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Wan H, Zhang J, Liu Z, Dong B, Tao Z, Wang G, Wang C. RING finger protein 5 protects against acute myocardial infarction by inhibiting ASK1. BMC Cardiovasc Disord 2024; 24:406. [PMID: 39098896 PMCID: PMC11299303 DOI: 10.1186/s12872-024-04070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Myocardial infarction (MI) is a major disease with high morbidity and mortality worldwide. However, existing treatments are far from satisfactory, making the exploration of potent molecular targets more imperative. The E3 ubiquitin ligase RING finger protein 5 (RNF5) has been previously reported to be involved in several diseases by regulating ubiquitination-mediated protein degradation. Nevertheless, few reports have focused on its function in cardiovascular diseases, including MI. METHODS In this study, we established RNF5 knockout mice through precise CRISPR-mediated genome editing and utilized left anterior descending coronary artery ligation in 9-11-week-old male C57BL/6 mice. Subsequently, serum biochemical analysis and histopathological examination of heart tissues were performed. Furthermore, we engineered adenoviruses for modulating RNF5 expression and subjected neonatal rat cardiomyocytes to oxygen-glucose deprivation (OGD) to mimic ischemic conditions, demonstrating the impact of RNF5 manipulation on cellular viability. Gene and protein expression analysis provided insights into the molecular mechanisms. Statistical methods were rigorously employed to assess the significance of experimental findings. RESULTS We found RNF5 was downregulated in infarcted heart tissue of mice and NRCMs subjected to OGD treatment. RNF5 knockout in mice resulted in exacerbated heart dysfunction, more severe inflammatory responses, and increased apoptosis after MI surgery. In vitro, RNF5 knockdown exacerbated the OGD-induced decline in cell activity, increased apoptosis, while RNF5 overexpression had the opposite effect. Mechanistically, it was proven that the kinase cascade initiated by apoptosis signal-regulating kinase 1 (ASK1) activation was closely regulated by RNF5 and mediated RNF5's protective function during MI. CONCLUSIONS We demonstrated the protective effect of RNF5 on myocardial infarction and its function was dependent on inhibiting the activation of ASK1, which adds a new regulatory component to the myocardial infarction associated network and promises to enable new therapeutic strategy.
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Affiliation(s)
- Hong Wan
- General practice medicine, Huanggang Central Hospital of Yangtze University, Huanggang, China
| | - Jianqing Zhang
- Department of central laboratory, Renmin hospital of Wuhan university, Wuhan, China
| | - Zhen Liu
- Department of Cardiology, Renmin hospital of Wuhan university, Wuhan, China
| | - Bizhen Dong
- Huanggang Institute of Translational Medicine, Huanggang, China
| | - Zhangqian Tao
- Department of Cardiology, Renmin hospital of Wuhan university, Wuhan, China
| | - Guanglin Wang
- Department of Cardiology, Huanggang Central Hospital of Yangtze University, Huanggang, China.
| | - Chihua Wang
- Huanggang Disease Control Center, Huanggang, China.
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Okiyoneda T, Borgo C, Bosello Travain V, Pedemonte N, Salvi M. Targeting ubiquitination machinery in cystic fibrosis: Where do we stand? Cell Mol Life Sci 2024; 81:271. [PMID: 38888668 PMCID: PMC11335196 DOI: 10.1007/s00018-024-05295-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in CFTR gene expressing the anion selective channel CFTR located at the plasma membrane of different epithelial cells. The most commonly investigated variant causing CF is F508del. This mutation leads to structural defects in the CFTR protein, which are recognized by the endoplasmic reticulum (ER) quality control system. As a result, the protein is retained in the ER and degraded via the ubiquitin-proteasome pathway. Although blocking ubiquitination to stabilize the CFTR protein has long been considered a potential pharmacological approach in CF, progress in this area has been relatively slow. Currently, no compounds targeting this pathway have entered clinical trials for CF. On the other hand, the emergence of Orkambi initially, and notably the subsequent introduction of Trikafta/Kaftrio, have demonstrated the effectiveness of molecular chaperone-based therapies for patients carrying the F508del variant and even showed efficacy against other variants. These treatments directly target the CFTR variant protein without interfering with cell signaling pathways. This review discusses the limits and potential future of targeting protein ubiquitination in CF.
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Affiliation(s)
- Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo, 669-1330, Japan.
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
- Department of Medicine, University of Padova, 35128, Padova, Italy
| | | | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy.
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small-molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. Mol Biol Cell 2024; 35:ar15. [PMID: 38019608 PMCID: PMC10881158 DOI: 10.1091/mbc.e23-08-0336] [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: 09/18/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small-molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase and demonstrated that CFTR-F508del ERAD is robust. Gene-drug interaction experiments illustrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA 94305
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4
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Ge J, Zhang L. RNF5: inhibiting antiviral immunity and shaping virus life cycle. Front Immunol 2024; 14:1324516. [PMID: 38250078 PMCID: PMC10796512 DOI: 10.3389/fimmu.2023.1324516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
RNF5 is an E3 ubiquitin ligase involved in various physiological processes such as protein localization and cancer progression. Recent studies have shown that RNF5 significantly inhibits antiviral innate immunity by promoting the ubiquitination and degradation of STING and MAVS, which are essential adaptor proteins, as well as their downstream signal IRF3. The abundance of RNF5 is delicately regulated by both host factors and viruses. Host factors have been found to restrict RNF5-mediated ubiquitination, maintaining the stability of STING or MAVS through distinct mechanisms. Meanwhile, viruses have developed ingenious strategies to hijack RNF5 to ubiquitinate and degrade immune proteins. Moreover, recent studies have revealed the multifaceted roles of RNF5 in the life cycle of various viruses, including SARS-CoV-2 and KSHV. Based on these emerging discoveries, RNF5 represents a novel means of modulating antiviral immunity. In this review, we summarize the latest research on the roles of RNF5 in antiviral immunity and virus life cycle. This comprehensive understanding could offer valuable insights into exploring potential therapeutic applications focused on targeting RNF5 during viral infections.
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Affiliation(s)
- Junyi Ge
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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5
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.556420. [PMID: 37745470 PMCID: PMC10515913 DOI: 10.1101/2023.09.15.556420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase, demonstrating that CFTR-F508del ERAD is highly buffered. Gene-drug interaction experiments demonstrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA, USA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA, USA 94305
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6
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Brusa I, Sondo E, Pesce E, Tomati V, Gioia D, Falchi F, Balboni B, Ortega Martínez JA, Veronesi M, Romeo E, Margaroli N, Recanatini M, Girotto S, Pedemonte N, Roberti M, Cavalli A. Innovative Strategy toward Mutant CFTR Rescue in Cystic Fibrosis: Design and Synthesis of Thiadiazole Inhibitors of the E3 Ligase RNF5. J Med Chem 2023. [PMID: 37440686 PMCID: PMC10388311 DOI: 10.1021/acs.jmedchem.3c00608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
In cystic fibrosis (CF), deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) is associated to misfolding and defective gating of the mutant channel. One of the most promising CF drug targets is the ubiquitin ligase RNF5, which promotes F508del-CFTR degradation. Recently, the first ever reported inhibitor of RNF5 was discovered, i.e., the 1,2,4-thiadiazol-5-ylidene inh-2. Here, we designed and synthesized a series of new analogues to explore the structure-activity relationships (SAR) of this class of compounds. SAR efforts ultimately led to compound 16, which showed a greater F508del-CFTR corrector activity than inh-2, good tolerability, and no toxic side effects. Analogue 16 increased the basal level of autophagy similar to what has been described with RNF5 silencing. Furthermore, co-treatment with 16 significantly improved the F508del-CFTR rescue induced by the triple combination elexacaftor/tezacaftor/ivacaftor in CFBE41o- cells. These findings validate the 1,2,4-thiadiazolylidene scaffold for the discovery of novel RNF5 inhibitors and provide evidence to pursue this unprecedented strategy for the treatment of CF.
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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
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Dario Gioia
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Beatrice Balboni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | | | - Marina Veronesi
- Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elisa Romeo
- Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Natasha Margaroli
- Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Stefania Girotto
- Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, 16163 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
- Centre Européen de Calcul Atomique et Moléculaire, EPFL CECAM, 1015 Lousanne, Switzerland
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7
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Tam A, Kulkarni J, An K, Li L, Dorscheid DR, Singhera GK, Bernatchez P, Reid G, Chan K, Witzigmann D, Cullis PR, Sin DD, Lim CJ. Lipid nanoparticle formulations for optimal RNA-based topical delivery to murine airways. Eur J Pharm Sci 2022; 176:106234. [PMID: 35688311 DOI: 10.1016/j.ejps.2022.106234] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Lipid nanoparticles (LNP) have been successfully used as a platform technology for delivering nucleic acids to the liver. To broaden the application of LNPs in targeting non-hepatic tissues, we developed LNP-based RNA therapies (siRNA or mRNA) for the respiratory tract. Such optimized LNP systems could offer an early treatment strategy for viral respiratory tract infections such as COVID-19. METHODS We generated a small library of six LNP formulations with varying helper lipid compositions and characterized their hydrodynamic diameter, size distribution and cargo entrapment properties. Next, we screened these LNP formulations for particle uptake and evaluated their potential for transfecting mRNA encoding green fluorescence protein (GFP) or SARS-CoV2 nucleocapsid-GFP fusion reporter gene in a human airway epithelial cell line in vitro. Following LNP-siGFP delivery, GFP protein knockdown efficiency was assessed by flow cytometry to determine %GFP+ cells and median fluorescence intensity (MFI) for GFP. Finally, lead LNP candidates were validated in Friend leukemia virus B (FVB) male mice via intranasal delivery of an mRNA encoding luciferase, using in vivo bioluminescence imaging. RESULTS Dynamic light scattering revealed that all LNP formulations contained particles with an average diameter of <100 nm and a polydispersity index of <0.2. Human airway epithelial cell lines in culture internalized LNPs with differential GFP transfection efficiencies (73-97%). The lead formulation LNP6 entrapping GFP or Nuc-GFP mRNA demonstrated the highest transfection efficiency (97%). Administration of LNP-GFP siRNA resulted in a significant reduction of GFP protein expression. For in vivo studies, intranasal delivery of LNPs containing helper lipids (DSPC, DOPC, ESM or DOPS) with luciferase mRNA showed significant increase in luminescence expression in nasal cavity and lungs by at least 10 times above baseline control. CONCLUSION LNP formulations enable the delivery of RNA payloads into human airway epithelial cells, and in the murine respiratory system; they can be delivered to nasal mucosa and lower respiratory tract via intranasal delivery. The composition of helper lipids in LNPs crucially modulates transfection efficiencies in airway epithelia, highlighting their importance in effective delivery of therapeutic products for airways diseases.
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Affiliation(s)
- A Tam
- NanoVation Therapeutics Inc. Vancouver, British Columbia, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia Vancouver, British Columbia, Canada; University of British Columbia (UBC) Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - J Kulkarni
- NanoVation Therapeutics Inc. Vancouver, British Columbia, Canada; NanoMedicines Innovation Network, Vancouver, British Columbia, Canada; University of British Columbia (UBC), Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada
| | - K An
- NanoVation Therapeutics Inc. Vancouver, British Columbia, Canada; University of British Columbia (UBC), Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada
| | - L Li
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia Vancouver, British Columbia, Canada
| | - D R Dorscheid
- University of British Columbia (UBC) Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - G K Singhera
- University of British Columbia (UBC) Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada; Department of Medicine (Division of Respirology), UBC, Vancouver, British Columbia, Canada
| | - P Bernatchez
- University of British Columbia (UBC) Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada; Department of Medicine (Division of Respirology), UBC, Vancouver, British Columbia, Canada; Department of Anesthesiology, Pharmacology & Therapeutics, University of British Columbia, 217-2176 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Gsd Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia Vancouver, British Columbia, Canada
| | - Kyt Chan
- NanoMedicines Innovation Network, Vancouver, British Columbia, Canada; University of British Columbia (UBC), Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada
| | - D Witzigmann
- NanoVation Therapeutics Inc. Vancouver, British Columbia, Canada; NanoMedicines Innovation Network, Vancouver, British Columbia, Canada; University of British Columbia (UBC), Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada
| | - P R Cullis
- NanoVation Therapeutics Inc. Vancouver, British Columbia, Canada; NanoMedicines Innovation Network, Vancouver, British Columbia, Canada; University of British Columbia (UBC), Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada
| | - D D Sin
- University of British Columbia (UBC) Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - C J Lim
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia Vancouver, British Columbia, Canada.
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8
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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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9
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Principi E, Sondo E, Bianchi G, Ravera S, Morini M, Tomati V, Pastorino C, Zara F, Bruno C, Eva A, Pedemonte N, Raffaghello L. Targeting of Ubiquitin E3 Ligase RNF5 as a Novel Therapeutic Strategy in Neuroectodermal Tumors. Cancers (Basel) 2022; 14:cancers14071802. [PMID: 35406574 PMCID: PMC8997491 DOI: 10.3390/cancers14071802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/27/2023] Open
Abstract
RNF5, an endoplasmic reticulum (ER) E3 ubiquitin ligase, participates to the ER-associated protein degradation guaranteeing the protein homeostasis. Depending on tumor model tested, RNF5 exerts pro- or anti-tumor activity. The aim of this study was to elucidate the controversial role of RNF5 in neuroblastoma and melanoma, two neuroectodermal tumors of infancy and adulthood, respectively. RNF5 gene levels are evaluated in publicly available datasets reporting the gene expression profile of melanoma and neuroblastoma primary tumors at diagnosis. The therapeutic effect of Analog-1, an RNF5 pharmacological activator, was investigated on in vitro and in vivo neuroblastoma and melanoma models. In both neuroblastoma and melanoma patients the high expression of RNF5 correlated with a better prognostic outcome. Treatment of neuroblastoma and melanoma cell lines with Analog-1 reduced cell viability by impairing the glutamine availability and energy metabolism through inhibition of F1Fo ATP-synthase activity. This latter event led to a marked increase in oxidative stress, which, in turn, caused cell death. Similarly, neuroblastoma- and melanoma-bearing mice treated with Analog-1 showed a significant delay of tumor growth in comparison to those treated with vehicle only. These findings validate RNF5 as an innovative drug target and support the development of Analog-1 in early phase clinical trials for neuroblastoma and melanoma patients.
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Affiliation(s)
- Elisa Principi
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Giovanna Bianchi
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Silvia Ravera
- Experimental Medicine Department, University of Genova, 16132 Genova, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Cristina Pastorino
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DI-NOGMI), University of Genoa, 16132 Genoa, Italy
| | - Federico Zara
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DI-NOGMI), University of Genoa, 16132 Genoa, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DI-NOGMI), University of Genoa, 16132 Genoa, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | | | - Lizzia Raffaghello
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
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10
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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11
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Borgo C, D'Amore C, Capurro V, Tomati V, Sondo E, Cresta F, Castellani C, Pedemonte N, Salvi M. Targeting the E1 ubiquitin-activating enzyme (UBA1) improves elexacaftor/tezacaftor/ivacaftor efficacy towards F508del and rare misfolded CFTR mutants. Cell Mol Life Sci 2022; 79:192. [PMID: 35292885 PMCID: PMC8924136 DOI: 10.1007/s00018-022-04215-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/08/2023]
Abstract
The advent of Trikafta (Kaftrio in Europe) (a triple-combination therapy based on two correctors—elexacaftor/tezacaftor—and the potentiator ivacaftor) has represented a revolution for the treatment of patients with cystic fibrosis (CF) carrying the most common misfolding mutation, F508del-CFTR. This therapy has proved to be of great efficacy in people homozygous for F508del-CFTR and is also useful in individuals with a single F508del allele. Nevertheless, the efficacy of this therapy needs to be improved, especially in light of the extent of its use in patients with rare class II CFTR mutations. Using CFBE41o- cells expressing F508del-CFTR, we provide mechanistic evidence that targeting the E1 ubiquitin-activating enzyme (UBA1) by TAK-243, a small molecule in clinical trials for other diseases, boosts the rescue of F508del-CFTR induced by CFTR correctors. Moreover, TAK-243 significantly increases the F508del-CFTR short-circuit current induced by elexacaftor/tezacaftor/ivacaftor in differentiated human primary airway epithelial cells, a gold standard for the pre-clinical evaluation of patients’ responsiveness to pharmacological treatments. This new combinatory approach also leads to an improvement in CFTR conductance on cells expressing other rare CF-causing mutations, including N1303K, for which Trikafta is not approved. These findings show that Trikafta therapy can be improved by the addition of a drug targeting the misfolding detection machinery at the beginning of the ubiquitination cascade and may pave the way for an extension of Trikafta to low/non-responding rare misfolded CFTR mutants.
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Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Valeria Capurro
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Federico Cresta
- Centro Fibrosi Cistica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Carlo Castellani
- Centro Fibrosi Cistica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy.
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
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12
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Strub MD, Gao L, Tan K, McCray PB. Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and ΔF508-CFTR rescue. BMC Med Genomics 2021; 14:258. [PMID: 34717611 PMCID: PMC8557508 DOI: 10.1186/s12920-021-01106-7] [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: 04/08/2021] [Accepted: 10/20/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND We previously reported that expression of a miR-138 mimic or knockdown of SIN3A in primary cultures of cystic fibrosis (CF) airway epithelia increased ΔF508-CFTR mRNA and protein levels, and partially restored CFTR-dependent chloride transport. Global mRNA transcript profiling in ΔF508-CFBE cells treated with miR-138 mimic or SIN3A siRNA identified two genes, SYVN1 and NEDD8, whose inhibition significantly increased ΔF508-CFTR trafficking, maturation, and function. Little is known regarding the dynamic changes in the CFTR gene network during such rescue events. We hypothesized that analysis of condition-specific gene networks from transcriptomic data characterizing ΔF508-CFTR rescue could help identify dynamic gene modules associated with CFTR biogenesis. METHODS We applied a computational method, termed M-module, to analyze multiple gene networks, each of which exhibited differential activity compared to a baseline condition. In doing so, we identified both unique and shared gene pathways across multiple differential networks. To construct differential networks, gene expression data from CFBE cells were divided into three groups: (1) siRNA inhibition of NEDD8 and SYVN1; (2) miR-138 mimic and SIN3A siRNA; and (3) temperature (27 °C for 24 h, 40 °C for 24 h, and 27 °C for 24 h followed by 40 °C for 24 h). RESULTS Interrogation of individual networks (e.g., NEDD8/SYVN1 network), combinations of two networks (e.g., NEDD8/SYVN1 + temperature networks), and all three networks yielded sets of 1-modules, 2-modules, and 3-modules, respectively. Gene ontology analysis revealed significant enrichment of dynamic modules in pathways including translation, protein metabolic/catabolic processes, protein complex assembly, and endocytosis. Candidate CFTR effectors identified in the analysis included CHURC1, GZF1, and RPL15, and siRNA-mediated knockdown of these genes partially restored CFTR-dependent transepithelial chloride current to ΔF508-CFBE cells. CONCLUSIONS The ability of the M-module to identify dynamic modules involved in ΔF508 rescue provides a novel approach for studying CFTR biogenesis and identifying candidate suppressors of ΔF508.
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Affiliation(s)
- Matthew D Strub
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA. .,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA.
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13
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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14
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Hodos RA, Strub MD, Ramachandran S, Li L, McCray PB, Dudley JT. Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue. Sci Rep 2020; 10:20553. [PMID: 33239626 PMCID: PMC7689470 DOI: 10.1038/s41598-020-76347-0] [Citation(s) in RCA: 5] [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: 12/26/2019] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF), caused by mutations to CFTR, leads to severe and progressive lung disease. The most common mutant, ΔF508-CFTR, undergoes proteasomal degradation, extinguishing its anion channel function. Numerous in vitro interventions have been identified to partially rescue ΔF508-CFTR function yet remain poorly understood. Improved understanding of both the altered state of CF cells and the mechanisms of existing rescue strategies could reveal novel therapeutic strategies. Toward this aim, we measured transcriptional profiles of established temperature, genetic, and chemical interventions that rescue ΔF508-CFTR and also re-analyzed public datasets characterizing transcription in human CF vs. non-CF samples from airway and whole blood. Meta-analysis yielded a core disease signature and two core rescue signatures. To interpret these through the lens of prior knowledge, we compiled a "CFTR Gene Set Library" from literature. The core disease signature revealed remarkably strong connections to genes with established effects on CFTR trafficking and function and suggested novel roles of EGR1 and SGK1 in the disease state. Our data also revealed an unexpected mechanistic link between several genetic rescue interventions and the unfolded protein response. Finally, we found that C18, an analog of the CFTR corrector compound Lumacaftor, induces almost no transcriptional perturbation despite its rescue activity.
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Affiliation(s)
- Rachel A Hodos
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
- BenevolentAI, Brooklyn, NY, USA
| | - Matthew D Strub
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Shyam Ramachandran
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Editas Medicine, Cambridge, MA, USA
| | - Li Li
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Paul B McCray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA.
| | - Joel T Dudley
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA.
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15
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Xu J, Zhao H, Wang T. Suppression of retinal degeneration by two novel ERAD ubiquitin E3 ligases SORDD1/2 in Drosophila. PLoS Genet 2020; 16:e1009172. [PMID: 33137101 PMCID: PMC7660902 DOI: 10.1371/journal.pgen.1009172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/12/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the gene rhodopsin are one of the major causes of autosomal dominant retinitis pigmentosa (adRP). Mutant forms of Rhodopsin frequently accumulate in the endoplasmic reticulum (ER), cause ER stress, and trigger photoreceptor cell degeneration. Here, we performed a genome-wide screen to identify suppressors of retinal degeneration in a Drosophila model of adRP, carrying a point mutation in the major rhodopsin, Rh1 (Rh1G69D). We identified two novel E3 ubiquitin ligases SORDD1 and SORDD2 that effectively suppressed Rh1G69D-induced photoreceptor dysfunction and retinal degeneration. SORDD1/2 promoted the ubiquitination and degradation of Rh1G69D through VCP (valosin containing protein) and independent of processes reliant on the HRD1 (HMG-CoA reductase degradation protein 1)/HRD3 complex. We further demonstrate that SORDD1/2 and HRD1 function in parallel and in a redundant fashion to maintain rhodopsin homeostasis and integrity of photoreceptor cells. These findings identify a new ER-associated protein degradation (ERAD) pathway and suggest that facilitating SORDD1/2 function may be a therapeutic strategy to treat adRP. Misfolded rhodopsins accumulated in endoplasmic reticulum (ER) could disrupt the homeostasis of the ER and cause ER stress. Chronic ER stress would finally lead to photoreceptor cell death and retinal degeneration. To diminish the stress and sustain homeostasis cells develop alternative strategies to clear the misfolded rhodopsins. Previous studies have suggested that ubiquitin E3 ligase HRD1 is involved in the degradation of misfolded rhodopsins. In this study, we define novel ubiquitin E3 ligase SORDD1/2 based on a genetic screen and demonstrate that SORDD1/2 promotes the degradation of misfolded rhodopsins through ER-associated degradation (ERAD) pathway. Furthermore, we demonstrate that SORDD1/2 function independently of HRD1 in misfolded rhodopsins degradation. We also show SORDD1/2 and HRD1 play redundant roles in rhodopsin homeostasis. Finally, we demonstrate that SORDD1 works well in a Drosophila disease model. Our studies identify a novel ERAD pathway that acts in parallel to HRD1, and suggest that SORDD1 is a good candidate therapeutic target.
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Affiliation(s)
- Jaiwei Xu
- College of Biological Sciences, China Agricultural University, China
- National Institute of Biological Sciences, China
| | - Haifang Zhao
- National Institute of Biological Sciences, China
| | - Tao Wang
- National Institute of Biological Sciences, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, China
- * E-mail:
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16
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Adir O, Bening-Abu-Shach U, Arbib S, Henis-Korenblit S, Broday L. Inactivation of the Caenorhabditis elegans RNF-5 E3 ligase promotes IRE-1-independent ER functions. Autophagy 2020; 17:2401-2414. [DOI: 10.1080/15548627.2020.1827778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Orit Adir
- Department of Cell and Developmental Biology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ulrike Bening-Abu-Shach
- Department of Cell and Developmental Biology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shir Arbib
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sivan Henis-Korenblit
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
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17
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Liessi N, Pedemonte N, Armirotti A, Braccia C. Proteomics and Metabolomics for Cystic Fibrosis Research. Int J Mol Sci 2020; 21:ijms21155439. [PMID: 32751630 PMCID: PMC7432297 DOI: 10.3390/ijms21155439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/18/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The aim of this review article is to introduce the reader to the state-of-the-art of the contribution that proteomics and metabolomics sciences are currently providing for cystic fibrosis (CF) research: from the understanding of cystic fibrosis transmembrane conductance regulator (CFTR) biology to biomarker discovery for CF diagnosis. Our work particularly focuses on CFTR post-translational modifications and their role in cellular trafficking as well as on studies that allowed the identification of CFTR molecular interactors. We also show how metabolomics is currently helping biomarker discovery in CF. The most recent advances in these fields are covered by this review, as well as some considerations on possible future scenarios for new applications.
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Affiliation(s)
- Nara Liessi
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Andrea Armirotti
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
- Correspondence: ; Tel.: +39-010-2896-938
| | - Clarissa Braccia
- D3PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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18
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Qin X, Denton WD, Huiting LN, Smith KS, Feng H. Unraveling the regulatory role of endoplasmic-reticulum-associated degradation in tumor immunity. Crit Rev Biochem Mol Biol 2020; 55:322-353. [PMID: 32633575 DOI: 10.1080/10409238.2020.1784085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During malignant transformation and cancer progression, tumor cells face both intrinsic and extrinsic stress, endoplasmic reticulum (ER) stress in particular. To survive and proliferate, tumor cells use multiple stress response pathways to mitigate ER stress, promoting disease aggression and treatment resistance. Among the stress response pathways is ER-associated degradation (ERAD), which consists of multiple components and steps working together to ensure protein quality and quantity. In addition to its established role in stress responses and tumor cell survival, ERAD has recently been shown to regulate tumor immunity. Here we summarize current knowledge on how ERAD promotes protein degradation, regulates immune cell development and function, participates in antigen presentation, exerts paradoxical roles on tumorigenesis and immunity, and thus impacts current cancer therapy. Collectively, ERAD is a critical protein homeostasis pathway intertwined with cancer development and tumor immunity. Of particular importance is the need to further unveil ERAD's enigmatic roles in tumor immunity to develop effective targeted and combination therapy for successful treatment of cancer.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - William D Denton
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Leah N Huiting
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Kaylee S Smith
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
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19
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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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20
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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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21
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Lopes-Pacheco M. CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision Medicine. Front Pharmacol 2020; 10:1662. [PMID: 32153386 PMCID: PMC7046560 DOI: 10.3389/fphar.2019.01662] [Citation(s) in RCA: 275] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal inherited disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which result in impairment of CFTR mRNA and protein expression, function, stability or a combination of these. Although CF leads to multifaceted clinical manifestations, the respiratory disorder represents the major cause of morbidity and mortality of these patients. The life expectancy of CF patients has substantially lengthened due to early diagnosis and improvements in symptomatic therapeutic regimens. Quality of life remains nevertheless limited, as these individuals are subjected to considerable clinical, psychosocial and economic burdens. Since the discovery of the CFTR gene in 1989, tremendous efforts have been made to develop therapies acting more upstream on the pathogenesis cascade, thereby overcoming the underlying dysfunctions caused by CFTR mutations. In this line, the advances in cell-based high-throughput screenings have been facilitating the fast-tracking of CFTR modulators. These modulator drugs have the ability to enhance or even restore the functional expression of specific CF-causing mutations, and they have been classified into five main groups depending on their effects on CFTR mutations: potentiators, correctors, stabilizers, read-through agents, and amplifiers. To date, four CFTR modulators have reached the market, and these pharmaceutical therapies are transforming patients' lives with short- and long-term improvements in clinical outcomes. Such breakthroughs have paved the way for the development of novel CFTR modulators, which are currently under experimental and clinical investigations. Furthermore, recent insights into the CFTR structure will be useful for the rational design of next-generation modulator drugs. This review aims to provide a summary of recent developments in CFTR-directed therapeutics. Barriers and future directions are also discussed in order to optimize treatment adherence, identify feasible and sustainable solutions for equitable access to these therapies, and continue to expand the pipeline of novel modulators that may result in effective precision medicine for all individuals with CF.
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Affiliation(s)
- Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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22
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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: 31] [Impact Index Per Article: 7.8] [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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23
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D'Antonio M, Reyna J, Jakubosky D, Donovan MKR, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. eLife 2019; 8:e48476. [PMID: 31746734 PMCID: PMC6904215 DOI: 10.7554/elife.48476] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account have substantially greater power compared with only using single variants. We examined the association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, postulating that downregulation of RNF5 expression is the likely causal mechanism. Our study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes.
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Affiliation(s)
- Matteo D'Antonio
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Joaquin Reyna
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - David Jakubosky
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
| | - Margaret KR Donovan
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical InformaticsUniversity of California, San DiegoSan DiegoUnited States
| | - Marc-Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Hiroko Matsui
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Naoki Nariai
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Agnieszka D'Antonio-Chronowska
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Kelly A Frazer
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
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24
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Amaral MD, Hutt DM, Tomati V, Botelho HM, Pedemonte N. CFTR processing, trafficking and interactions. J Cyst Fibros 2019; 19 Suppl 1:S33-S36. [PMID: 31680043 DOI: 10.1016/j.jcf.2019.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/04/2023]
Abstract
Mutations associated with cystic fibrosis (CF) have complex effects on the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The most common CF mutation, F508del, disrupts the processing to and stability at the plasma membrane and function as a Cl- channel. CFTR is surrounded by a dynamic network of interacting components, referred to as the CFTR Functional Landscape, that impact its synthesis, folding, stability, trafficking and function. CFTR interacting proteins can be manipulated by functional genomic approaches to rescue the trafficking and functional defects characteristic of CF. Here we review recent efforts to elucidate the impact of genetic variation on the ability of the nascent CFTR polypeptide to interact with the proteostatic environment. We also provide an overview of how specific components of this protein network can be modulated to rescue the trafficking and functional defects associated with the F508del variant of CFTR. The identification of novel proteins playing key roles in the processing of CFTR could pave the way for their use as novel therapeutic targets to provide synergistic correction of mutant CFTR for the greater benefit of individuals with CF.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla CA, USA
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy.
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25
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Bioactive Thymosin Alpha-1 Does Not Influence F508del-CFTR Maturation and Activity. Sci Rep 2019; 9:10310. [PMID: 31311979 PMCID: PMC6635361 DOI: 10.1038/s41598-019-46639-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/11/2022] Open
Abstract
Deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is the most frequent mutation causing cystic fibrosis (CF). F508del-CFTR is misfolded and prematurely degraded. Recently thymosin a-1 (Tα-1) was proposed as a single molecule-based therapy for CF, improving both F508del-CFTR maturation and function by restoring defective autophagy. However, three independent laboratories failed to reproduce these results. Lack of reproducibility has been ascribed by the authors of the original paper to the use of DMSO and to improper handling. Here, we address these potential issues by demonstrating that Tα-1 changes induced by DMSO are fully reversible and that Tα-1 peptides prepared from different stock solutions have equivalent biological activity. Considering the negative results here reported, six independent laboratories failed to demonstrate F508del-CFTR correction by Tα-1. This study also calls into question the autophagy modulator cysteamine, since no rescue of mutant CFTR function was detected following treatment with cysteamine, while deleterious effects were observed when bronchial epithelia were exposed to cysteamine plus the antioxidant food supplement EGCG. Although these studies do not exclude the possibility of beneficial immunomodulatory effects of thymosin α-1, they do not support its utility as a corrector of F508del-CFTR.
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26
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Huang Y, Arora K, Mun KS, Yang F, Moon C, Yarlagadda S, Jegga A, Weaver T, Naren AP. Targeting DNAJB9, a novel ER luminal co-chaperone, to rescue ΔF508-CFTR. Sci Rep 2019; 9:9808. [PMID: 31285458 PMCID: PMC6614449 DOI: 10.1038/s41598-019-46161-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/19/2019] [Indexed: 01/30/2023] Open
Abstract
The molecular mechanism of Endoplasmic Reticulum-associated degradation (ERAD) of Cystic fibrosis transmembrane-conductance regulator (CFTR) is largely unknown. Particularly, it is unknown what ER luminal factor(s) are involved in ERAD. Herein, we used ProtoArray to identify an ER luminal co-chaperone, DNAJB9, which can directly interact with CFTR. For both WT- and ΔF508 (deletion of phenylalanine at position 508, the most common CF-causing mutant)-CFTR, knockdown of DNAJB9 by siRNA increased their expression levels on the cell surface and, consequently, upregulated their function. Furthermore, genetic ablation of DNAJB9 in WT mice increased CFTR expression and enhanced CFTR-dependent fluid secretion in enteroids. Importantly, DNAJB9 deficiency upregulated enteroids' fluid secretion in CF mice (homozygous for ΔF508), and silencing one allele of DNAJB9 is sufficient to rescue ΔF508-CFTR in vitro and in vivo, suggesting that DNAJB9 may be a rate-limiting factor in CFTR ERAD pathway. Our studies identified the first ER luminal co-chaperone involved in CFTR ERAD, and DNAJB9 could be a novel therapeutic target for CF.
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Affiliation(s)
- Yunjie Huang
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Kavisha Arora
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Kyu Shik Mun
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Fanmuyi Yang
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - ChangSuk Moon
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Sunitha Yarlagadda
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Anil Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Timothy Weaver
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States.
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27
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28
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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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29
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Pesce E, Sondo E, Ferrera L, Tomati V, Caci E, Scudieri P, Musante I, Renda M, Baatallah N, Servel N, Hinzpeter A, di Bernardo D, Pedemonte N, Galietta LJV. The Autophagy Inhibitor Spautin-1 Antagonizes Rescue of Mutant CFTR Through an Autophagy-Independent and USP13-Mediated Mechanism. Front Pharmacol 2018; 9:1464. [PMID: 30618756 PMCID: PMC6300570 DOI: 10.3389/fphar.2018.01464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/29/2018] [Indexed: 12/21/2022] Open
Abstract
The mutation F508del, responsible for a majority of cystic fibrosis cases, provokes the instability and misfolding of the CFTR chloride channel. Pharmacological recovery of F508del-CFTR may be obtained with small molecules called correctors. However, treatment with a single corrector in vivo and in vitro only leads to a partial rescue, a consequence of cell quality control systems that still detect F508del-CFTR as a defective protein causing its degradation. We tested the effect of spautin-1 on F508del-CFTR since it is an inhibitor of USP10 deubiquitinase and of autophagy, a target and a biological process that have been associated with cystic fibrosis and mutant CFTR. We found that short-term treatment of cells with spautin-1 downregulates the function and expression of F508del-CFTR despite the presence of corrector VX-809, a finding obtained in multiple cell models and assays. In contrast, spautin-1 was ineffective on wild type CFTR. Silencing and upregulation of USP13 (another target of spautin-1) but not of USP10, had opposite effects on F508del-CFTR expression/function. In contrast, modulation of autophagy with known activators or inhibitors did not affect F508del-CFTR. Our results identify spautin-1 as a novel chemical probe to investigate the molecular mechanisms that prevent full rescue of mutant CFTR.
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Affiliation(s)
- Emanuela Pesce
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Elvira Sondo
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Loretta Ferrera
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Valeria Tomati
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Emanuela Caci
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Paolo Scudieri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Ilaria Musante
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Mario Renda
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Nesrine Baatallah
- INSERM, U1151, Institut Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
| | - Nathalie Servel
- INSERM, U1151, Institut Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
| | - Alexandre Hinzpeter
- INSERM, U1151, Institut Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
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30
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Braccia C, Tomati V, Caci E, Pedemonte N, Armirotti A. SWATH label-free proteomics for cystic fibrosis research. J Cyst Fibros 2018; 18:501-506. [PMID: 30348611 DOI: 10.1016/j.jcf.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Label-free proteomics is a powerful tool for biological investigation. The SWATH protocol, relying on the Pan Human ion library, currently represents the state-of-the-art methodology for this kind of analysis. We recently discovered that this tool is not perfectly suitable for proteomics research in the CF field, as it lacks assays for several proteins crucial for the CF biology, including CFTR. METHODS We extensively investigated the proteome of a very popular model for in vitro research on CF, CFBE41o-, and we used the corresponding data to improve the power of SWATH proteomics for CF investigation. We then used this improved tool to explore in depth the proteome of primary bronchial epithelial (BE) cells deriving from four CF individuals compared with that of four corresponding non-CF controls. By means of advanced bioinformatics tools, we outlined the presence of a number of protein networks being significantly altered by CF. RESULTS Our analysis on patients' BE cells identified 154 proteins dysregulated by the CF pathology (94 upregulated and 60 downregulated). Some known CFTR interactors are present among them, but our analysis also revealed the alteration of other proteins not previously known to be related with CF. CONCLUSIONS The present work outlines the power of SWATH label free proteomics applied to CF research.
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Affiliation(s)
- Clarissa Braccia
- D3Pharmachemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; Dipartimento di Chimica, Università degli Studi di Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Valeria Tomati
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Emanuela Caci
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
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31
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Moon HW, Han HG, Jeon YJ. Protein Quality Control in the Endoplasmic Reticulum and Cancer. Int J Mol Sci 2018; 19:E3020. [PMID: 30282948 PMCID: PMC6213883 DOI: 10.3390/ijms19103020] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/22/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is an essential compartment of the biosynthesis, folding, assembly, and trafficking of secretory and transmembrane proteins, and consequently, eukaryotic cells possess specialized machineries to ensure that the ER enables the proteins to acquire adequate folding and maturation for maintaining protein homeostasis, a process which is termed proteostasis. However, a large variety of physiological and pathological perturbations lead to the accumulation of misfolded proteins in the ER, which is referred to as ER stress. To resolve ER stress and restore proteostasis, cells have evolutionary conserved protein quality-control machineries of the ER, consisting of the unfolded protein response (UPR) of the ER, ER-associated degradation (ERAD), and autophagy. Furthermore, protein quality-control machineries of the ER play pivotal roles in the control of differentiation, progression of cell cycle, inflammation, immunity, and aging. Therefore, severe and non-resolvable ER stress is closely associated with tumor development, aggressiveness, and response to therapies for cancer. In this review, we highlight current knowledge in the molecular understanding and physiological relevance of protein quality control of the ER and discuss new insights into how protein quality control of the ER is implicated in the pathogenesis of cancer, which could contribute to therapeutic intervention in cancer.
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Affiliation(s)
- Hye Won Moon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
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32
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Stincardini C, Renga G, Villella V, Pariano M, Oikonomou V, Borghi M, Bellet MM, Sforna L, Costantini C, Goldstein AL, Garaci E, Romani L. Cellular proteostasis: a new twist in the action of thymosin α1. Expert Opin Biol Ther 2018; 18:43-48. [DOI: 10.1080/14712598.2018.1484103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Giorgia Renga
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Valeria Villella
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Marilena Pariano
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Vasilis Oikonomou
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Monica Borghi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Marina M. Bellet
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Luigi Sforna
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Claudio Costantini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Allan L. Goldstein
- Department of Biochemistry and Molecular Medicine, The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Enrico Garaci
- University San Raffaele and IRCCS San Raffaele, Rome, Italy
| | - Luigina Romani
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
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33
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Pharmacological Inhibition of the Ubiquitin Ligase RNF5 Rescues F508del-CFTR in Cystic Fibrosis Airway Epithelia. Cell Chem Biol 2018; 25:891-905.e8. [PMID: 29754957 DOI: 10.1016/j.chembiol.2018.04.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/22/2018] [Accepted: 04/09/2018] [Indexed: 12/20/2022]
Abstract
In cystic fibrosis (CF), deletion of phenylalanine 508 (F508del) in the CFTR channel is associated with misfolding and premature degradation of the mutant protein. Among the known proteins associated with F508del-CFTR processing, the ubiquitin ligase RNF5/RMA1 is particularly interesting. We previously demonstrated that genetic suppression of RNF5 in vivo leads to an attenuation of intestinal pathological phenotypes in CF mice, validating the relevance of RNF5 as a drug target for CF. Here, we used a computational approach, based on ligand docking and virtual screening, to discover inh-02, a drug-like small molecule that inhibits RNF5. In in vitro experiments, treatment with inh-02 modulated ATG4B and paxillin, both known RNF5 targets. In immortalized and primary bronchial epithelial cells derived from CF patients homozygous for the F508del mutation, long-term incubation with inh-02 caused significant F508del-CFTR rescue. This work validates RNF5 as a drug target for CF, providing evidence to support its druggability.
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Li H, Pesce E, Sheppard DN, Singh AK, Pedemonte N. Therapeutic approaches to CFTR dysfunction: From discovery to drug development. J Cyst Fibros 2018; 17:S14-S21. [DOI: 10.1016/j.jcf.2017.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 11/29/2022]
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Tomati V, Caci E, Ferrera L, Pesce E, Sondo E, Cholon DM, Quinney NL, Boyles SE, Armirotti A, Ravazzolo R, Galietta LJ, Gentzsch M, Pedemonte N. Thymosin α-1 does not correct F508del-CFTR in cystic fibrosis airway epithelia. JCI Insight 2018; 3:98699. [PMID: 29415893 DOI: 10.1172/jci.insight.98699] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/28/2017] [Indexed: 12/29/2022] Open
Abstract
In cystic fibrosis (CF), deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel causes misfolding and premature degradation. Considering the numerous effects of the F508del mutation on the assembly and processing of CFTR protein, combination therapy with several pharmacological correctors is likely to be required to treat CF patients. Recently, it has been reported that thymosin α-1 (Tα-1) has multiple beneficial effects that could lead to a single-molecule-based therapy for CF patients with F508del. Such effects include suppression of inflammation, improvement in F508del-CFTR maturation and gating, and stimulation of chloride secretion through the calcium-activated chloride channel (CaCC). Given the importance of such a drug, we aimed to characterize the underlying molecular mechanisms of action of Tα-1. In-depth analysis of Tα-1 effects was performed using well-established microfluorimetric, biochemical, and electrophysiological techniques on epithelial cell lines and primary bronchial epithelial cells from CF patients. The studies, which were conducted in 2 independent laboratories with identical outcome, demonstrated that Tα-1 is devoid of activity on mutant CFTR as well as on CaCC. Although Tα-1 may still be useful as an antiinflammatory agent, its ability to target defective anion transport in CF remains to be further investigated.
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Affiliation(s)
- Valeria Tomati
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Emanuela Caci
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Loretta Ferrera
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Emanuela Pesce
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Elvira Sondo
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy L Quinney
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Susan E Boyles
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrea Armirotti
- Fondazione Istituto Italiano di Tecnologia, Analytical Chemistry Lab, Genova, Italy
| | - Roberto Ravazzolo
- U.O.C. Genetica Medica, Istituto Giannina Gaslini, Genova, Italy.,University of Genova, DINOGMI Department, Genova, Italy
| | - Luis Jv Galietta
- Telethon Institute for Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Tomati V, Pesce E, Caci E, Sondo E, Scudieri P, Marini M, Amato F, Castaldo G, Ravazzolo R, Galietta LJV, Pedemonte N. High-throughput screening identifies FAU protein as a regulator of mutant cystic fibrosis transmembrane conductance regulator channel. J Biol Chem 2018; 293:1203-1217. [PMID: 29158263 PMCID: PMC5787799 DOI: 10.1074/jbc.m117.816595] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/19/2017] [Indexed: 01/01/2023] Open
Abstract
In cystic fibrosis, deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel causes misfolding and premature degradation. One possible approach to reducing the detrimental health effects of cystic fibrosis could be the identification of proteins whose suppression rescues F508del-CFTR function in bronchial epithelial cells. However, searches for these potential targets have not yet been conducted, particularly in a relevant airway background using a functional readout. To identify proteins associated with F508del-CFTR processing, we used a high-throughput functional assay to screen an siRNA library targeting 6,650 different cellular proteins. We identified 37 proteins whose silencing significantly rescued F508del-CFTR activity, as indicated by enhanced anion transport through the plasma membrane. These proteins included FAU, UBE2I, UBA52, MLLT6, UBA2, CHD4, PLXNA1, and TRIM24, among others. We focused our attention on FAU, a poorly characterized protein with unknown function. FAU knockdown increased the plasma membrane targeting and function of F508del-CFTR, but not of wild-type CFTR. Investigation into the mechanism of action revealed a preferential physical interaction of FAU with mutant CFTR, leading to its degradation. FAU and other proteins identified in our screening may offer a therapeutically relevant panel of drug targets to correct basic defects in F508del-CFTR processing.
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Affiliation(s)
- Valeria Tomati
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Emanuela Pesce
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Emanuela Caci
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Elvira Sondo
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Paolo Scudieri
- the Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Monica Marini
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Felice Amato
- the Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80138 Naples, Italy
- CEINGE-Advanced Biotechnology Scarl, 80145 Naples, Italy, and
| | - Giuseppe Castaldo
- the Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80138 Naples, Italy
- CEINGE-Advanced Biotechnology Scarl, 80145 Naples, Italy, and
| | - Roberto Ravazzolo
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy
- the Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DINOGMI), University of Genova, 16132 Genova, Italy
| | - Luis J V Galietta
- the Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Nicoletta Pedemonte
- From the Unità Operativa Complessa (U.O.C.) Genetica Medica, Istituto Giannina Gaslini, 16147 Genova, Italy,
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Yoo YS, Han HG, Jeon YJ. Unfolded Protein Response of the Endoplasmic Reticulum in Tumor Progression and Immunogenicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2969271. [PMID: 29430279 PMCID: PMC5752989 DOI: 10.1155/2017/2969271] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a pivotal regulator of folding, quality control, trafficking, and targeting of secreted and transmembrane proteins, and accordingly, eukaryotic cells have evolved specialized machinery to ensure that the ER enables these proteins to acquire adequate folding and maturation in the presence of intrinsic and extrinsic insults. This adaptive capacity of the ER to intrinsic and extrinsic perturbations is important for maintaining protein homeostasis, which is termed proteostasis. Failure in adaptation to these perturbations leads to accumulation of misfolded or unassembled proteins in the ER, which is termed ER stress, resulting in the activation of unfolded protein response (UPR) of the ER and the execution of ER-associated degradation (ERAD) to restore homeostasis. Furthermore, both of the two axes play key roles in the control of tumor progression, inflammation, immunity, and aging. Therefore, understanding UPR of the ER and subsequent ERAD will provide new insights into the pathogenesis of many human diseases and contribute to therapeutic intervention in these diseases.
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Affiliation(s)
- Yoon Seon Yoo
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
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Abstract
Newly synthesized transmembrane proteins undergo a series of steps to ensure that only the required amount of correctly folded protein is localized to the membrane. The regulation of protein quality and its abundance at the membrane are often controlled by ubiquitination, a multistep enzymatic process that results in the attachment of ubiquitin, or chains of ubiquitin to the target protein. Protein ubiquitination acts as a signal for sorting, trafficking, and the removal of membrane proteins via endocytosis, a process through which multiple ubiquitin ligases are known to specifically regulate the functions of a number of ion channels, transporters, and signaling receptors. Endocytic removal of these proteins through ubiquitin-dependent endocytosis provides a way to rapidly downregulate the physiological outcomes, and defects in such controls are directly linked to human pathologies. Recent evidence suggests that ubiquitination is also involved in the shedding of membranes and associated proteins as extracellular vesicles, thereby not only controlling the cell surface levels of some membrane proteins, but also their potential transport to neighboring cells. In this review, we summarize the mechanisms and functions of ubiquitination of membrane proteins and provide specific examples of ubiquitin-dependent regulation of membrane proteins.
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Affiliation(s)
- Natalie Foot
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Tanya Henshall
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, Australia
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Hegde RN, Subramanian A, Pothukuchi P, Parashuraman S, Luini A. Rare ER protein misfolding-mistrafficking disorders: Therapeutic developments. Tissue Cell 2017; 49:175-185. [PMID: 28222887 DOI: 10.1016/j.tice.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022]
Abstract
The presence of a functional protein at the appropriate location in the cell is the result of the processes of transcription, translation, folding and trafficking to the correct destination. There are numerous diseases that are caused by protein misfolding, mainly due to mutations in the respective gene. The consequences of this misfolding may be that proteins effectively lose their function, either by being removed by the cellular quality control machinery or by accumulating at the incorrect intracellular or extracellular location. A number of mutations that lead to protein misfolding and affect trafficking to the final destination, e.g. Cystic fibrosis, Wilson's disease, and Progressive Familial Intrahepatic 1 cholestasis, result in proteins that retain partial function if their folding and trafficking is restored either by molecular or pharmacological means. In this review, we discuss several mutant proteins within this class of misfolding diseases and provide an update on the status of molecular and therapeutic developments and potential therapeutic strategies being developed to counter these diseases.
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Affiliation(s)
| | - Advait Subramanian
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | | | | | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Naples, Italy; Istituto di Ricovero e Cura a Carattere Scientifico SDN, Naples, Italy
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Chung WJ, Goeckeler-Fried JL, Havasi V, Chiang A, Rowe SM, Plyler ZE, Hong JS, Mazur M, Piazza GA, Keeton AB, White EL, Rasmussen L, Weissman AM, Denny RA, Brodsky JL, Sorscher EJ. Increasing the Endoplasmic Reticulum Pool of the F508del Allele of the Cystic Fibrosis Transmembrane Conductance Regulator Leads to Greater Folding Correction by Small Molecule Therapeutics. PLoS One 2016; 11:e0163615. [PMID: 27732613 PMCID: PMC5061379 DOI: 10.1371/journal.pone.0163615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/12/2016] [Indexed: 12/19/2022] Open
Abstract
Small molecules that correct the folding defects and enhance surface localization of the F508del mutation in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) comprise an important therapeutic strategy for cystic fibrosis lung disease. However, compounds that rescue the F508del mutant protein to wild type (WT) levels have not been identified. In this report, we consider obstacles to obtaining robust and therapeutically relevant levels of F508del CFTR. For example, markedly diminished steady state amounts of F508del CFTR compared to WT CFTR are present in recombinant bronchial epithelial cell lines, even when much higher levels of mutant transcript are present. In human primary airway cells, the paucity of Band B F508del is even more pronounced, although F508del and WT mRNA concentrations are comparable. Therefore, to augment levels of “repairable” F508del CFTR and identify small molecules that then correct this pool, we developed compound library screening protocols based on automated protein detection. First, cell-based imaging measurements were used to semi-quantitatively estimate distribution of F508del CFTR by high content analysis of two-dimensional images. We evaluated ~2,000 known bioactive compounds from the NIH Roadmap Molecular Libraries Small Molecule Repository in a pilot screen and identified agents that increase the F508del protein pool. Second, we analyzed ~10,000 compounds representing diverse chemical scaffolds for effects on total CFTR expression using a multi-plate fluorescence protocol and describe compounds that promote F508del maturation. Together, our findings demonstrate proof of principle that agents identified in this fashion can augment the level of endoplasmic reticulum (ER) resident “Band B” F508del CFTR suitable for pharmacologic correction. As further evidence in support of this strategy, PYR-41—a compound that inhibits the E1 ubiquitin activating enzyme—was shown to synergistically enhance F508del rescue by C18, a small molecule corrector. Our combined results indicate that increasing the levels of ER-localized CFTR available for repair provides a novel route to correct F508del CFTR.
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Affiliation(s)
- W. Joon Chung
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jennifer L. Goeckeler-Fried
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Viktoria Havasi
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Annette Chiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Cellular, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zackery E. Plyler
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeong S. Hong
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Cellular, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Marina Mazur
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gary A. Piazza
- Oncologic Sciences, USA Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
| | - Adam B. Keeton
- Oncologic Sciences, USA Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
| | - E. Lucile White
- Drug Discovery Division, Southern Research Institute, Birmingham, Alabama, United States of America
| | - Lynn Rasmussen
- Drug Discovery Division, Southern Research Institute, Birmingham, Alabama, United States of America
| | - Allan M. Weissman
- Center for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - R. Aldrin Denny
- Worldwide Medicinal Chemistry, Pfizer, Cambridge, Massachusetts, United States of America
| | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Veltman M, Stolarczyk M, Radzioch D, Wojewodka G, De Sanctis JB, Dik WA, Dzyubachyk O, Oravecz T, de Kleer I, Scholte BJ. Correction of lung inflammation in a F508del CFTR murine cystic fibrosis model by the sphingosine-1-phosphate lyase inhibitor LX2931. Am J Physiol Lung Cell Mol Physiol 2016; 311:L1000-L1014. [PMID: 27663991 DOI: 10.1152/ajplung.00298.2016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/19/2016] [Indexed: 01/08/2023] Open
Abstract
Progressive lung disease with early onset is the main cause of mortality and morbidity in cystic fibrosis patients. Here we report a reduction of sphingosine-1-phosphate (S1P) in the lung of unchallenged Cftrtm1EUR F508del CFTR mutant mice. This correlates with enhanced infiltration by inducible nitric oxide synthase (iNOS)-expressing granulocytes, B cells, and T cells. Furthermore, the ratio of macrophage-derived dendritic cells (MoDC) to conventional dendritic cells (cDC) is higher in mutant mouse lung, consistent with unprovoked inflammation. Oral application of a S1P lyase inhibitor (LX2931) increases S1P levels in mutant mouse tissues. This normalizes the lung MoDC/cDC ratio and reduces B and T cell counts. Lung granulocytes are enhanced, but iNOS expression is reduced in this population. Although lung LyC6+ monocytes are enhanced by LX2931, they apparently do not differentiate to MoDC and macrophages. After challenge with bacterial toxins (LPS-fMLP) we observe enhanced levels of proinflammatory cytokines TNF-α, KC, IFNγ, and IL-12 and the inducible mucin MUC5AC in mutant mouse lung, evidence of deficient resolution of inflammation. LX2931 does not prevent transient inflammation or goblet cell hyperplasia after challenge, but it reduces MUC5AC and proinflammatory cytokine levels toward normal values. We conclude that lung pathology in homozygous mice expressing murine F508del CFTR, which represents the most frequent mutation in CF patients, is characterized by abnormal behavior of infiltrating myeloid cells and delayed resolution of induced inflammation. This phenotype can be partially corrected by a S1P lyase inhibitor, providing a rationale for therapeutic targeting of the S1P signaling pathway in CF patients.
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Affiliation(s)
- Mieke Veltman
- Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Danuta Radzioch
- Departments of Medicine and Human Genetics, McGill University, Montreal, Canada
| | - Gabriella Wojewodka
- Departments of Medicine and Human Genetics, McGill University, Montreal, Canada
| | - Juan B De Sanctis
- Faculty of Medicine. Universidad Central de Venezuela, Institute of Immunology, Caracas, Venezuela
| | - Willem A Dik
- Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Oleh Dzyubachyk
- Department of Radiology, Division of Image Processing, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ismé de Kleer
- Department of Pediatrics, Division of Respiratory Medicine, Erasmus MC, Rotterdam, The Netherlands; and.,Laboratory of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Bob J Scholte
- Cell Biology, Erasmus MC, Rotterdam, The Netherlands;
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