2
|
Differential CFTR-Interactome Proximity Labeling Procedures Identify Enrichment in Multiple SLC Transporters. Int J Mol Sci 2022; 23:ijms23168937. [PMID: 36012204 PMCID: PMC9408702 DOI: 10.3390/ijms23168937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins interacting with CFTR and its mutants have been intensively studied using different experimental approaches. These studies provided information on the cellular processes leading to proper protein folding, routing to the plasma membrane, recycling, activation and degradation. Recently, new approaches have been developed based on the proximity labeling of protein partners or proteins in close vicinity and their subsequent identification by mass spectrometry. In this study, we evaluated TurboID- and APEX2-based proximity labeling of WT CFTR and compared the obtained data to those reported in databases. The CFTR-WT interactome was then compared to that of two CFTR (G551D and W1282X) mutants and the structurally unrelated potassium channel KCNK3. The two proximity labeling approaches identified both known and additional CFTR protein partners, including multiple SLC transporters. Proximity labeling approaches provided a more comprehensive picture of the CFTR interactome and improved our knowledge of the CFTR environment.
Collapse
|
3
|
Pankonien I, Quaresma MC, Rodrigues CS, Amaral MD. CFTR, Cell Junctions and the Cytoskeleton. Int J Mol Sci 2022; 23:ijms23052688. [PMID: 35269829 PMCID: PMC8910340 DOI: 10.3390/ijms23052688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/05/2023] Open
Abstract
The multi-organ disease cystic fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, a cAMP regulated chloride (Cl−) and bicarbonate (HCO3−) ion channel expressed at the apical plasma membrane (PM) of epithelial cells. Reduced CFTR protein results in decreased Cl− secretion and excessive sodium reabsorption in epithelial cells, which consequently leads to epithelial dehydration and the accumulation of thick mucus within the affected organs, such as the lungs, pancreas, gastrointestinal (GI) tract, reproductive system and sweat glands. However, CFTR has been implicated in other functions besides transporting ions across epithelia. The rising number of references concerning its association to actin cytoskeleton organization, epithelial cell junctions and extracellular matrix (ECM) proteins suggests a role in the formation and maintenance of epithelial apical basolateral polarity. This review will focus on recent literature (the last 10 years) substantiating the role of CFTR in cell junction formation and actin cytoskeleton organization with its connection to the ECM.
Collapse
|
4
|
Farinha CM, Gentzsch M. Revisiting CFTR Interactions: Old Partners and New Players. Int J Mol Sci 2021; 22:13196. [PMID: 34947992 PMCID: PMC8703571 DOI: 10.3390/ijms222413196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress in CFTR research has led to the therapeutic development of modulators that rescue the basic defect in cystic fibrosis. There is continuous interest in studying CFTR molecular disease mechanisms as not all cystic fibrosis patients have a therapeutic option available. Addressing the basis of the problem by comprehensively understanding the critical molecular associations of CFTR interactions remains key. With the availability of CFTR modulators, there is interest in comprehending which interactions are critical to rescue CFTR and which are altered by modulators or CFTR mutations. Here, the current knowledge on interactions that govern CFTR folding, processing, and stability is summarized. Furthermore, we describe protein complexes and signal pathways that modulate the CFTR function. Primary epithelial cells display a spatial control of the CFTR interactions and have become a common system for preclinical and personalized medicine studies. Strikingly, the novel roles of CFTR in development and differentiation have been recently uncovered and it has been revealed that specific CFTR gene interactions also play an important role in transcriptional regulation. For a comprehensive understanding of the molecular environment of CFTR, it is important to consider CFTR mutation-dependent interactions as well as factors affecting the CFTR interactome on the cell type, tissue-specific, and transcriptional levels.
Collapse
Affiliation(s)
- Carlos M. Farinha
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Martina Gentzsch
- Marsico Lung Institute and Cystic Fibrosis Research Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pediatrics, Division of Pediatric Pulmonology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
5
|
Khodadadian A, Darzi S, Haghi-Daredeh S, Sadat Eshaghi F, Babakhanzadeh E, Mirabutalebi SH, Nazari M. Genomics and Transcriptomics: The Powerful Technologies in Precision Medicine. Int J Gen Med 2020; 13:627-640. [PMID: 32982380 PMCID: PMC7509479 DOI: 10.2147/ijgm.s249970] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022] Open
Abstract
In a clinical trial, people with the same disease can show different responses after treatment with the same drug and exactly under the same conditions. Some of them may improve, some may not show any response, and occasionally side effects may be observed. In other words, people with the same disease process under the same therapeutic conditions may have different responses. Today, some diseases are resistant to conventional (standard) treatment procedures. Why do people with the same disease show different responses to the treatment with the same drug? This is primarily due to differences in molecular pathways (especially genetic variations) associated with the disease. On the other hand, designing and delivery of a new drug is a time-consuming and costly process, so any mistake in any stage of this process can have irreparable consequences for pharmaceutical companies and consumer patients. Therefore, we can achieve more accurate and reliable treatments by acquiring precise insight into different aspects of precision medicine including genomics and transcriptomics. The aim of this paper is to address the role of genomics and transcriptomics in precision medicine.
Collapse
Affiliation(s)
- Ali Khodadadian
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Somaye Darzi
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Saeed Haghi-Daredeh
- Department of Medical Nanotechnology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Farzaneh Sadat Eshaghi
- Department of Medical Genetics, Biotechnology Research Center, International Campus, Shahid Sadoughi University of Science, Yazd, Iran
| | - Emad Babakhanzadeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Yazd Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Majid Nazari
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| |
Collapse
|
6
|
Hutt DM, Loguercio S, Campos AR, Balch WE. A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease. J Mol Biol 2018; 430:2951-2973. [PMID: 29924966 PMCID: PMC6097907 DOI: 10.1016/j.jmb.2018.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention. A comparative analysis of variant-specific proteomics allows us to identify a number of protein interactions contributing to the basic defects associated with F508del- and G551D-CFTR, two of the most common disease-associated variants in the patient population. We demonstrate that a number of these causal interactions are significantly altered in response to treatment with Vx809 and Vx770, small-molecule therapeutics that respectively target the F508del and G551D variants. ProVarA represents the first comparative proteomic analysis among multiple disease-causing mutations, thereby providing a methodological approach that provides a significant advancement to existing proteomic efforts in understanding the impact of variation in CF disease. We posit that the implementation of ProVarA for any familial or somatic mutation will provide a substantial increase in the knowledge base needed to implement a precision medicine-based approach for clinical management of disease.
Collapse
Affiliation(s)
- Darren M Hutt
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Salvatore Loguercio
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomic Core 10901 North Torrey Pines Road, La Jolla CA USA 92037
| | - William E Balch
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- Integrative Structural and Computational Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| |
Collapse
|
7
|
Huguet F, Calvez ML, Benz N, Le Hir S, Mignen O, Buscaglia P, Horgen FD, Férec C, Kerbiriou M, Trouvé P. Function and regulation of TRPM7, as well as intracellular magnesium content, are altered in cells expressing ΔF508-CFTR and G551D-CFTR. Cell Mol Life Sci 2016; 73:3351-73. [PMID: 26874684 PMCID: PMC11108291 DOI: 10.1007/s00018-016-2149-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 01/14/2016] [Accepted: 01/25/2016] [Indexed: 02/03/2023]
Abstract
Cystic fibrosis (CF), one of the most common fatal hereditary disorders, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CFTR gene product is a multidomain adenosine triphosphate-binding cassette (ABC) protein that functions as a chloride (Cl(-)) channel that is regulated by intracellular magnesium [Mg(2+)]i. The most common mutations in CFTR are a deletion of a phenylalanine residue at position 508 (ΔF508-CFTR, 70-80 % of CF phenotypes) and a Gly551Asp substitution (G551D-CFTR, 4-5 % of alleles), which lead to decreased or almost abolished Cl(-) channel function, respectively. Magnesium ions have to be finely regulated within cells for optimal expression and function of CFTR. Therefore, the melastatin-like transient receptor potential cation channel, subfamily M, member 7 (TRPM7), which is responsible for Mg(2+) entry, was studies and [Mg(2+)]i measured in cells stably expressing wildtype CFTR, and two mutant proteins (ΔF508-CFTR and G551D-CFTR). This study shows for the first time that [Mg(2+)]i is decreased in cells expressing ΔF508-CFTR and G551D-CFTR mutated proteins. It was also observed that the expression of the TRPM7 protein is increased; however, membrane localization was altered for both ΔF508del-CFTR and G551D-CFTR. Furthermore, both the function and regulation of the TRPM7 channel regarding Mg(2+) is decreased in the cells expressing the mutated CFTR. Ca(2+) influx via TRPM7 were also modified in cells expressing a mutated CFTR. Therefore, there appears to be a direct involvement of TRPM7 in CF physiopathology. Finally, we propose that the TRPM7 activator Naltriben is a new potentiator for G551D-CFTR as the function of this mutant increases upon activation of TRPM7 by Naltriben.
Collapse
Affiliation(s)
- F Huguet
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France
| | - M L Calvez
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France
- Association G. Saleun, Brest, 29218, France
| | - N Benz
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Association G. Saleun, Brest, 29218, France
| | - S Le Hir
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Laboratoire de Génétique Moléculaire, Hôpital Morvan, C.H.U. Brest, Brest, 29200, France
| | - O Mignen
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France
| | - P Buscaglia
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France
| | - F D Horgen
- Laboratory of Marine Biological Chemistry, Department of Natural Sciences, Hawaii Pacific University, Kaneohe, HI, 96744, USA
| | - C Férec
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France.
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France.
- Laboratoire de Génétique Moléculaire, Hôpital Morvan, C.H.U. Brest, Brest, 29200, France.
- Etablissement Français du Sang - Bretagne, Brest, 29200, France.
| | - M Kerbiriou
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France
- Faculté de Médecine et des sciences de la santé, Université de Bretagne Occidentale, Brest, 29200, France
| | - P Trouvé
- Inserm, UMR1078, 46, rue Félix le Dantec, CS 51819, 29218, Brest Cedex 2, France.
| |
Collapse
|