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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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Bulcaen M, Carlon MS. Genetic surgery for a cystic fibrosis-causing splicing mutation. Mol Ther Methods Clin Dev 2024; 32:101177. [PMID: 38261927 PMCID: PMC10797185 DOI: 10.1016/j.omtm.2023.101177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Affiliation(s)
- Mattijs Bulcaen
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Marianne S. Carlon
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
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Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling. Front Genet 2023; 14:1273994. [PMID: 37908590 PMCID: PMC10613999 DOI: 10.3389/fgene.2023.1273994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.
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Affiliation(s)
- Mirunalini Ravichandran
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
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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: 3] [Impact Index Per Article: 3.0] [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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Li T, Yang Y, Qi H, Cui W, Zhang L, Fu X, He X, Liu M, Li PF, Yu T. CRISPR/Cas9 therapeutics: progress and prospects. Signal Transduct Target Ther 2023; 8:36. [PMID: 36646687 PMCID: PMC9841506 DOI: 10.1038/s41392-023-01309-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/06/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene-editing technology is the ideal tool of the future for treating diseases by permanently correcting deleterious base mutations or disrupting disease-causing genes with great precision and efficiency. A variety of efficient Cas9 variants and derivatives have been developed to cope with the complex genomic changes that occur during diseases. However, strategies to effectively deliver the CRISPR system to diseased cells in vivo are currently lacking, and nonviral vectors with target recognition functions may be the focus of future research. Pathological and physiological changes resulting from disease onset are expected to serve as identifying factors for targeted delivery or targets for gene editing. Diseases are both varied and complex, and the choice of appropriate gene-editing methods and delivery vectors for different diseases is important. Meanwhile, there are still many potential challenges identified when targeting delivery of CRISPR/Cas9 technology for disease treatment. This paper reviews the current developments in three aspects, namely, gene-editing type, delivery vector, and disease characteristics. Additionally, this paper summarizes successful examples of clinical trials and finally describes possible problems associated with current CRISPR applications.
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Affiliation(s)
- Tianxiang Li
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Yanyan Yang
- grid.410645.20000 0001 0455 0905Department of Immunology, School of Basic Medicine, Qingdao University, 266021 Qingdao, People’s Republic of China
| | - Hongzhao Qi
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Weigang Cui
- grid.452710.5Department of Cardiology, People’s Hospital of Rizhao, No. 126 Taian Road, 276827 Rizhao, People’s Republic of China
| | - Lin Zhang
- Department of Microbiology, Linyi Center for Disease Control and Prevention, 276000 Linyi, People’s Republic of China
| | - Xiuxiu Fu
- grid.412521.10000 0004 1769 1119Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000 Qingdao, People’s Republic of China
| | - Xiangqin He
- grid.412521.10000 0004 1769 1119Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000 Qingdao, People’s Republic of China
| | - Meixin Liu
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Pei-feng Li
- grid.412521.10000 0004 1769 1119Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021 Qingdao, People’s Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 38 Dengzhou Road, 266021, Qingdao, People's Republic of China. .,Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, 266000, Qingdao, People's Republic of China.
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Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
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Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
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Assays of CFTR Function In Vitro, Ex Vivo and In Vivo. Int J Mol Sci 2022; 23:ijms23031437. [PMID: 35163362 PMCID: PMC8836180 DOI: 10.3390/ijms23031437] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis, a multi-organ genetic disease, is characterized by abnormal function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a chloride channel at the apical membrane of several epithelia. In recent years, therapeutic strategies have been developed to correct the CFTR defect. To evaluate CFTR function at baseline for diagnosis, or the efficacy of CFTR-restoring therapy, reliable tests are needed to measure CFTR function, in vitro, ex vivo and in vivo. In vitro techniques either directly or indirectly measure ion fluxes; direct measurement of ion fluxes and quenching of fluorescence in cell-based assays, change in transmembrane voltage or current in patch clamp or Ussing chamber, swelling of CFTR-containing organoids by secondary water influx upon CFTR activation. Several cell or tissue types can be used. Ex vivo and in vivo assays similarly evaluate current (intestinal current measurement) and membrane potential differences (nasal potential difference), on tissues from individual patients. In the sweat test, the most frequently used in vivo evaluation of CFTR function, chloride concentration or stimulated sweat rate can be directly measured. Here, we will describe the currently available bio-assays for quantitative evaluation of CFTR function, their indications, advantages and disadvantages, and correlation with clinical outcome measures.
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