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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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2
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Hodos RA, Strub MD, Ramachandran S, Meleshkevitch EA, Boudko DY, Bridges RJ, Dudley JT, McCray PB. Integrative chemogenomic analysis identifies small molecules that partially rescue ΔF508-CFTR for cystic fibrosis. CPT Pharmacometrics Syst Pharmacol 2021; 10:500-510. [PMID: 33934548 PMCID: PMC8129714 DOI: 10.1002/psp4.12626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Rare diseases affect 10% of the first-world population, yet over 95% lack even a single pharmaceutical treatment. In the present age of information, we need ways to leverage our vast data and knowledge to streamline therapeutic development and lessen this gap. Here, we develop and implement an innovative informatic approach to identify therapeutic molecules, using the Connectivity Map and LINCS L1000 databases and disease-associated transcriptional signatures and pathways. We apply this to cystic fibrosis (CF), the most common genetic disease in people of northern European ancestry leading to chronic lung disease and reduced lifespan. We selected and tested 120 small molecules in a CF cell line, finding 8 with activity, and confirmed 3 in primary CF airway epithelia. Although chemically diverse, the transcriptional profiles of the hits suggest a common mechanism associated with the unfolded protein response and/or TNFα signaling. This study highlights the power of informatics to help identify new therapies and reveal mechanistic insights while moving beyond target-centric drug discovery.
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Affiliation(s)
- Rachel A. Hodos
- Institute for Next Generation HealthcareMount Sinai School of MedicineNew YorkNYUSA
- Courant Institute for Mathematical SciencesNew York UniversityNew YorkNYUSA
- Present address:
BenevolentAINew YorkNYUSA
| | - Matthew D. Strub
- Department of PediatricsUniversity of IowaCarver College of MedicineIowa CityIAUSA
- Interdisciplinary Graduate Program in GeneticsUniversity of IowaIowa CityIAUSA
| | | | - Ella A. Meleshkevitch
- Department of Physiology and BiophysicsRosalind Franklin UniversityNorth ChicagoILUSA
| | - Dmitri Y. Boudko
- Department of Physiology and BiophysicsRosalind Franklin UniversityNorth ChicagoILUSA
| | - Robert J. Bridges
- Department of Physiology and BiophysicsRosalind Franklin UniversityNorth ChicagoILUSA
| | - Joel T. Dudley
- Institute for Next Generation HealthcareMount Sinai School of MedicineNew YorkNYUSA
| | - Paul B. McCray
- Department of PediatricsUniversity of IowaCarver College of MedicineIowa CityIAUSA
- Interdisciplinary Graduate Program in GeneticsUniversity of IowaIowa CityIAUSA
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3
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Bodas M, Vij N. Adapting Proteostasis and Autophagy for Controlling the Pathogenesis of Cystic Fibrosis Lung Disease. Front Pharmacol 2019; 10:20. [PMID: 30774592 PMCID: PMC6367269 DOI: 10.3389/fphar.2019.00020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Cystic fibrosis (CF), a fatal genetic disorder predominant in the Caucasian population, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (Cftr) gene. The most common mutation is the deletion of phenylalanine from the position-508 (F508del-CFTR), resulting in a misfolded-CFTR protein, which is unable to fold, traffic and retain its plasma membrane (PM) localization. The resulting CFTR dysfunction, dysregulates variety of key cellular mechanisms such as chloride ion transport, airway surface liquid (ASL) homeostasis, mucociliary-clearance, inflammatory-oxidative signaling, and proteostasis that includes ubiquitin-proteasome system (UPS) and autophagy. A collective dysregulation of these key homoeostatic mechanisms contributes to the development of chronic obstructive cystic fibrosis lung disease, instead of the classical belief focused exclusively on ion-transport defect. Hence, therapeutic intervention(s) aimed at rescuing chronic CF lung disease needs to correct underlying defect that mediates homeostatic dysfunctions and not just chloride ion transport. Since targeting all the myriad defects individually could be quite challenging, it will be prudent to identify a process which controls almost all disease-promoting processes in the CF airways including underlying CFTR dysfunction. There is emerging experimental and clinical evidence that supports the notion that impaired cellular proteostasis and autophagy plays a central role in regulating pathogenesis of chronic CF lung disease. Thus, correcting the underlying proteostasis and autophagy defect in controlling CF pulmonary disease, primarily via correcting the protein processing defect of F508del-CFTR protein has emerged as a novel intervention strategy. Hence, we discuss here both the rationale and significant therapeutic utility of emerging proteostasis and autophagy modulating drugs/compounds in controlling chronic CF lung disease, where targeted delivery is a critical factor-influencing efficacy.
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Affiliation(s)
- Manish Bodas
- Department of Medicine, University of Oklahoma, Oklahoma City, OK, United States
| | - Neeraj Vij
- Department of Pediatric Pulmonary Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- 4Dx Limited, Los Angeles, CA, United States
- VIJ Biotech LLC, Baltimore, MD, United States
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Canato S, Santos JD, Carvalho AS, Aloria K, Amaral MD, Matthiesen R, Falcao AO, Farinha CM. Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. Cell Mol Life Sci 2018; 75:4495-4509. [PMID: 30066085 PMCID: PMC11105581 DOI: 10.1007/s00018-018-2896-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 11/28/2022]
Abstract
Misfolded F508del-CFTR, the main molecular cause of the recessive disorder cystic fibrosis, is recognized by the endoplasmic reticulum (ER) quality control (ERQC) resulting in its retention and early degradation. The ERQC mechanisms rely mainly on molecular chaperones and on sorting motifs, whose presence and exposure determine CFTR retention or exit through the secretory pathway. Arginine-framed tripeptides (AFTs) are ER retention motifs shown to modulate CFTR retention. However, the interactions and regulatory pathways involved in this process are still largely unknown. Here, we used proteomic interaction profiling and global bioinformatic analysis to identify factors that interact differentially with F508del-CFTR and F508del-CFTR without AFTs (F508del-4RK-CFTR) as putative regulators of this specific ERQC checkpoint. Using LC-MS/MS, we identified kinesin family member C1 (KIFC1) as a stronger interactor with F508del-CFTR versus F508del-4RK-CFTR. We further validated this interaction showing that decreasing KIFC1 levels or activity stabilizes the immature form of F508del-CFTR by reducing its degradation. We conclude that the current approach is able to identify novel putative therapeutic targets that can be ultimately used to the benefit of CF patients.
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Affiliation(s)
- Sara Canato
- Department of Chemistry and Biochemistry & BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - João D Santos
- Department of Chemistry and Biochemistry & BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Ana S Carvalho
- CEDOC-Chronic Diseases Research Centre, Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana, 1150-082, Lisbon, Portugal
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country UPV/EHU, Barrio Sariena, 48940, Vizcaya, Spain
| | - Margarida D Amaral
- Department of Chemistry and Biochemistry & BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Rune Matthiesen
- CEDOC-Chronic Diseases Research Centre, Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana, 1150-082, Lisbon, Portugal
| | - André O Falcao
- Department of Chemistry and Biochemistry & BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- LASIGE, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Carlos M Farinha
- Department of Chemistry and Biochemistry & BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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Lim SH, Legere EA, Snider J, Stagljar I. Recent Progress in CFTR Interactome Mapping and Its Importance for Cystic Fibrosis. Front Pharmacol 2018; 8:997. [PMID: 29403380 PMCID: PMC5785726 DOI: 10.3389/fphar.2017.00997] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/26/2017] [Indexed: 12/25/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride channel found in secretory epithelia with a plethora of known interacting proteins. Mutations in the CFTR gene cause cystic fibrosis (CF), a disease that leads to progressive respiratory illness and other complications of phenotypic variance resulting from perturbations of this protein interaction network. Studying the collection of CFTR interacting proteins and the differences between the interactomes of mutant and wild type CFTR provides insight into the molecular machinery of the disease and highlights possible therapeutic targets. This mini review focuses on functional genomics and proteomics approaches used for systematic, high-throughput identification of CFTR-interacting proteins to provide comprehensive insight into CFTR regulation and function.
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Affiliation(s)
- Sang Hyun Lim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Jamie Snider
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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Puglia M, Landi C, Gagliardi A, Breslin L, Armini A, Brunetti J, Pini A, Bianchi L, Bini L. The proteome speciation of an immortalized cystic fibrosis cell line: New perspectives on the pathophysiology of the disease. J Proteomics 2018; 170:28-42. [DOI: 10.1016/j.jprot.2017.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/01/2017] [Accepted: 09/25/2017] [Indexed: 01/04/2023]
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Calumenin contributes to ER-Ca 2+ homeostasis in bronchial epithelial cells expressing WT and F508del mutated CFTR and to F508del-CFTR retention. Cell Calcium 2017; 62:47-59. [PMID: 28189267 DOI: 10.1016/j.ceca.2017.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 11/22/2022]
Abstract
Cystic Fibrosis (CF) is the most frequent fatal genetic disease in Caucasian populations. Mutations in the chloride channel CF Transmembrane Conductance Regulator (CFTR) gene are responsible for functional defects of the protein and multiple associated dysregulations. The most common mutation in patients with CF, F508del-CFTR, causes defective CFTR protein folding. Thus minimal levels of the receptor are expressed at the cell surface as the mutated CFTR is retained in the endoplasmic reticulum (ER) where it correlates with defective calcium (Ca2+) homeostasis. In this study, we discovered that the Ca2+ binding protein Calumenin (CALU) is a key regulator in the maintenance of ER-Ca2+ calcium homeostasis in both wild type and F508del-CFTR expressing cells. Calumenin modulates SERCA pump activity without drastically affecting ER-Ca2+ concentration. In addition, reducing Calumenin expression in CF cells results in a partial restoration of CFTR activity, highlighting a potential function of Calumenin in CFTR maturation. These findings demonstrate a pivotal role for Calumenin in CF cells, providing insights into how modulation of Calumenin expression or activity may be used as a potential therapeutic tool to correct defects in F508del-CFTR.
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Yan C, Lang Q, Huijuan L, Jiang X, Ming Y, Huaqin S, Wenming X. CFTR Deletion in Mouse Testis Induces VDAC1 Mediated Inflammatory Pathway Critical for Spermatogenesis. PLoS One 2016; 11:e0158994. [PMID: 27483469 PMCID: PMC4970767 DOI: 10.1371/journal.pone.0158994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/24/2016] [Indexed: 11/22/2022] Open
Abstract
Cystic fibrosis is the most common genetic disease among Caucasians and affects tissues including lung, pancreas and reproductive tracts. It has been shown that Endoplasmic Reticulum (ER) stress and heat shock response are two major deregulated functional modules related to CFTR dysfunction. To identify the impact of CFTR deletion during spermatogenesis, we examined the expression of spermiogenesis-related genes in the testis of CFTR mutant mice (CF mice). We confirmed expression changes of MSY2, a germ cell specific RNA binding protein, resulting from deletion of CFTR in testis. Furthermore, real time PCR and Western blot results showed that an inflammatory response was activated in CF mice testis, as reflected by the altered expression of cytokines. We demonstrate for the first time that expression of MSY2 is decreased in CF mice. Our results suggest that CFTR deletion in testis influences inflammatory responses and these features are likely to be due to the unique environment of the seminiferous tubule during the spermatogenesis process. The current study also suggests avenues to understand the pathophysiology of CFTR during spermatogenesis and provides targets for the possible treatment of CFTR-related infertility.
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Affiliation(s)
- Chen Yan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related disease of Women and Children, Ministry of Education (Sichuan University), West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qin Lang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Liao Huijuan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related disease of Women and Children, Ministry of Education (Sichuan University), West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xie Jiang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Third People’s Hospital of Chengdu, the Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, Sichuan, China
| | - Yang Ming
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related disease of Women and Children, Ministry of Education (Sichuan University), West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Sun Huaqin
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related disease of Women and Children, Ministry of Education (Sichuan University), West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xu Wenming
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related disease of Women and Children, Ministry of Education (Sichuan University), West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- * E-mail:
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Averna M, Bavestrello M, Cresta F, Pedrazzi M, De Tullio R, Minicucci L, Sparatore B, Salamino F, Pontremoli S, Melloni E. Abnormal activation of calpain and protein kinase Cα promotes a constitutive release of matrix metalloproteinase 9 in peripheral blood mononuclear cells from cystic fibrosis patients. Arch Biochem Biophys 2016; 604:103-12. [PMID: 27349634 DOI: 10.1016/j.abb.2016.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/25/2016] [Accepted: 06/23/2016] [Indexed: 12/17/2022]
Abstract
Matrix metalloproteinase 9 (MMP9) is physiologically involved in remodeling the extracellular matrix components but its abnormal release has been observed in several human pathologies. We here report that peripheral blood mononuclear cells (PBMCs), isolated from cystic fibrosis (CF) patients homozygous for F508del-cystic fibrosis transmembrane conductance regulator (CFTR), express constitutively and release at high rate MMP9 due to the alteration in their intracellular Ca(2+) homeostasis. This spontaneous and sustained MMP9 secretion may contribute to the accumulation of this protease in fluids of CF patients. Conversely, in PBMCs isolated from healthy donors, expression and secretion of MMP9 are undetectable but can be evoked, after 12 h of culture, by paracrine stimulation which also promotes an increase in [Ca(2+)]i. We also demonstrate that in both CF and control PBMCs the Ca(2+)-dependent MMP9 secretion is mediated by the concomitant activation of calpain and protein kinase Cα (PKCα), and that MMP9 expression involves extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) phosphorylation. Our results are supported by the fact that either the inhibition of Ca(2+) entry or chelation of [Ca(2+)]i as well as the inhibition of single components of the signaling pathway or the restoration of CFTR activity all promote the reduction of MMP9 secretion.
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Affiliation(s)
- Monica Averna
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy.
| | - Margherita Bavestrello
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Federico Cresta
- Cystic Fibrosis Pediatric Center, G. Gaslini Hospital, Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Science Mother and Child, University of Genova, Genova, Italy
| | - Marco Pedrazzi
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Roberta De Tullio
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy; Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Laura Minicucci
- Cystic Fibrosis Pediatric Center, G. Gaslini Hospital, Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Science Mother and Child, University of Genova, Genova, Italy
| | - Bianca Sparatore
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy; Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Franca Salamino
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy; Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Sandro Pontremoli
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy
| | - Edon Melloni
- Department of Experimental Medicine (DIMES) - Biochemistry Section, Viale Benedetto XV, 1, 16132, Genova, Italy; Center of Excellence for Biomedical Research (CEBR), University of Genova, Viale Benedetto XV, 1, 16132, Genova, Italy
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Personalized Medicine in Respiratory Disease: Role of Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:115-46. [PMID: 26827604 DOI: 10.1016/bs.apcsb.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Respiratory diseases affect humanity globally, with chronic lung diseases (e.g., asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, among others) and lung cancer causing extensive morbidity and mortality. These conditions are highly heterogeneous and require an early diagnosis. However, initial symptoms are nonspecific, and the clinical diagnosis is made late frequently. Over the last few years, personalized medicine has emerged as a medical care approach that uses novel technology aiming to personalize treatments according to the particular patient's medical needs. This review highlights the contributions of proteomics toward the understanding of personalized medicine in respiratory disease and its potential applications in the clinic.
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11
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Shen M, Wang L, Guo X, Xue Q, Huo C, Li X, Fan L, Wang X. A novel endoplasmic reticulum stress‑induced apoptosis model using tunicamycin in primary cultured neonatal rat cardiomyocytes. Mol Med Rep 2015; 12:5149-54. [PMID: 26151415 DOI: 10.3892/mmr.2015.4040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 05/06/2015] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is key in the development of cardiovascular diseases. However, there is a lack of a systemic ER stress‑induced cardiomyocyte apoptosis model. In the present study, primary cultured neonatal rat cardiomyocytes were exposed to tunicamycin. Cell viability was determined by an MTT assay, and cell damage was detected by a lactose dehydrogenase assay. Flow cytometry was used and the activity of caspase‑3 was analyzed in order to measure apoptosis. Reverse transcription-quantitative polymerase chain reaction and western blotting were used to examine the expression of glucose‑regulated protein 78‑kDa (GRP78) and C/EBP homologous protein (CHOP). As a result, tunicamycin significantly increased cardiomyocyte injury, which occurred in a time- and concentration‑dependent manner. In addition, tunicamycin treatment resulted in apoptosis of cardiomyocytes. Molecularly, tunicamycin (100 ng/ml) increased the levels of GRP78 and CHOP 6 h after administration. In addition, GRP78 and CHOP reached maximum mRNA and protein levels 24 h after administration. In conclusion, the results implicate that the tunicamycin‑induced ER stress‑induced apoptotic model was successfully constructed in cultured neonatal rat cardiomyocytes. A 100 ng/ml concentration of tunicamycin was selected, and MTT, LDH release and flow cytometry assay was at 72 h. In addition, GRP78 and GRP94 were detected 24 h following administration. The results of the present study indicate a novel experimental basis for the investigation of ERS-induced cardiac apoptosis.
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Affiliation(s)
- Mingzhi Shen
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xiaowang Guo
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Qiao Xue
- Department of Cardiology, Hainan Branch of PLA General Hospital, Sanya, Hainan 572013, P.R. China
| | - Cong Huo
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xing Li
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Li Fan
- Department of Geriatric Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Xiaoming Wang
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Lu WJ, Saxena N, Luk JM, Kaul SC, Wadhwa R. Circulating mortalin autoantibody--a new serological marker of liver cirrhosis. Cell Stress Chaperones 2015; 20:715-9. [PMID: 25905813 PMCID: PMC4463917 DOI: 10.1007/s12192-015-0592-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/02/2015] [Accepted: 04/10/2015] [Indexed: 12/14/2022] Open
Abstract
Mortalin is a stress chaperone belonging to the Hsp70 family of proteins. Frequently enriched in cancers, it is a multifunctional protein and regulates cell proliferation, apoptosis, mitochondrial functions, and the activity of tumor suppressor protein p53. In the present study, we investigated circulating mortalin and its autoantibody in normal, cirrhosis, and cancerous liver. We found that although mortalin is enriched in liver cancer cells and tumors, it is not detected in the serum of either the liver cirrhosis or cancer patients. In contrast, mortalin autoantibody was detected in patients' sera and showed significant correlation with the occurrence of cirrhosis. It is suggested as a potential noninvasive marker for liver cirrhosis.
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Affiliation(s)
- Wen-Jing Lu
- />Asian Liver Center, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305 USA
- />Department of Surgery, Queen Mary Hospital, University of Hong Kong, Pokfulam, Hong Kong
| | - Nishant Saxena
- />Drug Discovery and Assets Innovation, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - John M. Luk
- />Department of Surgery, Queen Mary Hospital, University of Hong Kong, Pokfulam, Hong Kong
| | - Sunil C. Kaul
- />Drug Discovery and Assets Innovation, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- />National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305 8562 Japan
| | - Renu Wadhwa
- />Drug Discovery and Assets Innovation, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- />National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305 8562 Japan
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Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl 2015; 9:134-46. [DOI: 10.1002/prca.201400122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/27/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sheemal Shanista Kumar
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Jashanpreet Kaur
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | | | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Mark P. Molloy
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
- Australian Proteome Analysis Facility; Macquarie University; Sydney Australia
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14
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Pranke IM, Sermet-Gaudelus I. Biosynthesis of cystic fibrosis transmembrane conductance regulator. Int J Biochem Cell Biol 2014; 52:26-38. [DOI: 10.1016/j.biocel.2014.03.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/19/2014] [Accepted: 03/20/2014] [Indexed: 01/19/2023]
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15
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Rauniyar N, Gupta V, Balch WE, Yates JR. Quantitative proteomic profiling reveals differentially regulated proteins in cystic fibrosis cells. J Proteome Res 2014; 13:4668-75. [PMID: 24818864 PMCID: PMC4224989 DOI: 10.1021/pr500370g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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The
most prevalent cause of cystic fibrosis (CF) is the deletion
of a phenylalanine residue at position 508 in CFTR (ΔF508-CFTR)
protein. The mutated protein fails to fold properly, is retained in
the endoplasmic reticulum via the action of molecular chaperones,
and is tagged for degradation. In this study, the differences in protein
expression levels in CF cell models were assessed using a systems
biology approach aided by the sensitivity of MudPIT proteomics. Analysis
of the differential proteome modulation without a priori hypotheses
has the potential to identify markers that have not yet been documented.
These may also serve as the basis for developing new diagnostic and
treatment modalities for CF. Several novel differentially expressed
proteins observed in our study are likely to play important roles
in the pathogenesis of CF and may serve as a useful resource for the
CF scientific community.
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Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, ‡Department of Cell and Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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16
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Santucci R, Sinibaldi F, Patriarca A, Santucci D, Fiorucci L. Misfolded proteins and neurodegeneration: role of non-native cytochrome c in cell death. Expert Rev Proteomics 2014; 7:507-17. [DOI: 10.1586/epr.10.50] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Ciavardelli D, D'Orazio M, Pieroni L, Consalvo A, Rossi C, Sacchetta P, Di Ilio C, Battistoni A, Urbani A. Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells. MOLECULAR BIOSYSTEMS 2013; 9:1117-26. [DOI: 10.1039/c3mb25594h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Blohmke CJ, Mayer ML, Tang AC, Hirschfeld AF, Fjell CD, Sze MA, Falsafi R, Wang S, Hsu K, Chilvers MA, Hogg JC, Hancock REW, Turvey SE. Atypical activation of the unfolded protein response in cystic fibrosis airway cells contributes to p38 MAPK-mediated innate immune responses. THE JOURNAL OF IMMUNOLOGY 2012; 189:5467-75. [PMID: 23105139 DOI: 10.4049/jimmunol.1103661] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Inflammatory lung disease is the major cause of morbidity and mortality in cystic fibrosis (CF); understanding what produces dysregulated innate immune responses in CF cells will be pivotal in guiding the development of novel anti-inflammatory therapies. To elucidate the molecular mechanisms that mediate exaggerated inflammation in CF following TLR signaling, we profiled global gene expression in immortalized human CF and non-CF airway cells at baseline and after microbial stimulation. Using complementary analysis methods, we observed a signature of increased stress levels in CF cells, specifically characterized by endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and MAPK signaling. Analysis of ER stress responses revealed an atypical induction of the UPR, characterized by the lack of induction of the PERK-eIF2α pathway in three complementary model systems: immortalized CF airway cells, fresh CF blood cells, and CF lung tissue. This atypical pattern of UPR activation was associated with the hyperinflammatory phenotype in CF cells, as deliberate induction of the PERK-eIF2α pathway with salubrinal attenuated the inflammatory response to both flagellin and Pseudomonas aeruginosa. IL-6 production triggered by ER stress and microbial stimulation were both dependent on p38 MAPK activity, suggesting a molecular link between both signaling events. These data indicate that atypical UPR activation fails to resolve the ER stress in CF and sensitizes the innate immune system to respond more vigorously to microbial challenge. Strategies to restore ER homeostasis and normalize the UPR activation profile may represent a novel therapeutic approach to minimize lung-damaging inflammation in CF.
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Affiliation(s)
- Christoph J Blohmke
- Department of Paediatrics, BC Children's Hospital and Child & Family Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4
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19
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Teng L, Kerbiriou M, Taiya M, Le Hir S, Mignen O, Benz N, Trouvé P, Férec C. Proteomic identification of calumenin as a G551D-CFTR associated protein. PLoS One 2012; 7:e40173. [PMID: 22768251 PMCID: PMC3387016 DOI: 10.1371/journal.pone.0040173] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 06/06/2012] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal autosomal recessive disease in the Caucasian population. It is due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. To date, over 1910 mutations have been identified in the CFTR gene. Among these mutations, the CF-causing missense mutation G551D-CFTR (approx. 5% of cases) encodes for a CFTR chloride channel with normal expression on the cell surface. Nevertheless, it is associated with severe disease due to its altered channel activation. The aim of the present study was to identify specific interacting proteins of G551D-CFTR. Co-immunoprecipitated proteins with G551D-CFTR were resolved by 2D-gel electrophoresis (2-DE). Mass Spectrometry revealed that calumenin was present in the protein complex linked to G551D-CFTR. Despite its basal expression was not modified in G551D-CFTR expressing cells when compared to Wt-CFTR expressing cells, it was more abundant in the G551D-CFTR complex detected by immunoprecipitation. The calumenin-CFTR interaction was also shown by Surface Plasmon Resonance and further confirmed by computational analysis of the predicted calumenin’s partners. Because in our cellular model calumenin was found in the endoplasmic reticulum (ER) by immunofluorescence experiments, we suggest that calumenin is likely involved in the mutated CFTR’s maturation. In conclusion, we showed for the first time that calumenin binds to CFTR and that it is increased in the G551D-CFTR complex. We suggest that it may be involved in the physiopathology of G551D-CFTR and that G551D-CFTR may follow a specific maturation and trafficking pathway. We also hypothesize that UPR may be triggered independently of the retention of G551D-CFTR in the ER because Grp78/Bip expression is increased in the cells. Finally, we propose here that Calumenin is a new CFTR chaperone.
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Affiliation(s)
- Ling Teng
- Inserm, UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Médecine et des sciences de la santé, Brest, France
| | - Mathieu Kerbiriou
- Inserm, UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Médecine et des sciences de la santé, Brest, France
| | - Mehdi Taiya
- Université de Bretagne Occidentale, Service commun de spectrométrie de masse, Brest, France
| | - Sophie Le Hir
- Inserm, UMR1078, Brest, France
- C.H.R.U. Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Olivier Mignen
- Inserm, UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Médecine et des sciences de la santé, Brest, France
| | - Nathalie Benz
- Inserm, UMR1078, Brest, France
- Association de Biogénétique Gaëtan Salaün, Brest, France
| | - Pascal Trouvé
- Inserm, UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Médecine et des sciences de la santé, Brest, France
- * E-mail: (PT); (CF)
| | - Claude Férec
- Inserm, UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Médecine et des sciences de la santé, Brest, France
- C.H.R.U. Morvan, Laboratoire de Génétique Moléculaire, Brest, France
- Etablissement Français du Sang, Brest, France
- * E-mail: (PT); (CF)
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20
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Alexandre BM, Charro N, Blonder J, Lopes C, Azevedo P, Bugalho de Almeida A, Chan KC, Prieto DA, Issaq H, Veenstra TD, Penque D. Profiling the erythrocyte membrane proteome isolated from patients diagnosed with chronic obstructive pulmonary disease. J Proteomics 2012; 76 Spec No.:259-69. [PMID: 22538302 DOI: 10.1016/j.jprot.2012.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/27/2012] [Accepted: 04/07/2012] [Indexed: 11/28/2022]
Abstract
Structural and metabolic alterations in erythrocytes play an important role in the pathophysiology of Chronic Obstructive Pulmonary Disease (COPD). Whether these dysfunctions are related to the modulation of erythrocyte membrane proteins in patients diagnosed with COPD remains to be determined. Herein, a comparative proteomic profiling of the erythrocyte membrane fraction isolated from peripheral blood of smokers diagnosed with COPD and smokers with no COPD was performed using differential (16)O/(18)O stable isotope labeling. A total of 219 proteins were quantified as being significantly differentially expressed within the erythrocyte membrane proteomes of smokers with COPD and healthy smokers. Functional pathway analysis showed that the most enriched biofunctions were related to cell-to-cell signaling and interaction, hematological system development, immune response, oxidative stress and cytoskeleton. Chorein (VPS13A), a cytoskeleton related protein whose defects had been associated with the presence of cell membrane deformation of circulating erythrocytes was found to be down-regulated in the membrane fraction of erythrocytes obtained from COPD patients. Methemoglobin reductase (CYB5R3) was also found to be underexpressed in these cells, suggesting that COPD patients may be at higher risk for developing methemoglobinemia. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Bruno M Alexandre
- Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge (INSA-IP), Lisboa, Portugal
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21
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Kowluru A, Klumpp S, Krieglstein J. Protein histidine [de]phosphorylation in insulin secretion: abnormalities in models of impaired insulin secretion. Naunyn Schmiedebergs Arch Pharmacol 2011; 384:383-90. [PMID: 21626002 DOI: 10.1007/s00210-011-0616-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 02/18/2011] [Indexed: 12/20/2022]
Abstract
In the majority of cell types, including the islet β-cell, transduction of extracellular signals involves ligand binding to a receptor, often followed by the activation G proteins and their effector modules. The islet β-cell is unusual in that glucose lacks an extracellular receptor. Instead, events consequent to glucose metabolism promote insulin secretion via the generation of diffusible second messengers and mobilization of calcium. A selective increase in intracellular calcium has been shown to regulate the phosphorylation status key islet proteins thereby facilitating insulin secretion. In addition to classical protein kinases [e.g., protein kinases A and C], recent studies from our laboratory have focused on the expression and function of various forms of NDPK/nm23-like histidine kinases in clonal β-cells, normal rodent, and human islets. Further, we recently reported localization of a cytosolic protein histidine phosphatase [PHP] in INS 832/13 cells, normal rat islets, and human islets. siRNA-mediated knock down of nm23-H1 and PHP in insulin-secreting INS 832/13 cells significantly attenuated glucose-induced insulin secretion. We also observed significant alterations in the expression and function of nm23-H1/PHP in β-cells chronically exposed to elevated levels of glucose and saturated fatty acids, such as palmitate (i.e., glucolipotoxicity). Similar changes were also noted in islets from the Goto-Kakizaki and Zucker Diabetic Fatty rats, two known models for type 2 diabetes. It is concluded that protein histidine phosphorylation-dephosphorylation cycles play novel regulatory roles in G protein-mediated physiological insulin secretion and that abnormalities in this signaling axis lead to impaired insulin secretion in glucolipotoxicity and type 2 diabetes.
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Affiliation(s)
- Anjaneyulu Kowluru
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, John D. Dingell VA Medical Center, Detroit, MI 48201, USA.
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22
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Signaling pathways of proteostasis network unraveled by proteomic approaches on the understanding of misfolded protein rescue. Methods Enzymol 2011. [PMID: 21329803 DOI: 10.1016/b978-0-12-385928-0.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Attempts to promote normal processing and function of F508del-CFTR, the most common mutant in cystic fibrosis (CF), have been described as potential therapeutic strategies in the management of this disease. Here we described the proteomic approaches, namely two-dimensional electrophoresis (2DE), mass spectrometry (MS), and bioinformatics tools used in our recent studies to gain insight into the proteins potentially involved in low-temperature or mutagenic treatment-induced rescue process of F508del-CFTR. The proteins identified are part of the proteostasis network, such as the unfolded protein response (UPR) signaling pathways that may regulate the processing of CF transmembrane conductance regulator (CFTR) through the folding and trafficking progression. The complete characterization of these signaling pathways and their regulators in CF will certainly contribute to the development of novel therapeutic strategies against CF.
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23
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Balch WE, Yates JR. Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis. Methods Mol Biol 2011; 742:227-247. [PMID: 21547736 DOI: 10.1007/978-1-61779-120-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.
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Affiliation(s)
- William E Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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24
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Henderson MJ, Singh OV, Zeitlin PL. Applications of proteomic technologies for understanding the premature proteolysis of CFTR. Expert Rev Proteomics 2010; 7:473-86. [PMID: 20653504 DOI: 10.1586/epr.10.42] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which encodes an ATP-dependent anion channel. Disease-causing mutations can affect channel biogenesis, trafficking or function, and result in reduced ion transport at the apical surface of many tissues. The most common CFTR mutation is a deletion of phenylalanine at position 508 (DeltaF508), which results in a misfolded protein that is prematurely targeted for degradation. This article focuses on how proteomic approaches have been utilized to explore the mechanisms of premature proteolysis in CF. Additionally, we emphasize the potential for proteomic-based technologies in expanding our understanding of CF pathophysiology and therapeutic approaches.
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Affiliation(s)
- Mark J Henderson
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
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25
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Collawn JF, Fu L, Bebok Z. Targets for cystic fibrosis therapy: proteomic analysis and correction of mutant cystic fibrosis transmembrane conductance regulator. Expert Rev Proteomics 2010; 7:495-506. [PMID: 20653506 DOI: 10.1586/epr.10.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Proteomic analysis has proved to be an important tool for understanding the complex nature of genetic disorders, such as cystic fibrosis (CF), by defining the cellular protein environment (proteome) associated with wild-type and mutant proteins. Proteomic screens identified the proteome of CF transmembrane conductance regulator (CFTR), and provided fundamental information to studies designed for understanding the crucial components of physiological CFTR function. Simultaneously, high-throughput screens for small-molecular correctors of CFTR mutants provided promising candidates for therapy. The majority of CF cases are caused by nucleotide deletions (DeltaF508 CFTR; >75%), resulting in CFTR misfolding, or insertion of premature termination codons ( approximately 10%), leading to unstable mRNA and reduced levels of truncated dysfunctional CFTR. In this article, we review recent results of proteomic screens, developments in identifying correctors for the most frequent CFTR mutants, and comment on how integration of the knowledge gained from these studies may aid in finding a cure for CF and a number of other genetic disorders.
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Affiliation(s)
- James F Collawn
- University of Alabama at Birmingham, Department of Cell Biology, Birmingham, AL, USA.
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26
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Gomes-Alves P, Penque D. Proteomics uncovering possible key players in F508del-CFTR processing and trafficking. Expert Rev Proteomics 2010; 7:487-94. [PMID: 20653505 DOI: 10.1586/epr.10.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The achievement and maintenance of a protein native conformation is a very complex cellular process involving a multitude of key factors whose contribution to a successful folding remains to be elucidated. On top of this, it is known that correct folding is crucial for proteins to play their normal role and, consequently, for the maintenance of cellular homeostasis or proteostasis. If the folding process is affected, the protein is unable to achieve its native conformation, compromising its life and function, and a pathological condition may arise. Protein-misfolding diseases are characterized by either formation of protein aggregates that are toxic to the cell (gain-of-toxic-function diseases) or by an incorrect processing of proteins, which leads to a deficiency in protein activity (loss-of-function diseases). In this article we have focused on proteomics advances in the molecular knowledge of protein-misfolding diseases with direct impact on possible key players in F508del-CFTR processing and trafficking.
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Affiliation(s)
- Patrícia Gomes-Alves
- Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge (INSA, I.P.), Av. Padre Cruz, Lisboa, Portugal
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27
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Supramolecular organizations in the aerobic respiratory chain of Escherichia coli. Biochimie 2010; 93:418-25. [PMID: 21040753 DOI: 10.1016/j.biochi.2010.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 10/20/2010] [Indexed: 12/26/2022]
Abstract
The organization of respiratory chain complexes in supercomplexes has been shown in the mitochondria of several eukaryotes and in the cell membranes of some bacteria. These supercomplexes are suggested to be important for oxidative phosphorylation efficiency and to prevent the formation of reactive oxygen species. Here we describe, for the first time, the identification of supramolecular organizations in the aerobic respiratory chain of Escherichia coli, including a trimer of succinate dehydrogenase. Furthermore, two heterooligomerizations have been shown: one resulting from the association of the NADH:quinone oxidoreductases NDH-1 and NDH-2, and another composed by the cytochrome bo(3) quinol:oxygen reductase, cytochrome bd quinol:oxygen reductase and formate dehydrogenase (fdo). These results are supported by blue native-electrophoresis, mass spectrometry and kinetic data of wild type and mutant E . coli strains.
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28
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Charro N, Hood BL, Faria D, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Couto FM, Conrads TP, Penque D. Serum proteomics signature of cystic fibrosis patients: a complementary 2-DE and LC-MS/MS approach. J Proteomics 2010; 74:110-26. [PMID: 20950718 DOI: 10.1016/j.jprot.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/17/2010] [Accepted: 10/05/2010] [Indexed: 01/01/2023]
Abstract
Complementary 2D-PAGE and 'shotgun' LC-MS/MS approaches were combined to identify medium and low-abundant proteins in sera of Cystic Fibrosis (CF) patients (mild or severe pulmonary disease) in comparison with healthy CF-carrier and non-CF carrier individuals aiming to gain deeper insights into the pathogenesis of this multifactorial genetic disease. 78 differentially expressed spots were identified from 2D-PAGE proteome profiling yielding 28 identifications and postulating the existence of post-translation modifications (PTM). The 'shotgun' approach highlighted altered levels of proteins actively involved in CF: abnormal tissue/airway remodeling, protease/antiprotease imbalance, innate immune dysfunction, chronic inflammation, nutritional imbalance and Pseudomonas aeruginosa colonization. Members of the apolipoproteins family (VDBP, ApoA-I, and ApoB) presented gradually lower expression from non-CF to CF-carrier individuals and from those to CF patients, results validated by an independent assay. The multifunctional enzyme NDKB was identified only in the CF group and independently validated by WB. Its functions account for ion sensor in epithelial cells, pancreatic secretion, neutrophil-mediated inflammation and energy production, highlighting its physiological significance in the context of CF. Complementary proteomics-based approaches are reliable tools to reveal pathways and circulating proteins actively involved in a heterogeneous disease such as CF.
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Affiliation(s)
- Nuno Charro
- Laboratório de Proteómica, Departamento de Genética, INSA, I.P., Lisboa, Portugal
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