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Hynds RE, Magin CM, Ikonomou L, Aschner Y, Beers MF, Burgess JK, Heise RL, Hume PS, Krasnodembskaya AD, Mei SHJ, Misharin AV, Park JA, Reynolds SD, Tschumperlin DJ, Tanneberger AE, Vaidyanathan S, Waters CM, Zettler PJ, Weiss DJ, Ryan AL. Stem cells, cell therapies, and bioengineering in lung biology and diseases 2023. Am J Physiol Lung Cell Mol Physiol 2024; 327:L327-L340. [PMID: 38772903 DOI: 10.1152/ajplung.00052.2024] [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: 02/14/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024] Open
Abstract
Repair and regeneration of a diseased lung using stem cells or bioengineered tissues is an exciting therapeutic approach for a variety of lung diseases and critical illnesses. Over the past decade, increasing evidence from preclinical models suggests that mesenchymal stromal cells, which are not normally resident in the lung, can be used to modulate immune responses after injury, but there have been challenges in translating these promising findings to the clinic. In parallel, there has been a surge in bioengineering studies investigating the use of artificial and acellular lung matrices as scaffolds for three-dimensional lung or airway regeneration, with some recent attempts of transplantation in large animal models. The combination of these studies with those involving stem cells, induced pluripotent stem cell derivatives, and/or cell therapies is a promising and rapidly developing research area. These studies have been further paralleled by significant increases in our understanding of the molecular and cellular events by which endogenous lung stem and/or progenitor cells arise during lung development and participate in normal and pathological remodeling after lung injury. For the 2023 Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Diseases Conference, scientific symposia were chosen to reflect the most cutting-edge advances in these fields. Sessions focused on the integration of "omics" technologies with function, the influence of immune cells on regeneration, and the role of the extracellular matrix in regeneration. The necessity for basic science studies to enhance fundamental understanding of lung regeneration and to design innovative translational studies was reinforced throughout the conference.
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Affiliation(s)
- Robert E Hynds
- Epithelial Cell Biology in ENT Research Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chelsea M Magin
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Laertis Ikonomou
- Department of Oral Biology, University at Buffalo, State University of New York, Buffalo, New York, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, United States
| | - Yael Aschner
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Michael F Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine and PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rebecca L Heise
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, United States
| | - Patrick S Hume
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Anna D Krasnodembskaya
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Shirley H J Mei
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Jin-Ah Park
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States
| | - Susan D Reynolds
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States
| | - Daniel J Tschumperlin
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, United States
| | - Alicia E Tanneberger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States
| | - Christopher M Waters
- Department of Physiology and Saha Cardiovascular Research Center, University of Kentucky, Lexington, Kentucky, United States
| | - Patricia J Zettler
- Moritz College of Law, Drug Enforcement and Policy Center, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
| | - Daniel J Weiss
- Department of Medicine, University of Vermont, Burlington, Vermont, United States
| | - Amy L Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
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2
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Stack JT, Rayner RE, Nouri R, Suarez CJ, Kim SH, Kanke KL, Vetter TA, Cormet-Boyaka E, Vaidyanathan S. DNA-PKcs Inhibition Improves Sequential Gene Insertion of the Full-Length CFTR cDNA in Airway Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607571. [PMID: 39185207 PMCID: PMC11343149 DOI: 10.1101/2024.08.12.607571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although many people with CF (pwCF) are treated using CFTR modulators, some are non-responsive due to their genotype or other uncharacterized reasons. Autologous airway stem cell therapies, in which the CFTR cDNA has been replaced, may enable a durable therapy for all pwCF. Previously, CRISPR-Cas9 with two AAVs was used to sequentially insert two halves of the CFTR cDNA and an enrichment cassette into the CFTR locus. However, the editing efficiency was <10% and required enrichment to restore CFTR function. Further improvement in gene insertion may enhance cell therapy production. To improve CFTR cDNA insertion in human airway basal stem cells (ABCs), we evaluated the use of the small molecules AZD7648 and ART558 which inhibit non-homologous end joining (NHEJ) and micro-homology mediated end joining (MMEJ). Adding AZD7648 alone improved gene insertion by 2-3-fold. Adding both ART558 and AZD7648 improved gene insertion but induced toxicity. ABCs edited in the presence of AZD7648 produced differentiated airway epithelial sheets with restored CFTR function after enrichment. Adding AZD7648 did not increase off-target editing. Further studies are necessary to validate if AZD7648 treatment enriches cells with oncogenic mutations.
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Affiliation(s)
- Jacob T. Stack
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Rachael E. Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Reza Nouri
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Carlos J. Suarez
- Department of Pathology, Stanford University, Palo Alto, CA 94305
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Karen L. Kanke
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Tatyana A. Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | | | - Sriram Vaidyanathan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210
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3
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Hui KK, Yamanaka S. iPS cell therapy 2.0: Preparing for next-generation regenerative medicine. Bioessays 2024:e2400072. [PMID: 38922935 DOI: 10.1002/bies.202400072] [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: 03/27/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
This year marks the tenth anniversary of the world's first transplantation of tissue generated from induced pluripotent stem cells (iPSCs). There is now a growing number of clinical trials worldwide examining the efficacy and safety of autologous and allogeneic iPSC-derived products for treating various pathologic conditions. As we patiently wait for the results from these and future clinical trials, it is imperative to strategize for the next generation of iPSC-based therapies. This review examines the lessons learned from the development of another advanced cell therapy, chimeric antigen receptor (CAR) T cells, and the possibility of incorporating various new bioengineering technologies in development, from RNA engineering to tissue fabrication, to apply iPSCs not only as a means to achieve personalized medicine but also as designer medical applications.
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Affiliation(s)
- Kelvin K Hui
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- CiRA Foundation, Kyoto, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
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4
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Hussen BM, Najmadden ZB, Abdullah SR, Rasul MF, Mustafa SA, Ghafouri-Fard S, Taheri M. CRISPR/Cas9 gene editing: a novel strategy for fighting drug resistance in respiratory disorders. Cell Commun Signal 2024; 22:329. [PMID: 38877530 PMCID: PMC11179281 DOI: 10.1186/s12964-024-01713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024] Open
Abstract
Respiratory disorders are among the conditions that affect the respiratory system. The healthcare sector faces challenges due to the emergence of drug resistance to prescribed medications for these illnesses. However, there is a technology called CRISPR/Cas9, which uses RNA to guide DNA targeting. This technology has revolutionized our ability to manipulate and visualize the genome, leading to advancements in research and treatment development. It can effectively reverse epigenetic alterations that contribute to drug resistance. Some studies focused on health have shown that targeting genes using CRISPR/Cas9 can be challenging when it comes to reducing drug resistance in patients with respiratory disorders. Nevertheless, it is important to acknowledge the limitations of this technology, such as off-target effects, immune system reactions to Cas9, and challenges associated with delivery methods. Despite these limitations, this review aims to provide knowledge about CRISPR/Cas9 genome editing tools and explore how they can help overcome resistance in patients with respiratory disorders. Additionally, this study discusses concerns related to applications of CRISPR and provides an overview of successful clinical trial studies.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Erbil, 44001, Kurdistan Region, Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Zana Baqi Najmadden
- Research Center, University of Halabja, Halabja, 46018, Kurdistan region, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Tishk International University, Kurdistan Region, Iraq
| | - Suhad A Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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5
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Porter JJ, Lueck JD. A cystic fibrosis gene editing approach that is on target. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102197. [PMID: 38766524 PMCID: PMC11101720 DOI: 10.1016/j.omtn.2024.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - John D. Lueck
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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6
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Bulcaen M, Kortleven P, Liu RB, Maule G, Dreano E, Kelly M, Ensinck MM, Thierie S, Smits M, Ciciani M, Hatton A, Chevalier B, Ramalho AS, Casadevall I Solvas X, Debyser Z, Vermeulen F, Gijsbers R, Sermet-Gaudelus I, Cereseto A, Carlon MS. Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Rep Med 2024; 5:101544. [PMID: 38697102 PMCID: PMC11148721 DOI: 10.1016/j.xcrm.2024.101544] [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: 07/26/2023] [Revised: 01/16/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: "detection of targeted editing of CFTR in organoids").
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Affiliation(s)
- Mattijs Bulcaen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium.
| | - Phéline Kortleven
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Ronald B Liu
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; School of Engineering, University of Edinburgh, EH9 3JL Edinburgh, UK
| | - Giulia Maule
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Elise Dreano
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Mairead Kelly
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Marjolein M Ensinck
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Sam Thierie
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Maxime Smits
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Matteo Ciciani
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Aurelie Hatton
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Benoit Chevalier
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Anabela S Ramalho
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | | | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - François Vermeulen
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; Department of Pediatrics, UZ Leuven, 3000 Leuven, Belgium
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Sermet-Gaudelus
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France; Cystic Fibrosis National Pediatric Reference Center, Pneumo-Allergologie Pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), 75015 Paris, France; European Reference Network, ERN-Lung CF, 60596 Frankfurt am Mein, Germany
| | - Anna Cereseto
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Marianne S Carlon
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium.
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7
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Selvaraj S, Feist WN, Viel S, Vaidyanathan S, Dudek AM, Gastou M, Rockwood SJ, Ekman FK, Oseghale AR, Xu L, Pavel-Dinu M, Luna SE, Cromer MK, Sayana R, Gomez-Ospina N, Porteus MH. High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition. Nat Biotechnol 2024; 42:731-744. [PMID: 37537500 DOI: 10.1038/s41587-023-01888-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Therapeutic applications of nuclease-based genome editing would benefit from improved methods for transgene integration via homology-directed repair (HDR). To improve HDR efficiency, we screened six small-molecule inhibitors of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key protein in the alternative repair pathway of non-homologous end joining (NHEJ), which generates genomic insertions/deletions (INDELs). From this screen, we identified AZD7648 as the most potent compound. The use of AZD7648 significantly increased HDR (up to 50-fold) and concomitantly decreased INDELs across different genomic loci in various therapeutically relevant primary human cell types. In all cases, the ratio of HDR to INDELs markedly increased, and, in certain situations, INDEL-free high-frequency (>50%) targeted integration was achieved. This approach has the potential to improve the therapeutic efficacy of cell-based therapies and broaden the use of targeted integration as a research tool.
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Affiliation(s)
- Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - William N Feist
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastien Viel
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Immunology Department, Lyon Sud University Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Sriram Vaidyanathan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sarah J Rockwood
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Freja K Ekman
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Aluya R Oseghale
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ruhi Sayana
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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8
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Dudek AM, Feist WN, Sasu EJ, Luna SE, Ben-Efraim K, Bak RO, Cepika AM, Porteus MH. A simultaneous knockout knockin genome editing strategy in HSPCs potently inhibits CCR5- and CXCR4-tropic HIV-1 infection. Cell Stem Cell 2024; 31:499-518.e6. [PMID: 38579682 PMCID: PMC11212398 DOI: 10.1016/j.stem.2024.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 12/29/2023] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Allogeneic hematopoietic stem and progenitor cell transplant (HSCT) of CCR5 null (CCR5Δ32) cells can be curative for HIV-1-infected patients. However, because allogeneic HSCT poses significant risk, CCR5Δ32 matched bone marrow donors are rare, and CCR5Δ32 transplant does not confer resistance to the CXCR4-tropic virus, it is not a viable option for most patients. We describe a targeted Cas9/AAV6-based genome editing strategy for autologous HSCT resulting in both CCR5- and CXCR4-tropic HIV-1 resistance. Edited human hematopoietic stem and progenitor cells (HSPCs) maintain multi-lineage repopulation capacity in vivo, and edited primary human T cells potently inhibit infection by both CCR5-tropic and CXCR4-tropic HIV-1. Modification rates facilitated complete loss of CCR5-tropic replication and up to a 2,000-fold decrease in CXCR4-tropic replication without CXCR4 locus disruption. This multi-factor editing strategy in HSPCs could provide a broad approach for autologous HSCT as a functional cure for both CCR5-tropic and CXCR4-tropic HIV-1 infections.
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Affiliation(s)
- Amanda M Dudek
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William N Feist
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena J Sasu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kaya Ben-Efraim
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rasmus O Bak
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000 Aarhus, Denmark
| | - Alma-Martina Cepika
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Vaidyanathan S, Kerschner JL, Paranjapye A, Sinha V, Lin B, Bedrosian TA, Thrasher AJ, Turchiano G, Harris A, Porteus MH. Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102134. [PMID: 38384445 PMCID: PMC10879780 DOI: 10.1016/j.omtn.2024.102134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
A "universal strategy" replacing the full-length CFTR cDNA may treat >99% of people with cystic fibrosis (pwCF), regardless of their specific mutations. Cas9-based gene editing was used to insert the CFTR cDNA and a truncated CD19 (tCD19) enrichment tag at the CFTR locus in airway basal stem cells. This strategy restores CFTR function to non-CF levels. Here, we investigate the safety of this approach by assessing genomic and regulatory changes after CFTR cDNA insertion. Safety was first assessed by quantifying genetic rearrangements using CAST-seq. After validating restored CFTR function in edited and enriched airway cells, the CFTR locus open chromatin profile was characterized using ATAC-seq. The regenerative potential and differential gene expression in edited cells was assessed using scRNA-seq. CAST-seq revealed a translocation in ∼0.01% of alleles primarily occurring at a nononcogenic off-target site and large indels in 1% of alleles. The open chromatin profile of differentiated airway epithelial cells showed no appreciable changes, except in the region corresponding to the CFTR cDNA and tCD19 cassette, indicating no detectable changes in gene regulation. Edited stem cells produced the same types of airway cells as controls with minimal alternations in gene expression. Overall, the universal strategy showed minor undesirable genomic changes.
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Affiliation(s)
- Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny L. Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vrishti Sinha
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Brian Lin
- Department of Developmental, Molecular, and Chemical Biology, Tufts University, Boston, MA 02111, USA
| | - Tracy A. Bedrosian
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Adrian J. Thrasher
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Giandomenico Turchiano
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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10
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Kerschner JL, Meckler F, Coatti GC, Vaghela N, Paranjapye A, Harris A. The impact of genomic distance on enhancer-promoter interactions at the CFTR locus. J Cell Mol Med 2024; 28:e18142. [PMID: 38372567 PMCID: PMC10875976 DOI: 10.1111/jcmm.18142] [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: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
We identified and characterized multiple cell-type selective enhancers of the CFTR gene promoter in previous work and demonstrated active looping of these elements to the promoter. Here we address the impact of genomic spacing on these enhancer:promoter interactions and on CFTR gene expression. Using CRISPR/Cas9, we generated clonal cell lines with deletions between the -35 kb airway enhancer and the CFTR promoter in the 16HBE14o- airway cell line, or between the intron 1 (185 + 10 kb) intestinal enhancer and the promoter in the Caco2 intestinal cell line. The effect of these deletions on CFTR transcript abundance, as well as the 3D looping structure of the locus was investigated in triplicate clones of each modification. Our results indicate that both small and larger deletions upstream of the promoter can perturb CFTR expression and -35 kb enhancer:promoter interactions in the airway cells, though the larger deletions are more impactful. In contrast, the small intronic deletions have no effect on CFTR expression and intron 1 enhancer:promoter interactions in the intestinal cells, whereas larger deletions do. Clonal variation following a specific CFTR modification is a confounding factor particularly in 16HBE14o- cells.
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Affiliation(s)
- Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Frederick Meckler
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Giuliana C. Coatti
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Alekh Paranjapye
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Present address:
Department of GeneticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
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11
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Kanke KL, Rayner RE, Abel E, Venugopalan A, Suu M, Stack JT, Nouri R, Guo G, Vetter TA, Cormet-Boyaka E, Hester ME, Vaidyanathan S. Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578476. [PMID: 38352420 PMCID: PMC10862822 DOI: 10.1101/2024.02.01.578476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Single-stranded DNA (ssDNA) templates along with Cas9 have been used for gene insertion but suffer from low efficiency. Here, we show that ssDNA with chemical modifications in 10-17% of internal bases (eDNA) is compatible with the homologous recombination machinery. Moreover, eDNA templates improve gene insertion by 2-3 fold compared to unmodified and end-modified ssDNA in airway basal stem cells (ABCs), hematopoietic stem and progenitor cells (HSPCs), T-cells and endothelial cells. Over 50% of alleles showed gene insertion in three clinically relevant loci (CFTR, HBB, and CCR5) in ABCs using eDNA and up to 70% of alleles showed gene insertion in the HBB locus in HSPCs. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. Knocking out TREX1 nuclease improved gene insertion using unmodified ssDNA but not eDNA suggesting that chemical modifications inhibit TREX1. This approach can be used for therapeutic applications and biological modeling.
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Affiliation(s)
- Karen L Kanke
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Rachael E Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
| | - Eli Abel
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Aparna Venugopalan
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Ma Suu
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Jacob T Stack
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Reza Nouri
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Gongbo Guo
- Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Tatyana A Vetter
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | | | - Mark E Hester
- Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University, Columbus, OH
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12
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Adegunsoye A, Gonzales NM, Gilad Y. Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility. Annu Rev Genet 2023; 57:341-360. [PMID: 37708421 DOI: 10.1146/annurev-genet-022123-090319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Many human phenotypes are impossible to recapitulate in model organisms or immortalized human cell lines. Induced pluripotent stem cells (iPSCs) offer a way to study disease mechanisms in a variety of differentiated cell types while circumventing ethical and practical issues associated with finite tissue sources and postmortem states. Here, we discuss the broad utility of iPSCs in genetic medicine and describe how they are being used to study musculoskeletal, pulmonary, neurologic, and cardiac phenotypes. We summarize the particular challenges presented by each organ system and describe how iPSC models are being used to address them. Finally, we discuss emerging iPSC-derived organoid models and the potential value that they can bring to studies of human disease.
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Affiliation(s)
- Ayodeji Adegunsoye
- Genetics, Genomics, and Systems Biology, Section of Pulmonary and Critical Care, and the Department of Medicine, University of Chicago, Chicago, Illinois, USA;
| | - Natalia M Gonzales
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA; ,
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA; ,
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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13
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Mention K, Cavusoglu-Doran K, Joynt AT, Santos L, Sanz D, Eastman AC, Merlo C, Langfelder-Schwind E, Scallan MF, Farinha CM, Cutting GR, Sharma N, Harrison PT. Use of adenine base editing and homology-independent targeted integration strategies to correct the cystic fibrosis causing variant, W1282X. Hum Mol Genet 2023; 32:3237-3248. [PMID: 37649273 PMCID: PMC10656707 DOI: 10.1093/hmg/ddad143] [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: 05/09/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023] Open
Abstract
Small molecule drugs known as modulators can treat ~90% of people with cystic fibrosis (CF), but do not work for premature termination codon variants such as W1282X (c.3846G>A). Here we evaluated two gene editing strategies, Adenine Base Editing (ABE) to correct W1282X, and Homology-Independent Targeted Integration (HITI) of a CFTR superexon comprising exons 23-27 (SE23-27) to enable expression of a CFTR mRNA without W1282X. In Flp-In-293 cells stably expressing a CFTR expression minigene bearing W1282X, ABE corrected 24% of W1282X alleles, rescued CFTR mRNA from nonsense mediated decay and restored protein expression. However, bystander editing at the adjacent adenine (c.3847A>G), caused an amino acid change (R1283G) that affects CFTR maturation and ablates ion channel activity. In primary human nasal epithelial cells homozygous for W1282X, ABE corrected 27% of alleles, but with a notably lower level of bystander editing, and CFTR channel function was restored to 16% of wild-type levels. Using the HITI approach, correct integration of a SE23-27 in intron 22 of the CFTR locus in 16HBEge W1282X cells was detected in 5.8% of alleles, resulting in 7.8% of CFTR transcripts containing the SE23-27 sequence. Analysis of a clonal line homozygous for the HITI-SE23-27 produced full-length mature protein and restored CFTR anion channel activity to 10% of wild-type levels, which could be increased three-fold upon treatment with the triple combination of CF modulators. Overall, these data demonstrate two different editing strategies can successfully correct W1282X, the second most common class I variant, with a concomitant restoration of CFTR function.
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Affiliation(s)
- Karen Mention
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Kader Cavusoglu-Doran
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Lúcia Santos
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - David Sanz
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Alice C Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, 1800 Orleans St, Baltimore, MD 21287, United States
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Lenox Hill Hospital, 100 E. 77th Street, 4E, New York, NY 10075, United States
| | - Martina F Scallan
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Carlos M Farinha
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Patrick T Harrison
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
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14
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Khlidj Y. What did CRISPR-Cas9 accomplish in its first 10 years? Biochem Med (Zagreb) 2023; 33:030601. [PMID: 37545694 PMCID: PMC10373057 DOI: 10.11613/bm.2023.030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/01/2023] [Indexed: 08/08/2023] Open
Abstract
It's been 10 years now from the debut of clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) era in which gene engineering has never been so accessible, precise and efficient. This technology, like a refined surgical procedure, has offered the ability of removing different types of disease causing mutations and restoring key proteins activity with ease of outperforming the previous resembling methods: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Additionally, CRISPR-Cas9 systems can systematically introduce genetic sequences to the specific sites in the human genome allowing to stimulate desired functions such as anti-tumoral and anti-infectious faculties. The present brief review provides an updated resume of CRISPR-Cas9's top achievements from its first appearance to the current date focusing on the breakthrough research including in vitro, in vivo and human studies. This enables the evaluation of the previous phase 'the proof-of-concept phase' and marks the beginning of the next phase which will probably bring a spate of clinical trials.
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15
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Oliver KE, Carlon MS, Pedemonte N, Lopes-Pacheco M. The revolution of personalized pharmacotherapies for cystic fibrosis: what does the future hold? Expert Opin Pharmacother 2023; 24:1545-1565. [PMID: 37379072 PMCID: PMC10528905 DOI: 10.1080/14656566.2023.2230129] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF), a potentially fatal genetic disease, is caused by loss-of-function mutations in the gene encoding for the CFTR chloride/bicarbonate channel. Modulator drugs rescuing mutant CFTR traffic and function are now in the clinic, providing unprecedented breakthrough therapies for people with CF (PwCF) carrying specific genotypes. However, several CFTR variants are unresponsive to these therapies. AREA COVERED We discussed several therapeutic approaches that are under development to tackle the fundamental cause of CF, including strategies targeting defective CFTR mRNA and/or protein expression and function. Alternatively, defective chloride secretion and dehydration in CF epithelia could be restored by exploiting pharmacological modulation of alternative targets, i.e., ion channels/transporters that concur with CFTR to maintain the airway surface liquid homeostasis (e.g., ENaC, TMEM16A, SLC26A4, SLC26A9, and ATP12A). Finally, we assessed progress and challenges in the development of gene-based therapies to replace or correct the mutant CFTR gene. EXPERT OPINION CFTR modulators are benefiting many PwCF responsive to these drugs, yielding substantial improvements in various clinical outcomes. Meanwhile, the CF therapy development pipeline continues to expand with the development of novel CFTR modulators and alternative therapeutic strategies with the ultimate goal of providing effective therapies for all PwCF in the foreseeable future.
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Affiliation(s)
- Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Marianne S. Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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16
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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: 1] [Impact Index Per Article: 1.0] [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.
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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.
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17
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Wang G. Genome Editing for Cystic Fibrosis. Cells 2023; 12:1555. [PMID: 37371025 DOI: 10.3390/cells12121555] [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: 04/01/2023] [Revised: 05/06/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenic recessive genetic disorder caused by mutations in the CF Transmembrane-conductance Regulator gene (CFTR). Remarkable progress in basic research has led to the discovery of highly effective CFTR modulators. Now ~90% of CF patients are treatable. However, these modulator therapies are not curative and do not cover the full spectrum of CFTR mutations. Thus, there is a continued need to develop a complete and durable therapy that can treat all CF patients once and for all. As CF is a genetic disease, the ultimate therapy would be in-situ repair of the genetic lesions in the genome. Within the past few years, new technologies, such as CRISPR/Cas gene editing, have emerged as an appealing platform to revise the genome, ushering in a new era of genetic therapy. This review provided an update on this rapidly evolving field and the status of adapting the technology for CF therapy.
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Affiliation(s)
- Guoshun Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, CSRB 607, 533 Bolivar Street, New Orleans, LA 70112, USA
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18
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Kerschner JL, Paranjapye A, Vaghela N, Wilson MD, Harris A. An ectopic enhancer restores CFTR expression through de novo chromatin looping. Gene Ther 2023; 30:478-486. [PMID: 36510002 PMCID: PMC11227122 DOI: 10.1038/s41434-022-00378-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/30/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Transcription of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is regulated by both ubiquitous and cell-type selective cis-regulatory elements (CREs). These CREs include extragenic and intronic enhancers that bind lineage-specific transcription factors, and architectural protein-marked structural elements. Deletion of the airway-selective -35 kb enhancer in 16HBE14o- lung epithelial cells was shown earlier to disrupt normal enhancer-promoter looping at the CFTR locus and nearly abolish its expression. Using a 16HBE14o- clone that lacks the endogenous -35 kb CRE, we explore the impact of relocating the functional core of this element to an ectopic site in intron 1. The -35 kb sequence establishes a de novo enhancer signature in chromatin at the insertion site, and augments CFTR expression, albeit not fully restoring WT levels. The relocated -35 kb enhancer also initiates de novo chromatin contacts with the CFTR promoter and other known CFTR CREs. These results are broadly relevant to therapeutic gene editing.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Michael D Wilson
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA.
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19
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Durrant MG, Fanton A, Tycko J, Hinks M, Chandrasekaran SS, Perry NT, Schaepe J, Du PP, Lotfy P, Bassik MC, Bintu L, Bhatt AS, Hsu PD. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol 2023; 41:488-499. [PMID: 36217031 PMCID: PMC10083194 DOI: 10.1038/s41587-022-01494-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022]
Abstract
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.
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Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michaela Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Nicholas T Perry
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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20
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Development of novel therapeutics for all individuals with CF (the future goes on). J Cyst Fibros 2023; 22 Suppl 1:S45-S49. [PMID: 36319570 DOI: 10.1016/j.jcf.2022.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/08/2022]
Abstract
Despite the major advances and successes in finding and establishing new treatments that tackle the basic defect in Cystic Fibrosis (CF), there is still an unmet need to bring these potentially curative therapies to all individuals with CF. Here, we review aspects of what is still missing to treat all individuals with CF by such approaches. On the one hand, we discuss novel holistic (high-throughput) approaches to elucidate mechanistic defects caused by distinct classes of mutations to identify novel drug targets. On the other hand, we examine therapeutic approaches to correct the gene in its own environment, i.e., in the genome.
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21
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Cromer MK, Barsan VV, Jaeger E, Wang M, Hampton JP, Chen F, Kennedy D, Xiao J, Khrebtukova I, Granat A, Truong T, Porteus MH. Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells. Nat Commun 2022; 13:4724. [PMID: 35953477 PMCID: PMC9372057 DOI: 10.1038/s41467-022-32233-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/22/2022] [Indexed: 12/25/2022] Open
Abstract
As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here, we employ a clinical next generation sequencing (NGS) workflow to achieve high sequencing depth and detect ultra-low frequency variants across exons of genes associated with cancer, all exons, and genome wide. In three separate primary human hematopoietic stem and progenitor cell (HSPC) donors assessed in technical triplicates, we electroporated high-fidelity Cas9 protein targeted to three loci (AAVS1, HBB, and ZFPM2) and harvested genomic DNA at days 4 and 10. Our results demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP in a gRNA spacer sequence is sufficient to eliminate Cas9 off-target activity in primary, repair-competent human HSPCs.
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Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
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22
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Harrison PT. CFTR RNA- and DNA-based therapies. Curr Opin Pharmacol 2022; 65:102247. [PMID: 35709547 DOI: 10.1016/j.coph.2022.102247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/20/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
This review provides an update on recent developments of RNA- and DNA-based methodologies and their intracellular targets in the context of cystic fibrosis (CF) lung disease. Ultimately, clinical success will require a suitable delivery system, but since the cargo for all these strategies is nucleic acid, it should hopefully be possible to exploit delivery breakthroughs from one study and apply these innovations to other experiments in order to identify the best strategy for everyone with CF. Ultimately, it may be the same approach for everyone, or possibly a number of different strategies tailored to particular mutations or classes/groups of mutations. And whilst the current focus is on CF lung disease, in the longer term the goal is to treat all affected organs in people with CF such as the pancreas, gut, and liver.
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Affiliation(s)
- Patrick T Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Ireland.
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Phadke MY, Sellers ZM. Current clinical opinion on CFTR dysfunction and patient risk of pancreatitis: diagnostic and therapeutic considerations. Expert Rev Gastroenterol Hepatol 2022; 16:499-509. [PMID: 35623009 PMCID: PMC9256802 DOI: 10.1080/17474124.2022.2084072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/26/2022] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cystic fibrosis transmembrane conductance regulator (CFTR)-mediated chloride and bicarbonate secretion is integral to the pancreas' ability to produce the alkaline pancreatic juice required for proper activation of enzymes for digestion. Disruption in this process increases the risk for pancreatitis. AREAS COVERED Using original basic and clinical research, as well as clinical case reports and recent reviews indexed in PubMed, we discuss why patients with CFTR dysfunction are at risk for pancreatitis. We also discuss diagnostic modalities for assessing CFTR function, as well as new therapeutic advancements and the impact these are having on pancreatic function, pancreatitis in particular. EXPERT OPINION CFTR-related pancreatitis occurs in the presence of monallelic or biallelic mutations and/or from toxin-mediated channel disruption. Research-based CFTR diagnostics have been expanded, yet all current methods rely on measuring CFTR chloride transport in non-pancreatic cells/tissue. Newer CFTR-directed therapies ('CFTR modulators') are both improving pancreatitis (pancreatic-sufficient CF patients) and increasing the risk for pancreatitis (previously pancreatic-insufficient CF patients). Our experiences with these drugs are enlightening us on how CFTR modulation can affect pancreatitis risk across a wide spectrum of pancreatic disease, and represents an opportunity for therapeutic relief from pancreatitis in those without CF, but who suffer from CFTR-related pancreatitis.
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Affiliation(s)
- Madhura Y. Phadke
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, 750 Welch Road, Suite 116, Palo Alto, CA
| | - Zachary M. Sellers
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, 750 Welch Road, Suite 116, Palo Alto, CA
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Barillà C, Suzuki S, Rab A, Sorscher EJ, Davis BR. Targeted Gene Insertion for Functional CFTR Restoration in Airway Epithelium. Front Genome Ed 2022; 4:847645. [PMID: 35330693 PMCID: PMC8940244 DOI: 10.3389/fgeed.2022.847645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic Fibrosis (CF) is caused by a diverse set of mutations distributed across the approximately 250 thousand base pairs of the CFTR gene locus, of which at least 382 are disease-causing (CFTR2.org). Although a variety of editing tools are now available for correction of individual mutations, a strong justification can be made for a more universal gene insertion approach, in principle capable of correcting virtually all CFTR mutations. Provided that such a methodology is capable of efficiently correcting relevant stem cells of the airway epithelium, this could potentially provide life-long correction for the lung. In this Perspective we highlight several requirements for efficient gene insertion into airway epithelial stem cells. In addition, we focus on specific features of the transgene construct and the endogenous CFTR locus that influence whether the inserted gene sequences will give rise to robust and physiologically relevant levels of CFTR function in airway epithelium. Finally, we consider how in vitro gene insertion methodologies may be adapted for direct in vivo editing.
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Affiliation(s)
- Cristina Barillà
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Shingo Suzuki
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Andras Rab
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
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Abdelnour SA, Xie L, Hassanin AA, Zuo E, Lu Y. The Potential of CRISPR/Cas9 Gene Editing as a Treatment Strategy for Inherited Diseases. Front Cell Dev Biol 2022; 9:699597. [PMID: 34977000 PMCID: PMC8715006 DOI: 10.3389/fcell.2021.699597] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising innovative technology for genomic editing that offers scientists the chance to edit DNA structures and change gene function. It has several possible uses consisting of editing inherited deficiencies, treating, and reducing the spread of disorders. Recently, reports have demonstrated the creation of synthetic RNA molecules and supplying them alongside Cas9 into genome of eukaryotes, since distinct specific regions of the genome can be manipulated and targeted. The therapeutic potential of CRISPR/Cas9 technology is great, especially in gene therapy, in which a patient-specific mutation is genetically edited, or in the treating of human disorders that are untreatable with traditional treatments. This review focused on numerous, in vivo, in vitro, and ex vivo uses of the CRISPR/Cas9 technology in human inherited diseases, discovering the capability of this versatile in medicine and examining some of the main limitations for its upcoming use in patients. In addition to introducing a brief impression of the biology of the CRISPR/Cas9 scheme and its mechanisms, we presented the utmost recent progress in the uses of CRISPR/Cas9 technology in editing and treating of human genetic diseases.
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Affiliation(s)
- Sameh A Abdelnour
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China.,Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Long Xie
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Abdallah A Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Erwei Zuo
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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Abstract
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
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Gene Editing in Pluripotent Stem Cells and Their Derived Organoids. Stem Cells Int 2021; 2021:8130828. [PMID: 34887928 PMCID: PMC8651378 DOI: 10.1155/2021/8130828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
With the rapid rise in gene-editing technology, pluripotent stem cells (PSCs) and their derived organoids have increasingly broader and practical applications in regenerative medicine. Gene-editing technologies, from large-scale nucleic acid endonucleases to CRISPR, have ignited a global research and development boom with significant implications in regenerative medicine. The development of regenerative medicine technologies, regardless of whether it is PSCs or gene editing, is consistently met with controversy. Are the tools for rewriting the code of life a boon to humanity or a Pandora's box? These technologies raise concerns regarding ethical issues, unexpected mutations, viral infection, etc. These concerns remain even as new treatments emerge. However, the potential negatives cannot obscure the virtues of PSC gene editing, which have, and will continue to, benefit mankind at an unprecedented rate. Here, we briefly introduce current gene-editing technology and its application in PSCs and their derived organoids, while addressing ethical concerns and safety risks and discussing the latest progress in PSC gene editing. Gene editing in PSCs creates visualized in vitro models, providing opportunities for examining mechanisms of known and unknown mutations and offering new possibilities for the treatment of cancer, genetic diseases, and other serious or refractory disorders. From model construction to treatment exploration, the important role of PSCs combined with gene editing in basic and clinical medicine studies is illustrated. The applications, characteristics, and existing challenges are summarized in combination with our lab experiences in this field in an effort to help gene-editing technology better serve humans in a regulated manner. Current preclinical and clinical trials have demonstrated initial safety and efficacy of PSC gene editing; however, for better application in clinical settings, additional investigation is warranted.
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