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Yavuz S, Elnazir B, Amin S, Sherif A, Saif S, Francis N. A Unique Mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Gene Causing Cystic Fibrosis in a Pakistani Child: A Case Highlighting the Need for More Awareness. Cureus 2024; 16:e54627. [PMID: 38524055 PMCID: PMC10959411 DOI: 10.7759/cureus.54627] [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] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Cystic fibrosis (CF) is a recessively inherited disease most commonly seen in Caucasians. The mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are responsible for the condition, and to date, more than 2000 mutations have been published in the literature. The most common mutation worldwide is F508del. Here, we reported a five-year-old child who presented to the clinic with a chronic cough. Her newborn screening for CF was negative, including 139 mutation panels done in India. The sweat chloride test was positive, and CF gene sequencing was reported as c.2489dup p. (Glu831GLYFS *5) homozygotes mutation in the CFTR gene (Online Mendelian Inheritance in Man (OMIM) *602421). To the best of our knowledge, this gene was first described and published in the literature.
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Affiliation(s)
- Sinan Yavuz
- Pediatrics/Pediatric Pulmonologist, Al Qassimi Women's and Children's Hospital, Sharjah, ARE
| | - Basil Elnazir
- Pediatrics, Children's Health Ireland (CHI) at Tallaght University Hospital, Dublin, IRL
- Pediatrics, Trinity College Dublin, Dublin, IRL
| | - Saista Amin
- Pediatric Gastroenterology, Al Qassimi Women's and Children's Hospital, Sharjah, ARE
| | - Amal Sherif
- Pediatrics/Pediatric Consultant, Al Qassimi Women's and Children's Hospital, Sharjah, ARE
| | - Safiya Saif
- Pediatrics/Pediatric Pulmonology, Al Qassimi Woman's and Children's Hospital, Sharjah, ARE
| | - Nader Francis
- Pediatrics/Pediatric Pulmonology, Al Qassimi Women's and Children's Hospital, Sharjah, ARE
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2
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Ondra M, Lenart L, Centorame A, Dumut DC, He A, Zaidi SSZ, Hanrahan JW, De Sanctis JB, Radzioch D, Hajduch M. CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane. Life Sci Alliance 2024; 7:e202302045. [PMID: 37918963 PMCID: PMC10622324 DOI: 10.26508/lsa.202302045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023] Open
Abstract
CFTR is a membrane protein that functions as an ion channel. Mutations that disrupt its biosynthesis, trafficking or function cause cystic fibrosis (CF). Here, we present a novel in vitro model system prepared using CRISPR/Cas9 genome editing with endogenously expressed WT-CFTR tagged with a HiBiT peptide. To enable the detection of CFTR in the plasma membrane of live cells, we inserted the HiBiT tag in the fourth extracellular loop of WT-CFTR. The 11-amino acid HiBiT tag binds with high affinity to a large inactive subunit (LgBiT), generating a reporter luciferase with bright luminescence. Nine homozygous clones with the HiBiT knock-in were identified from the 182 screened clones; two were genetically and functionally validated. In summary, this work describes the preparation and validation of a novel reporter cell line with the potential to be used as an ultimate building block for developing unique cellular CF models by CRISPR-mediated insertion of CF-causing mutations.
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Affiliation(s)
- Martin Ondra
- https://ror.org/04qxnmv42 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- https://ror.org/04qxnmv42 Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
| | - Lukas Lenart
- https://ror.org/04qxnmv42 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Amanda Centorame
- https://ror.org/01pxwe438 Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
- RI-MUHC, Montreal, Canada
| | - Daciana C Dumut
- https://ror.org/01pxwe438 Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
- RI-MUHC, Montreal, Canada
| | - Alexander He
- https://ror.org/01pxwe438 Physiology, McGill University, Montreal, Canada
| | | | - John W Hanrahan
- RI-MUHC, Montreal, Canada
- https://ror.org/01pxwe438 Physiology, McGill University, Montreal, Canada
| | - Juan Bautista De Sanctis
- https://ror.org/04qxnmv42 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Danuta Radzioch
- https://ror.org/04qxnmv42 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- https://ror.org/01pxwe438 Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
- RI-MUHC, Montreal, Canada
| | - Marian Hajduch
- https://ror.org/04qxnmv42 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- https://ror.org/04qxnmv42 Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, University Hospital Olomouc, Olomouc, Czech Republic
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3
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Tang D, Freudenberg J, Dahl A. Factorizing polygenic epistasis improves prediction and uncovers biological pathways in complex traits. Am J Hum Genet 2023; 110:1875-1887. [PMID: 37922884 PMCID: PMC10645564 DOI: 10.1016/j.ajhg.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Epistasis is central in many domains of biology, but it has not yet been proven useful for understanding the etiology of complex traits. This is partly because complex-trait epistasis involves polygenic interactions that are poorly captured in current models. To address this gap, we developed a model called Epistasis Factor Analysis (EFA). EFA assumes that polygenic epistasis can be factorized into interactions between a few epistasis factors (EFs), which represent latent polygenic components of the observed complex trait. The statistical goals of EFA are to improve polygenic prediction and to increase power to detect epistasis, while the biological goal is to unravel genetic effects into more-homogeneous units. We mathematically characterize EFA and use simulations to show that EFA outperforms current epistasis models when its assumptions approximately hold. Applied to predicting yeast growth rates, EFA outperforms the additive model for several traits with large epistasis heritability and uniformly outperforms the standard epistasis model. We replicate these prediction improvements in a second dataset. We then apply EFA to four previously characterized traits in the UK Biobank and find statistically significant epistasis in all four, including two that are robust to scale transformation. Moreover, we find that the inferred EFs partly recover pre-defined biological pathways for two of the traits. Our results demonstrate that more realistic models can identify biologically and statistically meaningful epistasis in complex traits, indicating that epistasis has potential for precision medicine and characterizing the biology underlying GWAS results.
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Affiliation(s)
- David Tang
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
| | - Jerome Freudenberg
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
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4
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Huang L, Lai HJ, Song J, Zhao Z, Lu Q, Murali SG, Brown DM, Worthey EA, Farrell PM. Impact of intrinsic and extrinsic risk factors on early-onset lung disease in cystic fibrosis. Pediatr Pulmonol 2023; 58:3071-3082. [PMID: 37539852 PMCID: PMC10592256 DOI: 10.1002/ppul.26625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Although respiratory pathology is known to develop in young children with cystic fibrosis (CF), the determinants of early-onset lung disease have not been elucidated. OBJECTIVE We aimed to determine the impact of potential intrinsic and extrinsic risk factors during the first 3 years of life, testing the hypothesis that both contribute significantly to early-onset CF lung disease. DESIGN We studied 104 infants born during 2012-2017, diagnosed through newborn screening by age 3 months, and evaluated comprehensively to 36 months of age. Lung disease manifestations were quantified with a new scoring system known as CFELD for Cystic Fibrosis Early-onset Lung Disease. The variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene were determined and categorized. Whole genome sequencing was performed on each subject and the data transformed to polygenic risk scores (PRS) that aggregate variants associated with lung function. Extrinsic factors included socioeconomic status (SES) indicators and environmental experiences such as exposures to smoking, pets, and daycare. RESULTS We found by univariate analysis that CFTR genotype and genetic modifiers aggregated by the PRS method were significantly associated with early-onset CF lung disease. Ordinal logistic regression analysis demonstrated that high and stable SES (maternal education ≥community college, stable 2-parent home, and not receiving Medicaid) and better growth (weight-for-age and height-for-age z-scores) reduced risks, while exposure to smoking and daycare ≥20 h/week increased the risk of CFELD severity. CONCLUSIONS Extrinsic, modifiable determinants are influential early and potentially as important as the intrinsic risk factors in the onset of CF lung disease.
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Affiliation(s)
- Leslie Huang
- Department of Pediatrics, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - HuiChuan J. Lai
- Department of Pediatrics, University of Wisconsin – Madison, Madison, Wisconsin, USA
- Department of Nutritional Sciences, University of Wisconsin – Madison, Madison, Wisconsin, USA
- Department of Population Health Sciences, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Jie Song
- Department of Statistics, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Zijie Zhao
- Department of Statistics, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Qiongshi Lu
- Department of Statistics, University of Wisconsin – Madison, Madison, Wisconsin, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Sangita G. Murali
- Department of Nutritional Sciences, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Donna M. Brown
- Departments of Pediatrics and Genetics, Center for Computational Genomics and Data Science at the UAB Marnix E. Heersink School of Medicine, Birmingham, AL, USA
| | - Elizabeth A. Worthey
- Departments of Pediatrics and Genetics, Center for Computational Genomics and Data Science at the UAB Marnix E. Heersink School of Medicine, Birmingham, AL, USA
| | - Philip M. Farrell
- Department of Pediatrics, University of Wisconsin – Madison, Madison, Wisconsin, USA
- Department of Population Health Sciences, University of Wisconsin – Madison, Madison, Wisconsin, USA
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Maroilley T, Rahit KMTH, Chida AR, Cotra F, Rodrigues Alves Barbosa V, Tarailo-Graovac M. Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad184. [PMID: 37585487 PMCID: PMC10627290 DOI: 10.1093/g3journal/jkad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Genetic modifiers are variants modulating phenotypic outcomes of a primary detrimental variant. They contribute to rare diseases phenotypic variability, but their identification is challenging. Genetic screening with model organisms is a widely used method for demystifying genetic modifiers. Forward genetics screening followed by whole genome sequencing allows the detection of variants throughout the genome but typically produces thousands of candidate variants making the interpretation and prioritization process very time-consuming and tedious. Despite whole genome sequencing is more time and cost-efficient, usage of computational pipelines specific to modifier identification remains a challenge for biological-experiment-focused laboratories doing research with model organisms. To facilitate a broader implementation of whole genome sequencing in genetic screens, we have developed Model Organism Modifier or MOM, a pipeline as a user-friendly Galaxy workflow. Model Organism Modifier analyses raw short-read whole genome sequencing data and implements tailored filtering to provide a Candidate Variant List short enough to be further manually curated. We provide a detailed tutorial to run the Galaxy workflow Model Organism Modifier and guidelines to manually curate the Candidate Variant Lists. We have tested Model Organism Modifier on published and validated Caenorhabditis elegans modifiers screening datasets. As whole genome sequencing facilitates high-throughput identification of genetic modifiers in model organisms, Model Organism Modifier provides a user-friendly solution to implement the bioinformatics analysis of the short-read datasets in laboratories without expertise or support in Bioinformatics.
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Affiliation(s)
- Tatiana Maroilley
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - K M Tahsin Hassan Rahit
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Afiya Razia Chida
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Filip Cotra
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Victoria Rodrigues Alves Barbosa
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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Ghigo A, De Santi C, Hart M, Mitash N, Swiatecka-Urban A. Cell signaling and regulation of CFTR expression in cystic fibrosis cells in the era of high efficiency modulator therapy. J Cyst Fibros 2023; 22 Suppl 1:S12-S16. [PMID: 36621372 DOI: 10.1016/j.jcf.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP- and protein kinase A (PKA)-regulated channel, expressed on the luminal surface of secretory and absorptive epithelial cells. CFTR has a complex, cell-specific regulatory network playing a major role in cAMP- and Ca2+-activated secretion of electrolytes. It secretes intracellular Cl- and bicarbonate and regulates absorption of electrolytes by differentially controlling the activity of the epithelial Na+ channel (ENaC) in colon, airways, and sweat ducts. The CFTR gene expression is regulated by cell-specific, time-dependent mechanisms reviewed elsewhere [1]. This review will focus on the transcriptional, post-transcriptional, and translational regulation of CFTR by cAMP-PKA, non-coding (nc)RNAs, and TGF-β signaling pathways in cystic fibrosis (CF) cells.
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Affiliation(s)
- Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, Via Nizza 52, Torino 10126, Italy.
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, 111St Stephen's Green, Dublin 2, Ireland
| | - Merrill Hart
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
| | - Nilay Mitash
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, United States
| | - Agnieszka Swiatecka-Urban
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
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7
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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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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.
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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.)
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9
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Moshirfar M, Brown AH, Sulit CA, Corbin WM, Ronquillo YC, Hoopes PC. Corneal Refractive Surgery Considerations in Patients with Cystic Fibrosis and Cystic Fibrosis Transmembrane Conductance Regulator-Related Disorders. Int Med Case Rep J 2022; 15:647-656. [PMID: 36388243 PMCID: PMC9656410 DOI: 10.2147/imcrj.s381078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
This article discusses common ocular manifestations of cystic fibrosis (CF) and cystic fibrosis transmembrane conductance regulator-related disorders (CFTR-RD). A structured approach for assessing and treating patients with CF/CFTR-RD seeking corneal refractive surgery is proposed, as well as a novel surgical risk scoring system. We also report two patients with various manifestations of CFTR dysfunction who presented for refractive surgery and the outcomes of the procedures. Surgeons seeking to perform refractive surgery on patients with CF/CFTR-RD should be aware of mild to severe clinical manifestations of CFTR dysfunction. Specific systemic and ocular manifestations of CF include chronic obstructive pulmonary disease (COPD), bronchiectasis, recurrent pulmonary infections, CF-related diabetes and liver disease, pancreatic insufficiency, conjunctival xerosis, night blindness, meibomian gland dysfunction (MGD), and blepharitis. Corneal manifestations include dry eye disease (DED), punctate keratitis (PK), filamentary keratitis (FK), xerophthalmia, and decreased endothelial cell density and central corneal thickness. Utilization of the appropriate review of systems (ROS) and screening tests will assist in determining if the patient is a suitable candidate for refractive surgery, as CF/CFTR-RD can impact the health of the cornea. Collaboration with other medical professionals who care for these patients is encouraged to ensure that their CF/CFTR-RD symptoms are best controlled via systemic and other treatment options. This will assist in reducing the severity of their ocular manifestations before and after surgery.
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Affiliation(s)
- Majid Moshirfar
- Hoopes Vision Research Center, Hoopes Vision, Draper, UT, USA
- John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
- Utah Lions Eye Bank, Murray, UT, USA
| | - Alex H Brown
- University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Christian A Sulit
- University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA
| | - Wyatt M Corbin
- Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
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10
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Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast. Proc Natl Acad Sci U S A 2022; 119:e2204206119. [PMID: 36067306 PMCID: PMC9478683 DOI: 10.1073/pnas.2204206119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In different individuals, the same mutation can lead to different phenotypes due to genetic background effects. This is commonly observed in various systems, including many human diseases. While isolated examples of such background effects have been observed, a systematic view across a large number of individuals is still lacking. Here, we surveyed genetic background effects associated with gene loss-of-function mutations across a population of natural isolates of the yeast Saccharomyces cerevisiae. We found that ∼15% of genes can display a background-dependent fitness change. Genes related to mitochondrial functions are significantly overrepresented, and showed reversed patterns of fitness gain or loss with genes involved in transcription and chromatin remodeling as well as in nuclear–cytoplasmic transport, suggesting a potential functional rewiring. In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared with the reference strain S288C. Out of these 632 genes with predicted background-dependent fitness effects, around 2/3 impact multiple backgrounds with a gradient of predicted fitness change while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear–cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All genes with background-dependent fitness effects tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.
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Evaluation of the quality of life and associated factors of a group of children and adolescents with cystic fibrosis in the northern region of Portugal: a cross-sectional pilot study. Porto Biomed J 2022; 7:e194. [DOI: 10.1097/j.pbj.0000000000000194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
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Rueda-Nieto S, Mondejar-Lopez P, Mira-Escolano MP, Cutillas-Tolín A, Maceda-Roldán LA, Arense-Gonzalo JJ, Palomar-Rodríguez JA. Analysis of the genotypic profile and its relationship with the clinical manifestations in people with cystic fibrosis: study from a rare disease registry. Orphanet J Rare Dis 2022; 17:222. [PMID: 35698092 PMCID: PMC9195274 DOI: 10.1186/s13023-022-02373-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cystic fibrosis (CF) has a vast and heterogeneous mutational spectrum in Europe. This variability has also been described in Spain, and there are numerous studies linking CFTR variants with the symptoms of the disease. Most of the studies analysed determinate clinical manifestations or specific sequence variants in patients from clinical units. Others used registry data without addressing the genotype–phenotype relationship. Therefore, the objective of this study is to describe the genetic and clinical characteristics of people with CF and to analyse the relationship between both using data from the rare disease registry of a region in southeastern Spain. Methods A cross-sectional study was carried out in people with a confirmed diagnosis of CF registered in the Rare Diseases Information System (SIER) of the Region of Murcia (Spain). The patients were classified into two genotypes according to the functional consequence that the genetic variants had on the CFTR protein. Results There were 192 people diagnosed with CF reported in the Region of Murcia as of 31 December 2018. Seventy-six genotypes and 49 different variants were described, with c.1521_1523delCTT (p. Phe508del) being the most common in 58.3% of the CF patients and 37.0% of the alleles. In addition, 67% of the patients were classified as a high-risk genotype, which was associated with a lower percentage of FEV1 (OR: 5.3; 95% CI: 1.2, 24.4), an increased risk of colonization by Pseudomonas aeruginosa (OR: 7.5; 95% CI: 1.7, 33.0) and the presence of pancreatic insufficiency (OR: 28.1; 95% CI: 9.3, 84.4) compared to those with a low-risk genotype. Conclusions This is the first study in Spain that describes the mutational spectrum and its association with clinical manifestations in patients with CF using data from a rare disease registry. The results obtained allow planning for the health resources needed by people with this disease, thus contributing to the development of personalized medicine that helps to optimize health care in CF patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02373-y.
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Affiliation(s)
- Senay Rueda-Nieto
- Teaching Unit of Preventive Medicine and Public Health, 30100, Murcia, Spain.
| | - Pedro Mondejar-Lopez
- Paediatric Pulmonology and Cystic Fibrosis Unit, Virgen de La Arrixaca Clinic University Hospital (Murcia), 30120, Murcia, Spain
| | - María-Pilar Mira-Escolano
- Rare Diseases Information System, Planning and Health Financing Department, Regional Health Council, 30001, Murcia, Spain
| | - Ana Cutillas-Tolín
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, University of Murcia School of Medicine, 30100, Murcia, Spain.,Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30120, El Palmar, Murcia, Spain
| | - Luis Alberto Maceda-Roldán
- Rare Diseases Information System, Planning and Health Financing Department, Regional Health Council, 30001, Murcia, Spain
| | - Julián Jesús Arense-Gonzalo
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, University of Murcia School of Medicine, 30100, Murcia, Spain.,Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30120, El Palmar, Murcia, Spain
| | - Joaquín A Palomar-Rodríguez
- Rare Diseases Information System, Planning and Health Financing Department, Regional Health Council, 30001, Murcia, Spain
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13
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Saint-Criq V, Guequén A, Philp AR, Villanueva S, Apablaza T, Fernández-Moncada I, Mansilla A, Delpiano L, Ruminot I, Carrasco C, Gray MA, Flores CA. Inhibition of the sodium-dependent HCO 3- transporter SLC4A4, produces a cystic fibrosis-like airway disease phenotype. eLife 2022; 11:e75871. [PMID: 35635440 PMCID: PMC9173743 DOI: 10.7554/elife.75871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Abstract
Bicarbonate secretion is a fundamental process involved in maintaining acid-base homeostasis. Disruption of bicarbonate entry into airway lumen, as has been observed in cystic fibrosis, produces several defects in lung function due to thick mucus accumulation. Bicarbonate is critical for correct mucin deployment and there is increasing interest in understanding its role in airway physiology, particularly in the initiation of lung disease in children affected by cystic fibrosis, in the absence of detectable bacterial infection. The current model of anion secretion in mammalian airways consists of CFTR and TMEM16A as apical anion exit channels, with limited capacity for bicarbonate transport compared to chloride. However, both channels can couple to SLC26A4 anion exchanger to maximise bicarbonate secretion. Nevertheless, current models lack any details about the identity of the basolateral protein(s) responsible for bicarbonate uptake into airway epithelial cells. We report herein that the electrogenic, sodium-dependent, bicarbonate cotransporter, SLC4A4, is expressed in the basolateral membrane of human and mouse airways, and that it's pharmacological inhibition or genetic silencing reduces bicarbonate secretion. In fully differentiated primary human airway cells cultures, SLC4A4 inhibition induced an acidification of the airways surface liquid and markedly reduced the capacity of cells to recover from an acid load. Studies in the Slc4a4-null mice revealed a previously unreported lung phenotype, characterized by mucus accumulation and reduced mucociliary clearance. Collectively, our results demonstrate that the reduction of SLC4A4 function induced a CF-like phenotype, even when chloride secretion remained intact, highlighting the important role SLC4A4 plays in bicarbonate secretion and mammalian airway function.
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Affiliation(s)
- Vinciane Saint-Criq
- Biosciences Institute, The Medical School, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Anita Guequén
- Centro de Estudios CientíficosValdiviaChile
- Universidad Austral de ChileValdiviaChile
| | - Amber R Philp
- Centro de Estudios CientíficosValdiviaChile
- Universidad Austral de ChileValdiviaChile
| | | | - Tábata Apablaza
- Centro de Estudios CientíficosValdiviaChile
- Universidad Austral de ChileValdiviaChile
| | | | - Agustín Mansilla
- Centro de Estudios CientíficosValdiviaChile
- Universidad Austral de ChileValdiviaChile
| | - Livia Delpiano
- Biosciences Institute, The Medical School, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Iván Ruminot
- Centro de Estudios CientíficosValdiviaChile
- Universidad San SebastiánValdiviaChile
| | - Cristian Carrasco
- Subdepartamento de Anatomía Patológica, Hospital Base de ValdiviaValdiviaChile
| | - Michael A Gray
- Biosciences Institute, The Medical School, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Carlos A Flores
- Centro de Estudios CientíficosValdiviaChile
- Universidad San SebastiánValdiviaChile
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14
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Blaconà G, Raso R, Castellani S, Pierandrei S, Del Porto P, Ferraguti G, Ascenzioni F, Conese M, Lucarelli M. Downregulation of epithelial sodium channel (ENaC) activity in cystic fibrosis cells by epigenetic targeting. Cell Mol Life Sci 2022; 79:257. [PMID: 35462606 PMCID: PMC9035428 DOI: 10.1007/s00018-022-04190-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 12/31/2022]
Abstract
The pathogenic mechanism of cystic fibrosis (CF) includes the functional interaction of the cystic fibrosis transmembrane conductance regulator (CFTR) protein with the epithelial sodium channel (ENaC). The reduction of ENaC activity may constitute a therapeutic option for CF. This hypothesis was evaluated using drugs that target the protease-dependent activation of the ENaC channel and the transcriptional activity of its coding genes. To this aim we used: camostat, a protease inhibitor; S-adenosyl methionine (SAM), showed to induce DNA hypermethylation; curcumin, known to produce chromatin condensation. SAM and camostat are drugs already clinically used in other pathologies, while curcumin is a common dietary compound. The experimental systems used were CF and non-CF immortalized human bronchial epithelial cell lines as well as human bronchial primary epithelial cells. ENaC activity and SCNN1A, SCNN1B and SCNN1G gene expression were analyzed, in addition to SCNN1B promoter methylation. In both immortalized and primary cells, the inhibition of extracellular peptidases and the epigenetic manipulations reduced ENaC activity. Notably, the reduction in primary cells was much more effective. The SCNN1B appeared to be the best target to reduce ENaC activity, in respect to SCNN1A and SCNN1G. Indeed, SAM treatment resulted to be effective in inducing hypermethylation of SCNN1B gene promoter and in lowering its expression. Importantly, CFTR expression was unaffected, or even upregulated, after treatments. These results open the possibility of CF patients’ treatment by epigenetic targeting.
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Affiliation(s)
- Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Roberto Raso
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Paola Del Porto
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy. .,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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15
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Nachtegael C, Gravel B, Dillen A, Smits G, Nowé A, Papadimitriou S, Lenaerts T. Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database. Database (Oxford) 2022; 2022:6566807. [PMID: 35411390 PMCID: PMC9216476 DOI: 10.1093/database/baac023] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 11/19/2022]
Abstract
Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, the ad hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published oligogenic literature. The application of this protocol on the oligogenic literature generated a new repository containing 916 oligogenic variant combinations linked to 159 distinct diseases. Information extracted from the scientific literature is supplemented with current knowledge support obtained from public databases. Each entry is an oligogenic combination linked to a disease, labelled with a confidence score based on the level of genetic and functional evidence that supports its involvement in this disease. These scores allow users to assess the relevance and proof of pathogenicity of each oligogenic combination in the database, constituting markers for reporting improvements on disease-causing oligogenic variant combinations. OLIDA follows the FAIR principles, providing detailed documentation, easy data access through its application programming interface and website, use of unique identifiers and links to existing ontologies.
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Affiliation(s)
- Charlotte Nachtegael
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, Brussels 1050, Belgium
| | - Barbara Gravel
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, Brussels 1050, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Arnau Dillen
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
- Human Physiology and Sports Physiotherapy research group, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Avenue Jean Joseph Crocq 15, Brussels 1020, Belgium
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, Brussels 1070, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, Brussels 1050, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Boulevard du Triomphe, CP 263, Brussels 1050, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, Brussels 1050, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
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16
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Rossi A, Kontarakis Z. Beyond Mendelian Inheritance: Genetic Buffering and Phenotype Variability. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:79-87. [PMID: 36939776 PMCID: PMC9590499 DOI: 10.1007/s43657-021-00030-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 06/18/2023]
Abstract
Understanding the way genes work amongst individuals and across generations to shape form and function is a common theme for many genetic studies. The recent advances in genetics, genome engineering and DNA sequencing reinforced the notion that genes are not the only players that determine a phenotype. Due to physiological or pathological fluctuations in gene expression, even genetically identical cells can behave and manifest different phenotypes under the same conditions. Here, we discuss mechanisms that can influence or even disrupt the axis between genotype and phenotype; the role of modifier genes, the general concept of genetic redundancy, genetic compensation, the recently described transcriptional adaptation, environmental stressors, and phenotypic plasticity. We furthermore highlight the usage of induced pluripotent stem cells (iPSCs), the generation of isogenic lines through genome engineering, and sequencing technologies can help extract new genetic and epigenetic mechanisms from what is hitherto considered 'noise'.
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Affiliation(s)
- Andrea Rossi
- Genome Engineering and Model Development Lab (GEMD), IUF-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Zacharias Kontarakis
- Genome Engineering and Measurement Laboratory (GEML), Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich of ETH Zurich, University of Zurich, 8093 Zurich, Switzerland
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17
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Narasimhan U, Janakiraman A, Puskur D, Anitha FS, Paul SFD, Koshy T. Case Report: A Disease Phenotype of Rett Syndrome and Neurofibromatosis Resulting from A Bilocus Variant Combination. J Autism Dev Disord 2022; 53:2138-2142. [PMID: 35122187 DOI: 10.1007/s10803-022-05458-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Udayakumar Narasimhan
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Abhinayaa Janakiraman
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Dedeepya Puskur
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Fatima Shirly Anitha
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Solomon Franklin Durairaj Paul
- Department of Human Genetics, Faculty of Biomedical Science and Technology, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Teena Koshy
- Department of Human Genetics, Faculty of Biomedical Science and Technology, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India.
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18
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Wang F, Panjwani N, Wang C, Sun L, Strug LJ. A flexible summary statistics-based colocalization method with application to the mucin cystic fibrosis lung disease modifier locus. Am J Hum Genet 2022; 109:253-269. [PMID: 35065708 PMCID: PMC8874229 DOI: 10.1016/j.ajhg.2021.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
Mucus obstruction is a central feature in the cystic fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Expression quantitative trait locus (eQTL) analysis using human nasal epithelia (HNE) from 94 CF-affected Canadians in the CFGMC demonstrated MUC4 eQTLs that mirrored the lung association pattern in the region, suggesting that MUC4 expression may mediate CF lung disease. Complications arose, however, with colocalization testing using existing methods: the locus is complex and the associated SNPs span a 0.2 Mb region with high linkage disequilibrium (LD) and evidence of allelic heterogeneity. We previously developed the Simple Sum (SS), a powerful colocalization test in regions with allelic heterogeneity, but SS assumed eQTLs to be present to achieve type I error control. Here we propose a two-stage SS (SS2) colocalization test that avoids a priori eQTL assumptions, accounts for multiple hypothesis testing and the composite null hypothesis, and enables meta-analysis. We compare SS2 to published approaches through simulation and demonstrate type I error control for all settings with the greatest power in the presence of high LD and allelic heterogeneity. Applying SS2 to the MUC20/MUC4 CF lung disease locus with eQTLs from CF HNE revealed significant colocalization with MUC4 (p = 1.31 × 10−5) rather than with MUC20. The SS2 is a powerful method to inform the responsible gene(s) at a locus and guide future functional studies. SS2 has been implemented in the application LocusFocus.
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Affiliation(s)
- Fan Wang
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5G 1Z5, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Cheng Wang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5G 1Z5, Canada; Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada.
| | - Lisa J Strug
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5G 1Z5, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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19
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Williamson DM, Sharma A. Cystic fibrosis in children: A pediatric anesthesiologist's perspective. Paediatr Anaesth 2022; 32:167-173. [PMID: 34963200 DOI: 10.1111/pan.14384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
Cystic fibrosis is a multi-systemic disease of impaired sodium and chloride transport across epithelial surfaces. Cystic fibrosis is one of the most common autosomal recessive diseases among Caucasian children. However, recent epidemiologic studies suggest that the disease in Hispanic, African American, and Asian American populations may be more common than previously recognized. The phenotypic expression is characterized by the constellation of pulmonary, pancreatic, hepatobiliary, and gastrointestinal dysfunction. Progressive obstructive lung disease is the hallmark of cystic fibrosis, and end-stage respiratory failure is the primary cause of morbidity and mortality. The most significant advance in the care has been the development of cystic fibrosis modulators, a class of drugs that restore cystic fibrosis transmembrane conductance regulator folding, intracellular processing, or function. Improved diagnostic abilities, a multidisciplinary approach to medical management, and the use of cystic fibrosis modulators have led to improvement in the quality of life and life expectancy. These patients undergo range of procedures such as nasal polypectomy, placement of gastrostomy tubes, vascular access device placement, transbronchial lung biopsies, and other thoracic surgeries. The anesthetic care of children with advanced cystic fibrosis disease is complex. Preoperative optimization can help improve postoperative outcomes. Strategies for pain control should rely on non-opiate, multimodal adjuncts, and regional or neuraxial techniques. Unfortunately for some children, a progressive respiratory disease often leads to end-stage respiratory failure and lung transplant surgery remains the only viable treatment option. Widespread use of lung transplant surgery as a treatment option is severely constraint by donor organ availability. Primary graft dysfunction is the most common cause of early death and can be seen within 48 h of surgery. Median long-term survival after lung transplant remains modest. Chronic lung allograft dysfunction, opportunistic infections, and post-transplant lymphoproliferative disorder are the most common causes of morbidity and mortality among long-term survivors.
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Affiliation(s)
- Danielle M Williamson
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California, USA
| | - Anshuman Sharma
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California, USA
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20
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Characterizing mucociliary clearance in young children with cystic fibrosis. Pediatr Res 2022; 91:612-620. [PMID: 33753897 PMCID: PMC8455702 DOI: 10.1038/s41390-021-01453-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/05/2022]
Abstract
BACKGROUND This research characterized mucociliary clearance (MCC) in young children with cystic fibrosis (CF). METHODS Fourteen children (5-7 years old) with CF underwent: two baseline MCC measurements (Visits 1 and 2); one MCC measurement approximately 1 year later (Visit 3); and measurements of lung clearance index (LCI), a measure of ventilation inhomogeneity. RESULTS Median (range) percent MCC through 60 min (MCC60) was similar on Visits 1 and 2 with 11.0 (0.9-33.7) and 12.8 (2.7-26.8), respectively (p = 0.95), and reproducible (Spearman Rho = 0.69; p = 0.007). Mucociliary clearance did not change significantly over 1 year with median percent MCC60 on Visit 3 [12.8 (3.7-17.6)] similar to Visit 2 (p = 0.58). Lower percent MCC60 on Visit 3 was significantly associated with higher LCI scores on Visit 3 (N = 14; Spearman Rho = -0.56; p = 0.04). CONCLUSIONS Tests of MCC were reproducible and reliable over a 2-week period and stable over a 1-year period in 5-7-year-old children with CF. Lower MCC values were associated with increased ventilation inhomogeneity. These results suggest that measurements of MCC could be used in short-term clinical trials of interventions designed to modulate MCC and as a new, non-invasive test to evaluate early lung pathology in children with CF. IMPACT This is the first study to characterize mucociliary clearance (MCC) in children with cystic fibrosis (CF) who were 5-7 years old. Measurements of mucociliary clearance were reproducible and reliable over a 2-week period and stable over a 1-year period. Variability in MCC between children was associated with differences in ventilation homogeneity, such that children with lower MCC values had increased ventilation inhomogeneity. These results suggest that measurements of MCC could be used in short-term clinical trials of interventions designed to modulate MCC and as a new, non-invasive test to evaluate early lung pathology in children with CF.
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21
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Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder caused by mutations in CFTR, the cystic fibrosis transmembrane conductance regulator gene. People with CF experience a wide variety of medical conditions that affect the pulmonary, endocrine, gastrointestinal, pancreatic, biliary, and reproductive systems. Traditionally, CF carriers, with one defective copy of CFTR, were not thought to be at risk for CF-associated diseases. However, an emerging body of literature suggests that heterozygotes are at increased risk for many of the same conditions as homozygotes. For example, heterozygotes appear to be at increased risk for chronic pancreatitis, atypical mycobacterial infections, and bronchiectasis. In the United States alone, there are almost 10 million CF carriers. Universal newborn screening and prenatal genetic screening will identify more. Thus, there is a critical need to develop more precise estimates of health risks attributable to the CF carrier state across the lifespan.
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Affiliation(s)
- Philip M. Polgreen
- Division of Infectious Diseases, Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Alejandro P. Comellas
- Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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22
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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.
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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.)
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23
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Hosoya M, Fujioka M, Nara K, Morimoto N, Masuda S, Sugiuchi T, Katsunuma S, Takagi A, Morita N, Ogawa K, Kaga K, Matsunaga T. Investigation of the hearing levels of siblings affected by a single GJB2 variant: Possibility of genetic modifiers. Int J Pediatr Otorhinolaryngol 2021; 149:110840. [PMID: 34293626 DOI: 10.1016/j.ijporl.2021.110840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/25/2021] [Accepted: 07/11/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Variants in GJB2 can cause autosomal recessive deafness (DFNB1). There is evidence for genotype-phenotype correlations of GJB2 variants; however, several genotypes can cause varying levels of hearing loss likely attributable to differences in genetic or environmental background. As siblings share approximately 50% of their genetic background and usually have a common environmental background, analysis of phenotypes of siblings with a specific GJB2 variant may reveal factors relevant to phenotypic variation. There have been no previous analyses of differences in hearing among siblings carrying a single GJB2 genotype. Here, we investigated hearing differences between siblings with a single GJB2 variant, which can cause various levels of hearing loss. METHODS We examined hearing levels in 16 pairs of siblings homozygous for the c.235delC variant of GJB2. Differences in hearing acuity between sibling pairs were detected by auditory evaluation. RESULTS Average differences in acoustic threshold >30 dB were observed between five pairs of siblings, whereas the remaining 11 pairs had average threshold values within approximately 10 dB of one another. Hearing loss varied from moderate to profound. CONCLUSION Our results indicate that auditory acuity associated with homozygosity for GJB2 c.235delC can vary in degree; however, in approximately 70% of younger siblings, it was approximately the same as that in the first child, despite a diverse spectrum of hearing loss among different families. These results suggest that differences in genetic background may modify the phenotype associated with homozygous GJB2 c.235delC.
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Affiliation(s)
- Makoto Hosoya
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masato Fujioka
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Noriko Morimoto
- Department of Otorhinolaryngology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Sawako Masuda
- Department of Otorhinolaryngology, National Hospital Organization Mie National Hospital, 357 Osato-Kubota, Tsu, Mie, 514-0125, Japan
| | - Tomoko Sugiuchi
- Department of Otorhinolaryngology, Kanto Rosai Hospital, 1-1 Kizukisumiyoshi-cho, Nakahara-ku, Kawasaki-shi, Kanagawa, 211-8510, Japan
| | - Sayaka Katsunuma
- Department of Otorhinolaryngology, Hyogo Prefectural Kobe Children's Hospital, 1-6-7 Minatojima-minamimachi, Chuo-ku, Kobe-shi, Hyogo, 650-0047, Japan
| | - Akira Takagi
- Department of Otorhinolaryngology, Shizuoka General Hospital, 4-27-1 Kita Ando Aoi-ku, Shizuoka-shi, Shizuoka, 420-8527, Japan
| | - Noriko Morita
- Department of Otorhinolaryngology, Teikyo University Hospital, 2-11-1 Kaga, Itabashi-Ku, Tokyo, 173-8606, Japan; Department of Otorhinolaryngology, Kobari General Hospital, 29-1 Yokouchi, Noda, Chiba, 278-8501, Japan
| | - Kaoru Ogawa
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kimitaka Kaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Tatsuo Matsunaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan; Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
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24
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Singh RS. Decoding 'Unnecessary Complexity': A Law of Complexity and a Concept of Hidden Variation Behind "Missing Heritability" in Precision Medicine. J Mol Evol 2021; 89:513-526. [PMID: 34341835 PMCID: PMC8327892 DOI: 10.1007/s00239-021-10023-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/20/2021] [Indexed: 01/06/2023]
Abstract
The high hopes for the Human Genome Project and personalized medicine were not met because the relationship between genotypes and phenotypes turned out to be more complex than expected. In a previous study we laid the foundation of a theory of complexity and showed that because of the blind nature of evolution, and molecular and historical contingency, cells have accumulated unnecessary complexity, complexity beyond what is necessary and sufficient to describe an organism. Here we provide empirical evidence and show that unnecessary complexity has become integrated into the genome in the form of redundancy and is relevant to molecular evolution of phenotypic complexity. Unnecessary complexity creates uncertainty between molecular and phenotypic complexity, such that phenotypic complexity (CP) is higher than molecular complexity (CM), which is higher than DNA complexity (CD). The qualitative inequality in complexity is based on the following hierarchy: CP > CM > CD. This law-like relationship holds true for all complex traits, including complex diseases. We present a hypothesis of two types of variation, namely open and closed (hidden) systems, show that hidden variation provides a hitherto undiscovered "third source" of phenotypic variation, beside genotype and environment, and argue that "missing heritability" for some complex diseases is likely to be a case of "diluted heritability". There is a need for radically new ways of thinking about the principles of genotype-phenotype relationship. Understanding how cells use hidden, pathway variation to respond to stress can shed light on why two individuals who share the same risk factors may not develop the same disease, or how cancer cells escape death.
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Affiliation(s)
- Rama S Singh
- Department of Biology, and Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada.
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25
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Consistent Assignment of Risk and Benign Allele at rs2303153 in the CF Modifier Gene SCNN1B in Three Independent F508del- CFTR Homozygous Patient Populations. Genes (Basel) 2021; 12:genes12101554. [PMID: 34680949 PMCID: PMC8535344 DOI: 10.3390/genes12101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
CFTR encodes for a chloride and bicarbonate channel expressed at the apical membrane of polarized epithelial cells. Transepithelial sodium transport mediated by the amiloride-sensitive sodium channel ENaC is thought to contribute to the manifestation of CF disease. Thus, ENaC is a therapeutic target in CF and a valid cystic fibrosis modifier gene. We have characterized SCNN1B as a genetic modifier in the three independent patient cohorts of F508del-CFTR homozygotes. We could identify a regulatory element at SCNN1B to the genomic segment rs168748-rs2303153-rs4968000 by fine-mapping (Pbest = 0.0177), consistently observing the risk allele rs2303153-C and the contrasting benign allele rs2303153-G in all three patient cohorts. Furthermore, our results show that expression levels of SCNN1B are associated with rs2303153 genotype in intestinal epithelia (p = 0.003). Our data confirm that the well-established biological role of SCNN1B can be recognized by an association study on informative endophenotypes in the rare disease cystic fibrosis and calls attention to reproducible results in association studies obtained from small, albeit carefully characterized patient populations.
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26
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Nykamp K, Truty R, Riethmaier D, Wilkinson J, Bristow SL, Aguilar S, Neitzel D, Faulkner N, Aradhya S. Elucidating clinical phenotypic variability associated with the polyT tract and TG repeats in CFTR. Hum Mutat 2021; 42:1165-1172. [PMID: 34196078 PMCID: PMC9292755 DOI: 10.1002/humu.24250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 02/05/2023]
Abstract
Biallelic pathogenic variants in CFTR manifest as cystic fibrosis (CF) or other CFTR-related disorders (CFTR-RDs). The 5T allele, causing alternative splicing and reduced protein activity, is modulated by the adjacent TG repeat element, though previous data have been limited to small, selective cohorts. Here, the risk and spectrum of phenotypes associated with the CFTR TG-T5 haplotype variants (TG11T5, TG12T5, and TG13T5) in the absence of the p.Arg117His variant are evaluated. Individuals who received physician-ordered next-generation sequencing of CFTR were included. TG[11-13]T5 variant frequencies (biallelic or with another CF-causing variant [CFvar]) were calculated. Clinical information reported by the ordering provider or the individual was examined. Among 548,300 individuals, the T5 minor allele frequency (MAF) was 4.2% (TG repeat distribution: TG11 = 68.1%, TG12 = 29.5%, TG13 = 2.4%). When present with a CFvar, each TG[11-13]T5 variant was significantly enriched in individuals with a high suspicion of CF or CFTR-RD (personal/family history of CF/CFTR-RD) compared to those with a low suspicion for CF or CFTR-RD (hereditary cancer screening, CFTR not requisitioned). Compared to CFvar/CFvar individuals, those with TG[11-13]T5/CFvar generally had single-organ involvement, milder symptoms, variable expressivity, and reduced penetrance. These data improve our understanding of disease risks associated with TG[11-13]T5 variants and have important implications for reproductive genetic counseling.
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27
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Walton NI, Zhang X, Soltis AR, Starr J, Dalgard CL, Wilkerson MD, Conrad D, Pollard HB. Tensin 1 (TNS1) is a modifier gene for low body mass index (BMI) in homozygous [F508del]CFTR patients. Physiol Rep 2021; 9:e14886. [PMID: 34086412 PMCID: PMC8176904 DOI: 10.14814/phy2.14886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/02/2021] [Indexed: 11/24/2022] Open
Abstract
Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in the CFTR gene, most commonly by the [F508del] variant. Although CF is a classical Mendelian disease, genetic variants in several modifier genes have been associated with variation of the clinical phenotype for pulmonary and gastrointestinal function and urogenital development. We hypothesized that whole genome sequencing of a well‐phenotyped CF populations might identify novel variants in known, or hitherto unknown, modifier genes. Whole genome sequencing was performed on the Illumina HiSeq X platform for 98 clinically diagnosed cystic fibrosis patient samples from the Adult CF Clinic at the University of California San Diego (UCSD). We compared protein‐coding, non‐silent variants genome wide between CFTR [F508del] homozygotes vs CFTR compound heterozygotes. Based on a single variant score test, we found 3 SNPs in common variants (MAF >5%) that occurred at significantly different rates between homozygous [F508del]CFTR and compound heterozygous [F508del]CFTR patients. The 3 SNPs were all located in one gene on chromosome 2: Tensin 1 (TNS1: rs3796028; rs2571445: and rs918949). We observed significantly lower BMIs in homozygous [F508del]CFTR patients who were also homozygous for Tensin 1 rs918949 (T/T) (p = 0.023) or rs2571445 (G/G) (p = 0.02) variants. The Tensin 1 gene is thus a potential modifier gene for low BMI in CF patients homozygous for the [F508del]CFTR variant.
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Affiliation(s)
- Nathan I Walton
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Consortium for Health and Military Performance, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Xijun Zhang
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anthony R Soltis
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Joshua Starr
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Douglas Conrad
- Department of Medicine, University of California, San Diego, CA, USA
| | - Harvey B Pollard
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Consortium for Health and Military Performance, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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28
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Rooj AK, Cormet-Boyaka E, Clark EB, Qadri YJ, Lee W, Boddu R, Agarwal A, Tambi R, Uddin M, Parpura V, Sorscher EJ, Fuller CM, Berdiev BK. Association of cystic fibrosis transmembrane conductance regulator with epithelial sodium channel subunits carrying Liddle's syndrome mutations. Am J Physiol Lung Cell Mol Physiol 2021; 321:L308-L320. [PMID: 34037494 DOI: 10.1152/ajplung.00298.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The association of the cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC) in the pathophysiology of cystic fibrosis (CF) is controversial. Previously, we demonstrated a close physical association between wild-type (WT) CFTR and WT ENaC. We have also shown that the F508del CFTR fails to associate with ENaC unless the mutant protein is rescued pharmacologically or by low temperature. In this study, we present the evidence for a direct physical association between WT CFTR and ENaC subunits carrying Liddle's syndrome mutations. We show that all three ENaC subunits bearing Liddle's syndrome mutations (both point mutations and the complete truncation of the carboxy terminus), could be coimmunoprecipitated with WT CFTR. The biochemical studies were complemented by fluorescence lifetime imaging microscopy (FLIM), a distance-dependent approach that monitors protein-protein interactions between fluorescently labeled molecules. Our measurements revealed significantly increased fluorescence resonance energy transfer between CFTR and all tested ENaC combinations as compared with controls (ECFP and EYFP cotransfected cells). Our findings are consistent with the notion that CFTR and ENaC are within reach of each other even in the setting of Liddle's syndrome mutations, suggestive of a direct intermolecular interaction between these two proteins.
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Affiliation(s)
- Arun K Rooj
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | - Edlira B Clark
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Yawar J Qadri
- Department of Anesthesiology, The Emory University School of Medicine, Atlanta, Georgia
| | - William Lee
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Ravindra Boddu
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Anupam Agarwal
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Eric J Sorscher
- Department of Pediatrics, The Emory University School of Medicine, Atlanta, Georgia
| | - Cathy M Fuller
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Bakhrom K Berdiev
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama.,College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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29
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Ekinci İB, Hızal M, Emiralioğlu N, Özçelik U, Yalçın E, Doğru D, Kiper N, Dayangaç-Erden D. Differentially expressed genes associated with disease severity in siblings with cystic fibrosis. Pediatr Pulmonol 2021; 56:910-920. [PMID: 33369261 DOI: 10.1002/ppul.25237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/26/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by CFTR gene mutations. Despite having the same mutation, CF patients may demonstrate clinical variability in severity and prognosis of the disease. In this study, we aimed to determine differentially expressed genes between mild and severe siblings with same genotype. We performed targeted real-time polymerase chain reaction based transcriptomic analysis of nasal epithelial cells obtained from two families with two siblings with Class II mutations (F508del/F508del) and (F508del/G85E), one family with three siblings with Class IV mutation (I1234V/I1234V). In severe siblings with Class II mutations, TNFRSF11A, KCNE1, STX1A, SLC9A3R2 were found to be up regulated. CXCL1, CFTR, CXCL2 were found to be down regulated. In the severe sibling with Class IV mutation; mainly genes responsible from complement and coagulation system were identified. Comparison of CF patients to non-CF control; showed that ICAM1 was up regulated whereas EZR, TNFRSF1A, HSPA1A were down regulated in patients. As a result of this study, differentially expressed genes responsible for clinical severity among affected siblings carrying the same mutation were identified. The results will provide an opportunity for the development of novel target molecules for treatment of disease.
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Affiliation(s)
- İlksen Berfin Ekinci
- Department of Medical Biology, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Mina Hızal
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Nagehan Emiralioğlu
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Uğur Özçelik
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Ebru Yalçın
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Deniz Doğru
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Nural Kiper
- Department of Pediatric Pulmonology, Ihsan Dogramaci Children's Hospital, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
| | - Didem Dayangaç-Erden
- Department of Medical Biology, Hacettepe University Faculty of Medicine, Sıhhiye, Ankara, Turkey
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Pierandrei S, Truglio G, Ceci F, Del Porto P, Bruno SM, Castellani S, Conese M, Ascenzioni F, Lucarelli M. DNA Methylation Patterns Correlate with the Expression of SCNN1A, SCNN1B, and SCNN1G (Epithelial Sodium Channel, ENaC) Genes. Int J Mol Sci 2021; 22:ijms22073754. [PMID: 33916525 PMCID: PMC8038451 DOI: 10.3390/ijms22073754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
The interplay between the cystic fibrosis transmembrane conductance regulator (CFTR) and the epithelial sodium channel (ENaC) in respiratory epithelia has a crucial role in the pathogenesis of cystic fibrosis (CF). The comprehension of the mechanisms of transcriptional regulation of ENaC genes is pivotal to better detail the pathogenic mechanism and the genotype-phenotype relationship in CF, as well as to realize therapeutic approaches based on the transcriptional downregulation of ENaC genes. Since we aimed to study the epigenetic transcriptional control of ENaC genes, an assessment of their expression and DNA methylation patterns in different human cell lines, nasal brushing samples, and leucocytes was performed. The mRNA expression of CFTR and ENaC subunits α, β and γ (respectively SCNN1A, SCNN1B, and SCNN1G genes) was studied by real time PCR. DNA methylation of 5'-flanking region of SCNN1A, SCNN1B, and SCNN1G genes was studied by HpaII/PCR. The levels of expression and DNA methylation of ENaC genes in the different cell lines, brushing samples, and leukocytes were very variable. The DNA regions studied of each ENaC gene showed different methylation patterns. A general inverse correlation between expression and DNA methylation was evidenced. Leukocytes showed very low expression of all the 3 ENaC genes corresponding to a DNA methylated pattern. The SCNN1A gene resulted to be the most expressed in some cell lines that, accordingly, showed a completely demethylated pattern. Coherently, a heavy and moderate methylated pattern of, respectively, SCNN1B and SCNN1G genes corresponded to low levels of expression. As exceptions, we found that dexamethasone treatment appeared to stimulate the expression of all the 3 ENaC genes, without an evident modulation of the DNA methylation pattern, and that in nasal brushing a considerable expression of all the 3 ENaC genes were found despite an apparent methylated pattern. At least part of the expression modulation of ENaC genes seems to depend on the DNA methylation patterns of specific DNA regions. This points to epigenetics as a controlling mechanism of ENaC function and as a possible therapeutic approach for CF.
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Affiliation(s)
- Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Gessica Truglio
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Fabrizio Ceci
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
| | - Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Via Napoli 121, 71122 Foggia, Italy;
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
- Correspondence: (F.A.); (M.L.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Viale Regina Elena 291, 00161 Roma, Italy
- Correspondence: (F.A.); (M.L.)
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31
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McKone EF, Ariti C, Jackson A, Zolin A, Carr SB, Orenti A, van Rens JG, Lemonnier L, Macek M, Keogh RH, Naehrlich L. Survival estimates in European cystic fibrosis patients and the impact of socioeconomic factors: a retrospective registry cohort study. Eur Respir J 2021; 58:13993003.02288-2020. [PMID: 33678607 DOI: 10.1183/13993003.02288-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/12/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Median survival for cystic fibrosis (CF) patients in Europe is unknown and is likely to be influenced by socioeconomic factors. Using the European CF Society Patient Registry (ECFSPR), median survival estimates were obtained for CF patients across Europe and the impact of socioeconomic status on survival was examined. METHODS CF subjects known to be alive and in the ECFSPR between 2010 and 2014 were included. Survival curves were estimated using the Kaplan-Meier method. Differences in the survival curves were assessed using the log-rank test. Cox regression was used to estimate the association between socioeconomic factors and the age-specific hazard of death, with adjustment for sex, age at diagnosis, CF transmembrane conductance regulator (CFTR) genotype and transplant status. RESULTS The final analysis included 13 countries with 31 987 subjects (135 833 person-years of follow-up) and 1435 deaths. Median survival age for these patients in the ECFSPR was 51.7 (95% CI 50.0-53.4) years. After adjusting for potential confounders age at diagnosis, sex, CFTR genotype and transplant status, there remained strong evidence of an association between socioeconomic factors and mortality (p<0.001). Countries in the highest third of healthcare spending had a 46% lower hazard of mortality (HR 0.54, 95% CI 0.45-0.64) than countries in the lowest third of healthcare spending. CONCLUSIONS Median survival for patients with CF in Europe is comparable to that reported in other jurisdictions and differs by socioeconomic factors.
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Affiliation(s)
- Edward F McKone
- St Vincent's University Hospital and University College Dublin School of Medicine, Dublin, Ireland
| | - Cono Ariti
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Anna Zolin
- Dept of Clinical Sciences and Community Health, Laboratory of Medical Statistics, Epidemiology and Biometry "G.A. Maccacaro", University of Milan, Milan, Italy
| | - Siobhán B Carr
- Royal Brompton Hospital and National Heart and Lung Institute, Imperial College London, London, UK
| | - Annalisa Orenti
- Dept of Clinical Sciences and Community Health, Laboratory of Medical Statistics, Epidemiology and Biometry "G.A. Maccacaro", University of Milan, Milan, Italy
| | - Jacqui G van Rens
- European Cystic Fibrosis Society Patient Registry, Karup, Denmark.,University Hospital Leuven, Leuven, Belgium
| | | | - Milan Macek
- Dept of Biology and Medical Genetics, Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czechia
| | - Ruth H Keogh
- London School of Hygiene and Tropical Medicine, London, UK
| | - Lutz Naehrlich
- Dept of Paediatrics, Justus Liebig University Giessen, Giessen, Germany
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32
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Two Siblings Homozygous for F508del-CFTR Have Varied Disease Phenotypes and Protein Biomarkers. Int J Mol Sci 2021; 22:ijms22052631. [PMID: 33807880 PMCID: PMC7961721 DOI: 10.3390/ijms22052631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/20/2021] [Accepted: 03/01/2021] [Indexed: 12/01/2022] Open
Abstract
Two siblings with CF are homozygous for F508del (referred to as Subject A and Subject B). Despite having the same CFTR genotype and similar environment, these two subjects exhibited different disease phenotypes. We analyzed their medical records and CF Foundation Registry data and measured inflammatory protein mediators in their sputum samples. Then, we examined the longitudinal relationships between inflammatory markers and disease severity for each subject and compared between them. Subject A presented a more severe disease than Subject B. During the study period, Subject A had two pulmonary exacerbations (PEs) whereas Subject B had one mild PE. The forced expiratory volume in 1 s (FEV1, % predicted) values for Subject A were between 34–45% whereas for Subject B varied between 48–90%. Inflammatory protein mediators associated with neutrophils, Th1, Th2, and Th17 responses were elevated in sputum of Subject A compared with Subject B, and also in samples collected prior to and during PEs for both subjects. Neutrophilic elastase (NE) seemed to be the most informative biomarkers. The infectious burden between these two subjects was different.
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33
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Choi P, Bauler L, Gregoire‐Bottex MM. Fighting diagnostic confirmation bias: Cystic fibrosis, allergic bronchopulmonary aspergillus, or both? Clin Case Rep 2021; 9:1379-1382. [PMID: 33768849 PMCID: PMC7981717 DOI: 10.1002/ccr3.3781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/26/2020] [Accepted: 09/06/2020] [Indexed: 11/12/2022] Open
Abstract
As diagnostic algorithms for cystic fibrosis (CF) continue to evolve, education of general practitioners is essential to prevent delayed diagnosis of CF and allow prompt referral to CF centers. For patients suffering from allergic bronchopulmonary aspergillosis (ABPA), CF should be at the top of the differential diagnosis.
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Affiliation(s)
- Patricia Choi
- Department of Pediatric and Adolescent MedicineWestern Michigan University Homer Stryker M.D. School of MedicineKalamazooMIUSA
- Present address:
Department of Internal MedicineSpectrum Health/Michigan State UniversityGrand RapidsMIUSA
| | - Laura Bauler
- Department of Biomedical SciencesWestern Michigan University Homer Stryker M.D. School of MedicineKalamazooMIUSA
| | - M. Myrtha Gregoire‐Bottex
- Department of Pediatric and Adolescent MedicineWestern Michigan University Homer Stryker M.D. School of MedicineKalamazooMIUSA
- Present address:
Department of PediatricsUniversity of MiamiMiller School of MedicineMiamiFLUSA
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34
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Royal CDM, Babyak M, Shah N, Srivatsa S, Stewart KA, Tanabe P, Wonkam A, Asnani M. Sickle cell disease is a global prototype for integrative research and healthcare. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10037. [PMID: 36618444 PMCID: PMC9744540 DOI: 10.1002/ggn2.10037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023]
Abstract
Differences in health outcomes and treatment responses within and between global populations have been well documented. There is growing recognition of the need to move beyond simple inventories and descriptions of these differences and our linear explanations for them, and gain a better understanding of the multifaceted systems and networks underlying them in order to develop more precise and effective remedies. Typical targets for such integrative research have been common multifactorial diseases. We propose sickle cell disease, one of the most common monogenic diseases, as an ideal candidate for elucidating the complexity of the influences of endogenous and exogenous factors on disease pathophysiology, phenotypic diversity, and variations in responses to treatments at both the individual and population levels. We provide data-informed representations of diverse contributors to sickle cell disease complications that could guide innovative efforts to advance scientific knowledge, clinical practice, and policy formulation related to the disease; help improve outcomes for people worldwide with sickle cell disease; and inform approaches to studying and addressing other diseases.
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Affiliation(s)
- Charmaine D. M. Royal
- Department of African & African American StudiesDuke UniversityDurhamNorth CarolinaUSA,Duke Global Health InstituteDuke UniversityDurhamNorth CarolinaUSA,Center on Genomics, Race, Identity, DifferenceDuke UniversityDurhamNorth CarolinaUSA
| | - Michael Babyak
- Department of Psychiatry and Behavioral SciencesDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Nirmish Shah
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Shantanu Srivatsa
- Center on Genomics, Race, Identity, DifferenceDuke UniversityDurhamNorth CarolinaUSA
| | | | - Paula Tanabe
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA,Duke University School of NursingDurhamNorth CarolinaUSA
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa,Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Monika Asnani
- Caribbean Institute for Health Research ‐ Sickle Cell UnitThe University of the West IndiesKingstonJamaica
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35
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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36
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Kamar A, Khalil A, Nemer G. The Digenic Causality in Familial Hypercholesterolemia: Revising the Genotype-Phenotype Correlations of the Disease. Front Genet 2021; 11:572045. [PMID: 33519890 PMCID: PMC7844333 DOI: 10.3389/fgene.2020.572045] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022] Open
Abstract
Genetically inherited defects in lipoprotein metabolism affect more than 10 million individuals around the globe with preponderance in some parts where consanguinity played a major role in establishing founder mutations. Mutations in four genes have been so far linked to the dominant and recessive form of the disease. Those players encode major proteins implicated in cholesterol regulation, namely, the low-density lipoprotein receptor (LDLR) and its associate protein 1 (LDLRAP1), the proprotein convertase substilin/kexin type 9 (PCSK9), and the apolipoprotein B (APOB). Single mutations or compound mutations in one of these genes are enough to account for a spectrum of mild to severe phenotypes. However, recently several reports have identified digenic mutations in familial cases that do not necessarily reflect a much severe phenotype. Yet, data in the literature supporting this notion are still lacking. Herein, we review all the reported cases of digenic mutations focusing on the biological impact of gene dosage and the potential protective effects of single-nucleotide polymorphisms linked to hypolipidemia. We also highlight the difficulty of establishing phenotype-genotype correlations in digenic familial hypercholesterolemia cases due to the complexity and heterogeneity of the phenotypes and the still faulty in silico pathogenicity scoring system. We finally emphasize the importance of having a whole exome/genome sequencing approach for all familial cases of familial hyperlipidemia to better understand the genetic and clinical course of the disease.
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Affiliation(s)
- Amina Kamar
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Athar Khalil
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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37
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Auslander N, Ramos DM, Zelaya I, Karathia H, Crawford TO, Schäffer AA, Sumner CJ, Ruppin E. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases. Mol Syst Biol 2020; 16:e9701. [PMID: 33438800 PMCID: PMC7754056 DOI: 10.15252/msb.20209701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre-mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient-derived cells leads to increased full-length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.
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Affiliation(s)
- Noam Auslander
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of HealthBethesdaMDUSA
| | - Daniel M Ramos
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivette Zelaya
- Interdepartmental Program in BioinformaticsUniversity of California Los AngelesLos AngelesCAUSA
| | - Hiren Karathia
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer InstituteNational Institutes of HealthMDUSA
| | - Thomas O. Crawford
- Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Charlotte J Sumner
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
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38
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Turton KB, Ingram RJ, Valvano MA. Macrophage dysfunction in cystic fibrosis: Nature or nurture? J Leukoc Biol 2020; 109:573-582. [PMID: 32678926 DOI: 10.1002/jlb.4ru0620-245r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) affect the homeostasis of chloride flux by epithelial cells. This has deleterious consequences, especially in respiratory epithelia, where the defect results in mucus accumulation distinctive of cystic fibrosis. CFTR is, however, also expressed in phagocytic cells, like macrophages. Immune cells are highly sensitive to conditioning by their environment; thus, CFTR dysfunction in epithelia influences macrophages by affecting the lung milieu, but the mutations also appear to be directly consequential for intrinsic macrophage functions. Particular mutations can alter CFTR's folding, traffic of the protein to the membrane and function. As such, understanding the intrinsic effects of CFTR mutation requires distinguishing the secondary effects of misfolded CFTR on cell stress pathways from the primary defect of CFTR dysfunction/absence. Investigations into CFTR's role in macrophages have exploited various models, each with their own advantages and limitations. This review summarizes these methodologic approaches, discussing their physiological correspondence and highlighting key findings. The controversy surrounding CFTR-dependent acidification is used as a case study to highlight difficulties in commensurability across model systems. Recent work in macrophage biology, including polarization and host-pathogen interaction studies, brought into the context of CFTR research, offers potential explanations for observed discrepancies between studies. Moreover, the rapid advancement of novel gene editing technologies and new macrophage model systems makes this assessment of the field's models and methodologies timely.
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Affiliation(s)
- Keren B Turton
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Rebecca J Ingram
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
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39
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Rang C, Keating D, Wilson J, Kotsimbos T. Re-imagining cystic fibrosis care: next generation thinking. Eur Respir J 2020; 55:13993003.02443-2019. [PMID: 32139465 DOI: 10.1183/13993003.02443-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/20/2020] [Indexed: 12/26/2022]
Abstract
Cystic fibrosis (CF) is a common multi-system genetically inherited condition, predominately found in individuals of Caucasian decent. Since the identification of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene in 1989, and the subsequent improvement in understanding of CF pathophysiology, significant increases in life-expectancy have followed. Initially this was related to improvements in the management and systems of care for treating the various affected organ systems. These cornerstone treatments are still essential for CF patients born today. However, over the last decade, the major advance has been in therapies that target the resultant genetic defect: the dysfunctional CFTR protein. Small molecule agents that target this dysfunctional protein via a variety of mechanisms have led to lung function improvements, reductions in pulmonary exacerbation rates and increases in weight and quality-of-life indices. As more patients receive these agents earlier and earlier in life, it is likely that general CF care will increasingly pivot around these specific therapies, although it is also likely that effects other than those identified in the initial trials will be discovered and need to be managed. Despite great excitement for modulator therapies, they are unlikely to be suitable or available for all; whether this is due to a lack of availability for specific CFTR mutations, drug-reactions or the health economic set-up in certain countries. Nevertheless, the CF community must be applauded for its ongoing focus on research and development for this life-limiting disease. With time, personalised individualised therapy would ideally be the mainstay of CF care.
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Affiliation(s)
- Catherine Rang
- Cystic Fibrosis Service, Dept of Respiratory Medicine, Alfred Health, Melbourne, Australia
| | - Dominic Keating
- Cystic Fibrosis Service, Dept of Respiratory Medicine, Alfred Health, Melbourne, Australia.,Dept of Medicine, Monash University, Alfred Campus, Melbourne, Australia
| | - John Wilson
- Cystic Fibrosis Service, Dept of Respiratory Medicine, Alfred Health, Melbourne, Australia.,Dept of Medicine, Monash University, Alfred Campus, Melbourne, Australia
| | - Tom Kotsimbos
- Cystic Fibrosis Service, Dept of Respiratory Medicine, Alfred Health, Melbourne, Australia.,Dept of Medicine, Monash University, Alfred Campus, Melbourne, Australia
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40
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Sun H, Guo Y, Lan X, Jia J, Cai X, Zhang G, Xie J, Liang Q, Li Y, Yu G. PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. Nucleic Acids Res 2020; 48:D977-D982. [PMID: 31642469 PMCID: PMC7145690 DOI: 10.1093/nar/gkz930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/05/2023] Open
Abstract
From clinical observations to large-scale sequencing studies, the phenotypic impact of genetic modifiers is evident. To better understand the full spectrum of the genetic contribution to human disease, concerted efforts are needed to construct a useful modifier resource for interpreting the information from sequencing data. Here, we present the PhenoModifier (https://www.biosino.org/PhenoModifier), a manually curated database that provides a comprehensive overview of human genetic modifiers. By manually curating over ten thousand published articles, 3078 records of modifier information were entered into the current version of PhenoModifier, related to 288 different disorders, 2126 genetic modifier variants and 843 distinct modifier genes. To help users probe further into the mechanism of their interested modifier genes, we extended the yeast genetic interaction data and yeast quantitative trait loci to the human and we also integrated GWAS data into the PhenoModifier to assist users in evaluating all possible phenotypes associated with a modifier allele. As the first comprehensive resource of human genetic modifiers, PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation. The portal has a broad scientific and clinical scope, spanning activities relevant to variant interpretation for research purposes as well as clinical decision making.
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Affiliation(s)
- Hong Sun
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yangfan Guo
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China.,School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoping Lan
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Jia Jia
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Xiaoshu Cai
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China.,Clinical Research Collaboration (K.-Y.H., J.-F.H.), Siemens Ltd., China Shanghai Branch, Shanghai 200120, China
| | - Guoqing Zhang
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200232, China
| | - Jingjing Xie
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Qian Liang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yixue Li
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200232, China
| | - Guangjun Yu
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
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Renaux A, Papadimitriou S, Versbraegen N, Nachtegael C, Boutry S, Nowé A, Smits G, Lenaerts T. ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. Nucleic Acids Res 2020; 47:W93-W98. [PMID: 31147699 PMCID: PMC6602484 DOI: 10.1093/nar/gkz437] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/01/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022] Open
Abstract
A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an essential task for the discovery of the causes of oligogenic diseases. ORVAL (the Oligogenic Resource for Variant AnaLysis), which is presented here, provides an answer to this problem by focusing on generating networks of candidate pathogenic variant combinations in gene pairs, as opposed to isolated variants in unique genes. This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information. ORVAL is the first web-based exploration platform dedicated to identifying networks of candidate pathogenic variant combinations with the sole ambition to help in uncovering oligogenic causes for patients that cannot rely on the classical disease analysis tools. ORVAL is available at https://orval.ibsquare.be.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Charlotte Nachtegael
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Simon Boutry
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Laboratory of Human Molecular Genetics, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Hôpital Universitaire des Enfants Reine Fabiola, 1020 Brussels, Belgium.,Center of Human Genetics, Hôpital Erasme, 1070 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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42
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Wang R, McCauley KB, Kotton DN, Hawkins F. Differentiation of human airway-organoids from induced pluripotent stem cells (iPSCs). Methods Cell Biol 2020; 159:95-114. [PMID: 32586451 DOI: 10.1016/bs.mcb.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There was significant progress over the last decade in the ability to generate induced pluripotent stem cell (iPSC)-derived airway organoids. We and others have developed step-wise, directed differentiation protocols to recapitulate the key milestones in human airway development, generating iPSC-derived airway organoids that possess the major human airway cell types. These organoids have already shown feasibility for genetic disease modeling. They have great future potential for modeling a wider spectrum of lung diseases, interrogating disease mechanisms, predicting personalized drug responses, studying developmental lung biology, and ultimately may serve as candidates for future cell-based therapies for lung regeneration and repair. Herein we detail a step-by-step laboratory protocol to generate human airway organoids.
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Affiliation(s)
- Ruobing Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States; Division of Respiratory Diseases, Department of Medicine, Boston Children's Hospital, Boston, MA, United States
| | - Katie B McCauley
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA, United States
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States; Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Finn Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States; Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States.
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43
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Sun T, Sun Z, Jiang Y, Ferguson AA, Pilewski JM, Kolls JK, Chen W, Chen K. Transcriptomic Responses to Ivacaftor and Prediction of Ivacaftor Clinical Responsiveness. Am J Respir Cell Mol Biol 2020; 61:643-652. [PMID: 30995102 DOI: 10.1165/rcmb.2019-0032oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ivacaftor is a drug that was recently approved by the U.S. Food and Drug Administration for the treatment of patients with cystic fibrosis (CF) and at least one copy of the G511D mutation in the CFTR (CF transmembrane conductance regulator) gene. The transcriptomic effect of ivacaftor in patients with CF remains unclear. Here, we sought to examine whether and how the transcriptome of patients is influenced by ivacaftor treatment, and to determine whether these data allow prediction of ivacaftor responsiveness. Our data originated from the G551D Observational Study (GOAL). We performed RNA sequencing (RNA-seq) on peripheral blood mononuclear cells (PBMCs) from 56 patients and compared the transcriptomic changes that occurred before and after ivacaftor treatment. We used consensus clustering to stratify patients into subgroups based on their clinical responses after treatment, and we determined differences between subgroups in baseline gene expression. A random forest model was built to predict ivacaftor responsiveness. We identified 239 genes (false discovery rate < 0.1) that were significantly influenced by ivacaftor in PBMCs. The functions of these genes relate to cell differentiation, microbial infection, inflammation, Toll-like receptor signaling, and metabolism. We classified patients into "good" and "moderate" responder groups based on their clinical response to ivacaftor. We identified a panel of signature genes and built a statistical model for predicting CFTR modulator responsiveness. Despite a limited sample size, adequate prediction performance was achieved with an accuracy of 0.92. In conclusion, for the first time, the present study demonstrates profound transcriptomic impacts of ivacaftor in PBMCs from patients with CF, and provides a pilot statistical model for predicting clinical responsiveness to ivacaftor before treatment.
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Affiliation(s)
- Tao Sun
- Pulmonary Medicine, Allergy, and Immunology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Biostatistics, School of Public Health, and
| | - Zhe Sun
- Pulmonary Medicine, Allergy, and Immunology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Biostatistics, School of Public Health, and
| | - Yale Jiang
- Pulmonary Medicine, Allergy, and Immunology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,School of Medicine, Tsinghua University, Beijing, China; and
| | - Annabel A Ferguson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joseph M Pilewski
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jay K Kolls
- Center for Translational Research in Infection and Inflammation, Tulane School of Medicine, New Orleans, Louisiana
| | - Wei Chen
- Pulmonary Medicine, Allergy, and Immunology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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44
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Paranjapye A, Ruffin M, Harris A, Corvol H. Genetic variation in CFTR and modifier loci may modulate cystic fibrosis disease severity. J Cyst Fibros 2020; 19 Suppl 1:S10-S14. [PMID: 31734115 PMCID: PMC7036019 DOI: 10.1016/j.jcf.2019.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
In patients with cystic fibrosis (CF), genetic variants within and outside the CFTR locus contribute to the variability of the disease severity. CFTR transcription is tightly regulated by cis-regulatory elements (CREs) that control the three-dimensional structure of the locus, chromatin accessibility and transcription factor recruitment. Variants within these CREs may contribute to the pathophysiology and to the phenotypic heterogeneity by altering CFTR transcript abundance. In addition to the CREs, variants outside the CFTR locus, namely "modifiers genes", may also be associated with the clinical variability. This review addresses variants at the CFTR locus itself and CFTR CREs, together with the outcomes of the latest modifier gene studies with respect to the different CF phenotypes.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Manon Ruffin
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA.
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France; AP-HP, Hôpital Trousseau, Service de Pneumologie Pédiatrique, Paris, France.
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45
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Cruz DF, Mitash N, Farinha CM, Swiatecka-Urban A. TGF-β1 Augments the Apical Membrane Abundance of Lemur Tyrosine Kinase 2 to Inhibit CFTR-Mediated Chloride Transport in Human Bronchial Epithelia. Front Cell Dev Biol 2020; 8:58. [PMID: 32117984 PMCID: PMC7018669 DOI: 10.3389/fcell.2020.00058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
The most common disease-causing mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, F508del, leads to cystic fibrosis (CF), by arresting CFTR processing and trafficking to the plasma membrane. The FDA-approved modulators partially restore CFTR function and slow down the progression of CF lung disease by increasing processing and delivery to the plasma membrane and improving activity of F508del-CFTR Cl– channels. However, the modulators do not correct compromised membrane stability of rescued F508del-CFTR. Transforming growth factor (TGF)-β1 is a well-established gene modifier of CF associated with worse lung disease in F508del-homozygous patients, by inhibiting CFTR biogenesis and blocking the functional rescue of F508del-CFTR. Lemur tyrosine kinase 2 (LMTK2) is a transmembrane protein localized at the apical and basolateral membrane domain of human bronchial epithelial cells. Phosphorylation of the apical membrane CFTR by LMTK2 triggers its endocytosis and reduces the abundance of membrane-associated CFTR, impairing the CFTR-mediated Cl– transport. We have previously shown that LMTK2 knockdown improves the pharmacologically rescued F508del-CFTR abundance and function. Thus, reducing the LMTK2 recruitment to the plasma membrane may provide a useful strategy to potentiate the pharmacological rescue of F508del-CFTR. Here, we elucidate the mechanism of LMTK2 recruitment to the apical plasma membrane in polarized CFBE41o- cells. TGF-β1 increased LMTK2 abundance selectively at the apical membrane by accelerating its recycling in Rab11-positive vesicles without affecting LMTK2 mRNA levels, protein biosynthesis, or endocytosis. Our data suggest that controlling TGF-β1 signaling may attenuate recruitment of LMTK2 to the apical membrane thereby improving stability of pharmacologically rescued F508del-CFTR.
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Affiliation(s)
- Daniel F Cruz
- BioSystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.,Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nilay Mitash
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Carlos M Farinha
- BioSystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Agnieszka Swiatecka-Urban
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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46
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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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47
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET RESPIRATORY MEDICINE 2020; 8:65-124. [DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
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48
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Han ST, Cutting GR. Molecular Genetics of Cystic Fibrosis. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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49
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Banjar H, Al-Mogarri I, Nizami I, Al-Haider S, AlMaghamsi T, Alkaf S, Al-Enazi A, Moghrabi N. Geographic distribution of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Saudi Arabia. Int J Pediatr Adolesc Med 2019; 8:25-28. [PMID: 33718573 PMCID: PMC7922840 DOI: 10.1016/j.ijpam.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/18/2019] [Accepted: 12/03/2019] [Indexed: 01/17/2023]
Abstract
Introduction Cystic fibrosis (CF) has been reported before in Saudi Arabia and the Gulf area. It has been found that screening for 10 most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations can detect 80% of positive CFTR cases. Objectives To determine the geographic distribution of the most common CFTR variants in 5 regions of Saudi Arabia. Methodology A retrospective chart review of all CFTR variants conducted from January 1, 1992 to December 1, 2017. Results The ten most common CFTR mutations in the Saudi population were as follows: p.Gly473GlufsX54 (17%), p.Phe508del (12%), p.Ile1234Val (12%), 3120+1G > A (11%), 711+1G > T (9%), p.His139Leu (6%), p.Gln637Hisfs (5%), p.Ser549Arg (3%), p.N1303K (3%), and delExon19-21 (2%) along with other variants 79 (20%). In terms of the highest frequency, the c.2988+1G > A (3120+1G > A) variant was found in the eastern province (7.3%) of Saudi Arabia, the c.1418delG (p.Gly473GlufsX54) variant in the northern province (6.8%), the c.579+1G > T (711+1G > T) variant in the southern province (4.8%), the c.3700A > G (p.Ile1234Val) variant in the central province (4.8%), and c.1521_1523delCTT (p.Phe508del) variant in the western province (4.3%). Conclusion The eastern and the northern provinces have the highest prevalence of CF, with the c.2988+1G > A (3120+1G > A) and c.1418delG (p.Gly473GlufsX54) variants showing the highest distribution in the Saudi CF population, which may reflect the effect of consanguinity within the same tribe. Proper family screening and counseling should be emphasized.
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Affiliation(s)
- Hanaa Banjar
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Ibrahim Al-Mogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Imran Nizami
- Organ Transplant Center, (King Faisal Specialist Hospital and Research Center), Riyadh, Saudi Arabia
| | - Sami Al-Haider
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Talal AlMaghamsi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Jeddah, Saudi Arabia
| | - Sara Alkaf
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Abdulaziz Al-Enazi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Nabil Moghrabi
- Department of Genetics, Molecular Diagnostic Laboratory, The Research Center, KFSHRC, Riyadh, Saudi Arabia
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50
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Andolfo I, Rosato BE, Marra R, De Rosa G, Manna F, Gambale A, Iolascon A, Russo R. The BMP-SMAD pathway mediates the impaired hepatic iron metabolism associated with the ERFE-A260S variant. Am J Hematol 2019; 94:1227-1235. [PMID: 31400017 DOI: 10.1002/ajh.25613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023]
Abstract
The erythroferrone (ERFE) is the erythroid regulator of hepatic iron metabolism by suppressing the expression of hepcidin. Congenital dyserythropoietic anemia type II (CDAII) is an inherited hyporegenerative anemia due to biallelic mutations in the SEC23B gene. Patients with CDAII exhibit marked clinical variability, even among individuals sharing the same pathogenic variants. The ERFE expression in CDAII is increased and related to abnormal erythropoiesis. We identified a recurrent low-frequency variant, A260S, in the ERFE gene in 12.5% of CDAII patients with a severe phenotype. We demonstrated that the ERFE-A260S variant leads to increased levels of ERFE, with subsequently marked impairment of iron regulation pathways at the hepatic level. Functional characterization of ERFE-A260S in the hepatic cell system demonstrated its modifier role in iron overload by impairing the BMP/SMAD pathway. We herein described for the first time an ERFE polymorphism as a genetic modifier variant. This was with a mild effect on disease expression, under a multifactorial-like model, in a condition of iron-loading anemia due to ineffective erythropoiesis.
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Affiliation(s)
- Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
| | - Barbara Eleni Rosato
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
| | - Roberta Marra
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
| | - Gianluca De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
| | | | - Antonella Gambale
- CEINGE Biotecnologie Avanzate Naples Italy
- Dipartimento Assistenziale di Medicina di Laboratorio (DAIMedLab)UOC Genetica Medica, AOU Federico II Naples Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico II Naples Italy
- CEINGE Biotecnologie Avanzate Naples Italy
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