1
|
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.
Collapse
Affiliation(s)
| | | | - Gagan D. Gupta
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada
| |
Collapse
|
2
|
Pereira R, Barbosa T, Cardoso AL, Sá R, Sousa M. Cystic fibrosis and primary ciliary dyskinesia: Similarities and differences. Respir Med 2023; 209:107169. [PMID: 36828173 DOI: 10.1016/j.rmed.2023.107169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 02/06/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023]
Abstract
Cystic fibrosis (CF) and Primary ciliary dyskinesia (PCD) are both rare chronic diseases, inherited disorders associated with multiple complications, namely respiratory complications, due to impaired mucociliary clearance that affect severely patients' lives. Although both are classified as rare diseases, PCD has a much lower prevalence than CF, particularly among Caucasians. As a result, CF is well studied, better recognized by clinicians, and with some therapeutic approaches already available. Whereas PCD is still largely unknown, and thus the approach is based on consensus guidelines, expert opinion, and extrapolation from the larger evidence base available for patients with CF. Both diseases have some clinical similarities but are very different, necessitating different treatment by specialists who are familiar with the complexities of each disease.This review aims to provide an overview of the knowledge about the two diseases with a focus on the similarities and differences between both in terms of disease mechanisms, common clinical manifestations, genetics and the most relevant therapeutic options. We hoped to raise clinical awareness about PCD, what it is, how it differs from CF, and how much information is still lacking. Furthermore, this review emphasises the fact that both diseases require ongoing research to find better treatments and, in particular for PCD, to fill the medical and scientific gaps.
Collapse
Affiliation(s)
- Rute Pereira
- Laboratory of Cell Biology, Department of Microscopy, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-UP/ ITR-Laboratory for Integrative and Translational Research in Population Health, UP, Porto, Portugal.
| | - Telma Barbosa
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-UP/ ITR-Laboratory for Integrative and Translational Research in Population Health, UP, Porto, Portugal; Department of Pediatrics, Maternal Child Centre of the North (CMIN), University Hospital Centre of Porto (CHUP), Largo da Maternidade, 4050-371, Porto, Portugal.
| | - Ana Lúcia Cardoso
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-UP/ ITR-Laboratory for Integrative and Translational Research in Population Health, UP, Porto, Portugal; Department of Pediatrics, Maternal Child Centre of the North (CMIN), University Hospital Centre of Porto (CHUP), Largo da Maternidade, 4050-371, Porto, Portugal.
| | - Rosália Sá
- Laboratory of Cell Biology, Department of Microscopy, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-UP/ ITR-Laboratory for Integrative and Translational Research in Population Health, UP, Porto, Portugal.
| | - Mário Sousa
- Laboratory of Cell Biology, Department of Microscopy, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-UP/ ITR-Laboratory for Integrative and Translational Research in Population Health, UP, Porto, Portugal.
| |
Collapse
|
3
|
Saber MM, Donner J, Levade I, Acosta N, Parkins MD, Boyle B, Levesque RC, Nguyen D, Shapiro BJ. Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis. Microb Genom 2023; 9. [PMID: 37052589 DOI: 10.1099/mgen.0.000981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
The severity and progression of lung disease are highly variable across individuals with cystic fibrosis (CF) and are imperfectly predicted by mutations in the human gene CFTR, lung microbiome variation or other clinical factors. The opportunistic pathogen Pseudomonas aeruginosa (Pa) dominates airway infections in most CF adults. Here we hypothesized that within-host genetic variation of Pa populations would be associated with lung disease severity. To quantify Pa genetic variation within CF sputum samples, we used deep amplicon sequencing (AmpliSeq) of 209 Pa genes previously associated with pathogenesis or adaptation to the CF lung. We trained machine learning models using Pa single nucleotide variants (SNVs), microbiome diversity data and clinical factors to classify lung disease severity at the time of sputum sampling, and to predict lung function decline after 5 years in a cohort of 54 adult CF patients with chronic Pa infection. Models using Pa SNVs alone classified lung disease severity with good sensitivity and specificity (area under the receiver operating characteristic curve: AUROC=0.87). Models were less predictive of lung function decline after 5 years (AUROC=0.74) but still significantly better than random. The addition of clinical data, but not sputum microbiome diversity data, yielded only modest improvements in classifying baseline lung function (AUROC=0.92) and predicting lung function decline (AUROC=0.79), suggesting that Pa AmpliSeq data account for most of the predictive value. Our work provides a proof of principle that Pa genetic variation in sputum tracks lung disease severity, moderately predicts lung function decline and could serve as a disease biomarker among CF patients with chronic Pa infections.
Collapse
Affiliation(s)
- Morteza M Saber
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jannik Donner
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Inès Levade
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brian Boyle
- Integrative Systems Biology Institute, University of Laval, Québec, QC, Canada
| | - Roger C Levesque
- Integrative Systems Biology Institute, University of Laval, Québec, QC, Canada
| | - Dao Nguyen
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Meakins Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
| |
Collapse
|
4
|
Recchia D, Stelitano G, Stamilla A, Gutierrez DL, Degiacomi G, Chiarelli LR, Pasca MR. Mycobacterium abscessus Infections in Cystic Fibrosis Individuals: A Review on Therapeutic Options. Int J Mol Sci 2023; 24:ijms24054635. [PMID: 36902066 PMCID: PMC10002592 DOI: 10.3390/ijms24054635] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/02/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Mycobacterium abscessus is an opportunistic pathogen that mainly colonizes and infects cystic fibrosis patients' lungs. M. abscessus is naturally resistant to many antibiotics such as rifamycin, tetracyclines and β-lactams. The current therapeutic regimens are not very effective and are mostly based on repurposed drugs used against Mycobacterium tuberculosis infections. Thus, new approaches and novel strategies are urgently needed. This review aims to provide an overview of the latest ongoing findings to fight M. abscessus infections by analyzing emerging and alternative treatments, novel drug delivery strategies, and innovative molecules.
Collapse
|
5
|
Allen L, Allen L, Carr SB, Davies G, Downey D, Egan M, Forton JT, Gray R, Haworth C, Horsley A, Smyth AR, Southern KW, Davies JC. Future therapies for cystic fibrosis. Nat Commun 2023; 14:693. [PMID: 36755044 PMCID: PMC9907205 DOI: 10.1038/s41467-023-36244-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
We are currently witnessing transformative change for people with cystic fibrosis with the introduction of small molecule, mutation-specific drugs capable of restoring function of the defective protein, cystic fibrosis transmembrane conductance regulator (CFTR). However, despite being a single gene disorder, there are multiple cystic fibrosis-causing genetic variants; mutation-specific drugs are not suitable for all genetic variants and also do not correct all the multisystem clinical manifestations of the disease. For many, there will remain a need for improved treatments. Those patients with gene variants responsive to CFTR modulators may have found these therapies to be transformational; research is now focusing on safely reducing the burden of symptom-directed treatment. However, modulators are not available in all parts of the globe, an issue which is further widening existing health inequalities. For patients who are not suitable for- or do not have access to- modulator drugs, alternative approaches are progressing through the trials pipeline. There will be challenges encountered in design and implementation of these trials, for which the established global CF infrastructure is a major advantage. Here, the Cystic Fibrosis National Research Strategy Group of the UK NIHR Respiratory Translational Research Collaboration looks to the future of cystic fibrosis therapies and consider priorities for future research and development.
Collapse
Affiliation(s)
| | | | - Siobhan B Carr
- Royal Brompton & Harefield Hospital, Guy's & St Thomas' Trust, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Gwyneth Davies
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children, London, UK
| | - Damian Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | | | - Julian T Forton
- Noah's Ark Children's Hospital for Wales, Cardiff, UK
- School of Medicine, Cardiff University, Cardiff, UK
| | - Robert Gray
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- Western General Hospital, Edinburgh, UK
| | - Charles Haworth
- Royal Papworth Hospital and Department of Medicine, Cambridge, UK
- University of Cambridge, Cambridge, UK
| | - Alexander Horsley
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
- Manchester Adult CF Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Alan R Smyth
- School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
- Institute in the Park, Alder Hey Children's Hospital, Liverpool, UK
| | - Jane C Davies
- Royal Brompton & Harefield Hospital, Guy's & St Thomas' Trust, London, UK.
- National Heart & Lung Institute, Imperial College London, London, UK.
| |
Collapse
|
6
|
Carneiro GV, de Oliveira FS, Pereira LA, Rezende ÉRMDA, Gonçalves LCP, Azevedo VMGDO. Association between phenotypic and genotypic characteristics and disease severity in individuals with cystic fibrosis. REVISTA PAULISTA DE PEDIATRIA 2022; 41:e2021286. [PMID: 36102402 PMCID: PMC9462412 DOI: 10.1590/1984-0462/2023/41/2021286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/05/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To analyze the association between phenotypic and genotypic characteristics and disease severity in individuals with cystic fibrosis treated at a reference center in Minas Gerais, Brazil. METHODS This is a retrospective study that collected clinical and laboratory data, respiratory and gastrointestinal manifestations, type of treatment, Shwachman-Kulczycki score, and mutations from the patients' medical records. RESULTS The sample included 50 participants aged one to 33 years, 50% of whom were female. Out of the one hundred alleles of the Cystic Fibrosis Transmembrane Conductance Regulator gene, the most prevalent mutations were DeltaF508 (45%) and S4X (18%). Mutation groups were only associated with pancreatic insufficiency (p=0.013) and not with disease severity (p=0.073). The latter presented an association with colonization by Pseudomonas aeruginosa and Staphylococcus aureus (p=0.007) and with underweight (p=0.036). Death was associated with age at diagnosis (p=0.016), respiratory symptomatology (p=0.013), colonization (p=0.024), underweight (p=0.017), and hospitalization (p=0.003). CONCLUSIONS We could identify the association of mutations with pancreatic insufficiency; the association of Staphylococcus aureus colonization and underweight with disease severity; and the lack of association between mutations and disease severity. Environmental factors should be investigated more thoroughly since they seem to have an important effect on disease severity.
Collapse
|
7
|
Kanaujia R, Arora A, Chakrabarti A, Rudramurthy SM, Agarwal R. Occurrence of Cystic Fibrosis Transmembrane Conductance Regulator Gene Mutations in Patients with Allergic Bronchopulmonary Aspergillosis Complicating Asthma. Mycopathologia 2022; 187:147-155. [DOI: 10.1007/s11046-022-00631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
|
8
|
Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients' Samples Reveals Perturbations in Tissue-Specific Pathways. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5262000. [PMID: 34901273 PMCID: PMC8660202 DOI: 10.1155/2021/5262000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/08/2021] [Indexed: 11/24/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder, caused by diverse genetic variants for the CF transmembrane conductance regulator (CFTR) protein. Among these, p.Phe508del is the most prevalent variant. The effects of this variant on the physiology of each tissue remains unknown. This study is aimed at predicting cell signaling pathways present in different tissues of fibrocystic patients, homozygous for p.Phe508del. The study involved analysis of two microarray datasets, E-GEOD-15568 and E-MTAB-360 corresponding to the rectal and bronchial epithelium, respectively, obtained from the ArrayExpress repository. Particularly, differentially expressed genes (DEGs) were predicted, protein-protein interaction (PPI) networks were designed, and centrality and functional interaction networks were analyzed. The study reported that p.Phe508del-mutated CFTR-allele in homozygous state influenced the whole gene expression in each tissue differently. Interestingly, gene ontology (GO) term enrichment analysis revealed that only “neutrophil activation” was shared between both tissues; however, nonshared DEGs were grouped into the same GO term. For further verification, functional interaction networks were generated, wherein no shared nodes were reported between these tissues. These results suggested that the p.Phe508del-mutated CFTR-allele in homozygous state promoted tissue-specific pathways in fibrocystic patients. The generated data might further assist in prediction diagnosis to define biomarkers or devising therapeutic strategies.
Collapse
|
9
|
Schamschula E, Lahnsteiner A, Assenov Y, Hagmann W, Zaborsky N, Wiederstein M, Strobl A, Stanke F, Muley T, Plass C, Tümmler B, Risch A. Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells. Epigenetics 2021; 17:837-860. [PMID: 34415821 PMCID: PMC9423854 DOI: 10.1080/15592294.2021.1959976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the Plakophilin-3 (PKP3) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of PKP3 which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
Collapse
Affiliation(s)
| | | | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hagmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Anna Strobl
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Frauke Stanke
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik Heidelberg, University of Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Angela Risch
- Department of Biosciences, University of Salzburg, Salzburg, Austria.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer Cluster Salzburg, Salzburg, Austria.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| |
Collapse
|
10
|
McLean SA, Cullen L, Gardam DJ, Schofield CJ, Laucirica DR, Sutanto EN, Ling KM, Stick SM, Peacock CS, Kicic A, Garratt LW. Cystic Fibrosis Clinical Isolates of Aspergillus fumigatus Induce Similar Muco-inflammatory Responses in Primary Airway Epithelial Cells. Pathogens 2021; 10:pathogens10081020. [PMID: 34451484 PMCID: PMC8399118 DOI: 10.3390/pathogens10081020] [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: 07/01/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus is increasingly associated with lung inflammation and mucus plugging in early cystic fibrosis (CF) disease during which conidia burden is low and strains appear to be highly diverse. It is unknown whether clinical Aspergillus strains vary in their capacity to induce epithelial inflammation and mucus production. We tested the hypothesis that individual colonising strains of Aspergillus fumigatus would induce different responses. Ten paediatric CF Aspergillus isolates were compared along with two systemically invasive clinical isolates and an ATCC reference strain. Isolates were first characterised by ITS gene sequencing and screened for antifungal susceptibility. Three clusters (A-C) of Aspergillus isolates were identified by ITS. Antifungal susceptibility was variable, particularly for itraconazole. Submerged CF and non-CF monolayers as well as differentiated primary airway epithelial cell cultures were incubated with conidia for 24 h to allow germination. None of the clinical isolates were found to significantly differ from one another in either IL-6 or IL-8 release or gene expression of secretory mucins. Clinical Aspergillus isolates appear to be largely homogenous in their mucostimulatory and immunostimulatory capacities and, therefore, only the antifungal resistance characteristics are likely to be clinically important.
Collapse
Affiliation(s)
- Samantha A. McLean
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Leilani Cullen
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Dianne J. Gardam
- PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch 6150, Australia;
| | - Craig J. Schofield
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Daniel R. Laucirica
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Erika N. Sutanto
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
| | - Kak-Ming Ling
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Stephen M. Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands 6009, Australia
| | - Christopher S. Peacock
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Faculty of Health and Medical Sciences, University of Western Australia, Crawley 6009, Australia; (L.C.); (C.S.P.)
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands 6009, Australia
- Occupation and Environment, School of Public Health, Curtin University, Bentley 6102, Australia
| | - Luke W. Garratt
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Crawley 6009, Australia; (S.A.M.); (C.J.S.); (D.R.L.); (E.N.S.); (K.-M.L.); (S.M.S.); (A.K.)
- Correspondence:
| | | | | |
Collapse
|
11
|
Quantification of Phenotypic Variability of Lung Disease in Children with Cystic Fibrosis. Genes (Basel) 2021; 12:genes12060803. [PMID: 34070354 PMCID: PMC8229033 DOI: 10.3390/genes12060803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) lung disease has the greatest impact on the morbidity and mortality of patients suffering from this autosomal-recessive multiorgan disorder. Although CF is a monogenic disorder, considerable phenotypic variability of lung disease is observed in patients with CF, even in those carrying the same mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene or CFTR mutations with comparable functional consequences. In most patients with CF, lung disease progresses from childhood to adulthood, but is already present in infants soon after birth. In addition to the CFTR genotype, the variability of early CF lung disease can be influenced by several factors, including modifier genes, age at diagnosis (following newborn screening vs. clinical symptoms) and environmental factors. The early onset of CF lung disease requires sensitive, noninvasive measures to detect and monitor changes in lung structure and function. In this context, we review recent progress with using multiple-breath washout (MBW) and lung magnetic resonance imaging (MRI) to detect and quantify CF lung disease from infancy to adulthood. Further, we discuss emerging data on the impact of variability of lung disease severity in the first years of life on long-term outcomes and the potential use of this information to improve personalized medicine for patients with CF.
Collapse
|
12
|
Hanssens LS, Cellauro S, Duchateau J, Casimir GJ. Immunoglobulin G: A useful outcome marker in the follow-up of cystic fibrosis patients? IMMUNITY INFLAMMATION AND DISEASE 2021; 9:608-614. [PMID: 33783131 PMCID: PMC8127551 DOI: 10.1002/iid3.426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/03/2023]
Abstract
Background and Methods Hypergammaglobulinemia (hyper‐IgG) and hypogammaglobulinemia (hypo‐IgG) have been reported in patients with cystic fibrosis (CF). Although the clinical respiratory course is paradoxically different, depending on the IgG status, this association remains elusive. Therefore, we performed a longitudinal study to assess the annual evolution of IgG profiles in a cohort of pediatric patients with CF, from their diagnosis until 2016. We then compared clinical findings with the patients’ IgG status to determine whether IgG status could reflect the respiratory clinical course of patients with CF. Results Among the 66 patients with CF that were aged between 12 months and 18 years in 2016 (mean age: 9.3 years [SD: 5.2]), hypo‐IgG was observed in 15.2% and no hyper‐IgG was identified. Longitudinal assessment since diagnosis revealed no hyper‐IgG but 33.3% of patients had at least one sample showing hypo‐IgG, among which two patients displayed persistent hypo‐IgG. The number of pulmonary exacerbations, duration of antibiotic therapy, and erythrocyte sedimentation rate were all lower in hypo‐IgG patients. No difference was observed for the genotype, chronic Pseudomonas aeruginosa or Staphylococcus aureus infection, and in the parameters of lung function. Conclusion The IgG profile of pediatric patients with CF has changed over recent decades, particularly with regard to hyper‐IgG. In a significant portion of the pediatric CF population, hypo‐IgG is transient and only identifiable in longitudinal assessments. This study reinforces that hypo‐IgG patients paradoxically present a more favorable course of clinical status. Therefore, IgG levels could be a useful outcome marker in the follow‐up of patients with CF. Abnormal immunoglobulin G (IgG) levels have been described in patients with cystic fibrosis (CF). With this longitudinal study, we sought to determine whether IgG status could reflect the respiratory clinical course of CF patients. The assessment in 2016 identified 15.2% of 66 pediatric patients as hypo‐IgG, whereas no hyper‐IgG was highlighted. The longitudinal assessment of IgG since diagnosis revealed no hyper‐IgG and hypo‐IgG was transient in at least one‐third of our patients, except for two, who both displayed persistent hypo‐IgG. Therefore, three populations can be identified, according to the patient's IgG profile during their follow‐up: a first with persistent hypo‐IgG since diagnosis; a second with a transient deficiency, which likely normalizes in adolescence; a third whose IgG remains within a normal range. CF patients with hypo‐IgG appear to be protected from pulmonary exacerbations and therefore could present a more favorable respiratory course, even with low IgG levels since diagnosis. This suggests that IgG levels could be a useful outcome marker in CF patient follow‐up in order to predict their respiratory clinical course.
Collapse
Affiliation(s)
- Laurence S Hanssens
- Department of Pediatric Pulmonology and Cystic Fibrosis Clinic, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sarah Cellauro
- Department of Pediatric Pulmonology and Cystic Fibrosis Clinic, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean Duchateau
- Laboratoire Académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Georges J Casimir
- Department of Pediatric Pulmonology and Cystic Fibrosis Clinic, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Laboratoire Académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| |
Collapse
|
13
|
Kawai K, Dombrowski N, Sawicki GS, Adil EA. Improvement of Pulmonary Function in Cystic Fibrosis Patients following Endoscopic Sinus Surgery. Laryngoscope 2021; 131:1930-1938. [PMID: 33538334 DOI: 10.1002/lary.29409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/03/2021] [Accepted: 01/06/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE/HYPOTHESIS To compare pre-and post-operative pulmonary function relative to disease severity in cystic fibrosis (CF) patients following endoscopic sinus surgery (ESS). STUDY DESIGN Retrospective chart review. METHODS Patients with CF who underwent ESS between January 1996 and July 2018 were identified, with subsequent study exclusions based upon surgical indications or incomplete records. CF disease severity was based upon percentage predicted of forced expiratory volume in 1 second (%FEV1) with <40% considered severe disease, 40% to 70% as moderate disease, and >70% as mild disease. The changes in %FEV1 before and after ESS were examined using multivariable mixed-effects models controlling for age, gender, genotype, medications, nutritional status, diabetes status, microbiology results, extent of surgery, and number of surgeries. RESULTS A total of 427 surgeries were performed in 188 patients during the study period. Mean age at first ESS was 12.7 years (SD 6.0 years, range 4-38) and 54.8% were females. The effect of ESS varied by severity of lung disease. After surgery, %FEV1 increased by 8.1% (95% CI: 2.3, 13.9%) among patients with severe lung disease and by 3.0% (95% CI: 0.7, 5.2%) among patients with moderate disease. %FEV1 also increased by 7.3% (95% CI: 4.2, 10.5%) among patients with mild disease whose %FEV1 value was 70% to 80% at baseline. No improvement was observed in patients with a baseline %FEV1 >80%. CONCLUSIONS When controlling for important confounding factors, lung function improved following ESS among CF patients with severe and moderate disease and in select patients with mild disease. This improvement was sustained at 12 months following surgery. LEVEL OF EVIDENCE 4 Laryngoscope, 131:1930-1938, 2021.
Collapse
Affiliation(s)
- Kosuke Kawai
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Natasha Dombrowski
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A
| | - Gregory S Sawicki
- Division of Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts, U.S.A
| | - Eelam A Adil
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, U.S.A
| |
Collapse
|
14
|
|
15
|
Auslander N, Ramos DM, Zelaya I, Karathia H, Crawford TO, Schäffer AA, Sumner CJ, Ruppin E. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases. Mol Syst Biol 2020; 16:e9701. [PMID: 33438800 PMCID: PMC7754056 DOI: 10.15252/msb.20209701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre-mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient-derived cells leads to increased full-length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.
Collapse
Affiliation(s)
- Noam Auslander
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of HealthBethesdaMDUSA
| | - Daniel M Ramos
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivette Zelaya
- Interdepartmental Program in BioinformaticsUniversity of California Los AngelesLos AngelesCAUSA
| | - Hiren Karathia
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer InstituteNational Institutes of HealthMDUSA
| | - Thomas O. Crawford
- Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Charlotte J Sumner
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| |
Collapse
|
16
|
Filbrun AG, Enochs C, Caverly L, Rajala K, Powell C, Merrick E, Nasr SZ. Quality improvement initiative to improve pulmonary function in pediatric cystic fibrosis patients. Pediatr Pulmonol 2020; 55:3039-3045. [PMID: 32770822 DOI: 10.1002/ppul.25017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/05/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Our Cystic Fibrosis (CF) Center initiated a Quality Improvement (QI) project in November 2017 with the goal of improving our patients' forced expiratory volume in 1 second (FEV1) percent predicted (pp) and continued for 1 year. Our specific aim was to increase the relative mean FEV1 pp by 5% in 12 months for CF patients 6 to 21 years old with FEV1 ≤ 80 pp. METHODS We identified patients with FEV1 ≤ 80 pp, developed cause and effect diagrams (fishbones) to identify contributing factors to FEV1 ≤ 80 pp, and created flowcharts to address barriers. The barriers to adherence that may result in FEV1 ≤ 80 pp were studied using a fishbone. A standardized approach across providers was implemented to individualize care for each patient. Each discipline developed a flowchart to address barriers to improving FEV1. RESULTS Forty patients were identified (43% male). Their mean age was 16.8 years (range 8.2-21.5 years). Mean FEV1 pp at baseline was 58.6 (range 30-80). The fishbone identified needs for continuing education for patients/families, and providing a treatment plan at each clinic visit. After 6 months of implementation, patients had an improvement in mean FEV1 pp by 6.4% (CI, 0.4%-12.9%). At 12 months, mean FEV1 pp had improved by 14% (CI, 6.5%-21.4%), which exceeded our goal of 5%. CONCLUSION Through this ongoing project, team members, patients, and families partnered to improve lung function in pediatric CF patients. Flowcharts facilitated a standardized approach across providers to develop individualized treatment plans for patients, which resulted in improved lung function.
Collapse
Affiliation(s)
- Amy G Filbrun
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| | - Catherine Enochs
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| | - Lindsay Caverly
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| | - Kelsey Rajala
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| | - Corey Powell
- Center for Statistics, Computing and Analytics Research (CSCAR), University of Michigan, Ann Arbor, Michigan
| | - Emily Merrick
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| | - Samya Z Nasr
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
17
|
Briottet M, Shum M, Urbach V. The Role of Specialized Pro-Resolving Mediators in Cystic Fibrosis Airways Disease. Front Pharmacol 2020; 11:1290. [PMID: 32982730 PMCID: PMC7493015 DOI: 10.3389/fphar.2020.01290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022] Open
Abstract
Cystic Fibrosis (CF) is a recessive genetic disease due to mutations of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene encoding the CFTR chloride channel. The ion transport abnormalities related to CFTR mutation generate a dehydrated airway surface liquid (ASL) layer, which is responsible for an altered mucociliary clearance, favors infections and persistent inflammation that lead to progressive lung destruction and respiratory failure. The inflammatory response is normally followed by an active resolution phase to return to tissue homeostasis, which involves specialized pro-resolving mediators (SPMs). SPMs promote resolution of inflammation, clearance of microbes, tissue regeneration and reduce pain, but do not evoke unwanted immunosuppression. The airways of CF patients showed a decreased production of SPMs even in the absence of pathogens. SPMs levels in the airway correlated with CF patients' lung function. The prognosis for CF has greatly improved but there remains a critical need for more effective treatments that prevent excessive inflammation, lung damage, and declining pulmonary function for all CF patients. This review aims to highlight the recent understanding of CF airway inflammation and the possible impact of SPMs on functions that are altered in CF airways.
Collapse
Affiliation(s)
| | | | - Valerie Urbach
- Institut national de la santé et de la recherche médicale (Inserm) U955, Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| |
Collapse
|
18
|
Strong toll-like receptor responses in cystic fibrosis patients are associated with higher lung function. J Cyst Fibros 2019; 19:608-613. [PMID: 31813753 DOI: 10.1016/j.jcf.2019.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) airways disease varies widely among patients with identical cystic fibrosis transmembrane conductance regulator (CFTR) genotypes. Robust airway inflammation is thought to be deleterious in CF; inter-individual variation in Toll-like receptor (TLR)-mediated innate immune inflammatory responses (TMIIR) might account for a portion of the phenotypic variation. We tested if TMIIR in people with CF are different than those of healthy controls, and whether higher TMIIR in people with CF are associated with reduced lung function. METHODS We cultured whole blood from clinically stable subjects with CF (n = 76) and healthy controls (n = 45) with TLR agonists, and measured cytokine production and expression of TLR-associated genes. We tested for differences in TLR-stimulated cytokine levels between subjects with CF and healthy subjects, and for associations between cytokine and gene expression levels with baseline lung function (forced expiratory volume in one second percent predicted (FEV1%)) and decline in FEV1% over time. RESULTS TMIIR in blood from subjects with CF were lower than in healthy controls. Expression of TLR regulators SARM1, TOLLIP, and AKT1 were downregulated in CF. In subjects with CF we found that lower TLR4-agonist-induced IL-8 was associated with lower FEV1% at enrollment (p<0.001) and with greater five year FEV1% decline (p<0.001). CONCLUSIONS TMIIR were lower in people with CF relative to healthy controls; however, unexpectedly, greater whole blood TMIIR were positively associated with lung function in people with CF. These findings suggest a complex interaction between inflammation and disease in people with CF.
Collapse
|