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Farinha CM, Santos L, Ferreira JF. Cell type-specific regulation of CFTR trafficking-on the verge of progress. Front Cell Dev Biol 2024; 12:1338892. [PMID: 38505263 PMCID: PMC10949533 DOI: 10.3389/fcell.2024.1338892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein is a complex process that starts with its biosynthesis and folding in the endoplasmic reticulum. Exit from the endoplasmic reticulum (ER) is coupled with the acquisition of a compact structure that can be processed and traffic through the secretory pathway. Once reaching its final destination-the plasma membrane, CFTR stability is regulated through interaction with multiple protein partners that are involved in its post-translation modification, connecting the channel to several signaling pathways. The complexity of the process is further boosted when analyzed in the context of the airway epithelium. Recent advances have characterized in detail the different cell types that compose the surface epithelium and shifted the paradigm on which cells express CFTR and on their individual and combined contribution to the total expression (and function) of this chloride/bicarbonate channel. Here we review CFTR trafficking and its relationship with the knowledge on the different cell types of the airway epithelia. We explore the crosstalk between these two areas and discuss what is still to be clarified and how this can be used to develop more targeted therapies for CF.
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Affiliation(s)
- Carlos M. Farinha
- Faculty of Sciences, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
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2
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Cao L, Wu Y, Gong Y, Zhou Q. Small molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR): Structure, classification, and mechanisms. Eur J Med Chem 2024; 265:116120. [PMID: 38194776 DOI: 10.1016/j.ejmech.2023.116120] [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: 11/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
The advent of small molecule modulators targeting the cystic fibrosis transmembrane conductance regulator (CFTR) has revolutionized the treatment of persons with cystic fibrosis (CF) (pwCF). Presently, these small molecule CFTR modulators have gained approval for usage in approximately 90 % of adult pwCF. Ongoing drug development endeavors are focused on optimizing the therapeutic benefits while mitigating potential adverse effects associated with this treatment approach. Based on their mode of interaction with CFTR, these drugs can be classified into two distinct categories: specific CFTR modulators and non-specific CFTR modulators. Specific CFTR modulators encompass potentiators and correctors, whereas non-specific CFTR modulators encompass activators, proteostasis modulators, stabilizers, reader-through agents, and amplifiers. Currently, four small molecule modulators, all classified as potentiators and correctors, have obtained marketing approval. Furthermore, numerous novel small molecule modulators, exhibiting diverse mechanisms of action, are currently undergoing development. This review aims to explore the classification, mechanisms of action, molecular structures, developmental processes, and interrelationships among small molecule CFTR modulators.
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Affiliation(s)
- Luyang Cao
- China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yong Wu
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China
| | - Yanchun Gong
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China.
| | - Qingfa Zhou
- China Pharmaceutical University, Nanjing, 210009, PR China.
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3
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McDonald EF, Meiler J, Plate L. CFTR Folding: From Structure and Proteostasis to Cystic Fibrosis Personalized Medicine. ACS Chem Biol 2023; 18:2128-2143. [PMID: 37730207 PMCID: PMC10595991 DOI: 10.1021/acschembio.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023]
Abstract
Cystic fibrosis (CF) is a lethal genetic disease caused by mutations in the chloride ion channel cystic fibrosis transmembrane conductance regulator (CFTR). Class-II mutants of CFTR lack intermolecular interactions important for CFTR structural stability and lead to misfolding. Misfolded CFTR is detected by a diverse suite of proteostasis factors that preferentially bind and route mutant CFTR toward premature degradation, resulting in reduced plasma membrane CFTR levels and impaired chloride ion conductance associated with CF. CF treatment has been vastly improved over the past decade by the availability of small molecules called correctors. Correctors directly bind CFTR, stabilize its structure by conferring thermodynamically favorable interactions that compensate for mutations, and thereby lead to downstream folding fidelity. However, each of over 100 Class-II CF causing mutations causes unique structural defects and shows a unique response to drug treatment, described as theratype. Understanding CFTR structural defects, the proteostasis factors evaluating those defects, and the stabilizing effects of CFTR correctors will illuminate a path toward personalized medicine for CF. Here, we review recent advances in our understanding of CFTR folding, focusing on structure, corrector binding sites, the mechanisms of proteostasis factors that evaluate CFTR, and the implications for CF personalized medicine.
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Affiliation(s)
- Eli Fritz McDonald
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Institute
for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Lars Plate
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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4
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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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5
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Railean V, Rodrigues CS, Ramalho SS, Silva IAL, Bartosch J, Farinha CM, Pankonien I, Amaral MD. Personalized medicine: Function of CFTR variant p.Arg334Trp is rescued by currently available CFTR modulators. Front Mol Biosci 2023; 10:1155705. [PMID: 37006619 PMCID: PMC10063961 DOI: 10.3389/fmolb.2023.1155705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Most of the 2,100 CFTR gene variants reported to date are still unknown in terms of their disease liability in Cystic Fibrosis (CF) and their molecular and cellular mechanism that leads to CFTR dysfunction. Since some rare variants may respond to currently approved modulators, characterizing their defect and response to these drugs is essential for effective treatment of people with CF (pwCF) not eligible for the current treatment. Here, we assessed how the rare variant, p.Arg334Trp, impacts on CFTR traffic and function and its response to existing CFTR modulators. To this end, we performed the forskolin-induced swelling (FIS) assay on intestinal organoids from 10 pwCF bearing the p.Arg334Trp variant in one or both alleles of the CFTR gene. In parallel, a novel p.Arg334Trp-CFTR expressing CFBE cell line was generated to characterize the variant individually. Results show that p.Arg334Trp-CFTR does not significantly affect the plasma membrane traffic of CFTR and evidences residual CFTR function. This CFTR variant is rescued by currently available CFTR modulators independently of the variant in the second allele. The study, predicting clinical benefit for CFTR modulators in pwCF with at least one p.Arg334Trp variant, demonstrates the high potential of personalized medicine through theranostics to extend the label of approved drugs for pwCF carrying rare CFTR variants. We recommend that this personalized approach should be considered for drug reimbursement policies by health insurance systems/national health services.
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Santos L, Nascimento R, Duarte A, Railean V, Amaral MD, Harrison PT, Gama-Carvalho M, Farinha CM. Mutation-class dependent signatures outweigh disease-associated processes in cystic fibrosis cells. Cell Biosci 2023; 13:26. [PMID: 36759923 PMCID: PMC9912517 DOI: 10.1186/s13578-023-00975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The phenotypic heterogeneity observed in Cystic Fibrosis (CF) patients suggests the involvement of other genes, besides CFTR. Here, we combined transcriptome and proteome analysis to understand the global gene expression patterns associated with five prototypical CFTR mutations. RESULTS Evaluation of differentially expressed genes and proteins unveiled common and mutation-specific changes revealing functional signatures that are much more associated with the specific molecular defects associated with each mutation than to the CFTR loss-of-function phenotype. The combination of both datasets revealed that mutation-specific detected translated-transcripts (Dtt) have a high level of consistency. CONCLUSIONS This is the first combined transcriptomic and proteomic study focusing on prototypical CFTR mutations. Analysis of Dtt provides novel insight into the pathophysiology of CF, and the mechanisms through which each mutation class causes disease and will likely contribute to the identification of new therapeutic targets and/or biomarkers for CF.
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Affiliation(s)
- Lúcia Santos
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal ,grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Rui Nascimento
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Aires Duarte
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Violeta Railean
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Margarida D. Amaral
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Patrick T. Harrison
- grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Margarida Gama-Carvalho
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Carlos M. Farinha
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
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7
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Amaral MD. Using the genome to correct the ion transport defect in cystic fibrosis. J Physiol 2022; 601:1573-1582. [PMID: 36068724 DOI: 10.1113/jp282308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Human genome information can help finding drugs for human diseases. 'Omics' allow unbiased identification of novel drug targets. High-throughput (HT) approaches provide a global view on disease mechanisms. As a monogenic disease CF has led the way in multiple 'Omic' studies. 'Multi-omics' integration will generate maximal biological significance. ABSTRACT Today Biomedicine faces one of its greatest challenges, i.e. treating diseases through their causative dysfunctional processes and not just their symptoms. However, we still miss a global view of mechanisms and pathways involved in pathophysiology of most diseases. In fact, disease mechanisms and pathways can be achieved by holistic studies provided by 'Omic' approaches. Cystic Fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes an anion channel, is paradigmatic for monogenic disorders, namely channelopathies. A high number of 'omics studies' have focussed on CF, namely several cell-based high-throughput (HT) approaches were developed and applied towards a global mechanistic characterization of CF pathophysiology and the identification of novel and 'unbiased' drug targets. Notwithstanding, it is likely that, through the integration of all these 'layers' of large datasets into comprehensive disease maps that biological significance can be extracted so that the enormous potential of these approaches to identifying dysfunctional mechanisms and novel drugs may become a reality. Abstract figure legend Schematic overview of the 3 main approaches to discovery of new drugs/drug targets. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande-C8 bdg, Lisboa, 1749-016, Portugal
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8
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Molecular mechanisms of Cystic Fibrosis - how mutations lead to misfunction and guide therapy. Biosci Rep 2022; 42:231430. [PMID: 35707985 PMCID: PMC9251585 DOI: 10.1042/bsr20212006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cystic fibrosis, the most common autosomal recessive disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a cAMP-activated chloride and bicarbonate channel that regulates ion and water transport in secretory epithelia. Although all mutations lead to the lack or reduction in channel function, the mechanisms through which this occurs are diverse – ranging from lack of full-length mRNA, reduced mRNA levels, impaired folding and trafficking, targeting to degradation, decreased gating or conductance, and reduced protein levels to decreased half-life at the plasma membrane. Here, we review the different molecular mechanisms that cause cystic fibrosis and detail how these differences identify theratypes that can inform the use of directed therapies aiming at correcting the basic defect. In summary, we travel through CFTR life cycle from the gene to function, identifying what can go wrong and what can be targeted in terms of the different types of therapeutic approaches.
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9
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Rare Trafficking CFTR Mutations Involve Distinct Cellular Retention Machineries and Require Different Rescuing Strategies. Int J Mol Sci 2021; 23:ijms23010024. [PMID: 35008443 PMCID: PMC8744605 DOI: 10.3390/ijms23010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/12/2022] Open
Abstract
Most of the ~2100 CFTR variants so far reported are very rare and still uncharacterized regarding their cystic fibrosis (CF) disease liability. Since some may respond to currently approved modulators, characterizing their defect and response to these drugs is essential. Here we aimed characterizing the defect associated with four rare missense (likely Class II) CFTR variants and assess their rescue by corrector drugs. We produced CFBE cell lines stably expressing CFTR with W57G, R560S, H1079P and Q1100P, assessed their effect upon CFTR expression and maturation and their rescue by VX-661/VX-445 correctors. Results were validated by forskolin-induced swelling assay (FIS) using intestinal organoids from individuals bearing these variants. Finally, knock-down (KD) of genes previously shown to rescue F508del-CFTR was assessed on these mutants. Results show that all the variants preclude the production of mature CFTR, confirming them as Class II mutations. None of the variants responded to VX-661 but the combination rescued H1079P- and Q1100P-CFTR. The KD of factors that correct F508del-CFTR retention only marginally rescued R560S- and H1079P-CFTR. Overall, data evidence that Class II mutations induce distinct molecular defects that are neither rescued by the same corrector compounds nor recognized by the same cellular machinery, thus requiring personalized drug discovery initiatives.
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10
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Farinha CM, Gentzsch M. Revisiting CFTR Interactions: Old Partners and New Players. Int J Mol Sci 2021; 22:13196. [PMID: 34947992 PMCID: PMC8703571 DOI: 10.3390/ijms222413196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress in CFTR research has led to the therapeutic development of modulators that rescue the basic defect in cystic fibrosis. There is continuous interest in studying CFTR molecular disease mechanisms as not all cystic fibrosis patients have a therapeutic option available. Addressing the basis of the problem by comprehensively understanding the critical molecular associations of CFTR interactions remains key. With the availability of CFTR modulators, there is interest in comprehending which interactions are critical to rescue CFTR and which are altered by modulators or CFTR mutations. Here, the current knowledge on interactions that govern CFTR folding, processing, and stability is summarized. Furthermore, we describe protein complexes and signal pathways that modulate the CFTR function. Primary epithelial cells display a spatial control of the CFTR interactions and have become a common system for preclinical and personalized medicine studies. Strikingly, the novel roles of CFTR in development and differentiation have been recently uncovered and it has been revealed that specific CFTR gene interactions also play an important role in transcriptional regulation. For a comprehensive understanding of the molecular environment of CFTR, it is important to consider CFTR mutation-dependent interactions as well as factors affecting the CFTR interactome on the cell type, tissue-specific, and transcriptional levels.
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Affiliation(s)
- Carlos M. Farinha
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Martina Gentzsch
- Marsico Lung Institute and Cystic Fibrosis Research Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pediatrics, Division of Pediatric Pulmonology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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11
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Pereira C, Mazein A, Farinha CM, Gray MA, Kunzelmann K, Ostaszewski M, Balaur I, Amaral MD, Falcao AO. CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. Sci Rep 2021; 11:22223. [PMID: 34782688 PMCID: PMC8592983 DOI: 10.1038/s41598-021-01618-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a life-threatening autosomal recessive disease caused by more than 2100 mutations in the CF transmembrane conductance regulator (CFTR) gene, generating variability in disease severity among individuals with CF sharing the same CFTR genotype. Systems biology can assist in the collection and visualization of CF data to extract additional biological significance and find novel therapeutic targets. Here, we present the CyFi-MAP-a disease map repository of CFTR molecular mechanisms and pathways involved in CF. Specifically, we represented the wild-type (wt-CFTR) and the F508del associated processes (F508del-CFTR) in separate submaps, with pathways related to protein biosynthesis, endoplasmic reticulum retention, export, activation/inactivation of channel function, and recycling/degradation after endocytosis. CyFi-MAP is an open-access resource with specific, curated and continuously updated information on CFTR-related pathways available online at https://cysticfibrosismap.github.io/ . This tool was developed as a reference CF pathway data repository to be continuously updated and used worldwide in CF research.
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Affiliation(s)
- Catarina Pereira
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- LASIGE, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- CIRI UMR5308, CNRS-ENS-UCBL-INSERM, European Institute for Systems Biology and Medicine, Université de Lyon, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Carlos M Farinha
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Michael A Gray
- Biosciences Institute, University Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- CIRI UMR5308, CNRS-ENS-UCBL-INSERM, European Institute for Systems Biology and Medicine, Université de Lyon, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Margarida D Amaral
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Andre O Falcao
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
- LASIGE, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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12
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Santos L, Mention K, Cavusoglu-Doran K, Sanz DJ, Bacalhau M, Lopes-Pacheco M, Harrison PT, Farinha CM. Comparison of Cas9 and Cas12a CRISPR editing methods to correct the W1282X-CFTR mutation. J Cyst Fibros 2021; 21:181-187. [PMID: 34103250 DOI: 10.1016/j.jcf.2021.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND W1282X-CFTR variant (c.3846G>A) is the second most common nonsense cystic fibrosis (CF)-causing mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Even though remarkable breakthroughs have been done towards CF treatment with the approval of four CFTR protein modulators, none of these are approved for patients with nonsense mutations. CRISPR gene editing tools can be of great value to permanently correct the genetic defects caused by these mutations. METHODS We compared the capacity of homology-directed repair (HDR) mediated by Cas9 or Cas12a to correct W1282X CFTR mutation in the CFF-16HBEge W1282X CFTR cell line (obtained from CFF), using Cas9/gRNA and Cas12a/gRNA ribonucleoproteins (RNPs) and single strand DNA (ssODN) oligonucleotide donors. RESULTS Cas9 shows higher levels of correction than Cas12a as, by electroporating cells with Cas9 RNPs and ssODN donor, nearly 18% of precise editing was achieved compared to just 8% for Cas12a. Such levels of correction increase the abundance of CFTR mRNA and protein, and partially restore CFTR function in the pool of edited cells to 18% of WT CFTR function. Moreover, homozygous corrected clones produced levels of mRNA, protein, and function comparable to those of cells expressing WT CFTR. CONCLUSION Altogether, this work demonstrates the potential of gene editing as a therapeutic strategy for CF directly correcting the root cause of the disease.
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Affiliation(s)
- Lúcia Santos
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal; Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Karen Mention
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | | | - David J Sanz
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Mafalda Bacalhau
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Miquéias Lopes-Pacheco
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Patrick T Harrison
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Carlos M Farinha
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.
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13
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Amaral MD. How to determine the mechanism of action of CFTR modulator compounds: A gateway to theranostics. Eur J Med Chem 2020; 210:112989. [PMID: 33190956 DOI: 10.1016/j.ejmech.2020.112989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The greatest challenge of 21st century biology is to fully understand mechanisms of disease to drive new approaches and medical innovation. Parallel to this is the huge biomedical endeavour of treating people through personalized medicine. Until now all CFTR modulator drugs that have entered clinical trials have been genotype-dependent. An emerging alternative is personalized/precision medicine in CF, i.e., to determine whether rare CFTR mutations respond to existing (or novel) CFTR modulator drugs by pre-assessing them directly on patient's tissues ex vivo, an approach also now termed theranostics. To administer the right drug to the right person it is essential to understand how drugs work, i.e., to know their mechanism of action (MoA), so as to predict their applicability, not just in certain mutations but also possibly in other diseases that share the same defect/defective pathway. Moreover, an understanding the MoA of a drug before it is tested in clinical trials is the logical path to drug discovery and can increase its chance for success and hence also approval. In conclusion, the most powerful approach to determine the MoA of a compound is to understand the underlying biology. Novel large datasets of intervenients in most biological processes, namely those emerging from the post-genomic era tools, are available and should be used to help in this task.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal.
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Silva IAL, Doušová T, Ramalho S, Centeio R, Clarke LA, Railean V, Botelho HM, Holubová A, Valášková I, Yeh JT, Hwang TC, Farinha CM, Kunzelmann K, Amaral MD. Organoids as a personalized medicine tool for ultra-rare mutations in cystic fibrosis: The case of S955P and 1717-2A>G. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165905. [PMID: 32730979 PMCID: PMC7484254 DOI: 10.1016/j.bbadis.2020.165905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND For most of the >2000 CFTR gene variants reported, neither the associated disease liability nor the underlying basic defect are known, and yet these are essential for disease prognosis and CFTR-based therapeutics. Here we aimed to characterize two ultra-rare mutations - 1717-2A > G (c.1585-2A > G) and S955P (p.Ser955Pro) - as case studies for personalized medicine. METHODS Patient-derived rectal biopsies and intestinal organoids from two individuals with each of these mutations and F508del (p.Phe508del) in the other allele were used to assess CFTR function, response to modulators and RNA splicing pattern. In parallel, we used cellular models to further characterize S955P independently of F508del and to assess its response to CFTR modulators. RESULTS Results in both rectal biopsies and intestinal organoids from both patients evidence residual CFTR function. Further characterization shows that 1717-2A > G leads to alternative splicing generating <1% normal CFTR mRNA and that S955P affects CFTR gating. Finally, studies in organoids predict that both patients are responders to VX-770 alone and even more to VX-770 combined with VX-809 or VX-661, although to different levels. CONCLUSION This study demonstrates the high potential of personalized medicine through theranostics to extend the label of approved drugs to patients with rare mutations.
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Affiliation(s)
- Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Tereza Doušová
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84,Prague 5, 150 06 Prague, Czech Republic
| | - Sofia Ramalho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Raquel Centeio
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Violeta Railean
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Andrea Holubová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84,Prague 5, 150 06 Prague, Czech Republic
| | - Iveta Valášková
- Department of Medical Genetics, Masaryk University Brno and University Hospital Brno, Jihlavská 20, Brno 625 00, Czech Republic
| | - Jiunn-Tyng Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, United States of America
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, United States of America
| | - Carlos M Farinha
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Karl Kunzelmann
- Institut für Physiologie, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal.
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Characterization of the mechanism of action of RDR01752, a novel corrector of F508del-CFTR. Biochem Pharmacol 2020; 180:114133. [DOI: 10.1016/j.bcp.2020.114133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022]
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16
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Cytoskeleton regulators CAPZA2 and INF2 associate with CFTR to control its plasma membrane levels under EPAC1 activation. Biochem J 2020; 477:2561-2580. [PMID: 32573649 DOI: 10.1042/bcj20200287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023]
Abstract
Cystic Fibrosis (CF), the most common lethal autosomic recessive disorder among Caucasians, is caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein, a cAMP-regulated chloride channel expressed at the apical surface of epithelial cells. Cyclic AMP regulates both CFTR channel gating through a protein kinase A (PKA)-dependent process and plasma membane (PM) stability through activation of the exchange protein directly activated by cAMP1 (EPAC1). This cAMP effector, when activated promotes the NHERF1:CFTR interaction leading to an increase in CFTR at the PM by decreasing its endocytosis. Here, we used protein interaction profiling and bioinformatic analysis to identify proteins that interact with CFTR under EPAC1 activation as possible regulators of this CFTR PM anchoring. We identified an enrichment in cytoskeleton related proteins among which we characterized CAPZA2 and INF2 as regulators of CFTR trafficking to the PM. We found that CAPZA2 promotes wt-CFTR trafficking under EPAC1 activation at the PM whereas reduction of INF2 levels leads to a similar trafficking promotion effect. These results suggest that CAPZA2 is a positive regulator and INF2 a negative one for the increase of CFTR at the PM after an increase of cAMP and concomitant EPAC1 activation. Identifying the specific interactions involving CFTR and elicited by EPAC1 activation provides novel insights into late CFTR trafficking, insertion and/or stabilization at the PM and highlighs new potential therapeutic targets to tackle CF disease.
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Sousa L, Pankonien I, Clarke LA, Silva I, Kunzelmann K, Amaral MD. KLF4 Acts as a wt-CFTR Suppressor through an AKT-Mediated Pathway. Cells 2020; 9:cells9071607. [PMID: 32630830 PMCID: PMC7408019 DOI: 10.3390/cells9071607] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic Fibrosis (CF) is caused by >2000 mutations in the CF transmembrane conductance regulator (CFTR) gene, but one mutation-F508del-occurs in ~80% of patients worldwide. Besides its main function as an anion channel, the CFTR protein has been implicated in epithelial differentiation, tissue regeneration, and, when dysfunctional, cancer. However, the mechanisms that regulate such relationships are not fully elucidated. Krüppel-like factors (KLFs) are a family of transcription factors (TFs) playing central roles in development, stem cell differentiation, and proliferation. Herein, we hypothesized that these TFs might have an impact on CFTR expression and function, being its missing link to differentiation. Our results indicate that KLF4 (but not KLF2 nor KLF5) is upregulated in CF vs. non-CF cells and that it negatively regulates wt-CFTR expression and function. Of note, F508del-CFTR expressing cells are insensitive to KLF4 modulation. Next, we investigated which KLF4-related pathways have an effect on CFTR. Our data also show that KLF4 modulates wt-CFTR (but not F508del-CFTR) via both the serine/threonine kinase AKT1 (AKT) and glycogen synthase kinase 3 beta (GSK3β) signaling. While AKT acts positively, GSK3β is a negative regulator of CFTR. This crosstalk between wt-CFTR and KLF4 via AKT/ GSK3β signaling, which is disrupted in CF, constitutes a novel mechanism linking CFTR to the epithelial differentiation.
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Affiliation(s)
- Luis Sousa
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Ines Pankonien
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Luka A Clarke
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Iris Silva
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Karl Kunzelmann
- Department of Physiology, University of Regensburg, 93053 Regensburg, Germany;
| | - Margarida D Amaral
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
- Correspondence: ; Tel.: +351-21-750-08-61; Fax: +351-21-750-00-88
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Callebaut I, Mense M, Farinha CM. Exploring the basic mechanisms in Cystic Fibrosis: Promoting data presentation and discussion at the 16th ECFS Basic Science Conference. J Cyst Fibros 2020; 19 Suppl 1:S1-S4. [PMID: 31932104 DOI: 10.1016/j.jcf.2019.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The revolution in cystic fibrosis treatment is rooted in tremendous interdisciplinary research efforts, which led in recent years to significant progress in precision medicine. Since 2004, a key annual event for the CF research community is the ECFS Basic Science Conference (BSC), which is an ideal venue for deep discussions around topical subjects and fosters basic CF-related research in Europe and beyond. This special issue explores topics that were featured at the 16th ECFS BSC, held in Dubrovnik in March 2019 and provides an overview of recent progress in various fields for understanding disease mechanisms, developing relevant cell and animal models and designing breakthrough therapies. The special issue also identifies a number of the key issues and challenges in the future development of transformative therapies for all patients with CF.
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Affiliation(s)
- Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France.
| | - Martin Mense
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Carlos M Farinha
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande 1749-016, Lisboa, Portugal
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Amaral MD, Hutt DM, Tomati V, Botelho HM, Pedemonte N. CFTR processing, trafficking and interactions. J Cyst Fibros 2019; 19 Suppl 1:S33-S36. [PMID: 31680043 DOI: 10.1016/j.jcf.2019.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/04/2023]
Abstract
Mutations associated with cystic fibrosis (CF) have complex effects on the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The most common CF mutation, F508del, disrupts the processing to and stability at the plasma membrane and function as a Cl- channel. CFTR is surrounded by a dynamic network of interacting components, referred to as the CFTR Functional Landscape, that impact its synthesis, folding, stability, trafficking and function. CFTR interacting proteins can be manipulated by functional genomic approaches to rescue the trafficking and functional defects characteristic of CF. Here we review recent efforts to elucidate the impact of genetic variation on the ability of the nascent CFTR polypeptide to interact with the proteostatic environment. We also provide an overview of how specific components of this protein network can be modulated to rescue the trafficking and functional defects associated with the F508del variant of CFTR. The identification of novel proteins playing key roles in the processing of CFTR could pave the way for their use as novel therapeutic targets to provide synergistic correction of mutant CFTR for the greater benefit of individuals with CF.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla CA, USA
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy.
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21
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Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum. Cells 2019; 8:cells8040353. [PMID: 31014000 PMCID: PMC6523853 DOI: 10.3390/cells8040353] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
The most common cystic fibrosis-causing mutation (F508del, present in ~85% of CF patients) leads to CFTR misfolding, which is recognized by the endoplasmic reticulum (ER) quality control (ERQC), resulting in ER retention and early degradation. It is known that CFTR exit from the ER is mediated by specific retention/sorting signals that include four arginine-framed tripeptide (AFT) retention motifs and a diacidic (DAD) exit code that controls the interaction with the COPII machinery. Here, we aim at obtaining a global view of the protein interactors that regulate CFTR exit from the ER. We used mass spectrometry-based interaction proteomics and bioinformatics analyses to identify and characterize proteins interacting with selected CFTR peptide motifs or full-length CFTR variants retained or bypassing these ERQC checkpoints. We conclude that these ERQC trafficking checkpoints rely on fundamental players in the secretory pathway, detecting key components of the protein folding machinery associated with the AFT recognition and of the trafficking machinery recognizing the diacidic code. Furthermore, a greater similarity in terms of interacting proteins is observed for variants sharing the same folding defect over those reaching the same cellular location, evidencing that folding status is dominant over ER escape in shaping the CFTR interactome.
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