a fundamental role on DLX pharmacokinetic profile and tissue distribution in mice. Clinical studies suggested that CYP1A2 has more effects on DLX systemic exposure than CYP2D6. Further studies in liver humanized mice or clinical studies concerning CYP2D6 inhibitors-DLX interaction study could clarify the roles of CYP2D6 on DLX pharmacokinetics and toxicity in human.
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Affiliation(s)
- Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cen Xie
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelton R Boyd
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mercedes Barzi
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27708, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27708, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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16
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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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17
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Mackenzie M, Fower A, Allan AJ, Codner GF, Bunton-Stasyshyn RK, Teboul L. Genotyping Genome-Edited Founders and Subsequent Generation. Methods Mol Biol 2023; 2631:103-134. [PMID: 36995665 DOI: 10.1007/978-1-0716-2990-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Targeted nucleases allow the production of many types of genetic mutations directly in the early embryo. However, the outcome of their activity is a repair event of unpredictable nature, and the founder animals that are produced are generally of a mosaic nature. Here, we present the molecular assays and genotyping strategies that will support the screening of the first generation for potential founders and the validation of positive animals in the subsequent generation, according to the type of mutation generated.
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Affiliation(s)
| | - Alex Fower
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK
| | | | | | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK.
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18
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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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19
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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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20
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Garza S, Paik R. CRISPR/Cas9 Endonuclease-Mediated Mouse Genome Editing of One-Cell and/or Two-Cell Embryos by Electroporation, and the Use of Rad51 to Enhance Knock-In Allele Homozygosity via Interhomolog Repair Mechanism. Methods Mol Biol 2023; 2631:253-266. [PMID: 36995671 DOI: 10.1007/978-1-0716-2990-1_10] [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
Electroporation of mouse embryos with CRISPR/Cas9 endonuclease tool is a facile and efficient method to edit endogenous genome sequences for generating genetically engineered mouse models (GEMMs). Common genome engineering projects, such as knock-out (KO), conditional knock-out (cKO), point mutation, and small foreign DNA (<1 Kb) knock-in (KI) alleles, can be effectively accomplished with a simple electroporation procedure. The use of electroporation in sequential gene editing at the one-cell (0.7 days post-coitum (dpc)) and at two-cell (1.5 dpc) embryonic stages provides a fast and compelling protocol to safely introduce multiple gene modifications on the same chromosome by limiting chromosomal fractures. In addition, the co-electroporation of the ribonucleoprotein (RNP) complex and single-stranded oligodeoxynucleotide (ssODN) donor DNA with the strand exchange protein Rad51 can significantly increase the number of homozygous founders. Here we describe a comprehensive guideline for mouse embryo electroporation to generate GEMMs and the implementation of Rad51 in RNP/ssODN complex EP medium protocol.
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Affiliation(s)
- Selika Garza
- Rodent Genome Engineering Core, University of Texas Health San Antonio, San Antonio, TX, USA
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21
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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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22
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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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23
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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] [MESH Headings] [Grants] [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
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan.
| | - Keiko Yokoyama
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Hideki Hayashi
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Sanae Isaki
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Kanae Kitatani
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Ting Wang
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Hisako Kawata
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Hideyuki Matsuzawa
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
- Genome Editing and Education Center Nebraska (GEEC-Nebraska), College of Medicine, 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
| | - Hiromi Miura
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan.
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan.
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24
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Aulicino F, Pelosse M, Toelzer C, Capin J, Ilegems E, Meysami P, Rollarson R, Berggren PO, Dillingham M, Schaffitzel C, Saleem M, Welsh G, Berger I. Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus. Nucleic Acids Res 2022; 50:7783-7799. [PMID: 35801912 PMCID: PMC9303279 DOI: 10.1093/nar/gkac587] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
CRISPR-based precise gene-editing requires simultaneous delivery of multiple components into living cells, rapidly exceeding the cargo capacity of traditional viral vector systems. This challenge represents a major roadblock to genome engineering applications. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck in human cells. By encoding Cas9, sgRNA and Donor DNAs on a single, rapidly assembled baculoviral vector, we achieve with up to 30% efficacy whole-exon replacement in the intronic β-actin (ACTB) locus, including site-specific docking of very large DNA payloads. We use our approach to rescue wild-type podocin expression in steroid-resistant nephrotic syndrome (SRNS) patient derived podocytes. We demonstrate single baculovirus vectored delivery of single and multiplexed prime-editing toolkits, achieving up to 100% cleavage-free DNA search-and-replace interventions without detectable indels. Taken together, we provide a versatile delivery platform for single base to multi-gene level genome interventions, addressing the currently unmet need for a powerful delivery system accommodating current and future CRISPR technologies without the burden of limited cargo capacity.
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Affiliation(s)
- Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Martin Pelosse
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christine Toelzer
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Julien Capin
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Erwin Ilegems
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Parisa Meysami
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Ruth Rollarson
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Mark Simon Dillingham
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christiane Schaffitzel
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Moin A Saleem
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Gavin I Welsh
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Imre Berger
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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25
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Hillen AEJ, Hruzova M, Rothgangl T, Breur M, Bugiani M, van der Knaap MS, Schwank G, Heine VM. In vivo targeting of a variant causing vanishing white matter using CRISPR/Cas9. Mol Ther Methods Clin Dev 2022; 25:17-25. [PMID: 35317047 PMCID: PMC8917273 DOI: 10.1016/j.omtm.2022.02.006] [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: 08/27/2021] [Accepted: 02/19/2022] [Indexed: 11/17/2022]
Abstract
Vanishing white matter (VWM) is a leukodystrophy caused by recessive variants in subunits of eIF2B. At present, no curative treatment is available and patients often die at young age. Due to its monogenic nature, VWM is a promising candidate for the development of CRISPR/Cas9-mediated gene therapy. Here we tested a dual-AAV approach in VWM mice encoding CRISPR/Cas9 and a DNA donor template to correct a pathogenic variant in Eif2b5. We performed sequencing analysis to assess gene correction rates and examined effects on the VWM phenotype, including motor behavior. Sequence analysis demonstrated that over 90% of CRISPR/Cas9-induced edits at the targeted locus are insertion or deletion (indel) mutations, rather than precise corrections from the DNA donor template by homology-directed repair. Around half of the CRISPR/Cas9-treated animals died prematurely. VWM mice showed no improvement in motor skills, weight, or neurological scores at 7 months of age, and CRISPR/Cas9-treated controls displayed an induced VWM phenotype. In conclusion, CRISPR/Cas9-induced DNA double-strand breaks (DSBs) at the Eif2b5 locus did not lead to sufficient correction of the VWM variant. Moreover, indel formation in Eif2b5 induced an exacerbated VWM phenotype. Therefore, DSB-independent strategies like base- or prime editing might better suited for VWM correction.
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Affiliation(s)
- Anne E J Hillen
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Marjolein Breur
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marianna Bugiani
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vivi M Heine
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands.,Department of Child and Adolescence Psychiatry, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
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26
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Bernas G, Ouellet M, Barrios A, Jamann H, Larochelle C, Lévy É, Schmouth JF. Introduction of loxP sites by electroporation in the mouse genome; a simple approach for conditional allele generation in complex targeting loci. BMC Biotechnol 2022; 22:14. [PMID: 35549895 PMCID: PMC9097428 DOI: 10.1186/s12896-022-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
Background The discovery of the CRISPR-Cas9 system and its applicability in mammalian embryos has revolutionized the way we generate genetically engineered animal models. To date, models harbouring conditional alleles (i.e. two loxP sites flanking an exon or a critical DNA sequence of interest) are amongst the most widely requested project type that are challenging to generate as they require simultaneous cleavage of the genome using two guides in order to properly integrate the repair template. An approach, using embryo sequential electroporation has been reported in the literature to successfully introduce loxP sites on the same allele. Here, we describe a modification of this sequential electroporation procedure that demonstrated the production of conditional allele mouse models for eight different genes via one of two possible strategies: either by consecutive sequential electroporation (strategy A) or non-consecutive sequential electroporation (strategy B). This latest strategy originated from using the by-product produced when using consecutive sequential electroporation (i.e. mice with a single targeted loxP site) to complete the project.
Results By using strategy A, we demonstrated successful generation of conditional allele models for three different genes (Icam1, Lox, and Sar1b), with targeting efficiencies varying between 5 and 13%. By using strategy B, we generated five conditional allele models (Loxl1, Pard6a, Pard6g, Clcf1, and Mapkapk5), with targeting efficiencies varying between 3 and 25%. Conclusion Our modified electroporation-based approach, involving one of the two alternative strategies, allowed the production of conditional allele models for eight different genes via two different possible paths. This reproducible method will serve as another reliable approach in addition to other well-established methodologies in the literature for conditional allele mouse model generation.
Supplementary Information The online version contains supplementary material available at 10.1186/s12896-022-00744-8.
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Affiliation(s)
- Guillaume Bernas
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada
| | - Mariette Ouellet
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada
| | - Andréa Barrios
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada
| | - Hélène Jamann
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada.,Département de Neurosciences, Université de Montréal, Montréal, Canada
| | - Catherine Larochelle
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada.,Département de Neurosciences, Université de Montréal, Montréal, Canada
| | - Émile Lévy
- Centre de recherche du CHU Ste-Justine, Université de Montréal, Montréal, Canada.,Département de Pharmacologie et physiologie, Université de Montréal, Montréal, Canada.,Département de Nutrition, Université de Montréal, Montréal, Canada
| | - Jean-François Schmouth
- Centre de recherche du CHUM, Université de Montréal, Montréal, Canada. .,Département de Neurosciences, Université de Montréal, Montréal, Canada.
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27
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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28
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Ang JXD, Nevard K, Ireland R, Purusothaman DK, Verkuijl SAN, Shackleford L, Gonzalez E, Anderson MAE, Alphey L. Considerations for homology-based DNA repair in mosquitoes: Impact of sequence heterology and donor template source. PLoS Genet 2022; 18:e1010060. [PMID: 35180218 PMCID: PMC8893643 DOI: 10.1371/journal.pgen.1010060] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/03/2022] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
The increasing prevalence of insecticide resistance and the ongoing global burden of vector-borne diseases have encouraged new efforts in mosquito control. For Aedes aegypti, the most important arboviral vector, integration rates achieved in Cas9-based knock-ins so far have been rather low, highlighting the need to understand gene conversion patterns and other factors that influence homology-directed repair (HDR) events in this species. In this study, we report the effects of sequence mismatches or donor template forms on integration rates. We found that modest sequence differences between construct homology arms [DNA sequence in the donor template which resembles the region flanking the target cut] and genomic target comprising 1.2% nucleotide dissimilarity (heterology) significantly reduced integration rates. While most integrations (59-88%) from plasmid templates were the result of canonical [on target, perfect repair] HDR events, no canonical events were identified from other donor types (i.e. ssDNA, biotinylated ds/ssDNA). Sequencing of the transgene flanking region in 69 individuals with canonical integrations revealed 60% of conversion tracts to be unidirectional and extend up to 220 bp proximal to the break, though in three individuals bidirectional conversion of up to 725 bp was observed.
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Affiliation(s)
| | | | | | | | - Sebald A. N. Verkuijl
- The Pirbright Institute, Pirbright, Woking, United Kingdom
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Luke Alphey
- The Pirbright Institute, Pirbright, Woking, United Kingdom
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29
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Kuno A, Ikeda Y, Ayabe S, Kato K, Sakamoto K, Suzuki SR, Morimoto K, Wakimoto A, Mikami N, Ishida M, Iki N, Hamada Y, Takemura M, Daitoku Y, Tanimoto Y, Dinh TTH, Murata K, Hamada M, Muratani M, Yoshiki A, Sugiyama F, Takahashi S, Mizuno S. DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biol 2022; 20:e3001507. [PMID: 35041655 PMCID: PMC8765641 DOI: 10.1371/journal.pbio.3001507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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Affiliation(s)
- Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Ikeda
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Sakamoto
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Sayaka R. Suzuki
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Arata Wakimoto
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Natsuki Mikami
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Natsumi Iki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Megumi Takemura
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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Abstract
The emergence of an array of genome-editing tools in recent years has facilitated the introduction of genetic modifications directly into the embryo, increasing the ease, efficiency and catalogue of alleles accessible to researchers across a range of species. Bypassing the requirement for a selection cassette and resulting in a broad range of outcomes besides the desired allele, genome editing has altered the allele validation process both temporally and technically. Whereas traditional gene targeting relies upon selection and allows allele validation at the embryonic stem cell modification stage, screening for the presence of the intended allele now occurs in the (frequently mosaic) founder animals. Final confirmation of the edited allele can only take place at the subsequent G1 generation and the validation strategy must differentiate the desired allele from a range of unintended outcomes. Here we present some of the challenges posed by gene editing, strategies for validation and considerations for animal colony management.
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Affiliation(s)
| | - Gemma F Codner
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, UK
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31
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Gertsenstein M, Nutter LMJ. Production of knockout mouse lines with Cas9. Methods 2021; 191:32-43. [PMID: 33524495 DOI: 10.1016/j.ymeth.2021.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/05/2020] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
Knockout mice are used extensively to explore the phenotypic effects of mammalian gene dysfunction. With the application of RNA-guided Cas9 nuclease technology for the production of knockout mouse lines, the time, as well as the resources needed, to progress from identification of a gene of interest to production of a knockout line is significantly reduced. Here we present our standard methodology to produce knockout mouse lines by the electroporation of Cas9 ribonucleoprotein (RNP) into mouse zygotes. Using this protocol, we have obtained an 80% success rate in the generation of founders for null alleles with a subsequent 93% germline transmission rate. These methods rely on equipment already present in the majority of transgenic facilities and should be straightforward to implement where appropriate embryo handling expertise exists.
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Affiliation(s)
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto M5T 3H7, Canada; The Hospital for Sick Children, Toronto M5G 1X8, Canada
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32
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O'Hagan D, Kruger RE, Gu B, Ralston A. Efficient generation of endogenous protein reporters for mouse development. Development 2021; 148:269311. [PMID: 34036333 PMCID: PMC8276983 DOI: 10.1242/dev.197418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/20/2021] [Indexed: 01/09/2023]
Abstract
Fluorescent proteins and epitope tags can reveal protein localization in cells and animals, yet the large size of many tags hinders efficient genome targeting. Accordingly, many studies have relied on characterizing overexpressed proteins, which might not recapitulate endogenous protein activities. Here, we present two strategies for higher throughput production of endogenous protein reporters in mice, focusing on the blastocyst model of development. Our first strategy makes use of a split fluorescent protein, mNeonGreen2 (mNG2). Knock-in of a small portion of the mNG2 gene, in frame with gene coding regions of interest, was highly efficient in embryos, potentially obviating the need to establish mouse lines. When complemented by the larger portion of the mNG2 gene, fluorescence was reconstituted and endogenous protein localization faithfully reported in living embryos. Our second strategy achieves in-frame knock-in of a relatively small protein tag, which provides high efficiency and higher sensitivity protein reporting. Together, these two approaches provide complementary advantages and enable broad downstream applications.
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Affiliation(s)
- Daniel O'Hagan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robin E Kruger
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI 48824, USA
| | - Bin Gu
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Amy Ralston
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI 48824, USA
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Zhang X, Li T, Ou J, Huang J, Liang P. Homology-based repair induced by CRISPR-Cas nucleases in mammalian embryo genome editing. Protein Cell 2021; 13:316-335. [PMID: 33945139 PMCID: PMC9008090 DOI: 10.1007/s13238-021-00838-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genome editing, especially CRISPR-Cas nucleases, have revolutionized both laboratory research and clinical therapeutics. CRISPR-Cas nucleases, together with the DNA damage repair pathway in cells, enable both genetic diversification by classical non-homologous end joining (c-NHEJ) and precise genome modification by homology-based repair (HBR). Genome editing in zygotes is a convenient way to edit the germline, paving the way for animal disease model generation, as well as human embryo genome editing therapy for some life-threatening and incurable diseases. HBR efficiency is highly dependent on the DNA donor that is utilized as a repair template. Here, we review recent progress in improving CRISPR-Cas nuclease-induced HBR in mammalian embryos by designing a suitable DNA donor. Moreover, we want to provide a guide for producing animal disease models and correcting genetic mutations through CRISPR-Cas nuclease-induced HBR in mammalian embryos. Finally, we discuss recent developments in precise genome-modification technology based on the CRISPR-Cas system.
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Affiliation(s)
- Xiya Zhang
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Tao Li
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Jianping Ou
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China.
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Webster NJ, Maywald RL, Benton SM, Dawson EP, Murillo OD, LaPlante EL, Milosavljevic A, Lanza DG, Heaney JD. Testicular germ cell tumors arise in the absence of sex-specific differentiation. Development 2021; 148:260592. [PMID: 33912935 DOI: 10.1242/dev.197111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/22/2021] [Indexed: 01/09/2023]
Abstract
In response to signals from the embryonic testis, the germ cell intrinsic factor NANOS2 coordinates a transcriptional program necessary for the differentiation of pluripotent-like primordial germ cells toward a unipotent spermatogonial stem cell fate. Emerging evidence indicates that genetic risk factors contribute to testicular germ cell tumor initiation by disrupting sex-specific differentiation. Here, using the 129.MOLF-Chr19 mouse model of testicular teratomas and a NANOS2 reporter allele, we report that the developmental phenotypes required for tumorigenesis, including failure to enter mitotic arrest, retention of pluripotency and delayed sex-specific differentiation, were exclusive to a subpopulation of germ cells failing to express NANOS2. Single-cell RNA sequencing revealed that embryonic day 15.5 NANOS2-deficient germ cells and embryonal carcinoma cells developed a transcriptional profile enriched for MYC signaling, NODAL signaling and primed pluripotency. Moreover, lineage-tracing experiments demonstrated that embryonal carcinoma cells arose exclusively from germ cells failing to express NANOS2. Our results indicate that NANOS2 is the nexus through which several genetic risk factors influence tumor susceptibility. We propose that, in the absence of sex specification, signals native to the developing testis drive germ cell transformation.
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Affiliation(s)
- Nicholas J Webster
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca L Maywald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Benton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily P Dawson
- Department of Cell Biology, New York University, New York, NY 10003, USA
| | - Oscar D Murillo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily L LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Chenouard V, Remy S, Tesson L, Ménoret S, Ouisse LH, Cherifi Y, Anegon I. Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. Front Genet 2021; 12:615491. [PMID: 33959146 PMCID: PMC8093876 DOI: 10.3389/fgene.2021.615491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
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Affiliation(s)
- Vanessa Chenouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- genOway, Lyon, France
| | - Séverine Remy
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Laurent Tesson
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Séverine Ménoret
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes Université, Nantes, France
| | - Laure-Hélène Ouisse
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | | | - Ignacio Anegon
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
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Cox AR, Chernis N, Kim KH, Masschelin PM, Saha PK, Briley SM, Sharp R, Li X, Felix JB, Sun Z, Moore DD, Pangas SA, Hartig SM. Ube2i deletion in adipocytes causes lipoatrophy in mice. Mol Metab 2021; 48:101221. [PMID: 33771728 PMCID: PMC8080079 DOI: 10.1016/j.molmet.2021.101221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Objective White adipose tissue (WAT) expansion regulates energy balance and overall metabolic homeostasis. The absence or loss of WAT occurring through lipodystrophy and lipoatrophy contributes to the development of hepatic steatosis and insulin resistance. We previously demonstrated that sole small ubiquitin-like modifier (SUMO) E2-conjugating enzyme Ube2i represses human adipocyte differentiation. The role of Ube2i during WAT development remains unknown. Methods To determine how Ube2i impacts body composition and energy balance, we generated adipocyte-specific Ube2i knockout mice (Ube2ia-KO). CRISPR/Cas9 gene editing inserted loxP sites flanking exons 3 and 4 at the Ube2i locus. Subsequent genetic crosses to Adipoq-Cre transgenic mice allowed deletion of Ube2i in white and brown adipocytes. We measured multiple metabolic endpoints that describe energy balance and carbohydrate metabolism in Ube2ia-KO and littermate controls during postnatal growth. Results Surprisingly, Ube2ia-KO mice developed hyperinsulinemia and hepatic steatosis. Global energy balance defects emerged from dysfunctional WAT marked by pronounced local inflammation, loss of serum adipokines, hepatomegaly, and near absence of major adipose tissue depots. We observed progressive lipoatrophy that commences in the early adolescent period. Conclusions Our results demonstrate that Ube2i expression in mature adipocytes allows WAT expansion during postnatal growth. Deletion of Ube2i in fat cells compromises and diminishes adipocyte function that induces WAT inflammation and ectopic lipid accumulation in the liver. Our findings reveal an indispensable role for Ube2i during white adipocyte expansion and endocrine control of energy balance. A new mouse model reveals that Ube2i loss in fat cells impacts body composition. Ube2i fat-specific knockout (Ube2ia-KO) causes fatty liver and hyperinsulinemia. Ube2ia-KO mice develop metabolic inflexibility and cold intolerance. Inflammation and caspase activation of cell death occur in Ube2ia-KO adipocytes.
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Affiliation(s)
- Aaron R Cox
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Natasha Chernis
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Kang Ho Kim
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Peter M Masschelin
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pradip K Saha
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Shawn M Briley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robert Sharp
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xin Li
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jessica B Felix
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Zheng Sun
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David D Moore
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie A Pangas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Sean M Hartig
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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Generation of mouse conditional knockout alleles in one step using the i-GONAD method. Genome Res 2020; 31:121-130. [PMID: 33328166 PMCID: PMC7849380 DOI: 10.1101/gr.265439.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
The Cre/loxP system is a powerful tool for gene function study in vivo. Regulated expression of Cre recombinase mediates precise deletion of genetic elements in a spatially– and temporally–controlled manner. Despite the robustness of this system, it requires a great amount of effort to create a conditional knockout model for each individual gene of interest where two loxP sites must be simultaneously inserted in cis. The current undertaking involves labor-intensive embryonic stem (ES) cell–based gene targeting and tedious micromanipulations of mouse embryos. The complexity of this workflow poses formidable technical challenges, thus limiting wider applications of conditional genetics. Here, we report an alternative approach to generate mouse loxP alleles by integrating a unique design of CRISPR donor with the new oviduct electroporation technique i-GONAD. Showing the potential and simplicity of this method, we created floxed alleles for five genes in one attempt with relatively low costs and a minimal equipment setup. In addition to the conditional alleles, constitutive knockout alleles were also obtained as byproducts of these experiments. Therefore, the wider applications of i-GONAD may promote gene function studies using novel murine models.
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38
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Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
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Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
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39
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CRISPR-mediated knock-in in the mouse embryo using long single stranded DNA donors synthesised by biotinylated PCR. Methods 2020; 191:3-14. [PMID: 33172594 DOI: 10.1016/j.ymeth.2020.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/21/2020] [Accepted: 10/18/2020] [Indexed: 12/26/2022] Open
Abstract
Successful gene knock-in by CRISPR-Cas9 in the mouse zygote requires three components; guideRNA, Cas9 protein and a suitable donor template, which usually comprises homology flanked insert sequence. Recently, long single stranded DNA (lssDNA) donors have emerged as a popular choice of DNA donor, outperforming dsDNA templates in terms of knock-in efficiency for gene tagging and generating conditional alleles. The generation of these donors can be achieved through several methods that may introduce errors in the sequence, result in poor yields, and contain dsDNA contamination. We have developed our own cost-effective lssDNA synthesis methodology that results in high purity, sequence verified, low contamination lssDNA donors. We provide a detailed methodology on the design and generation of such donors for gene tagging experiments and generating conditional alleles.
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Stroup BM, Marom R, Li X, Hsu CW, Chang CY, Truong LD, Dawson B, Grafe I, Chen Y, Jiang MM, Lanza D, Green JR, Sun Q, Barrish JP, Ani S, Christiansen AE, Seavitt JR, Dickinson ME, Kheradmand F, Heaney JD, Lee B, Burrage LC. A global Slc7a7 knockout mouse model demonstrates characteristic phenotypes of human lysinuric protein intolerance. Hum Mol Genet 2020; 29:2171-2184. [PMID: 32504080 PMCID: PMC7399531 DOI: 10.1093/hmg/ddaa107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/30/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022] Open
Abstract
Lysinuric protein intolerance (LPI) is an inborn error of cationic amino acid (arginine, lysine, ornithine) transport caused by biallelic pathogenic variants in SLC7A7, which encodes the light subunit of the y+LAT1 transporter. Treatments for the complications of LPI, including growth failure, renal disease, pulmonary alveolar proteinosis, autoimmune disorders and osteoporosis, are limited. Given the early lethality of the only published global Slc7a7 knockout mouse model, a viable animal model to investigate global SLC7A7 deficiency is needed. Hence, we generated two mouse models with global Slc7a7 deficiency (Slc7a7em1Lbu/em1Lbu; Slc7a7Lbu/Lbu and Slc7a7em1(IMPC)Bay/em1(IMPC)Bay; Slc7a7Bay/Bay) using CRISPR/Cas9 technology by introducing a deletion of exons 3 and 4. Perinatal lethality was observed in Slc7a7Lbu/Lbu and Slc7a7Bay/Bay mice on the C57BL/6 and C57BL/6NJ inbred genetic backgrounds, respectively. We noted improved survival of Slc7a7Lbu/Lbu mice on the 129 Sv/Ev × C57BL/6 F2 background, but postnatal growth failure occurred. Consistent with human LPI, these Slc7a7Lbu/Lbu mice exhibited reduced plasma and increased urinary concentrations of the cationic amino acids. Histopathological assessment revealed loss of brush border and lipid vacuolation in the renal cortex of Slc7a7Lbu/Lbu mice, which combined with aminoaciduria suggests proximal tubular dysfunction. Micro-computed tomography of L4 vertebrae and skeletal radiographs showed delayed skeletal development and suggested decreased mineralization in Slc7a7Lbu/Lbu mice, respectively. In addition to delayed skeletal development and delayed development in the kidneys, the lungs and liver were observed based on histopathological assessment. Overall, our Slc7a7Lbu/Lbu mouse model on the F2 mixed background recapitulates multiple human LPI phenotypes and may be useful for future studies of LPI pathology.
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Affiliation(s)
- Bridget M Stroup
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiaohui Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cheng-Yen Chang
- Department of Medicine-Pulmonary, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luan D Truong
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Brian Dawson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ingo Grafe
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Endocrinology, Diabetes, and Bone Diseases, Department of Medicine III, Center for Healthy Aging, University Clinic, Dresden D-01307, Germany
| | - Yuqing Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ming-Ming Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Denise Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennie Rose Green
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - J P Barrish
- Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Safa Ani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Audrey E Christiansen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Department of Medicine-Pulmonary, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
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41
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Levi T, Sloutskin A, Kalifa R, Juven-Gershon T, Gerlitz O. Efficient In Vivo Introduction of Point Mutations Using ssODN and a Co-CRISPR Approach. Biol Proced Online 2020; 22:14. [PMID: 32684853 PMCID: PMC7362497 DOI: 10.1186/s12575-020-00123-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Background The generation of point mutations is a major tool for evaluating the roles of specific nucleotides or amino acids within the regulatory or functional landscape. However, examination of these mutations in vivo requires the generation of animals carrying only the relevant point mutations at the endogenous genomic loci, which is technically challenging. The CRISPR-Cas9 based genome editing greatly facilitates the generation of such genetically modified animals; however, most of the described methods use double-strand DNA (dsDNA) as the donor template. The dsDNA plasmids frequently undergo undesired integration events into the targeted genomic locus. The use of a single-strand oligodeoxynucleotide (ssODN) as the donor template prevents this complication and is therefore the preferred choice for introducing point mutations, as well as short sequences such as protein tags. Results We successfully applied the CRISPR-based white co-conversion strategy with a ssODN template, instead of the originally described dsDNA plasmid, to create genetically modified Drosophila melanogaster strains. We used the technique to easily introduce point mutations in two distinct chromosomes. Using the generated flies, we were able to demonstrate the in vivo importance of the respective mutations. For the Nucleoporin107 (Nup107) gene, the 1090G > A mutation was confirmed to affect ovarian development, while for the tinman (tin) gene, the regulatory role of the downstream core promoter element (DPE) was demonstrated within the developing Drosophila melanogaster embryo. Conclusions The described approach has facilitated the successful generation of point mutations in two different chromosomes, by two different labs. Distinct phenotypes associated with the newly-generated genotype were identified, thus exemplifying the importance of investigating the in vivo role of specific nucleotides. In addition, detailed guidelines, recommendations and crossing schemes are provided in order to support the generation of additional genetically modified animals by the scientific community.
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Affiliation(s)
- Tgst Levi
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rachel Kalifa
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Offer Gerlitz
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel
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42
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Taylor CA, Shawlot W, Ren JX, Mukhopadhyay S. Generation and Validation of Tissue-Specific Knockout Strains for Toxicology Research. ACTA ACUST UNITED AC 2020; 81:e86. [PMID: 31529798 DOI: 10.1002/cptx.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Tissue-specific knockout mice are widely used throughout scientific research. A principle method for generating tissue-specific knockout mice is the Cre-loxP system. Here, we give a detailed description of the steps required to generate and validate tissue-specific knockout mice using the Cre-loxP system. The first protocol describes how to use gene targeting in mouse embryonic stem cells to generate mice with conditional alleles. Subsequent protocols describe how to recover Cre transgenic mice from cryopreserved sperm using in vitro fertilization and present a breeding strategy for obtaining tissue-specific knockouts. Finally, methods are provided for validating the knockout mice using PCR of genomic DNA, reverse-transcription PCR and quantitative reverse-transcription PCR of mRNA, and immunoblot analysis of proteins. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Cherish A Taylor
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology and Institute for Neuroscience, University of Texas at Austin, Austin, Texas
| | - William Shawlot
- Mouse Genetic Engineering Facility, University of Texas at Austin, Austin, Texas
| | - Jin Xiang Ren
- Mouse Genetic Engineering Facility, University of Texas at Austin, Austin, Texas
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology and Institute for Neuroscience, University of Texas at Austin, Austin, Texas
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43
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Hu Y, Li J, Zhu Y, Li M, Lin J, Yang L, Wang C, Lu Z. Development and characterization of an Otp conditional loss of function allele. Genesis 2020; 58:e23370. [PMID: 32468663 DOI: 10.1002/dvg.23370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 01/11/2023]
Abstract
Orthopedia (Otp) is a homeodomain transcription factor that plays an essential role in the development of hypothalamic neurosecretory systems. Loss of Otp results in the failure of differentiation of key hypothalamic neuroendocrine cell types, and pups die soon after birth. Although the constitutive knockout Otp mouse model (Otp KO ) has significantly expanded our understanding of Otp's function in vivo, a conditional loss of function Otp allele that enables tissue or cell-type specific ablation of Otp has not been developed. Here, we used CRISPR/Cas9 gene-editing technology to generate a conditional Otp knockout mouse line in which exon 2 of the murine Otp gene is flanked by LoxP sites (Otp f/f ). Crossing the Otp f/f mouse with Agrp-Ires-cre mouse, we demonstrate the requirement for Otp in the continuous differentiation of AgRP neurons after cell fate determination. We also show that the residual AgRP neurons in Agrp-Ires-cre;Otp f/f mice project to similar downstream target regions. This newly developed Otp f/f mouse can be used to explore the functions of Otp with cell-type or temporal specificity.
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Affiliation(s)
- Yu Hu
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Jiamin Li
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Zhu
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,Shenzhen Key Lab of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mengqi Li
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,Shenzhen Key Lab of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianbang Lin
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lixin Yang
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuan Wang
- Naval Medical Center of PLA, Shanghai, China
| | - Zhonghua Lu
- Shenzhen Key Laboratory for Molecular Biology of Neural Development, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
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44
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Mizuno-Iijima S, Ayabe S, Kato K, Matoba S, Ikeda Y, Dinh TTH, Le HT, Suzuki H, Nakashima K, Hasegawa Y, Hamada Y, Tanimoto Y, Daitoku Y, Iki N, Ishida M, Ibrahim EAE, Nakashiba T, Hamada M, Murata K, Miwa Y, Okada-Iwabu M, Iwabu M, Yagami KI, Ogura A, Obata Y, Takahashi S, Mizuno S, Yoshiki A, Sugiyama F. Efficient production of large deletion and gene fragment knock-in mice mediated by genome editing with Cas9-mouse Cdt1 in mouse zygotes. Methods 2020; 191:23-31. [PMID: 32334080 DOI: 10.1016/j.ymeth.2020.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Genetically modified mouse models are essential for in vivo investigation of gene function and human disease research. Targeted mutations can be introduced into mouse embryos using genome editing technology such as CRISPR-Cas. Although mice with small indel mutations can be produced, the production of mice carrying large deletions or gene fragment knock-in alleles remains inefficient. We introduced the nuclear localisation property of Cdt1 protein into the CRISPR-Cas system for efficient production of genetically engineered mice. Mouse Cdt1-connected Cas9 (Cas9-mC) was present in the nucleus of HEK293T cells and mouse embryos. Cas9-mC induced a bi-allelic full deletion of Dmd, GC-rich fragment knock-in, and floxed allele knock-in with high efficiency compared to standard Cas9. These results indicate that Cas9-mC is a useful tool for producing mouse models carrying targeted mutations.
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Affiliation(s)
- Saori Mizuno-Iijima
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
| | - Kanako Kato
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshihisa Ikeda
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Charles River Laboratories Japan, Inc., 955 Kamibayashi, Ishioka 315-0138, Japan
| | - Tra Thi Huong Dinh
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hoai Thu Le
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hayate Suzuki
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshikazu Hasegawa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuko Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Natsumi Iki
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miyuki Ishida
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Elzeftawy Abdelaziz Elsayed Ibrahim
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Toshiaki Nakashiba
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Michito Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshihiro Miwa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miki Okada-Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masato Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken-Ichi Yagami
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuichi Obata
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Takahashi
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Fumihiro Sugiyama
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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45
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Fleischer A, Vallejo-Díez S, Martín-Fernández JM, Sánchez-Gilabert A, Castresana M, Del Pozo A, Esquisabel A, Ávila S, Castrillo JL, Gaínza E, Pedraz JL, Viñas M, Bachiller D. iPSC-Derived Intestinal Organoids from Cystic Fibrosis Patients Acquire CFTR Activity upon TALEN-Mediated Repair of the p.F508del Mutation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:858-870. [PMID: 32373648 PMCID: PMC7195499 DOI: 10.1016/j.omtm.2020.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is the main genetic cause of death among the Caucasian population. The disease is characterized by abnormal fluid and electrolyte mobility across secretory epithelia. The first manifestations occur within hours of birth (meconium ileus), later extending to other organs, generally affecting the respiratory tract. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encodes a cyclic adenosine monophosphate (cAMP)-dependent, phosphorylation-regulated chloride channel required for transport of chloride and other ions through cell membranes. There are more than 2,000 mutations described in the CFTR gene, but one of them, phenylalanine residue at amino acid position 508 (p.F508del), a recessive allele, is responsible for the vast majority of CF cases worldwide. Here, we present the results of the application of genome-editing techniques to the restoration of CFTR activity in p.F508del patient-derived induced pluripotent stem cells (iPSCs). Gene-edited iPSCs were subsequently used to produce intestinal organoids on which the physiological activity of the restored gene was tested in forskolin-induced swelling tests. The seamless restoration of the p.F508del mutation resulted in normal expression of the mature CFTR glycoprotein, full recovery of CFTR activity, and a normal response of the repaired organoids to treatment with two approved CF therapies: VX-770 and VX-809.
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Affiliation(s)
- Aarne Fleischer
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | - Sara Vallejo-Díez
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
| | | | | | - Mónica Castresana
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | | | - Amaia Esquisabel
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Silvia Ávila
- Genetadi Biotech S.L., Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, University of Barcelona, 08097 Barcelona, Spain
| | - Daniel Bachiller
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
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46
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Lanigan TM, Kopera HC, Saunders TL. Principles of Genetic Engineering. Genes (Basel) 2020; 11:E291. [PMID: 32164255 PMCID: PMC7140808 DOI: 10.3390/genes11030291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering is the use of molecular biology technology to modify DNA sequence(s) in genomes, using a variety of approaches. For example, homologous recombination can be used to target specific sequences in mouse embryonic stem (ES) cell genomes or other cultured cells, but it is cumbersome, poorly efficient, and relies on drug positive/negative selection in cell culture for success. Other routinely applied methods include random integration of DNA after direct transfection (microinjection), transposon-mediated DNA insertion, or DNA insertion mediated by viral vectors for the production of transgenic mice and rats. Random integration of DNA occurs more frequently than homologous recombination, but has numerous drawbacks, despite its efficiency. The most elegant and effective method is technology based on guided endonucleases, because these can target specific DNA sequences. Since the advent of clustered regularly interspaced short palindromic repeats or CRISPR/Cas9 technology, endonuclease-mediated gene targeting has become the most widely applied method to engineer genomes, supplanting the use of zinc finger nucleases, transcription activator-like effector nucleases, and meganucleases. Future improvements in CRISPR/Cas9 gene editing may be achieved by increasing the efficiency of homology-directed repair. Here, we describe principles of genetic engineering and detail: (1) how common elements of current technologies include the need for a chromosome break to occur, (2) the use of specific and sensitive genotyping assays to detect altered genomes, and (3) delivery modalities that impact characterization of gene modifications. In summary, while some principles of genetic engineering remain steadfast, others change as technologies are ever-evolving and continue to revolutionize research in many fields.
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Affiliation(s)
- Thomas M. Lanigan
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C. Kopera
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Biomedical Research Core Facilities, Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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47
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Golovko A, Adams J, Guo H, Ballard J, Gonzales A, Morpurgo B. Consistent Production of Mice with Conditional Knockout Alleles by CRISPR/Cas9-Mediated Genome Editing Using Two Guides/Two Oligos Approach. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Abstract
A transgenic mouse carries within its genome an artificial DNA construct (transgene) that is deliberately introduced by an experimentalist. These animals are widely used to understand gene function and protein function. When addressing the history of transgenic mouse technology, it is apparent that a number of basic science research areas laid the groundwork for success. These include reproductive science, genetics and molecular biology, and micromanipulation and microscopy equipment. From reproductive physiology came applications on how to optimize mouse breeding, how to superovulate mice to produce zygotes for DNA microinjection or preimplantation embryos for combination with embryonic stem (ES) cells, and how to return zygotes and embryos to a pseudopregnant surrogate dam for gestation and birth. From developmental biology, it was learned how to micromanipulate embryos for morula aggregation and blastocyst microinjection and how to establish germline competent ES cells. From genetics came the foundational principles governing the inheritance of genes, the interactions of gene products, and an understanding of the phenotypic consequences of genetic mutations. From molecular biology came a panoply of tools and reagents that are used to clone DNA transgenes, to detect the presence of transgenes, to assess gene expression by measuring transcription, and to detect proteins in cells and tissues. Technical advances in light microscopes, micromanipulators, micropipette pullers, and ancillary equipment made it possible for experimentalists to insert thin glass needles into zygotes or embryos under controlled conditions to inject DNA solutions or ES cells. To fully discuss the breadth of contributions of these numerous scientific disciplines to a comprehensive history of transgenic science is beyond the scope of this work. Examples will be used to illustrate scientific developments central to the foundation of transgenic technology and that are in use today.
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Affiliation(s)
- Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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49
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García-García MJ. A History of Mouse Genetics: From Fancy Mice to Mutations in Every Gene. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:1-38. [PMID: 32304067 DOI: 10.1007/978-981-15-2389-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The laboratory mouse has become the model organism of choice in numerous areas of biological and biomedical research, including the study of congenital birth defects. The appeal of mice for these experimental studies stems from the similarities between the physiology, anatomy, and reproduction of these small mammals with our own, but it is also based on a number of practical reasons: mice are easy to maintain in a laboratory environment, are incredibly prolific, and have a relatively short reproductive cycle. Another compelling reason for choosing mice as research subjects is the number of tools and resources that have been developed after more than a century of working with these small rodents in laboratory environments. As will become obvious from the reading of the different chapters in this book, research in mice has already helped uncover many of the genes and processes responsible for congenital birth malformations and human diseases. In this chapter, we will provide an overview of the methods, scientific advances, and serendipitous circumstances that have made these discoveries possible, with a special emphasis on how the use of genetics has propelled scientific progress in mouse research and paved the way for future discoveries.
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Pineault KM, Novoa A, Lozovska A, Wellik DM, Mallo M. Two CRISPR/Cas9-mediated methods for targeting complex insertions, deletions, or replacements in mouse. MethodsX 2019; 6:2088-2100. [PMID: 31667107 PMCID: PMC6812322 DOI: 10.1016/j.mex.2019.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/05/2019] [Indexed: 12/01/2022] Open
Abstract
Genetically modified model organisms are valuable tools for probing gene function, dissecting complex signaling networks, studying human disease, and more. CRISPR/Cas9 technology has significantly democratized and reduced the time and cost of generating genetically modified models to the point that small gene edits are now routinely and efficiently generated in as little as two months. However, generation of larger and more sophisticated gene-modifications continues to be inefficient. Alternative ways to provide the replacement DNA sequence, method of Cas9 delivery, and tethering the template sequence to Cas9 or the guide RNA (gRNA) have all been tested in an effort to maximize homology-directed repair for precise modification of the genome. We present two CRISPR/Cas9 methods that have been used to successfully generate large and complex gene-edits in mouse. In the first method, the Cas9 enzyme is used in conjunction with two sgRNAs and a long single-stranded DNA (lssDNA) template prepared by an alternative protocol. The second method utilizes a tethering approach to couple a biotinylated, double-stranded DNA (dsDNA) template to a Cas9-streptavidin fusion protein. Alternative method for generating long, single-stranded DNA templates for CRISPR/Cas9 editing. Demonstration that using two sgRNAs with Cas9-streptavidin/biotinylated-dsDNA is feasible for large DNA modifications.
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Affiliation(s)
- Kyriel M Pineault
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, USA.,Instituto Gulbenkian de Ciência, Portugal
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Portugal
| | | | - Deneen M Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, USA
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