1
|
Hale M, Takehara KK, Thouvenel CD, Moustafa DA, Repele A, Fontana MF, Netland J, McNamara S, Gibson RL, Goldberg JB, Rawlings DJ, Pepper M. Monoclonal antibodies derived from B cells in subjects with cystic fibrosis reduce Pseudomonas aeruginosa burden in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588618. [PMID: 38645147 PMCID: PMC11030358 DOI: 10.1101/2024.04.08.588618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across 3 donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.
Collapse
|
2
|
Rosenfeld M, Faino AV, Qu P, Onchiri FM, Blue EE, Collaco JM, Gordon WW, Szczesniak R, Zhou YH, Bamshad MJ, Gibson RL. Association of Pseudomonas aeruginosa infection stage with lung function trajectory in children with cystic fibrosis. J Cyst Fibros 2023; 22:857-863. [PMID: 37217389 DOI: 10.1016/j.jcf.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/25/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa (Pa) infection in cystic fibrosis (CF) is characterized in stages: never (prior to first positive culture) to incident (first positive culture) to chronic. The association of Pa infection stage with lung function trajectory is poorly understood and the impact of age on this association has not been examined. We hypothesized that FEV1 decline would be slowest prior to Pa infection, intermediate after incident infection and greatest after chronic Pa infection. METHODS Participants in a large US prospective cohort study diagnosed with CF prior to age 3 contributed data through the U.S. CF Patient Registry. Cubic spline linear mixed effects models were used to evaluate the longitudinal association of Pa stage (never, incident, chronic using 4 different definitions) with FEV1 adjusted for relevant covariates. Models contained interaction terms between age and Pa stage. RESULTS 1,264 subjects born 1992-2006 provided a median 9.5 (IQR 0.25 to 15.75) years of follow up through 2017. 89% developed incident Pa; 39-58% developed chronic Pa depending on the definition. Compared to never Pa, incident Pa infection was associated with greater annual FEV1 decline and chronic Pa infection with the greatest FEV1 decline. The most rapid FEV1 decline and strongest association with Pa infection stage was seen in early adolescence (ages 12-15). CONCLUSIONS Annual FEV1 decline worsens significantly with each Pa infection stage in children with CF. Our findings suggest that measures to prevent chronic infection, particularly during the high-risk period of early adolescence, could mitigate FEV1 decline and improve survival.
Collapse
Affiliation(s)
- Margaret Rosenfeld
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA.
| | - Anna V Faino
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Pingping Qu
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William W Gordon
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Rhonda Szczesniak
- Department of Pediatrics, Cincinnati Children's Hospital and Medical Center, Cincinnati, OH USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Hospital, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA USA
| | - Ronald L Gibson
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| |
Collapse
|
3
|
Mésinèle J, Ruffin M, Guillot L, Corvol H. Modifier Factors of Cystic Fibrosis Phenotypes: A Focus on Modifier Genes. Int J Mol Sci 2022; 23:ijms232214205. [PMID: 36430680 PMCID: PMC9698440 DOI: 10.3390/ijms232214205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Although cystic fibrosis (CF) is recognized as a monogenic disease, due to variants within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene, an extreme clinical heterogeneity is described among people with CF (pwCF). Apart from the exocrine pancreatic status, most studies agree that there is little association between CFTR variants and disease phenotypes. Environmental factors have been shown to contribute to this heterogeneity, accounting for almost 50% of the variability of the lung function of pwCF. Nevertheless, pwCF with similar CFTR variants and sharing the same environment (such as in siblings) may have highly variable clinical manifestations not explained by CFTR variants, and only partly explained by environmental factors. It is recognized that genetic variants located outside the CFTR locus, named "modifier genes", influence the clinical expression of the disease. This short review discusses the latest studies that have described modifier factors associated with the various CF phenotypes as well as the response to the recent CFTR modulator therapies.
Collapse
Affiliation(s)
- Julie Mésinèle
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Inovarion, 75005 Paris, France
| | - Manon Ruffin
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
| | - Loïc Guillot
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
| | - Harriet Corvol
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Trousseau, Service de Pneumologie Pédiatrique, 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
| |
Collapse
|
4
|
Butnariu LI, Țarcă E, Cojocaru E, Rusu C, Moisă ȘM, Leon Constantin MM, Gorduza EV, Trandafir LM. Genetic Modifying Factors of Cystic Fibrosis Phenotype: A Challenge for Modern Medicine. J Clin Med 2021; 10:5821. [PMID: 34945117 PMCID: PMC8707808 DOI: 10.3390/jcm10245821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disease caused by cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations. CF is characterized by a high phenotypic variability present even in patients with the same genotype. This is due to the intervention of modifier genes that interact with both the CFTR gene and environmental factors. The purpose of this review is to highlight the role of non-CFTR genetic factors (modifier genes) that contribute to phenotypic variability in CF. We analyzed literature data starting with candidate gene studies and continuing with extensive studies, such as genome-wide association studies (GWAS) and whole exome sequencing (WES). The results of both types of studies revealed that the number of modifier genes in CF patients is impressive. Their identification offers a new perspective on the pathophysiological mechanisms of the disease, paving the way for the understanding of other genetic disorders. In conclusion, in the future, genetic analysis, such as GWAS and WES, should be performed routinely. A challenge for future research is to integrate their results in the process of developing new classes of drugs, with a goal to improve the prognosis, increase life expectancy, and enhance quality of life among CF patients.
Collapse
Affiliation(s)
- Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Elena Țarcă
- Department of Surgery II—Pediatric Surgery, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaşi, Romania
| | - Elena Cojocaru
- Department of Morphofunctional Sciences I, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaşi, Romania
| | - Cristina Rusu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Ștefana Maria Moisă
- Department of Mother and Child, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (Ș.M.M.); (L.M.T.)
| | | | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Laura Mihaela Trandafir
- Department of Mother and Child, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (Ș.M.M.); (L.M.T.)
| |
Collapse
|
5
|
Raraigh KS, Aksit MA, Hetrick K, Pace RG, Ling H, O'Neal W, Blue E, Zhou YH, Bamshad MJ, Blackman SM, Gibson RL, Knowles MR, Cutting GR. Complete CFTR gene sequencing in 5,058 individuals with cystic fibrosis informs variant-specific treatment. J Cyst Fibros 2021; 21:463-470. [PMID: 34782259 DOI: 10.1016/j.jcf.2021.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is a recessive condition caused by variants in each CF transmembrane conductance regulator (CFTR) allele. Clinically affected individuals without two identified causal variants typically have no further interrogation of CFTR beyond examination of coding regions, but the development of variant-specific CFTR-targeted treatments necessitates complete understanding of CFTR genotype. METHODS Whole genome sequences were analyzed on 5,058 individuals with CF. We focused on the full CFTR gene sequence and identified disease-causing variants in three phases: screening for known and structural variants; discovery of novel loss-of-function variants; and investigation of remaining variants. RESULTS All variants identified in the first two phases and coding region variants found in the third phase were interpreted according to CFTR2 or ACMG criteria (n = 371; 16 [4.3%] previously unreported). Full gene sequencing enabled delineation of 18 structural variants (large insertions or deletions), of which two were novel. Additional CFTR variants of uncertain effect were found in 76 F508del homozygotes and in 21 individuals with other combinations of CF-causing variants. Both causative variants were identified in 98.1% (n = 4,960) of subjects, an increase of 2.3 percentage points from the 95.8% (n = 4,847) who had a registry- or chart-reported disease-causing CFTR genotype. Of the remaining 98 individuals, 78 carried one variant that has been associated with CF (CF-causing [n = 70] or resulting in varying clinical consequences n = 8]). CONCLUSIONS Complete CFTR gene sequencing in 5,058 individuals with CF identified at least one DNA variant in 99.6% of the cohort that is targetable by current molecular or emerging gene-based therapeutic technologies.
Collapse
Affiliation(s)
- Karen S Raraigh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Melis A Aksit
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Kurt Hetrick
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Hua Ling
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Wanda O'Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Elizabeth Blue
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Yi-Hui Zhou
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, United States
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States; Department of Pediatrics, University of Washington, Seattle, WA 98195, United States; Brotman-Baty Institute, Seattle, WA 98195, United States
| | - Scott M Blackman
- Division of Pediatric Endocrinology and Diabetes, Johns Hopkins University, Baltimore, MD 21287, United States
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
| | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States.
| |
Collapse
|
6
|
Rosenfeld M, Faino AV, Onchiri F, Aksit MA, Blackman SM, Blue EE, Collaco JM, Gordon WW, Pace RG, Raraigh KS, Zhou YH, Cutting GR, Knowles MR, Bamshad MJ, Gibson RL. Comparing encounter-based and annualized chronic pseudomonas infection definitions in cystic fibrosis. J Cyst Fibros 2021; 21:40-44. [PMID: 34393091 DOI: 10.1016/j.jcf.2021.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/07/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Chronic Pseudomonas aeruginosa (Pa) infection is associated with increased morbidity and mortality in people with cystic fibrosis (CF). There is no gold standard definition of chronic Pa infection in CF. We compared chronic Pa definitions using encounter-based versus annualized data in the Early Pseudomonas Infection Control (EPIC) Observational study cohort, and subsequently compared annualized chronic Pa definitions across a range of U.S. cohorts spanning decades of CF care. We found that an annualized chronic Pa definition requiring at least 1 Pa+ culture in 3 of 4 consecutive years ("Green 3/4") resulted in chronic Pa metrics similar to established encounter-based modified Leeds criteria definitions, including a similar age at and proportion who fulfilled chronic Pa criteria, and a similar proportion with sustained Pa infection after meeting the chronic Pa definition. The Green 3/4 chronic Pa definition will be valuable for longitudinal analyses in cohorts with limited culture frequency.
Collapse
Affiliation(s)
- Margaret Rosenfeld
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
| | - Anna V Faino
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Frankline Onchiri
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Melis A Aksit
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Scott M Blackman
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - William W Gordon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rhonda G Pace
- Marsico Lung Institute/Cystic Fibrosis Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen S Raraigh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Michael R Knowles
- Marsico Lung Institute/Cystic Fibrosis Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
7
|
Abstract
PURPOSE OF REVIEW To compile data from the past 10 years regarding the role of modifying genes in cystic fibrosis (CF). RECENT FINDINGS CF is a model disease for understanding of the action of modifying genes. Although it is a monogenic (CFTR) autosomal recessive disease, CF presents with wide phenotypic variability. In CF, variability occurs with different intensity among patients by each organ, being organ-specific, resulting from the mutual interaction of environmental and genetic factors, including CFTR mutations and various other genes, most of which are associated with inflammatory processes. In individuals, using precision medicine, gene modification studies have revealed individualized responses to drugs depending on particular CFTR mutations and modifying genes, most of which are alternative ion channels. SUMMARY Studies of modifying genes in CF allow: understanding of clinical variability among patients with the same CFTR genotype; evaluation of precision medicine; understanding of environmental and genetic effects at the organ level; understanding the involvement of genetic variants in inflammatory responses; improvements in genetic counseling; understanding the involvement of genetic variants in inflammatory responses in lung diseases, such as asthma; and understanding the individuality of the person with the disease.
Collapse
|
8
|
Terlizzi V, Lucarelli M, Salvatore D, Angioni A, Bisogno A, Braggion C, Buzzetti R, Carnovale V, Casciaro R, Castaldo G, Cirilli N, Collura M, Colombo C, Di Lullo AM, Elce A, Lucidi V, Madarena E, Padoan R, Quattrucci S, Raia V, Seia M, Termini L, Zarrilli F. Clinical expression of cystic fibrosis in a large cohort of Italian siblings. BMC Pulm Med 2018; 18:196. [PMID: 30577776 PMCID: PMC6303904 DOI: 10.1186/s12890-018-0766-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/12/2018] [Indexed: 02/10/2023] Open
Abstract
Background A clinical heterogeneity was reported in patients with Cystic Fibrosis (CF) with the same CFTR genotype and between siblings with CF. Methods We investigated all clinical aspects in a cohort of 101 pairs of siblings with CF (including 6 triplets) followed since diagnosis. Results Severe lung disease had a 22.2% concordance in sib-pairs, occurred early and the FEV1% at 12 years was predictive of the severity of lung disease in the adulthood. Similarly, CF liver disease occurred early (median: 15 years) and showed a concordance of 27.8% in sib-pairs suggesting a scarce contribution of genetic factors; in fact, only 2/15 patients with liver disease in discordant sib-pairs had a deficiency of alpha-1-antitrypsin (a known modifier gene of CF liver phenotype). CF related diabetes was found in 22 pairs (in 6 in both the siblings). It occurred later (median: 32.5 years) and is strongly associated with liver disease. Colonization by P. aeruginosa and nasal polyposis that required surgery had a concordance > 50% in sib-pairs and were poorly correlated to other clinical parameters. The pancreatic status was highly concordant in pairs of siblings (i.e., 95.1%) but a different pancreatic status was observed in patients with the same CFTR mutations. This suggests a close relationship of the pancreatic status with the “whole” CFTR genotype, including mutations in regulatory regions that may modulate the levels of CFTR expression. Finally, a severe course of CF was evident in a number of patients with pancreatic sufficiency. Conclusions Physicians involved in care of patients with CF and in genetic counseling must be aware of the clinical heterogeneity of CF even in sib-pairs that, at the state of the art, is difficult to explain. Electronic supplementary material The online version of this article (10.1186/s12890-018-0766-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vito Terlizzi
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy.
| | - Marco Lucarelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Donatello Salvatore
- Centro Regionale Fibrosi Cistica, Centro Pediatrico Bambino Gesù Basilicata, AOR San Carlo, Potenza, Italy
| | - Adriano Angioni
- Laboratorio di Genetica Medica, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Arianna Bisogno
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Cesare Braggion
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy
| | | | - Vincenzo Carnovale
- Centro Regionale Fibrosi Cistica Adulti, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Rosaria Casciaro
- Centro Regionale Fibrosi Cistica, U.O.C. Pneumologia, IRCCS G. Gaslini, Genua, Italy
| | - Giuseppe Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie avanzate, Naples, Italy
| | - Natalia Cirilli
- Centro Regionale Fibrosi Cistica, Dipartimento Materno-Infantile, Ospedali Riuniti Ancona, Ancona, Italy
| | - Mirella Collura
- CRR Fibrosi Cistica, Ospedale dei Bambini, ARNAS Civico, Palermo, Italy
| | - Carla Colombo
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Antonella Miriam Di Lullo
- Dipartimento di Neuroscienze, Scienze Riproduttive ed Odontostomatologica, Università di Napoli Federico II, Naples, Italy
| | | | - Vincenzina Lucidi
- Unità Regionale di Fibrosi Cistica, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Elisa Madarena
- Centro Regionale Fibrosi Cistica, Ospedale Giovanni Paolo II, Lamezia, Italy
| | - Rita Padoan
- Centro Regionale di supporto Fibrosi Cistica, Dipartimento di Pediatria, Università di Brescia, AO Spedali Civili, Brescia, Italy
| | - Serena Quattrucci
- Centro Fibrosi Cistica Regione Lazio, Dipartimento di Pediatria e Neuropsichiatria Infantile, Sapienza Università-Policlinico Umberto I, Rome, Italy
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Sezione Pediatrica, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Manuela Seia
- Laboratorio di Genetica Medica, Fondazione IRCCS Policlinico Ca' Granda Ospedale, Milan, Italy
| | - Lisa Termini
- Ospedale dei Bambini G. Di Cristina, Centro Regionale Fibrosi Cistica, Palermo, Italy
| | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
| |
Collapse
|
9
|
O'Neal WK, Knowles MR. Cystic Fibrosis Disease Modifiers: Complex Genetics Defines the Phenotypic Diversity in a Monogenic Disease. Annu Rev Genomics Hum Genet 2018; 19:201-222. [DOI: 10.1146/annurev-genom-083117-021329] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In many respects, genetic studies in cystic fibrosis (CF) serve as a paradigm for a human Mendelian genetic success story. From recognition of the condition as a heritable pathological entity to implementation of personalized treatments based on genetic findings, this multistep pathway of progress has focused on the genetic underpinnings of CF clinical disease. Along this path was the recognition that not all CFTR gene mutations produce the same disease and the recognition of the complex, multifactorial nature of CF genotype–phenotype relationships. The non- CFTR genetic components (gene modifiers) that contribute to variation in phenotype are the focus of this review. A multifaceted approach involving candidate gene studies, genome-wide association studies, and gene expression studies has revealed significant gene modifiers for multiple CF phenotypes. The bold challenges for the future are to integrate the findings into our understanding of CF pathogenesis and to use the knowledge to develop novel therapies.
Collapse
Affiliation(s)
- Wanda K. O'Neal
- Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;,
| | - Michael R. Knowles
- Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;,
| |
Collapse
|
10
|
Sontag MK. Sweat Chloride: The Critical Biomarker for Cystic Fibrosis Trials. Am J Respir Crit Care Med 2017; 194:1311-1313. [PMID: 27905852 DOI: 10.1164/rccm.201606-1286ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Marci K Sontag
- 1 Colorado School of Public Health University of Colorado Anschutz Medical Campus Aurora, Colorado
| |
Collapse
|
11
|
Psoter KJ, De Roos AJ, Wakefield J, Mayer JD, Rosenfeld M. Air pollution exposure is associated with MRSA acquisition in young U.S. children with cystic fibrosis. BMC Pulm Med 2017; 17:106. [PMID: 28750627 PMCID: PMC5530959 DOI: 10.1186/s12890-017-0449-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/19/2017] [Indexed: 01/21/2023] Open
Abstract
Background The role of air pollution in increasing susceptibility to respiratory tract infections in the cystic fibrosis (CF) population has not been well described. We recently demonstrated that chronic PM2.5 exposure is associated with an increased risk of initial Pseudomonas aeruginosa acquisition in young children with CF. The purpose of this study was to determine whether PM2.5 exposure is a risk factor for acquisition of other respiratory pathogens in young children with CF. Methods We conducted a retrospective study of initial acquisition of methicillin susceptible and methicillin resistant Staphylococcus aureus (MSSA and MRSA), Stenotrophomonas maltophilia and Achromobacter xylosoxidans in U.S. children <6 years of age with CF using the CF Foundation Patient Registry, 2003–2009. Multivariable Weibull regression with interval-censored outcomes was used to evaluate the association of PM2.5 concentration in the year prior to birth and risk of acquisition of each organism. Results During follow-up 63%, 17%, 24%, and 5% of children acquired MSSA, MRSA, S. maltophilia, and A. xylosoxidans, respectively. A 10 μg/m3 increase in PM2.5 exposure was associated with a 68% increased risk of MRSA acquisition (Hazard Ratio: 1.68; 95% Confidence Interval: 1.24, 2.27). PM2.5 was not associated with acquisition of other respiratory pathogens. Conclusions Fine particulate matter is an independent risk factor for initial MRSA acquisition in young children with CF. These results support the increasing evidence that air pollution contributes to pulmonary morbidities in the CF community.
Collapse
Affiliation(s)
- Kevin J Psoter
- Department of Pediatrics, School of Medicine, The Johns Hopkins University Bayview Medical Center, 5200 Eastern Ave, Mason F. Lord Bldg, Center Towers, Suite 4200, Baltimore, MD, 21224, USA.
| | - Anneclaire J De Roos
- Department of Environmental and Occupational Health, Drexel University School of Public Health, Philadelphia, PA, USA
| | - Jon Wakefield
- Departments of Biostatistics and Statistics, University of Washington, Seattle, WA, USA
| | - Jonathan D Mayer
- Departments of Epidemiology, Geography, Global Health, Medicine (Allergy and Infectious Diseases), Family Medicine, and Health Services, University of Washington, Seattle, WA, USA
| | - Margaret Rosenfeld
- Division of Pulmonary Medicine, University of Washington School of Medicine, Seattle, WA, USA
| |
Collapse
|
12
|
Castellani C, Assael BM. Cystic fibrosis: a clinical view. Cell Mol Life Sci 2017; 74:129-140. [PMID: 27709245 PMCID: PMC11107741 DOI: 10.1007/s00018-016-2393-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
Abstract
Cystic fibrosis (CF), a monogenic disease caused by mutations in the CFTR gene on chromosome 7, is complex and greatly variable in clinical expression. Airways, pancreas, male genital system, intestine, liver, bone, and kidney are involved. The lack of CFTR or its impaired function causes fat malabsorption and chronic pulmonary infections leading to bronchiectasis and progressive lung damage. Previously considered lethal in infancy and childhood, CF has now attained median survivals of 50 years of age, mainly thanks to the early diagnosis through neonatal screening, recognition of mild forms, and an aggressive therapeutic attitude. Classical treatment includes pancreatic enzyme replacement, respiratory physiotherapy, mucolitics, and aggressive antibiotic therapy. A significant proportion of patients with severe symptoms still requires lung or, less frequently, liver transplantation. The great number of mutations and their diverse effects on the CFTR protein account only partially for CF clinical variability, and modifier genes have a role in modulating the clinical expression of the disease. Despite the increasing understanding of CFTR functioning, several aspects of CF need still to be clarified, e.g., the worse outcome in females, the risk of malignancies, the pathophysiology, and best treatment of comorbidities, such as CF-related diabetes or CF-related bone disorder. Research is focusing on new drugs restoring CFTR function, some already available and with good clinical impact, others showing promising preliminary results that need to be confirmed in phase III clinical trials.
Collapse
Affiliation(s)
- Carlo Castellani
- Verona Cystic Fibrosis Centre, Piazzale Stefani 1, 37126, Verona, Italy.
| | - Baroukh M Assael
- Adult Cystic Fibrosis Center, Via Francesco Sforza, 20100, Milano, Italy
| |
Collapse
|
13
|
The Effect of Strict Segregation on Pseudomonas aeruginosa in Cystic Fibrosis Patients. PLoS One 2016; 11:e0157189. [PMID: 27280467 PMCID: PMC4900627 DOI: 10.1371/journal.pone.0157189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/25/2016] [Indexed: 01/20/2023] Open
Abstract
Introduction Segregation of patients with cystic fibrosis (CF) was implemented to prevent chronic infection with epidemic Pseudomonas aeruginosa strains with presumed detrimental clinical effects, but its effectiveness has not been carefully evaluated. Methods The effect of strict segregation on the incidence of P. aeruginosa infection in CF patients was investigated through longitudinal protocolized follow-up of respiratory tract infection before and after segregation. In two nested cross-sectional studies in 2007 and 2011 the P. aeruginosa population structure was investigated and clinical parameters were determined in patients with and without infection with the Dutch epidemic P. aeruginosa clone (ST406). Results Of 784 included patients 315 and 382 were at risk for acquiring chronic P. aeruginosa infection before and after segregation. Acquisition rates were, respectively, 0.14 and 0.05 per 1,000 days at risk (HR: 0.66, 95% CI [0.2548–1.541]; p = 0.28). An exploratory subgroup analysis indicated lower acquisition after segregation in children < 15 years of age (HR: 0.43, 95% CI[0.21–0.95]; p = 0.04). P. aeruginosa population structure did not change after segregation and ST406 was not associated with lung function decline, death or lung transplantation. Conclusions Strict segregation was not associated with a statistically significant lower acquisition of chronic P. aeruginosa infection and ST406 was not associated with adverse clinical outcome. After segregation there were no new acquisitions of ST406. In an unplanned exploratory analysis chronic acquisition of P. aeruginosa was lower after implementation of segregation in patients under 15 years of age.
Collapse
|
14
|
Paul-Smith MC, Bell RV, Alton WE, Alton EW, Griesenbach U. Gene therapy for cystic fibrosis: recent progress and current aims. Expert Opin Orphan Drugs 2016. [DOI: 10.1080/21678707.2016.1180974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Michael C. Paul-Smith
- Department of Gene Therapy and the UK Cystic Fibrosis Gene Therapy Consortium, Imperial College, London, UK
| | - Robyn V. Bell
- Department of Gene Therapy and the UK Cystic Fibrosis Gene Therapy Consortium, Imperial College, London, UK
| | - William E. Alton
- Department of Gene Therapy and the UK Cystic Fibrosis Gene Therapy Consortium, Imperial College, London, UK
| | - Eric W.F.W. Alton
- Department of Gene Therapy and the UK Cystic Fibrosis Gene Therapy Consortium, Imperial College, London, UK
| | - Uta Griesenbach
- Department of Gene Therapy and the UK Cystic Fibrosis Gene Therapy Consortium, Imperial College, London, UK
| |
Collapse
|
15
|
Alanin M, Nielsen K, von Buchwald C, Skov M, Aanaes K, Høiby N, Johansen H. A longitudinal study of lung bacterial pathogens in patients with primary ciliary dyskinesia. Clin Microbiol Infect 2015; 21:1093.e1-7. [DOI: 10.1016/j.cmi.2015.08.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/21/2015] [Accepted: 08/21/2015] [Indexed: 12/22/2022]
|
16
|
Association of meteorological and geographical factors and risk of initial Pseudomonas aeruginosa acquisition in young children with cystic fibrosis. Epidemiol Infect 2015; 144:1075-83. [PMID: 26449886 DOI: 10.1017/s0950268815002411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Initial infection with the sentinel respiratory pathogen in children with cystic fibrosis (CF), Pseudomonas aeruginosa (Pa), is generally with environmental strains of this ubiquitous organism. The purpose of this study was to evaluate the associations between meteorological and geographical factors and risk of initial Pa acquisition in young children with CF. Using the U.S. Cystic Fibrosis Foundation Patient Registry from 2003 to 2009, 3463 patients met inclusion criteria, of which 48% (n = 1659) acquired Pa during follow-up. From multivariable Weibull regression, increased risk of Pa acquisition was associated with increasing temperature [hazard ratio (HR) per 1 °C: 1·13; 95% confidence interval (CI) 1·08-1·13], dew point (HR per 1 °C: 1·10, 95% CI 1·07-1·13), rainfall (HR per cm: 1·10, 95% CI 1·07-1·12), latitude (HR per 1 °C northing: 1·15, 95% CI 1·11-1·20), longitude (HR per 1 °C easting: 1·01, 95% CI 1·01-1·02) and elevation (HR per 100 m: 1·05, 95% CI 1·03-1·07). These results suggest that environmental factors may play a previously unrecognized role in the aetiology of initial Pa acquisition.
Collapse
|
17
|
Lorè NI, Iraqi FA, Bragonzi A. Host genetic diversity influences the severity of Pseudomonas aeruginosa pneumonia in the Collaborative Cross mice. BMC Genet 2015; 16:106. [PMID: 26310945 PMCID: PMC4551369 DOI: 10.1186/s12863-015-0260-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/03/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is one of the top three causes of opportunistic infections in humans. Patients with a compromised immune system, due to immunosuppressive therapies or underlying diseases such as cancer, AIDS or the hereditary disease cystic fibrosis, are at risk of developing P. aeruginosa infection. However, clinical evidence indicates extremely variable outcomes of P. aeruginosa infections in individuals at risk, suggesting that host multi-complex genetic traits may influence the severity of this opportunistic infection. Here, we have used an innovative experimental model to dissect whether host genetic background, such as those found in the outbred population, could influence the risk of morbidity and mortality to P. aeruginosa pneumonia. RESULTS A highly genetically-diverse mouse resource population, Collaborative Cross (CC) mice, was infected with a clinical strain of P. aeruginosa and subsequently monitored for mortality, mean survival time, and morbidity, change in body weight for seven days post infection. Disease phenotypes ranged from complete resistance and recovery of body weight to lethal disease. Initial variables, including body weight, age and gender, have limited influence on P. aeruginosa outcome, emphasizing the role of host genetic background in defining the risk of morbidity and mortality. When broad-sense heritability of phenotypic traits was evaluated, it confirmed the influence of genetic profile rather than environmental factors among the CC lines during P. aeruginosa infection. CONCLUSION This innovative model system can potentially reproduce the variables responses of disease severity observed in humans during P. aeruginosa pneumonia. Our results demonstrated that a widely-marked differential response to P. aeruginosa airway infection in term of morbidity and mortality, is mainly affected by host genetic factors, as multiple genetic loci or polymorphic variations.
Collapse
Affiliation(s)
- Nicola Ivan Lorè
- Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS - San Raffaele Scientific Institute, Milan, Italy.
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel.
| | - Alessandra Bragonzi
- Infection and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS - San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
18
|
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.
Collapse
|
19
|
Abstract
Cystic fibrosis is an autosomal recessive, monogenetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The gene defect was first described 25 years ago and much progress has been made since then in our understanding of how CFTR mutations cause disease and how this can be addressed therapeutically. CFTR is a transmembrane protein that transports ions across the surface of epithelial cells. CFTR dysfunction affects many organs; however, lung disease is responsible for the vast majority of morbidity and mortality in patients with cystic fibrosis. Prenatal diagnostics, newborn screening and new treatment algorithms are changing the incidence and the prevalence of the disease. Until recently, the standard of care in cystic fibrosis treatment focused on preventing and treating complications of the disease; now, novel treatment strategies directly targeting the ion channel abnormality are becoming available and it will be important to evaluate how these treatments affect disease progression and the quality of life of patients. In this Primer, we summarize the current knowledge, and provide an outlook on how cystic fibrosis clinical care and research will be affected by new knowledge and therapeutic options in the near future. For an illustrated summary of this Primer, visit: http://go.nature.com/4VrefN.
Collapse
|
20
|
LaBonte ML, Beers MA. An alternative laboratory designed to address ethical concerns associated with traditional TAS2R38 student genotyping. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 43:100-109. [PMID: 25704857 DOI: 10.1002/bmb.20846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/27/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
The TAS2R38 alleles that code for the PAV/AVI T2R38 proteins have long been viewed as benign taste receptor variants. However, recent studies have demonstrated an expanding and medically relevant role for TAS2R38. The AVI variant of T2R38 is associated with an increased risk of both colorectal cancer and Pseudomonas aeruginosa-associated sinus infection and T2R38 variants have been implicated in off-target drug responses. To address ethical concerns associated with continued student TAS2R38 gene testing, we developed an alternative to the traditional laboratory genotyping exercise. Instead of determining their own genotype, introductory level students isolated plasmid DNA containing a section of the human TAS2R38 gene from Escherichia coli. Following PCR-mediated amplification of a section of the TAS2R38 gene spanning the SNP at position 785, students determined their assigned genotype by restriction enzyme digestion and agarose gel electrophoresis. Using the course wide genotype and phenotype data, students found that there was an association between TAS2R38 genotype and the age of persistent P. aeruginosa acquisition in cystic fibrosis "patients." Assessment data demonstrated that students taking part in this new TAS2R38 laboratory activity made clear learning gains.
Collapse
Affiliation(s)
- Michelle L LaBonte
- Department of the History of Science, Harvard University, Cambridge, Massachusetts, 02138
| | | |
Collapse
|
21
|
Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes. Am J Hum Genet 2015; 96:318-28. [PMID: 25640674 DOI: 10.1016/j.ajhg.2014.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/23/2014] [Indexed: 11/23/2022] Open
Abstract
Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease.
Collapse
|
22
|
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.
Collapse
|
23
|
Psoter KJ, Rosenfeld M, De Roos AJ, Mayer JD, Wakefield J. Differential geographical risk of initial Pseudomonas aeruginosa acquisition in young US children with cystic fibrosis. Am J Epidemiol 2014; 179:1503-13. [PMID: 24875373 DOI: 10.1093/aje/kwu077] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas aeruginosa is the sentinel respiratory pathogen in cystic fibrosis patients. We conducted a retrospective study to examine whether state of residence affected risk of P. aeruginosa acquisition among US children under 6 years of age with cystic fibrosis by using data from the Cystic Fibrosis Foundation National Patient Registry, 2003-2009. The outcome was time to first isolation of P. aeruginosa from a respiratory culture. We used a Bayesian hierarchical Weibull regression model with interval-censored outcomes. Spatial random effects, included at the state level and modeled using an intrinsic conditional autoregressive prior, allowed estimation of the residual spatial correlation. The regression portion of the model was adjusted for demographic and disease characteristics potentially affecting P. aeruginosa acquisition. A total of 3,608 children met the inclusion criteria and were followed for an average of 2.1 (standard deviation, 1.6) years. P. aeruginosa was cultured in 1,714 (48%) subjects. There was a moderately elevated spatial residual relative risk. An estimated 95% credible interval for the residual hazard ratio under 1 of the fitted models was 0.64-1.57; the strongest positive association was observed in the Southern states. The fact that risk for P. aeruginosa acquisition displayed spatial dependence suggests that regional factors, such as climate, may play an important role in P. aeruginosa acquisition.
Collapse
|
24
|
Hampton TH, Green DM, Cutting GR, Morrison HG, Sogin ML, Gifford AH, Stanton BA, O’Toole GA. The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. MICROBIOME 2014; 2:14. [PMID: 25071935 PMCID: PMC4113139 DOI: 10.1186/2049-2618-2-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is caused by mutations in the CFTR gene that predispose the airway to infection. Chronic infection by pathogens such as Pseudomonas aeruginosa leads to inflammation that gradually degrades lung function, resulting in morbidity and early mortality. In a previous study of CF monozygotic twins, we demonstrate that genetic modifiers significantly affect the establishment of persistent P. aeruginosa colonization in CF. Recognizing that bacteria other than P. aeruginosa contribute to the CF microbiome and associated pathology, we used deep sequencing of sputum from pediatric monozygotic twins and nontwin siblings with CF to characterize pediatric bacterial communities and the role that genetics plays in their evolution. FINDINGS We found that the microbial communities in sputum from pediatric patients living together were much more alike than those from pediatric individuals living apart, regardless of whether samples were taken from monozygous twins or from nontwin CF siblings living together, which we used as a proxy for dizygous twins. In contrast, adult communities were comparatively monolithic and much less diverse than the microbiome of pediatric patients. CONCLUSION Taken together, these data and other recent studies suggest that as patients age, the CF microbiome becomes less diverse, more refractory to treatment and dominated by mucoid P. aeruginosa, as well as being associated with accelerated pulmonary decline. Our studies show that the microbiome of pediatric patients is susceptible to environmental influences, suggesting that interventions to preserve the community structure found in young CF patients might be possible, perhaps slowing disease progression.
Collapse
Affiliation(s)
- Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 615 Remsen Building, N. College St., Hanover, NH 03755, USA
| | - Deanna M Green
- Division of Pediatric Pulmonary and Sleep Medicine, Duke University Medical Center, 350 Hanes House, DUMC Box 102360, Durham NC, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 1800 Orleans St., Baltimore MD, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Alex H Gifford
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 615 Remsen Building, N. College St., Hanover, NH 03755, USA
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 615 Remsen Building, N. College St., Hanover, NH 03755, USA
| | - George A O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 202 Remsen Building, N. College St., Hanover, NH 03755, USA
| |
Collapse
|
25
|
Grasemann H, Ratjen F. Early lung disease in cystic fibrosis. THE LANCET RESPIRATORY MEDICINE 2013; 1:148-57. [PMID: 24429095 DOI: 10.1016/s2213-2600(13)70026-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Lung disease in patients with cystic fibrosis is characterised by inflammation and recurrent and chronic infections leading to progressive loss in pulmonary function and respiratory failure. Early management of disease results in substantially improved pulmonary function at first testing (at roughly 6 years of age), but the annual decline in pulmonary function tests in older patients has remained unchanged showing how important the early years are in the disease process. Treatment regimens for patients with cystic fibrosis have changed from predominantly symptomatic treatment to preventive or causal (ie, treatments that address the underlying mechanisms of disease) therapeutic interventions. The infant and preschool age (2-5 years) could represent a unique period of opportunity to postpone or even prevent the onset of cystic fibrosis lung disease. We summarise the current knowledge and the methods used to characterise and quantify early lung disease. We discuss treatment strategies including new drugs that are being developed and their potential role in the treatment of early lung disease in patients with cystic fibrosis.
Collapse
Affiliation(s)
- Hartmut Grasemann
- Division of Respiratory Medicine, Department of Paediatrics, and Programme in Physiology and Experimental Medicine, Research Institute, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Felix Ratjen
- Division of Respiratory Medicine, Department of Paediatrics, and Programme in Physiology and Experimental Medicine, Research Institute, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- Michael R Knowles
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
| | | |
Collapse
|