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Komori T, Hata S, Mabuchi A, Genova M, Harada T, Fukuyama M, Chinen T, Kitagawa D. A CRISPR-del-based pipeline for complete gene knockout in human diploid cells. J Cell Sci 2023; 136:286993. [PMID: 36762651 PMCID: PMC10038147 DOI: 10.1242/jcs.260000] [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: 03/07/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
The advance of CRISPR/Cas9 technology has enabled us easily to generate gene knockout cell lines by introducing insertion-deletion mutations (indels) at the target site via the error-prone non-homologous end joining repair system. Frameshift-promoting indels can disrupt gene functions by generation of a premature stop codon. However, there is growing evidence that targeted genes are not always knocked out by the indel-based gene disruption. Here, we established a pipeline of CRISPR-del, which induces a large chromosomal deletion by cutting two different target sites, to perform 'complete' gene knockout efficiently in human diploid cells. Quantitative analyses show that the frequency of gene deletion with this approach is much higher than that of conventional CRISPR-del methods. The lengths of the deleted genomic regions demonstrated in this study are longer than those of 95% of the human protein-coding genes. Furthermore, the pipeline enabled the generation of a model cell line having a bi-allelic cancer-associated chromosomal deletion. Overall, these data lead us to propose that the CRISPR-del pipeline is an efficient and practical approach for producing 'complete' gene knockout cell lines in human diploid cells.
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Affiliation(s)
- Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, 102-8666 Saitama, Japan
| | - Akira Mabuchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Mariya Genova
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, 69120 Heidelberg, Germany
| | - Tomoki Harada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
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Brasil S, Allocca M, Magrinho SCM, Santos I, Raposo M, Francisco R, Pascoal C, Martins T, Videira PA, Pereira F, Andreotti G, Jaeken J, Kantautas KA, Perlstein EO, Ferreira VDR. Systematic Review: Drug Repositioning for Congenital Disorders of Glycosylation (CDG). Int J Mol Sci 2022; 23:ijms23158725. [PMID: 35955863 PMCID: PMC9369176 DOI: 10.3390/ijms23158725] [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: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022] Open
Abstract
Advances in research have boosted therapy development for congenital disorders of glycosylation (CDG), a group of rare genetic disorders affecting protein and lipid glycosylation and glycosylphosphatidylinositol anchor biosynthesis. The (re)use of known drugs for novel medical purposes, known as drug repositioning, is growing for both common and rare disorders. The latest innovation concerns the rational search for repositioned molecules which also benefits from artificial intelligence (AI). Compared to traditional methods, drug repositioning accelerates the overall drug discovery process while saving costs. This is particularly valuable for rare diseases. AI tools have proven their worth in diagnosis, in disease classification and characterization, and ultimately in therapy discovery in rare diseases. The availability of biomarkers and reliable disease models is critical for research and development of new drugs, especially for rare and heterogeneous diseases such as CDG. This work reviews the literature related to repositioned drugs for CDG, discovered by serendipity or through a systemic approach. Recent advances in biomarkers and disease models are also outlined as well as stakeholders’ views on AI for therapy discovery in CDG.
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Affiliation(s)
- Sandra Brasil
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Mariateresa Allocca
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Institute of Biomolecular Chemistry, National Research Council of Italy, 80078 Pozzuoli, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Salvador C. M. Magrinho
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- LAQV-Requimte, Chemistry Department, School of Science and Technology, Nova University of Lisbon, 2819-516 Caparica, Portugal
| | - Inês Santos
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Sci and Volunteer Program from School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Madalena Raposo
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Sci and Volunteer Program from School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Rita Francisco
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Carlota Pascoal
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Tiago Martins
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Sci and Volunteer Program from School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Paula A. Videira
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Florbela Pereira
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- LAQV-Requimte, Chemistry Department, School of Science and Technology, Nova University of Lisbon, 2819-516 Caparica, Portugal
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry, National Research Council of Italy, 80078 Pozzuoli, Italy
| | - Jaak Jaeken
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Center for Metabolic Diseases, Department of Pediatrics, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Vanessa dos Reis Ferreira
- UCIBIO—Applied Molecular Biosciences Unit, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Nova University of Lisbon, 2829-516 Caparica, Portugal
- CDG & Allies PPAIN—Professionals and Patient Associations International Network, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Correspondence:
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4
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Zhang W, Brosh R, McCulloch LH, Zhu Y, Ashe H, Ellis G, Camellato BR, Kim SY, Maurano MT, Boeke JD. A conditional counterselectable Piga knockout in mouse embryonic stem cells for advanced genome writing applications. iScience 2022; 25:104438. [PMID: 35692632 PMCID: PMC9184564 DOI: 10.1016/j.isci.2022.104438] [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: 09/04/2021] [Revised: 03/18/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
Overwriting counterselectable markers is an efficient strategy for removing wild-type DNA or replacing it with payload DNA of interest. Currently, one bottleneck of efficient genome engineering in mammals is the shortage of counterselectable (negative selection) markers that work robustly without affecting organismal developmental potential. Here, we report a conditional Piga knockout strategy that enables efficient proaerolysin-based counterselection in mouse embryonic stem cells. The conditional Piga knockout cells show similar proaerolysin resistance as full (non-conditional) Piga deletion cells, which enables the use of a PIGA transgene as a counterselectable marker for genome engineering purposes. Native Piga function is readily restored in conditional Piga knockout cells to facilitate subsequent mouse development. We also demonstrate the generality of our strategy by engineering a conditional knockout of endogenous Hprt. Taken together, our work provides a new tool for advanced mouse genome writing and mouse model establishment.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Laura H McCulloch
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Hannah Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | | | - Sang Yong Kim
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
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6
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Brosh R, Laurent JM, Ordoñez R, Huang E, Hogan MS, Hitchcock AM, Mitchell LA, Pinglay S, Cadley JA, Luther RD, Truong DM, Boeke JD, Maurano MT. A versatile platform for locus-scale genome rewriting and verification. Proc Natl Acad Sci U S A 2021; 118:e2023952118. [PMID: 33649239 PMCID: PMC7958457 DOI: 10.1073/pnas.2023952118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Routine rewriting of loci associated with human traits and diseases would facilitate their functional analysis. However, existing DNA integration approaches are limited in terms of scalability and portability across genomic loci and cellular contexts. We describe Big-IN, a versatile platform for targeted integration of large DNAs into mammalian cells. CRISPR/Cas9-mediated targeting of a landing pad enables subsequent recombinase-mediated delivery of variant payloads and efficient positive/negative selection for correct clones in mammalian stem cells. We demonstrate integration of constructs up to 143 kb, and an approach for one-step scarless delivery. We developed a staged pipeline combining PCR genotyping and targeted capture sequencing for economical and comprehensive verification of engineered stem cells. Our approach should enable combinatorial interrogation of genomic functional elements and systematic locus-scale analysis of genome function.
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Affiliation(s)
- Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Jon M Laurent
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | | | - Leslie A Mitchell
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - John A Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Raven D Luther
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - David M Truong
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016;
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn 11201, NY
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
- Department of Pathology, NYU Langone Health, New York, NY 10016
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