1
|
Chen Y, Wang P, Ma S, Yue C, Liu X, Cheng Y, Liu K, Zhao T, Shyh‐Chang N. Genetically Engineered Hypoimmune Human Muscle Progenitor Cells Can Reduce Immune Rejection. Cell Prolif 2025; 58:e13802. [PMID: 39777760 PMCID: PMC11969239 DOI: 10.1111/cpr.13802] [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: 11/22/2024] [Revised: 12/18/2024] [Accepted: 12/24/2024] [Indexed: 01/11/2025] Open
Abstract
Cells face two challenges after transplantation: recognition and killing by lymphocytes, and cell apoptosis induced by the transplantation environment. Our hypoimmune cells aim to address these two challenges through editing of immunomodulatory proteins and overexpression of anti-apoptotic proteins.
Collapse
Affiliation(s)
- Yu Chen
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Peng Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Shilin Ma
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Chenran Yue
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Xupeng Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Yeqian Cheng
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Kun Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Tongbiao Zhao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Ng Shyh‐Chang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| |
Collapse
|
2
|
Aguilar G, Bauer M, Vigano MA, Schnider ST, Brügger L, Jiménez-Jiménez C, Guerrero I, Affolter M. Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing. Dev Cell 2024; 59:2672-2686.e5. [PMID: 38971155 DOI: 10.1016/j.devcel.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/06/2023] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
CRISPR-Cas greatly facilitated the integration of exogenous sequences into specific loci. However, knockin generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Here, we describe SEED/Harvest, a method to generate knockins in Drosophila, based on CRISPR-Cas and the single-strand annealing (SSA) repair pathway. In SEED (from "scarless editing by element deletion"), a switchable cassette is first integrated into the target locus. In a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knockin generation of both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatiotemporal control of protein labeling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knockins, we developed a genetic toolbox by functionalizing the ALFA nanobody.
Collapse
Affiliation(s)
- Gustavo Aguilar
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Milena Bauer
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - M Alessandra Vigano
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Sophie T Schnider
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Lukas Brügger
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Carlos Jiménez-Jiménez
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Isabel Guerrero
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Markus Affolter
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| |
Collapse
|
3
|
Hosseini SY, Mallick R, Mäkinen P, Ylä-Herttuala S. Insights into Prime Editing Technology: A Deep Dive into Fundamentals, Potentials, and Challenges. Hum Gene Ther 2024; 35:649-668. [PMID: 38832869 DOI: 10.1089/hum.2024.043] [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: 06/06/2024] Open
Abstract
As the most versatile and precise gene editing technology, prime editing (PE) can establish a durable cure for most human genetic disorders. Several generations of PE have been developed based on an editor machine or prime editing guide RNA (pegRNA) to achieve any kind of genetic correction. However, due to the early stage of development, PE complex elements need to be optimized for more efficient editing. Smart optimization of editor proteins as well as pegRNA has been contemplated by many researchers, but the universal PE machine's current shortcomings remain to be solved. The modification of PE elements, fine-tuning of the host genes, manipulation of epigenetics, and blockage of immune responses could be used to reach more efficient PE. Moreover, the host factors involved in the PE process, such as repair and innate immune system genes, have not been determined, and PE cell context dependency is still poorly understood. Regarding the large size of the PE elements, delivery is a significant challenge and the development of a universal viral or nonviral platform is still far from complete. PE versions with shortened variants of reverse transcriptase are still too large to fit in common viral vectors. Overall, PE faces challenges in optimization for efficiency, high context dependency during the cell cycling, and delivery due to the large size of elements. In addition, immune responses, unpredictability of outcomes, and off-target effects further limit its application, making it essential to address these issues for broader use in nonpersonalized gene editing. Besides, due to the limited number of suitable animal models and computational modeling, the prediction of the PE process remains challenging. In this review, the fundamentals of PE, including generations, potential, optimization, delivery, in vivo barriers, and the future landscape of the technology are discussed.
Collapse
Affiliation(s)
- Seyed Younes Hosseini
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| |
Collapse
|
4
|
Karwacki-Neisius V, Jang A, Cukuroglu E, Tai A, Jiao A, Predes D, Yoon J, Brookes E, Chen J, Iberg A, Halbritter F, Õunap K, Gecz J, Schlaeger TM, Ho Sui S, Göke J, He X, Lehtinen MK, Pomeroy SL, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature 2024; 627:594-603. [PMID: 38383780 PMCID: PMC10954547 DOI: 10.1038/s41586-024-07067-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: 01/07/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Although KDM5C is one of the most frequently mutated genes in X-linked intellectual disability1, the exact mechanisms that lead to cognitive impairment remain unknown. Here we use human patient-derived induced pluripotent stem cells and Kdm5c knockout mice to conduct cellular, transcriptomic, chromatin and behavioural studies. KDM5C is identified as a safeguard to ensure that neurodevelopment occurs at an appropriate timescale, the disruption of which leads to intellectual disability. Specifically, there is a developmental window during which KDM5C directly controls WNT output to regulate the timely transition of primary to intermediate progenitor cells and consequently neurogenesis. Treatment with WNT signalling modulators at specific times reveal that only a transient alteration of the canonical WNT signalling pathway is sufficient to rescue the transcriptomic and chromatin landscapes in patient-derived cells and to induce these changes in wild-type cells. Notably, WNT inhibition during this developmental period also rescues behavioural changes of Kdm5c knockout mice. Conversely, a single injection of WNT3A into the brains of wild-type embryonic mice cause anxiety and memory alterations. Our work identifies KDM5C as a crucial sentinel for neurodevelopment and sheds new light on KDM5C mutation-associated intellectual disability. The results also increase our general understanding of memory and anxiety formation, with the identification of WNT functioning in a transient nature to affect long-lasting cognitive function.
Collapse
Affiliation(s)
- Violetta Karwacki-Neisius
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ahram Jang
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Engin Cukuroglu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
- Data Intensive Studies Center, Tufts University, Medford, MA, USA
| | - Alan Jiao
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danilo Predes
- Department of Neurology, F. M Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joon Yoon
- Department of Biostatistics, The Harvard Chan School of Public Health, Bioinformatics Core, Cambridge, MA, USA
| | - Emily Brookes
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jiekai Chen
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Aimee Iberg
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Halbritter
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Katrin Õunap
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shannan Ho Sui
- Department of Biostatistics, The Harvard Chan School of Public Health, Bioinformatics Core, Cambridge, MA, USA
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xi He
- Department of Neurology, F. M Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Scott L Pomeroy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
5
|
Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
Collapse
Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| |
Collapse
|
6
|
Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
Collapse
Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
| |
Collapse
|
7
|
Cuevas-Ocaña S, Yang JY, Aushev M, Schlossmacher G, Bear CE, Hannan NRF, Perkins ND, Rossant J, Wong AP, Gray MA. A Cell-Based Optimised Approach for Rapid and Efficient Gene Editing of Human Pluripotent Stem Cells. Int J Mol Sci 2023; 24:10266. [PMID: 37373413 PMCID: PMC10299534 DOI: 10.3390/ijms241210266] [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: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Introducing or correcting disease-causing mutations through genome editing in human pluripotent stem cells (hPSCs) followed by tissue-specific differentiation provide sustainable models of multiorgan diseases, such as cystic fibrosis (CF). However, low editing efficiency resulting in extended cell culture periods and the use of specialised equipment for fluorescence activated cell sorting (FACS) make hPSC genome editing still challenging. We aimed to investigate whether a combination of cell cycle synchronisation, single-stranded oligodeoxyribonucleotides, transient selection, manual clonal isolation, and rapid screening can improve the generation of correctly modified hPSCs. Here, we introduced the most common CF mutation, ΔF508, into the CFTR gene, using TALENs into hPSCs, and corrected the W1282X mutation using CRISPR-Cas9, in human-induced PSCs. This relatively simple method achieved up to 10% efficiency without the need for FACS, generating heterozygous and homozygous gene edited hPSCs within 3-6 weeks in order to understand genetic determinants of disease and precision medicine.
Collapse
Affiliation(s)
- Sara Cuevas-Ocaña
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
- Biodiscovery Institute, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Jin Ye Yang
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Magomet Aushev
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Biomedicine West Wing, Centre for Life, Times Square, Newcastle upon Tyne NE1 3BZ, UK;
| | - George Schlossmacher
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
| | - Christine E. Bear
- Programme in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Nicholas R. F. Hannan
- Biodiscovery Institute, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Neil D. Perkins
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
| | - Janet Rossant
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Amy P. Wong
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Michael A. Gray
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
| |
Collapse
|
8
|
Establishment of isogenic induced pluripotent stem cells with or without pathogenic mutation for understanding the pathogenesis of myeloproliferative neoplasms. Exp Hematol 2023; 118:12-20. [PMID: 36511286 DOI: 10.1016/j.exphem.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Identification and functional characterization of disease-associated genetic traits are crucial for understanding the pathogenesis of hematologic malignancies. Various in vitro and in vivo models, including cell lines, primary cells, and animal models, have been established to examine these genetic alterations. However, their nonphysiologic conditions, diverse genetic backgrounds, and species-specific differences often limit data interpretation. To evaluate somatic mutations in myeloproliferative neoplasms (MPNs), we used CRISPR/Cas9 combined with the piggyBac transposon system to establish isogenic induced pluripotent stem (iPS) cell lines with or without JAK2V617F mutation, a driver mutation of MPNs. We induced hematopoietic stem/progenitor cells (HSPCs) from these iPS cells and observed phenotypic differences during hematopoiesis using fluorescence-activated cell sorting analysis. HSPCs with pathogenic mutations exhibited cell-autonomous erythropoiesis and megakaryopoiesis, which are hallmarks in the bone marrow of patients with MPNs. Furthermore, we used these HSPCs as a model to validate therapeutic compounds and showed that interferon alpha selectively inhibited erythropoiesis and megakaryopoiesis in mutant HSPCs. These results demonstrate that genome editing is feasible for establishing isogenic iPS cells, studying genetic elements to understand the pathogenesis of MPNs, and evaluating therapeutic compounds against MPNs.
Collapse
|
9
|
Ercu M, Mücke MB, Pallien T, Markó L, Sholokh A, Schächterle C, Aydin A, Kidd A, Walter S, Esmati Y, McMurray BJ, Lato DF, Yumi Sunaga-Franze D, Dierks PH, Flores BIM, Walker-Gray R, Gong M, Merticariu C, Zühlke K, Russwurm M, Liu T, Batolomaeus TUP, Pautz S, Schelenz S, Taube M, Napieczynska H, Heuser A, Eichhorst J, Lehmann M, Miller DC, Diecke S, Qadri F, Popova E, Langanki R, Movsesian MA, Herberg FW, Forslund SK, Müller DN, Borodina T, Maass PG, Bähring S, Hübner N, Bader M, Klussmann E. Mutant Phosphodiesterase 3A Protects From Hypertension-Induced Cardiac Damage. Circulation 2022; 146:1758-1778. [PMID: 36259389 DOI: 10.1161/circulationaha.122.060210] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/24/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Phosphodiesterase 3A (PDE3A) gain-of-function mutations cause hypertension with brachydactyly (HTNB) and lead to stroke. Increased peripheral vascular resistance, rather than salt retention, is responsible. It is surprising that the few patients with HTNB examined so far did not develop cardiac hypertrophy or heart failure. We hypothesized that, in the heart, PDE3A mutations could be protective. METHODS We studied new patients. CRISPR-Cas9-engineered rat HTNB models were phenotyped by telemetric blood pressure measurements, echocardiography, microcomputed tomography, RNA-sequencing, and single nuclei RNA-sequencing. Human induced pluripotent stem cells carrying PDE3A mutations were established, differentiated to cardiomyocytes, and analyzed by Ca2+ imaging. We used Förster resonance energy transfer and biochemical assays. RESULTS We identified a new PDE3A mutation in a family with HTNB. It maps to exon 13 encoding the enzyme's catalytic domain. All hitherto identified HTNB PDE3A mutations cluster in exon 4 encoding a region N-terminally from the catalytic domain of the enzyme. The mutations were recapitulated in rat models. Both exon 4 and 13 mutations led to aberrant phosphorylation, hyperactivity, and increased PDE3A enzyme self-assembly. The left ventricles of our patients with HTNB and the rat models were normal despite preexisting hypertension. A catecholamine challenge elicited cardiac hypertrophy in HTNB rats only to the level of wild-type rats and improved the contractility of the mutant hearts, compared with wild-type rats. The β-adrenergic system, phosphodiesterase activity, and cAMP levels in the mutant hearts resembled wild-type hearts, whereas phospholamban phosphorylation was decreased in the mutants. In our induced pluripotent stem cell cardiomyocyte models, the PDE3A mutations caused adaptive changes of Ca2+ cycling. RNA-sequencing and single nuclei RNA-sequencing identified differences in mRNA expression between wild-type and mutants, affecting, among others, metabolism and protein folding. CONCLUSIONS Although in vascular smooth muscle, PDE3A mutations cause hypertension, they confer protection against hypertension-induced cardiac damage in hearts. Nonselective PDE3A inhibition is a final, short-term option in heart failure treatment to increase cardiac cAMP and improve contractility. Our data argue that mimicking the effect of PDE3A mutations in the heart rather than nonselective PDE3 inhibition is cardioprotective in the long term. Our findings could facilitate the search for new treatments to prevent hypertension-induced cardiac damage.
Collapse
Affiliation(s)
- Maria Ercu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
| | - Michael B Mücke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
| | - Tamara Pallien
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
| | - Lajos Markó
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Anastasiia Sholokh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
| | - Carolin Schächterle
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Atakan Aydin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Alexa Kidd
- Clinical Genetics Ltd, Christchurch, New Zealand (A.K.)
| | | | - Yasmin Esmati
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Brandon J McMurray
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada (B.J.M., D.F.L., P.G.M.)
| | - Daniella F Lato
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada (B.J.M., D.F.L., P.G.M.)
| | - Daniele Yumi Sunaga-Franze
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Philip H Dierks
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Barbara Isabel Montesinos Flores
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Ryan Walker-Gray
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Maolian Gong
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Claudia Merticariu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Kerstin Zühlke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Michael Russwurm
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät MA N1, Ruhr-Universität Bochum, Germany (M.R.)
| | - Tiannan Liu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Theda U P Batolomaeus
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Sabine Pautz
- Department of Biochemistry, University of Kassel, Germany (S.P., F.W.H.)
| | - Stefanie Schelenz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Martin Taube
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Hanna Napieczynska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Arnd Heuser
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany (J.E., M.L.)
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany (J.E., M.L.)
| | - Duncan C Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Berlin Institute of Health (BIH), Germany (S.D., S.K.F.)
| | - Fatimunnisa Qadri
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Elena Popova
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Reika Langanki
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | | | | | - Sofia K Forslund
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
- Berlin Institute of Health (BIH), Germany (S.D., S.K.F.)
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany (S.K.F.)
| | - Dominik N Müller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Tatiana Borodina
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
| | - Philipp G Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada (B.J.M., D.F.L., P.G.M.)
- Department of Molecular Genetics, University of Toronto, ON, Canada (P.G.M.)
| | - Sylvia Bähring
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Universitätsmedizin Berlin, Germany (L.M., Y.E., M.G., T.U.P.B., S.K.F., D.N.M., S.B.)
| | - Norbert Hübner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (M.B.M., L.M., A.S., Y.E., T.U.P.B., S.K.F., S.B., N.H., M.B.)
- Institute for Biology, University of Lübeck, Germany (M.B.)
| | - Enno Klussmann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.E., M.B.M., T.P., A.S., C.S., A.A., D.Y.S.-F., P.H.D., B.I.M.F., R.W.-G., M.G., C.M., K.Z., T.L., S.S., M.T., H.N., A.H., D.C.M., S.D., F.Q., E.P., R.L., S.K.F., D.N.M., T.B., S.B., N.H., M.B., E.K.)
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (M.E., M.B.M., T.P., L.M., A.S., Y.E., T.U.P.B., D.C.M., S.D., S.K.F., D.N.M., N.H., M.B., E.K.)
| |
Collapse
|
10
|
Benati D, Leung A, Perdigao P, Toulis V, van der Spuy J, Recchia A. Induced Pluripotent Stem Cells and Genome-Editing Tools in Determining Gene Function and Therapy for Inherited Retinal Disorders. Int J Mol Sci 2022; 23:ijms232315276. [PMID: 36499601 PMCID: PMC9735568 DOI: 10.3390/ijms232315276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal disorders (IRDs) affect millions of people worldwide and are a major cause of irreversible blindness. Therapies based on drugs, gene augmentation or transplantation approaches have been widely investigated and proposed. Among gene therapies for retinal degenerative diseases, the fast-evolving genome-editing CRISPR/Cas technology has emerged as a new potential treatment. The CRISPR/Cas system has been developed as a powerful genome-editing tool in ophthalmic studies and has been applied not only to gain proof of principle for gene therapies in vivo, but has also been extensively used in basic research to model diseases-in-a-dish. Indeed, the CRISPR/Cas technology has been exploited to genetically modify human induced pluripotent stem cells (iPSCs) to model retinal disorders in vitro, to test in vitro drugs and therapies and to provide a cell source for autologous transplantation. In this review, we will focus on the technological advances in iPSC-based cellular reprogramming and gene editing technologies to create human in vitro models that accurately recapitulate IRD mechanisms towards the development of treatments for retinal degenerative diseases.
Collapse
Affiliation(s)
- Daniela Benati
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Amy Leung
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Pedro Perdigao
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | | | | | - Alessandra Recchia
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: (J.v.d.S.); (A.R.)
| |
Collapse
|
11
|
Thomsen EA, Skipper KA, Andersen S, Haslund D, Skov TW, Mikkelsen JG. CRISPR-Cas9-directed gene tagging using a single integrase-defective lentiviral vector carrying a transposase-based Cas9 off switch. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:563-576. [PMID: 36090759 PMCID: PMC9403905 DOI: 10.1016/j.omtn.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022]
Abstract
Locus-directed DNA cleavage induced by the CRISPR-Cas9 system triggers DNA repair mechanisms allowing gene repair or targeted insertion of foreign DNA. For gene insertion to be successful, availability of a homologous donor template needs to be timed with cleavage of the DNA by the Cas9 endonuclease guided by a target-specific single guide RNA (sgRNA). We present a novel approach for targeted gene insertion based on a single integrase-defective lentiviral vector (IDLV) carrying a Cas9 off switch. Gene insertion using this approach benefits from transposon-based stable Cas9 expression, which is switched off by excision-only transposase protein co-delivered in IDLV particles carrying a combined sgRNA/donor vector. This one-vector approach supports potent (up to >80%) knockin of a full-length EGFP gene sequence. This traceless cell engineering method benefits from high stable levels of Cas9, timed intracellular availability of the molecular tools, and a built-in feature to turn off Cas9 expression after DNA cleavage. The simple technique is based on transduction with a single IDLV, which holds the capacity to transfer larger donor templates, allowing robust gene knockin or tagging of genes in a single step.
Collapse
Affiliation(s)
- Emil Aagaard Thomsen
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Kristian Alsbjerg Skipper
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Sofie Andersen
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Didde Haslund
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Thomas Wisbech Skov
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Jacob Giehm Mikkelsen
- Department of Biomedicine, HEALTH, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Corresponding author Jacob Giehm Mikkelson, Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark.
| |
Collapse
|
12
|
Harlow CE, Gandawijaya J, Bamford RA, Martin ER, Wood AR, van der Most PJ, Tanaka T, Leonard HL, Etheridge AS, Innocenti F, Beaumont RN, Tyrrell J, Nalls MA, Simonsick EM, Garimella PS, Shiroma EJ, Verweij N, van der Meer P, Gansevoort RT, Snieder H, Gallins PJ, Jima DD, Wright F, Zhou YH, Ferrucci L, Bandinelli S, Hernandez DG, van der Harst P, Patel VV, Waterworth DM, Chu AY, Oguro-Ando A, Frayling TM. Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies. Am J Hum Genet 2022; 109:1638-1652. [PMID: 36055212 PMCID: PMC9502050 DOI: 10.1016/j.ajhg.2022.08.004] [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: 04/14/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) are currently under clinical development for treating anemia in chronic kidney disease (CKD), but it is important to monitor their cardiovascular safety. Genetic variants can be used as predictors to help inform the potential risk of adverse effects associated with drug treatments. We therefore aimed to use human genetics to help assess the risk of adverse cardiovascular events associated with therapeutically altered EPO levels to help inform clinical trials studying the safety of HIF-PHIs. By performing a genome-wide association meta-analysis of EPO (n = 6,127), we identified a cis-EPO variant (rs1617640) lying in the EPO promoter region. We validated this variant as most likely causal in controlling EPO levels by using genetic and functional approaches, including single-base gene editing. Using this variant as a partial predictor for therapeutic modulation of EPO and large genome-wide association data in Mendelian randomization tests, we found no evidence (at p < 0.05) that genetically predicted long-term rises in endogenous EPO, equivalent to a 2.2-unit increase, increased risk of coronary artery disease (CAD, OR [95% CI] = 1.01 [0.93, 1.07]), myocardial infarction (MI, OR [95% CI] = 0.99 [0.87, 1.15]), or stroke (OR [95% CI] = 0.97 [0.87, 1.07]). We could exclude increased odds of 1.15 for cardiovascular disease for a 2.2-unit EPO increase. A combination of genetic and functional studies provides a powerful approach to investigate the potential therapeutic profile of EPO-increasing therapies for treating anemia in CKD.
Collapse
Affiliation(s)
- Charli E Harlow
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Josan Gandawijaya
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Rosemary A Bamford
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Emily-Rose Martin
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Andrew R Wood
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Peter J van der Most
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen 9713, the Netherlands
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy S Etheridge
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | | | - Robin N Beaumont
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eleanor M Simonsick
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Pranav S Garimella
- Division of Nephrology-Hypertension, University of California San Diego, San Diego, CA, USA
| | - Eric J Shiroma
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD 20892, USA
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713, the Netherlands
| | - Peter van der Meer
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713, the Netherlands
| | - Ron T Gansevoort
- University of Groningen, University Medical Center Groningen, Department of Nephrology, Groningen 9713, the Netherlands
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen 9713, the Netherlands
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
| | - Fred Wright
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | | | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | | | | | | | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK.
| | - Timothy M Frayling
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK.
| |
Collapse
|
13
|
Sen T, Thummer RP. CRISPR and iPSCs: Recent Developments and Future Perspectives in Neurodegenerative Disease Modelling, Research, and Therapeutics. Neurotox Res 2022; 40:1597-1623. [PMID: 36044181 PMCID: PMC9428373 DOI: 10.1007/s12640-022-00564-w] [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: 03/21/2022] [Revised: 06/17/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
Neurodegenerative diseases are prominent causes of pain, suffering, and death worldwide. Traditional approaches modelling neurodegenerative diseases are deficient, and therefore, improved strategies that effectively recapitulate the pathophysiological conditions of neurodegenerative diseases are the need of the hour. The generation of human-induced pluripotent stem cells (iPSCs) has transformed our ability to model neurodegenerative diseases in vitro and provide an unlimited source of cells (including desired neuronal cell types) for cell replacement therapy. Recently, CRISPR/Cas9-based genome editing has also been gaining popularity because of the flexibility they provide to generate and ablate disease phenotypes. In addition, the recent advancements in CRISPR/Cas9 technology enables researchers to seamlessly target and introduce precise modifications in the genomic DNA of different human cell lines, including iPSCs. CRISPR-iPSC-based disease modelling, therefore, allows scientists to recapitulate the pathological aspects of most neurodegenerative processes and investigate the role of pathological gene variants in healthy non-patient cell lines. This review outlines how iPSCs, CRISPR/Cas9, and CRISPR-iPSC-based approaches accelerate research on neurodegenerative diseases and take us closer to a cure for neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Amyotrophic Lateral Sclerosis, and so forth.
Collapse
Affiliation(s)
- Tirthankar Sen
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
| |
Collapse
|
14
|
Feuer KL, Wahbeh MH, Yovo C, Rabie E, Lam ATN, Abdollahi S, Young LJ, Rike B, Umamageswaran A, Avramopoulos D. CRISPR Del/Rei: a simple, flexible, and efficient pipeline for scarless genome editing. Sci Rep 2022; 12:11928. [PMID: 35831384 PMCID: PMC9279498 DOI: 10.1038/s41598-022-16004-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022] Open
Abstract
Scarless genome editing of induced pluripotent stem cells (iPSCs) is crucial for the precise modeling of genetic disease. Here we present CRISPR Del/Rei, a two-step deletion-reinsertion strategy with high editing efficiency and simple PCR-based screening that generates isogenic clones in ~ 2 months. We apply our strategy to edit iPSCs at 3 loci with only rare off target editing.
Collapse
Affiliation(s)
- Kyra L Feuer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
- Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, USA
| | - Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
- Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Eman Rabie
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
- Biotechnology Program, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt
| | - Anh-Thu N Lam
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Sara Abdollahi
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Lindsay J Young
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Akul Umamageswaran
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA.
| |
Collapse
|
15
|
Lee OH, Lee S, Park M, Moon S, Hwang S, Kim B, Kim CY, Lee DR, Shim SH, Park KH, Chung HM, Choi Y. Generation of a B2M homozygous knockout human somatic cell nuclear transfer-derived embryonic stem cell line using the CRISPR/Cas9 system. Stem Cell Res 2022; 59:102643. [PMID: 34971932 DOI: 10.1016/j.scr.2021.102643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/23/2021] [Accepted: 12/26/2021] [Indexed: 10/19/2022] Open
Abstract
Beta2-microglobulin (B2M) is a subunit of human leukocyte antigen class-I (HLA-I) heterodimer that mediates immune rejection through activation of cytotoxic T cells. B2M binding to HLA-I proteins is essential for functional HLA-I on the cell surface. Here, we generated a B2M homozygous knockout somatic cell nuclear transfer-induced embryonic stem cell (SCNT-ESC) line using CRISPR/Cas9-mediated gene targeting. B2M KO cell line, which does not express HLA-I molecules on cell surface, has pluripotency and differentiation ability to three germ layers. This cell line provides a useful cell source for investigating immunogenicity of allogeneic ESCs and their derivatives for tissue regeneration.
Collapse
Affiliation(s)
- Ok-Hee Lee
- Department of Biomedical Science, CHA University, Seongnam-si, Gyeonggi-do 13488, Republic of Korea; Department of Veterinary Physiology, College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Siyoung Lee
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Miseon Park
- Fertility Center of CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06135, Republic of Korea
| | - Sohyeon Moon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Semi Hwang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Byeongseok Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - C-Yoon Kim
- Department of Veterinary Physiology, College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Dong Ryul Lee
- Department of Biomedical Science, CHA University, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, CHA University, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Keun-Hong Park
- Department of Biomedical Science, CHA University, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Hyung Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| |
Collapse
|
16
|
Wei R, Yang J, Cheng CW, Ho WI, Li N, Hu Y, Hong X, Fu J, Yang B, Liu Y, Jiang L, Lai WH, Au KW, Tsang WL, Tse YL, Ng KM, Esteban MA, Tse HF. CRISPR-targeted genome editing of human induced pluripotent stem cell-derived hepatocytes for the treatment of Wilson's disease. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2021; 4:100389. [PMID: 34877514 PMCID: PMC8633686 DOI: 10.1016/j.jhepr.2021.100389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 09/28/2021] [Accepted: 10/18/2021] [Indexed: 02/07/2023]
Abstract
Background & Aims Wilson’s disease (WD) is an autosomal recessive disorder of copper metabolism caused by loss-of-function mutations in ATP7B, which encodes a copper-transporting protein. It is characterized by excessive copper deposition in tissues, predominantly in the liver and brain. We sought to investigate whether gene-corrected patient-specific induced pluripotent stem cell (iPSC)-derived hepatocytes (iHeps) could serve as an autologous cell source for cellular transplantation therapy in WD. Methods We first compared the in vitro phenotype and cellular function of ATP7B before and after gene correction using CRISPR/Cas9 and single-stranded oligodeoxynucleotides (ssODNs) in iHeps (derived from patients with WD) which were homozygous for the ATP7B R778L mutation (ATP7BR778L/R778L). Next, we evaluated the in vivo therapeutic potential of cellular transplantation of WD gene-corrected iHeps in an immunodeficient WD mouse model (Atp7b-/-/ Rag2-/-/ Il2rg-/-; ARG). Results We successfully created iPSCs with heterozygous gene correction carrying 1 allele of the wild-type ATP7B gene (ATP7BWT/-) using CRISPR/Cas9 and ssODNs. Compared with ATP7BR778L/R778L iHeps, gene-corrected ATP7BWT/- iHeps restored in vitro ATP7B subcellular localization, its subcellular trafficking in response to copper overload and its copper exportation function. Moreover, in vivo cellular transplantation of ATP7BWT/- iHeps into ARG mice via intra-splenic injection significantly attenuated the hepatic manifestations of WD. Liver function improved and liver fibrosis decreased due to reductions in hepatic copper accumulation and consequently copper-induced hepatocyte toxicity. Conclusions Our findings demonstrate that gene-corrected patient-specific iPSC-derived iHeps can rescue the in vitro and in vivo disease phenotypes of WD. These proof-of-principle data suggest that iHeps derived from gene-corrected WD iPSCs have potential use as an autologous ex vivo cell source for in vivo therapy of WD as well as other inherited liver disorders. Lay summary Gene correction restored ATP7B function in hepatocytes derived from induced pluripotent stem cells that originated from a patient with Wilson’s disease. These gene-corrected hepatocytes are potential cell sources for autologous cell therapy in patients with Wilson’s disease. Correction of the ATP7B R778L mutation restored the subcellular localization of ATP7B in iHeps. The copper exportation capability of ATP7B was restored in gene-corrected iHeps. Gene-corrected iHeps reduced hepatic copper accumulation and copper-induced hepatic toxicity in mice with Wilson’s disease. Gene-corrected iHeps are potential ex vivo cell sources for therapy in Wilson’s disease.
Collapse
Key Words
- AFP, alpha-fetoprotein
- ALB, albumin
- ATP7B, ATPase copper transporting beta
- ATPase copper transporting beta polypeptide (ATP7B)
- Clustered regularly interspaced palindromic repeats (CRISPR)/Cas9
- EB, embryoid body
- RFLP, restriction fragment length polymorphism
- Single-stranded Oligodeoxynucleotide (ssODN)
- TGN, trans-Golgi network
- WD, Wilson’s disease
- Wilson’s disease
- cell therapy
- gene correction
- iHep(s), iPSC-derived hepatocyte(s)
- iPSC, induced pluripotent stem cell
- iPSC-derived hepatocytes (iHeps)
- induced pluripotent stem cell (iPSC)
- sgRNA, single guide RNA
- ssODN, single-stranded oligodeoxynucleotide
Collapse
Affiliation(s)
- Rui Wei
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
- Center for Translational Stem Cell Biology, Hong Kong, China
| | - Jiayin Yang
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Cell Inspire Therapeutics Co., Ltd and Cell Inspire Biotechnology Co., Ltd, Shenzhen 518102, China
| | - Chi-Wa Cheng
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Wai-In Ho
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Na Li
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Yang Hu
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Xueyu Hong
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jian Fu
- Cell Inspire Therapeutics Co., Ltd and Cell Inspire Biotechnology Co., Ltd, Shenzhen 518102, China
| | - Bo Yang
- Cell Inspire Therapeutics Co., Ltd and Cell Inspire Biotechnology Co., Ltd, Shenzhen 518102, China
| | - Yuqing Liu
- Cell Inspire Therapeutics Co., Ltd and Cell Inspire Biotechnology Co., Ltd, Shenzhen 518102, China
| | - Lixiang Jiang
- Cell Inspire Therapeutics Co., Ltd and Cell Inspire Biotechnology Co., Ltd, Shenzhen 518102, China
| | - Wing-Hon Lai
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Ka-Wing Au
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Wai-Ling Tsang
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yiu-Lam Tse
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
| | - Kwong-Man Ng
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
- Center for Translational Stem Cell Biology, Hong Kong, China
| | - Miguel A. Esteban
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China
- Corresponding authors. Address: Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China; Tel.: (852) 2255-4694, fax: (852) 2818-6304.
| | - Hung-Fat Tse
- The Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Hong Kong-Guangdong Stem Cell and Regenerative Medicine Research Centre, The University of Hong Kong and Guangzhou Institutes of Biomedicine and Health, Hong Kong, China
- Center for Translational Stem Cell Biology, Hong Kong, China
- Heart and Vascular Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
- Corresponding authors. Address: Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China; Tel.: (852) 2255-4694, fax: (852) 2818-6304.
| |
Collapse
|
17
|
Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
Collapse
Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
| |
Collapse
|
18
|
Chin YW, Shin SC, Han S, Jang HW, Kim HJ. CRISPR/Cas9-mediated Inactivation of arginase in a yeast strain isolated from Nuruk and its impact on the whole genome. J Biotechnol 2021; 341:163-167. [PMID: 34601018 DOI: 10.1016/j.jbiotec.2021.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/30/2021] [Accepted: 09/26/2021] [Indexed: 12/22/2022]
Abstract
Despite the advantages of CRISPR/Cas9 technology in the food industry, controversy over its off-target effects exists. We engineered an industrial Saccharomyces cerevisiae strain isolated from a Korean rice wine starter, Nuruk, using CRISPR/Cas9 to decrease ethyl carbamate (EC) formation. We disrupted the CAR1 gene encoding arginase, which plays a key role in EC formation. Subsequently, we compared the whole genome of the engineered strain to that of the wild type by analyzing heterozygous and homozygous mutations through variant calling. Homozygous mutations in the genome of the engineered strains were identified as the target mutations in CAR1 induced by CRISPR/Cas9, and no other off-target effects were observed. Our findings have critical implications for the use of CRISRP/Cas9 technology in yeasts in the food industry.
Collapse
Affiliation(s)
- Young-Wook Chin
- Research Group of Traditional Food, Research Division of Strategic Food Technology, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Seung Chul Shin
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Suk Han
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Hae Won Jang
- Research Group of Traditional Food, Research Division of Strategic Food Technology, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; Department of Food Science and Biotechnology, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Hyo Jin Kim
- Research Group of Traditional Food, Research Division of Strategic Food Technology, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea.
| |
Collapse
|
19
|
Kyrousi C, O’Neill AC, Brazovskaja A, He Z, Kielkowski P, Coquand L, Di Giaimo R, D’ Andrea P, Belka A, Forero Echeverry A, Mei D, Lenge M, Cruceanu C, Buchsbaum IY, Khattak S, Fabien G, Binder E, Elmslie F, Guerrini R, Baffet AD, Sieber SA, Treutlein B, Robertson SP, Cappello S. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nat Commun 2021; 12:6298. [PMID: 34728600 PMCID: PMC8564519 DOI: 10.1038/s41467-021-26447-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.
Collapse
Affiliation(s)
- Christina Kyrousi
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5216.00000 0001 2155 0800Present Address: First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Greece and University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Adam C. O’Neill
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Agnieska Brazovskaja
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Zhisong He
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Pavel Kielkowski
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377 München, Germany
| | - Laure Coquand
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Rossella Di Giaimo
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pierpaolo D’ Andrea
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander Belka
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Davide Mei
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Matteo Lenge
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Cristiana Cruceanu
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Isabel Y. Buchsbaum
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5252.00000 0004 1936 973XGraduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich Planegg, Germany
| | - Shahryar Khattak
- grid.4488.00000 0001 2111 7257DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany ,grid.4912.e0000 0004 0488 7120Present Address: Royal College of Surgeons Ireland (RCSI) in Bahrain, Adliya, Kingdom of Bahrain
| | - Guimiot Fabien
- grid.50550.350000 0001 2175 4109Unité de Foetopathologie, Assistance Publique-Hôpitaux de Paris, CHU Robert Debré, F-75019 Paris, France
| | - Elisabeth Binder
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Frances Elmslie
- grid.4464.20000 0001 2161 2573South West Thames Regional Genetics Service, St George’s, University of London, London, SW17 0RE UK
| | - Renzo Guerrini
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Alexandre D. Baffet
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Stephan A. Sieber
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Barbara Treutlein
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Stephen P. Robertson
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Silvia Cappello
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| |
Collapse
|
20
|
Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
Collapse
|
21
|
Nami F, Ramezankhani R, Vandenabeele M, Vervliet T, Vogels K, Urano F, Verfaillie C. Fast and Efficient Generation of Isogenic Induced Pluripotent Stem Cell Lines Using Adenine Base Editing. CRISPR J 2021; 4:502-518. [PMID: 34406036 DOI: 10.1089/crispr.2021.0006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Isogenic induced pluripotent stem cell (iPSC) lines are currently mostly created by homology directed repair evoked by a double-strand break (DSB) generated by CRISPR-Cas9. However, this process is in general lengthy and inefficient. This problem can be overcome, specifically for correction or insertion of transition mutations, by using base editing (BE). BE does not require DSB formation, hence avoiding creation of genomic off-target breaks and insertions and deletions, and as it is highly efficient, it also does not require integration of selection cassettes in the genome to enrich for edited cells. BE has been successfully used in many cell types as well as in some in vivo settings to correct or insert mutations, but very few studies have reported generation of isogenic iPSC lines using BE. Here, we describe a simple and fast workflow to generate isogenic iPSCs efficiently with a compound heterozygous or a homozygous Wolfram syndrome 1 (WFS1) mutation using adenine BE, without the need to include a genomic selection cassette and without off-target modifications. We demonstrated that correctly base-edited clones can be generated by screening only five cell clones in less than a month, provided that the mutation is positioned in a correct place with regards to the protospacer adjacent motif sequence and no putative bystander bases exist.
Collapse
Affiliation(s)
- Fatemeharefeh Nami
- Department of Development and Regeneration, KU Leuven, Stamcelinstituut, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| | - Roya Ramezankhani
- Department of Development and Regeneration, KU Leuven, Stamcelinstituut, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marjan Vandenabeele
- Department of Development and Regeneration, KU Leuven, Stamcelinstituut, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, KU Leuven, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Cellular and Molecular Medicine, Campus Gasthuisberg, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kristy Vogels
- Department of Development and Regeneration, KU Leuven, Stamcelinstituut, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| | - Fumihiko Urano
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, USA; and Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Catherine Verfaillie
- Department of Development and Regeneration, KU Leuven, Stamcelinstituut, Leuven, Belgium; Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
22
|
Thues C, Valadas JS, Deaulmerie L, Geens A, Chouhan AK, Duran-Romaña R, Schymkowitz J, Rousseau F, Bartusel M, Rehimi R, Rada-Iglesias A, Verstreken P, Van Esch H. MAPRE2 mutations result in altered human cranial neural crest migration, underlying craniofacial malformations in CSC-KT syndrome. Sci Rep 2021; 11:4976. [PMID: 33654163 PMCID: PMC7925611 DOI: 10.1038/s41598-021-83771-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Circumferential skin creases (CSC-KT) is a rare polymalformative syndrome characterised by intellectual disability associated with skin creases on the limbs, and very characteristic craniofacial malformations. Previously, heterozygous and homozygous mutations in MAPRE2 were found to be causal for this disease. MAPRE2 encodes for a member of evolutionary conserved microtubule plus end tracking proteins, the end binding (EB) family. Unlike MAPRE1 and MAPRE3, MAPRE2 is not required for the persistent growth and stabilization of microtubules, but plays a role in other cellular processes such as mitotic progression and regulation of cell adhesion. The mutations identified in MAPRE2 all reside within the calponin homology domain, responsible to track and interact with the plus-end tip of growing microtubules, and previous data showed that altered dosage of MAPRE2 resulted in abnormal branchial arch patterning in zebrafish. In this study, we developed patient derived induced pluripotent stem cell lines for MAPRE2, together with isogenic controls, using CRISPR/Cas9 technology, and differentiated them towards neural crest cells with cranial identity. We show that changes in MAPRE2 lead to alterations in neural crest migration in vitro but also in vivo, following xenotransplantation of neural crest progenitors into developing chicken embryos. In addition, we provide evidence that changes in focal adhesion might underlie the altered cell motility of the MAPRE2 mutant cranial neural crest cells. Our data provide evidence that MAPRE2 is involved in cellular migration of cranial neural crest and offers critical insights into the mechanism underlying the craniofacial dysmorphisms and cleft palate present in CSC-KT patients. This adds the CSC-KT disorder to the growing list of neurocristopathies.
Collapse
Affiliation(s)
- Cedric Thues
- Laboratory for the Genetics of Cognition, Department of Human Genetics, Center for Human Genetics, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Jorge S Valadas
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Liesbeth Deaulmerie
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Ann Geens
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Amit K Chouhan
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931, Cologne, Germany
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St., Cambridge, MA, 02142, USA
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931, Cologne, Germany
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011, Santander, Spain
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hilde Van Esch
- Laboratory for the Genetics of Cognition, Department of Human Genetics, Center for Human Genetics, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
23
|
Gruber JJ, Chen J, Geller B, Jäger N, Lipchik AM, Wang G, Kurian AW, Ford JM, Snyder MP. Chromatin Remodeling in Response to BRCA2-Crisis. Cell Rep 2020; 28:2182-2193.e6. [PMID: 31433991 DOI: 10.1016/j.celrep.2019.07.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 06/05/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022] Open
Abstract
Individuals with a single functional copy of the BRCA2 tumor suppressor have elevated risks for breast, ovarian, and other solid tumor malignancies. The exact mechanisms of carcinogenesis due to BRCA2 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function ("BRCA2-crisis"), which may contribute to disease. Here, we establish an in vitro model for BRCA2-crisis that demonstrates chromatin remodeling and activation of an NF-κB survival pathway in response to transient BRCA2 depletion. Mechanistically, we identify BRCA2 chromatin binding, histone acetylation, and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis. These chromatin alterations are reflected in transcriptional profiles of pre-malignant tissues from BRCA2 carriers and, therefore, may reflect natural steps in human disease. By modeling BRCA2-crisis in vitro, we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.
Collapse
Affiliation(s)
- Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Oncology Division, Stanford University, Stanford, CA 94305, USA
| | - Justin Chen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Benjamin Geller
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Natalie Jäger
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andrew M Lipchik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Allison W Kurian
- Department of Medicine, Oncology Division, Stanford University, Stanford, CA 94305, USA
| | - James M Ford
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Oncology Division, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
24
|
Kumar D, Anand T, Talluri TR, Kues WA. Potential of transposon-mediated cellular reprogramming towards cell-based therapies. World J Stem Cells 2020; 12:527-544. [PMID: 32843912 PMCID: PMC7415244 DOI: 10.4252/wjsc.v12.i7.527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/09/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem (iPS) cells present a seminal discovery in cell biology and promise to support innovative treatments of so far incurable diseases. To translate iPS technology into clinical trials, the safety and stability of these reprogrammed cells needs to be shown. In recent years, different non-viral transposon systems have been developed for the induction of cellular pluripotency, and for the directed differentiation into desired cell types. In this review, we summarize the current state of the art of different transposon systems in iPS-based cell therapies.
Collapse
Affiliation(s)
- Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India.
| | - Taruna Anand
- NCVTC, ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Thirumala R Talluri
- Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner 334001, India
| | - Wilfried A Kues
- Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics, Department of Biotechnology, Mariensee 31535, Germany
| |
Collapse
|
25
|
Trevisan M, Masi G, Palù G. Genome editing technologies to treat rare liver diseases. Transl Gastroenterol Hepatol 2020; 5:23. [PMID: 32258527 DOI: 10.21037/tgh.2019.10.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Liver has a central role in protein and lipid metabolism, and diseases involving hepatocytes have often repercussions on multiple organs and systems. Hepatic disorders are frequently characterized by production of defective or non-functional proteins, and traditional gene therapy approaches have been attempted for years to restore adequate protein levels through delivery of transgenes. Recently, many different genome editing platforms have been developed aimed at correcting at DNA level the defects underlying the diseases. In this Review we discuss the latest applications of these tools applied to develop therapeutic strategies for rare liver disorders, in particular updating the literature with the most recent strategies relying on base editors technology.
Collapse
Affiliation(s)
- Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| |
Collapse
|
26
|
Kim J, Lana B, Torelli S, Ryan D, Catapano F, Ala P, Luft C, Stevens E, Konstantinidis E, Louzada S, Fu B, Paredes‐Redondo A, Chan AWE, Yang F, Stemple DL, Liu P, Ketteler R, Selwood DL, Muntoni F, Lin Y. A new patient-derived iPSC model for dystroglycanopathies validates a compound that increases glycosylation of α-dystroglycan. EMBO Rep 2019; 20:e47967. [PMID: 31566294 PMCID: PMC6832011 DOI: 10.15252/embr.201947967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/24/2019] [Accepted: 08/29/2019] [Indexed: 12/24/2022] Open
Abstract
Dystroglycan, an extracellular matrix receptor, has essential functions in various tissues. Loss of α-dystroglycan-laminin interaction due to defective glycosylation of α-dystroglycan underlies a group of congenital muscular dystrophies often associated with brain malformations, referred to as dystroglycanopathies. The lack of isogenic human dystroglycanopathy cell models has limited our ability to test potential drugs in a human- and neural-specific context. Here, we generated induced pluripotent stem cells (iPSCs) from a severe dystroglycanopathy patient with homozygous FKRP (fukutin-related protein gene) mutation. We showed that CRISPR/Cas9-mediated gene correction of FKRP restored glycosylation of α-dystroglycan in iPSC-derived cortical neurons, whereas targeted gene mutation of FKRP in wild-type cells disrupted this glycosylation. In parallel, we screened 31,954 small molecule compounds using a mouse myoblast line for increased glycosylation of α-dystroglycan. Using human FKRP-iPSC-derived neural cells for hit validation, we demonstrated that compound 4-(4-bromophenyl)-6-ethylsulfanyl-2-oxo-3,4-dihydro-1H-pyridine-5-carbonitrile (4BPPNit) significantly augmented glycosylation of α-dystroglycan, in part through upregulation of LARGE1 glycosyltransferase gene expression. Together, isogenic human iPSC-derived cells represent a valuable platform for facilitating dystroglycanopathy drug discovery and therapeutic development.
Collapse
Affiliation(s)
- Jihee Kim
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Beatrice Lana
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Silvia Torelli
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - David Ryan
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | | | - Pierpaolo Ala
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - Christin Luft
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | | | - Evangelos Konstantinidis
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | | | - Beiyuan Fu
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | - Amaia Paredes‐Redondo
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - AW Edith Chan
- The Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | | | | | - Pentao Liu
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - David L Selwood
- The Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | - Francesco Muntoni
- UCL Great Ormond Street Institute of Child HealthLondonUK
- NIHR Biomedical Research Centre at Great Ormond Street HospitalLondonUK
| | - Yung‐Yao Lin
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| |
Collapse
|
27
|
Naphade S, Tshilenge KT, Ellerby LM. Modeling Polyglutamine Expansion Diseases with Induced Pluripotent Stem Cells. Neurotherapeutics 2019; 16:979-998. [PMID: 31792895 PMCID: PMC6985408 DOI: 10.1007/s13311-019-00810-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polyglutamine expansion disorders, which include Huntington's disease, have expanded CAG repeats that result in polyglutamine expansions in affected proteins. How this specific feature leads to distinct neuropathies in 11 different diseases is a fascinating area of investigation. Most proteins affected by polyglutamine expansions are ubiquitously expressed, yet their mechanisms of selective neurotoxicity are unknown. Induced pluripotent stem cells have emerged as a valuable tool to model diseases, understand molecular mechanisms, and generate relevant human neural and glia subtypes, cocultures, and organoids. Ideally, this tool will generate specific neuronal populations that faithfully recapitulate specific polyglutamine expansion disorder phenotypes and mimic the selective vulnerability of a given disease. Here, we review how induced pluripotent technology is used to understand the effects of the disease-causing polyglutamine protein on cell function, identify new therapeutic targets, and determine how polyglutamine expansion affects human neurodevelopment and disease. We will discuss ongoing challenges and limitations in our use of induced pluripotent stem cells to model polyglutamine expansion diseases.
Collapse
Affiliation(s)
- Swati Naphade
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | | | - Lisa M Ellerby
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA.
| |
Collapse
|
28
|
Bertero A, Fields PA, Smith AST, Leonard A, Beussman K, Sniadecki NJ, Kim DH, Tse HF, Pabon L, Shendure J, Noble WS, Murry CE. Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. J Cell Biol 2019; 218:2919-2944. [PMID: 31395619 PMCID: PMC6719452 DOI: 10.1083/jcb.201902117] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/20/2019] [Accepted: 07/10/2019] [Indexed: 01/16/2023] Open
Abstract
Mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared with gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape segregation to the nuclear lamina and inactivation during cardiogenesis. These regions exhibit up-regulation of multiple noncardiac genes including CACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. However, chromatin compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. Thus, global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency.
Collapse
Affiliation(s)
- Alessandro Bertero
- Department of Pathology, University of Washington, Seattle, WA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Paul A Fields
- Department of Pathology, University of Washington, Seattle, WA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Alec S T Smith
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Andrea Leonard
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Mechanical Engineering, University of Washington, Seattle, WA
| | - Kevin Beussman
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Mechanical Engineering, University of Washington, Seattle, WA
| | - Nathan J Sniadecki
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
- Department of Mechanical Engineering, University of Washington, Seattle, WA
| | - Deok-Ho Kim
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Hung-Fat Tse
- Cardiology Division, Department of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lil Pabon
- Department of Pathology, University of Washington, Seattle, WA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Charles E Murry
- Department of Pathology, University of Washington, Seattle, WA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
- Department of Medicine/Cardiology, University of Washington, Seattle, WA
| |
Collapse
|
29
|
One-Step Generation of Seamless Luciferase Gene Knockin Using CRISPR/Cas9 Genome Editing in Human Pluripotent Stem Cells. Methods Mol Biol 2019; 1942:61-69. [PMID: 30900175 DOI: 10.1007/978-1-4939-9080-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Human pluripotent stem cells (hPSCs) offer powerful platforms for studying mechanisms of human diseases and for evaluating potential treatments. Genome editing, particularly the CRISPR/Cas9-based method, is highly effective for generating cell and animal models to study genetic human diseases. However, the procedure for generating gene-edited hPSCs is laborious, time consuming and unintentional genetic changes may confound the consequent experiments and conclusions. Here we describe one-step knockin of the NanoLuc luciferase gene (Nluc) to the fragile X syndrome gene, FMR1, in a human embryonic stem cell line (hESC), H1, and a fragile X disease model human induced pluripotent stem cell line (hiPSC), FX-iPSC. The luciferase reporter cell lines provide new platforms for exploring potential treatments for fragile X syndrome. The shortened and scarless targeting method described here can be effectively applied to other genes.
Collapse
|
30
|
Bollen Y, Post J, Koo BK, Snippert HJG. How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing. Nucleic Acids Res 2019; 46:6435-6454. [PMID: 29955892 PMCID: PMC6061873 DOI: 10.1093/nar/gky571] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Abstract
Model systems with defined genetic modifications are powerful tools for basic research and translational disease modelling. Fortunately, generating state-of-the-art genetic model systems is becoming more accessible to non-geneticists due to advances in genome editing technologies. As a consequence, solely relying on (transient) overexpression of (mutant) effector proteins is no longer recommended since scientific standards increasingly demand genetic modification of endogenous loci. In this review, we provide up-to-date guidelines with respect to homology-directed repair (HDR)-mediated editing of mammalian model systems, aimed at assisting researchers in designing an efficient genome editing strategy.
Collapse
Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands.,Medical Cell BioPhysics, MIRA Institute, University of Twente, Enschede, The Netherlands
| | - Jasmin Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| |
Collapse
|
31
|
Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC. Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation. iScience 2019; 16:206-217. [PMID: 31185456 PMCID: PMC6556878 DOI: 10.1016/j.isci.2019.05.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
During mammalian development, liver differentiation is driven by signals that converge on multiple transcription factor networks. The hepatocyte nuclear factor signaling network is known to be essential for hepatocyte specification and maintenance. In this study, we have generated deletion and point mutants of hepatocyte nuclear factor-4alpha (HNF4α) to precisely evaluate the function of protein domains during hepatocyte specification from human pluripotent stem cells. We demonstrate that nuclear HNF4α is essential for hepatic progenitor specification, and the introduction of point mutations in HNF4α's Small Ubiquitin-like Modifier (SUMO) consensus motif leads to disrupted hepatocyte differentiation. Taking a multiomics approach, we identified key deficiencies in cell biology, which included dysfunctional metabolism, substrate adhesion, tricarboxylic acid cycle flux, microRNA transport, and mRNA processing. In summary, the combination of genome editing and multiomics analyses has provided valuable insight into the diverse functions of HNF4α during pluripotent stem cell entry into the hepatic lineage and during hepatocellular differentiation.
Collapse
Affiliation(s)
- Yu Wang
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology eV-Hans-Knoll Institute, Jena, Germany
| | - Carolyn Swann
- National Institute for Biological Standards and Control (MHRA), Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK
| | - Karamjit Singh-Dolt
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Jose Meseguer-Ripolles
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Baltasar Lucendo-Villarin
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Tilo Kunath
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Timothy R Rudd
- National Institute for Biological Standards and Control (MHRA), Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK
| | - Andrew J H Smith
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Jan G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Patricio Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David C Hay
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK.
| |
Collapse
|
32
|
Doi M, Shimatani H, Atobe Y, Murai I, Hayashi H, Takahashi Y, Fustin JM, Yamaguchi Y, Kiyonari H, Koike N, Yagita K, Lee C, Abe M, Sakimura K, Okamura H. Non-coding cis-element of Period2 is essential for maintaining organismal circadian behaviour and body temperature rhythmicity. Nat Commun 2019; 10:2563. [PMID: 31189882 PMCID: PMC6561950 DOI: 10.1038/s41467-019-10532-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/16/2019] [Indexed: 12/22/2022] Open
Abstract
Non-coding cis-regulatory elements are essential determinants of development, but their exact impacts on behavior and physiology in adults remain elusive. Cis-element-based transcriptional regulation is believed to be crucial for generating circadian rhythms in behavior and physiology. However, genetic evidence supporting this model is based on mutations in the protein-coding sequences of clock genes. Here, we report generation of mutant mice carrying a mutation only at the E'-box cis-element in the promoter region of the core clock gene Per2. The Per2 E'-box mutation abolishes sustainable molecular clock oscillations and renders circadian locomotor activity and body temperature rhythms unstable. Without the E'-box, Per2 messenger RNA and protein expression remain at mid-to-high levels. Our work delineates the Per2 E'-box as a critical nodal element for keeping sustainable cell-autonomous circadian oscillation and reveals the extent of the impact of the non-coding cis-element in daily maintenance of animal locomotor activity and body temperature rhythmicity.
Collapse
Affiliation(s)
- Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
| | - Hiroyuki Shimatani
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yuta Atobe
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Iori Murai
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.,Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Hida Hayashi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yukari Takahashi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Jean-Michel Fustin
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiaki Yamaguchi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Kiyonari
- Laboratories for Animal Resource Development and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Choogon Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Hitoshi Okamura
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan. .,Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
| |
Collapse
|
33
|
Use of human pluripotent stem cell-derived cells for neurodegenerative disease modeling and drug screening platform. Future Med Chem 2019; 11:1305-1322. [DOI: 10.4155/fmc-2018-0520] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most neurodegenerative diseases are characterized by a complex and mostly still unresolved pathology. This fact, together with the lack of reliable disease models, has precluded the development of effective therapies counteracting the disease progression. The advent of human pluripotent stem cells has revolutionized the field allowing the generation of disease-relevant neural cell types that can be used for disease modeling, drug screening and, possibly, cell transplantation purposes. In this Review, we discuss the applications of human pluripotent stem cells, the development of efficient protocols for the derivation of the different neural cells and their applicability for robust in vitro disease modeling and drug screening platforms for most common neurodegenerative conditions.
Collapse
|
34
|
Salvarani N, Crasto S, Miragoli M, Bertero A, Paulis M, Kunderfranco P, Serio S, Forni A, Lucarelli C, Dal Ferro M, Larcher V, Sinagra G, Vezzoni P, Murry CE, Faggian G, Condorelli G, Di Pasquale E. The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. Nat Commun 2019; 10:2267. [PMID: 31118417 PMCID: PMC6531493 DOI: 10.1038/s41467-019-09929-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/06/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in LMNA, which encodes the nuclear proteins Lamin A/C, can cause cardiomyopathy and conduction disorders. Here, we employ induced pluripotent stem cells (iPSCs) generated from human cells carrying heterozygous K219T mutation on LMNA to develop a disease model. Cardiomyocytes differentiated from these iPSCs, and which thus carry K219T-LMNA, have altered action potential, reduced peak sodium current and diminished conduction velocity. Moreover, they have significantly downregulated Nav1.5 channel expression and increased binding of Lamin A/C to the promoter of SCN5A, the channel's gene. Coherently, binding of the Polycomb Repressive Complex 2 (PRC2) protein SUZ12 and deposition of the repressive histone mark H3K27me3 are increased at SCN5A. CRISPR/Cas9-mediated correction of the mutation re-establishes sodium current density and SCN5A expression. Thus, K219T-LMNA cooperates with PRC2 in downregulating SCN5A, leading to decreased sodium current density and slower conduction velocity. This mechanism may underlie the conduction abnormalities associated with LMNA-cardiomyopathy.
Collapse
Affiliation(s)
- Nicolò Salvarani
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Silvia Crasto
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Michele Miragoli
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
- Department of Medicine and Surgery, University of Parma, Parma, 43121, Italy
| | - Alessandro Bertero
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, 98109, WA, USA
| | - Marianna Paulis
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Paolo Kunderfranco
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Simone Serio
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Alberto Forni
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Carla Lucarelli
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Matteo Dal Ferro
- Cardiovascular Department, "Ospedali Riuniti" and University of Trieste, Trieste, 34129, Italy
| | - Veronica Larcher
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Gianfranco Sinagra
- Cardiovascular Department, "Ospedali Riuniti" and University of Trieste, Trieste, 34129, Italy
| | - Paolo Vezzoni
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, 98109, WA, USA
| | - Giuseppe Faggian
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Gianluigi Condorelli
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy.
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy.
- Humanitas University, Rozzano (MI), 20089, Italy.
| | - Elisa Di Pasquale
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy.
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy.
| |
Collapse
|
35
|
Jarazo J, Qing X, Schwamborn JC. Guidelines for Fluorescent Guided Biallelic HDR Targeting Selection With PiggyBac System Removal for Gene Editing. Front Genet 2019; 10:190. [PMID: 30930935 PMCID: PMC6425911 DOI: 10.3389/fgene.2019.00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
The development of new and easy-to-use nucleases, such as CRISPR/Cas9, made tools for gene editing widely accessible to the scientific community. Cas9-based gene editing protocols are robust for creating knock-out models, but the generation of single nucleotide transitions or transversions remains challenging. This is mainly due to the low frequency of homology directed repair, which leads to the screening of a high number of clones to identify positive events. Moreover, lack of simultaneous biallelic modifications, frequently results in second-allele indels. For example, while one allele might undergo homology directed repair, the second can undergo non-homologous end joining repair. Here we present a step-wise protocol for biallelic gene editing. It uses two donors carrying a combination of fluorescent reporters alongside homology arms directed to the same genomic region for biallelic targeting. These homology arms carry the desired composite of modifications to be introduced (homozygous or heterozygous changes). Plus, the backbone of the plasmid carries a third fluorescent reporter for negative selection (to discard random integration events). Fluorescent selection of non-random biallelic targeted clones can be performed by microscopy guided picking or cell sorting (FACS). The positive selection module (PSM), carrying the fluorescence reporter and an antibiotic resistance, is flanked by inverted terminal repeats (ITR) that are recognized by transposase. Upon purification of the clones correctly modified, transfection of the excision-only transposase allows the removal of the PSM resulting in the integration of only the desired modifications.
Collapse
Affiliation(s)
- Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Xiaobing Qing
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| |
Collapse
|
36
|
Schumann GG, Fuchs NV, Tristán-Ramos P, Sebe A, Ivics Z, Heras SR. The impact of transposable element activity on therapeutically relevant human stem cells. Mob DNA 2019; 10:9. [PMID: 30899334 PMCID: PMC6408843 DOI: 10.1186/s13100-019-0151-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.
Collapse
Affiliation(s)
- Gerald G Schumann
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Nina V Fuchs
- 2Host-Pathogen Interactions, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Pablo Tristán-Ramos
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Attila Sebe
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Zoltán Ivics
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Sara R Heras
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| |
Collapse
|
37
|
Alateeq S, Ovchinnikov D, Tracey T, Whitworth D, Al-Rubaish A, Al-Ali A, Wolvetang E. Identification of on-target mutagenesis during correction of a beta-thalassemia splice mutation in iPS cells with optimised CRISPR/Cas9-double nickase reveals potential safety concerns. APL Bioeng 2018; 2:046103. [PMID: 31069325 PMCID: PMC6481731 DOI: 10.1063/1.5048625] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Precise and accurate gene correction is crucial for enabling iPSC-based therapies, and Cas9-Nickase based approaches are increasingly considered for in vivo correction of diseases such as beta-thalassemia. Here, we generate footprint-free induced pluripotent stem cells from a patient with a beta-thalassemia mutation (IVSII-1 G > A) and employ a double Cas9nickase-mediated correction strategy combined with a piggyBac transposon-modified donor vector for gene correction. Our approach further aimed to minimize the formation of adjacent single-strand breaks at the targeted allele through the destruction of the binding site for one guide and the use of a synonymous protospacer adjacent motif blocking mutation (canonical PAM sequence 5'-NGG-3' is changed to 5'-NCG-3', where N indicates any nucleobase) for the other guide. We show that this strategy indeed not only permits bi-allelic seamless repair of the beta-globin gene splice site mutation and negligible off-target mutagenesis or re-editing of the targeted allele but also results in unexpected on-target mutagenesis with some guide RNAs (gRNAs) in several targeted clones. This study thus not only validates a framework for seamless gene correction with enhanced specificity and accuracy but also highlights potential safety concerns associated with Cas9-nickase based gene correction.
Collapse
Affiliation(s)
| | - Dmitry Ovchinnikov
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Timothy Tracey
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Deanne Whitworth
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Abdullah Al-Rubaish
- Department of Internal Medicine, College of Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 31451, Kingdom of Saudi Arabia
| | - Amein Al-Ali
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31451, Kingdom of Saudi Arabia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| |
Collapse
|
38
|
Abstract
Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness. [1-6] Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts. Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the gene-centred views of evolution popularized by George Williams[7] and Richard Dawkins,[8] two papers were published back-to-back in Nature in 1980-by Leslie Orgel and Francis Crick[9] and Ford Doolittle and Carmen Sapienza[10] respectively-introducing the concept of selfish genetic elements (at the time called "selfish DNA") to the wider scientific community. Both papers emphasized that genes can spread in a population regardless of their effect on organismal fitness as long as they have a transmission advantage. Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission.[11] Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.[12].
Collapse
Affiliation(s)
- J. Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
| |
Collapse
|
39
|
Ren C, Xu K, Segal DJ, Zhang Z. Strategies for the Enrichment and Selection of Genetically Modified Cells. Trends Biotechnol 2018; 37:56-71. [PMID: 30135027 DOI: 10.1016/j.tibtech.2018.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023]
Abstract
Programmable artificial nucleases have transitioned over the past decade from ZFNs and TALENs to CRISPR/Cas systems, which have been ubiquitously used with great success to modify genomes. The efficiencies of knockout and knockin vary widely among distinct cell types and genomic loci and depend on the nuclease delivery and cleavage efficiencies. Moreover, genetically modified cells are almost phenotypically indistinguishable from normal counterparts, making screening and isolating positive cells rather challenging and time-consuming. To address this issue, we review several strategies for the enrichment and selection of genetically modified cells, including transfection-positive selection, nuclease-positive selection, genome-targeted positive selection, and knockin-positive selection, to provide a reference for future genome research and gene therapy studies.
Collapse
Affiliation(s)
- Chonghua Ren
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China; College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA; These authors contributed equally to this article
| | - Kun Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; These authors contributed equally to this article
| | - David Jay Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
40
|
Generation of a human induced pluripotent stem cell-based model for tauopathies combining three microtubule-associated protein TAU mutations which displays several phenotypes linked to neurodegeneration. Alzheimers Dement 2018; 14:1261-1280. [PMID: 30036493 DOI: 10.1016/j.jalz.2018.05.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/28/2018] [Accepted: 05/13/2018] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Tauopathies are neurodegenerative diseases characterized by TAU protein-related pathology, including frontotemporal dementia and Alzheimer's disease among others. Mutant TAU animal models are available, but none of them faithfully recapitulates human pathology and are not suitable for drug screening. METHODS To create a new in vitro tauopathy model, we generated a footprint-free triple MAPT-mutant human induced pluripotent stem cell line (N279K, P301L, and E10+16 mutations) using clustered regularly interspaced short palindromic repeats-FokI and piggyBac transposase technology. RESULTS Mutant neurons expressed pathogenic 4R and phosphorylated TAU, endogenously triggered TAU aggregation, and had increased electrophysiological activity. TAU-mutant cells presented deficiencies in neurite outgrowth, aberrant sequence of differentiation to cortical neurons, and a significant activation of stress response pathways. RNA sequencing confirmed stress activation, demonstrated a shift toward GABAergic identity, and an upregulation of neurodegenerative pathways. DISCUSSION In summary, we generated a novel in vitro human induced pluripotent stem cell TAU-mutant model displaying neurodegenerative disease phenotypes that could be used for disease modeling and drug screening.
Collapse
|
41
|
HIV-1 inhibition in cells with CXCR4 mutant genome created by CRISPR-Cas9 and piggyBac recombinant technologies. Sci Rep 2018; 8:8573. [PMID: 29872154 PMCID: PMC5988798 DOI: 10.1038/s41598-018-26894-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/22/2018] [Indexed: 01/15/2023] Open
Abstract
The C-X-C chemokine receptor type 4 (CXCR4) is one of the major co-receptors for human immunodeficiency virus type 1 (HIV-1) entry and is considered an important therapeutic target. However, its function in maintaining the development of hematopoietic stem cells (HSC) makes it difficult to be used for HIV-1 gene therapy with HSC transplantation. A previous report showed that the natural CXCR4 P191A mutant inhibits HIV-1 infection without any defect in HSC differentiation, which could provide a basis for the development of new approaches for HIV-1 gene therapy. In the present study, we used CRISPR-Cas9 combined with the piggyBac transposon technologies to efficiently induce the expression of the CXCR4 P191A mutant in an HIV-1 reporter cell line, leading to no detectable exogenous sequences. In addition, no off-target effects were detected in the genome-edited cells. The decline of HIV-1 replication in biallelic CXCR4 gene-edited cells suggests that individuals equipped with homologous recombination of the CXCR4 P191A mutant could prevent or reduce HIV-1 infection. This study provides an effective approach to create a CXCR4 mutation with HIV-1 infection inhibition function and without leaving any genetic footprint inside cells, thereby shedding light on an application in HIV-1 gene therapy and avoiding side effects caused by deficiency or destruction of CXCR4 function.
Collapse
|
42
|
Wagner JM, Williams EV, Alper HS. Developing a piggyBac Transposon System and Compatible Selection Markers for Insertional Mutagenesis and Genome Engineering in Yarrowia lipolytica. Biotechnol J 2018; 13:e1800022. [PMID: 29493878 DOI: 10.1002/biot.201800022] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/17/2018] [Indexed: 12/30/2022]
Abstract
Yarrowia lipolytica is a non-conventional yeast of interest to the biotechnology industry. However, the physiology, metabolism, and genetic regulation of Y. lipolytica diverge significantly from more well-studied and characterized yeasts such as Saccharomyces cerevisiae. To develop additional genetic tools for this industrially relevant host, the piggyBac transposon system to enable efficient generation of genome-wide insertional mutagenesis libraries and introduction of scarless, footprint-free genomic modifications in Y. lipolytica. Specifically, we demonstrate piggyBac transposition in Y. lipolytica, and then use the approach to screen transposon insertion libraries for rapid isolation of mutations that confer altered canavanine resistance, pigment formation, and neutral lipid accumulation. We also develop a variety of piggyBac compatible selection markers for footprint-free genome engineering, including a novel dominant marker cassette (Escherichia coli guaB) for effective Y. lipolytica selection using mycophenolic acid. We utilize these marker cassettes to construct a piggyBac vector set that allows for auxotrophic selection (uracil or tryptophan biosynthesis) or dominant selection (hygromycin, nourseothricin, chlorimuron ethyl, or mycophenolic acid resistance) and subsequent marker excision. These new genetic tools and techniques will help to facilitate and accelerate the engineering of Y. lipolytica strains for efficient and sustainable production of a wide variety of small molecules and proteins.
Collapse
Affiliation(s)
- James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Eden V Williams
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
| |
Collapse
|
43
|
Skipper KA, Nielsen MG, Andersen S, Ryø LB, Bak RO, Mikkelsen JG. Time-Restricted PiggyBac DNA Transposition by Transposase Protein Delivery Using Lentivirus-Derived Nanoparticles. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:253-262. [PMID: 29858060 PMCID: PMC5992343 DOI: 10.1016/j.omtn.2018.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 01/12/2023]
Abstract
Continuous innovation of revolutionizing genome engineering technologies calls for an intensified focus on new delivery technologies that not only match the inventiveness of genome editors but also enable the combination of potent delivery and time-restricted action of genome-modifying bits and tools. We have previously demonstrated the use of lentivirus-derived nanoparticles (LNPs) as a protein delivery vehicle, incorporating and transferring DNA transposases, designer nucleases, or RNA-guided endonucleases fused to the N terminus of the Gag/GagPol polypeptide. Here, we establish LNP-directed transfer of the piggyBac DNA transposase protein by fusing the transposase to the integrase protein in the C-terminal end of GagPol. We show protein incorporation and proteolytic release of the DNA transposase within matured LNPs, resulting in high levels of DNA transposition activity in LNP-treated cells. Importantly, as opposed to conventional delivery methods based on transfection of plasmid DNA or in-vitro-transcribed mRNA, protein delivery by LNPs effectively results in time-restricted action of the protein (<24 hr) without compromising overall potency. Our findings refine LNP-directed piggyBac transposase delivery, at present the only available direct delivery strategy for this particular protein, and demonstrate a novel strategy for restricting and fine-tuning the exposure of the genome to DNA-modifying enzymes.
Collapse
Affiliation(s)
| | | | - Sofie Andersen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Laura Barrett Ryø
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark
| | | |
Collapse
|
44
|
Kondrashov A, Duc Hoang M, Smith JGW, Bhagwan JR, Duncan G, Mosqueira D, Munoz MB, Vo NTN, Denning C. Simplified Footprint-Free Cas9/CRISPR Editing of Cardiac-Associated Genes in Human Pluripotent Stem Cells. Stem Cells Dev 2018; 27:391-404. [PMID: 29402189 PMCID: PMC5882176 DOI: 10.1089/scd.2017.0268] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Modeling disease with human pluripotent stem cells (hPSCs) is hindered because the impact on cell phenotype from genetic variability between individuals can be greater than from the pathogenic mutation. While “footprint-free” Cas9/CRISPR editing solves this issue, existing approaches are inefficient or lengthy. In this study, a simplified PiggyBac strategy shortened hPSC editing by 2 weeks and required one round of clonal expansion and genotyping rather than two, with similar efficiencies to the longer conventional process. Success was shown across four cardiac-associated loci (ADRB2, GRK5, RYR2, and ACTC1) by genomic cleavage and editing efficiencies of 8%–93% and 8%–67%, respectively, including mono- and/or biallelic events. Pluripotency was retained, as was differentiation into high-purity cardiomyocytes (CMs; 88%–99%). Using the GRK5 isogenic lines as an exemplar, chronic stimulation with the β-adrenoceptor agonist, isoprenaline, reduced beat rate in hPSC-CMs expressing GRK5-Q41 but not GRK5-L41; this was reversed by the β-blocker, propranolol. This shortened, footprint-free approach will be useful for mechanistic studies.
Collapse
Affiliation(s)
- Alexander Kondrashov
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Minh Duc Hoang
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - James G W Smith
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Jamie R Bhagwan
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Gary Duncan
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Diogo Mosqueira
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Maria Barbadillo Munoz
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Nguyen T N Vo
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Chris Denning
- Department of Stem Cell Biology, Centre of Biomolecular Sciences, University of Nottingham , Nottingham, United Kingdom
| |
Collapse
|
45
|
Kobayashi Y, Hayashi R, Quantock AJ, Nishida K. Generation of a TALEN-mediated, p63 knock-in in human induced pluripotent stem cells. Stem Cell Res 2017; 25:256-265. [PMID: 29179035 DOI: 10.1016/j.scr.2017.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 09/12/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022] Open
Abstract
The expression of p63 in surface ectodermal cells during development of the cornea, skin, oral mucosa and olfactory placodes is integral to the process of cellular self-renewal and the maintenance of the epithelial stem cell status. Here, we used TALEN technology to generate a p63 knock-in (KI) human induced pluripotent stem (hiPS) cell line in which p63 expression can be visualized via enhanced green fluorescent protein (EGFP) expression. The KI-hiPS cells maintained pluripotency and expressed the stem cell marker gene, ΔNp63α. They were also able to successfully differentiate into functional corneal epithelial cells as assessed by p63 expression in reconstructed corneal epithelium. This approach enables the tracing of p63-expressing cell lineages throughout epithelial development, and represents a promising application in the field of stem cell research.
Collapse
Affiliation(s)
- Yuki Kobayashi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuhei Hayashi
- Department of Ophthalmology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Stem Cells and Applied Medicine, Osaka University Graduate School of Medicine, 2-2 Yamdaoka, Suita, Osaka 565-0871, Japan.
| | - Andrew J Quantock
- Structural Biophysics Group, School of Optometry and Vision Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
46
|
Shin JW, Lee JM. The prospects of CRISPR-based genome engineering in the treatment of neurodegenerative disorders. Ther Adv Neurol Disord 2017; 11:1756285617741837. [PMID: 29399048 PMCID: PMC5784517 DOI: 10.1177/1756285617741837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022] Open
Abstract
Over the past few decades, as gene discovery methods and sequencing technologies have evolved, many genetic variations that significantly increase the risk of or cause neurodegenerative diseases have been identified. However, knowledge of those pathogenic mutations and subsequent mechanism-focused studies has rarely yielded effective treatments, warranting alternative strategies for refining rational therapeutic targets. Nevertheless, with the evolution of gene targeting methods, it has been increasingly recognized that the disease-causing gene itself is the best therapeutic target even when we do not have a full understanding of its biological functions. Considering this, CRISPR/Cas gene editing technology offers the promise of permanently silencing or correcting the disease-causing mutations, potentially overcoming key limitations of RNA-targeting approaches. The versatile CRISPR/Cas-based strategies have the potential to become treatment options for challenging disorders such as neurodegenerative diseases. Here, we summarize recent reports of preclinical applications of CRISPR/Cas in models of neurodegenerative disorders to provide perspectives on therapeutic gene editing for diseases of the nervous system.
Collapse
Affiliation(s)
- Jun Wan Shin
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Medical and Population Genetics Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Department of Neurology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
47
|
Tipanee J, VandenDriessche T, Chuah MK. Transposons: Moving Forward from Preclinical Studies to Clinical Trials. Hum Gene Ther 2017; 28:1087-1104. [DOI: 10.1089/hum.2017.128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jaitip Tipanee
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| |
Collapse
|
48
|
Miyamoto T, Akutsu SN, Matsuura S. Updated summary of genome editing technology in human cultured cells linked to human genetics studies. J Hum Genet 2017; 63:133-143. [PMID: 29167553 DOI: 10.1038/s10038-017-0349-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 12/22/2022]
Abstract
Current deep-sequencing technology provides a mass of nucleotide variations associated with human genetic disorders to accelerate the identification of causative mutations. To understand the etiology of genetic disorders, reverse genetics in human cultured cells is a useful approach for modeling a disease in vitro. However, gene targeting in human cultured cells is difficult because of their low activity of homologous recombination. Engineered endonucleases enable enhancement of the local activation of DNA repair pathways at the human genome target site to rewrite the desired sequence, thereby efficiently generating disease-modeling cultured cell clones. These edited cells can be used to explore the molecular functions of a causative gene product to uncover the etiological mechanisms. The correction of mutations in patient cells using genome editing technology could contribute to the development of unique gene therapies. This technology can also be applied to screening causative mutations. Rare genetic disorders and non-exonic mutation-caused diseases remain frontier in the field of human genetics as it is difficult to validate whether the extracted nucleotide variants are mutation or polymorphism. When isogenic human cultured cells with a candidate variant reproduce the pathogenic phenotypes, it is confirmed that the variant is a causative mutation.
Collapse
Affiliation(s)
- Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.
| | - Silvia Natsuko Akutsu
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
49
|
Abstract
It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments-the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success.
Collapse
Affiliation(s)
- Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research and Department of Biology, MIT, Cambridge, MA 02142, USA
| |
Collapse
|
50
|
One-Step piggyBac Transposon-Based CRISPR/Cas9 Activation of Multiple Genes. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 8:64-76. [PMID: 28918057 PMCID: PMC5485764 DOI: 10.1016/j.omtn.2017.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/09/2017] [Accepted: 06/10/2017] [Indexed: 11/26/2022]
Abstract
Neural cell fate is determined by a tightly controlled transcription regulatory network during development. The ability to manipulate the expression of multiple transcription factors simultaneously is required to delineate the complex picture of neural cell development. Because of the limited carrying capacity of the commonly used viral vectors, such as lentiviral or retroviral vectors, it is often challenging to perform perturbation experiments on multiple transcription factors. Here we have developed a piggyBac (PB) transposon-based CRISPR activation (CRISPRa) all-in-one system, which allows for simultaneous and stable endogenous transactivation of multiple transcription factors and long non-coding RNAs. As a proof of principle, we showed that the PB-CRISPRa system could accelerate the differentiation of human induced pluripotent stem cells into neurons and astrocytes by triggering endogenous expression of different sets of transcription factors. The PB-CRISPRa system has the potential to become a convenient and robust tool in neuroscience, which can meet the needs of a variety of in vitro and in vivo gain-of-function applications.
Collapse
|