1
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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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2
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Premchandar A, Ming R, Baiad A, Da Fonte DF, Xu H, Faubert D, Veit G, Lukacs GL. Readthrough-induced misincorporated amino acid ratios guide mutant-specific therapeutic approaches for two CFTR nonsense mutations. Front Pharmacol 2024; 15:1389586. [PMID: 38725656 PMCID: PMC11079177 DOI: 10.3389/fphar.2024.1389586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Premature termination codons (PTCs) represent ∼9% of CF mutations that typically cause severe expression defects of the CFTR anion channel. Despite the prevalence of PTCs as the underlying cause of genetic diseases, understanding the therapeutic susceptibilities of their molecular defects, both at the transcript and protein levels remains partially elucidated. Given that the molecular pathologies depend on the PTC positions in CF, multiple pharmacological interventions are required to suppress the accelerated nonsense-mediated mRNA decay (NMD), to correct the CFTR conformational defect caused by misincorporated amino acids, and to enhance the inefficient stop codon readthrough. The G418-induced readthrough outcome was previously investigated only in reporter models that mimic the impact of the local sequence context on PTC mutations in CFTR. To identify the misincorporated amino acids and their ratios for PTCs in the context of full-length CFTR readthrough, we developed an affinity purification (AP)-tandem mass spectrometry (AP-MS/MS) pipeline. We confirmed the incorporation of Cys, Arg, and Trp residues at the UGA stop codons of G542X, R1162X, and S1196X in CFTR. Notably, we observed that the Cys and Arg incorporation was favored over that of Trp into these CFTR PTCs, suggesting that the transcript sequence beyond the proximity of PTCs and/or other factors can impact the amino acid incorporation and full-length CFTR functional expression. Additionally, establishing the misincorporated amino acid ratios in the readthrough CFTR PTCs aided in maximizing the functional rescue efficiency of PTCs by optimizing CFTR modulator combinations. Collectively, our findings contribute to the understanding of molecular defects underlying various CFTR nonsense mutations and provide a foundation to refine mutation-dependent therapeutic strategies for various CF-causing nonsense mutations.
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Affiliation(s)
| | - Ruiji Ming
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Abed Baiad
- Department of Physiology, McGill University, Montréal, QC, Canada
| | | | - Haijin Xu
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Denis Faubert
- IRCM Mass Spectrometry and Proteomics Platform, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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3
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Cui G, Strickland KM, Vazquez Cegla AJ, McCarty NA. Comparing ATPase activity of ATP-binding cassette subfamily C member 4, lamprey CFTR, and human CFTR using an antimony-phosphomolybdate assay. Front Pharmacol 2024; 15:1363456. [PMID: 38440176 PMCID: PMC10910009 DOI: 10.3389/fphar.2024.1363456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction: ATP-binding cassette (ABC) transporters use the hydrolysis of ATP to power the active transport of molecules, but paradoxically the cystic fibrosis transmembrane regulator (CFTR, ABCC7) forms an ion channel. We previously showed that ATP-binding cassette subfamily C member 4 (ABCC4) is the closest mammalian paralog to CFTR, compared to other ABC transporters. In addition, Lamprey CFTR (Lp-CFTR) is the oldest known CFTR ortholog and has unique structural and functional features compared to human CFTR (hCFTR). The availability of these evolutionarily distant orthologs gives us the opportunity to study the changes in ATPase activity that may be related to their disparate functions. Methods: We utilized the baculovirus expression system with Sf9 insect cells and made use of the highly sensitive antimony-phosphomolybdate assay for testing the ATPase activity of human ABCC4 (hABCC4), Lp-CFTR, and hCFTR under similar experimental conditions. This assay measures the production of inorganic phosphate (Pi) in the nanomolar range. Results: Crude plasma membranes were purified, and protein concentration, determined semi-quantitatively, of hABCC4, Lp-CFTR, and hCFTR ranged from 0.01 to 0.36 μg/μL. No significant difference in expression level was found although hABCC4 trended toward the highest level. hABCC4 was activated by ATP with the equilibrium constant (Kd) 0.55 ± 0.28 mM (n = 8). Estimated maximum ATPase rate (Vmax) for hABCC4 was about 0.2 nmol/μg/min when the protein was activated with 1 mM ATP at 37°C (n = 7). Estimated maximum ATPase rate for PKA-phosphorylated Lp-CFTR reached about half of hCFTR levels in the same conditions. Vmax for both Lp-CFTR and hCFTR were significantly increased in high PKA conditions compared to low PKA conditions. Maximum intrinsic ATPase rate of hABCC4 in the absence of substrate was twice that of hCFTR when activated in 1 mM ATP. Conclusion: The findings here suggest that while both ABCC4 and hCFTR bear one consensus and one degenerate ATPase site, the hCFTR exhibited a reduced intrinsic ATPase activity. In addition, ATPase activity in the CFTR lineage increased from Lp-CFTR to hCFTR. Finally, the studies pave the way to purify hABCC4, Lp-CFTR, and hCFTR from Sf9 cells for their structural investigation, including by cryo-EM, and for studies of evolution in the ABC transporter superfamily.
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Affiliation(s)
| | | | | | - Nael A. McCarty
- Division of Pulmonology, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory + Children’s Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
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4
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McDonald EF, Meiler J, Plate L. CFTR Folding: From Structure and Proteostasis to Cystic Fibrosis Personalized Medicine. ACS Chem Biol 2023; 18:2128-2143. [PMID: 37730207 PMCID: PMC10595991 DOI: 10.1021/acschembio.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023]
Abstract
Cystic fibrosis (CF) is a lethal genetic disease caused by mutations in the chloride ion channel cystic fibrosis transmembrane conductance regulator (CFTR). Class-II mutants of CFTR lack intermolecular interactions important for CFTR structural stability and lead to misfolding. Misfolded CFTR is detected by a diverse suite of proteostasis factors that preferentially bind and route mutant CFTR toward premature degradation, resulting in reduced plasma membrane CFTR levels and impaired chloride ion conductance associated with CF. CF treatment has been vastly improved over the past decade by the availability of small molecules called correctors. Correctors directly bind CFTR, stabilize its structure by conferring thermodynamically favorable interactions that compensate for mutations, and thereby lead to downstream folding fidelity. However, each of over 100 Class-II CF causing mutations causes unique structural defects and shows a unique response to drug treatment, described as theratype. Understanding CFTR structural defects, the proteostasis factors evaluating those defects, and the stabilizing effects of CFTR correctors will illuminate a path toward personalized medicine for CF. Here, we review recent advances in our understanding of CFTR folding, focusing on structure, corrector binding sites, the mechanisms of proteostasis factors that evaluate CFTR, and the implications for CF personalized medicine.
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Affiliation(s)
- Eli Fritz McDonald
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Institute
for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Lars Plate
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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5
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Taniguchi S, Fukuda R, Okiyoneda T. The multiple ubiquitination mechanisms in CFTR peripheral quality control. Biochem Soc Trans 2023:233016. [PMID: 37140364 DOI: 10.1042/bst20221468] [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: 03/07/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated anion channel, which is expressed on the apical plasma membrane (PM) of epithelial cells. Mutations in the CFTR gene cause cystic fibrosis (CF), one of the most common genetic diseases among Caucasians. Most CF-associated mutations result in misfolded CFTR proteins that are degraded by the endoplasmic reticulum quality control (ERQC) mechanism. However, the mutant CFTR reaching the PM through therapeutic agents is still ubiquitinated and degraded by the peripheral protein quality control (PeriQC) mechanism, resulting in reduced therapeutic efficacy. Moreover, certain CFTR mutants that can reach the PM under physiological conditions are degraded by PeriQC. Thus, it may be beneficial to counteract the selective ubiquitination in PeriQC to enhance therapeutic outcomes for CF. Recently, the molecular mechanisms of CFTR PeriQC have been revealed, and several ubiquitination mechanisms, including both chaperone-dependent and -independent pathways, have been identified. In this review, we will discuss the latest findings related to CFTR PeriQC and propose potential novel therapeutic strategies for CF.
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Affiliation(s)
- Shogo Taniguchi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo 669-1330, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo 669-1330, Japan
| | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo 669-1330, Japan
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6
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Tosaka T, Kamiya K. Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes. Int J Mol Sci 2023; 24:ijms24087231. [PMID: 37108393 PMCID: PMC10138308 DOI: 10.3390/ijms24087231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.
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Affiliation(s)
- Toshiyuki Tosaka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
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7
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The COPD-Associated Polymorphism Impairs the CFTR Function to Suppress Excessive IL-8 Production upon Environmental Pathogen Exposure. Int J Mol Sci 2023; 24:ijms24032305. [PMID: 36768629 PMCID: PMC9916815 DOI: 10.3390/ijms24032305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
COPD is a lifestyle-related disease resulting from irreversible damage to respiratory tissues mostly due to chronic exposure to environmental pollutants, including cigarette smoke. Environmental pathogens and pollutants induce the acquired dysfunction of the CFTR Cl- channel, which is invoked in COPD. Despite the increased incidence of CFTR polymorphism R75Q or M470V in COPD patients, the mechanism of how the CFTR variant affects COPD pathogenesis remains unclear. Here, we investigated the impact of CFTR polymorphisms (R75Q, M470V) on the CFTR function in airway epithelial cell models. While wild-type (WT) CFTR suppressed the proinflammatory cytokine production induced by COPD-related pathogens including pyocyanin (PYO), R75Q- or M470V-CFTR failed. Mechanistically, the R75Q- or M470V-CFTR fractional PM activity (FPMA) was significantly lower than WT-CFTR in the presence of PYO. Notably, the CF drug Trikafta corrected the PM expression of R75Q- or M470V-CFTR even upon PYO exposure and consequently suppressed the excessive IL-8 production. These results suggest that R75Q or M470V polymorphism impairs the CFTR function to suppress the excessive proinflammatory response to environmental pathogens associated with COPD. Moreover, Trikafta may be useful to prevent the COPD pathogenesis associated with acquired CFTR dysfunction.
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8
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Sagarika P, Yadav K, Sahi C. Volleying plasma membrane proteins from birth to death: Role of J-domain proteins. Front Mol Biosci 2022; 9:1072242. [PMID: 36589230 PMCID: PMC9798423 DOI: 10.3389/fmolb.2022.1072242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
The function, stability, and turnover of plasma membrane (PM) proteins are crucial for cellular homeostasis. Compared to soluble proteins, quality control of plasma membrane proteins is extremely challenging. Failure to meet the high quality control standards is detrimental to cellular and organismal health. J-domain proteins (JDPs) are among the most diverse group of chaperones that collaborate with other chaperones and protein degradation machinery to oversee cellular protein quality control (PQC). Although fragmented, the available literature from different models, including yeast, mammals, and plants, suggests that JDPs assist PM proteins with their synthesis, folding, and trafficking to their destination as well as their degradation, either through endocytic or proteasomal degradation pathways. Moreover, some JDPs interact directly with the membrane to regulate the stability and/or functionality of proteins at the PM. The deconvoluted picture emerging is that PM proteins are relayed from one JDP to another throughout their life cycle, further underscoring the versatility of the Hsp70:JDP machinery in the cell.
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9
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Hillenaar T, Beekman J, van der Sluijs P, Braakman I. Redefining Hypo- and Hyper-Responding Phenotypes of CFTR Mutants for Understanding and Therapy. Int J Mol Sci 2022; 23:ijms232315170. [PMID: 36499495 PMCID: PMC9735543 DOI: 10.3390/ijms232315170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Mutations in CFTR cause misfolding and decreased or absent ion-channel function, resulting in the disease Cystic Fibrosis. Fortunately, a triple-modulator combination therapy (Trikafta) has been FDA-approved for 178 mutations, including all patients who have F508del on one allele. That so many CFTR mutants respond well to modulators developed for a single mutation is due to the nature of the folding process of this multidomain protein. We have addressed the question 'What characterizes the exceptions: the mutants that functionally respond either not or extremely well'. A functional response is the product of the number of CFTR molecules on the cell surface, open probability, and conductivity of the CFTR chloride channel. By combining biosynthetic radiolabeling with protease-susceptibility assays, we have followed CF-causing mutants during the early and late stages of folding in the presence and absence of modulators. Most CFTR mutants showed typical biochemical responses for each modulator, such as a TMD1 conformational change or an increase in (cell-surface) stability, regardless of a functional response. These modulators thus should still be considered for hypo-responder genotypes. Understanding both biochemical and functional phenotypes of outlier mutations will boost our insights into CFTR folding and misfolding, and lead to improved therapeutic strategies.
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Affiliation(s)
- Tamara Hillenaar
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
| | - Jeffrey Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands;
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
- Correspondence: ; Tel.: +31-30-253-2759
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10
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Vasconcelos-Cardoso M, Batista-Almeida D, Rios-Barros LV, Castro-Gomes T, Girao H. Cellular and molecular mechanisms underlying plasma membrane functionality and integrity. J Cell Sci 2022; 135:275922. [PMID: 35801807 DOI: 10.1242/jcs.259806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasma membrane not only protects the cell from the extracellular environment, acting as a selective barrier, but also regulates cellular events that originate at the cell surface, playing a key role in various biological processes that are essential for the preservation of cell homeostasis. Therefore, elucidation of the mechanisms involved in the maintenance of plasma membrane integrity and functionality is of utmost importance. Cells have developed mechanisms to ensure the quality of proteins that inhabit the cell surface, as well as strategies to cope with injuries inflicted to the plasma membrane. Defects in these mechanisms can lead to the development or onset of several diseases. Despite the importance of these processes, a comprehensive and holistic perspective of plasma membrane quality control is still lacking. To tackle this gap, in this Review, we provide a thorough overview of the mechanisms underlying the identification and targeting of membrane proteins that are to be removed from the cell surface, as well as the membrane repair mechanisms triggered in both physiological and pathological conditions. A better understanding of the mechanisms underlying protein quality control at the plasma membrane can reveal promising and unanticipated targets for the development of innovative therapeutic approaches.
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Affiliation(s)
- Maria Vasconcelos-Cardoso
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Daniela Batista-Almeida
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Laura Valeria Rios-Barros
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Thiago Castro-Gomes
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Henrique Girao
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
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11
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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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12
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Anglès F, Wang C, Balch WE. Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold. Commun Biol 2022; 5:356. [PMID: 35418593 PMCID: PMC9008016 DOI: 10.1038/s42003-022-03302-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although the impact of genome variation on the thermodynamic properties of function on the protein fold has been studied in vitro, it remains a challenge to assign these relationships across the entire polypeptide sequence in vivo. Using the Gaussian process regression based principle of Spatial CoVariance, we globally assign on a residue-by-residue basis the biological thermodynamic properties that contribute to the functional fold of CFTR in the cell. We demonstrate the existence of a thermodynamically sensitive region of the CFTR fold involving the interface between NBD1 and ICL4 that contributes to its export from endoplasmic reticulum. At the cell surface a new set of residues contribute uniquely to the management of channel function. These results support a general ‘quality assurance’ view of global protein fold management as an SCV principle describing the differential pre- and post-ER residue interactions contributing to compartmentalization of the energetics of the protein fold for function. Our results set the stage for future analyses of the quality systems managing protein sequence-to-function-to-structure broadly encompassing genome design leading to protein function in complex cellular relationships responsible for diversity and fitness in biology in response to the environment. Spatial covariance analysis shows how each residue in the critical fold region of chloride channel CFTR, defective in cystic fibrosis patients, contributes to CFTR’s export from the endoplasmic reticulum and function in the cell.
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Affiliation(s)
- Frédéric Anglès
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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13
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Brusa I, Sondo E, Falchi F, Pedemonte N, Roberti M, Cavalli A. Proteostasis Regulators in Cystic Fibrosis: Current Development and Future Perspectives. J Med Chem 2022; 65:5212-5243. [PMID: 35377645 PMCID: PMC9014417 DOI: 10.1021/acs.jmedchem.1c01897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In cystic fibrosis (CF), the deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) leads to misfolding and premature degradation of the mutant protein. These defects can be targeted with pharmacological agents named potentiators and correctors. During the past years, several efforts have been devoted to develop and approve new effective molecules. However, their clinical use remains limited, as they fail to fully restore F508del-CFTR biological function. Indeed, the search for CFTR correctors with different and additive mechanisms has recently increased. Among them, drugs that modulate the CFTR proteostasis environment are particularly attractive to enhance therapy effectiveness further. This Perspective focuses on reviewing the recent progress in discovering CFTR proteostasis regulators, mainly describing the design, chemical structure, and structure-activity relationships. The opportunities, challenges, and future directions in this emerging and promising field of research are discussed, as well.
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Affiliation(s)
- Irene Brusa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | | | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
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14
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Wang BB, Xu H, Isenmann S, Huang C, Elorza-Vidal X, Rychkov GY, Estévez R, Schittenhelm RB, Lukacs GL, Apaja PM. Ubr1-induced selective endophagy/autophagy protects against the endosomal and Ca 2+-induced proteostasis disease stress. Cell Mol Life Sci 2022; 79:167. [PMID: 35233680 PMCID: PMC8888484 DOI: 10.1007/s00018-022-04191-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
Abstract
The cellular defense mechanisms against cumulative endo-lysosomal stress remain incompletely understood. Here, we identify Ubr1 as a protein quality control (QC) E3 ubiquitin-ligase that counteracts proteostasis stresses by facilitating endosomal cargo-selective autophagy for lysosomal degradation. Astrocyte regulatory cluster membrane protein MLC1 mutations cause endosomal compartment stress by fusion and enlargement. Partial lysosomal clearance of mutant endosomal MLC1 is accomplished by the endosomal QC ubiquitin ligases, CHIP and Ubr1 via ESCRT-dependent route. As a consequence of the endosomal stress, a supportive QC mechanism, dependent on both Ubr1 and SQSTM1/p62 activities, targets ubiquitinated and arginylated MLC1 mutants for selective endosomal autophagy (endophagy). This QC pathway is also activated for arginylated Ubr1-SQSTM1/p62 autophagy cargoes during cytosolic Ca2+-assault. Conversely, the loss of Ubr1 and/or arginylation elicited endosomal compartment stress. These findings underscore the critical housekeeping role of Ubr1 and arginylation-dependent endophagy/autophagy during endo-lysosomal proteostasis perturbations and suggest a link of Ubr1 to Ca2+ homeostasis and proteins implicated in various diseases including cancers and brain disorders.
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Affiliation(s)
- Ben B Wang
- Lifelong Health, Organelle Proteostasis Diseases, South Australian Health and Medical Research Institute (SAHMRI), 5000 North Terrace, Adelaide, SA, 5000, Australia.,EMBL Australia, Adelaide, South Australia, 5000, Australia
| | - Haijin Xu
- Department of Physiology and Cell Information Systems, McGill University, 3655 Promenade Sir-William-Osler, Montréal, QC, H3G 1Y6, Canada
| | - Sandra Isenmann
- Lifelong Health, Organelle Proteostasis Diseases, South Australian Health and Medical Research Institute (SAHMRI), 5000 North Terrace, Adelaide, SA, 5000, Australia.,EMBL Australia, Adelaide, South Australia, 5000, Australia
| | - Cheng Huang
- Monash Biomedical Proteomics Facility, Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Xabier Elorza-Vidal
- Unitat de Fisiologia, Departament de Ciències Fisiològiques, IDIBELL-Institute of Neurosciences, L'Hospitalet de Llobregat, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Grigori Y Rychkov
- Lifelong Health, Organelle Proteostasis Diseases, South Australian Health and Medical Research Institute (SAHMRI), 5000 North Terrace, Adelaide, SA, 5000, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Raúl Estévez
- Unitat de Fisiologia, Departament de Ciències Fisiològiques, IDIBELL-Institute of Neurosciences, L'Hospitalet de Llobregat, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility, Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Gergely L Lukacs
- Department of Physiology and Cell Information Systems, McGill University, 3655 Promenade Sir-William-Osler, Montréal, QC, H3G 1Y6, Canada. .,Department of Biochemistry, McGill University, Montréal, QC, H3G 1Y6, Canada.
| | - Pirjo M Apaja
- Lifelong Health, Organelle Proteostasis Diseases, South Australian Health and Medical Research Institute (SAHMRI), 5000 North Terrace, Adelaide, SA, 5000, Australia. .,EMBL Australia, Adelaide, South Australia, 5000, Australia. .,Department of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia. .,College of Public Health and Medicine, Molecular Biosciences Theme, Flinders University, Bedford Park, SA, 5042, Australia.
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15
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Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi. Int J Mol Sci 2022; 23:ijms23052442. [PMID: 35269585 PMCID: PMC8910062 DOI: 10.3390/ijms23052442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Deletion of phenylalanine 508 (∆F508) of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel protein is the leading cause of Cystic Fibrosis (CF). Here, we report the analysis of CFTR and ∆F508-CFTR interactomes using BioID (proximity-dependent biotin identification), a technique that can also detect transient associations. We identified 474 high-confidence CFTR proximity-interactors, 57 of which have been previously validated, with the remainder representing novel interaction space. The ∆F508 interactome, comprising 626 proximity-interactors was markedly different from its wild type counterpart, with numerous alterations in protein associations categorized in membrane trafficking and cellular stress functions. Furthermore, analysis of the ∆F508 interactome in cells treated with Orkambi identified several interactions that were altered as a result of this drug therapy. We examined two candidate CFTR proximity interactors, VAPB and NOS1AP, in functional assays designed to assess surface delivery and overall chloride efflux. VAPB depletion impacted both CFTR surface delivery and chloride efflux, whereas NOS1AP depletion only affected the latter. The wild type and ∆F508-CFTR interactomes represent rich datasets that could be further mined to reveal additional candidates for the functional rescue of ∆F508-CFTR.
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16
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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17
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Sabbadini R, Pesce E, Parodi A, Mustorgi E, Bruzzone S, Pedemonte N, Casale M, Millo E, Cichero E. Probing Allosteric Hsp70 Inhibitors by Molecular Modelling Studies to Expedite the Development of Novel Combined F508del CFTR Modulators. Pharmaceuticals (Basel) 2021; 14:ph14121296. [PMID: 34959696 PMCID: PMC8709398 DOI: 10.3390/ph14121296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis (CF) is caused by different mutations related to the cystic fibrosis transmembrane regulator protein (CFTR), with F508del being the most common. Pioneering the development of CFTR modulators, thanks to the development of effective correctors or potentiators, more recent studies deeply encouraged the administration of triple combination therapeutics. However, combinations of molecules interacting with other proteins involved in functionality of the CFTR channel recently arose as a promising approach to address a large rescue of F508del-CFTR. In this context, the design of compounds properly targeting the molecular chaperone Hsp70, such as the allosteric inhibitor MKT-077, proved to be effective for the development of indirect CFTR modulators, endowed with ability to amplify the accumulation of the rescued protein. Herein we performed structure-based studies of a number of allosteric HSP70 inhibitors, considering the recent X-ray crystallographic structure of the human enzyme. This allowed us to point out the main interaction supporting the binding mode of MKT-077, as well as of the related analogues. In particular, cation-π and π-π stacking with the conserve residue Tyr175 deeply stabilized inhibitor binding at the HSP70 cavity. Molecular docking studies had been followed by QSAR analysis and then by virtual screening of aminoaryl thiazoles (I-IIIa) as putative HSP70 inhibitors. Their effectiveness as CFTR modulators has been verified by biological assays, in combination with VX-809, whose positive results confirmed the reliability of the whole applied computational method. Along with this, the "in-silico" prediction of absorption, distribution, metabolism, and excretion (ADME) properties highlighted, once more, that AATs may represent a chemical class to be further investigated for the rational design of novel combination of compounds for CF treatment.
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Affiliation(s)
- Roberto Sabbadini
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy;
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 5, 16147 Genova, Italy; (E.P.); (N.P.)
| | - Alice Parodi
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
| | - Eleonora Mustorgi
- Department of Pharmacy, Section of Chemistry and Food and Pharmaceutical Technologies, University of Genoa, Viale Cembrano, 4, 16148 Genoa, Italy; (E.M.); (M.C.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 5, 16147 Genova, Italy; (E.P.); (N.P.)
| | - Monica Casale
- Department of Pharmacy, Section of Chemistry and Food and Pharmaceutical Technologies, University of Genoa, Viale Cembrano, 4, 16148 Genoa, Italy; (E.M.); (M.C.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
- Correspondence: (E.M.); (E.C.); Tel.: +10-335-3032-3033 (E.M.); +39-010-353-8350 (E.C.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy;
- Correspondence: (E.M.); (E.C.); Tel.: +10-335-3032-3033 (E.M.); +39-010-353-8350 (E.C.)
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18
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Farinha CM, Gentzsch M. Revisiting CFTR Interactions: Old Partners and New Players. Int J Mol Sci 2021; 22:13196. [PMID: 34947992 PMCID: PMC8703571 DOI: 10.3390/ijms222413196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress in CFTR research has led to the therapeutic development of modulators that rescue the basic defect in cystic fibrosis. There is continuous interest in studying CFTR molecular disease mechanisms as not all cystic fibrosis patients have a therapeutic option available. Addressing the basis of the problem by comprehensively understanding the critical molecular associations of CFTR interactions remains key. With the availability of CFTR modulators, there is interest in comprehending which interactions are critical to rescue CFTR and which are altered by modulators or CFTR mutations. Here, the current knowledge on interactions that govern CFTR folding, processing, and stability is summarized. Furthermore, we describe protein complexes and signal pathways that modulate the CFTR function. Primary epithelial cells display a spatial control of the CFTR interactions and have become a common system for preclinical and personalized medicine studies. Strikingly, the novel roles of CFTR in development and differentiation have been recently uncovered and it has been revealed that specific CFTR gene interactions also play an important role in transcriptional regulation. For a comprehensive understanding of the molecular environment of CFTR, it is important to consider CFTR mutation-dependent interactions as well as factors affecting the CFTR interactome on the cell type, tissue-specific, and transcriptional levels.
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Affiliation(s)
- Carlos M. Farinha
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Martina Gentzsch
- Marsico Lung Institute and Cystic Fibrosis Research Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pediatrics, Division of Pediatric Pulmonology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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19
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Civera M, Moroni E, Sorrentino L, Vasile F, Sattin S. Chemical and Biophysical Approaches to Allosteric Modulation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monica Civera
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche Giulio Natta, SCITEC Via Mario Bianco 9 20131 Milan Italy
| | - Luca Sorrentino
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Francesca Vasile
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Sara Sattin
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
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20
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Marx DC, Fleming KG. Membrane proteins enter the fold. Curr Opin Struct Biol 2021; 69:124-130. [PMID: 33975156 DOI: 10.1016/j.sbi.2021.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 11/19/2022]
Abstract
Membrane proteins have historically been recalcitrant to biophysical folding studies. However, recent adaptations of methods from the soluble protein folding field have found success in their applications to transmembrane proteins composed of both α-helical and β-barrel conformations. Avoiding aggregation is critical for the success of these experiments. Altogether these studies are leading to discoveries of folding trajectories, foundational stabilizing forces and better-defined endpoints that enable more accurate interpretation of thermodynamic data. Increased information on membrane protein folding in the cell shows that the emerging biophysical principles are largely recapitulated even in the complex biological environment.
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Affiliation(s)
- Dagan C Marx
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States
| | - Karen G Fleming
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States.
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21
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Kleizen B, van Willigen M, Mijnders M, Peters F, Grudniewska M, Hillenaar T, Thomas A, Kooijman L, Peters KW, Frizzell R, van der Sluijs P, Braakman I. Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain. J Mol Biol 2021; 433:166955. [PMID: 33771570 DOI: 10.1016/j.jmb.2021.166955] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
ABC transporters transport a wealth of molecules across membranes and consist of transmembrane and cytosolic domains. Their activity cycle involves a tightly regulated and concerted domain choreography. Regulation is driven by the cytosolic domains and function by the transmembrane domains. Folding of these polytopic multidomain proteins to their functional state is a challenge for cells, which is mitigated by co-translational and sequential events. We here reveal the first stages of co-translational domain folding and assembly of CFTR, the ABC transporter defective in the most abundant rare inherited disease cystic fibrosis. We have combined biosynthetic radiolabeling with protease-susceptibility assays and domain-specific antibodies. The most N-terminal domain, TMD1 (transmembrane domain 1), folds both its hydrophobic and soluble helices during translation: the transmembrane helices pack tightly and the cytosolic N- and C-termini assemble with the first cytosolic helical loop ICL1, leaving only ICL2 exposed. This N-C-ICL1 assembly is strengthened by two independent events: (i) assembly of ICL1 with the N-terminal subdomain of the next domain, cytosolic NBD1 (nucleotide-binding domain 1); and (ii) in the presence of corrector drug VX-809, which rescues cell-surface expression of a range of disease-causing CFTR mutants. Both lead to increased shielding of the CFTR N-terminus, and their additivity implies different modes of action. Early assembly of NBD1 and TMD1 is essential for CFTR folding and positions both domains for the required assembly with TMD2. Altogether, we have gained insights into this first, nucleating, VX-809-enhanced domain-assembly event during and immediately after CFTR translation, involving structures conserved in type-I ABC exporters.
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Affiliation(s)
- Bertrand Kleizen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Marcel van Willigen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands; Julius Clinical Ltd, Broederplein 41-43, 3703 CD Zeist, the Netherlands(‡)
| | - Marjolein Mijnders
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands‡
| | - Florence Peters
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Magda Grudniewska
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands; GenomeScan B.V, Plesmanlaan 1d, 2333 BZ Leiden, the Netherlands‡
| | - Tamara Hillenaar
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Ann Thomas
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands; UniQure, Paasheuvelweg 25a, 1105 BP Amsterdam, the Netherlands‡
| | - Laurens Kooijman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands; Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland‡
| | - Kathryn W Peters
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Raymond Frizzell
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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22
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Lumacaftor and Matrine: Possible Therapeutic Combination to Counteract the Inflammatory Process in Cystic Fibrosis. Biomolecules 2021; 11:biom11030422. [PMID: 33805605 PMCID: PMC7999856 DOI: 10.3390/biom11030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/03/2022] Open
Abstract
Cystic fibrosis is a monogenic, autosomal, recessive disease characterized by an alteration of chloride transport caused by mutations in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene. The loss of Phe residue in position 508 (ΔF508-CFTR) causes an incorrect folding of the protein causing its degradation and electrolyte imbalance. CF patients are extremely predisposed to the development of a chronic inflammatory process of the bronchopulmonary system. When the cells of a tissue are damaged, the immune cells are activated and trigger the production of free radicals, provoking an inflammatory process. In addition to routine therapies, today drugs called correctors are available for mutations such as ΔF508-CFTR as well as for others less frequent ones. These active molecules are supposed to facilitate the maturation of the mutant CFTR protein, allowing it to reach the apical membrane of the epithelial cell. Matrine induces ΔF508-CFTR release from the endoplasmic reticulum to cell cytosol and its localization on the cell membrane. We now have evidence that Matrine and Lumacaftor not only restore the transport of mutant CFTR protein, but probably also counteract the inflammatory process by improving the course of the disease.
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23
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Serapian SA, Triveri A, Marchetti F, Castelli M, Colombo G. Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us? ChemMedChem 2021; 16:1593-1599. [PMID: 33443306 DOI: 10.1002/cmdc.202000960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 01/03/2023]
Abstract
Advances in genomics and proteomics have unveiled an ever-growing number of key proteins and provided mechanistic insights into the genesis of pathologies. This wealth of data showed that changes in expression levels of specific proteins, mutations, and post-translational modifications can result in (often subtle) perturbations of functional protein-protein interaction networks, which ultimately determine disease phenotypes. Although many such validated pathogenic proteins have emerged as ideal drug targets, there are also several that escape traditional pharmacological regulation; these proteins have thus been labeled "undruggable". The challenges posed by undruggable targets call for new sorts of molecular intervention. One fascinating solution is to perturb a pathogenic protein's expression levels, rather than blocking its activities. In this Concept paper, we shall discuss chemical interventions aimed at recruiting undruggable proteins to the ubiquitin proteasome system, or aimed at disrupting protein-protein interactions in the chaperone-mediated cellular folding machinery: both kinds of intervention lead to a decrease in the amount of active pathogenic protein expressed. Specifically, we shall discuss the role of computational strategies in understanding the molecular determinants characterizing the function of synthetic molecules typically designed for either type of intervention. Finally, we shall provide our perspectives and views on the current limitations and possibilities to expand the scope of rational approaches to the design of chemical regulators of protein levels.
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Affiliation(s)
- Stefano A Serapian
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Alice Triveri
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Filippo Marchetti
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
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24
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Dougherty PG, Wellmerling JH, Koley A, Lukowski JK, Hummon AB, Cormet-Boyaka E, Pei D. Cyclic Peptidyl Inhibitors against CAL/CFTR Interaction for Treatment of Cystic Fibrosis. J Med Chem 2020; 63:15773-15784. [PMID: 33314931 PMCID: PMC8011814 DOI: 10.1021/acs.jmedchem.0c01528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, encoding for a chloride ion channel. Membrane expression of CFTR is negatively regulated by CFTR-associated ligand (CAL). We previously showed that inhibition of the CFTR/CAL interaction with a cell-permeable peptide improves the function of rescued F508del-CFTR. In this study, optimization of the peptidyl inhibitor yielded PGD97, which exhibits a KD value of 6 nM for the CAL PDZ domain, ≥ 130-fold selectivity over closely related PDZ domains, and a serum t1/2 of >24 h. In patient-derived F508del homozygous cells, PGD97 (100 nM) increased short-circuit currents by ∼3-fold and further potentiated the therapeutic effects of small-molecule correctors (e.g., VX-661) by ∼2-fold (with an EC50 of ∼10 nM). Our results suggest that PGD97 may be used as a novel treatment for CF, either as a single agent or in combination with small-molecule correctors/potentiators.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States,Current address: Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Jack H. Wellmerling
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica K. Lukowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States,Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA,Corresponding Author: To whom correspondence should be addressed. Estelle Cormet-Boyaka: . Dehua Pei: Phone: (614) 688-4068;
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States,Corresponding Author: To whom correspondence should be addressed. Estelle Cormet-Boyaka: . Dehua Pei: Phone: (614) 688-4068;
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25
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Geisler M, Hegedűs T. A twist in the ABC: regulation of ABC transporter trafficking and transport by FK506-binding proteins. FEBS Lett 2020; 594:3986-4000. [PMID: 33125703 DOI: 10.1002/1873-3468.13983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 01/07/2023]
Abstract
Post-transcriptional regulation of ATP-binding cassette (ABC) proteins has been so far shown to encompass protein phosphorylation, maturation, and ubiquitination. Yet, recent accumulating evidence implicates FK506-binding proteins (FKBPs), a type of peptidylprolyl cis-trans isomerase (PPIase) proteins, in ABC transporter regulation. In this perspective article, we summarize current knowledge on ABC transporter regulation by FKBPs, which seems to be conserved over kingdoms and ABC subfamilies. We uncover striking functional similarities but also differences between regulatory FKBP-ABC modules in plants and mammals. We dissect a PPIase- and HSP90-dependent and independent impact of FKBPs on ABC biogenesis and transport activity. We propose and discuss a putative new mode of transient ABC transporter regulation by cis-trans isomerization of X-prolyl bonds.
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Affiliation(s)
- Markus Geisler
- Department of Biology, University of Fribourg, Switzerland
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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26
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Bhattacharya K, Weidenauer L, Luengo TM, Pieters EC, Echeverría PC, Bernasconi L, Wider D, Sadian Y, Koopman MB, Villemin M, Bauer C, Rüdiger SGD, Quadroni M, Picard D. The Hsp70-Hsp90 co-chaperone Hop/Stip1 shifts the proteostatic balance from folding towards degradation. Nat Commun 2020; 11:5975. [PMID: 33239621 PMCID: PMC7688965 DOI: 10.1038/s41467-020-19783-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Hop/Stip1/Sti1 is thought to be essential as a co-chaperone to facilitate substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Despite this proposed key function for protein folding and maturation, it is not essential in a number of eukaryotes and bacteria lack an ortholog. We set out to identify and to characterize its eukaryote-specific function. Human cell lines and the budding yeast with deletions of the Hop/Sti1 gene display reduced proteasome activity due to inefficient capping of the core particle with regulatory particles. Unexpectedly, knock-out cells are more proficient at preventing protein aggregation and at promoting protein refolding. Without the restraint by Hop, a more efficient folding activity of the prokaryote-like Hsp70-Hsp90 complex, which can also be demonstrated in vitro, compensates for the proteasomal defect and ensures the proteostatic equilibrium. Thus, cells may act on the level and/or activity of Hop to shift the proteostatic balance between folding and degradation. Hop, also known as Stip1 or Sti1, facilitates substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Characterization of proteostasis-related pathways in STIP1 knock-out cell lines reveals that in eukaryotes Stip1 modulates the balance between protein folding and degradation.
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Affiliation(s)
- Kaushik Bhattacharya
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Ellis C Pieters
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Pablo C Echeverría
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.,European Association for the Study of the Liver, 1203, Genève, Switzerland
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Diana Wider
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Yashar Sadian
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Margreet B Koopman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Matthieu Villemin
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Christoph Bauer
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.
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27
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Shishido H, Yoon JS, Yang Z, Skach WR. CFTR trafficking mutations disrupt cotranslational protein folding by targeting biosynthetic intermediates. Nat Commun 2020; 11:4258. [PMID: 32848127 PMCID: PMC7450043 DOI: 10.1038/s41467-020-18101-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/04/2020] [Indexed: 02/03/2023] Open
Abstract
Protein misfolding causes a wide spectrum of human disease, and therapies that target misfolding are transforming the clinical care of cystic fibrosis. Despite this success, however, very little is known about how disease-causing mutations affect the de novo folding landscape. Here we show that inherited, disease-causing mutations located within the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) have distinct effects on nascent polypeptides. Two of these mutations (A455E and L558S) delay compaction of the nascent NBD1 during a critical window of synthesis. The observed folding defect is highly dependent on nascent chain length as well as its attachment to the ribosome. Moreover, restoration of the NBD1 cotranslational folding defect by second site suppressor mutations also partially restores folding of full-length CFTR. These findings demonstrate that nascent folding intermediates can play an important role in disease pathogenesis and thus provide potential targets for pharmacological correction.
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Affiliation(s)
- Hideki Shishido
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Jae Seok Yoon
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Zhongying Yang
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - William R Skach
- Cystic Fibrosis Foundation, 4550 Montgomery Ave., Suite 1100N, Bethesda, MD, 20814, USA.
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28
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Degrugillier F, Aissat A, Prulière-Escabasse V, Bizard L, Simonneau B, Decrouy X, Jiang C, Rotin D, Fanen P, Simon S. Phosphorylation of the Chaperone-Like HspB5 Rescues Trafficking and Function of F508del-CFTR. Int J Mol Sci 2020; 21:ijms21144844. [PMID: 32650630 PMCID: PMC7402320 DOI: 10.3390/ijms21144844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cystic Fibrosis is a lethal monogenic autosomal recessive disease linked to mutations in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. The most frequent mutation is the deletion of phenylalanine at position 508 of the protein. This F508del-CFTR mutation leads to misfolded protein that is detected by the quality control machinery within the endoplasmic reticulum and targeted for destruction by the proteasome. Modulating quality control proteins as molecular chaperones is a promising strategy for attenuating the degradation and stabilizing the mutant CFTR at the plasma membrane. Among the molecular chaperones, the small heat shock protein HspB1 and HspB4 were shown to promote degradation of F508del-CFTR. Here, we investigated the impact of HspB5 expression and phosphorylation on transport to the plasma membrane, function and stability of F508del-CFTR. We show that a phosphomimetic form of HspB5 increases the transport to the plasma membrane, function and stability of F508del-CFTR. These activities are further enhanced in presence of therapeutic drugs currently used for the treatment of cystic fibrosis (VX-770/Ivacaftor, VX-770+VX-809/Orkambi). Overall, this study highlights the beneficial effects of a phosphorylated form of HspB5 on F508del-CFTR rescue and its therapeutic potential in cystic fibrosis.
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Affiliation(s)
- Fanny Degrugillier
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
| | - Abdel Aissat
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
- AP-HP, Hôpital Henri Mondor, Département de Génétique, F-94010 Creteil, France
| | - Virginie Prulière-Escabasse
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
- Centre Hospitalier Intercommunal de Creteil, Service d’ORL et de Chirurgie Cervico-Faciale, F-94010 Creteil, France
| | - Lucie Bizard
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
| | - Benjamin Simonneau
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
| | - Xavier Decrouy
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
| | - Chong Jiang
- The Hospital for Sick Children and the University of Toronto, Toronto, ON M5G 0A4, Canada; (C.J.); (D.R.)
| | - Daniela Rotin
- The Hospital for Sick Children and the University of Toronto, Toronto, ON M5G 0A4, Canada; (C.J.); (D.R.)
| | - Pascale Fanen
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
- AP-HP, Hôpital Henri Mondor, Département de Génétique, F-94010 Creteil, France
| | - Stéphanie Simon
- Univ Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France; (F.D.); (A.A.); (V.P.-E.); (L.B.); (B.S.); (X.D.); (P.F.)
- Correspondence: ; Tel.: +33-1-49-81-68-55
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29
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Ubiquitination of disease-causing CFTR variants in a microsome-based assay. Anal Biochem 2020; 604:113829. [PMID: 32621804 DOI: 10.1016/j.ab.2020.113829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Abstract
Soluble secreted proteins and membrane proteins are subjected to protein quality control pathways during their synthesis in the endoplasmic reticulum (ER) and delivery to other destinations. Foremost among these quality control pathways is the selection of misfolded proteins for ER-associated degradation (ERAD). A growing number of diseases, including Cystic Fibrosis, are linked to the ERAD pathway. In most cases, a membrane protein known as the Cystic Fibrosis Transmembrane Conductance Regulator, or CFTR, is prematurely degraded by ERAD. Cell-based assays and in vitro studies have elucidated factors required for the recognition and degradation of CFTR, yet mechanistic details on how these factors target specific disease-causing variants is limited. Given the possibility that variants might exhibit unique susceptibilities to ubiquitin modification, which is required for proteasome-mediated degradation, we devised an assay that recapitulates this event. Here, we demonstrate that ER-enriched membranes from transfected human cells support CFTR ubiquitination when combined with radiolabeled ubiquitin and isolated enzymes in the ubiquitination cascade. We also show that select disease-causing variants are ubiquitinated more extensively than wild-type channels and to varying degrees. Our system provides a platform to examine how other purified factors impact CFTR ubiquitination and the ubiquitination of additional disease-associated membrane proteins.
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30
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Strub MD, McCray, Jr. PB. Transcriptomic and Proteostasis Networks of CFTR and the Development of Small Molecule Modulators for the Treatment of Cystic Fibrosis Lung Disease. Genes (Basel) 2020; 11:genes11050546. [PMID: 32414011 PMCID: PMC7288469 DOI: 10.3390/genes11050546] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The diversity of mutations and the multiple ways by which the protein is affected present challenges for therapeutic development. The observation that the Phe508del-CFTR mutant protein is temperature sensitive provided proof of principle that mutant CFTR could escape proteosomal degradation and retain partial function. Several specific protein interactors and quality control checkpoints encountered by CFTR during its proteostasis have been investigated for therapeutic purposes, but remain incompletely understood. Furthermore, pharmacological manipulation of many CFTR interactors has not been thoroughly investigated for the rescue of Phe508del-CFTR. However, high-throughput screening technologies helped identify several small molecule modulators that rescue CFTR from proteosomal degradation and restore partial function to the protein. Here, we discuss the current state of CFTR transcriptomic and biogenesis research and small molecule therapy development. We also review recent progress in CFTR proteostasis modulators and discuss how such treatments could complement current FDA-approved small molecules.
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Affiliation(s)
- Matthew D. Strub
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA;
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USA
| | - Paul B. McCray, Jr.
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA;
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USA
- Correspondence: ; Tel.: +1-(319)-335-6844
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31
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Juarez-Navarro K, Ayala-Garcia VM, Ruiz-Baca E, Meneses-Morales I, Rios-Banuelos JL, Lopez-Rodriguez A. Assistance for Folding of Disease-Causing Plasma Membrane Proteins. Biomolecules 2020; 10:biom10050728. [PMID: 32392767 PMCID: PMC7277483 DOI: 10.3390/biom10050728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
An extensive catalog of plasma membrane (PM) protein mutations related to phenotypic diseases is associated with incorrect protein folding and/or localization. These impairments, in addition to dysfunction, frequently promote protein aggregation, which can be detrimental to cells. Here, we review PM protein processing, from protein synthesis in the endoplasmic reticulum to delivery to the PM, stressing the main repercussions of processing failures and their physiological consequences in pathologies, and we summarize the recent proposed therapeutic strategies to rescue misassembled proteins through different types of chaperones and/or small molecule drugs that safeguard protein quality control and regulate proteostasis.
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32
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Fukuda R, Okiyoneda T. Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Ubiquitylation as a Novel Pharmaceutical Target for Cystic Fibrosis. Pharmaceuticals (Basel) 2020; 13:ph13040075. [PMID: 32331485 PMCID: PMC7243099 DOI: 10.3390/ph13040075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/22/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene decrease the structural stability and function of the CFTR protein, resulting in cystic fibrosis. Recently, the effect of CFTR-targeting combination therapy has dramatically increased, and it is expected that add-on drugs that modulate the CFTR surrounding environment will further enhance their effectiveness. Various interacting proteins have been implicated in the structural stability of CFTR and, among them, molecules involved in CFTR ubiquitylation are promising therapeutic targets as regulators of CFTR degradation. This review focuses on the ubiquitylation mechanism that contributes to the stability of mutant CFTR at the endoplasmic reticulum (ER) and post-ER compartments and discusses the possibility as a pharmacological target for cystic fibrosis (CF).
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33
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Baaklini I, Gonçalves CDC, Lukacs GL, Young JC. Selective Binding of HSC70 and its Co-Chaperones to Structural Hotspots on CFTR. Sci Rep 2020; 10:4176. [PMID: 32144307 PMCID: PMC7060200 DOI: 10.1038/s41598-020-61107-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) channel cause cystic fibrosis. Chaperones, including HSC70, DNAJA1 and DNAJA2, play key roles in both the folding and degradation of wild-type and mutant CFTR at multiple cellular locations. DNAJA1 and HSC70 promote the folding of newly synthesized CFTR at the endoplasmic reticulum (ER), but are required for the rapid turnover of misfolded channel at the plasma membrane (PM). DNAJA2 and HSC70 are also involved in the ER-associated degradation (ERAD) of misfolded CFTR, while they assist the refolding of destabilized channel at the PM. These outcomes may depend on the binding of chaperones to specific sites within CFTR, which would be exposed in non-native states. A CFTR peptide library was used to identify binding sites for HSC70, DNAJA1 and DNAJA2, validated by competition and functional assays. Each chaperone had a distinct binding pattern, and sites were distributed between the surfaces of the CFTR cytosolic domains, and domain interfaces known to be important for channel assembly. The accessibility of sites to chaperones will depend on the degree of CFTR folding or unfolding. Different folded states may be recognized by unique combinations of HSC70, DNAJA1 and DNAJA2, leading to divergent biological effects.
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Affiliation(s)
- Imad Baaklini
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada
| | | | - Gergely L Lukacs
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada.,McGill University, Department of Physiology, Montreal, H3G 1Y6, Canada
| | - Jason C Young
- McGill University, Department of Biochemistry, Montreal, H3G 1Y6, Canada.
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34
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Regulation of CFTR Biogenesis by the Proteostatic Network and Pharmacological Modulators. Int J Mol Sci 2020; 21:ijms21020452. [PMID: 31936842 PMCID: PMC7013518 DOI: 10.3390/ijms21020452] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal inherited disease among Caucasians in North America and a significant portion of Europe. The disease arises from one of many mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator, or CFTR. The most common disease-associated allele, F508del, along with several other mutations affect the folding, transport, and stability of CFTR as it transits from the endoplasmic reticulum (ER) to the plasma membrane, where it functions primarily as a chloride channel. Early data demonstrated that F508del CFTR is selected for ER associated degradation (ERAD), a pathway in which misfolded proteins are recognized by ER-associated molecular chaperones, ubiquitinated, and delivered to the proteasome for degradation. Later studies showed that F508del CFTR that is rescued from ERAD and folds can alternatively be selected for enhanced endocytosis and lysosomal degradation. A number of other disease-causing mutations in CFTR also undergo these events. Fortunately, pharmacological modulators of CFTR biogenesis can repair CFTR, permitting its folding, escape from ERAD, and function at the cell surface. In this article, we review the many cellular checkpoints that monitor CFTR biogenesis, discuss the emergence of effective treatments for CF, and highlight future areas of research on the proteostatic control of CFTR.
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35
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Mutation-specific dual potentiators maximize rescue of CFTR gating mutants. J Cyst Fibros 2019; 19:236-244. [PMID: 31678009 DOI: 10.1016/j.jcf.2019.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND The potentiator ivacaftor (VX-770) has been approved for therapy of 38 cystic fibrosis (CF) mutations (∼10% of the patient population) associated with a gating defect of the CF transmembrane conductance regulator (CFTR). Despite the success of VX-770 treatment of patients carrying at least one allele of the most common gating mutation G551D-CFTR, some lung function decline and P. aeruginosa colonization persist. This study aims at identifying potentiator combinations that can considerably enhance the limited channel activity of a panel of CFTR gating mutants over monotherapy. METHODS The functional response of 13 CFTR mutants to single potentiators or systematic potentiator combinations was determined in the human bronchial epithelial cell line CFBE41o- and a subset of them was confirmed in primary human nasal epithelia (HNE). RESULTS In six out of thirteen CFTR missense mutants the fractional plasma membrane (PM) activity, a surrogate measure of CFTR channel gating, reached only ∼10-50% of WT channel activity upon VX-770 treatment, indicating incomplete gating correction. Combinatorial potentiator profiling and cluster analysis of mutant responses to 24 diverse investigational potentiators identified several compound pairs that improved the gating activity of R352Q-, S549R-, S549N-, G551D-, and G1244E-CFTR to ∼70-120% of the WT. Similarly, the potentiator combinations were able to confer WT-like function to G551D-CFTR in patient-derived human nasal epithelia. CONCLUSION This study suggests that half of CF patients with missense mutations approved for VX-770 administration, could benefit from the development of dual potentiator therapy.
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36
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Phosphorylation-dependent modulation of CFTR macromolecular signalling complex activity by cigarette smoke condensate in airway epithelia. Sci Rep 2019; 9:12706. [PMID: 31481727 PMCID: PMC6722123 DOI: 10.1038/s41598-019-48971-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic and acquired loss-of-function defect of the cystic fibrosis transmembrane conductance regulator (CFTR) compromise airway surface liquid homeostasis and mucociliary clearance (MCC), culminating in recurrent lung inflammation/infection. While chronic cigarette smoke (CS), CS extract (CSE; water-soluble compounds) and CS condensate (CSC; particulate, organic fraction) exposure inhibit CFTR activity at transcriptional, biochemical, and functional levels, the acute impact of CSC remains incompletely understood. We report that CSC transiently activates CFTR chloride secretion in airway epithelia. The comparable CFTR phospho-occupancy after CSC- and forskolin-exposure, determined by affinity-enriched tandem mass spectrometry and pharmacology, suggest that localised cAMP-dependent protein kinase (PKA) stimulation by CSC causes the channel opening. Due to the inhibition of the MRP4/ABCC4, a cAMP-exporter confined to the CFTR macromolecular signalling-complex, PKA activation is accomplished by the subcompartmentalised elevation of cytosolic cAMP. In line, MRP4 inhibition results in CFTR activation and phospho-occupancy similar to that by forskolin. In contrast, acute CSC exposure reversibly inhibits the phosphorylated CFTR both in vivo and in phospholipid bilayers, without altering its cell surface density and phospho-occupancy. We propose that components of CSC elicit both a transient protective CFTR activation, as well as subsequent channel block in airway epithelia, contributing to the subacute MCC defect in acquired CF lung diseases.
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37
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Kim Chiaw P, Hantouche C, Wong MJH, Matthes E, Robert R, Hanrahan JW, Shrier A, Young JC. Hsp70 and DNAJA2 limit CFTR levels through degradation. PLoS One 2019; 14:e0220984. [PMID: 31408507 PMCID: PMC6692068 DOI: 10.1371/journal.pone.0220984] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/26/2019] [Indexed: 11/18/2022] Open
Abstract
Cystic Fibrosis is caused by mutations in the CFTR anion channel, many of which cause its misfolding and degradation. CFTR folding depends on the Hsc70 and Hsp70 chaperones and their co-chaperone DNAJA1, but Hsc70/Hsp70 is also involved in CFTR degradation. Here, we address how these opposing functions are balanced. DNAJA2 and DNAJA1 were both important for CFTR folding, however overexpressing DNAJA2 but not DNAJA1 enhanced CFTR degradation at the endoplasmic reticulum by Hsc70/Hsp70 and the E3 ubiquitin ligase CHIP. Excess Hsp70 also promoted CFTR degradation, but this occurred through the lysosomal pathway and required CHIP but not complex formation with HOP and Hsp90. Notably, the Hsp70 inhibitor MKT077 enhanced levels of mature CFTR and the most common disease variant ΔF508-CFTR, by slowing turnover and allowing delayed maturation, respectively. MKT077 also boosted the channel activity of ΔF508-CFTR when combined with the corrector compound VX809. Thus, the Hsp70 system is the major determinant of CFTR degradation, and its modulation can partially relieve the misfolding phenotype.
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Affiliation(s)
- Patrick Kim Chiaw
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
| | - Christine Hantouche
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Michael J. H. Wong
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
| | - Elizabeth Matthes
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Renaud Robert
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - John W. Hanrahan
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Alvin Shrier
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Jason C. Young
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Overeem AW, Klappe K, Parisi S, Klöters-Planchy P, Mataković L, du Teil Espina M, Drouin CA, Weiss KH, van IJzendoorn SCD. Pluripotent stem cell-derived bile canaliculi-forming hepatocytes to study genetic liver diseases involving hepatocyte polarity. J Hepatol 2019; 71:344-356. [PMID: 30965071 DOI: 10.1016/j.jhep.2019.03.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 03/15/2019] [Accepted: 03/31/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Hepatocyte polarity is essential for the development of bile canaliculi and for safely transporting bile and waste products from the liver. Functional studies of autologous mutated proteins in the context of the polarized hepatocyte have been challenging because of the lack of appropriate cell models. The aims of this study were to obtain a patient-specific hepatocyte model that recapitulated hepatocyte polarity and to employ this model to study endogenous mutant proteins in liver diseases that involve hepatocyte polarity. METHODS Urine cell-derived pluripotent stem cells, taken from a patient with a homozygous mutation in ATP7B and a patient with a heterozygous mutation, were differentiated towards hepatocyte-like cells (hiHeps). HiHeps were also derived from a patient with MEDNIK syndrome. RESULTS Polarized hiHeps that formed in vivo-like bile canaliculi could be generated from embryonic and patient urine cell-derived pluripotent stem cells. HiHeps recapitulated polarized protein trafficking processes, exemplified by the Cu2+-induced redistribution of the copper transporter protein ATP7B to the bile canalicular domain. We demonstrated that, in contrast to the current dogma, the most frequent yet enigmatic Wilson disease-causing ATP7B-H1069Q mutation per se did not preclude trafficking of ATP7B to the trans-Golgi Network. Instead, it prevented its Cu2+-induced polarized redistribution to the bile canalicular domain, which could not be reversed by pharmacological folding chaperones. Finally, we demonstrate that hiHeps from a patient with MEDNIK syndrome, suffering from liver copper overload of unclear etiology, showed no defect in the Cu2+-induced redistribution of ATP7B to the bile canaliculi. CONCLUSIONS Functional cell polarity can be achieved in patient pluripotent stem cell-derived hiHeps, enabling, for the first time, the study of the endogenous mutant proteins, patient-specific pathogenesis and drug responses for diseases where hepatocyte polarity is a key factor. LAY SUMMARY This study demonstrates that cells that are isolated from urine can be reprogrammed in a dish towards hepatocytes that display architectural characteristics similar to those seen in the intact liver. The application of this methodology to cells from patients diagnosed with inherited copper metabolism-related liver diseases (that is, Wilson disease and MEDNIK syndrome) revealed unexpected and novel insights into patient mutation-specific disease mechanisms and drug responses.
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Affiliation(s)
- Arend W Overeem
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Karin Klappe
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Silvia Parisi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Lavinija Mataković
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marines du Teil Espina
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Christian A Drouin
- Service de Dermatologie, Centre Hospitalier du Grand Portage, Rivière du Loup, Québec, Canada
| | - Karl Heinz Weiss
- University Hospital Heidelberg, Internal Medicine IV, Heidelberg, Germany
| | - Sven C D van IJzendoorn
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Hanrahan JW, Sato Y, Carlile GW, Jansen G, Young JC, Thomas DY. Cystic Fibrosis: Proteostatic correctors of CFTR trafficking and alternative therapeutic targets. Expert Opin Ther Targets 2019; 23:711-724. [PMID: 31169041 DOI: 10.1080/14728222.2019.1628948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cystic fibrosis (CF) is the most frequent lethal orphan disease and is caused by mutations in the CFTR gene. The most frequent mutation F508del-CFTR affects multiple organs; infections and subsequent infections and complications in the lung lead to death. Areas covered: This review focuses on new targets and mechanisms that are attracting interest for the development of CF therapies. The F508del-CFTR protein is retained in the endoplasmic reticulum (ER) but has some function if it can traffic to the plasma membrane. Cell-based assays have been used to screen chemical libraries for small molecule correctors that restore its trafficking. Pharmacological chaperones are correctors that bind directly to the F508del-CFTR mutant and promote its folding and trafficking. Other correctors fall into a heterogeneous class of proteostasis modulators that act indirectly by altering cellular homeostasis. Expert opinion: Pharmacological chaperones have so far been the most successful correctors of F508del-CFTR trafficking, but their level of correction means that more than one corrector is required. Proteostasis modulators have low levels of correction but hold promise because some can correct several different CFTR mutations. Identification of their cellular targets and the potential for development may lead to new therapies for CF.
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Affiliation(s)
- John W Hanrahan
- a Department of Physiology , McGill University , Montréal , QC , Canada.,c Research Institute of the McGill University Health Centre , McGill University , Montréal , QC , Canada
| | - Yukiko Sato
- a Department of Physiology , McGill University , Montréal , QC , Canada.,b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada
| | - Graeme W Carlile
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - Gregor Jansen
- d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - Jason C Young
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - David Y Thomas
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada.,e Department of Human Genetics , McGill University , Montréal , QC , Canada
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Bidaud-Meynard A, Bossard F, Schnúr A, Fukuda R, Veit G, Xu H, Lukacs GL. Transcytosis maintains CFTR apical polarity in the face of constitutive and mutation-induced basolateral missorting. J Cell Sci 2019; 132:jcs.226886. [PMID: 30975917 DOI: 10.1242/jcs.226886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
Apical polarity of cystic fibrosis transmembrane conductance regulator (CFTR) is essential for solute and water transport in secretory epithelia and can be impaired in human diseases. Maintenance of apical polarity in the face of CFTR non-polarized delivery and inefficient apical retention of mutant CFTRs lacking PDZ-domain protein (NHERF1, also known as SLC9A3R1) interaction, remains enigmatic. Here, we show that basolateral CFTR delivery originates from biosynthetic (∼35%) and endocytic (∼65%) recycling missorting. Basolateral channels are retrieved via basolateral-to-apical transcytosis (hereafter denoted apical transcytosis), enhancing CFTR apical expression by two-fold and suppressing its degradation. In airway epithelia, CFTR transcytosis is microtubule-dependent but independent of Myo5B, Rab11 proteins and NHERF1 binding to its C-terminal DTRL motif. Increased basolateral delivery due to compromised apical recycling and accelerated internalization upon impaired NHERF1-CFTR association is largely counterbalanced by efficient CFTR basolateral internalization and apical transcytosis. Thus, transcytosis represents a previously unrecognized, but indispensable, mechanism for maintaining CFTR apical polarity that acts by attenuating its constitutive and mutation-induced basolateral missorting.
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Affiliation(s)
| | - Florian Bossard
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Andrea Schnúr
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Ryosuke Fukuda
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Guido Veit
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Haijin Xu
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montréal, QC, H3G 1Y6, Canada .,Department of Biochemistry, McGill University, Montréal, QC, H3G 1Y6, Canada
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Mutation-specific peripheral and ER quality control of hERG channel cell-surface expression. Sci Rep 2019; 9:6066. [PMID: 30988392 PMCID: PMC6465299 DOI: 10.1038/s41598-019-42331-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
Impaired functional plasma membrane (PM) expression of the hERG K+-channel is associated with Long-QT syndrome type-2 (LQT2) and increased risk of cardiac arrhythmia. Reduced PM-expression is primarily attributed to retention and degradation of misfolded channels by endoplasmic reticulum (ER) protein quality control (QC) systems. However, as the molecular pathogenesis of LQT2 was defined using severely-misfolded hERG variants with limited PM-expression, the potential contribution of post-ER (peripheral) QC pathways to the disease phenotype remains poorly established. Here, we investigate the cellular processing of mildly-misfolded Per-Arnt-Sim (PAS)-domain mutant hERGs, which display incomplete ER-retention and PM-expression defects at physiological temperature. We show that the attenuated PM-expression of hERG is dictated by mutation-specific contributions from both the ER and peripheral QC systems. At the ER, PAS-mutants experience inefficient conformational maturation coupled with rapid ubiquitin-dependent proteasomal degradation. In post-ER compartments, they are rapidly endocytosed from the PM via a ubiquitin-independent mechanism and rapidly targeted for lysosomal degradation. Conformational destabilization underlies aberrant cellular processing at both ER- and post-ER compartments, since conformational correction by a hERG-specific pharmacochaperone or low-temperatures can restore WT-like trafficking. Our results demonstrate that the post-ER QC alone or jointly with the ER QC determines the loss-of-PM-expression phenotype of a subset of LQT2 mutations.
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Chen Y, Li X, Liao H, Leung X, He J, Wang X, Li F, Yue H, Xu W. CFTR mutation compromises spermatogenesis by enhancing miR-15b maturation and suppressing its regulatory target CDC25A†. Biol Reprod 2019; 101:50-62. [PMID: 30985893 DOI: 10.1093/biolre/ioz062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/17/2018] [Accepted: 04/14/2019] [Indexed: 01/27/2023] Open
Abstract
Abstract
MicroRNAs (miRNAs) have recently been shown to be important for spermatogenesis; both DROSHA and Dicer1 KO mice exhibit infertility due to abnormal miRNA expression. However, the roles of individual miRNAs in spermatogenesis remain elusive. Here we demonstrated that miR-15b, a member of the miR-15/16 family, is primarily expressed in testis. A miR-15b transgenic mouse model was constructed to investigate the role of miR-15b in spermatogenesis. Impaired spermatogenesis was observed in miR-15b transgenic mice, suggesting that appropriate expression of miR-15b is vital for spermatogenesis. Furthermore, we demonstrated that overexpression of miR-15b reduced CDC25A gene post-transcriptional activity by targeting the 3′-UTR region of CDC25A, thus regulating spermatogenesis. In vitro results further demonstrated that a mutation in CFTR could affect the interaction between Ago2 with Dicer1 and that Dicer1 activity regulates miR-15b expression. We extended our study to azoospermia patients and found that infertile patients have a significantly higher level of miR-15b in semen and plasma samples. Taken together, we propose that CFTR regulation of miR-15b could be involved in the post-transcriptional regulation of CDC25A in mammalian testis and that miR-15b is important for spermatogenesis.
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Affiliation(s)
- Yan Chen
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaoliang Li
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
| | - Huijuan Liao
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaotong Leung
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Epithelial Cell Biology Research Center, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Jiabei He
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiang Wang
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
| | - Fuping Li
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Huanxun Yue
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wenming Xu
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, P.R. China
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Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, Hunt JF. Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator. J Biol Chem 2018; 293:17685-17704. [PMID: 29903914 PMCID: PMC6240863 DOI: 10.1074/jbc.ra117.000819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/31/2018] [Indexed: 01/07/2023] Open
Abstract
Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.
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Affiliation(s)
- Chi Wang
- From the Departments of Biological Sciences and
| | - Andrei A. Aleksandrov
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Zhengrong Yang
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | | | - Elizabeth A. Proctor
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pradeep Kota
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jianli An
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | - Anna Kaplan
- From the Departments of Biological Sciences and
| | - Netaly Khazanov
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Brent R. Stockwell
- From the Departments of Biological Sciences and ,Chemistry, Columbia University, New York, New York 10027
| | - Hanoch Senderowitz
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Nikolay V. Dokholyan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R. Riordan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - John F. Hunt
- From the Departments of Biological Sciences and , To whom correspondence should be addressed. Tel.:
212-854-5443; Fax:
212-865-8246; E-mail:
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Wang Y, Cai Z, Gosling M, Sheppard DN. Potentiation of the cystic fibrosis transmembrane conductance regulator Cl− channel by ivacaftor is temperature independent. Am J Physiol Lung Cell Mol Physiol 2018; 315:L846-L857. [DOI: 10.1152/ajplung.00235.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ivacaftor is the first drug to target directly defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which causes cystic fibrosis (CF). To understand better how ivacaftor potentiates CFTR channel gating, here we investigated the effects of temperature on its action. As a control, we studied the benzimidazolone UCCF-853, which potentiates CFTR by a different mechanism. Using the patch-clamp technique and cells expressing recombinant CFTR, we studied the single-channel behavior of wild-type and F508del-CFTR, the most common CF mutation. Raising the temperature of the intracellular solution from 23 to 37°C increased the frequency but reduced the duration of wild-type and F508del-CFTR channel openings. Although the open probability ( Po) of wild-type CFTR increased progressively as temperature was elevated, the relationship between Po and temperature for F508del-CFTR was bell-shaped with a maximum Po at ~30°C. For wild-type CFTR and to a greatly reduced extent F508del-CFTR, the temperature dependence of channel gating was asymmetric with the opening rate demonstrating greater temperature sensitivity than the closing rate. At all temperatures tested, ivacaftor and UCCF-853 potentiated wild-type and F508del-CFTR. Strikingly, ivacaftor but not UCCF-853 abolished the asymmetric temperature dependence of CFTR channel gating. At all temperatures tested, Po values of wild-type CFTR in the presence of ivacaftor were approximately double those of F508del-CFTR, which were equivalent to or greater than those of wild-type CFTR at 37°C in the absence of the drug. We conclude that the principal effect of ivacaftor is to promote channel opening to abolish the temperature dependence of CFTR channel gating.
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Affiliation(s)
- Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Martin Gosling
- Enterprise Therapeutics, Sussex Innovation Centre, University of Sussex, Science Park Square, Brighton, United Kingdom
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - David N. Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
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Abstract
Cystic fibrosis (CF) is the most common life-limiting genetic disease in Caucasian patients. Continued advances have led to improved survival, and adults with CF now outnumber children. As our understanding of the disease improves, new therapies have emerged that improve the basic defect, enabling patient-specific treatment and improved outcomes. However, recurrent exacerbations continue to lead to morbidity and mortality, and new pathogens have been identified that may lead to worse outcomes. In addition, new complications, such as CF-related diabetes and increased risk of gastrointestinal cancers, are creating new challenges in management. For patients with end-stage disease, lung transplantation has remained one of the few treatment options, but challenges in identifying the most appropriate patients remain.
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Affiliation(s)
- Michael M Rey
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Michael P Bonk
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Denis Hadjiliadis
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
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Veit G, Xu H, Dreano E, Avramescu RG, Bagdany M, Beitel LK, Roldan A, Hancock MA, Lay C, Li W, Morin K, Gao S, Mak PA, Ainscow E, Orth AP, McNamara P, Edelman A, Frenkiel S, Matouk E, Sermet-Gaudelus I, Barnes WG, Lukacs GL. Structure-guided combination therapy to potently improve the function of mutant CFTRs. Nat Med 2018; 24:1732-1742. [PMID: 30297908 PMCID: PMC6301090 DOI: 10.1038/s41591-018-0200-x] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 08/08/2018] [Indexed: 12/17/2022]
Abstract
Available corrector drugs are unable to effectively rescue the folding defects of CFTR-ΔF508 (or CFTR-F508del), the most common disease-causing mutation of the cystic fibrosis transmembrane conductance regulator, a plasma membrane (PM) anion channel, and thus to substantially ameliorate clinical phenotypes of cystic fibrosis (CF). To overcome the corrector efficacy ceiling, here we show that compounds targeting distinct structural defects of CFTR can synergistically rescue mutant expression and function at the PM. High-throughput cell-based screens and mechanistic analysis identified three small-molecule series that target defects at nucleotide-binding domain (NBD1), NBD2 and their membrane-spanning domain (MSD) interfaces. Although individually these compounds marginally improve ΔF508-CFTR folding efficiency, function and stability, their combinations lead to ~50-100% of wild-type-level correction in immortalized and primary human airway epithelia and in mouse nasal epithelia. Likewise, corrector combinations were effective against rare missense mutations in various CFTR domains, probably acting via structural allostery, suggesting a mechanistic framework for their broad application.
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Affiliation(s)
- Guido Veit
- Department of Physiology, McGill University, Montréal, Quebec, Canada.
| | - Haijin Xu
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Elise Dreano
- Institut Necker-Enfants Malades (INEM)-INSERM U1151, Paris, France
| | - Radu G Avramescu
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Miklos Bagdany
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Lenore K Beitel
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Ariel Roldan
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Mark A Hancock
- SPR-MS Facility, McGill University, Montréal, Quebec, Canada
| | - Cecilia Lay
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Wei Li
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Katelin Morin
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Sandra Gao
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Puiying A Mak
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Edward Ainscow
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anthony P Orth
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Peter McNamara
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | | | - Saul Frenkiel
- Department of Otolaryngology - Head and Neck Surgery, McGill University, Montréal, Quebec, Canada
| | - Elias Matouk
- Adult Cystic Fibrosis Clinic, Montreal Chest Institute, McGill University, Montréal, Quebec, Canada
| | | | - William G Barnes
- Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montréal, Quebec, Canada. .,Department of Biochemistry, McGill University, Montréal, Quebec, Canada. .,Groupe de Recherche Axé sur la Structure des Protéines (GRASP), McGill University, Montréal, Quebec, Canada.
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Fukuda R, Okiyoneda T. Peripheral Protein Quality Control as a Novel Drug Target for CFTR Stabilizer. Front Pharmacol 2018; 9:1100. [PMID: 30319426 PMCID: PMC6170605 DOI: 10.3389/fphar.2018.01100] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Conformationally defective cystic fibrosis transmembrane conductance regulator (CFTR) including rescued ΔF508-CFTR is rapidly eliminated from the plasma membrane (PM) even in the presence of a CFTR corrector and potentiator, limiting the therapeutic effort of the combination therapy. CFTR elimination from the PM is determined by the conformation-dependent ubiquitination as a part of the peripheral quality control (PQC) mechanism. Recently, the molecular machineries responsible for the CFTR PQC mechanism which includes molecular chaperones and ubiquitination enzymes have been revealed. This review summarizes the molecular mechanism of the CFTR PQC and discusses the possibility that the peripheral ubiquitination mechanism becomes a novel drug target to develop the CFTR stabilizer as a novel class of CFTR modulator.
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Affiliation(s)
- Ryosuke Fukuda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Nishinomiya, Japan
| | - Tsukasa Okiyoneda
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Nishinomiya, Japan
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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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