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Martínez García de la Torre RA, Vallverdú J, Xu Z, Ariño S, Ferrer-Lorente R, Zanatto L, Mercado-Gómez M, Aguilar-Bravo B, Ruiz-Blázquez P, Fernandez-Fernandez M, Navarro-Gascon A, Blasco-Roset A, Sànchez-Fernàndez-de-Landa P, Pera J, Romero-Moya D, Ayuso Garcia P, Martínez Sánchez C, Sererols Viñas L, Cantallops Vilà P, Cárcamo Giráldez CI, McQuillin A, Morgan MY, Moya-Rull D, Montserrat N, Eberlé D, Staels B, Antoine B, Azkargorta M, Lozano JJ, Martínez-Chantar ML, Giorgetti A, Elortza F, Planavila A, Varela-Rey M, Woodhoo A, Zorzano A, Graupera I, Moles A, Coll M, Affo S, Sancho-Bru P. Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis. Nat Commun 2025; 16:1489. [PMID: 39929812 PMCID: PMC11811062 DOI: 10.1038/s41467-025-56024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 01/07/2025] [Indexed: 02/13/2025] Open
Abstract
Defining the trajectory of cells during differentiation and disease is key for uncovering the mechanisms driving cell fate and identity. However, trajectories of human cells remain largely unexplored due to the challenges of studying them with human samples. In this study, we investigate the proteome trajectory of iPSCs differentiation to hepatic stellate cells (diHSCs) and identify RORA as a key transcription factor governing the metabolic reprogramming of HSCs necessary for diHSCs' commitment, identity, and activation. Using RORA deficient iPSCs and pharmacologic interventions, we show that RORA is required for early differentiation and prevents diHSCs activation by reducing the high energetic state of the cells. While RORA knockout mice have enhanced fibrosis, RORA agonists rescue multi-organ fibrosis in in vivo models. Notably, RORA expression correlates negatively with liver fibrosis and HSCs activation markers in patients with liver disease. This study reveals that RORA regulates cell metabolic plasticity, important for mesoderm differentiation, pericyte quiescence, and fibrosis, influencing cell commitment and disease.
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Affiliation(s)
| | - Julia Vallverdú
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Zhenqing Xu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Silvia Ariño
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Raquel Ferrer-Lorente
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Zanatto
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Maria Mercado-Gómez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Beatriz Aguilar-Bravo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Paloma Ruiz-Blázquez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
| | - Maria Fernandez-Fernandez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
| | - Artur Navarro-Gascon
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Spain
- CIBER Fisitopatologia de la Obesidad y Nutrición, Instituto de Salud Carlos III, Barcelona, Spain
| | - Albert Blasco-Roset
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Spain
- CIBER Fisitopatologia de la Obesidad y Nutrición, Instituto de Salud Carlos III, Barcelona, Spain
| | - Paula Sànchez-Fernàndez-de-Landa
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Joan Pera
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Damia Romero-Moya
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Paula Ayuso Garcia
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Celia Martínez Sánchez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Laura Sererols Viñas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Paula Cantallops Vilà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | | | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, WC1E 6DE, UK
| | - Marsha Y Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London, NW3 2PF, UK
| | - Daniel Moya-Rull
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri i Reixac, 15-21, Barcelona, Spain
| | - Núria Montserrat
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri i Reixac, 15-21, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, Barcelona, Spain
| | - Delphine Eberlé
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, 59000, Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, 59000, Lille, France
| | - Bénédicte Antoine
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012, Paris, France
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Proteomics Platform, CIC BioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, Derio, Spain
| | - Juan-José Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Maria L Martínez-Chantar
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, Derio, Spain
| | - Alessandra Giorgetti
- Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Barcelona University, Barcelona, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Proteomics Platform, CIC BioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, Derio, Spain
| | - Anna Planavila
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Spain
- CIBER Fisitopatologia de la Obesidad y Nutrición, Instituto de Salud Carlos III, Barcelona, Spain
| | - Marta Varela-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, Spain
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Barcelona University, Barcelona, Spain
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, Spain
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
- Oportunius Research Professor at CIMUS/USC, Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, A Coruña, Spain
| | - Antonio Zorzano
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Spain
- CIBER Fisitopatologia de la Obesidad y Nutrición, Instituto de Salud Carlos III, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel Graupera
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Hospital Clínic, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Anna Moles
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
| | - Mar Coll
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Medicine Department, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Silvia Affo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | - Pau Sancho-Bru
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
- Medicine Department, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
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Petazzi P, Gutierrez-Agüera F, Roca-Ho H, Castaño J, Bueno C, Alvarez N, Forrester LM, Sevilla A, Fidanza A, Menendez P. Generation of an inducible dCas9-SAM human PSC line for endogenous gene activation. Front Cell Dev Biol 2024; 12:1484955. [PMID: 39676795 PMCID: PMC11638181 DOI: 10.3389/fcell.2024.1484955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 11/11/2024] [Indexed: 12/17/2024] Open
Abstract
The CRISPR/Cas9 system has transformed genome editing by enabling precise modifications for diverse applications. Recent advancements, including base editing and prime editing, have expanded its utility beyond conventional gene knock-out and knock-in strategies. Additionally, several catalytically dead Cas9 (dCas9) proteins fused to distinct activation domains have been developed to modulate endogenous gene expression when directed to their regulatory regions by specific single-guide RNAs. Here, we report the development of the H9 human pluripotent stem cell (hPSC) line expressing an inducible dCas9-SAM activator (H9-iCas9.SAM), designed to activate transcription of endogenous genes. The H9-iCas9.SAM cells were generated through targeted integration of an inducible CRISPR/Cas9-based gene activator cassette into the AAVS1 "safe-harbour" locus. Molecular analyses confirmed precise and specific integration, ensuring minimal off-target effects. Functional characterization revealed that H9-iCas9.SAM cells retain pluripotency and display inducible endogenous gene activation upon doxycycline treatment. The versatility of H9-iCas9.SAM cells was demonstrated in directed in vitro differentiation assays, yielding neural stem cells (ectoderm), hematopoietic progenitor cells (mesoderm), and hepatocytes (endoderm). This underscores their potential in developmental biology studies and cell therapy applications. The engineered H9-iCas9.SAM line provides a robust platform for investigating gene function and advancing next-generation cell-based therapies.
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Affiliation(s)
- Paolo Petazzi
- Josep Carreras Leukemia Research Institute, Campus Clinic-UB, Casanova 143, Barcelona, Spain
| | | | - Heleia Roca-Ho
- Josep Carreras Leukemia Research Institute, Campus Clinic-UB, Casanova 143, Barcelona, Spain
| | - Julio Castaño
- Josep Carreras Leukemia Research Institute, Campus Clinic-UB, Casanova 143, Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, Campus Clinic-UB, Casanova 143, Barcelona, Spain
- Spanish Network for Advanced Cell Therapies (TERAV), Carlos III Health Institute, Barcelona, Spain
- Spanish Cancer Network (CIBERONC), Carlos III Health Institute, Barcelona, Spain
| | - Niuska Alvarez
- Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Lesley M Forrester
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ana Sevilla
- Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Antonella Fidanza
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute, Campus Clinic-UB, Casanova 143, Barcelona, Spain
- Spanish Network for Advanced Cell Therapies (TERAV), Carlos III Health Institute, Barcelona, Spain
- Spanish Cancer Network (CIBERONC), Carlos III Health Institute, Barcelona, Spain
- Department of Biomedicine, School of Medicine, Casanova 143, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
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3
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Sheridan SD, Horng JE, Yeh H, McCrea L, Wang J, Fu T, Perlis RH. Loss of Function in the Neurodevelopmental Disease and Schizophrenia-Associated Gene CYFIP1 in Human Microglia-like Cells Supports a Functional Role in Synaptic Engulfment. Biol Psychiatry 2024; 95:676-686. [PMID: 37573007 PMCID: PMC10874584 DOI: 10.1016/j.biopsych.2023.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND The CYFIP1 gene, located in the neurodevelopmental risk locus 15q11.2, is highly expressed in microglia, but its role in human microglial function as it relates to neurodevelopment is not well understood. METHODS We generated multiple CRISPR (clustered regularly interspaced short palindromic repeat) knockouts of CYFIP1 in patient-derived models of microglia to characterize function and phenotype. Using microglia-like cells reprogrammed from peripheral blood mononuclear cells, we quantified phagocytosis of synaptosomes (isolated and purified synaptic vesicles) from human induced pluripotent stem cell (iPSC)-derived neuronal cultures as an in vitro model of synaptic pruning. We repeated these analyses in human iPSC-derived microglia-like cells derived from 3 isogenic wild-type/knockout line pairs derived from 2 donors and further characterized microglial development and function through morphology and motility. RESULTS CYFIP1 knockout using orthogonal CRISPR constructs in multiple patient-derived cell lines was associated with a statistically significant decrease in synaptic vesicle phagocytosis in microglia-like cell models derived from both peripheral blood mononuclear cells and iPSCs. Morphology was also shifted toward a more ramified profile, and motility was significantly reduced. However, iPSC-CYFIP1 knockout lines retained the ability to differentiate to functional microglia. CONCLUSIONS The changes in microglial phenotype and function due to the loss of function of CYFIP1 observed in this study implicate a potential impact on processes such as synaptic pruning that may contribute to CYFIP1-related neurodevelopmental disorders. Investigating risk genes in a range of central nervous system cell types, not solely neurons, may be required to fully understand the way in which common and rare variants intersect to yield neuropsychiatric disorders.
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Affiliation(s)
- Steven D Sheridan
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Joy E Horng
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Hana Yeh
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Liam McCrea
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Jennifer Wang
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Ting Fu
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Roy H Perlis
- Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Psychiatry, Harvard Medical School, Boston, Massachusetts.
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4
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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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5
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Davis-Anderson K, Micheva-Viteva S, Solomon E, Hovde B, Cirigliano E, Harris J, Twary S, Iyer R. CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function. Int J Mol Sci 2023; 24:16161. [PMID: 38003351 PMCID: PMC10671572 DOI: 10.3390/ijms242216161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegeneration causes a significant disease burden and there are few therapeutic interventions available for reversing or slowing the disease progression. Induced pluripotent stem cells (iPSCs) hold significant potential since they are sourced from adult tissue and have the capacity to be differentiated into numerous cell lineages, including motor neurons. This differentiation process traditionally relies on cell lineage patterning factors to be supplied in the differentiation media. Genetic engineering of iPSC with the introduction of recombinant master regulators of motor neuron (MN) differentiation has the potential to shorten and streamline cell developmental programs. We have established stable iPSC cell lines with transient induction of exogenous LHX3 and ISL1 from the Tet-activator regulatory region and have demonstrated that induction of the transgenes is not sufficient for the development of mature MNs in the absence of neuron patterning factors. Comparative global transcriptome analysis of MN development from native and Lhx-ISL1 modified iPSC cultures demonstrated that the genetic manipulation helped to streamline the neuronal patterning process. However, leaky gene expression of the exogenous MN master regulators in iPSC resulted in the premature activation of genetic pathways characteristic of the mature MN function. Dysregulation of metabolic and regulatory pathways within the developmental process affected the MN electrophysiological responses.
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Affiliation(s)
- Katie Davis-Anderson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Sofiya Micheva-Viteva
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Emilia Solomon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Blake Hovde
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Elisa Cirigliano
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer Harris
- Information Systems and Modeling Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA; (K.D.-A.); (E.S.)
| | - Rashi Iyer
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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6
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Lotfi M, Morshedi Rad D, Mashhadi SS, Ashouri A, Mojarrad M, Mozaffari-Jovin S, Farrokhi S, Hashemi M, Lotfi M, Ebrahimi Warkiani M, Abbaszadegan MR. Recent Advances in CRISPR/Cas9 Delivery Approaches for Therapeutic Gene Editing of Stem Cells. Stem Cell Rev Rep 2023; 19:2576-2596. [PMID: 37723364 PMCID: PMC10661828 DOI: 10.1007/s12015-023-10585-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 09/20/2023]
Abstract
Rapid advancement in genome editing technologies has provided new promises for treating neoplasia, cardiovascular, neurodegenerative, and monogenic disorders. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has emerged as a powerful gene editing tool offering advantages, including high editing efficiency and low cost over the conventional approaches. Human pluripotent stem cells (hPSCs), with their great proliferation and differentiation potential into different cell types, have been exploited in stem cell-based therapy. The potential of hPSCs and the capabilities of CRISPR/Cas9 genome editing has been paradigm-shifting in medical genetics for over two decades. Since hPSCs are categorized as hard-to-transfect cells, there is a critical demand to develop an appropriate and effective approach for CRISPR/Cas9 delivery into these cells. This review focuses on various strategies for CRISPR/Cas9 delivery in stem cells.
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Affiliation(s)
- Malihe Lotfi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Dorsa Morshedi Rad
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Samaneh Sharif Mashhadi
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Ashouri
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Farrokhi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Hashemi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Lotfi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia.
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, Australia.
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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7
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Tamura R, Miyoshi H, Imaizumi K, Yo M, Kase Y, Sato T, Sato M, Morimoto Y, Sampetrean O, Kohyama J, Shinozaki M, Miyawaki A, Yoshida K, Saya H, Okano H, Toda M. Gene therapy using genome-edited iPS cells for targeting malignant glioma. Bioeng Transl Med 2023; 8:e10406. [PMID: 37693056 PMCID: PMC10487333 DOI: 10.1002/btm2.10406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/08/2022] Open
Abstract
Glioblastoma is characterized by diffuse infiltration into the normal brain. Invasive glioma stem cells (GSCs) are an underlying cause of treatment failure. Despite the use of multimodal therapies, the prognosis remains dismal. New therapeutic approach targeting invasive GSCs is required. Here, we show that neural stem cells (NSCs) derived from CRISRP/Cas9-edited human-induced pluripotent stem cell (hiPSC) expressing a suicide gene had higher tumor-trophic migratory capacity compared with mesenchymal stem cells (MSCs), leading to marked in vivo antitumor effects. High migratory capacity in iPSC-NSCs was related to self-repulsive action and pathotropism involved in EphB-ephrinB and CXCL12-CXCR4 signaling. The gene insertion to ACTB provided higher and stable transgene expression than other common insertion sites, such as GAPDH or AAVS1. Ferroptosis was associated with enhanced antitumor immune responses. The thymidylate synthase and dihydroprimidine dehydrogenase expressions predicted the treatment efficacy of therapeutic hiPSC-NSCs. Our results indicate the potential benefit of genome-edited iPS cells based gene therapy for invasive GSCs. Furthermore, the present research concept may become a platform to promote clinical studies using hiPSC.
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Affiliation(s)
- Ryota Tamura
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | | | - Kent Imaizumi
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Masahiro Yo
- Laboratory for Cell Function and Dynamics, RIKEN Center for Brain ScienceWako, SaitamaJapan
| | - Yoshitaka Kase
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
- Department of Geriatric MedicineGraduate School of Medicine, The University of TokyoBunkyo‐ku, TokyoJapan
| | - Tsukika Sato
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Mizuto Sato
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Yukina Morimoto
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Oltea Sampetrean
- Division of Gene RegulationKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Jun Kohyama
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Munehisa Shinozaki
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, RIKEN Center for Brain ScienceWako, SaitamaJapan
| | - Kazunari Yoshida
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Hideyuki Saya
- Division of Gene RegulationKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Hideyuki Okano
- Department of PhysiologyKeio University School of MedicineShinjuku‐ku, TokyoJapan
| | - Masahiro Toda
- Department of NeurosurgeryKeio University School of MedicineShinjuku‐ku, TokyoJapan
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8
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Alonso-Gil D, Cuadrado A, Giménez-Llorente D, Rodríguez-Corsino M, Losada A. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2. Nat Commun 2023; 14:1326. [PMID: 36898992 PMCID: PMC10006224 DOI: 10.1038/s41467-023-36900-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesin's ATPase and is essential for loop extrusion, but its requirement for cohesin loading is unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data are consistent with a model in which NIPBL may not be required for chromatin association of cohesin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 binds chromatin and becomes stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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9
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Khabarova A, Koksharova G, Salnikov P, Belokopytova P, Mungalov R, Pristyazhnuk I, Nurislamov A, Gridina M, Fishman V. A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells. Chromosome Res 2023; 31:11. [PMID: 36842155 DOI: 10.1007/s10577-023-09719-7] [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: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
Alterations of human karyotype caused by chromosomal rearrangements are often associated with considerable phenotypic effects. Studying molecular mechanisms underlying these effects requires an efficient and scalable experimental model. Here, we propose a Cre-LoxP-based approach for the generation of combinatorial diversity of chromosomal rearrangements. We demonstrate that using the developed system, both intra- and inter-chromosomal rearrangements can be induced in the human haploid HAP1 cells, although the latter is significantly less effective. The obtained genetically modified HAP1 cell line can be used to dissect genomic effects associated with intra-chromosomal structural variations.
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Affiliation(s)
| | - Galina Koksharova
- Institute of Cytology and Genetics, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Pavel Salnikov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina Belokopytova
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | - Artem Nurislamov
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Maria Gridina
- Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- Artificial Intelligence Research Institute, AIRI, Moscow, Russia
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10
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Inderbitzin A, Loosli T, Kouyos RD, Metzner KJ. Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9-based approach reveals high transcriptional variation. Mol Ther Methods Clin Dev 2022; 26:107-118. [PMID: 35795775 PMCID: PMC9234542 DOI: 10.1016/j.omtm.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022]
Abstract
Genomic safe harbors (GSH) are defined as sites in the host genome that allow stable expression of inserted transgenes while having no adverse effects on the host cell, making them ideal for use in basic research and therapeutic applications. Silencing and fluctuations in transgene expression would be highly undesirable effects. We have previously shown that transgene expression in Jurkat T cells is not silenced for up to 160 days after CRISPR-Cas9-mediated insertion of reporter genes into the adeno-associated virus site 1 (AAVS1), a commonly used GSH. Here, we studied fluctuations in transgene expression upon targeted insertion into the GSH AAVS1. We have developed an efficient method to generate and validate highly complex barcoded plasmid libraries to study transgene expression on the single-cell level. Its applicability is demonstrated by inserting the barcoded transgene Cerulean into the AAVS1 locus in Jurkat T cells via the CRISPR-Cas9 technology followed by next-generation sequencing of the transcribed barcodes. We observed large transcriptional variations over two logs for transgene expression in the GSH AAVS1. This barcoded transgene insertion model is a powerful tool to investigate fluctuations in transgene expression at any GSH site.
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Affiliation(s)
- Anne Inderbitzin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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11
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Engineering off-the-shelf universal CAR T cells: A silver lining in the cloud. Cytokine 2022; 156:155920. [DOI: 10.1016/j.cyto.2022.155920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
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12
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Fehér A, Schnúr A, Muenthaisong S, Bellák T, Ayaydin F, Várady G, Kemter E, Wolf E, Dinnyés A. Establishment and characterization of a novel human induced pluripotent stem cell line stably expressing the iRFP720 reporter. Sci Rep 2022; 12:9874. [PMID: 35701501 PMCID: PMC9198085 DOI: 10.1038/s41598-022-12956-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Stem cell therapy has great potential for replacing beta-cell loss in diabetic patients. However, a key obstacle to cell therapy’s success is to preserve viability and function of the engrafted cells. While several strategies have been developed to improve engrafted beta-cell survival, tools to evaluate the efficacy within the body by imaging are limited. Traditional labeling tools, such as GFP-like fluorescent proteins, have limited penetration depths in vivo due to tissue scattering and absorption. To circumvent this limitation, a near-infrared fluorescent mutant version of the DrBphP bacteriophytochrome, iRFP720, has been developed for in vivo imaging and stem/progenitor cell tracking. Here, we present the generation and characterization of an iRFP720 expressing human induced pluripotent stem cell (iPSC) line, which can be used for real-time imaging in various biological applications. To generate the transgenic cells, the CRISPR/Cas9 technology was applied. A puromycin resistance gene was inserted into the AAVS1 locus, driven by the endogenous PPP1R12C promoter, along with the CAG-iRFP720 reporter cassette, which was flanked by insulator elements. Proper integration of the transgene into the targeted genomic region was assessed by comprehensive genetic analysis, verifying precise genome editing. Stable expression of iRFP720 in the cells was confirmed and imaged by their near-infrared fluorescence. We demonstrated that the reporter iPSCs exhibit normal stem cell characteristics and can be efficiently differentiated towards the pancreatic lineage. As the genetically modified reporter cells show retained pluripotency and multilineage differentiation potential, they hold great potential as a cellular model in a variety of biological and pharmacological applications.
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Affiliation(s)
- Anita Fehér
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
| | - Andrea Schnúr
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
| | | | - Tamás Bellák
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary.,Department of Anatomy, Histology and Embryology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6724, Hungary
| | - Ferhan Ayaydin
- Functional Cell Biology and Immunology Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, University of Szeged (HCEMM-USZ), Szeged, 6720, Hungary.,Laboratory of Cellular Imaging, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - György Várady
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, 1117, Hungary
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Centre and Department of Veterinary Sciences, LMU Munich, 81377, Munich, Germany.,Centre for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764, Oberschleißheim, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Centre and Department of Veterinary Sciences, LMU Munich, 81377, Munich, Germany.,Centre for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764, Oberschleißheim, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - András Dinnyés
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary. .,HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged, 6723, Hungary. .,Department of Cell Biology and Molecular Medicine, University of Szeged, Szeged, 6720, Hungary. .,Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary.
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13
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Domingo-Reinés J, Martínez-Navajas G, Montes R, Lamolda M, Simón I, Castaño J, Ríos-Pelegrina R, Lopez-Hidalgo JL, García del Moral R, Marchal JA, Real PJ, Ramos-Mejía V. Generation of a H9 Clonal Cell Line With Inducible Expression of NUP98-KDM5A Fusion Gene in the AAVS1 Safe Harbor Locus. Front Cell Dev Biol 2022; 10:846092. [PMID: 35721502 PMCID: PMC9200071 DOI: 10.3389/fcell.2022.846092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Pediatric acute myeloid leukemia (AML) is a rare and heterogeneous disease that remains the major cause of mortality in children with leukemia. To improve the outcome of pediatric AML we need to gain knowledge on the biological bases of this disease. NUP98-KDM5A (NK5A) fusion protein is present in a particular subgroup of young pediatric patients with poor outcome. We report the generation and characterization of human Embryonic Stem Cell (hESC) clonal lines with inducible expression of NK5A. Temporal control of NK5A expression during hematopoietic differentiation from hESC will be critical for elucidating its participation during the leukemogenic process.
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Affiliation(s)
- Joan Domingo-Reinés
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Gonzalo Martínez-Navajas
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Faculty of Science, Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Rosa Montes
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Faculty of Sciences, Department of Cell Biology, University of Granada, Granada, Spain
| | - Mar Lamolda
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Iris Simón
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Faculty of Science, Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Julio Castaño
- Advanced Cell Therapy Service, Banc de Sang I Teixits, Edifici Dr. Frederic Duran I Jordà, Barcelona, Spain
| | - Rosa Ríos-Pelegrina
- Unidad de Anatomía Patológica, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Javier Luis Lopez-Hidalgo
- Unidad de Anatomía Patológica, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Raimundo García del Moral
- Unidad de Anatomía Patológica, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Juan A. Marchal
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, Granada, Spain
- Faculty of Medicine, Department of Human Anatomy and Embryology, University of Granada, Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Granada, Spain
| | - Pedro J. Real
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Faculty of Science, Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Verónica Ramos-Mejía
- GENYO, Centre for Genomics and Oncological Research Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- *Correspondence: Verónica Ramos-Mejía,
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14
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Petazzi P, Menéndez P, Sevilla A. CRISPR/Cas9-Mediated Gene Knockout and Knockin Human iPSCs. Methods Mol Biol 2022; 2454:559-574. [PMID: 33190185 DOI: 10.1007/7651_2020_337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The realization of the full potential of human pluripotent stem cells (hPSCs), including human induced PSCs (iPSC), relies on the ability to precisely edit their genome in a locus-specific and multiplex manner. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) serve as a guide for the endonuclease Cas9 (CRISPR-associated protein 9) to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. CRISPR/Cas9-mediated editing has become the gold standard for precise genome manipulation as it offers a unique, versatile, and limitless tool for fast, robust, and efficient genome editing. Here, we provide a protocol to successfully generate gene knockout and/or knockin iPSCs. We include detailed information on the design of guide RNAs (gRNAs), T7 endonuclease assay to detect on-target CRISPR/Cas9 editing events, DNA electroporation of the iPSCs with a ribonucleoprotein complex, and single-cell cloning steps for the selection of the genome-edited iPSC clones.
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Affiliation(s)
- Paolo Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer-CIBER-ONC, ISCIII, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ana Sevilla
- Departament de Biología Cellular, Fisiología i Immunología, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain.
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15
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Zhang W, Wang Q, Du H, Jiang S. CRISPR/cas9-mediated overexpression of long non-coding RNA SRY-box transcription factor 21 antisense divergent transcript 1 regulates the proliferation of osteosarcoma by increasing the expression of mechanistic target of rapamycin kinase and Kruppel like factor 4. Bioengineered 2021; 13:6678-6687. [PMID: 34696664 PMCID: PMC8973734 DOI: 10.1080/21655979.2021.1995106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Osteosarcoma, derived from primitive mesenchymal cells, is the most common primary solid malignant tumor of bone. The cause of osteosarcoma remains unclear. In recent years, the role of non-coding sequences in regulating protein expression in tumors has been paid more and more attention, especially long non-coding RNA (lncRNA). We speculate that SRY-box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1) can regulate the expression of the mechanistic target of rapamycin kinase (mTOR) and Kruppel-like factor 4 (KLF4) through sponging hsa-mir-7-5p and hsa-mir-145-5p. We knocked lncRNA SOX21-AS1 into the genome of 143B cells through CRISPR/Cas9, then screened out a monoclonal cell line. Detect the transcription level and protein expression level of the above-mentioned related genes, and cell proliferation. Then, ginsenoside Rg3 was added to culture the cell line knocked into lncRNA SOX21-AS1, and the expression levels of lncRNA SOX21-AS1, hsa-mir-7-5p, hsa-mir-145-5p, mTOR, and KLF4 were detected by RT-qPCR and Western blot. Cell proliferation method detects cell viability, explores the molecular mechanism of lncRNA SOX21-AS1 in osteosarcoma, and checks whether it can be used as a potential drug target for the treatment of osteosarcoma. Our results demonstrate that the overexpression of lncRNA SOX21-AS1 up-regulates mTOR and KLF4 by sponging hsa-mir-7-5p and hsa-mir-145-5p, and ultimately regulates the proliferation of osteosarcoma. It is proved that ginsenoside Rg3 can inhibit the cell proliferation of osteosarcoma by reducing the expression level of lncRNA SOX21-AS1. It provides an alternative for the treatment of osteosarcoma in the future.
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Affiliation(s)
- Weiying Zhang
- Health Management Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Qiang Wang
- Department of human resources, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Haibo Du
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Shichao Jiang
- Department of orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China.,Department of orthopedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
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16
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Nanobody-based chimeric antigen receptor T cells designed by CRISPR/Cas9 technology for solid tumor immunotherapy. Signal Transduct Target Ther 2021; 6:80. [PMID: 33627635 PMCID: PMC7904846 DOI: 10.1038/s41392-021-00462-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 11/09/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Chimeric antigen receptor-based T-cell immunotherapy is a promising strategy for treatment of hematological malignant tumors; however, its efficacy towards solid cancer remains challenging. We therefore focused on developing nanobody-based CAR-T cells that treat the solid tumor. CD105 expression is upregulated on neoangiogenic endothelial and cancer cells. CD105 has been developed as a drug target. Here we show the generation of a CD105-specific nanobody, an anti-human CD105 CAR-T cells, by inserting the sequences for anti-CD105 nanobody-linked standard cassette genes into AAVS1 site using CRISPR/Cas9 technology. Co-culture with CD105+ target cells led to the activation of anti-CD105 CAR-T cells that displayed the typically activated cytotoxic T-cell characters, ability to proliferate, the production of pro-inflammatory cytokines, and the specific killing efficacy against CD105+ target cells in vitro. The in vivo treatment with anti-CD105 CAR-T cells significantly inhibited the growth of implanted CD105+ tumors, reduced tumor weight, and prolonged the survival time of tumor-bearing NOD/SCID mice. Nanobody-based CAR-T cells can therefore function as an antitumor agent in human tumor xenograft models. Our findings determined that the strategy of nanobody-based CAR-T cells engineered by CRISPR/Cas9 system has a certain potential to treat solid tumor through targeting CD105 antigen.
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17
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Hayashi H, Kubo Y, Izumida M, Matsuyama T. Efficient viral delivery of Cas9 into human safe harbor. Sci Rep 2020; 10:21474. [PMID: 33293588 PMCID: PMC7722726 DOI: 10.1038/s41598-020-78450-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Gene editing using CRISPR/Cas9 is a promising method to cure many human genetic diseases. We have developed an efficient system to deliver Cas9 into the adeno-associated virus integration site 1 (AAVS1) locus, known as a safe harbor, using lentivirus and AAV viral vectors, as a step toward future in vivo transduction. First, we introduced Cas9v1 (derived from Streptococcus pyogenes) at random into the genome using a lentiviral vector. Cas9v1 activity was used when the N-terminal 1.9 kb, and C-terminal 2.3 kb fragments of another Cas9v2 (human codon-optimized) were employed sequentially with specific single-guide RNAs (sgRNAs) and homology donors carried by AAV vectors into the AAVS1 locus. Then, Cas9v1 was removed from the genome by another AAV vector containing sgRNA targeting the long terminal repeat of the lentivirus vector. The reconstituted Cas9v2 in the AAVS1 locus was functional and gene editing was efficient.
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Affiliation(s)
- Hideki Hayashi
- Medical University Research Administrator, Nagasaki University School of Medicine, Nagasaki, Japan.
| | - Yoshinao Kubo
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Mai Izumida
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Toshifumi Matsuyama
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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18
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Bhagwan JR, Collins E, Mosqueira D, Bakar M, Johnson BB, Thompson A, Smith JG, Denning C. Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour. F1000Res 2019; 8:1911. [PMID: 32789000 PMCID: PMC7401084 DOI: 10.12688/f1000research.19894.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Diseases such as hypertrophic cardiomyopathy (HCM) can lead to severe outcomes including sudden death. The generation of human induced pluripotent stem cell (hiPSC) reporter lines can be useful for disease modelling and drug screening by providing physiologically relevant in vitro models of disease. The AAVS1 locus is cited as a safe harbour that is permissive for stable transgene expression, and hence is favoured for creating gene targeted reporter lines. Methods: We generated hiPSC reporters using a plasmid-based CRISPR/Cas9 nickase strategy. The first intron of PPP1R12C, the AAVS1 locus, was targeted with constructs expressing a genetically encoded calcium indicator (R-GECO1.0) or HOXA9-T2A-mScarlet reporter under the control of a pCAG or inducible pTRE promoter, respectively. Transgene expression was compared between clones before, during and/or after directed differentiation to mesodermal lineages. Results: Successful targeting to AAVS1 was confirmed by PCR and sequencing. Of 24 hiPSC clones targeted with pCAG-R-GECO1.0, only 20 expressed the transgene and in these, the percentage of positive cells ranged from 0% to 99.5%. Differentiation of a subset of clones produced cardiomyocytes, wherein the percentage of cells positive for R-GECO1.0 ranged from 2.1% to 93.1%. In the highest expressing R-GECO1.0 clones, transgene silencing occurred during cardiomyocyte differentiation causing a decrease in expression from 98.93% to 1.3%. In HOXA9-T2A-mScarlet hiPSC reporter lines directed towards mesoderm lineages, doxycycline induced a peak in transgene expression after two days but this reduced by up to ten-thousand-fold over the next 8-10 days. Nevertheless, for R-GECO1.0 lines differentiated into cardiomyocytes, transgene expression was rescued by continuous puromycin drug selection, which allowed the Ca 2+ responses associated with HCM to be investigated in vitro using single cell analysis. Conclusions: Targeted knock-ins to AAVS1 can be used to create reporter lines but variability between clones and transgene silencing requires careful attention by researchers seeking robust reporter gene expression.
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Affiliation(s)
- Jamie R. Bhagwan
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Emma Collins
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Diogo Mosqueira
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Mine Bakar
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Benjamin B. Johnson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander Thompson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James G.W. Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Chris Denning
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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19
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Bhagwan JR, Collins E, Mosqueira D, Bakar M, Johnson BB, Thompson A, Smith JG, Denning C. Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour. F1000Res 2019; 8:1911. [PMID: 32789000 PMCID: PMC7401084 DOI: 10.12688/f1000research.19894.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2020] [Indexed: 01/11/2023] Open
Abstract
Background: Diseases such as hypertrophic cardiomyopathy (HCM) can lead to severe outcomes including sudden death. The generation of human induced pluripotent stem cell (hiPSC) reporter lines can be useful for disease modelling and drug screening by providing physiologically relevant in vitro models of disease. The AAVS1 locus is cited as a safe harbour that is permissive for stable transgene expression, and hence is favoured for creating gene targeted reporter lines. Methods: We generated hiPSC reporters using a plasmid-based CRISPR/Cas9 nickase strategy. The first intron of PPP1R12C, the AAVS1 locus, was targeted with constructs expressing a genetically encoded calcium indicator (R-GECO1.0) or HOXA9-T2A-mScarlet reporter under the control of a pCAG or inducible pTRE promoter, respectively. Transgene expression was compared between clones before, during and/or after directed differentiation to mesodermal lineages. Results: Successful targeting to AAVS1 was confirmed by PCR and sequencing. Of 24 hiPSC clones targeted with pCAG-R-GECO1.0, only 20 expressed the transgene and in these, the percentage of positive cells ranged from 0% to 99.5%. Differentiation of a subset of clones produced cardiomyocytes, wherein the percentage of cells positive for R-GECO1.0 ranged from 2.1% to 93.1%. In the highest expressing R-GECO1.0 clones, transgene silencing occurred during cardiomyocyte differentiation causing a decrease in expression from 98.93% to 1.3%. In HOXA9-T2A-mScarlet hiPSC reporter lines directed towards mesoderm lineages, doxycycline induced a peak in transgene expression after two days but this reduced by up to ten-thousand-fold over the next 8-10 days. Nevertheless, for R-GECO1.0 lines differentiated into cardiomyocytes, transgene expression was rescued by continuous puromycin drug selection, which allowed the Ca 2+ responses associated with HCM to be investigated in vitro using single cell analysis. Conclusions: Targeted knock-ins to AAVS1 can be used to create reporter lines but variability between clones and transgene silencing requires careful attention by researchers seeking robust reporter gene expression.
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Affiliation(s)
- Jamie R. Bhagwan
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Emma Collins
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Diogo Mosqueira
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Mine Bakar
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Benjamin B. Johnson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander Thompson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James G.W. Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Chris Denning
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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20
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Papasavva P, Kleanthous M, Lederer CW. Rare Opportunities: CRISPR/Cas-Based Therapy Development for Rare Genetic Diseases. Mol Diagn Ther 2019; 23:201-222. [PMID: 30945166 PMCID: PMC6469594 DOI: 10.1007/s40291-019-00392-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rare diseases pose a global challenge, in that their collective impact on health systems is considerable, whereas their individually rare occurrence impedes research and development of efficient therapies. In consequence, patients and their families are often unable to find an expert for their affliction, let alone a cure. The tide is turning as pharmaceutical companies embrace gene therapy development and as serviceable tools for the repair of primary mutations separate the ability to create cures from underlying disease expertise. Whereas gene therapy by gene addition took decades to reach the clinic by incremental disease-specific refinements of vectors and methods, gene therapy by genome editing in its basic form merely requires certainty about the causative mutation. Suddenly we move from concept to trial in 3 years instead of 30: therapy development in the fast lane, with all the positive and negative implications of the phrase. Since their first application to eukaryotic cells in 2013, the proliferation and refinement in particular of tools based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) prokaryotic RNA-guided nucleases has prompted a landslide of therapy-development studies for rare diseases. An estimated thousands of orphan diseases are up for adoption, and legislative, entrepreneurial, and research initiatives may finally conspire to find many of them a good home. Here we summarize the most significant recent achievements and remaining hurdles in the application of CRISPR/Cas technology to rare diseases and take a glimpse at the exciting road ahead.
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Affiliation(s)
- Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, Cyprus School of Molecular Medicine and The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, 1683, Nicosia, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, Cyprus School of Molecular Medicine and The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, 1683, Nicosia, Cyprus
| | - Carsten W Lederer
- Department of Molecular Genetics Thalassaemia, Cyprus School of Molecular Medicine and The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, 1683, Nicosia, Cyprus.
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21
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Feasible development of stable HEK293 clones by CRISPR/Cas9-mediated site-specific integration for biopharmaceuticals production. Biotechnol Lett 2019; 41:941-950. [DOI: 10.1007/s10529-019-02702-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022]
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22
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Pinheiro EA, Fetterman KA, Burridge PW. hiPSCs in cardio-oncology: deciphering the genomics. Cardiovasc Res 2019; 115:935-948. [PMID: 30689737 PMCID: PMC6452310 DOI: 10.1093/cvr/cvz018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 01/21/2019] [Indexed: 12/18/2022] Open
Abstract
The genomic predisposition to oncology-drug-induced cardiovascular toxicity has been postulated for many decades. Only recently has it become possible to experimentally validate this hypothesis via the use of patient-specific human-induced pluripotent stem cells (hiPSCs) and suitably powered genome-wide association studies (GWAS). Identifying the individual single nucleotide polymorphisms (SNPs) responsible for the susceptibility to toxicity from a specific drug is a daunting task as this precludes the use of one of the most powerful tools in genomics: comparing phenotypes to close relatives, as these are highly unlikely to have been treated with the same drug. Great strides have been made through the use of candidate gene association studies (CGAS) and increasingly large GWAS studies, as well as in vivo whole-organism studies to further our mechanistic understanding of this toxicity. The hiPSC model is a powerful technology to build on this work and identify and validate causal variants in mechanistic pathways through directed genomic editing such as CRISPR. The causative variants identified through these studies can then be implemented clinically to identify those likely to experience cardiovascular toxicity and guide treatment options. Additionally, targets identified through hiPSC studies can inform future drug development. Through careful phenotypic characterization, identification of genomic variants that contribute to gene function and expression, and genomic editing to verify mechanistic pathways, hiPSC technology is a critical tool for drug discovery and the realization of precision medicine in cardio-oncology.
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Affiliation(s)
- Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
| | - K Ashley Fetterman
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
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23
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Hasegawa Y, Ikeno M, Suzuki N, Nakayama M, Ohara O. Improving the efficiency of gene insertion in a human artificial chromosome vector and its transfer in human-induced pluripotent stem cells. Biol Methods Protoc 2018; 3:bpy013. [PMID: 32161806 PMCID: PMC6994043 DOI: 10.1093/biomethods/bpy013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/15/2018] [Accepted: 11/26/2018] [Indexed: 01/24/2023] Open
Abstract
A human artificial chromosome (HAC) vector has potential to overcome the problems of stable gene expression associated with plasmid, transposon, and virus-based vectors, such as insertional mutagenesis, position effect, uncontrollable copy number, unstable gene expression, and DNA size limitation. The main advantages of the HAC are its episomal nature and ability to accommodate DNA inserts of any size. However, HAC vectors have two disadvantages: low efficiency of gene insertion and lack of reports regarding the successful HAC transfer to human-induced pluripotent stem cells (iPSCs). We here provide the first report of a method for the efficient transfer of HAC to human iPSCs for obtaining reproducible experimental results. Moreover, we achieved a 10% increase in the gene insertion efficiency in the HAC vector using our new site-specific recombination systems VCre/VloxP and SCre/SloxP.
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Affiliation(s)
- Yoshinori Hasegawa
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | | | | | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Osamu Ohara
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
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24
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Dubois VP, Zotova D, Parkins KM, Swick C, Hamilton AM, Kelly JJ, Ronald JA. Safe Harbor Targeted CRISPR-Cas9 Tools for Molecular-Genetic Imaging of Cells in Living Subjects. CRISPR J 2018; 1:440-449. [PMID: 31021241 DOI: 10.1089/crispr.2018.0030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Noninvasive molecular-genetic imaging of cells expressing imaging reporter genes is an invaluable approach for longitudinal monitoring of the biodistribution and viability of cancer cells and cell-based therapies in preclinical models and patients. However, labeling cells with reporter genes often relies on using gene transfer methods that randomly integrate the reporter genes into the genome, which may cause unwanted and serious detrimental effects. To overcome this, we have developed CRISPR-Cas9 tools to edit cells at the adeno-associated virus site 1 (AAVS1) safe harbour with a large donor construct (∼6.3 kilobases) encoding an antibiotic resistance gene and reporter genes for bioluminescence (BLI) and fluorescence imaging. HEK293T cells were transfected with a dual plasmid system encoding the Cas9 endonuclease and an AAVS1-targeted guide RNA in one plasmid, and a donor plasmid encoding a puromycin resistance gene, tdTomato and firefly luciferase flanked by AAVS1 homology arms. Puromycin-resistant clonal cells were isolated and AAVS1 integration was confirmed via PCR and sequencing of the PCR product. In vitro BLI signal correlated well to cell number (R2 = 0.9988; p < 0.05) and was stable over multiple passages. Engineered cells (2.5 × 106) were injected into the left hind flank of nude mice and in vivo BLI was performed on days 0, 7, 14, 21, and 28. BLI signal trended down from day 0 to day 7, but significantly increased by day 28 due to cell growth (p < 0.05). This describes the first CRISPR-Cas9 system for AAVS1 integration of large gene constructs for molecular-genetic imaging of cells in vivo. With further development, including improving editing efficiency, use of clinically relevant reporters, and evaluation in other cell populations that can be readily expanded in culture (e.g., immortalized cells or T cells), this CRISPR-Cas9 reporter gene system could be broadly applied to a number of in vivo cell tracking studies.
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Affiliation(s)
- Veronica P Dubois
- 1 Department of Medical Biophysics, Western University , London, Ontario, Canada.,2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada
| | - Darya Zotova
- 2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada
| | - Katie M Parkins
- 1 Department of Medical Biophysics, Western University , London, Ontario, Canada
| | - Connor Swick
- 2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada
| | - Amanda M Hamilton
- 2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada
| | - John J Kelly
- 2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada
| | - John A Ronald
- 1 Department of Medical Biophysics, Western University , London, Ontario, Canada.,2 Imaging Research Laboratories, Robarts Research Institute , London, Ontario, Canada.,3 Lawson Health Research Institute, London, Ontario, Canada
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