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Zemanick ET, Rosas-Salazar C. The Role of the Microbiome in Pediatric Respiratory Diseases. Clin Chest Med 2024; 45:587-597. [PMID: 39069323 DOI: 10.1016/j.ccm.2024.02.026] [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] [Indexed: 07/30/2024]
Abstract
Numerous studies have examined the role of the microbiome and microbiome-based therapeutics in many childhood airway and lung diseases. In this narrative review, the authors first give a brief overview of the current methods used in microbiome research. The authors then review the literature linking the microbiome with (1) early-life acute respiratory infections due to respiratory syncytial virus, (2) childhood asthma onset, (3) cystic fibrosis, and (4) bronchopulmonary dysplasia, focusing on recent studies that have used culture-independent methods to characterize the respiratory or gut microbiome in the pediatric population.
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Affiliation(s)
- Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 East 16th Avenue, B-395, Aurora, CO 80045, USA
| | - Christian Rosas-Salazar
- Department of Pediatrics, Vanderbilt University Medical Center and Monroe Carell Jr. Children's Hospital at Vanderbilt, 2200 Children's Way, Doctors' Office Tower, Suite 11215, Nashville, TN 37232, USA.
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2
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Bae H, Kim BR, Jung S, Le J, van der Heide D, Yu W, Park SH, Hilkin BM, Gansemer ND, Powers LS, Kang T, Meyerholz DK, Schuster VL, Jang C, Welsh MJ. Arteriovenous metabolomics in pigs reveals CFTR regulation of metabolism in multiple organs. J Clin Invest 2024; 134:e174500. [PMID: 38743489 PMCID: PMC11213515 DOI: 10.1172/jci174500] [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: 08/04/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), a multiorgan disease that is characterized by diverse metabolic defects. However, other than specific CFTR mutations, the factors that influence disease progression and severity remain poorly understood. Aberrant metabolite levels have been reported, but whether CFTR loss itself or secondary abnormalities (infection, inflammation, malnutrition, and various treatments) drive metabolic defects is uncertain. Here, we implemented comprehensive arteriovenous metabolomics in newborn CF pigs, and the results revealed CFTR as a bona fide regulator of metabolism. CFTR loss impaired metabolite exchange across organs, including disruption of lung uptake of fatty acids, yet enhancement of uptake of arachidonic acid, a precursor of proinflammatory cytokines. CFTR loss also impaired kidney reabsorption of amino acids and lactate and abolished renal glucose homeostasis. These and additional unexpected metabolic defects prior to disease manifestations reveal a fundamental role for CFTR in controlling multiorgan metabolism. Such discovery informs a basic understanding of CF, provides a foundation for future investigation, and has implications for developing therapies targeting only a single tissue.
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Affiliation(s)
- Hosung Bae
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
| | - Bo Ram Kim
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Howard Hughes Medical Institute, University of Iowa, Iowa City, Iowa, USA
| | - Sunhee Jung
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
| | - Johnny Le
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
| | | | - Wenjie Yu
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Howard Hughes Medical Institute, University of Iowa, Iowa City, Iowa, USA
| | - Sang Hee Park
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
| | - Brieanna M. Hilkin
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Nicholas D. Gansemer
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Linda S. Powers
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Taekyung Kang
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
| | - David K. Meyerholz
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Victor L. Schuster
- Department of Internal Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California – Irvine, Irvine, California, USA
- Center for Complex Biological Systems and
- Center for Epigenetics and Metabolism, University of California – Irvine, Irvine, California, USA
| | - Michael J. Welsh
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Howard Hughes Medical Institute, University of Iowa, Iowa City, Iowa, USA
- Department of Molecular Physiology and Biophysics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, Iowa, USA
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3
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Chu T, Cui J, Sun L, Zhang X, Sun L, Tong J, Li L, Xiao Y, Xu L, Zhang L, Song Y. The disordered extracellular matrix landscape induced endometrial fibrosis of sheep: A multi-omics integrative analysis. Int J Biol Macromol 2024; 265:130845. [PMID: 38503376 DOI: 10.1016/j.ijbiomac.2024.130845] [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: 01/08/2024] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Endometrial fibrosis leads to the destruction of endometrial function and affects reproductive performance. However, mechanisms underlying the development of endometrial fibrosis in sheep remain unclear. We use transcriptomic, proteomic, and metabolomic studies to reveal the formation mechanisms of endometrial fibrosis. The results showed that the fibrotic endometrial tissue phenotype presented fewer glands, accompanied by collagen deposition. Transcriptomic results indicated alterations in genes associated with the synthesis and degradation of extracellular matrix components, which alter metabolite homeostasis, especially in glycerophospholipid metabolism. Moreover, differentially expressed metabolites may play regulatory roles in key metabolic processes during fibrogenesis, including protein digestion and absorption, and amino acid synthesis. Affected by the aberrant genes, protein levels related to the extracellular matrix components were altered. In addition, based on Kyoto Encyclopedia of Genes and Genomes analysis of differentially expressed genes, metabolites and proteins, amino acid biosynthesis, glutathione, glycerophospholipid, arginine and proline metabolism, and cell adhesion are closely associated with fibrogenesis. Finally, we analyzed the dynamic changes in serum differential metabolites at different time points during fibrosis. Taken together, fibrosis development is related to metabolic obstacles in extracellular matrix synthesis and degradation triggered by disturbed gene and protein levels.
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Affiliation(s)
- Tingting Chu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jiuzeng Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lei Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaoyu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Le Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jiashun Tong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Long Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Yuhang Xiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Liang Xu
- Weinan Agricultural Product Quality and Safety Inspection and Testing Center, PR China
| | - Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Iazzi M, Sadeghi S, Gupta GD. A Proteomic Survey of the Cystic Fibrosis Transmembrane Conductance Regulator Surfaceome. Int J Mol Sci 2023; 24:11457. [PMID: 37511222 PMCID: PMC10380767 DOI: 10.3390/ijms241411457] [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: 06/07/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The aim of this review article is to collate recent contributions of proteomic studies to cystic fibrosis transmembrane conductance regulator (CFTR) biology. We summarize advances from these studies and create an accessible resource for future CFTR proteomic efforts. We focus our attention on the CFTR interaction network at the cell surface, thus generating a CFTR 'surfaceome'. We review the main findings about CFTR interactions and highlight several functional categories amongst these that could lead to the discovery of potential biomarkers and drug targets for CF.
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Affiliation(s)
| | | | - Gagan D. Gupta
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada
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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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Santos L, Nascimento R, Duarte A, Railean V, Amaral MD, Harrison PT, Gama-Carvalho M, Farinha CM. Mutation-class dependent signatures outweigh disease-associated processes in cystic fibrosis cells. Cell Biosci 2023; 13:26. [PMID: 36759923 PMCID: PMC9912517 DOI: 10.1186/s13578-023-00975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The phenotypic heterogeneity observed in Cystic Fibrosis (CF) patients suggests the involvement of other genes, besides CFTR. Here, we combined transcriptome and proteome analysis to understand the global gene expression patterns associated with five prototypical CFTR mutations. RESULTS Evaluation of differentially expressed genes and proteins unveiled common and mutation-specific changes revealing functional signatures that are much more associated with the specific molecular defects associated with each mutation than to the CFTR loss-of-function phenotype. The combination of both datasets revealed that mutation-specific detected translated-transcripts (Dtt) have a high level of consistency. CONCLUSIONS This is the first combined transcriptomic and proteomic study focusing on prototypical CFTR mutations. Analysis of Dtt provides novel insight into the pathophysiology of CF, and the mechanisms through which each mutation class causes disease and will likely contribute to the identification of new therapeutic targets and/or biomarkers for CF.
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Affiliation(s)
- Lúcia Santos
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal ,grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Rui Nascimento
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Aires Duarte
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Violeta Railean
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Margarida D. Amaral
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Patrick T. Harrison
- grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Margarida Gama-Carvalho
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Carlos M. Farinha
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
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Steinke E, Sommerburg O, Graeber SY, Joachim C, Labitzke C, Nissen G, Ricklefs I, Rudolf I, Kopp MV, Dittrich AM, Mall MA, Stahl M. TRACK-CF prospective cohort study: Understanding early cystic fibrosis lung disease. Front Med (Lausanne) 2023; 9:1034290. [PMID: 36687447 PMCID: PMC9853074 DOI: 10.3389/fmed.2022.1034290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Background Lung disease as major cause for morbidity in patients with cystic fibrosis (CF) starts early in life. Its large phenotypic heterogeneity is partially explained by the genotype but other contributing factors are not well delineated. The close relationship between mucus, inflammation and infection, drives morpho-functional alterations already early in pediatric CF disease, The TRACK-CF cohort has been established to gain insight to disease onset and progression, assessed by lung function testing and imaging to capture morpho-functional changes and to associate these with risk and protective factors, which contribute to the variation of the CF lung disease progression. Methods and design TRACK-CF is a prospective, longitudinal, observational cohort study following patients with CF from newborn screening or clinical diagnosis throughout childhood. The study protocol includes monthly telephone interviews, quarterly visits with microbiological sampling and multiple-breath washout and as well as a yearly chest magnetic resonance imaging. A parallel biobank has been set up to enable the translation from the deeply phenotyped cohort to the validation of relevant biomarkers. The main goal is to determine influencing factors by the combined analysis of clinical information and biomaterials. Primary endpoints are the lung clearance index by multiple breath washout and semi-quantitative magnetic resonance imaging scores. The frequency of pulmonary exacerbations, infection with pro-inflammatory pathogens and anthropometric data are defined as secondary endpoints. Discussion This extensive cohort includes children after diagnosis with comprehensive monitoring throughout childhood. The unique composition and the use of validated, sensitive methods with the attached biobank bears the potential to decisively advance the understanding of early CF lung disease. Ethics and trial registration The study protocol was approved by the Ethics Committees of the University of Heidelberg (approval S-211/2011) and each participating site and is registered at clinicaltrials.gov (NCT02270476).
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Affiliation(s)
- Eva Steinke
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany,German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany,Berlin Institute of Health (BIH) at Charité, Berlin, Germany,*Correspondence: Eva Steinke ✉
| | - Olaf Sommerburg
- Division of Pediatric Pulmonology and Allergy and Cystic Fibrosis Center, Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Simon Y. Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany,German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany,Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | - Cornelia Joachim
- Division of Pediatric Pulmonology and Allergy and Cystic Fibrosis Center, Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christiane Labitzke
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Gyde Nissen
- Division of Pediatric Pneumology and Allergology, University of Lübeck, Lübeck, Germany,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Lübeck, Germany
| | - Isabell Ricklefs
- Division of Pediatric Pneumology and Allergology, University of Lübeck, Lübeck, Germany,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Lübeck, Germany
| | - Isa Rudolf
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Matthias V. Kopp
- Division of Pediatric Pneumology and Allergology, University of Lübeck, Lübeck, Germany,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Lübeck, Germany,Division of Respiratory Medicine, Department of Pediatrics, University Children's Hospital, Inselspital, University of Bern, Bern, Switzerland
| | - Anna-Maria Dittrich
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany,German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany,Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | - Mirjam Stahl
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany,German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany,Berlin Institute of Health (BIH) at Charité, Berlin, Germany
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Amaral MD. Using the genome to correct the ion transport defect in cystic fibrosis. J Physiol 2022; 601:1573-1582. [PMID: 36068724 DOI: 10.1113/jp282308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Human genome information can help finding drugs for human diseases. 'Omics' allow unbiased identification of novel drug targets. High-throughput (HT) approaches provide a global view on disease mechanisms. As a monogenic disease CF has led the way in multiple 'Omic' studies. 'Multi-omics' integration will generate maximal biological significance. ABSTRACT Today Biomedicine faces one of its greatest challenges, i.e. treating diseases through their causative dysfunctional processes and not just their symptoms. However, we still miss a global view of mechanisms and pathways involved in pathophysiology of most diseases. In fact, disease mechanisms and pathways can be achieved by holistic studies provided by 'Omic' approaches. Cystic Fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes an anion channel, is paradigmatic for monogenic disorders, namely channelopathies. A high number of 'omics studies' have focussed on CF, namely several cell-based high-throughput (HT) approaches were developed and applied towards a global mechanistic characterization of CF pathophysiology and the identification of novel and 'unbiased' drug targets. Notwithstanding, it is likely that, through the integration of all these 'layers' of large datasets into comprehensive disease maps that biological significance can be extracted so that the enormous potential of these approaches to identifying dysfunctional mechanisms and novel drugs may become a reality. Abstract figure legend Schematic overview of the 3 main approaches to discovery of new drugs/drug targets. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande-C8 bdg, Lisboa, 1749-016, Portugal
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Chandler JD, Esther CR. Metabolomics of airways disease in cystic fibrosis. Curr Opin Pharmacol 2022; 65:102238. [PMID: 35649321 PMCID: PMC10068587 DOI: 10.1016/j.coph.2022.102238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
While discovery metabolomic studies have identified many potential biomarkers of cystic fibrosis (CF) airways disease, relatively few have been validated. We review the recent literature to identify the most promising metabolomic findings as those repeatedly observed over multiple studies. Reproducible metabolomic findings include increased airway amino acids and small peptides in CF airways, as well as changes in phospholipids and sphingolipids. Other commonly altered pathways include adenosine metabolism, polyamine synthesis, and oxidative stress. These pathways represent potential biomarkers and therapeutic targets, though findings require reevaluation in the era of highly effective modulator therapies. Analysis of airway biomarkers in exhaled breath holds promise for non-invasive detection, though technical challenges will need to be overcome.
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Affiliation(s)
- Joshua D Chandler
- Pediatrics, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis, and Sleep Medicine, Emory University, Atlanta, GA, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Charles R Esther
- Pediatric Pulmonology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Braccia C, Christopher JA, Crook OM, Breckels LM, Queiroz RML, Liessi N, Tomati V, Capurro V, Bandiera T, Baldassari S, Pedemonte N, Lilley KS, Armirotti A. CFTR Rescue by Lumacaftor (VX-809) Induces an Extensive Reorganization of Mitochondria in the Cystic Fibrosis Bronchial Epithelium. Cells 2022; 11:1938. [PMID: 35741067 PMCID: PMC9222197 DOI: 10.3390/cells11121938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cystic Fibrosis (CF) is a genetic disorder affecting around 1 in every 3000 newborns. In the most common mutation, F508del, the defective anion channel, CFTR, is prevented from reaching the plasma membrane (PM) by the quality check control of the cell. Little is known about how CFTR pharmacological rescue impacts the cell proteome. METHODS We used high-resolution mass spectrometry, differential ultracentrifugation, machine learning and bioinformatics to investigate both changes in the expression and localization of the human bronchial epithelium CF model (F508del-CFTR CFBE41o-) proteome following treatment with VX-809 (Lumacaftor), a drug able to improve the trafficking of CFTR. RESULTS The data suggested no stark changes in protein expression, yet subtle localization changes of proteins of the mitochondria and peroxisomes were detected. We then used high-content confocal microscopy to further investigate the morphological and compositional changes of peroxisomes and mitochondria under these conditions, as well as in patient-derived primary cells. We profiled several thousand proteins and we determined the subcellular localization data for around 5000 of them using the LOPIT-DC spatial proteomics protocol. CONCLUSIONS We observed that treatment with VX-809 induces extensive structural and functional remodelling of mitochondria and peroxisomes that resemble the phenotype of healthy cells. Our data suggest additional rescue mechanisms of VX-809 beyond the correction of aberrant folding of F508del-CFTR and subsequent trafficking to the PM.
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Affiliation(s)
- Clarissa Braccia
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (C.B.); (T.B.)
| | - Josie A. Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Oliver M. Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
- Department of Statistics, University of Oxford, 29 St Giles’, Oxford OX1 3LB, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Nara Liessi
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Valeria Capurro
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Tiziano Bandiera
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (C.B.); (T.B.)
| | - Simona Baldassari
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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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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12
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Nutrition in Cystic Fibrosis—Some Notes on the Fat Recommendations. Nutrients 2022; 14:nu14040853. [PMID: 35215502 PMCID: PMC8875685 DOI: 10.3390/nu14040853] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Nutrition is important in cystic fibrosis (CF) because the disease is associated with a higher energy consumption, special nutritional deficiencies, and malabsorption mainly related to pancreatic insufficiency. The clinical course with deterioration of lung function has been shown to relate to nutrition. Despite general recommendation of high energy intake, the clinical deterioration is difficult to restrain suggesting that special needs have not been identified and specified. It is well-known that the CF phenotype is associated with lipid abnormalities, especially in the essential or conditionally essential fatty acids. This review will concentrate on the qualitative aspects of fat metabolism, which has mainly been neglected in dietary fat recommendations focusing on fat quantity. For more than 60 years it has been known and confirmed that the patients have a deficiency of linoleic acid, an n-6 essential fatty acid of importance for membrane structure and function. The ratio between arachidonic acid and docosahexaenoic acid, conditionally essential fatty acids of the n-6 and n-3 series, respectively, is often increased. The recently discovered relations between the CFTR modulators and lipid metabolism raise new interests in this field and together with new technology provide possibilities to specify further specify personalized therapy.
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13
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Graf AC, Striesow J, Pané-Farré J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, Riedel K. An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum. Front Cell Infect Microbiol 2021; 11:724569. [PMID: 34513734 PMCID: PMC8432295 DOI: 10.3389/fcimb.2021.724569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
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Affiliation(s)
- Alexander C Graf
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Johanna Striesow
- Research Group ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Thomas Sura
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Martina Wurster
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Dietmar H Pieper
- Research Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
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14
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Hardouin P, Chiron R, Marchandin H, Armengaud J, Grenga L. Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives. Genes (Basel) 2021; 12:892. [PMID: 34207804 PMCID: PMC8227082 DOI: 10.3390/genes12060892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.
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Affiliation(s)
- Pauline Hardouin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols-sur-Cèze, France;
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Raphael Chiron
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France;
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
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15
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Proteome Characterization of BALF Extracellular Vesicles in Idiopathic Pulmonary Fibrosis: Unveiling Undercover Molecular Pathways. Int J Mol Sci 2021; 22:ijms22115696. [PMID: 34071777 PMCID: PMC8199247 DOI: 10.3390/ijms22115696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
In the longtime challenge of identifying specific, easily detectable and reliable biomarkers of IPF, BALF proteomics is providing interesting new insights into its pathogenesis. To the best of our knowledge, the present study is the first shotgun proteomic investigation of EVs isolated from BALF of IPF patients. Our main aim was to characterize the proteome of the vesicular component of BALF and to explore its individual impact on the pathogenesis of IPF. To this purpose, ultracentrifugation was chosen as the EVs isolation technique, and their purification was assessed by TEM, 2DE and LC-MS/MS. Our 2DE data and scatter plots showed considerable differences between the proteome of EVs and that of whole BALF and of its fluid component. Analysis of protein content and protein functions evidenced that EV proteins are predominantly involved in cytoskeleton remodeling, adenosine signaling, adrenergic signaling, C-peptide signaling and lipid metabolism. Our findings may suggest a wider system involvement in the disease pathogenesis and support the importance of pre-fractioning of complex samples, such as BALF, in order to let low-abundant proteins-mediated pathways emerge.
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16
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Thavamani A, Salem I, Sferra TJ, Sankararaman S. Impact of Altered Gut Microbiota and Its Metabolites in Cystic Fibrosis. Metabolites 2021; 11:metabo11020123. [PMID: 33671639 PMCID: PMC7926988 DOI: 10.3390/metabo11020123] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal, multisystemic genetic disorder in Caucasians. Mutations in the gene encoding the cystic fibrosis transmembrane regulator (CFTR) protein are responsible for impairment of epithelial anionic transport, leading to impaired fluid regulation and pH imbalance across multiple organs. Gastrointestinal (GI) manifestations in CF may begin in utero and continue throughout the life, resulting in a chronic state of an altered intestinal milieu. Inherent dysfunction of CFTR leads to dysbiosis of the gut. This state of dysbiosis is further perpetuated by acquired factors such as use of antibiotics for recurrent pulmonary exacerbations. Since the gastrointestinal microbiome and their metabolites play a vital role in nutrition, metabolic, inflammatory, and immune functions, the gut dysbiosis will in turn impact various manifestations of CF-both GI and extra-GI. This review focuses on the consequences of gut dysbiosis and its metabolic implications on CF disease and possible ways to restore homeostasis.
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Affiliation(s)
- Aravind Thavamani
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Iman Salem
- Center for Medial Mycology, Case Western Reserve University School of Medicine, UH Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Thomas J. Sferra
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Senthilkumar Sankararaman
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
- Correspondence: ; Tel.: +1-216-844-1765
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17
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Awatade NT, Wong SL, Capraro A, Pandzic E, Slapetova I, Zhong L, Turgutoglu N, Fawcett LK, Whan RM, Jaffe A, Waters SA. Significant functional differences in differentiated Conditionally Reprogrammed (CRC)- and Feeder-free Dual SMAD inhibited-expanded human nasal epithelial cells. J Cyst Fibros 2021; 20:364-371. [PMID: 33414087 DOI: 10.1016/j.jcf.2020.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Patient-derived airway cells differentiated at Air Liquid Interface (ALI) are valuable models for Cystic fibrosis (CF) precision therapy. Different culture expansion methods have been established to extend expansion capacity of airway basal cells, while retaining functional airway epithelium physiology. Considerable variation in response to CFTR modulators is observed in cultures even within the same CFTR genotype and despite the use of similar ALI culture techniques. We aimed to address culture expansion method impact on differentiation. METHODS Nasal epithelial brushings from 14 individuals (CF=9; non-CF=5) were collected, then equally divided and expanded under conditional reprogramming culture (CRC) and feeder-serum-free "dual-SMAD inhibition" (SMADi) methods. Expanded cells from each culture were differentiated with proprietary PneumaCult™-ALI media. Morphology (Immunofluorescence), global proteomics (LC-MS/MS) and function (barrier integrity, cilia motility, and ion transport) were compared in CRCALI and SMADiALI under basal and CFTR corrector treated (VX-809) conditions. RESULTS No significant difference in the structural morphology or baseline global proteomics profile were observed. Barrier integrity and cilia motility were significantly different, despite no difference in cell junction morphology or cilia abundance. Epithelial Sodium Channels and Calcium-activated Chloride Channel activity did not differ but CFTR mediated chloride currents were significantly reduced in SMADiALI compare to their CRCALI counterparts. CONCLUSION Alteration of cellular physiological function in vitro were more prominent than structural and differentiation potential in airway ALI. Since initial expansion culture conditions significantly influence CFTR activity, this could lead to false conclusions if data from different labs are compared against each other without specific reference ranges.
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Affiliation(s)
- Nikhil T Awatade
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Sharon L Wong
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Alexander Capraro
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Elvis Pandzic
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Iveta Slapetova
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Nihan Turgutoglu
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Laura K Fawcett
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Renee M Whan
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Shafagh A Waters
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia.
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18
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Zardini Buzatto A, Abdel Jabar M, Nizami I, Dasouki M, Li L, Abdel Rahman AM. Lipidome Alterations Induced by Cystic Fibrosis, CFTR Mutation, and Lung Function. J Proteome Res 2020; 20:549-564. [PMID: 33089695 DOI: 10.1021/acs.jproteome.0c00556] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis is a genetic pathology characterized by abnormal accumulation of mucus in the respiratory, gastrointestinal, and reproductive tracts, caused by mutations in the CFTR gene. Although the classical presentation of the condition is well known, there is still a need for a better characterization of metabolic alterations related to cystic fibrosis and different genotypic mutations. We employed untargeted, comprehensive lipidomics of blood serum samples to investigate alterations in the lipid metabolism related to the pathology, mutation classes, and lung function decline. Six unique biomarker candidates were able to independently differentiate diseased individuals from healthy controls with excellent performance. Cystic fibrosis patients showed dyslipidemia for most lipid subclasses, with significantly elevated odd-chain and polyunsaturated fatty acyl lipids. Phosphatidic acids and diacylglycerols were particularly affected by different genotypic mutation classes. We selected a biomarker panel composed of four lipids, including two ceramides, one sphingomyelin, and one fatty acid, which correctly classified all validation samples from classes III and IV. A biomarker panel of five oxidized lipids was further selected to differentiate patients with reduced lung function, measured as predicted FEV1%. Our results indicate that cystic fibrosis is deeply related to lipid metabolism and provide new clues for the investigation of the disease mechanisms and therapeutic targets.
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Affiliation(s)
| | - Mai Abdel Jabar
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Imran Nizami
- Lung Transplant Section, Organ Transplant Center, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Majed Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Anas M Abdel Rahman
- Department of Genetics, King Faisal Specialist Hospital and Research Centre (KFSHRC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh 11533, Saudi Arabia.,Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
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