1
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Hastings CJ, Syed SS, Marques CNH. Subversion of the Complement System by Pseudomonas aeruginosa. J Bacteriol 2023; 205:e0001823. [PMID: 37436150 PMCID: PMC10464199 DOI: 10.1128/jb.00018-23] [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: 07/13/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen heavily implicated in chronic diseases. Immunocompromised patients that become infected with P. aeruginosa usually are afflicted with a lifelong chronic infection, leading to worsened patient outcomes. The complement system is an integral piece of the first line of defense against invading microorganisms. Gram-negative bacteria are thought to be generally susceptible to attack from complement; however, P. aeruginosa can be an exception, with certain strains being serum resistant. Various molecular mechanisms have been described that confer P. aeruginosa unique resistance to numerous aspects of the complement response. In this review, we summarize the current published literature regarding the interactions of P. aeruginosa and complement, as well as the mechanisms used by P. aeruginosa to exploit various complement deficiencies and the strategies used to disrupt or hijack normal complement activities.
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Affiliation(s)
- Cody James Hastings
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
| | - Shazrah Salim Syed
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
| | - Cláudia Nogueira Hora Marques
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
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2
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Horani A, Gupta DK, Xu J, Xu H, del Carmen Puga-Molina L, Santi CM, Ramagiri S, Brennan SK, Pan J, Koenitzer JR, Huang T, Hyland RM, Gunsten SP, Tzeng SC, Strahle JM, Mill P, Mahjoub MR, Dutcher SK, Brody SL. The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes. JCI Insight 2023; 8:e168836. [PMID: 37104040 PMCID: PMC10393236 DOI: 10.1172/jci.insight.168836] [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: 01/13/2023] [Accepted: 04/20/2023] [Indexed: 04/28/2023] Open
Abstract
DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift-null deletion in Dnaaf5. Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partially preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. Transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. These findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies.
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Affiliation(s)
- Amjad Horani
- Department of Pediatrics
- Department of Cell Biology and Physiology
| | | | | | | | | | | | - Sruthi Ramagiri
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | | | | | | | | | | | | | - Jennifer M. Strahle
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pleasantine Mill
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Moe R. Mahjoub
- Department of Cell Biology and Physiology
- Department of Medicine
| | - Susan K. Dutcher
- Department of Cell Biology and Physiology
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
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3
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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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4
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Horani A, Gupta DK, Xu J, Xu H, Del Carmen Puga-Molina L, Santi CM, Ramagiri S, Brennen SK, Pan J, Huang T, Hyland RM, Gunsten SP, Tzeng SC, Strahle JM, Mill P, Mahjoub MR, Dutcher SK, Brody SL. The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523966. [PMID: 36712068 PMCID: PMC9882222 DOI: 10.1101/2023.01.13.523966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift null deletion in Dnaaf5 . Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partial preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. While transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. Together, these findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies. Brief Summary A mouse model of human DNAAF5 primary ciliary dyskinesia variants reveals gene dosage effects of mutant alleles and tissue-specific molecular requirements for cilia motor assembly.
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5
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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]
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Bojanowski CM, Lu S, Kolls JK. Mucosal Immunity in Cystic Fibrosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2901-2912. [PMID: 35802761 PMCID: PMC9270582 DOI: 10.4049/jimmunol.2100424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/21/2021] [Indexed: 05/27/2023]
Abstract
The highly complex and variable genotype-phenotype relationships observed in cystic fibrosis (CF) have been an area of growing interest since the discovery of the CF transmembrane conductance regulator (CFTR) gene >30 y ago. The consistently observed excessive, yet ineffective, activation of both the innate and adaptive host immune systems and the establishment of chronic infections within the lung, leading to destruction and functional decline, remain the primary causes of morbidity and mortality in CF. The fact that both inflammation and pathogenic bacteria persist despite the introduction of modulator therapies targeting the defective protein, CFTR, highlights that we still have much to discover regarding mucosal immunity determinants in CF. Gene modifier studies have overwhelmingly implicated immune genes in the pulmonary phenotype of the disease. In this context, we aim to review recent advances in our understanding of the innate and adaptive immune systems in CF lung disease.
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Affiliation(s)
- Christine M Bojanowski
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Department of Medicine, Tulane University School of Medicine, New Orleans, LA;
| | - Shiping Lu
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA; and
| | - Jay K Kolls
- Center for Translational Research in Infection and Inflammation, Department of Medicine, Tulane University School of Medicine, New Orleans, LA
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7
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Sepahzad A, Morris-Rosendahl DJ, Davies JC. Cystic Fibrosis Lung Disease Modifiers and Their Relevance in the New Era of Precision Medicine. Genes (Basel) 2021; 12:genes12040562. [PMID: 33924524 PMCID: PMC8069009 DOI: 10.3390/genes12040562] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
Our understanding of cystic fibrosis (CF) has grown exponentially since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989. With evolving genetic and genomic tools, we have come to better understand the role of CFTR genotypes in the pathophysiology of the disease. This, in turn, has paved the way for the development of modulator therapies targeted at mutations in the CFTR, which are arguably one of the greatest advances in the treatment of CF. These modulator therapies, however, do not target all the mutations in CFTR that are seen in patients with CF and, furthermore, a variation in response is seen in patients with the same genotype who are taking modulator therapies. There is growing evidence to support the role of non-CFTR modifiers, both genetic and environmental, in determining the variation seen in CF morbidity and mortality and also in the response to existing therapies. This review focusses on key findings from studies using candidate gene and genome-wide approaches to identify CF modifier genes of lung disease in cystic fibrosis and considers the interaction between modifiers and the response to modulator therapies. As the use of modulator therapies expands and we gain data around outcomes, it will be of great interest to investigate this interaction further. Going forward, it will also be crucial to better understand the relative influence of genomic versus environmental factors. With this understanding, we can truly begin to deliver personalised care by better profiling the likely disease phenotype for each patient and their response to treatment.
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Affiliation(s)
- Afsoon Sepahzad
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
| | | | - Jane C. Davies
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
- National Heart & Lung Institute, Imperial College London, Emmanuel Kay Building, 1b Manresa Rd, London SW3 6LR, UK
- Correspondence:
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8
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Garred P, Tenner AJ, Mollnes TE. Therapeutic Targeting of the Complement System: From Rare Diseases to Pandemics. Pharmacol Rev 2021; 73:792-827. [PMID: 33687995 PMCID: PMC7956994 DOI: 10.1124/pharmrev.120.000072] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The complement system was discovered at the end of the 19th century as a heat-labile plasma component that "complemented" the antibodies in killing microbes, hence the name "complement." Complement is also part of the innate immune system, protecting the host by recognition of pathogen-associated molecular patterns. However, complement is multifunctional far beyond infectious defense. It contributes to organ development, such as sculpting neuron synapses, promoting tissue regeneration and repair, and rapidly engaging and synergizing with a number of processes, including hemostasis leading to thromboinflammation. Complement is a double-edged sword. Although it usually protects the host, it may cause tissue damage when dysregulated or overactivated, such as in the systemic inflammatory reaction seen in trauma and sepsis and severe coronavirus disease 2019 (COVID-19). Damage-associated molecular patterns generated during ischemia-reperfusion injuries (myocardial infarction, stroke, and transplant dysfunction) and in chronic neurologic and rheumatic disease activate complement, thereby increasing damaging inflammation. Despite the long list of diseases with potential for ameliorating complement modulation, only a few rare diseases are approved for clinical treatment targeting complement. Those currently being efficiently treated include paroxysmal nocturnal hemoglobinuria, atypical hemolytic-uremic syndrome, myasthenia gravis, and neuromyelitis optica spectrum disorders. Rare diseases, unfortunately, preclude robust clinical trials. The increasing evidence for complement as a pathogenetic driver in many more common diseases suggests an opportunity for future complement therapy, which, however, requires robust clinical trials; one ongoing example is COVID-19 disease. The current review aims to discuss complement in disease pathogenesis and discuss future pharmacological strategies to treat these diseases with complement-targeted therapies. SIGNIFICANCE STATEMENT: The complement system is the host's defense friend by protecting it from invading pathogens, promoting tissue repair, and maintaining homeostasis. Complement is a double-edged sword, since when dysregulated or overactivated it becomes the host's enemy, leading to tissue damage, organ failure, and, in worst case, death. A number of acute and chronic diseases are candidates for pharmacological treatment to avoid complement-dependent damage, ranging from the well established treatment for rare diseases to possible future treatment of large patient groups like the pandemic coronavirus disease 2019.
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Affiliation(s)
- Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (P.G.); Departments of Molecular Biology and Biochemistry, Neurobiology and Behavior, and Pathology and Laboratory Medicine, University of California, Irvine, California (A.J.T.); and Research Laboratory, Nordland Hospital, Bodø, Norway, Faculty of Health Sciences, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway (T.E.M.); Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway (T.E.M.); and Department of Immunology, Oslo University Hospital and University of Oslo, Oslo, Norway (T.E.M.)
| | - Andrea J Tenner
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (P.G.); Departments of Molecular Biology and Biochemistry, Neurobiology and Behavior, and Pathology and Laboratory Medicine, University of California, Irvine, California (A.J.T.); and Research Laboratory, Nordland Hospital, Bodø, Norway, Faculty of Health Sciences, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway (T.E.M.); Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway (T.E.M.); and Department of Immunology, Oslo University Hospital and University of Oslo, Oslo, Norway (T.E.M.)
| | - Tom E Mollnes
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (P.G.); Departments of Molecular Biology and Biochemistry, Neurobiology and Behavior, and Pathology and Laboratory Medicine, University of California, Irvine, California (A.J.T.); and Research Laboratory, Nordland Hospital, Bodø, Norway, Faculty of Health Sciences, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway (T.E.M.); Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway (T.E.M.); and Department of Immunology, Oslo University Hospital and University of Oslo, Oslo, Norway (T.E.M.)
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9
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Almughem FA, Aldossary AM, Tawfik EA, Alomary MN, Alharbi WS, Alshahrani MY, Alshehri AA. Cystic Fibrosis: Overview of the Current Development Trends and Innovative Therapeutic Strategies. Pharmaceutics 2020; 12:E616. [PMID: 32630625 PMCID: PMC7407299 DOI: 10.3390/pharmaceutics12070616] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Cystic Fibrosis (CF), an autosomal recessive genetic disease, is caused by a mutation in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). This mutation reduces the release of chloride ions (Cl-) in epithelial tissues, and hyperactivates the epithelial sodium channels (ENaC) which aid in the absorption of sodium ions (Na+). Consequently, the mucus becomes dehydrated and thickened, making it a suitable medium for microbial growth. CF causes several chronic lung complications like thickened mucus, bacterial infection and inflammation, progressive loss of lung function, and ultimately, death. Until recently, the standard of clinical care in CF treatment had focused on preventing and treating the disease complications. In this review, we have summarized the current knowledge on CF pathogenesis and provided an outlook on the current therapeutic approaches relevant to CF (i.e., CFTR modulators and ENaC inhibitors). The enormous potential in targeting bacterial biofilms using antibiofilm peptides, and the innovative therapeutic strategies in using the CRISPR/Cas approach as a gene-editing tool to repair the CFTR mutation have been reviewed. Finally, we have discussed the wide range of drug delivery systems available, particularly non-viral vectors, and the optimal properties of nanocarriers which are essential for successful drug delivery to the lungs.
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Affiliation(s)
- Fahad A. Almughem
- National Centre for Pharmaceutical Technology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia; (F.A.A.); (E.A.T.)
| | - Ahmad M. Aldossary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia; (A.M.A.); (M.N.A.)
| | - Essam A. Tawfik
- National Centre for Pharmaceutical Technology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia; (F.A.A.); (E.A.T.)
| | - Mohammad N. Alomary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia; (A.M.A.); (M.N.A.)
| | - Waleed S. Alharbi
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia;
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia;
| | - Abdullah A. Alshehri
- National Centre for Pharmaceutical Technology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia; (F.A.A.); (E.A.T.)
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10
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The Role of MicroRNA in the Airway Surface Liquid Homeostasis. Int J Mol Sci 2020; 21:ijms21113848. [PMID: 32481719 PMCID: PMC7312818 DOI: 10.3390/ijms21113848] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
Mucociliary clearance, mediated by a coordinated function of cilia bathing in the airway surface liquid (ASL) on the surface of airway epithelium, protects the host from inhaled pathogens and is an essential component of the innate immunity. ASL is composed of the superficial mucus layer and the deeper periciliary liquid. Ion channels, transporters, and pumps coordinate the transcellular and paracellular movement of ions and water to maintain the ASL volume and mucus hydration. microRNA (miRNA) is a class of non-coding, short single-stranded RNA regulating gene expression by post-transcriptional mechanisms. miRNAs have been increasingly recognized as essential regulators of ion channels and transporters responsible for ASL homeostasis. miRNAs also influence the airway host defense. We summarize the most up-to-date information on the role of miRNAs in ASL homeostasis and host-pathogen interactions in the airway and discuss concepts for miRNA-directed therapy.
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11
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Poschet JF, Perkett EA, Timmins GS, Deretic V. Azithromycin and ciprofloxacin have a chloroquine-like effect on respiratory epithelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.29.008631. [PMID: 32511331 PMCID: PMC7239066 DOI: 10.1101/2020.03.29.008631] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is interest in the use of chloroquine/hydroxychloroquine (CQ/HCQ) and azithromycin (AZT) in COVID-19 therapy. Employing cystic fibrosis respiratory epithelial cells, here we show that drugs AZT and ciprofloxacin (CPX) act as acidotropic lipophilic weak bases and confer in vitro effects on intracellular organelles similar to the effects of CQ. These seemingly disparate FDA-approved antimicrobials display a common property of modulating pH of endosomes and trans-Golgi network. We believe this may in part help understand the potentially beneficial effects of CQ/HCQ and AZT in COVID-19, and that the present considerations of HCQ and AZT for clinical trials should be extended to CPX.
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Affiliation(s)
- Jens F. Poschet
- Departments of Molecular Genetics and Microbiology, University of New Mexico Health Science Center
| | - Elizabeth A. Perkett
- Departments of Pediatrics, University of New Mexico Health Science Center
- Departments of Internal Medicine, University of New Mexico Health Science Center
| | - Graham S. Timmins
- Pharmaceutical Sciences, University of New Mexico Health Science Center
| | - Vojo Deretic
- Departments of Molecular Genetics and Microbiology, University of New Mexico Health Science Center
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Science Center
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12
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Wilk MA, Braun AT, Farrell PM, Laxova A, Brown DM, Holt JM, Birch CL, Sosonkina N, Wilk BM, Worthey EA. Applying whole-genome sequencing in relation to phenotype and outcomes in siblings with cystic fibrosis. Cold Spring Harb Mol Case Stud 2020; 6:a004531. [PMID: 32014855 PMCID: PMC6996517 DOI: 10.1101/mcs.a004531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 12/18/2022] Open
Abstract
Variations in disease onset and/or severity have often been observed in siblings with cystic fibrosis (CF), despite the same CFTR genotype and environment. We postulated that genomic variation (modifier and/or pharmacogenomic variants) might explain these clinical discordances. From a cohort of patients included in the Wisconsin randomized clinical trial (RCT) of newborn screening (NBS) for CF, we identified two brothers who showed discordant lung disease courses as children, with one milder and the other more severe than average, and a third, eldest brother, who also has severe lung disease. Leukocytes were harvested as the source of DNA, and whole-genome sequencing (WGS) was performed. Variants were identified and analyzed using in-house-developed informatics tools. Lung disease onset and severity were quantitatively different between brothers during childhood. The youngest, less severely affected brother is homozygous for HFE p.H63D. He also has a very rare PLG p.D238N variant that may influence host-pathogen interaction during chronic lung infection. Other variants of interest were found differentially between the siblings. Pharmacogenomics findings were consistent with the middle, most severely affected brother having poor outcomes to common CF treatments. We conclude that genomic variation between siblings with CF is expected. Variable lung disease severity may be associated with differences acting as genetic modifiers and/or pharmacogenomic factors, but large cohort studies are needed to assess this hypothesis.
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Affiliation(s)
- Melissa A Wilk
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Andrew T Braun
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
| | - Philip M Farrell
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
| | - Anita Laxova
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
| | - Donna M Brown
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - James M Holt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Camille L Birch
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Nadiya Sosonkina
- Department of Genetics, University of Alabama-Birmingham, Birmingham, Alabama 35233, USA
| | - Brandon M Wilk
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Elizabeth A Worthey
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
- Department of Genetics, University of Alabama-Birmingham, Birmingham, Alabama 35233, USA
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13
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Sharma N, Cutting GR. The genetics and genomics of cystic fibrosis. J Cyst Fibros 2019; 19 Suppl 1:S5-S9. [PMID: 31879237 DOI: 10.1016/j.jcf.2019.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023]
Abstract
Genetics is the branch of biology concerned with study of individual genes and how they work whereas genomics is involved with the analysis of all genes and their interactions. Both of these approaches have been applied extensively to CF. Identification of the CFTR gene initiated the dissection of CF genetics at the molecular level. Subsequently, thousands of variants were found in the gene and the functional consequences of a subset have been studied in detail. The completion of the human genome ushered in a new phase of study where the role of genes beyond CFTR could be evaluated for their contribution to the severity of CF. This will be a brief overview of the contribution of these complementary methods to our understanding of CF pathogenesis.
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Affiliation(s)
- N Sharma
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - G R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
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14
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Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells. Int J Mol Sci 2019; 20:ijms20194933. [PMID: 31590401 PMCID: PMC6801718 DOI: 10.3390/ijms20194933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/27/2019] [Accepted: 10/05/2019] [Indexed: 12/23/2022] Open
Abstract
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene lead to cystic fibrosis (CF). The most common mutation F508del inhibits folding and processing of CFTR protein. FDA-approved correctors rescue the biosynthetic processing of F508del-CFTR protein, while potentiators improve the rescued CFTR channel function. Transforming growth factor (TGF-β1), overexpressed in many CF patients, blocks corrector/potentiator rescue by inhibiting CFTR mRNA in vitro. Increased TGF-β1 signaling and acquired CFTR dysfunction are present in other lung diseases. To study the mechanism of TGF-β1 repression of CFTR, we used molecular, biochemical, and functional approaches in primary human bronchial epithelial cells from over 50 donors. TGF-β1 destabilized CFTR mRNA in cells from lungs with chronic disease, including CF, and impaired F508del-CFTR rescue by new-generation correctors. TGF-β1 increased the active pool of selected micro(mi)RNAs validated as CFTR inhibitors, recruiting them to the RNA-induced silencing complex (RISC). Expression of F508del-CFTR globally modulated TGF-β1-induced changes in the miRNA landscape, creating a permissive environment required for degradation of F508del-CFTR mRNA. In conclusion, TGF-β1 may impede the full benefit of corrector/potentiator therapy in CF patients. Studying miRNA recruitment to RISC under disease-specific conditions may help to better characterize the miRNAs utilized by TGF-β1 to destabilize CFTR mRNA.
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15
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Levy H, Jia S, Pan A, Zhang X, Kaldunski M, Nugent ML, Reske M, Feliciano RA, Quintero D, Renda MM, Woods KJ, Murkowski K, Johnson K, Verbsky J, Dasu T, Ideozu JE, McColley S, Quasney MW, Dahmer MK, Avner E, Farrell PM, Cannon CL, Jacob H, Simpson PM, Hessner MJ. Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. Physiol Genomics 2018; 51:27-41. [PMID: 30540547 DOI: 10.1152/physiolgenomics.00109.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Although cystic fibrosis (CF) is attributed to dysfunction of a single gene, the relationships between the abnormal gene product and the development of inflammation and progression of lung disease are not fully understood, which limits our ability to predict an individual patient's clinical course and treatment response. To better understand CF progression, we characterized the molecular signatures of CF disease status with plasma-based functional genomics. Peripheral blood mononuclear cells (PBMCs) from healthy donors were cultured with plasma samples from CF patients ( n = 103) and unrelated, healthy controls ( n = 31). Gene expression levels were measured with an Affymetrix microarray (GeneChip Human Genome U133 Plus 2.0). Peripheral blood samples from a subset of the CF patients ( n = 40) were immunophenotyped by flow cytometry, and the data were compared with historical data for age-matched healthy controls ( n = 351). Plasma samples from another subset of CF patients ( n = 56) and healthy controls ( n = 16) were analyzed by multiplex enzyme-linked immunosorbent assay (ELISA) for numerous cytokines and chemokines. Principal component analysis and hierarchical clustering of induced transcriptional data revealed disease-specific plasma-induced PBMC profiles. Among 1,094 differentially expressed probe sets, 51 genes were associated with pancreatic sufficient status, and 224 genes were associated with infection with Pseudomonas aeruginosa. The flow cytometry and ELISA data confirmed that various immune modulators are relevant contributors to the CF molecular signature. This study provides strong evidence for distinct molecular signatures among CF patients. An understanding of these molecular signatures may lead to unique molecular markers that will enable more personalized prognoses, individualized treatment plans, and rapid monitoring of treatment response.
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Affiliation(s)
- Hara Levy
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago , Chicago, Illinois.,Division of Pulmonary Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Shuang Jia
- Division of Endocrinology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin.,Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Amy Pan
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin.,Division of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Xi Zhang
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago , Chicago, Illinois.,Division of Pulmonary Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Mary Kaldunski
- Division of Endocrinology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin.,Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Melodee L Nugent
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin.,Division of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Melissa Reske
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin
| | - Rachel A Feliciano
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin
| | - Diana Quintero
- Division of Pulmonology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Michael M Renda
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin
| | - Katherine J Woods
- Division of Pediatric Critical Care Medicine, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Kathy Murkowski
- Division of Pediatric Critical Care Medicine, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Keven Johnson
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago , Chicago, Illinois
| | - James Verbsky
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Trivikram Dasu
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Justin Eze Ideozu
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute of Chicago , Chicago, Illinois.,Division of Pulmonary Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Susanna McColley
- Division of Pulmonary Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Michael W Quasney
- Division of Pediatric Critical Care Medicine, University of Michigan Medical School , Ann Arbor, Michigan
| | - Mary K Dahmer
- Division of Pediatric Critical Care Medicine, University of Michigan Medical School , Ann Arbor, Michigan
| | - Ellis Avner
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin.,Division of Nephrology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Philip M Farrell
- Department of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health , Madison, Wisconsin
| | - Carolyn L Cannon
- Division of Pulmonary Medicine, Department of Pediatrics, Baylor College of Medicine , Houston, Texas
| | - Howard Jacob
- Genomic Medicine, Institute for Biotechnology, Hudson Alpha, Huntsville, Alabama
| | - Pippa M Simpson
- Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin.,Division of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Martin J Hessner
- Division of Endocrinology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin.,Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin.,Children's Research Institute of the Children's Hospital of Wisconsin , Milwaukee, Wisconsin
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16
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Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. Am J Hum Genet 2018; 103:535-552. [PMID: 30290150 DOI: 10.1016/j.ajhg.2018.08.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/28/2018] [Indexed: 01/29/2023] Open
Abstract
Although recent studies provide evidence for a common genetic basis between complex traits and Mendelian disorders, a thorough quantification of their overlap in a phenotype-specific manner remains elusive. Here, we have quantified the overlap of genes identified through large-scale genome-wide association studies (GWASs) for 62 complex traits and diseases with genes containing mutations known to cause 20 broad categories of Mendelian disorders. We identified a significant enrichment of genes linked to phenotypically matched Mendelian disorders in GWAS gene sets; of the total 1,240 comparisons, a higher proportion of phenotypically matched or related pairs (n = 50 of 92 [54%]) than phenotypically unmatched pairs (n = 27 of 1,148 [2%]) demonstrated significant overlap, confirming a phenotype-specific enrichment pattern. Further, we observed elevated GWAS effect sizes near genes linked to phenotypically matched Mendelian disorders. Finally, we report examples of GWAS variants localized at the transcription start site or physically interacting with the promoters of genes linked to phenotypically matched Mendelian disorders. Our results are consistent with the hypothesis that genes that are disrupted in Mendelian disorders are dysregulated by non-coding variants in complex traits and demonstrate how leveraging findings from related Mendelian disorders and functional genomic datasets can prioritize genes that are putatively dysregulated by local and distal non-coding GWAS variants.
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17
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The impact of host genetic background in the Pseudomonas aeruginosa respiratory infections. Mamm Genome 2018; 29:550-557. [PMID: 29947963 PMCID: PMC7087806 DOI: 10.1007/s00335-018-9753-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/05/2018] [Indexed: 12/27/2022]
Abstract
Understanding the significance of human genetic diversity in modulating host susceptibility to opportunistic infections is an emerging challenge in the field of respiratory illnesses. While it is recognized that diverse bacterial strains account for differential disease manifestations, emerging data indicate that host genetic diversity is an important determinant factor that influences the severity of opportunistic infections. With particular regard to respiratory illnesses mediated by the gram-negative bacterium Pseudomonas aeruginosa, diverse genetic background is also emerging as a key contributor. Human-genome-wide association studies are a common approach for determining the inter-individual genetic variation associated with variability of the pulmonary infections. Historically, diverse murine inbred mouse strains and ex-vivo cellular models were considered complementary to human studies for establishing the contribution of genetic background to P. aeruginosa respiratory infections. More recently, the development of a new mouse model of infection, mirroring human airway diseases, combined with innovative murine resource populations, modelling human genetic variation, provides additional insights into the mechanisms of genetic susceptibility. In this review, we cover the recent state of the art of human and animal studies and we discuss future potential challenges in the field of P. aeruginosa respiratory infections.
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18
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Lutful Kabir F, Ambalavanan N, Liu G, Li P, Solomon GM, Lal CV, Mazur M, Halloran B, Szul T, Gerthoffer WT, Rowe SM, Harris WT. MicroRNA-145 Antagonism Reverses TGF-β Inhibition of F508del CFTR Correction in Airway Epithelia. Am J Respir Crit Care Med 2018; 197:632-643. [PMID: 29232160 PMCID: PMC6005236 DOI: 10.1164/rccm.201704-0732oc] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022] Open
Abstract
RATIONALE MicroRNAs (miRNAs) destabilize mRNA transcripts and inhibit protein translation. miR-145 is of particular interest in cystic fibrosis (CF) as it has a direct binding site in the 3'-untranslated region of CFTR (cystic fibrosis transmembrane conductance regulator) and is upregulated by the CF genetic modifier TGF (transforming growth factor)-β. OBJECTIVES To demonstrate that miR-145 mediates TGF-β inhibition of CFTR synthesis and function in airway epithelia. METHODS Primary human CF (F508del homozygous) and non-CF airway epithelial cells were grown to terminal differentiation at the air-liquid interface on permeable supports. TGF-β (5 ng/ml), a miR-145 mimic (20 nM), and a miR-145 antagonist (20 nM) were used to manipulate CFTR function. In CF cells, lumacaftor (3 μM) and ivacaftor (10 μM) corrected mutant F508del CFTR. Quantification of CFTR mRNA, protein, and function was done by standard techniques. MEASUREMENTS AND MAIN RESULTS miR-145 is increased fourfold in CF BAL fluid compared with non-CF (P < 0.01) and increased 10-fold in CF primary airway epithelial cells (P < 0.01). Exogenous TGF-β doubles miR-145 expression (P < 0.05), halves wild-type CFTR mRNA and protein levels (P < 0.01), and nullifies lumacaftor/ivacaftor F508del CFTR correction. miR-145 overexpression similarly decreases wild-type CFTR protein synthesis (P < 0.01) and function (P < 0.05), and eliminates F508del corrector benefit. miR-145 antagonism blocks TGF-β suppression of CFTR and enhances lumacaftor correction of F508del CFTR. CONCLUSIONS miR-145 mediates TGF-β inhibition of CFTR synthesis and function in airway epithelia. Specific antagonists to miR-145 interrupt TGF-β signaling to restore F508del CFTR modulation. miR-145 antagonism may offer a novel therapeutic opportunity to enhance therapeutic benefit of F508del CFTR correction in CF epithelia.
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Affiliation(s)
| | | | | | - Peng Li
- Department of Biostatistics, and
| | - George M. Solomon
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama; and
| | | | - Marina Mazur
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama; and
| | | | - Tomasz Szul
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - William T. Gerthoffer
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama
| | - Steven M. Rowe
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - William T. Harris
- Department of Pediatrics
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama; and
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19
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Constrictive Bronchiolitis in Cystic Fibrosis Adolescents with Refractory Pulmonary Decline. Ann Am Thorac Soc 2018; 13:2174-2183. [PMID: 27684511 DOI: 10.1513/annalsats.201412-594oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RATIONALE Refractory lung function decline in association with recurrent pulmonary exacerbations is a common, yet poorly explained finding in cystic fibrosis (CF). To investigate the histopathologic mechanisms of pulmonary deterioration during adolescence and early adulthood, we reviewed clinically-indicated lung biopsy specimens obtained during a period of persistent decline. OBJECTIVES To determine if peribronchiolar remodeling is prominent in lung biopsy specimens obtained in adolescents with CF refractory to conventional therapy. METHODS Six adolescents with CF (mean age, 16.2 y; mean FEV1, 52% predicted at biopsy) with significant pulmonary deterioration over 12-24 months (mean FEV1 decline of 14% predicted/year) despite aggressive intervention underwent computed tomography imaging and ultimately lung biopsy to aid clinical management. In addition to routine clinical evaluation, histopathologic investigation included staining for transforming growth factor-β (TGF-β, a genetic modifier of CF lung disease), collagen deposition (a marker of fibrosis), elastin (to evaluate for bronchiectasis), and α-smooth muscle actin (to identify myofibroblasts). MEASUREMENTS AND MAIN RESULTS All computed tomography scans demonstrated a mix of bronchiectasis and hyperinflation that was variable across lung regions and within patients. Lung biopsy revealed significant peribronchiolar remodeling, particularly in patients with more advanced disease, with near complete obliteration of the peribronchiolar lumen (constrictive bronchiolitis). Myofibroblast differentiation (a TGF-β-dependent process) was prominent in specimens with significant airway remodeling. CONCLUSIONS Constrictive bronchiolitis is widely present in the lung tissue of adolescents with CF with advanced disease and may contribute to impaired lung function that is refractory to conventional therapy (antibiotics, antiinflammatories, and mucolytics). TGF-β-dependent myofibroblast differentiation is prominent in areas of active fibrogenesis and may foster small airway remodeling in CF lung disease.
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20
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Kormann MSD, Dewerth A, Eichner F, Baskaran P, Hector A, Regamey N, Hartl D, Handgretinger R, Antony JS. Transcriptomic profile of cystic fibrosis patients identifies type I interferon response and ribosomal stalk proteins as potential modifiers of disease severity. PLoS One 2017; 12:e0183526. [PMID: 28846703 PMCID: PMC5573219 DOI: 10.1371/journal.pone.0183526] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/04/2017] [Indexed: 12/25/2022] Open
Abstract
Cystic Fibrosis (CF) is the most common monogenic disease among people of Western European descent and caused by mutations in the CFTR gene. However, the disease severity is immensely variable even among patients with similar CFTR mutations due to the possible effect of 'modifier genes'. To identify genetic modifiers, we applied RNA-seq based transcriptomic analyses in CF patients with a mild and severe lung phenotype. Global gene expression and enrichment analyses revealed that genes of the type I interferon response and ribosomal stalk proteins are potential modifiers of CF related lung dysfunction. The results provide a new set of CF modifier genes with possible implications as new therapeutic targets for the treatment of CF.
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Affiliation(s)
- Michael S. D. Kormann
- Department of Pediatrics I, Pediatric Infectiology and Immunology, Translational Genomics and Gene Therapy in Pediatrics, University of Tuebingen, Tuebingen, Germany
| | - Alexander Dewerth
- Department of Pediatrics I, Pediatric Infectiology and Immunology, Translational Genomics and Gene Therapy in Pediatrics, University of Tuebingen, Tuebingen, Germany
| | - Felizitas Eichner
- Department of Pediatrics I, Pediatric Infectiology and Immunology, Translational Genomics and Gene Therapy in Pediatrics, University of Tuebingen, Tuebingen, Germany
| | - Praveen Baskaran
- Center for Quantitative Biology, University of Tuebingen, Tuebingen, Germany
| | - Andreas Hector
- University Children's Clinic Department of Paediatrics I, Paediatric Infectiology & Immunology, University of Tuebingen, Tuebingen, Germany
| | - Nicolas Regamey
- Division of Paediatric Respiratory Medicine and Department of Clinical Research, University of Bern, Bern, Switzerland
- Children’s Hopsital of Lucerne, Paediatric Pulmonology, Lucerne, Switzerland
| | - Dominik Hartl
- University Children's Clinic Department of Paediatrics I, Paediatric Infectiology & Immunology, University of Tuebingen, Tuebingen, Germany
| | - Rupert Handgretinger
- University Children's Clinic Department of Paediatrics I, Hematology and Oncology, University of Tuebingen, Tuebingen, Germany
| | - Justin S. Antony
- Department of Pediatrics I, Pediatric Infectiology and Immunology, Translational Genomics and Gene Therapy in Pediatrics, University of Tuebingen, Tuebingen, Germany
- * E-mail:
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21
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Strug LJ, Gonska T, He G, Keenan K, Ip W, Boëlle PY, Lin F, Panjwani N, Gong J, Li W, Soave D, Xiao B, Tullis E, Rabin H, Parkins MD, Price A, Zuberbuhler PC, Corvol H, Ratjen F, Sun L, Bear CE, Rommens JM. Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics. Hum Mol Genet 2016; 25:4590-4600. [PMID: 28171547 PMCID: PMC5886039 DOI: 10.1093/hmg/ddw290] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/12/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis is realizing the promise of personalized medicine. Recent advances in drug development that target the causal CFTR directly result in lung function improvement, but variability in response is demanding better prediction of outcomes to improve management decisions. The genetic modifier SLC26A9 contributes to disease severity in the CF pancreas and intestine at birth and here we assess its relationship with disease severity and therapeutic response in the airways. SLC26A9 association with lung disease was assessed in individuals from the Canadian and French CF Gene Modifier consortia with CFTR-gating mutations and in those homozygous for the common Phe508del mutation. Variability in response to a CFTR-directed therapy attributed to SLC26A9 genotype was assessed in Canadian patients with gating mutations. A primary airway model system determined if SLC26A9 shows modification of Phe508del CFTR function upon treatment with a CFTR corrector. In those with gating mutations that retain cell surface-localized CFTR we show that SLC26A9 modifies lung function while this is not the case in individuals homozygous for Phe508del where cell surface expression is lacking. Treatment response to ivacaftor, which aims to improve CFTR-channel opening probability in patients with gating mutations, shows substantial variability in response, 28% of which can be explained by rs7512462 in SLC26A9 (P = 0.0006). When homozygous Phe508del primary bronchial cells are treated to restore surface CFTR, SLC26A9 likewise modifies treatment response (P = 0.02). Our findings indicate that SLC26A9 airway modification requires CFTR at the cell surface, and that a common variant in SLC26A9 may predict response to CFTR-directed therapeutics.
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Affiliation(s)
- Lisa J. Strug
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tanja Gonska
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Katherine Keenan
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wan Ip
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre-Yves Boëlle
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital St. Antoine, Biostatistics Department; Inserm U1136, Paris, France
| | - Fan Lin
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Weili Li
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Soave
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Bowei Xiao
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth Tullis
- Department of Respiratory Medicine and Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Harvey Rabin
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- The Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - Michael D. Parkins
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- The Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - April Price
- Division of Paediatric Respirology, Department of Paediatrics, Children's Hospital at London Health Sciences Centre, London, Ontario, Canada
| | | | - Harriet Corvol
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, Paris, France
- AP-HP, Hôpital Trousseau, Pediatric Pulmonary Department; Institut National de la Santé et al Recherche Medicale (INSERM) U938, Paris, France
| | - Felix Ratjen
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Christine E. Bear
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartments of
- Biochemistry
- Physiology
| | - Johanna M. Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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22
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miR-1343 attenuates pathways of fibrosis by targeting the TGF-β receptors. Biochem J 2015; 473:245-56. [PMID: 26542979 DOI: 10.1042/bj20150821] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/05/2015] [Indexed: 12/18/2022]
Abstract
Irreversible respiratory obstruction resulting from progressive airway damage, inflammation and fibrosis is a feature of several chronic respiratory diseases, including cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). The cytokine transforming growth factor β (TGF-β) has a pivotal role in promoting lung fibrosis and is implicated in respiratory disease severity. In the present study, we show that a previously uncharacterized miRNA, miR-1343, reduces the expression of both TGF-β receptor 1 and 2 by directly targeting their 3'-UTRs. After TGF-β exposure, elevated intracellular miR-1343 significantly decreases levels of activated TGF-β effector molecules, pSMAD2 (phosphorylated SMAD2) and pSMAD3 (phosphorylated SMAD3), when compared with a non-targeting control miRNA. As a result, the abundance of fibrotic markers is reduced, cell migration into a scratch wound impaired and epithelial-to-mesenchymal transition (EMT) repressed. Mature miR-1343 is readily detected in human neutrophils and HL-60 cells and is activated in response to stress in A549 lung epithelial cells. miR-1343 may have direct therapeutic applications in fibrotic lung disease.
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23
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Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis. Nat Commun 2015; 6:8382. [PMID: 26417704 PMCID: PMC4589222 DOI: 10.1038/ncomms9382] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 08/17/2015] [Indexed: 02/06/2023] Open
Abstract
The identification of small molecules that target specific CFTR variants has ushered in a new era of treatment for cystic fibrosis (CF), yet optimal, individualized treatment of CF will require identification and targeting of disease modifiers. Here we use genome-wide association analysis to identify genetic modifiers of CF lung disease, the primary cause of mortality. Meta-analysis of 6,365 CF patients identifies five loci that display significant association with variation in lung disease. Regions on chr3q29 (MUC4/MUC20; P=3.3 × 10(-11)), chr5p15.3 (SLC9A3; P=6.8 × 10(-12)), chr6p21.3 (HLA Class II; P=1.2 × 10(-8)) and chrXq22-q23 (AGTR2/SLC6A14; P=1.8 × 10(-9)) contain genes of high biological relevance to CF pathophysiology. The fifth locus, on chr11p12-p13 (EHF/APIP; P=1.9 × 10(-10)), was previously shown to be associated with lung disease. These results provide new insights into potential targets for modulating lung disease severity in CF.
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Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis. PLoS Genet 2015; 11:e1005273. [PMID: 26047157 PMCID: PMC4457883 DOI: 10.1371/journal.pgen.1005273] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/12/2015] [Indexed: 12/22/2022] Open
Abstract
Discovery of rare or low frequency variants in exome or genome data that are associated with complex traits often will require use of very large sample sizes to achieve adequate statistical power. For a fixed sample size, sequencing of individuals sampled from the tails of a phenotype distribution (i.e., extreme phenotypes design) maximizes power and this approach was recently validated empirically with the discovery of variants in DCTN4 that influence the natural history of P. aeruginosa airway infection in persons with cystic fibrosis (CF; MIM219700). The increasing availability of large exome/genome sequence datasets that serve as proxies for population-based controls affords the opportunity to test an alternative, potentially more powerful and generalizable strategy, in which the frequency of rare variants in a single extreme phenotypic group is compared to a control group (i.e., extreme phenotype vs. control population design). As proof-of-principle, we applied this approach to search for variants associated with risk for age-of-onset of chronic P. aeruginosa airway infection among individuals with CF and identified variants in CAV2 and TMC6 that were significantly associated with group status. These results were validated using a large, prospective, longitudinal CF cohort and confirmed a significant association of a variant in CAV2 with increased age-of-onset of P. aeruginosa airway infection (hazard ratio = 0.48, 95% CI=[0.32, 0.88]) and variants in TMC6 with diminished age-of-onset of P. aeruginosa airway infection (HR = 5.4, 95% CI=[2.2, 13.5]) A strong interaction between CAV2 and TMC6 variants was observed (HR=12.1, 95% CI=[3.8, 39]) for children with the deleterious TMC6 variant and without the CAV2 protective variant. Neither gene showed a significant association using an extreme phenotypes design, and conditions for which the power of an extreme phenotype vs. control population design was greater than that for the extreme phenotypes design were explored. Whole exome and whole genome sequencing provide the opportunity to test for associations between expressed traits and genetic variants that cannot be tested with chip technology, particularly variants that are too rare to be included on chips designed for genome-wide association analysis. We used exome sequencing to identify variants in CAV2 and TMC6 that modify the age-of-onset of chronic Pseudomonas aeruginosa infection among children with cystic fibrosis, and validated our findings in a large cohort of children with cystic fibrosis. For a fixed number of study participants, it is known that the extreme phenotypes design provides greater statistical power than a random sampling design. In the extreme phenotypes design, one compares the frequency of a given set of genetic variants in one extreme of age-of-onset (early onset) to that in the other extreme (late onset). Here, we employed an alternative design that compares genetic frequencies in exomes sampled from one extreme to that among exomes from a large set of controls. We show that this design confers substantially greater statistical power for discovery of CAV2 and TMC6 and provide general conditions under which this single extreme versus control design is more powerful than the extreme phenotypes design.
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Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Hum Mol Genet 2014; 24:1908-17. [PMID: 25489051 DOI: 10.1093/hmg/ddu607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Predicting the impact of genetic variation on human health remains an important and difficult challenge. Often, algorithmic classifiers are tasked with predicting binary traits (e.g. positive or negative for a disease) from missense variation. Though useful, this arrangement is limiting and contrived, because human diseases often comprise a spectrum of severities, rather than a discrete partitioning of patient populations. Furthermore, labeling variants as causal or benign can be error prone, which is problematic for training supervised learning algorithms (the so-called garbage in, garbage out phenomenon). We explore the potential value of training classifiers using continuous-valued quantitative measurements, rather than binary traits. Using 20 variants from cystic fibrosis transmembrane conductance regulator (CFTR) nucleotide-binding domains and six quantitative measures of cystic fibrosis (CF) severity, we trained classifiers to predict CF severity from CFTR variants. Employing cross validation, classifier prediction and measured clinical/functional values were significantly correlated for four of six quantitative traits (correlation P-values from 1.35 × 10(-4) to 4.15 × 10(-3)). Classifiers were also able to stratify variants by three clinically relevant risk categories with 85-100% accuracy, depending on which of the six quantitative traits was used for training. Finally, we characterized 11 additional CFTR variants using clinical sweat chloride testing, two functional assays, or all three diagnostics, and validated our classifier using blind prediction. Predictions were within the measured sweat chloride range for seven of eight variants, and captured the differential impact of specific variants on the two functional assays. This work demonstrates a promising and novel framework for assessing the impact of genetic variation.
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Affiliation(s)
- David L Masica
- Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | - Rachel Karchin
- Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Abstract
The availability of the human genome sequence and tools for interrogating individual genomes provide an unprecedented opportunity to apply genetics to medicine. Mendelian conditions, which are caused by dysfunction of a single gene, offer powerful examples that illustrate how genetics can provide insights into disease. Cystic fibrosis, one of the more common lethal autosomal recessive Mendelian disorders, is presented here as an example. Recent progress in elucidating disease mechanism and causes of phenotypic variation, as well as in the development of treatments, demonstrates that genetics continues to play an important part in cystic fibrosis research 25 years after the discovery of the disease-causing gene.
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Sun H, Harris WT, Kortyka S, Kotha K, Ostmann AJ, Rezayat A, Sridharan A, Sanders Y, Naren AP, Clancy JP. Tgf-beta downregulation of distinct chloride channels in cystic fibrosis-affected epithelia. PLoS One 2014; 9:e106842. [PMID: 25268501 PMCID: PMC4182049 DOI: 10.1371/journal.pone.0106842] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/05/2014] [Indexed: 01/15/2023] Open
Abstract
Rationale The cystic fibrosis transmembrane conductance regulator (CFTR) and Calcium-activated Chloride Conductance (CaCC) each play critical roles in maintaining normal hydration of epithelial surfaces including the airways and colon. TGF-beta is a genetic modifier of cystic fibrosis (CF), but how it influences the CF phenotype is not understood. Objectives We tested the hypothesis that TGF-beta potently downregulates chloride-channel function and expression in two CF-affected epithelia (T84 colonocytes and primary human airway epithelia) compared with proteins known to be regulated by TGF-beta. Measurements and Main Results TGF-beta reduced CaCC and CFTR-dependent chloride currents in both epithelia accompanied by reduced levels of TMEM16A and CFTR protein and transcripts. TGF-beta treatment disrupted normal regulation of airway-surface liquid volume in polarized primary human airway epithelia, and reversed F508del CFTR correction produced by VX-809. TGF-beta effects on the expression and activity of TMEM16A, wtCFTR and corrected F508del CFTR were seen at 10-fold lower concentrations relative to TGF-beta effects on e-cadherin (epithelial marker) and vimentin (mesenchymal marker) expression. TGF-beta downregulation of TMEM16A and CFTR expression were partially reversed by Smad3 and p38 MAPK inhibition, respectively. Conclusions TGF-beta is sufficient to downregulate two critical chloride transporters in two CF-affected tissues that precedes expression changes of two distinct TGF-beta regulated proteins. Our results provide a plausible mechanism for CF-disease modification by TGF-beta through effects on CaCC.
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Affiliation(s)
- Hongtao Sun
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - William T. Harris
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Stephanie Kortyka
- University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Kavitha Kotha
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Alicia J. Ostmann
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Amir Rezayat
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Anusha Sridharan
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yan Sanders
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Anjaparavanda P. Naren
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - John P. Clancy
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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Gallati S. Disease-modifying genes and monogenic disorders: experience in cystic fibrosis. APPLICATION OF CLINICAL GENETICS 2014; 7:133-46. [PMID: 25053892 PMCID: PMC4104546 DOI: 10.2147/tacg.s18675] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The mechanisms responsible for the determination of phenotypes are still not well understood; however, it has become apparent that modifier genes must play a considerable role in the phenotypic heterogeneity of Mendelian disorders. Significant advances in genetic technologies and molecular medicine allow huge amounts of information to be generated from individual samples within a reasonable time frame. This review focuses on the role of modifier genes using the example of cystic fibrosis, the most common lethal autosomal recessive disorder in the white population, and discusses the advantages and limitations of candidate gene approaches versus genome-wide association studies. Moreover, the implications of modifier gene research for other monogenic disorders, as well as its significance for diagnostic, prognostic, and therapeutic approaches are summarized. Increasing insight into modifying mechanisms opens up new perspectives, dispelling the idea of genetic disorders being caused by one single gene.
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Affiliation(s)
- Sabina Gallati
- Division of Human Genetics, Department of Pediatrics, and Department of Clinical Research, Inselspital, University of Berne, Berne, Switzerland
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Coutinho CAAC, Marson FAL, Marcelino ARB, Bonadia LC, Carlin MP, Ribeiro AF, Ribeiro JD, Bertuzzo CS. TNF-alpha polymorphisms as a potential modifier gene in the cystic fibrosis. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2014; 5:87-99. [PMID: 24959313 PMCID: PMC4065397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/21/2014] [Indexed: 06/03/2023]
Abstract
Modifier genes, as the TNF-α gene, can modulate the cystic fibrosis (CF) severity. Thus, -238G>A and -308G>A polymorphisms of TNF-α gene were analyzed as modifiers of CF. In this context, the present study enrolled 49 CF patients (diagnosis performed by sweat test and complete CFTR screening). The -238G>A polymorphism analysis was performed by ARMS-PCR, and -308G>A, by PCR-RFLP. In our data, the -238G>A polymorphism was not associated with clinical variability. The AA genotype for -308G>A polymorphism was a risk factor for early gastrointestinal symptoms (OR=5.98, 95%CI=1.06-49.68) and protection for the first Pseudomonas aeruginosa (OR=0.05, 95%CI=0.0003-0.007). For the first P. aeruginosa, GA genotype was a risk factor (OR=10.2, 95%CI=1.86-84.09); for the same genotype, the diagnosis was made in minor time than the AA genotype (p=0.031). Considering the -308G>A polymorphism alleles, the G allele was a risk factor for early pulmonary symptoms (OR=3.81, 95%CI=1.13-12.97) and P. aeruginosa (OR=66.77, 95%CI=15.18-482.7); however, the same allele showed better transcutaneous oxygen saturation (OR=9.24, 95%CI=1.53-206.1). The A allele was a protective factor for early pulmonary symptoms (OR=12.26, 95%CI=0.08-0.89) and P. aeruginosa (OR=12.15, 95%CI=0002-0007), however, the same allele was a risk factor for worst transcutaneous oxygen saturation (OR=7.01, 95%CI=1.14-157.4). As conclusion, the -308G>A polymorphism of the TNF-α gene was associated with the CF severity.
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Affiliation(s)
- Cyntia AAC Coutinho
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Fernando AL Marson
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
- Department of Pediatrics, School of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Aline RB Marcelino
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Luciana C Bonadia
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Marcelo P Carlin
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Antonio F Ribeiro
- Department of Pediatrics, School of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Jose D Ribeiro
- Department of Pediatrics, School of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
| | - Carmen S Bertuzzo
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas13081-970, P.O. Box: 6111, Campinas, SP, Brazil
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Harris WT, Kelly DR, Zhou Y, Wang D, MacEwen M, Hagood JS, Clancy JP, Ambalavanan N, Sorscher EJ. Myofibroblast differentiation and enhanced TGF-B signaling in cystic fibrosis lung disease. PLoS One 2013; 8:e70196. [PMID: 23950911 PMCID: PMC3741283 DOI: 10.1371/journal.pone.0070196] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/14/2013] [Indexed: 12/15/2022] Open
Abstract
Rationale TGF-β, a mediator of pulmonary fibrosis, is a genetic modifier of CF respiratory deterioration. The mechanistic relationship between TGF-β signaling and CF lung disease has not been determined. Objective To investigate myofibroblast differentiation in CF lung tissue as a novel pathway by which TGF-β signaling may contribute to pulmonary decline, airway remodeling and tissue fibrosis. Methods Lung samples from CF and non-CF subjects were analyzed morphometrically for total TGF-β1, TGF-β signaling (Smad2 phosphorylation), myofibroblast differentiation (α-smooth muscle actin), and collagen deposition (Masson trichrome stain). Results TGF-β signaling and fibrosis are markedly increased in CF (p<0.01), and the presence of myofibroblasts is four-fold higher in CF vs. normal lung tissue (p<0.005). In lung tissue with prominent TGF-β signaling, both myofibroblast differentiation and tissue fibrosis are significantly augmented (p<0.005). Conclusions These studies establish for the first time that a pathogenic mechanism described previously in pulmonary fibrosis is also prominent in cystic fibrosis lung disease. The presence of TGF-β dependent signaling in areas of prominent myofibroblast proliferation and fibrosis in CF suggests that strategies under development for other pro-fibrotic lung conditions may also be evaluated for use in CF.
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Affiliation(s)
- William T Harris
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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Alonso A, Marsal S, Tortosa R, Canela-Xandri O, Julià A. GStream: improving SNP and CNV coverage on genome-wide association studies. PLoS One 2013; 8:e68822. [PMID: 23844243 PMCID: PMC3700900 DOI: 10.1371/journal.pone.0068822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/03/2013] [Indexed: 11/22/2022] Open
Abstract
We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.
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Affiliation(s)
- Arnald Alonso
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
- Department of ESAII, Polytechnical University of Catalonia, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Raül Tortosa
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Oriol Canela-Xandri
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
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Dysregulated proinflammatory and fibrogenic phenotype of fibroblasts in cystic fibrosis. PLoS One 2013; 8:e64341. [PMID: 23734196 PMCID: PMC3667188 DOI: 10.1371/journal.pone.0064341] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/27/2013] [Indexed: 11/19/2022] Open
Abstract
Morbi-mortality in cystic fibrosis (CF) is mainly related to chronic lung infection and inflammation, uncontrolled tissue rearrangements and fibrosis, and yet the underlying mechanisms remain largely unknown. We evaluated inflammatory and fibrosis responses to bleomycin in F508del homozygous and wild-type mice, and phenotype of fibroblasts explanted from mouse lungs and skin. The effect of vardenafil, a cGMP-specific phosphodiesterase type 5 inhibitor, was tested in vivo and in culture. Responses of proinflammatory and fibrotic markers to bleomycin were enhanced in lungs and skin of CF mice and were prevented by treatment with vardenafil. Purified lung and skin fibroblasts from CF mice proliferated and differentiated into myofibroblasts more prominently and displayed higher sensitivity to growth factors than those recovered from wild-type littermates. Under inflammatory stimulation, mRNA and protein expression of proinflammatory mediators were higher in CF than in wild-type fibroblasts, in which CFTR expression reached similar levels to those observed in other non-epithelial cells, such as macrophages. Increased proinflammatory responses in CF fibroblasts were reduced by half with submicromolar concentrations of vardenafil. Proinflammatory and fibrogenic functions of fibroblasts are upregulated in CF and are reduced by vardenafil. This study provides compelling new support for targeting cGMP signaling pathway in CF pharmacotherapy.
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Tgf-β1 inhibits Cftr biogenesis and prevents functional rescue of ΔF508-Cftr in primary differentiated human bronchial epithelial cells. PLoS One 2013; 8:e63167. [PMID: 23671668 PMCID: PMC3650079 DOI: 10.1371/journal.pone.0063167] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
CFTR is an integral transmembrane glycoprotein and a cAMP-activated Cl(-) channel. Mutations in the CFTR gene lead to Cystic Fibrosis (CF)-an autosomal recessive disease with majority of the morbidity and mortality resulting from airway infection, inflammation, and fibrosis. The most common disease-associated mutation in the CFTR gene-deletion of Phe508 (ΔF508) leads to a biosynthetic processing defect of CFTR. Correction of the defect and delivery of ΔF508-CFTR to the cell surface has been highly anticipated as a disease modifying therapy. Compared to promising results in cultured cell this approach was much less effective in CF patients in an early clinical trial. Although the cause of failure to rescue ΔF508-CFTR in the clinical trial has not been determined, presence of factor(s) that interfere with the rescue in vivo could be considered. The cytokine TGF-β1 is frequently elevated in CF patients. TGF-β1 has pleiotropic effects in different disease models and genetic backgrounds and little is known about TGF-β1 effects on CFTR in human airway epithelial cells. Moreover, there are no published studies examining TGF-β1 effects on the functional rescue of ΔF508-CFTR. Here we found that TGF-β1 inhibits CFTR biogenesis by reducing mRNA levels and protein abundance in primary differentiated human bronchial epithelial (HBE) cells from non-CF individuals. TGF-β1 inhibits CFTR biogenesis without compromising the epithelial phenotype or integrity of HBE cells. TGF-β1 also inhibits biogenesis and impairs the functional rescue of ΔF508-CFTR in HBE cells from patients homozygous for the ΔF508 mutation. Our data indicate that activation of TGF-β1 signaling may inhibit CFTR function in non-CF individuals and may interfere with therapies directed at correcting the processing defect of ΔF508-CFTR in CF patients.
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Weiler CA, Drumm ML. Genetic influences on cystic fibrosis lung disease severity. Front Pharmacol 2013; 4:40. [PMID: 23630497 PMCID: PMC3632778 DOI: 10.3389/fphar.2013.00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/21/2013] [Indexed: 12/19/2022] Open
Abstract
Understanding the causes of variation in clinical manifestations of disease should allow for design of new or improved therapeutic strategies to treat the disease. If variation is caused by genetic differences between individuals, identifying the genes involved should present therapeutic targets, either in the proteins encoded by those genes or the pathways in which they function. The technology to identify and genotype the millions of variants present in the human genome has evolved rapidly over the past two decades. Originally only a small number of polymorphisms in a small number of subjects could be studied realistically, but speed and scope have increased nearly as dramatically as cost has decreased, making it feasible to determine genotypes of hundreds of thousands of polymorphisms in thousands of subjects. The use of such genetic technology has been applied to cystic fibrosis (CF) to identify genetic variation that alters the outcome of this single gene disorder. Candidate gene strategies to identify these variants, referred to as “modifier genes,” has yielded several genes that act in pathways known to be important in CF and for these the clinical implications are relatively clear. More recently, whole-genome surveys that probe hundreds of thousands of variants have been carried out and have identified genes and chromosomal regions for which a role in CF is not at all clear. Identification of these genes is exciting, as it provides the possibility for new areas of therapeutic development.
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Affiliation(s)
- Colleen A Weiler
- Department of Pediatrics, Case Western Reserve University Cleveland, OH, USA
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Clinical and molecular characterization of the potential CF disease modifier syntaxin 1A. Eur J Hum Genet 2013; 21:1462-6. [PMID: 23572023 DOI: 10.1038/ejhg.2013.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/25/2013] [Accepted: 02/22/2013] [Indexed: 02/02/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator gene (CFTR). Disease severity in CF varies greatly, and sibling studies strongly indicate that genes other than CFTR modify disease outcome. Syntaxin 1A (STX1A) has been reported as a negative regulator of CFTR and other ion channels. We hypothesized that STX1A variants act as a CF modifier by influencing the remaining function of mutated CFTR. We identified STX1A variants by genomic resequencing patients from the Bernese CF Patient Data Registry and applied linear mixed model analysis to establish genotype-phenotype correlations, revealing STX1A rs4363087 (c.467-38A>G) to significantly influence lung function. The same STX1A risk allele was recognized in the European CF Twin and Sibling Study (P=0.0027), demonstrating that the genotype-phenotype association of STX1A to CF disease severity is robust enough to allow replication in two independent CF populations. rs4363087 is in linkage disequilibrium to the exonic variant rs2228607 (c.204C>T). Considering that neither rs4363087 nor rs2228607 changes the amino-acid sequence of STX1A, we investigated their effects on mRNA level. We show that rs2228607 reinforces aberrant splicing of STX1A mRNA, leading to nonsense-mediated mRNA decay. In conclusion, we demonstrate the clinical relevance of STX1A variants in CF, and evidence the functional relevance of STX1A variant rs2228607 at molecular level. Our findings show that genes interacting with CFTR can modify CF disease progression.
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36
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Knowles MR, Drumm M. The influence of genetics on cystic fibrosis phenotypes. Cold Spring Harb Perspect Med 2012; 2:a009548. [PMID: 23209180 DOI: 10.1101/cshperspect.a009548] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Technological advances in genetics have made feasible and affordable large studies to identify genetic variants that cause or modify a trait. Genetic studies have been carried out to assess variants in candidate genes, as well as polymorphisms throughout the genome, for their associations with heritable clinical outcomes of cystic fibrosis (CF), such as lung disease, meconium ileus, and CF-related diabetes. The candidate gene approach has identified some predicted relationships, while genome-wide surveys have identified several genes that would not have been obvious disease-modifying candidates, such as a methionine sulfoxide transferase gene that influences intestinal obstruction, or a region on chromosome 11 proximate to genes encoding a transcription factor and an apoptosis controller that associates with lung function. These unforeseen associations thus provide novel insight into disease pathophysiology, as well as suggesting new therapeutic strategies for CF.
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Affiliation(s)
- Michael R Knowles
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
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Green DM, Collaco JM, McDougal KE, Naughton KM, Blackman SM, Cutting GR. Heritability of respiratory infection with Pseudomonas aeruginosa in cystic fibrosis. J Pediatr 2012; 161:290-5.e1. [PMID: 22364820 PMCID: PMC3682831 DOI: 10.1016/j.jpeds.2012.01.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 10/21/2011] [Accepted: 01/19/2012] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To quantify the relative contribution of factors other than cystic fibrosis transmembrane conductance regulator genotype and environment on the acquisition of Pseudomonas aeruginosa (Pa) by patients with cystic fibrosis. STUDY DESIGN Lung infection with Pa and mucoid Pa was assessed using a co-twin study design of 44 monozygous (MZ) and 17 dizygous (DZ) twin pairs. Two definitions were used to establish infection: first positive culture and persistent positive culture. Genetic contribution to infection (ie, heritability) was estimated based on concordance analysis, logistic regression, and age at onset of infection through comparison of intraclass correlation coefficients. RESULTS Concordance for persistent Pa infection was higher in MZ (0.83; 25 of 30 pairs) than DZ twins (0.45; 5 of 11 pairs), generating a heritability of 0.76. Logistic regression adjusted for age corroborated genetic control of persistent Pa infection. The correlation for age at persistent Pa infection was higher in MZ twins (0.589; 95% CI, 0.222-0.704) than in DZ twins (0.162; 95% CI, -0.352 to 0.607), generating a heritability of 0.85. CONCLUSION Genetic modifiers play a significant role in the establishment and timing of persistent Pa infection in individuals with cystic fibrosis.
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Affiliation(s)
- Deanna M. Green
- Division of Pediatric Pulmonary and Sleep Medicine, Duke University Medical Center, Durham, NC
| | - J. Michael Collaco
- Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine
| | - Kathryn E. McDougal
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University School of Medicine
| | - Kathleen M. Naughton
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Scott M. Blackman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) functions as a channel that regulates the transport of ions and the movement of water across the epithelial barrier. Mutations in CFTR, which form the basis for the clinical manifestations of cystic fibrosis, affect the epithelial innate immune function in the lung, resulting in exaggerated and ineffective airway inflammation that fails to eradicate pulmonary pathogens. Compounding the effects of excessive neutrophil recruitment, the mutant CFTR channel does not transport antioxidants to counteract neutrophil-associated oxidative stress. Whereas mutant CFTR expression in leukocytes outside of the lung does not markedly impair their function, the expected regulation of inflammation in the airways is clearly deficient in cystic fibrosis. The resulting bacterial infections, which are caused by organisms that have substantial genetic and metabolic flexibility, can resist multiple classes of antibiotics and evade phagocytic clearance. The development of animal models that approximate the human pulmonary phenotypes-airway inflammation and spontaneous infection-may provide the much-needed tools to establish how CFTR regulates mucosal immunity and to test directly the effect of pharmacologic potentiation and correction of mutant CFTR function on bacterial clearance.
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Cordovado S, Hendrix M, Greene C, Mochal S, Earley M, Farrell P, Kharrazi M, Hannon W, Mueller P. CFTR mutation analysis and haplotype associations in CF patients. Mol Genet Metab 2012; 105:249-54. [PMID: 22137130 PMCID: PMC3551260 DOI: 10.1016/j.ymgme.2011.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/20/2011] [Accepted: 10/20/2011] [Indexed: 11/24/2022]
Abstract
Most newborn screening (NBS) laboratories use second-tier molecular tests for cystic fibrosis (CF) using dried blood spots (DBS). The Centers for Disease Control and Prevention's NBS Quality Assurance Program offers proficiency testing (PT) in DBS for CF transmembrane conductance regulator (CFTR) gene mutation detection. Extensive molecular characterization on 76 CF patients, family members or screen positive newborns was performed for quality assurance. The coding, regulatory regions and portions of all introns were sequenced and large insertions/deletions were characterized as well as two intronic di-nucleotide microsatellites. For CF patient samples, at least two mutations were identified/verified and four specimens contained three likely CF-associated mutations. Thirty-four sequence variations in 152 chromosomes were identified, five of which were not previously reported. Twenty-seven of these variants were used to predict haplotypes from the major haplotype block defined by HapMap data that spans the promoter through intron 19. Chromosomes containing the F508del (p.Phe508del), G542X (p.Gly542X) and N1303K (p.Asn1303Lys) mutations shared a common haplotype subgroup, consistent with a common ancient European founder. Understanding the haplotype background of CF-associated mutations in the U.S. population provides a framework for future phenotype/genotype studies and will assist in determining a likely cis/trans phase of the mutations without need for parent studies.
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Affiliation(s)
- S.K. Cordovado
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
- Corresponding author. Fax: +1 770 488 4005, (S.K. Cordovado)
| | - M. Hendrix
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - C.N. Greene
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - S. Mochal
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - M.C. Earley
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - P.M. Farrell
- University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, Madison, WI, USA
| | - M. Kharrazi
- California Department of Public Health, Richmond, CA 94804, USA
| | - W.H. Hannon
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - P.W. Mueller
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
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40
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Drumm ML, Ziady AG, Davis PB. Genetic variation and clinical heterogeneity in cystic fibrosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2011; 7:267-82. [PMID: 22017581 DOI: 10.1146/annurev-pathol-011811-120900] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis (CF), a lethal genetic disease, is characterized by substantial clinical heterogeneity. Work over the past decade has established that much of the variation is genetically conferred, and recent studies have begun to identify chromosomal locations that identify specific genes as contributing to this variation. Transcriptomic and proteomic data, sampling hundreds and thousands of genes and their products, point to pathways that are altered in the cells and tissues of CF patients. Genetic studies have examined more than half a million polymorphic sites and have identified regions, and probably genes, that contribute to the clinical heterogeneity. The combination of these approaches has great potential because genetic profiling identifies putative disease-modifying processes, and transcript and protein profiling is shedding light on the biology involved. Such studies are providing new insights into the disease, such as altered apoptotic responses, oxidative stress dysregulation, and neuronal involvement, all of which may open new therapeutic avenues to exploration.
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Affiliation(s)
- Mitchell L Drumm
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.
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41
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Harris WT, Muhlebach MS, Oster RA, Knowles MR, Clancy JP, Noah TL. Plasma TGF-β₁ in pediatric cystic fibrosis: potential biomarker of lung disease and response to therapy. Pediatr Pulmonol 2011; 46:688-95. [PMID: 21337732 PMCID: PMC3115503 DOI: 10.1002/ppul.21430] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 12/21/2010] [Accepted: 12/23/2010] [Indexed: 11/11/2022]
Abstract
INTRODUCTION Transforming growth factor beta-1 (TGF-β₁) is an important genetic modifier of lung disease severity in cystic fibrosis (CF), yet the mechanism behind this disease association remains unknown. Initial steps in the investigation of the relationship between TGF-β₁ and CF lung disease include determining the most appropriate available biospecimen for TGF-β₁ protein measurement. HYPOTHESIS In hospitalized pediatric CF patients, plasma TGF-β₁ is increased in association with clinical parameters of lung disease severity. METHODS Serum and plasma were obtained pre- and post-intravenous antibiotic therapy in pediatric CF patients hospitalized for a pulmonary exacerbation. Total TGF-β₁ , measured via ELISA, was compared with markers of lung disease, including airway microbiology, lung function, and response to therapy. RESULTS Forty CF children were studied, 15 of whom underwent bronchoalveolar lavage (BAL) at the time of admission. Plasma TGF-β₁ positively correlated with BAL fluid (BALF) TGF-β₁ (r=0.59, P<0.05). Admission plasma TGF-β₁ was increased in subjects positive for Pseudomonas aeruginosa (P=0.014) and was inversely associated with diminished lung function (P<0.038) after therapy. Treatment with antibiotics significantly decreased plasma TGF-β(1) (P<0.001). Serum TGF-β₁ was not associated with plasma TGF-β(1) , BALF TGF-β₁, or these clinical parameters of lung disease. CONCLUSION In pediatric CF, plasma (but not serum) TGF-β₁ is increased in association with Pseudomonas infection and lung disease, and is reduced in response to therapy. These findings emphasize the importance of optimizing biospecimen selection for future studies investigating the role of TGF-β(1) in CF lung disease.
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Affiliation(s)
- William T Harris
- Division of Pulmonology, Department of Pediatrics, University of Alabama at Birmingham, 1600 7th Avenue South, Birmingham, AL 35233-1711, USA.
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Özgüç M. Genetic testing: predictive value of genotyping for diagnosis and management of disease. EPMA J 2011; 2:173-9. [PMID: 23199147 PMCID: PMC3405385 DOI: 10.1007/s13167-011-0077-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/29/2011] [Indexed: 12/13/2022]
Abstract
This article describes predictive, preventive value of genetic tests and the implication of the use of testing for personalized treatment. This year marks the 10th anniversity of publishing of the sequence of the human genome. One important area of application of this mega project is a development of genetic tests for mutation detection in single gene disorders that has impact for pediatric age group patients and analyzing susceptibility genes as risk factors in common disorders. Types of genetic tests, new emerging technologies will enable developments of high-throughput approaches by microarrays of great application capacity as described here. As it is usual for all technologies used in health care, bioethical concerns has to be delt with. The ethical, social and governance issues associated with genetic testing are discussed.
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Affiliation(s)
- Meral Özgüç
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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43
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Wright FA, Strug LJ, Doshi VK, Commander CW, Blackman SM, Sun L, Berthiaume Y, Cutler D, Cojocaru A, Collaco JM, Corey M, Dorfman R, Goddard K, Green D, Kent JW, Lange EM, Lee S, Li W, Luo J, Mayhew GM, Naughton KM, Pace RG, Paré P, Rommens JM, Sandford A, Stonebraker JR, Sun W, Taylor C, Vanscoy LL, Zou F, Blangero J, Zielenski J, O'Neal WK, Drumm ML, Durie PR, Knowles MR, Cutting GR. Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet 2011; 43:539-46. [PMID: 21602797 PMCID: PMC3296486 DOI: 10.1038/ng.838] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
Abstract
A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.
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Affiliation(s)
- Fred A Wright
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Abstract
In the past three decades, scientists have had immense success in identifying genes and their variants that contribute to an array of diseases. While the identification of such genetic variants has informed our knowledge of the etiologic bases of diseases, there continues to be a substantial gap in our understanding of the factors that modify disease severity. Monogenic diseases provide an opportunity to identify modifiers as they have uniform etiology, detailed phenotyping of affected individuals, and familial clustering. Cystic fibrosis (CF) is among the more common life-shortening recessive disorders that displays wide variability in clinical features and survival. Considerable progress has been made in elucidating the contribution of genetic and nongenetic factors to CF. Allelic variation in CFTR, the gene responsible for CF, correlates with some aspects of the disease. However, lung function, neonatal intestinal obstruction, diabetes, and anthropometry display strong genetic control independent of CFTR, and candidate gene studies have revealed genetic modifiers underlying these traits. The application of genome-wide techniques holds great promise for the identification of novel genetic variants responsible for the heritable features and complications of CF. Since the genetic modifiers are known to alter the course of disease, their protein products become immediate targets for therapeutic intervention.
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Affiliation(s)
- Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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45
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Kong X, Cho MH, Anderson W, Coxson HO, Muller N, Washko G, Hoffman EA, Bakke P, Gulsvik A, Lomas DA, Silverman EK, Pillai SG. Genome-wide association study identifies BICD1 as a susceptibility gene for emphysema. Am J Respir Crit Care Med 2011; 183:43-9. [PMID: 20709820 PMCID: PMC3040393 DOI: 10.1164/rccm.201004-0541oc] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 08/12/2010] [Indexed: 01/17/2023] Open
Abstract
RATIONALE chronic obstructive pulmonary disease (COPD), characterized by airflow limitation, is a disorder with high phenotypic and genetic heterogeneity. Pulmonary emphysema is a major but variable component of COPD; familial data suggest that different components of COPD, such as emphysema, may be influenced by specific genetic factors. OBJECTIVES to identify genetic determinants of emphysema assessed through high-resolution chest computed tomography in individuals with COPD. METHODS we performed a genome-wide association study (GWAS) of emphysema determined from chest computed tomography scans with a total of 2,380 individuals with COPD in three independent cohorts of white individuals from (1) a cohort from Bergen, Norway, (2) the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) Study, and (3) the National Emphysema Treatment Trial (NETT). We tested single-nucleotide polymorphism associations with the presence or absence of emphysema determined by radiologist assessment in two of the three cohorts and a quantitative emphysema trait (percentage of lung voxels less than -950 Hounsfield units) in all three cohorts. MEASUREMENTS AND MAIN RESULTS we identified association of a single-nucleotide polymorphism in BICD1 with the presence or absence of emphysema (P = 5.2 × 10(-7) with at least mild emphysema vs. control subjects; P = 4.8 × 10(-8) with moderate and more severe emphysema vs. control subjects). CONCLUSIONS our study suggests that genetic variants in BICD1 are associated with qualitative emphysema in COPD. Variants in BICD1 are associated with length of telomeres, which suggests that a mechanism linked to accelerated aging may be involved in the pathogenesis of emphysema. Clinical trial registered with www.clinicaltrials.gov (NCT00292552).
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Affiliation(s)
- Xiangyang Kong
- Research and Development, GlaxoSmithKline, 709 Swedeland Road, UW2230, King of Prussia, PA 19406, USA.
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46
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Collaco JM, Blackman SM, McGready J, Naughton KM, Cutting GR. Quantification of the relative contribution of environmental and genetic factors to variation in cystic fibrosis lung function. J Pediatr 2010; 157:802-7.e1-3. [PMID: 20580019 PMCID: PMC2948620 DOI: 10.1016/j.jpeds.2010.05.018] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 02/23/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To assess the relative contributions of environmental and genetic factors to variation in cystic fibrosis (CF) lung disease. STUDY DESIGN Genetic and environmental contributions were quantified by use of intrapair correlations and differences in CF-specific forced expiratory volume in 1 second measures from 134 monozygous twins and 272 dizygous twins and siblings while in different living environments (ie, living with parents vs living alone), as well as by use of intraindividual differences in pulmonary function from a separate group of 80 siblings. RESULTS Pulmonary function among monozygous twins was more similar than among dizygous twin and sibling pairs, regardless of living environment, affirming the role of genetic modifiers in CF pulmonary function. Regression modeling revealed that genetic factors account for 50% of pulmonary function variation, unique environmental or stochastic factors (36%), and shared environmental factors (14%; P < .0001). The intraindividual analysis produced similar estimates for the contributions of the unique and shared environment. The shared environment effects appeared primarily because of living with a sibling with CF (P = .003), rather than factors within the parental household (P = .310). CONCLUSIONS Genetic and environmental factors contribute equally to pulmonary function variation in CF. Environmental effects are dominated by unique and stochastic effects rather than common exposures.
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Affiliation(s)
- J. Michael Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University, Baltimore, Maryland 21287 (U.S.A.)
| | - Scott M. Blackman
- Division of Pediatric Endocrinology, Johns Hopkins University, Baltimore, Maryland 21287 (U.S.A.)
| | - John McGready
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21287 (U.S.A.)
| | - Kathleen M. Naughton
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287 (U.S.A.)
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287 (U.S.A.)
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Use of a modeling framework to evaluate the effect of a modifier gene (MBL2) on variation in cystic fibrosis. Eur J Hum Genet 2010; 18:680-4. [PMID: 20068595 DOI: 10.1038/ejhg.2009.226] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Variants in mannose-binding lectin (MBL2; protein MBL) have shown association with different aspects (eg, lung function, infection, survival) of cystic fibrosis (CF) in some studies but not others. Inconsistent results may be due to confounding among disease variables that were not fully accounted for in each study. To account for these relationships, we derived a modeling framework incorporating CFTR genotype, age, Pseudomonas aeruginosa (Pa) infection, and lung function from 788 patients in the US CF Twin and Sibling Study. This framework was then used to identify confounding variables when testing the effect of MBL2 variation on specific CF traits. MBL2 genotypes corresponding to low levels of MBL associated with Pa infection 1.94 years earlier than did MBL2 genotypes corresponding to high levels of MBL (P=0.0034). In addition, Pa-infected patients with MBL2 genotypes corresponding to low levels of MBL underwent conversion to mucoid Pa 2.72 years earlier than did patients with genotypes corresponding to high levels of MBL (P=0.0003). MBL2 was not associated with the time to transition from infection to conversion or with lung function. Thus, use of a modeling framework that identified confounding among disease variables revealed that variation in MBL2 associates with age at infection with Pa and age at conversion to mucoid Pa in CF.
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Stanke F, Becker T, Hedtfeld S, Tamm S, Wienker TF, Tümmler B. Hierarchical fine mapping of the cystic fibrosis modifier locus on 19q13 identifies an association with two elements near the genes CEACAM3 and CEACAM6. Hum Genet 2010; 127:383-94. [PMID: 20047061 DOI: 10.1007/s00439-009-0779-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/18/2009] [Indexed: 12/23/2022]
Abstract
On 19q13, TGFB1 and the cystic fibrosis modifier 1 locus (CFM1) have been identified as modifiers of the course of the monogenic disease cystic fibrosis (CF). Recently, we have described a transmission disequilibrium at the microsatellite D19S197, localized between TGFB1 and CFM1. To map the corresponding molecular variants, we have selected informative SNP markers within a 600-kb area and compared two-marker-haplotype-distributions between phenotypically contrasting sib pair groups, intending to type only phylogenetically old markers by aiming for close-to-maximal polymorphism information content of the SNPs. Starting with a seed set of five SNPs that cover intermarker distances of up to 50 kb, we have iteratively added more SNPs to the map, until we could identify two genomic fragments of 3,289 and 2,052 bp for which pairs with contrasting phenotypes showed different haplotype distributions on the final 17-SNP-map (P(raw) = 0.0002, P(corr17SNPs) = 0.0106 and P(raw) = 0.0008, P(corr17SNPs) = 0.0469, respectively). Resequencing of these fragments of four unrelated individuals for each element showed that the mildly and severely affected pairs differ in seven SNPs and concordant pairs differ from discordant pairs in five SNPs. Annotation of these variants indicate that CEACAM6 and a regulatory element near the 3' end of CEACAM3 are associated with CF disease severity and intrapair discordance, respectively. While our approach was only guided by the markers' position, the involvement of genes from the CEACAM family in host defense and innate immunity designates these proteins as likely modifiers of the multi-organ disease cystic fibrosis which is known for its cytokine imbalance and pro-inflammatory phenotype.
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Affiliation(s)
- Frauke Stanke
- Department of Pediatrics, Hannover Medical School, Hannover, Germany.
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49
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Darrah R, McKone E, O'Connor C, Rodgers C, Genatossio A, McNamara S, Gibson R, Stuart Elborn J, Ennis M, Gallagher CG, Kalsheker N, Aitken M, Wiese D, Dunn J, Smith P, Pace R, Londono D, Goddard KAB, Knowles MR, Drumm ML. EDNRA variants associate with smooth muscle mRNA levels, cell proliferation rates, and cystic fibrosis pulmonary disease severity. Physiol Genomics 2009; 41:71-7. [PMID: 20028935 DOI: 10.1152/physiolgenomics.00185.2009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Airway inflammation and pulmonary disease are heterogeneous phenotypes in cystic fibrosis (CF) patients, even among patients with the same cystic fibrosis transmembrane conductance regulator (CFTR) genotype. Endothelin, a proinflammatory peptide and smooth muscle agonist, is increased in CF airways, potentially contributing to the pulmonary phenotype. Four cohorts of CF patients were screened for variants in endothelin pathway genes to determine whether any of these variants associated with pulmonary function. An initial cohort of 808 CF patients homozygous for the common CF mutation, DeltaF508, showed significant association for polymorphisms in the endothelin receptor A gene, EDNRA (P = 0.04), but not in the related endothelin genes (EDN1, EDN2, EDN3, or EDNRB) or NOS1, NOS2A, or NOS3. Variants within EDNRA were examined in three additional cohorts of CF patients, 238 patients from Seattle, WA, 303 from Ireland and the U.K., and 228 from Cleveland, OH, for a total of 1,577 CF patients. The three additional groups each demonstrated a significant association between EDNRA 3'-untranslated region (UTR) variant rs5335 and pulmonary function (P = 0.002). At the molecular level, single nucleotide primer extension assays suggest that the effect of the variants is quantitative. EDNRA mRNA levels from cultured primary tracheal smooth muscle cells are greater for the allele that appears to be deleterious to lung function than for the protective allele, suggesting a mechanism by which increased receptor function is harmful to the CF airway. Finally, cell proliferation studies using human airway smooth muscle cells demonstrated that cells homozygous for the deleterious allele proliferate at a faster rate than those homozygous for the protective allele.
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Affiliation(s)
- Rebecca Darrah
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Keating CL, Liu X, Dimango EA. Classic respiratory disease but atypical diagnostic testing distinguishes adult presentation of cystic fibrosis. Chest 2009; 137:1157-63. [PMID: 19965956 DOI: 10.1378/chest.09-1352] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The majority of new cases of cystic fibrosis (CF) are diagnosed before age 2 years. Diagnoses in older individuals have increased because of improved genetic testing and increased awareness of the disease. A comprehensive description of clinical, genetic, and microbiologic characteristics of adult-age presentation of CF does not exist. We compare newly diagnosed CF in adults with newly diagnosed CF in children and adolescents in the United States. METHODS This is a cross-sectional study of new CF diagnoses from the Cystic Fibrosis Foundation Patient Registry between 1995 and 2005. Diagnostic, microbiologic, and clinical features during year of diagnosis were analyzed for subjects by age group. Descriptive statistics were calculated for variables on characteristics by age group. RESULTS A total of 9,766 new diagnoses of CF were reported to the Registry between 1995 and 2005. The proportion of adult diagnoses increased significantly in the years 2001 to 2005 as compared with 1995 to 2000 (9.0% vs 7.7%, P = .012). FEV(1)% predicted decreased with increasing age at diagnosis (P < .001). Infection with Pseudomonas aeruginosa was most common in adults (P < .001). Both the number of positive sweat chloride tests and prevalence of DeltaF508 mutation, the most common mutation in the United States, decreased significantly with older age at diagnosis (P < .001). CONCLUSIONS Between 1995 and 2005, the proportion of new diagnoses of CF in adults in the United States increased significantly. Adults present with commonly described CF respiratory disease (Pseudomonas aeruginosa infection and reduced lung function), but have lower sweat chloride values and lower frequency of DeltaF508 mutation. Knowledge of clinical characteristics and diagnostic limitations of adult patients presenting with CF will hopefully lead to earlier recognition and intervention.
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Affiliation(s)
- Claire L Keating
- Columbia University Medical Center, 622 W 168th St, PH 8, New York, NY 10032, USA.
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