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Anglès F, Gupta V, Wang C, Balch WE. COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation. Sci Rep 2024; 14:10160. [PMID: 38698045 PMCID: PMC11065896 DOI: 10.1038/s41598-024-60687-2] [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: 07/12/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
How information flow is coordinated for managing transit of 1/3 of the genome through endomembrane pathways by the coat complex II (COPII) system in response to human variation remains an enigma. By examining the interactome of the COPII cage-assembly component Sec13, we show that it is simultaneously associated with multiple protein complexes that facilitate different features of a continuous program of chromatin organization, transcription, translation, trafficking, and degradation steps that are differentially sensitive to Sec13 levels. For the trafficking step, and unlike other COPII components, reduction of Sec13 expression decreased the ubiquitination and degradation of wild-type (WT) and F508del variant cargo protein cystic fibrosis transmembrane conductance regulator (CFTR) leading to a striking increase in fold stability suggesting that the events differentiating export from degradation are critically dependent on COPII cage assembly at the ER Golgi intermediate compartment (ERGIC) associated recycling and degradation step linked to COPI exchange. Given Sec13's multiple roles in protein complex assemblies that change in response to its expression, we suggest that Sec13 serves as an unanticipated master regulator coordinating information flow from the genome to the proteome to facilitate spatial covariant features initiating and maintaining design and function of membrane architecture in response to human variation.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Vijay Gupta
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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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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Di Mambro T, Pellielo G, Agyapong ED, Carinci M, Chianese D, Giorgi C, Morciano G, Patergnani S, Pinton P, Rimessi A. The Tricky Connection between Extracellular Vesicles and Mitochondria in Inflammatory-Related Diseases. Int J Mol Sci 2023; 24:ijms24098181. [PMID: 37175888 PMCID: PMC10179665 DOI: 10.3390/ijms24098181] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Mitochondria are organelles present in almost all eukaryotic cells, where they represent the main site of energy production. Mitochondria are involved in several important cell processes, such as calcium homeostasis, OXPHOS, autophagy, and apoptosis. Moreover, they play a pivotal role also in inflammation through the inter-organelle and inter-cellular communications, mediated by the release of mitochondrial damage-associated molecular patterns (mtDAMPs). It is currently well-documented that in addition to traditional endocrine and paracrine communication, the cells converse via extracellular vesicles (EVs). These small membrane-bound particles are released from cells in the extracellular milieu under physio-pathological conditions. Importantly, EVs have gained much attention for their crucial role in inter-cellular communication, translating inflammatory signals into recipient cells. EVs cargo includes plasma membrane and endosomal proteins, but EVs also contain material from other cellular compartments, including mitochondria. Studies have shown that EVs may transport mitochondrial portions, proteins, and/or mtDAMPs to modulate the metabolic and inflammatory responses of recipient cells. Overall, the relationship between EVs and mitochondria in inflammation is an active area of research, although further studies are needed to fully understand the mechanisms involved and how they may be targeted for therapeutic purposes. Here, we have reported and discussed the latest studies focused on this fascinating and recent area of research, discussing of tricky connection between mitochondria and EVs in inflammatory-related diseases.
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Affiliation(s)
- Tommaso Di Mambro
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Giulia Pellielo
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Esther Densu Agyapong
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Marianna Carinci
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Diego Chianese
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Carlotta Giorgi
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Giampaolo Morciano
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Simone Patergnani
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Pinton
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
- Center of Research for Innovative Therapies in Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
| | - Alessandro Rimessi
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
- Center of Research for Innovative Therapies in Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
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Zacarias S, Batista MSP, Ramalho SS, Victor BL, Farinha CM. Rescue of Rare CFTR Trafficking Mutants Highlights a Structural Location-Dependent Pattern for Correction. Int J Mol Sci 2023; 24:ijms24043211. [PMID: 36834620 PMCID: PMC9961391 DOI: 10.3390/ijms24043211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) channel. Currently, more than 2100 variants have been identified in the gene, with a large number being very rare. The approval of modulators that act on mutant CFTR protein, correcting its molecular defect and thus alleviating the burden of the disease, revolutionized the field of CF. However, these drugs do not apply to all patients with CF, especially those with rare mutations-for which there is a lack of knowledge on the molecular mechanisms of the disease and the response to modulators. In this work, we evaluated the impact of several rare putative class II mutations on the expression, processing, and response of CFTR to modulators. Novel cell models consisting of bronchial epithelial cell lines expressing CFTR with 14 rare variants were created. The variants studied are localized at Transmembrane Domain 1 (TMD1) or very close to the signature motif of Nucleotide Binding Domain 1 (NBD1). Our data show that all mutations analyzed significantly decrease CFTR processing and while TMD1 mutations respond to modulators, those localized in NBD1 do not. Molecular modeling calculations confirm that the mutations in NBD1 induce greater destabilization of CFTR structure than those in TMD1. Furthermore, the structural proximity of TMD1 mutants to the reported binding site of CFTR modulators such as VX-809 and VX-661, make them more efficient in stabilizing the CFTR mutants analyzed. Overall, our data suggest a pattern for mutation location and impact in response to modulators that correlates with the global effect of the mutations on CFTR structure.
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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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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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Wang C, Anglès F, Balch WE. Triangulating variation in the population to define mechanisms for precision management of genetic disease. Structure 2022; 30:1190-1207.e5. [PMID: 35714602 PMCID: PMC9357173 DOI: 10.1016/j.str.2022.05.011] [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: 09/01/2021] [Revised: 04/18/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
To understand mechanistically how the protein fold is shaped by therapeutics to inform precision management of disease, we developed variation-capture (VarC) mapping. VarC triangulates sparse sequence variation information found in the population using Gaussian process regression (GPR)-based machine learning to define the combined pairwise-residue interactions contributing to dynamic protein function in the individual in response to therapeutics. Using VarC mapping, we now reveal the pairwise-residue covariant relationships across the entire protein fold of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) to define the molecular mechanisms of clinically approved CF chemical modulators. We discover an energetically destabilized covariant core containing a di-acidic YKDAD endoplasmic reticulum (ER) exit code that is only weakly corrected by current therapeutics. Our results illustrate that VarC provides a generalizable tool to triangulate information from genetic variation in the population to mechanistically discover therapeutic strategies that guide precision management of the individual.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Frédéric Anglès
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.
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Amaral MD. Precision medicine for rare diseases: The times they are A-Changin'. Curr Opin Pharmacol 2022; 63:102201. [DOI: 10.1016/j.coph.2022.102201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
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Roda J, Teixeira T, Ai Silva I, Silva TR, Ferreira R, Amaral MD, Oliveira G. Pediatric population with cystic fibrosis in the centre of Portugal: candidates for new therapies. J Pediatr (Rio J) 2022; 98:212-217. [PMID: 34252371 PMCID: PMC9432345 DOI: 10.1016/j.jped.2021.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Cystic fibrosis (CF) is a severe autosomal recessive disease that results from mutations in a gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein, a chloride channel. This study aims to characterize the clinical and genetic features of a cohort of pediatric people with CF (PwCF) in the center of Portugal and to determine which ones are candidates for the new drugs modulating the CFTR channel. METHODS A review of the demographic, genetic and clinical characteristics of PwCF undergoing follow-up at a CF reference center was carried out. RESULTS Twenty-three PwCF (12 male), with a median age of 12 years, were followed up. All patients carry the F508del mutation in at least one allele. Fifteen PwCF were F508del-homozygous, median BMI z-score was -0.13, all are pancreatic insufficient and median FEV1 value was 78.1%. These PwCF are eligible for dual therapy (lumacaftor/tezacaftor+ivacaftor) and for triple therapy (tezacaftor+ivacaftor+elexacaftor). PwCF with 711 +1G->T (n = 2), 2184insA (n = 1) mutations and a novel mutation c.3321dup (n = 1) have minimal function mutation and patients with a residual function mutation: R334W (n = 3) and P5L (n = 1) have a less severe phenotype. All these patients, because they also carry F508del mutation, are elegible to triple therapy. CONCLUSIONS Genetic and molecular characterization of PwCF poses an important step not just for CF diagnosis and prognosis which is tightly correlated with the clinical phenotype, but also for the eligibility of CFTR modulator drugs.
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Affiliation(s)
- Juliana Roda
- Centro Hospitalar e Universitário de Coimbra, Hospital Pediátrico, Unidade de Gastroenterologia e Nutrição Pediátrica, Coimbra, Portugal; Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal.
| | - Teresa Teixeira
- Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal
| | - Iris Ai Silva
- Universidade de Lisboa, Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas (BioISI), Lisbon, Portugal
| | - Teresa Reis Silva
- Centro Hospitalar e Universitário de Coimbra, Centro de Referência em Fibrose Cística, Unidade Pediátrica, Coimbra, Portugal
| | - Ricardo Ferreira
- Centro Hospitalar e Universitário de Coimbra, Hospital Pediátrico, Unidade de Gastroenterologia e Nutrição Pediátrica, Coimbra, Portugal
| | - Margarida D Amaral
- Universidade de Lisboa, Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas (BioISI), Lisbon, Portugal
| | - Guiomar Oliveira
- Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal; Centro Hospitalar e Universitário de Coimbra, Centro de Desenvolvimento da Criança e Centro de Investigação e Formação Clínica, Hospital Pediátrico, Coimbra, Portugal
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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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Peters KW, Gong X, Frizzell RA. Cystic Fibrosis Transmembrane Conductance Regulator Folding Mutations Reveal Differences in Corrector Efficacy Linked to Increases in Immature Cystic Fibrosis Transmembrane Conductance Regulator Expression. Front Physiol 2021; 12:695767. [PMID: 34764878 PMCID: PMC8576290 DOI: 10.3389/fphys.2021.695767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Most cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that lead to protein misfolding and degradation by the ubiquitin–proteasome system. Previous studies demonstrated that PIAS4 facilitates the modification of wild-type (WT) and F508del CFTR by small ubiquitin-like modifier (SUMO)-1, enhancing CFTR biogenesis by slowing immature CFTR degradation and producing increased immature CFTR band B. Methods: We evaluated two correction strategies using misfolding mutants, including the common variant, F508del. We examined the effects on mutant expression of co-expression with PIAS4 (E3 SUMO ligase), and/or the corrector, C18. To study the impact of these correction conditions, we transfected CFBE410- cells, a bronchial epithelial cell line, with a CFTR mutant plus: (1) empty vector, (2) empty vector plus overnight 5 μM C18, (3) PIAS4, and (4) PIAS4 plus C18. We assessed expression at steady state by immunoblot of CFTR band B, and if present, band C, and the corresponding C:B band ratio. The large PIAS4-induced increase in band B expression allowed us to ask whether C18 could act on the now abundant immature protein to enhance correction above the control level, as reported by the C:B ratio. Results: The data fell into three mutant CFTR categories as follows: (1) intransigent: no observable band C under any condition (i.e., C:B = 0); (2) throughput responsive: a C:B ratio less than control, but suggesting that the increased band C resulted from PIAS4-induced increases in band B production; and (3) folding responsive: a C:B ratio greater than control, reflecting C18-induced folding greater than that expected from increased throughput due to the PIAS4-induced band B level. Conclusion: These results suggest that the immature forms of CFTR folding intermediates occupy different loci within the energetic/kinetic folding landscape of CFTR. The evaluation of their properties could assist in the development of correctors that can target the more difficult-to-fold mutant conformations that occupy different sites within the CFTR folding pathway.
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Affiliation(s)
- Kathryn W Peters
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Xiaoyan Gong
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Raymond A Frizzell
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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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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Stanton BA, Hampton TH, Ashare A. SARS-CoV-2 (COVID-19) and cystic fibrosis. Am J Physiol Lung Cell Mol Physiol 2020; 319:L408-L415. [PMID: 32668165 PMCID: PMC7518058 DOI: 10.1152/ajplung.00225.2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene. Although viral respiratory tract infections are, in general, more severe in patients with CF compared with the general population, a small number of studies indicate that SARS-CoV-2 does not cause a worse infection in CF. This is surprising since comorbidities including preexisting lung disease have been reported to be associated with worse outcomes in SARS-CoV-2 infections. Several recent studies provide insight into why SARS-CoV-2 may not produce more severe outcomes in CF. First, ACE and ACE2, genes that play key roles in SARS-CoV-2 infection, have some variants that are predicted to reduce the severity of SARS-CoV-2 infection. Second, mRNA for ACE2 is elevated and mRNA for TMPRSS2, a serine protease, is decreased in CF airway epithelial cells. Increased ACE2 is predicted to enhance SARS-CoV-2 binding to cells but would increase conversion of angiotensin II, which is proinflammatory, to angiotensin-1-7, which is anti-inflammatory. Thus, increased ACE2 would reduce inflammation and lung damage due to SARS-CoV-2. Moreover, decreased TMPRSS2 would reduce SARS-CoV-2 entry into airway epithelial cells. Second, many CF patients are treated with azithromycin, which suppresses viral infection and lung inflammation and inhibits the activity of furin, a serine protease. Finally, the CF lung contains high levels of serine protease inhibitors including ecotin and SERPINB1, which are predicted to reduce the ability of TMPRSS2 to facilitate SARS-CoV-2 entry into airway epithelial cells. Thus, a variety of factors may mitigate the severity of SARS-CoV-2 in CF.
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Affiliation(s)
- Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
- Section of Pulmonology, Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
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14
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Ricard-Blum S, Miele AE. Omic approaches to decipher the molecular mechanisms of fibrosis, and design new anti-fibrotic strategies. Semin Cell Dev Biol 2020; 101:161-169. [DOI: 10.1016/j.semcdb.2019.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
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15
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Useckaite Z, Ward MP, Trappe A, Reilly R, Lennon J, Davage H, Matallanas D, Cassidy H, Dillon ET, Brennan K, Doyle SL, Carter S, Donnelly S, Linnane B, McKone EF, McNally P, Coppinger JA. Increased extracellular vesicles mediate inflammatory signalling in cystic fibrosis. Thorax 2020; 75:449-458. [PMID: 32265339 PMCID: PMC7279202 DOI: 10.1136/thoraxjnl-2019-214027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/09/2020] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
Abstract
Rationale Mutations in the cystic fibrosis transmembrane regulator (CFTR) gene form the basis of cystic fibrosis (CF). There remains an important knowledge gap in CF as to how diminished CFTR activity leads to the dominant inflammatory response within CF airways. Objectives To investigate if extracellular vesicles (EVs) contribute to inflammatory signalling in CF. Methods EVs released from CFBE41o-, CuFi-5, 16HBE14o- and NuLi-1 cells were characterised by nanoparticle tracking analysis (NTA). EVs isolated from bronchoalveolar lavage fluid (BALF) from 30 people with CF (PWCF) were analysed by NTA and mass spectrometry and compared with controls. Neutrophils were isolated from the blood of 8 PWCF to examine neutrophil migration in the presence of CFBE41o- EVs. Results A significantly higher level of EVs were released from CFBE41o- (p<0.0001) and CuFi-5 (p=0.0209) relative to control cell lines. A significantly higher level of EVs were detected in BALF of PWCF, in three different age groups relative to controls (p=0.01, 0.001, 0.002). A significantly lower level of EVs were released from CFBE41o- (p<0.001) and CuFi-5 (p=0.0002) cell lines treated with CFTR modulators. Significant changes in the protein expression of 126 unique proteins was determined in EVs obtained from the BALF of PWCF of different age groups (p<0.001–0.05). A significant increase in chemotaxis of neutrophils derived from PWCF was observed in the presence of CFBE41o EVs (p=0.0024) compared with controls. Conclusion This study demonstrates that EVs are produced in CF airway cells, have differential protein expression at different ages and drive neutrophil recruitment in CF.
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Affiliation(s)
- Zivile Useckaite
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Mark P Ward
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Anne Trappe
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Rebecca Reilly
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Jenny Lennon
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - Holly Davage
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
| | - David Matallanas
- Systems Biology Ireland, UCD School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Hilary Cassidy
- Systems Biology Ireland, UCD School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland.,School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Eugene T Dillon
- UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kiva Brennan
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Sarah L Doyle
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | | | - Seamas Donnelly
- Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Barry Linnane
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland.,Paediatrics, University Hospital Limerick, Limerick, Ireland
| | - Edward F McKone
- UCD Conway Institute, University College Dublin, Dublin 4, Ireland.,St. Vincent's University Hospital, Dublin 4, Ireland
| | - Paul McNally
- National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland.,Paediatrics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Judith A Coppinger
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland .,National Children's Research Centre, Children's Health Ireland (CHI) at Crumlin, Dublin 12, Ireland
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16
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Anglès F, Hutt DM, Balch WE. HDAC inhibitors rescue multiple disease-causing CFTR variants. Hum Mol Genet 2020; 28:1982-2000. [PMID: 30753450 DOI: 10.1093/hmg/ddz026] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/21/2018] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Understanding the role of the epigenome in protein-misfolding diseases remains a challenge in light of genetic diversity found in the world-wide population revealed by human genome sequencing efforts and the highly variable response of the disease population to therapeutics. An ever-growing body of evidence has shown that histone deacetylase (HDAC) inhibitors (HDACi) can have significant benefit in correcting protein-misfolding diseases that occur in response to both familial and somatic mutation. Cystic fibrosis (CF) is a familial autosomal recessive disease, caused by genetic diversity in the CF transmembrane conductance regulator (CFTR) gene, a cyclic Adenosine MonoPhosphate (cAMP)-dependent chloride channel expressed at the apical plasma membrane of epithelial cells in multiple tissues. The potential utility of HDACi in correcting the phenylalanine 508 deletion (F508del) CFTR variant as well as the over 2000 CF-associated variants remains controversial. To address this concern, we examined the impact of US Food and Drug Administration-approved HDACi on the trafficking and function of a panel of CFTR variants. Our data reveal that panobinostat (LBH-589) and romidepsin (FK-228) provide functional correction of Class II and III CFTR variants, restoring cell surface chloride channel activity in primary human bronchial epithelial cells. We further demonstrate a synergistic effect of these HDACi with Vx809, which can significantly restore channel activity for multiple CFTR variants. These data suggest that HDACi can serve to level the cellular playing field for correcting CF-causing mutations, a leveling effect that might also extend to other protein-misfolding diseases.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA.,Skaggs Institute of Chemical Biology, North Torrey Pines Rd, La Jolla, CA, USA
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17
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Wang C, Balch WE. Bridging Genomics to Phenomics at Atomic Resolution through Variation Spatial Profiling. Cell Rep 2020; 24:2013-2028.e6. [PMID: 30134164 PMCID: PMC6261431 DOI: 10.1016/j.celrep.2018.07.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 01/04/2023] Open
Abstract
To understand the impact of genome sequence variation (the genotype) responsible for biological diversity and human health (the phenotype) including cystic fibrosis and Alzheimer's disease, we developed a Gaussian-process-based machine learning (ML) approach, variation spatial profiling (VSP). VSP uses a sparse collection of known variants found in the population that perturb the protein fold to define unknown variant function based on the emergent general principle of spatial covariance (SCV). SCV quantitatively captures the role of proximity in genotype-to-phenotype spatial-temporal relationships. Phenotype landscapes generated through SCV provide a platform that can be used to describe the functional properties that drive sequence-to-function-to-structure design of the polypeptide fold at atomic resolution. We provide proof of principle that SCV can enable the use of population-based genomic platforms to define the origins and mechanism of action of genotype-to-phenotype transformations contributing to the health and disease of an individual.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.
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18
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Wang C, Zhao P, Sun S, Teckman J, Balch WE. Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2020; 7:224-246. [PMID: 32726074 DOI: 10.15326/jcopdf.7.3.2019.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep medicine is rapidly moving towards a high-definition approach for therapeutic management of the patient as an individual given the rapid progress of genome sequencing technologies and machine learning algorithms. While considered a monogenic disease, alpha-1 antitrypsin (AAT) deficiency (AATD) patients present with complex and variable phenotypes we refer to as the "hallmarks of AATD" that involve distinct molecular mechanisms in the liver, plasma and lung tissues, likely due to both coding and non-coding variation as well as genetic and environmental modifiers in different individuals. Herein, we briefly review the current therapeutic strategies for the management of AATD. To embrace genetic diversity in the management of AATD, we provide an overview of the disease phenotypes of AATD patients harboring different AAT variants. Linking genotypic diversity to phenotypic diversity illustrates the potential for sequence-specific regions of AAT protein fold design to play very different roles during nascent synthesis in the liver and/or function in post-liver plasma and lung environments. We illustrate how to manage diversity with recently developed machine learning (ML) approaches that bridge sequence-to-function-to-structure knowledge gaps based on the principle of spatial covariance (SCV). SCV relationships provide a deep understanding of the genotype to phenotype transformation initiated by AAT variation in the population to address the role of genetic and environmental modifiers in the individual. Embracing the complexity of AATD in the population is critical for risk management and therapeutic intervention to generate a high definition medicine approach for the patient.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Jeffrey Teckman
- Pediatrics and Biochemistry, Saint Louis University, and Cardinal Glennon Children's Medical Center, St. Louis, Missouri
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California
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19
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Tosco A, Villella VR, Raia V, Kroemer G, Maiuri L. Cystic Fibrosis: New Insights into Therapeutic Approaches. CURRENT RESPIRATORY MEDICINE REVIEWS 2020. [DOI: 10.2174/1573398x15666190702151613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the identification of Cystic Fibrosis (CF) as a disease in 1938 until 2012, only
therapies to treat symptoms rather than etiological therapies have been used to treat the disease. Over
the last few years, new technologies have been developed, and gene editing strategies are now
moving toward a one-time cure. This review will summarize recent advances in etiological therapies
that target the basic defect in the CF Transmembrane Receptor (CFTR), the protein that is mutated in
CF. We will discuss how newly identified compounds can directly target mutated CFTR to improve
its function. Moreover, we will discuss how proteostasis regulators can modify the environment in
which the mutant CFTR protein is synthesized and decayed, thus restoring CFTR function. The
future of CF therapies lies in combinatory therapies that may be personalized for each CF patient.
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Affiliation(s)
- Antonella Tosco
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Valeria R. Villella
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Valeria Raia
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Guido Kroemer
- Equipe11 labellisee Ligue Nationale Contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Luigi Maiuri
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
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20
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET RESPIRATORY MEDICINE 2020; 8:65-124. [DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
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21
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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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22
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Pierandrei S, Blaconà G, Fabrizzi B, Cimino G, Cirilli N, Caporelli N, Angeloni A, Cipolli M, Lucarelli M. Two novel and correlated CF-causing insertions in the (TG)mTn tract of the CFTR gene. PLoS One 2019; 14:e0222838. [PMID: 31593572 PMCID: PMC6782095 DOI: 10.1371/journal.pone.0222838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023] Open
Abstract
Two novel and related pathogenic variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene were structurally and functionally characterized. These alterations have not been previously described in literature. Two patients with diagnosis of Cystic Fibrosis (CF) based on the presence of one mutated allele, p.Phe508del, pathological sweat test and clinical symptoms were studied. To complete the genotypes of both patients, an extensive genetic and functional analysis of the CFTR gene was performed. Extensive genetic characterization confirmed the presence of p.Phe508del pathogenic variant and revealed, in both patients, the presence of an insertion of part of intron 10 in intron 9 of the CFTR gene, within the (TG)m repeat, with a variable poly-T stretch. The molecular lesions resulted to be very similar in both patients, with only a difference in the number of T in the poly-T stretch. The functional characterization at RNA level revealed a complete anomalous splicing, without exon 10, from the allele with the insertion of both patients. Consequently, the alleles with the insertions are expected not to contribute to the formation of a functional CFTR protein. Molecular and functional features of these alterations are compatible with the definition of novel CF-causing variants of the CFTR gene. This also allowed the completion of the genetic characterization of both patients.
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Affiliation(s)
- Silvia Pierandrei
- Dept. of Mother-Child and Urologic Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Blaconà
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Care Center, Umberto I Hospital, Rome, Italy
| | - Natalia Cirilli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Antonio Angeloni
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Cipolli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
- * E-mail:
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23
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Shanthikumar S, Neeland MN, Saffery R, Ranganathan S. Gene modifiers of cystic fibrosis lung disease: A systematic review. Pediatr Pulmonol 2019; 54:1356-1366. [PMID: 31140758 DOI: 10.1002/ppul.24366] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Lung disease is the major source of morbidity and mortality in cystic fibrosis (CF), with large variability in severity between patients. Although accurate prediction of lung disease severity would be extremely useful, no robust methods exist. Twin and sibling studies have highlighted the importance of non-cystic fibrosis transmembrane conductance regulator (CFTR) genes in determining lung disease severity but how these impact on the severity in CF remains unclear. METHODS A systematic review was undertaken to answer the question "In patients with CF which non-CFTR genes modify the severity of lung disease?" The method for this systematic review was based upon the "Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)" statement, with a narrative synthesis of results planned. RESULTS A total of 1168 articles were screened for inclusion, with 275 articles undergoing detailed assessment for inclusion. One hundred and forty articles were included. Early studies focused on candidate genes, whereas more recent studies utilized genome-wide approaches and also examined epigenetic mechanisms, gene expression, and therapeutic response. DISCUSSION A large body of evidence regarding non-CFTR gene modifiers of lung disease severity has been generated, examining a wide array of genes. Limitations to existing studies include heterogeneity in outcome measures used, limited replication, and relative lack of clinical impact. Future work examining non-CFTR gene modifiers will have to overcome these limitations if gene modifiers are to have a meaningful role in the care of patients with CF.
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Affiliation(s)
- Shivanthan Shanthikumar
- Respiratory and Sleep Medicine Department, Royal Children's Hospital, Melbourne, Australia.,Respiratory Diseases Department, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Australia
| | - Melanie N Neeland
- Department of Paediatrics, The University of Melbourne, Australia.,Centre of Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Australia.,Cancer & Disease Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Sarath Ranganathan
- Respiratory and Sleep Medicine Department, Royal Children's Hospital, Melbourne, Australia.,Respiratory Diseases Department, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Australia
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24
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Amaral MD, de Boeck K. Theranostics by testing CFTR modulators in patient-derived materials: The current status and a proposal for subjects with rare CFTR mutations. J Cyst Fibros 2019; 18:685-692. [PMID: 31326274 DOI: 10.1016/j.jcf.2019.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022]
Abstract
The last decade has witnessed developments in the CF drug pipeline which are both exciting and unprecedented, bringing with them previously unconsidered challenges. The Task Force group came together to consider these challenges and possible strategies to address them. Over the last 18 months, we have discussed internally and gathered views from a broad range of individuals representing patient organizations, clinical and research teams, the pharmaceutical industry and regulatory agencies. In this and the accompanying article, we discuss two main areas of focus: i) optimising trial design and delivery for speed/efficiency; ii) drug development for patients with rare CFTR mutations. We propose some strategies to tackle the challenges ahead and highlight areas where further thought is needed. We see this as the start of a process rather than the end and hope herewith to engage the wider community in seeking solutions to improved treatments for all patients with CF.
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25
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Villella VR, Tosco A, Esposito S, Ferrari E, Bona G, Kroemer G, Raia V, Maiuri L. Personalization of therapies in rare diseases: a translational approach for the treatment of cystic fibrosis. Minerva Pediatr 2019; 71:362-370. [PMID: 30761822 DOI: 10.23736/s0026-4946.19.05511-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High variability in the response rates to treatments can make the interpretation of data from clinical trials very difficult, particularly in rare genetic diseases in which the enrolment of thousands of patients is problematic. Personalized medicine largely depends on the establishment of appropriate early detectors of drug efficacy that may guide the administration (or discontinuation) of specific treatments. Such biomarkers should be capable of predicting the therapeutic response of individual patients and of monitoring early benefits of candidate drugs before late clinical benefits become evident. The identification of these biomarkers implies a rigorous stepwise process of translation from preclinical evaluation in cultured cells, suitable animal models or patient-derived freshly isolated cells to clinical application. In this review, we will discuss how a process of research translation can lead to the implementation of functional and mechanistic disease-relevant biomarkers. Moreover, we will address how preclinical data can be translated into the clinic in a personalized medical approach that can provide the right drug to the right patient within the right timeframe.
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Affiliation(s)
- Valeria R Villella
- European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Tosco
- Regional Cystic Fibrosis Center, Unit of Pediatrics, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Speranza Esposito
- European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Ferrari
- European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy.,Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gianni Bona
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Guido Kroemer
- Equipe11 Labellisée Ligue Nationale contre le Cancer, Cordeliers Research Center, Paris, France.,INSERM U1138, Cordeliers Research Center, Paris, France.,Paris Descartes University, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Institute, Villejuif, France.,Section of Biology, Georges Pompidou European Hospital, Assistance Publique, Hôpitaux de Paris (AP-HP), Paris, France.,Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Valeria Raia
- Regional Cystic Fibrosis Center, Unit of Pediatrics, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Luigi Maiuri
- European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan, Italy - .,Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
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26
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Pollard BS, Pollard HB. Induced pluripotent stem cells for treating cystic fibrosis: State of the science. Pediatr Pulmonol 2018; 53:S12-S29. [PMID: 30062693 DOI: 10.1002/ppul.24118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are a recently developed technology in which fully differentiated cells such as fibroblasts from individual CF patients can be repaired with [wildtype] CFTR, and reprogrammed to differentiate into fully differentiated cells characteristic of the proximal and distal airways. Here, we review properties of different epithelial cells in the airway, and the in vitro genetic roadmap which iPSCs follow as they are step-wise differentiated into either basal stem cells, for the proximal airway, or into Type II Alveolar cells for the distal airways. The central theme is that iPSC-derived basal stem cells, are penultimately dependent on NOTCH signaling for differentiation into club cells, goblet cells, ciliated cells, and neuroendocrine cells. Furthermore, given the proper matrix, these cellular progenies are also able to self-assemble into a fully functional pseudostratified squamous proximal airway epithelium. By contrast, club cells are reserve stem cells which are able to either differentiate into goblet or ciliated cells, but also to de-differentiate into basal stem cells. Variant club cells, located at the transition between airway and alveoli, may also be responsible for differentiation into Type II Alveolar cells, which then differentiate into Type I Alveolar cells for gas exchange in the distal airway. Using gene editing, the mutant CFTR gene in iPSCs from CF patients can be repaired, and fully functional epithelial cells can thus be generated through directed differentiation. However, there is a limitation in that the lung has other CFTR-dependent cells besides epithelial cells. Another limitation is that there are CFTR-dependent cells in other organs which would continue to contribute to CF disease. Furthermore, there are also bystander or modifier genes which affect disease outcome, not only in the lung, but specifically in other CF-affected organs. Finally, we discuss future personalized applications of the iPSC technology, many of which have already survived the "proof-of-principle" test. These include (i) patient-derived iPSCs used as a "lung-on-a-chip" tool for personalized drug discovery; (ii) replacement of mutant lung cells by wildtype lung cells in the living lung; and (iii) development of bio-artificial lungs. It is hoped that this review will give the reader a roadmap through the most complicated of the obstacles, and foster a guardedly optimistic view of how some of the remaining obstacles might one day be overcome.
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Affiliation(s)
| | - Harvey B Pollard
- Department of Cell Biology and Genetics, Uniformed Services University School of Medicine-America's Medical School, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Hutt DM, Loguercio S, Campos AR, Balch WE. A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease. J Mol Biol 2018; 430:2951-2973. [PMID: 29924966 PMCID: PMC6097907 DOI: 10.1016/j.jmb.2018.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention. A comparative analysis of variant-specific proteomics allows us to identify a number of protein interactions contributing to the basic defects associated with F508del- and G551D-CFTR, two of the most common disease-associated variants in the patient population. We demonstrate that a number of these causal interactions are significantly altered in response to treatment with Vx809 and Vx770, small-molecule therapeutics that respectively target the F508del and G551D variants. ProVarA represents the first comparative proteomic analysis among multiple disease-causing mutations, thereby providing a methodological approach that provides a significant advancement to existing proteomic efforts in understanding the impact of variation in CF disease. We posit that the implementation of ProVarA for any familial or somatic mutation will provide a substantial increase in the knowledge base needed to implement a precision medicine-based approach for clinical management of disease.
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Affiliation(s)
- Darren M Hutt
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Salvatore Loguercio
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomic Core 10901 North Torrey Pines Road, La Jolla CA USA 92037
| | - William E Balch
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- Integrative Structural and Computational Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
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Hutt DM, Loguercio S, Roth DM, Su AI, Balch WE. Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation. J Biol Chem 2018; 293:13477-13495. [PMID: 30006345 DOI: 10.1074/jbc.ra118.003192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/05/2018] [Indexed: 12/31/2022] Open
Abstract
Inherited and somatic rare diseases result from >200,000 genetic variants leading to loss- or gain-of-toxic function, often caused by protein misfolding. Many of these misfolded variants fail to properly interact with other proteins. Understanding the link between factors mediating the transcription, translation, and protein folding of these disease-associated variants remains a major challenge in cell biology. Herein, we utilized the cystic fibrosis transmembrane conductance regulator (CFTR) protein as a model and performed a proteomics-based high-throughput screen (HTS) to identify pathways and components affecting the folding and function of the most common cystic fibrosis-associated mutation, the F508del variant of CFTR. Using a shortest-path algorithm we developed, we mapped HTS hits to the CFTR interactome to provide functional context to the targets and identified the eukaryotic translation initiation factor 3a (eIF3a) as a central hub for the biogenesis of CFTR. Of note, siRNA-mediated silencing of eIF3a reduced the polysome-to-monosome ratio in F508del-expressing cells, which, in turn, decreased the translation of CFTR variants, leading to increased CFTR stability, trafficking, and function at the cell surface. This finding suggested that eIF3a is involved in mediating the impact of genetic variations in CFTR on the folding of this protein. We posit that the number of ribosomes on a CFTR mRNA transcript is inversely correlated with the stability of the translated polypeptide. Polysome-based translation challenges the capacity of the proteostasis environment to balance message fidelity with protein folding, leading to disease. We suggest that this deficit can be corrected through control of translation initiation.
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Affiliation(s)
| | | | | | - Andrew I Su
- Integrative Structural and Computational Biology and
| | - William E Balch
- From the Departments of Molecular Medicine and .,the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
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Hutt DM, Mishra SK, Roth DM, Larsen MB, Angles F, Frizzell RA, Balch WE. Silencing of the Hsp70-specific nucleotide-exchange factor BAG3 corrects the F508del-CFTR variant by restoring autophagy. J Biol Chem 2018; 293:13682-13695. [PMID: 29986884 DOI: 10.1074/jbc.ra118.002607] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/05/2018] [Indexed: 01/11/2023] Open
Abstract
The protein chaperones heat shock protein 70 (Hsp70) and Hsp90 are required for de novo folding of proteins and protect against misfolding-related cellular stresses by directing misfolded or slowly folding proteins to the ubiquitin/proteasome system (UPS) or autophagy/lysosomal degradation pathways. Here, we examined the role of the Bcl2-associated athanogene (BAG) family of Hsp70-specific nucleotide-exchange factors in the biogenesis and functional correction of genetic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) whose mutations cause cystic fibrosis (CF). We show that siRNA-mediated silencing of BAG1 and -3, two BAG members linked to the clearance of misfolded proteins via the UPS and autophagy pathways, respectively, leads to functional correction of F508del-CFTR and other disease-associated CFTR variants. BAG3 silencing was the most effective, leading to improved F508del-CFTR stability, trafficking, and restoration of cell-surface function, both alone and in combination with the FDA-approved CFTR corrector, VX-809. We also found that the BAG3 silencing-mediated correction of F508del-CFTR restores the autophagy pathway, which is defective in F508del-CFTR-expressing cells, likely because of the maladaptive stress response in CF pathophysiology. These results highlight the potential therapeutic benefits of targeting the cellular chaperone system to improve the functional folding of CFTR variants contributing to CF and possibly other protein-misfolding-associated diseases.
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Affiliation(s)
- Darren M Hutt
- From the Department of Molecular Medicine, Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California 92037 and
| | - Sanjay Kumar Mishra
- the Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Daniela Martino Roth
- From the Department of Molecular Medicine, Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California 92037 and
| | - Mads Breum Larsen
- the Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Frédéric Angles
- From the Department of Molecular Medicine, Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California 92037 and
| | - Raymond A Frizzell
- the Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - William E Balch
- From the Department of Molecular Medicine, Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California 92037 and
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Tosco A, Villella VR, Castaldo A, Kroemer G, Maiuri L, Raia V. Repurposing therapies for the personalised treatment of cystic fibrosis. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1483231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Antonella Tosco
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Valeria R. Villella
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Alice Castaldo
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Guido Kroemer
- Equipe11 labellisée Ligue Nationale Contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Paris, Sorbonne Paris Cité, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, HôpitalEuropéen Georges Pompidou, AP-HP, Paris, France
| | - Luigi Maiuri
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Valeria Raia
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
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Lim SH, Legere EA, Snider J, Stagljar I. Recent Progress in CFTR Interactome Mapping and Its Importance for Cystic Fibrosis. Front Pharmacol 2018; 8:997. [PMID: 29403380 PMCID: PMC5785726 DOI: 10.3389/fphar.2017.00997] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/26/2017] [Indexed: 12/25/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride channel found in secretory epithelia with a plethora of known interacting proteins. Mutations in the CFTR gene cause cystic fibrosis (CF), a disease that leads to progressive respiratory illness and other complications of phenotypic variance resulting from perturbations of this protein interaction network. Studying the collection of CFTR interacting proteins and the differences between the interactomes of mutant and wild type CFTR provides insight into the molecular machinery of the disease and highlights possible therapeutic targets. This mini review focuses on functional genomics and proteomics approaches used for systematic, high-throughput identification of CFTR-interacting proteins to provide comprehensive insight into CFTR regulation and function.
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Affiliation(s)
- Sang Hyun Lim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Jamie Snider
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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Pfaar O, Bonini S, Cardona V, Demoly P, Jakob T, Jutel M, Kleine-Tebbe J, Klimek L, Klysner S, Kopp MV, Kuna P, Larché M, Muraro A, Schmidt-Weber CB, Shamji MH, Simonsen K, Somoza C, Valovirta E, Zieglmayer P, Zuberbier T, Wahn U. Perspectives in allergen immunotherapy: 2017 and beyond. Allergy 2018; 73 Suppl 104:5-23. [PMID: 29171712 DOI: 10.1111/all.13355] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2017] [Indexed: 01/01/2023]
Abstract
The Future of the Allergists and Specific Immunotherapy (FASIT) workshop provides a regular platform for global experts from academia, allergy clinics, regulatory authorities and industry to review developments in the field of allergen immunotherapy (AIT). The most recent meeting, held in February 2017, had two main themes: advances in AIT and hot topics in AIT from the regulatory point of view. The first theme covered opportunities for personalized AIT, advances in adjuvants and delivery systems, and the development of new molecules and future vaccines for AIT. Key topics in the second part of the meeting were the effects of the enactment of European Directive 2001/83 on the availability of allergens for therapy and diagnosis across the EU, the challenges of conducting Phase 3 studies in the field, the future role of allergen exposure chambers in AIT studies and specific considerations in performing AIT studies in the paediatric population. Finally, the group highlighted the forthcoming EAACI guidelines and their particular importance for the standardization of practice in the treatment of allergies. This review presents a comprehensive insight into those panel discussions and highlights unmet needs and also possible solutions to them for the future.
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Affiliation(s)
- O. Pfaar
- Department of Otorhinolaryngology; Head and Neck Surgery; Universitätsmedizin Mannheim; Medical Faculty Mannheim; Heidelberg University; Mannheim Germany
- Center for Rhinology and Allergology; Wiesbaden Germany
| | - S. Bonini
- Italian National Research Council; Institute of Translational Pharmacology; Rome, and University of Campania ‘Luigi Vanvitelli’; Naples Italy
- Expert-on Secondment at the European Medicines Agency; London UK
| | - V. Cardona
- Hospital Vall D'Hebron, S. Allergologia, S. Medicina Interna; Barcelona Spain
| | - P. Demoly
- Departement de Pneumologie et Addictologie; Hopital Arnaud de Villeneuve; University Hospital of Montpellier; Montpellier France
| | - T. Jakob
- Department of Dermatology and Allergology; University Medical Center Giessen (UKGM); Justus-Liebig-University Giessen; Giessen Germany
- Allergy Research Group; Department of Dermatology; Medical Center - University Freiburg; Freiburg Germany
| | - M. Jutel
- Department of Clinical Immunology; Wroclaw Medical University; Wroclaw Poland
- All-Med Medical Research Institute; Wroclaw Poland
| | - J. Kleine-Tebbe
- Allergy & Asthma Center Westend; Outpatient Clinic and Clinical Research Center; Berlin Germany
| | - L. Klimek
- Center for Rhinology and Allergology; Wiesbaden Germany
| | - S. Klysner
- Expres ion Biotechnologies Aps; Hørsholm Denmark
| | - M. V. Kopp
- Department of Pediatric Allergy and Pulmonology; University of Luebeck; Luebeck Germany
- Airway Research Center North (ARCN); Member of the Deutsches Zentrum für Lungenforschung (DZL); Luebeck Germany
| | - P. Kuna
- Department of Internal Medicine, Asthma and Allergy; Barlicki University Hospital; Medical University of Lodz; Lodz Poland
| | - M. Larché
- Divisions of Clinical Immunology & Allergy, and Respirology; Department of Medicine and Firestone Institute for Respiratory Health; McMaster University; Hamilton ON Canada
| | - A. Muraro
- Food Allergy Referral Centre; Padua University Hospital; Padua Italy
| | - C. B. Schmidt-Weber
- Center of Allergy and Environment (ZAUM); Member of the German Center for Lung Research (DZL); Technical University of Munich and Helmholtz Center Munich; Munich Germany
| | - M. H. Shamji
- Immunomodulation and Tolerance Group; Allergy and Clinical Immunology; Inflammation Repair and Development; National Heart and Lung Institute; Imperial College; London UK
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma; London UK
| | | | - C. Somoza
- Biological Products and Biotechnology Division; Medicines for Human Use Department; Agencia Española de Medicamentos y Productos Sanitarios (AEMPS); Madrid Spain
| | - E. Valovirta
- Department of Lung Disease and Clinical Allergology; University of Turku and Terveystalo Allergy Clinic; Turku Finland
| | - P. Zieglmayer
- Allergy Center Vienna West; Vienna Challenge Chamber; Vienna Austria
| | - T. Zuberbier
- Comprehensive Allergy-Centre-Charité; Department of Dermatology and Allergy; Charité - Universitätsmedizin Berlin; Berlin Germany
- Member of Global Allergy and Asthma European Network (GA LEN); GA LEN coordinating Office; Charité - Universitätsmedizin Berlin; Germany
| | - U. Wahn
- Department for Pediatric Pneumology and Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
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Strategies for the etiological therapy of cystic fibrosis. Cell Death Differ 2017; 24:1825-1844. [PMID: 28937684 PMCID: PMC5635223 DOI: 10.1038/cdd.2017.126] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 12/14/2022] Open
Abstract
Etiological therapies aim at repairing the underlying cause of cystic fibrosis (CF), which is the functional defect of the cystic fibrosis transmembrane conductance regulator (CFTR) protein owing to mutations in the CFTR gene. Among these, the F508del CFTR mutation accounts for more than two thirds of CF cases worldwide. Two somehow antinomic schools of thought conceive CFTR repair in a different manner. According to one vision, drugs should directly target the mutated CFTR protein to increase its plasma membrane expression (correctors) or improve its ion transport function (potentiators). An alternative strategy consists in modulating the cellular environment and proteostasis networks in which the mutated CFTR protein is synthesized, traffics to its final destination, the plasma membrane, and is turned over. We will analyze distinctive advantages and drawbacks of these strategies in terms of their scientific and clinical dimensions, and we will propose a global strategy for CF research and development based on a reconciliatory approach. Moreover, we will discuss the utility of preclinical biomarkers that may guide the personalized, patient-specific implementation of CF therapies.
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Biobanking: towards increased access of biomaterials in cystic fibrosis. Report on the pre-conference meeting to the 13th ECFS Basic Science Conference, Pisa, 30 March-2 April, 2016. J Cyst Fibros 2017; 16:616-621. [DOI: 10.1016/j.jcf.2017.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/01/2017] [Accepted: 04/08/2017] [Indexed: 01/06/2023]
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35
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Targeting the PI3K/Akt/mTOR signalling pathway in Cystic Fibrosis. Sci Rep 2017; 7:7642. [PMID: 28794469 PMCID: PMC5550428 DOI: 10.1038/s41598-017-06588-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022] Open
Abstract
Deletion of phenylalanine 508 of the cystic fibrosis transmembrane conductance regulator (ΔF508 CFTR) is a major cause of cystic fibrosis (CF), one of the most common inherited childhood diseases. ΔF508 CFTR is a trafficking mutant that is retained in the endoplasmic reticulum (ER) and unable to reach the plasma membrane. Efforts to enhance exit of ΔF508 CFTR from the ER and improve its trafficking are of utmost importance for the development of treatment strategies. Using protein interaction profiling and global bioinformatics analysis we revealed mammalian target of rapamycin (mTOR) signalling components to be associated with ∆F508 CFTR. Our results demonstrated upregulated mTOR activity in ΔF508 CF bronchial epithelial (CFBE41o-) cells. Inhibition of the Phosphatidylinositol 3-kinase/Akt/Mammalian Target of Rapamycin (PI3K/Akt/mTOR) pathway with 6 different inhibitors demonstrated an increase in CFTR stability and expression. Mechanistically, we discovered the most effective inhibitor, MK-2206 exerted a rescue effect by restoring autophagy in ΔF508 CFBE41o- cells. We identified Bcl-2-associated athanogene 3 (BAG3), a regulator of autophagy and aggresome clearance to be a potential mechanistic target of MK-2206. These data further link the CFTR defect to autophagy deficiency and demonstrate the potential of the PI3K/Akt/mTOR pathway for therapeutic targeting in CF.
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Ferrari E, Monzani R, Villella VR, Esposito S, Saluzzo F, Rossin F, D'Eletto M, Tosco A, De Gregorio F, Izzo V, Maiuri MC, Kroemer G, Raia V, Maiuri L. Cysteamine re-establishes the clearance of Pseudomonas aeruginosa by macrophages bearing the cystic fibrosis-relevant F508del-CFTR mutation. Cell Death Dis 2017; 8:e2544. [PMID: 28079883 PMCID: PMC5386380 DOI: 10.1038/cddis.2016.476] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/17/2016] [Accepted: 12/16/2016] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF), the most common lethal monogenic disease in Caucasians, is characterized by recurrent bacterial infections and colonization, mainly by Pseudomonas aeruginosa, resulting in unresolved airway inflammation. CF is caused by mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR) protein, which functions as a chloride channel in epithelial cells, macrophages, and other cell types. Impaired bacterial handling by macrophages is a feature of CF airways, although it is still debated how defective CFTR impairs bacterial killing. Recent evidence indicates that a defective autophagy in CF macrophages leads to alterations of bacterial clearance upon infection. Here we use bone marrow-derived macrophages from transgenic mice to provide the genetic proof that defective CFTR compromises both uptake and clearance of internalized Pseudomonas aeruginosa. We demonstrate that the proteostasis regulator cysteamine, which rescues the function of the most common F508del-CFTR mutant and hence reduces lung inflammation in CF patients, can also repair the defects of CF macrophages, thus restoring both bacterial internalization and clearance through a process that involves upregulation of the pro-autophagic protein Beclin 1 and re-establishment of the autophagic pathway. Altogether these results indicate that cysteamine restores the function of several distinct cell types, including that of macrophages, which might contribute to its beneficial effects on CF.
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Affiliation(s)
- Eleonora Ferrari
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy
| | - Romina Monzani
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy
| | - Valeria R Villella
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy
| | - Speranza Esposito
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy
| | - Francesca Saluzzo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy
| | - Federica Rossin
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Manuela D'Eletto
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Antonella Tosco
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, FedericoII University Naples 80131, Italy
| | - Fabiola De Gregorio
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy.,Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, FedericoII University Naples 80131, Italy
| | - Valentina Izzo
- Equipe11 labellisée Ligue Nationale contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Maria C Maiuri
- Equipe11 labellisée Ligue Nationale contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Guido Kroemer
- Equipe11 labellisée Ligue Nationale contrele Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.,Université Paris Descartes, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôlede Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, Franceand.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Valeria Raia
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, FedericoII University Naples 80131, Italy
| | - Luigi Maiuri
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, European Institute for Research in Cystic Fibrosis, Milan 20132, Italy.,SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara 28100, Italy
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37
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De Boeck K, Amaral MD. Progress in therapies for cystic fibrosis. THE LANCET RESPIRATORY MEDICINE 2016; 4:662-674. [DOI: 10.1016/s2213-2600(16)00023-0] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/19/2022]
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Vij N, Min T, Bodas M, Gorde A, Roy I. Neutrophil targeted nano-drug delivery system for chronic obstructive lung diseases. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:2415-2427. [PMID: 27381067 DOI: 10.1016/j.nano.2016.06.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 01/13/2023]
Abstract
The success of drug delivery to target airway cell(s) remains a significant challenge due to the limited ability of nanoparticle (NP) systems to circumvent protective airway-defense mechanisms. The size, density, surface and physical-chemical properties of nanoparticles are the key features that determine their ability to navigate across the airway-barrier. We evaluated here the efficacy of a PEGylated immuno-conjugated PLGA-nanoparticle (PINP) to overcome this challenge and selectively deliver drug to specific inflammatory cells (neutrophils). We first characterized the size, shape, surface-properties and neutrophil targeting using dynamic laser scattering, transmission electron microscopy and flow cytometry. Next, we assessed the efficacy of neutrophil-targeted PINPs in transporting through the airway followed by specific binding and release of drug to neutrophils. Finally, our results demonstrate the efficacy of PINP mediated non-steroidal anti-inflammatory drug-(ibuprofen) delivery to neutrophils in murine models of obstructive lung diseases, based on its ability to control neutrophilic-inflammation and resulting lung disease.
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Affiliation(s)
- Neeraj Vij
- Department of Pediatric Respiratory Science, The Johns Hopkins University School of Medicine, Baltimore, MD; College of Medicine, Central Michigan University, Mt Pleasant, MI.
| | - Taehong Min
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD; Genentech, 1 DNA Way, San Francisco, CA
| | - Manish Bodas
- Department of Pediatric Respiratory Science, The Johns Hopkins University School of Medicine, Baltimore, MD; College of Medicine, Central Michigan University, Mt Pleasant, MI
| | - Aakruti Gorde
- Department of Pediatric Respiratory Science, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Indrajit Roy
- Department of Chemistry, State University of New York, Buffalo, NY
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Esposito S, Tosco A, Villella VR, Raia V, Kroemer G, Maiuri L. Manipulating proteostasis to repair the F508del-CFTR defect in cystic fibrosis. Mol Cell Pediatr 2016; 3:13. [PMID: 26976279 PMCID: PMC4791443 DOI: 10.1186/s40348-016-0040-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal monogenic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that entails the (diagnostic) increase in sweat electrolyte concentrations, progressive lung disease with chronic inflammation and recurrent bacterial infections, pancreatic insufficiency, and male infertility. Therapies aimed at restoring the CFTR defect have emerged. Thus, a small molecule which facilitates chloride channel opening, the potentiator Ivacaftor, has been approved for the treatment of CF patients bearing a particular class of rare CFTR mutations. However, small molecules that directly target the most common misfolded CFTR mutant, F508del, and improve its intracellular trafficking in vitro, have been less effective than expected when tested in CF patients, even in combination with Ivacaftor. Thus, new strategies are required to circumvent the F508del-CFTR defect. Airway and intestinal epithelial cells from CF patients bearing the F508del-CFTR mutation exhibit an impressive derangement of cellular proteostasis, with oxidative stress, overactivation of the tissue transglutaminase (TG2), and disabled autophagy. Proteostasis regulators such as cysteamine can rescue and stabilize a functional F508del-CFTR protein through suppressing TG2 activation and restoring autophagy in vivo in F508del-CFTR homozygous mice, in vitro in CF patient-derived cell lines, ex vivo in freshly collected primary patient’s nasal cells, as well as in a pilot clinical trial involving homozygous F508del-CFTR patients. Here, we discuss how the therapeutic normalization of defective proteostasis can be harnessed for the treatment of CF patients with the F508del-CFTR mutation.
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Affiliation(s)
- Speranza Esposito
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Antonella Tosco
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, 80131, Italy
| | - Valeria R Villella
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Valeria Raia
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, 80131, Italy.
| | - Guido Kroemer
- Equipe 11 labellisée par la Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France. .,Cell Biology and Metabolomics Platforms, GustaveRoussy Comprehensive Cancer Center, Villejuif, France. .,INSERM, U1138, Paris, France. .,Université Paris Descartes, Sorbonne Paris Cité, Paris, France. .,Université Pierre et Marie Curie, Paris, France. .,Pôle de Biologie, HôpitalEuropéen Georges Pompidou, AP-HP, Paris, France. .,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Luigi Maiuri
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy. .,SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, 28100, Italy.
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Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A. PLoS One 2016; 11:e0149097. [PMID: 26950439 PMCID: PMC4780765 DOI: 10.1371/journal.pone.0149097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/27/2016] [Indexed: 02/05/2023] Open
Abstract
Cystic fibrosis results from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP-dependent protein kinase A (PKA) and ATP-regulated chloride channel. Here, we demonstrate that nucleoside diphosphate kinase B (NDPK-B, NM23-H2) forms a functional complex with CFTR. In airway epithelia forskolin/IBMX significantly increases NDPK-B co-localisation with CFTR whereas PKA inhibitors attenuate complex formation. Furthermore, an NDPK-B derived peptide (but not its NDPK-A equivalent) disrupts the NDPK-B/CFTR complex in vitro (19-mers comprising amino acids 36–54 from NDPK-B or NDPK-A). Overlay (Far-Western) and Surface Plasmon Resonance (SPR) analysis both demonstrate that NDPK-B binds CFTR within its first nucleotide binding domain (NBD1, CFTR amino acids 351–727). Analysis of chloride currents reflective of CFTR or outwardly rectifying chloride channels (ORCC, DIDS-sensitive) showed that the 19-mer NDPK-B peptide (but not its NDPK-A equivalent) reduced both chloride conductances. Additionally, the NDPK-B (but not NDPK-A) peptide also attenuated acetylcholine-induced intestinal short circuit currents. In silico analysis of the NBD1/NDPK-B complex reveals an extended interaction surface between the two proteins. This binding zone is also target of the 19-mer NDPK-B peptide, thus confirming its capability to disrupt NDPK-B/CFTR complex. We propose that NDPK-B forms part of the complex that controls chloride currents in epithelia.
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Colemeadow J, Joyce H, Turcanu V. Precise treatment of cystic fibrosis – current treatments and perspectives for using CRISPR. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1146077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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