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Scalia F, Culletta G, Barreca M, Caruso Bavisotto C, Bivacqua R, D'Amico G, Alberti G, Spanò V, Tutone M, Almerico AM, Cappello F, Montalbano A, Barraja P. Chaperoning system: Intriguing target to modulate the expression of CFTR in cystic fibrosis. Eur J Med Chem 2024; 278:116809. [PMID: 39226706 DOI: 10.1016/j.ejmech.2024.116809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
The correction of protein folding is fundamental for cellular functionality and its failure can lead to severe diseases. In this context, molecular chaperones are crucial players involved in the tricky process of assisting in protein folding, stabilization, and degradation. Chaperones, such as heat shock proteins (HSP) 90, 70, and 60, operate within complex systems, interacting with co-chaperones both to prevent protein misfolding and direct to the correct folding. Chaperone targeting drugs could represent a challenging approach for the treatment of cystic fibrosis (CF), an autosomal recessive genetic disease caused by mutations in the CFTR gene, encoding for the CFTR chloride channel. In this review, we discuss the potential role of molecular chaperones as proteostasis modulators affecting CFTR biogenesis. In particular, we focused on HSP90 and HSP70, for their key role in CFTR folding and trafficking, as well as on HSP60 for its involvement in the inflammation process.
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Affiliation(s)
- Federica Scalia
- Section of Human Anatomy and Histology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, via del Vespro 129, 90127 Palermo, Italy
| | - Giulia Culletta
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Marilia Barreca
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Celeste Caruso Bavisotto
- Section of Human Anatomy and Histology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, via del Vespro 129, 90127 Palermo, Italy; Euro-Mediterranean Institute of Science and Technology (IEMEST), via Michele Miraglia 20, 90139 Palermo, Italy
| | - Roberta Bivacqua
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Giuseppa D'Amico
- Section of Human Anatomy and Histology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, via del Vespro 129, 90127 Palermo, Italy
| | - Giusi Alberti
- Section of Human Anatomy and Histology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, via del Vespro 129, 90127 Palermo, Italy
| | - Virginia Spanò
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Marco Tutone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Maria Almerico
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Francesco Cappello
- Section of Human Anatomy and Histology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, via del Vespro 129, 90127 Palermo, Italy; Euro-Mediterranean Institute of Science and Technology (IEMEST), via Michele Miraglia 20, 90139 Palermo, Italy
| | - Alessandra Montalbano
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy.
| | - Paola Barraja
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
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Chatterjee P, Moss CT, Omar S, Dhillon E, Hernandez Borges CD, Tang AC, Stevens DA, Hsu JL. Allergic Bronchopulmonary Aspergillosis (ABPA) in the Era of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Modulators. J Fungi (Basel) 2024; 10:656. [PMID: 39330416 PMCID: PMC11433030 DOI: 10.3390/jof10090656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/11/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Allergic bronchopulmonary aspergillosis (ABPA) is a hypersensitivity disease caused by Aspergillus fumigatus (Af), prevalent in persons with cystic fibrosis (CF) or asthma. In ABPA, Af proteases drive a T-helper cell-2 (Th2)-mediated allergic immune response leading to inflammation that contributes to permanent lung damage. Corticosteroids and antifungals are the mainstays of therapies for ABPA. However, their long-term use has negative sequelae. The treatment of patients with CF (pwCF) has been revolutionized by the efficacy of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy. Pharmacological improvement in CFTR function with highly effective elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes of pwCF. The mechanism behind the improvement in patient outcomes is a continued topic of investigation as our understanding of the role of CFTR function evolves. As ETI therapy gains traction in CF management, understanding its potential impact on ABPA, especially on the allergic immune response pathways and Af infection becomes increasingly crucial for optimizing patient outcomes. This literature review aims to examine the extent of these findings and expand our understanding of the already published research focusing on the intersection between ABPA therapeutic approaches in CF and the rapid impact of the evolving CFTR modulator landscape. While our literature search yielded limited reports specifically focusing on the role of CFTR modulator therapy on CF-ABPA, findings from epidemiologic and retrospective studies suggest the potential for CFTR modulator therapies to positively influence pulmonary outcomes by addressing the underlying pathophysiology of CF-ABPA, especially by decreasing inflammatory response and Af colonization. Thus, this review highlights the promising scope of CFTR modulator therapy in decreasing the overall prevalence and incidence of CF-ABPA.
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Affiliation(s)
- Paulami Chatterjee
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | - Carson Tyler Moss
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sarah Omar
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | - Ekroop Dhillon
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
| | | | - Alan C. Tang
- Department of Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA;
| | - David A. Stevens
- Division of Infectious Diseases and Geographic Medicine, Stanford University Medical School, Stanford, CA 94305, USA;
| | - Joe L. Hsu
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.C.); (S.O.); (E.D.)
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Yıldız CA, Selçuk Balcı M, Karabulut Ş, Başer ZM, Kalyoncu M, Metin Çakar N, Akkitap Yiğit MM, Baysal EE, Özdemircioğlu F, Uzunoğlu B, Taştan G, Ergenekon P, Gökdemir Y, Erdem Eralp E, Karakoç F, Ata P, Karadağ B. Exploring Turkey's mosaic of novel variants and complex alleles in cystic fibrosis genetics. Pediatr Pulmonol 2024. [PMID: 39291770 DOI: 10.1002/ppul.27249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 08/09/2024] [Accepted: 08/31/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUNDS Genetic variants in CF transmembrane conductance regulator (CFTR) gene causes cystic fibrosis (CF), a prevalent autosomal recessive disorder. More than 2000 variants in CFTR have been described as disease causative. This study aims to delineate the genotypic and phenotypic landscape of CF among people with CF (pwCF) followed at the largest CF center in Turkey. METHODS We conducted a descriptive and retrospective analysis of 481 patients registered with the European CF Society Patient Registry and followed at Marmara University Selim Çöremen CF Center from 2015 onwards. Comprehensive CFTR analysis was utilized for genetic diagnosis. Besides the whole cohort, novel variants and complex alleles were also described. RESULTS Our cohort exhibited a broad spectrum of CFTR variants, with 136 different variants detected, indicating substantial genetic diversity. The F508del variant was less prevalent in our cohort compared to US and European averages, which could reflect unique genetic and demographic characteristics of the Turkish population. Additionally, we identified nine novel variants in 12 alleles, which enhances the understanding of CF's genetic complexity in this region, and complex alleles in 32 pwCF. CONCLUSION Our research underscores the heterogeneity of CFTR variants in Turkey and highlights the necessity for extensive genetic profiling particularly for diverse populations to provide effective personalized treatment strategies. It is crucial to understand the full spectrum of CFTR variants with the advent of CFTR modulators.
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Affiliation(s)
- Ceren Ayça Yıldız
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Merve Selçuk Balcı
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Şeyda Karabulut
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Zeynep Münteha Başer
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul, Turkey
| | - Mine Kalyoncu
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Neval Metin Çakar
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | | | - Eda Esra Baysal
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Fulya Özdemircioğlu
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Burcu Uzunoğlu
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Gamze Taştan
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Pınar Ergenekon
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Yasemin Gökdemir
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Ela Erdem Eralp
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Fazilet Karakoç
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
| | - Pınar Ata
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul, Turkey
| | - Bülent Karadağ
- Division of Pediatric Pulmonology, Marmara University School of Medicine, Istanbul, Turkey
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Yanus GA, Suspitsin EN, Imyanitov EN. The Spectrum of Disease-Associated Alleles in Countries with a Predominantly Slavic Population. Int J Mol Sci 2024; 25:9335. [PMID: 39273284 PMCID: PMC11394759 DOI: 10.3390/ijms25179335] [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: 07/18/2024] [Revised: 08/21/2024] [Accepted: 08/25/2024] [Indexed: 09/15/2024] Open
Abstract
There are more than 260 million people of Slavic descent worldwide, who reside mainly in Eastern Europe but also represent a noticeable share of the population in the USA and Canada. Slavic populations, particularly Eastern Slavs and some Western Slavs, demonstrate a surprisingly high degree of genetic homogeneity, and, consequently, remarkable contribution of recurrent alleles associated with hereditary diseases. Along with pan-European pathogenic variants with clearly elevated occurrence in Slavic people (e.g., ATP7B c.3207C>A and PAH c.1222C>T), there are at least 52 pan-Slavic germ-line mutations (e.g., NBN c.657_661del and BRCA1 c.5266dupC) as well as several disease-predisposing alleles characteristic of the particular Slavic communities (e.g., Polish SDHD c.33C>A and Russian ARSB c.1562G>A variants). From a clinical standpoint, Slavs have some features of a huge founder population, thus providing a unique opportunity for efficient genetic studies.
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Affiliation(s)
- Grigoriy A Yanus
- Laboratory of Molecular Diagnostics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N Suspitsin
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
| | - Evgeny N Imyanitov
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
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Guo R, Zou Y, Guo Y, Gao W. Compound heterozygous CFTR variants (Q1352H and 5T; TG13) in a Chinese patient with cystic fibrosis. Diagn Pathol 2024; 19:107. [PMID: 39107787 PMCID: PMC11302081 DOI: 10.1186/s13000-024-01531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive inherited disease caused by variants of cystic fibrosis transmembrane conductance regulation (CFTR) gene. This report presents a case of a Chinese boy diagnosed with CF, attributed to the presence of two specific CFTR gene variations: 4056G > C (NM_000492.4) (p.Gln1352His, legacy: Q1352H) and c.1210-34TG[13]T[5] (NM_000492.4)(legacy: 5T; TG13). A ten-year-old boy was admitted to the hospital due to recurrent pneumonia, cough, and intermittent fever for seven years. Lung auscultation revealed rales, and a lung CT scan indicated parenchymal transformation with infection in both lungs. Whole Exome Sequencing (WES) identified two CFTR gene variants, Q1352H and 5T; TG13, which were significantly associated with clinical phenotype. Following a two-year course of azithromycin combined with inhalation therapy with budesonide, the patient experienced no further episodes of respiratory infections. Moreover, significant improvements were observed in pulmonary function, pulmonary infection, and bronchiectasis. The occurrence of combined variations, Q1352H and 5T; TG13, in the CFTR gene is rare and specific to Chinese populations. WES proves to be a valuable diagnostic tool for detecting CFTR gene variants.
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Affiliation(s)
- Run Guo
- Department of Pulmonology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Machang compus, 225 Machang Road, Hexi District, Tianjin, 300074, China
| | - Yingxue Zou
- Department of Pulmonology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Machang compus, 225 Machang Road, Hexi District, Tianjin, 300074, China.
| | - Yongsheng Guo
- Department of Pulmonology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Machang compus, 225 Machang Road, Hexi District, Tianjin, 300074, China
| | - Weiwei Gao
- Department of Pulmonology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Machang compus, 225 Machang Road, Hexi District, Tianjin, 300074, China
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Anwar S, Peng JL, Zahid KR, Zhou YM, Ali Q, Qiu CR. Cystic Fibrosis: Understanding Cystic Fibrosis Transmembrane Regulator Mutation Classification and Modulator Therapies. Adv Respir Med 2024; 92:263-277. [PMID: 39051188 PMCID: PMC11270331 DOI: 10.3390/arm92040026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
A common life-threatening hereditary disease, Cystic Fibrosis (CF), affects primarily Caucasian infants. High sweat-salt levels are observed as a result of a single autosomal mutation in chromosome 7 that affects the critical function of the cystic fibrosis transmembrane regulator (CFTR). For establishing tailored treatment strategies, it is important to understand the broad range of CFTR mutations and their impacts on disease pathophysiology. This study thoroughly investigates the six main classes of classification of CFTR mutations based on their functional effects. Each class is distinguished by distinct molecular flaws, such as poor protein synthesis, misfolding, gating defects, conduction defects, and decreased CFTR expression at the apical membrane. Furthermore, this paper focuses on the emerging field of CFTR modulators, which intend to restore CFTR function or mitigate its consequences. These modulators, which are characterized by the mode of action and targeted mutation class, have the potential to provide personalized therapy regimens in CF patients. This review provides valuable insights into the genetic basis of CF pathology, and highlights the potential for precision medicine methods in CF therapy by thoroughly investigating CFTR mutation classification and related modulators.
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Affiliation(s)
- Saba Anwar
- Centre for Applied Molecular Biology, University of the Punjab Lahore, Lahore 53700, Pakistan;
| | - Jin-Liang Peng
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
| | - Kashif Rafiq Zahid
- Department of Radiation Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianaapolis, IN 46202, USA;
| | - Yu-Ming Zhou
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Chong-Rong Qiu
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou 341000, China; (J.-L.P.); (Y.-M.Z.)
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Ahting S, Nährlich L, Held I, Henn C, Krill A, Landwehr K, Meister J, Nährig S, Nolde A, Remke K, Ruppel R, Sauer-Heilborn A, Schebek M, Schopper G, Schulte-Hubbert B, Schwarz C, Smaczny C, Wege S, Hentschel J. Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry. J Cyst Fibros 2024; 23:774-781. [PMID: 37867076 DOI: 10.1016/j.jcf.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards. METHODS To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus. RESULTS Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics. CONCLUSION Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.
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Affiliation(s)
- Simone Ahting
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Inka Held
- Pediatric Practice Friesenweg, Cystic Fibrosis Center Altona, Hamburg, Germany
| | - Constance Henn
- Division of pediatric Pulmonology and Allergology, Hospital for children and adolescents, University Medical Center Leipzig, Leipzig, Germany
| | - Angelika Krill
- Division of Pneumology, University Medical Center Homburg, Homburg/Saar, Germany
| | - Kerstin Landwehr
- Division of Allergology and Pediatric Pneumology, University Children's Hospital Bethel, University Medical Center Ostwestfalen-Lippe, Bielefeld, Germany
| | - Jochen Meister
- Division of Pneumology, Allergology and Psychotherapy, Children's Hospital, Helios Hospital Aue, Aue, Germany
| | - Susanne Nährig
- Cystic Fibrosis Center for Adults, Med. Klinik V, University Hospital LMU, Munich, Germany
| | - Anna Nolde
- Division of Pneumology, II. Department of Medicine and University Transplant Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Remke
- Department for General Paediatrics, Neonatology and Paediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Renate Ruppel
- University Children's Hospital, University Medical Center Erlangen, Erlangen, Germany
| | | | - Martin Schebek
- Division of Pediatric Pneumology, Center for Pediatric and Women's Medicine Kassel, Kassel, Germany
| | - Gudrun Schopper
- University Children's Hospital Schwabing, Technical University of Munich, Munich, Germany
| | - Bernhard Schulte-Hubbert
- Department of medical clinic I, Medical Center Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Carsten Schwarz
- Department Medicine, HMU-Health and Medical University Potsdam and Director CF Center Westbrandenburg, Division Cystic Fibrosis, Clinic Westbrandenburg, Potsdam, Germany
| | - Christina Smaczny
- Christiane Herzog CF-centre Frankfurt/Main, University Medical Center Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Sabine Wege
- Cystic Fibrosis Center, Thoraxklinik Heidelberg, University Medical Center Heidelberg, Heidelberg, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
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Iyer AG, Yu B, Reddy A, Khera M. Optimizing sexual reproductive health of men and women with cystic fibrosis: A systematic review. J Cyst Fibros 2024; 23:633-638. [PMID: 38311513 DOI: 10.1016/j.jcf.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 02/06/2024]
Abstract
This systematic review summarizes the impact of cystic fibrosis (CF) on sexual and reproductive health (SRH) in males and females, covering pubertal development, hormonal function, family planning, and fertility. Included articles featured historical CF diagnostic criteria, preclinical or clinical data (retrospective cohorts or open label trials), while excluded articles lacked full text availability, explicit methodology, or comparisons between CF and non-CF patients. Genotype differences in CFTR mutations influenced symptom severity. Males with CF experienced delayed puberty, hypogonadism, infertility from obstructive azoospermia, and semen parameter issues. Female CF patients showed decreased fertility, possibly linked to disrupted ionic balance and ovarian cystic disease. Assistive reproductive technologies addressed fertility issues, but success varied based on disease severity and genotype. CFTR modulators aided pulmonary function and sexual health but require further assessment for fertility benefits.
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Affiliation(s)
- Anand G Iyer
- School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229, USA.
| | - Benjamin Yu
- Department of Urology, Baylor College of Medicine, 2457 S Braeswood Blvd, Houston, TX 77030, USA
| | - Amit Reddy
- Department of Urology, Baylor College of Medicine, 2457 S Braeswood Blvd, Houston, TX 77030, USA
| | - Mohit Khera
- Department of Urology, Baylor College of Medicine, 2457 S Braeswood Blvd, Houston, TX 77030, USA
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9
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Okiyoneda T, Borgo C, Bosello Travain V, Pedemonte N, Salvi M. Targeting ubiquitination machinery in cystic fibrosis: Where do we stand? Cell Mol Life Sci 2024; 81:271. [PMID: 38888668 PMCID: PMC11335196 DOI: 10.1007/s00018-024-05295-z] [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: 03/27/2024] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in CFTR gene expressing the anion selective channel CFTR located at the plasma membrane of different epithelial cells. The most commonly investigated variant causing CF is F508del. This mutation leads to structural defects in the CFTR protein, which are recognized by the endoplasmic reticulum (ER) quality control system. As a result, the protein is retained in the ER and degraded via the ubiquitin-proteasome pathway. Although blocking ubiquitination to stabilize the CFTR protein has long been considered a potential pharmacological approach in CF, progress in this area has been relatively slow. Currently, no compounds targeting this pathway have entered clinical trials for CF. On the other hand, the emergence of Orkambi initially, and notably the subsequent introduction of Trikafta/Kaftrio, have demonstrated the effectiveness of molecular chaperone-based therapies for patients carrying the F508del variant and even showed efficacy against other variants. These treatments directly target the CFTR variant protein without interfering with cell signaling pathways. This review discusses the limits and potential future of targeting protein ubiquitination in CF.
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Affiliation(s)
- Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Hyogo, 669-1330, Japan.
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
- Department of Medicine, University of Padova, 35128, Padova, Italy
| | | | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy.
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Kasmi I, Kasmi G, Basholli B, Sefa HS, Vevecka E. The Spectrum and Frequency of Cystic Fibrosis Mutations in Albanian Patients. Balkan J Med Genet 2024; 27:31-36. [PMID: 39345797 PMCID: PMC11432417 DOI: 10.2478/bjmg-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a genetic disease characterized by a wide spectrum of severity, resulting from the inheritance of a mutant allele of the gene for cystic fibrosis transmembrane conductance regulator (CFTR). The aim of the study was to present a CFTR mutation analysis among the Albanian population and to identify rare variants. METHODS We identified CFTR mutations in a representative cohort of CF patients comprising of Albanian patients and some Kosovo patients followed up by the Department of Pediatrics at the University Hospital Center "Mother Theresa" (UHCMT). Compiled clinical and genotypic data include 133 previously analyzed patients, of whom 116 have two identified mutations, 6 have only one known mutation, and 11 are unexamined. RESULTS The most frequent mutation is F508del (83.19%), followed by 621+1G>T (2.45%). Other mutations identified in decrease order are E822X, G85E, G542X, R1066C, R1070Q, R1158X, G1349D, N1303K, S466X, 1811+1G->C, E831X, CFTRdele2,3(21kb). CONCLUSIONS The data suggest that most of these patients can benefit from new modulatory therapies targeting CFTR mutations, translating to very hopeful prospects for these patients.The Albanian population would benefit from Cystic Fibrosis neonatal screening, since outcomes can be improved through early diagnosis.
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Affiliation(s)
- I Kasmi
- University Hospital Center “Mother Teresa” (UHCMT), Pediatric Department, Tirana
| | - G Kasmi
- University of Medicine, Tirana (UMT), Laboratory Department
| | - B Basholli
- University Hospital Center “Mother Teresa” (UHCMT), Pediatric Department, Tirana
| | - HS Sefa
- Laboratory Department, Catholic Hospital “Our Lady of Good Counsel”, Tirana, Albania
| | - E Vevecka
- University Hospital Center “Mother Teresa” (UHCMT), Pediatric Department, Tirana
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11
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Terlizzi V, Farrell PM. Update on advances in cystic fibrosis towards a cure and implications for primary care clinicians. Curr Probl Pediatr Adolesc Health Care 2024; 54:101637. [PMID: 38811287 DOI: 10.1016/j.cppeds.2024.101637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
During the past quarter century, the diagnosis and treatment of cystic fibrosis (CF) have been transformed by molecular sciences that initiated a new era with discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The knowledge gained from that breakthrough has had dramatic clinical impact. Although once a diagnostic dilemma with long delays, preventable deaths, and irreversible pathology, CF can now be routinely diagnosed shortly after birth through newborn screening programs. This strategy of pre-symptomatic identification has eliminated the common diagnostic "odyssey" that was a failure of the healthcare delivery system causing psychologically traumatic experiences for parents. Therapeutic advances of many kinds have culminated in CFTR modulator treatment that can reduce the effects of or even correct the molecular defect in the chloride channel -the basic cause of CF. This astonishing advance has transformed CF care as described fully herein. Despite this impressive progress, there are challenges and controversies in the delivery of care. Issues include how best to achieve high sensitivity newborn screening with acceptable specificity; what course of action is appropriate for children who are identified through the unavoidable incidental findings of screening tests (CFSPID/CRMS cases and heterozygote carriers); how best to ensure genetic counseling; when to initiate the very expensive but life-saving CFTR modulator drugs; how to identify new CFTR modulator drugs for patients with non-responsive CFTR variants; how to adjust other therapeutic modalities; and how to best partner with primary care clinicians. Progress always brings new challenges, and this has been evident worldwide for CF. Consequently, this article summarizes the major advances of recent years along with controversies and describes their implications with an international perspective.
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Affiliation(s)
- Vito Terlizzi
- Department of Pediatric Medicine, Meyer Children's Hospital IRCCS, Cystic Fibrosis Regional Reference Center, Viale Gaetano Pieraccini 24, Florence, Italy
| | - Philip M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Clinical Sciences Center (K4/948), 600 Highland Avenue, Madison, WI 53792, USA.
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12
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Ramananda Y, Naren AP, Arora K. Functional Consequences of CFTR Interactions in Cystic Fibrosis. Int J Mol Sci 2024; 25:3384. [PMID: 38542363 PMCID: PMC10970640 DOI: 10.3390/ijms25063384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 09/01/2024] Open
Abstract
Cystic fibrosis (CF) is a fatal autosomal recessive disorder caused by the loss of function mutations within a single gene for the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CFTR is a chloride channel that regulates ion and fluid transport across various epithelia. The discovery of CFTR as the CF gene and its cloning in 1989, coupled with extensive research that went into the understanding of the underlying biological mechanisms of CF, have led to the development of revolutionary therapies in CF that we see today. The highly effective modulator therapies have increased the survival rates of CF patients and shifted the epidemiological landscape and disease prognosis. However, the differential effect of modulators among CF patients and the presence of non-responders and ineligible patients underscore the need to develop specialized and customized therapies for a significant number of patients. Recent advances in the understanding of the CFTR structure, its expression, and defined cellular compositions will aid in developing more precise therapies. As the lifespan of CF patients continues to increase, it is becoming critical to clinically address the extra-pulmonary manifestations of CF disease to improve the quality of life of the patients. In-depth analysis of the molecular signature of different CF organs at the transcriptional and post-transcriptional levels is rapidly advancing and will help address the etiological causes and variability of CF among patients and develop precision medicine in CF. In this review, we will provide an overview of CF disease, leading to the discovery and characterization of CFTR and the development of CFTR modulators. The later sections of the review will delve into the key findings derived from single-molecule and single-cell-level analyses of CFTR, followed by an exploration of disease-relevant protein complexes of CFTR that may ultimately define the etiological course of CF disease.
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Affiliation(s)
- Yashaswini Ramananda
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anjaparavanda P. Naren
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kavisha Arora
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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13
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Tupayachi Ortiz MG, Baumlin N, Yoshida M, Salathe M. Response to Elexacaftor/Tezacaftor/Ivacaftor in people with cystic fibrosis with the N1303K mutation: Case report and review of the literature. Heliyon 2024; 10:e26955. [PMID: 38463894 PMCID: PMC10920363 DOI: 10.1016/j.heliyon.2024.e26955] [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: 07/11/2023] [Revised: 11/15/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Cystic fibrosis (CF) is caused by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Thousands of CFTR mutations have been identified, but only a fraction are known to cause CF, with the most common being the prototypical class II CFTR mutation F508del. Elexacaftor-Tezacaftor-Ivacaftor (ETI) is a CFTR modulator that significantly increases ppFEV1 and reduces exacerbation frequencies. It is indicated for people with CF (pwCF) 2 years or older with at least one copy of F508del or one copy of the other 177 CFTR mutations that are responsive to ETI based on clinical or in vitro data. N1303K is the second most common class II mutation in the U.S. but is not yet FDA-approved for CFTR modulator therapy. However, N1303K is very similar to the F508del mutation and reveals variable in vitro responses to ETI. Theratyping provides an opportunity to consider ETI therapy for pwCF with mutations currently not approved by the FDA. We describe the case of an adult CF patient with W1282X and N1303K CFTR mutations and advanced CF lung disease (ACFLD) and declining lung function in which ETI was started after theratyping of nasal cells showed a meaningful response to ETI (current enhanced to over 10% of WT CFTR). The patient experienced clinical improvement with a 5% improvement in ppFEV1 and 10% increase in weight. However, there was no change in sweat chloride and the increase in ppFEV1 was less than what has been described for ACFLD patients with more typical ETI-amenable mutations. However, the response was in line with a few other cases described in the literature. This suggests a partial functional CFTR rescue like first-generation modulators for F508del. Thus, pwCF with N1303K CFTR variant could be considered for ETI eligibility.
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Affiliation(s)
- Maria G Tupayachi Ortiz
- Division of Pulmonary and Critical Care Medicine, University of Miami Miller School of Medicine, 1951 NW 7th Ave, Suite 2278, Miami, FL, 33136, United States
| | - Nathalie Baumlin
- Department of Internal Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, United States
| | - Makoto Yoshida
- Department of Internal Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, United States
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, United States
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14
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Miller AC, Harris LM, Winthrop KL, Cavanaugh JE, Abou Alaiwa MH, Hornick DB, Stoltz DA, Polgreen PM. Cystic Fibrosis Carrier States Are Associated With More Severe Cases of Bronchiectasis. Open Forum Infect Dis 2024; 11:ofae024. [PMID: 38390464 PMCID: PMC10883289 DOI: 10.1093/ofid/ofae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/12/2024] [Indexed: 02/24/2024] Open
Abstract
Background People with cystic fibrosis (CF) are at increased risk for bronchiectasis, and several reports suggest that CF carriers may also be at higher risk for developing bronchiectasis. The purpose of this study was to determine if CF carriers are at risk for more severe courses or complications of bronchiectasis. Methods Using MarketScan data (2001-2021), we built a cohort consisting of 105 CF carriers with bronchiectasis and 300 083 controls with bronchiectasis but without a CF carrier diagnosis. We evaluated if CF carriers were more likely to be hospitalized for bronchiectasis. In addition, we examined if CF carriers were more likely to be infected with Pseudomonas aeruginosa or nontuberculous mycobacteria (NTM) or to have filled more antibiotic prescriptions. We considered regression models for incident and rate outcomes that controlled for age, sex, smoking status, and comorbidities. Results The odds of hospitalization were almost 2.4 times higher (95% CI, 1.116-5.255) for CF carriers with bronchiectasis when compared with non-CF carriers with bronchiectasis. The estimated odds of being diagnosed with a Pseudomonas infection for CF carriers vs noncarriers was about 4.2 times higher (95% CI, 2.417-7.551) and 5.4 times higher (95% CI, 3.398-8.804) for being diagnosed with NTM. The rate of distinct antibiotic fill dates was estimated to be 2 times higher for carriers as compared with controls (95% CI, 1.735-2.333), and the rate ratio for the total number of days of antibiotics supplied was estimated as 2.8 (95% CI, 2.290-3.442). Conclusions CF carriers with bronchiectasis required more hospitalizations and more frequent administration of antibiotics as compared with noncarriers. Given that CF carriers were also more likely to be diagnosed with Pseudomonas and NTM infections, CF carriers with bronchiectasis may have a phenotype more resembling CF-related bronchiectasis than non-CF bronchiectasis.
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Affiliation(s)
- Aaron C Miller
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Logan M Harris
- Department of Biostatistics, University of Iowa, Iowa City, Iowa, USA
| | - Kevin L Winthrop
- Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA
| | | | | | - Douglas B Hornick
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David A Stoltz
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Philip M Polgreen
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
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15
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small-molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. Mol Biol Cell 2024; 35:ar15. [PMID: 38019608 PMCID: PMC10881158 DOI: 10.1091/mbc.e23-08-0336] [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: 09/18/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small-molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase and demonstrated that CFTR-F508del ERAD is robust. Gene-drug interaction experiments illustrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA 94305
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16
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El Makhzen N, Daimi H, Bouguenouch L, Abriel H. The burden of cystic fibrosis in North Africa. Front Genet 2024; 14:1295008. [PMID: 38269366 PMCID: PMC10806102 DOI: 10.3389/fgene.2023.1295008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Background: Over 200 pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are associated with cystic fibrosis (CF)-the most prevalent autosomal recessive disease globally, the p.Phe508del variant being the most commonly observed. Main text: Recent epidemiological studies suggest a higher global prevalence of CF than previously thought. Nevertheless, comprehensive CF data remains extremely scarce among African populations, contributing to a significant information gap within the African healthcare system. Consequently, the underestimation of CF among children from African populations is likely. The goal of this article is to review the pathogenesis of CF and its prevalence in the countries of North Africa. Conclusion: The prevalence of CF in North African countries is likely underestimated due to the complexity of the disease and the lack of a timely, proper clinical and genetic investigation that allows the early identification of CF patients and thus facilitates therapeutic recommendations. Therefore, specific genetic and epidemiological studies on African individuals showing CF symptoms should be conducted to enhance the diagnostic yield of CF in Africa.
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Affiliation(s)
- Nada El Makhzen
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Houria Daimi
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Department of Biology, Faculty of Sciences, University of Gabes, Gabès, Tunisia
| | - Laila Bouguenouch
- Laboratory of Medical Genetics and Oncogenetics, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hugues Abriel
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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17
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da Silva LVRF, Athanazio RA, Tonon CR, Ferreira JC, Tanni SE. Use of elexacaftor+tezacaftor+ivacaftor in individuals with cystic fibrosis and at least one F508del allele: a systematic review and meta-analysis. J Bras Pneumol 2024; 49:e20230187. [PMID: 38198345 PMCID: PMC10760416 DOI: 10.36416/1806-3756/e20230187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/11/2023] [Indexed: 01/12/2024] Open
Abstract
OBJECTIVE To evaluate the effect of treatment with the combination of three cystic fibrosis transmembrane conductance regulator (CFTR) modulators-elexacaftor+tezacaftor+ivacaftor (ETI)-on important clinical endpoints in individuals with cystic fibrosis. METHODS This was a systematic review and meta-analysis of randomized clinical trials that compared the use of ETI in individuals with CF and at least one F508del allele with that of placebo or with an active comparator such as other combinations of CFTR modulators, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations and the Patients of interest, Intervention to be studied, Comparison of interventions, and Outcome of interest (PICO) methodology. We searched the following databases: MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov from their inception to December 26th, 2022. The risk of bias was assessed using the Cochrane risk-of-bias tool, and the quality of evidence was based on the Grading of Recommendations Assessment, Development and Evaluation (GRADE). RESULTS We retrieved 54 studies in the primary search. Of these, 6 met the inclusion criteria and were analyzed (1,127 patients; 577 and 550 in the intervention and control groups, respectively). The meta-analysis revealed that the use of ETI increased FEV1% [risk difference (RD), +10.47%; 95% CI, 6.88-14.06], reduced the number of acute pulmonary exacerbations (RD, -0.16; 95% CI, -0.28 to -0.04), and improved quality of life (RD, +14.93; 95% CI, 9.98-19.89) and BMI (RD, +1.07 kg/m2; 95% CI, 0.90-1.25). Adverse events did not differ between groups (RD, -0.03; 95% CI, -0.08 to 0.01), and none of the studies reported deaths. CONCLUSIONS Our findings demonstrate that ETI treatment substantially improves clinically significant, patient-centered outcomes.
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Affiliation(s)
- Luiz Vicente Ribeiro Ferreira da Silva
- . Unidade de Pneumologia Pediátrica, Instituto da Criança e do Adolescente, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Rodrigo Abensur Athanazio
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | | | - Juliana Carvalho Ferreira
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Suzana Erico Tanni
- . Departamento de Clínica Médica, Faculdade de Medicina de Botucatu, Botucatu, (SP) Brasil
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18
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Dobra R, Pinnell S, Jones A, Madge S, Simmonds NJ, Davies JC. How representative are clinical trial cohorts of the general CF population? Implications for trial planning. J Cyst Fibros 2024; 23:68-72. [PMID: 38040535 DOI: 10.1016/j.jcf.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 12/03/2023]
Abstract
Understanding the number of patients eligible to participate in research is important to design protocols and define research priorities. We reviewed the records of all patients with CF, age 12+, who receive care at our centre. We assessed their eligibility for trial participation based on common trial inclusion/exclusion criteria. 643 patients were included in the analysis, 31 were modulator ineligible(MI). Only 198(31 %) of the total cohort and 7(23 %) of the MI cohort were eligible for participation based on the hypothetical criteria. The most common reason for ineligibility was ppFEV1 ≥90 % followed by clinical instability, complex comorbidity and anticipated inability to adhere to the protocol. We suggest this would be a useful exercise for centres planning to either participate in, or refer subjects into, upcoming trials to undertake for their own cohort. We also make suggestions for protocol designs that optimise the number of patients who are eligible to participate.
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19
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Li C, Liu Z, Anderson J, Liu Z, Tang L, Li Y, Peng N, Chen J, Liu X, Fu L, Townes TM, Rowe SM, Bedwell DM, Guimbellot J, Zhao R. Prime editing-mediated correction of the CFTR W1282X mutation in iPSCs and derived airway epithelial cells. PLoS One 2023; 18:e0295009. [PMID: 38019847 PMCID: PMC10686454 DOI: 10.1371/journal.pone.0295009] [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: 07/07/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing, a novel CRISPR-based genomic editing method, can be a potential therapeutic modality to correct nonsense CFTR mutations. We generated iPSCs from a CF patient homozygous for the CFTR W1282X mutation. We demonstrated that prime editing corrected one mutant allele in iPSCs, which effectively restored CFTR function in iPSC-derived airway epithelial cells and organoids. We further demonstrated that prime editing may directly repair mutations in iPSC-derived airway epithelial cells when the prime editing machinery is efficiently delivered by helper-dependent adenovirus (HDAd). Together, our data demonstrated that prime editing may potentially be applied to correct CFTR mutations such as W1282X.
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Affiliation(s)
- Chao Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zhong Liu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Justin Anderson
- Department of Pediatrics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zhongyu Liu
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Liping Tang
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yao Li
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ning Peng
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jianguo Chen
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Xueming Liu
- Key Laboratory of Imaging Processing and Intelligent Control, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David M. Bedwell
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jennifer Guimbellot
- Department of Pediatrics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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20
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Malik SS, Padmanabhan D, Hull-Meichle RL. Pancreas and islet morphology in cystic fibrosis: clues to the etiology of cystic fibrosis-related diabetes. Front Endocrinol (Lausanne) 2023; 14:1269139. [PMID: 38075070 PMCID: PMC10704027 DOI: 10.3389/fendo.2023.1269139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/03/2023] [Indexed: 12/18/2023] Open
Abstract
Cystic fibrosis (CF) is a multi-organ disease caused by loss-of-function mutations in CFTR (which encodes the CF transmembrane conductance regulator ion channel). Cystic fibrosis related diabetes (CFRD) occurs in 40-50% of adults with CF and is associated with significantly increased morbidity and mortality. CFRD arises from insufficient insulin release from β cells in the pancreatic islet, but the mechanisms underlying the loss of β cell function remain understudied. Widespread pathological changes in the CF pancreas provide clues to these mechanisms. The exocrine pancreas is the epicenter of pancreas pathology in CF, with ductal pathology being the initiating event. Loss of CFTR function results in ductal plugging and subsequent obliteration. This in turn leads to destruction of acinar cells, fibrosis and fatty replacement. Despite this adverse environment, islets remain relatively well preserved. However, islet composition and arrangement are abnormal, including a modest decrease in β cells and an increase in α, δ and γ cell abundance. The small amount of available data suggest that substantial loss of pancreatic/islet microvasculature, autonomic nerve fibers and intra-islet macrophages occur. Conversely, T-cell infiltration is increased and, in CFRD, islet amyloid deposition is a frequent occurrence. Together, these pathological changes clearly demonstrate that CF is a disease of the pancreas/islet microenvironment. Any or all of these changes are likely to have a dramatic effect on the β cell, which relies on positive signals from all of these neighboring cell types for its normal function and survival. A thorough characterization of the CF pancreas microenvironment is needed to develop better therapies to treat, and ultimately prevent CFRD.
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Affiliation(s)
- Sarah S. Malik
- Department of Pharmacology, University of Washington, Seattle, WA, United States
- Research Service, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
| | - Diksha Padmanabhan
- Research Service, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Seattle Institute for Biomedical and Clinical Research, Seattle, WA, United States
| | - Rebecca L. Hull-Meichle
- Department of Pharmacology, University of Washington, Seattle, WA, United States
- Research Service, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Seattle Institute for Biomedical and Clinical Research, Seattle, WA, United States
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington, Seattle, WA, United States
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21
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Heneghan M, Southern KW, Murphy J, Sinha IP, Nevitt SJ. Corrector therapies (with or without potentiators) for people with cystic fibrosis with class II CFTR gene variants (most commonly F508del). Cochrane Database Syst Rev 2023; 11:CD010966. [PMID: 37983082 PMCID: PMC10659105 DOI: 10.1002/14651858.cd010966.pub4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is a common life-shortening genetic condition caused by a variant in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. A class II CFTR variant F508del is the commonest CF-causing variant (found in up to 90% of people with CF (pwCF)). The F508del variant lacks meaningful CFTR function - faulty protein is degraded before reaching the cell membrane, where it needs to be to effect transepithelial salt transport. Corrective therapy could benefit many pwCF. This review evaluates single correctors (monotherapy) and any combination of correctors (most commonly lumacaftor, tezacaftor, elexacaftor, VX-659, VX-440 or VX-152) and a potentiator (e.g. ivacaftor) (dual and triple therapies). OBJECTIVES To evaluate the effects of CFTR correctors (with or without potentiators) on clinically important benefits and harms in pwCF of any age with class II CFTR mutations (most commonly F508del). SEARCH METHODS We searched the Cochrane CF Trials Register (28 November 2022), reference lists of relevant articles and online trials registries (3 December 2022). SELECTION CRITERIA Randomised controlled trials (RCTs) (parallel design) comparing CFTR correctors to control in pwCF with class II mutations. DATA COLLECTION AND ANALYSIS Two authors independently extracted data, assessed risk of bias and judged evidence certainty (GRADE); we contacted investigators for additional data. MAIN RESULTS We included 34 RCTs (4781 participants), lasting between 1 day and 48 weeks; an extension of two lumacaftor-ivacaftor studies provided additional 96-week safety data (1029 participants). We assessed eight monotherapy RCTs (344 participants) (4PBA, CPX, lumacaftor, cavosonstat and FDL169), 16 dual-therapy RCTs (2627 participants) (lumacaftor-ivacaftor or tezacaftor-ivacaftor) and 11 triple-therapy RCTs (1804 participants) (elexacaftor-tezacaftor-ivacaftor/deutivacaftor; VX-659-tezacaftor-ivacaftor/deutivacaftor; VX-440-tezacaftor-ivacaftor; VX-152-tezacaftor-ivacaftor). Participants in 21 RCTs had the genotype F508del/F508del, in seven RCTs they had F508del/minimal function (MF), in one RCT F508del/gating genotypes, in one RCT either F508del/F508del genotypes or F508del/residual function genotypes, in one RCT either F508del/gating or F508del/residual function genotypes, and in three RCTs either F508del/F508del genotypes or F508del/MF genotypes. Risk of bias judgements varied across different comparisons. Results from 16 RCTs may not be applicable to all pwCF due to age limits (e.g. adults only) or non-standard designs (converting from monotherapy to combination therapy). Monotherapy Investigators reported no deaths or clinically relevant improvements in quality of life (QoL). There was insufficient evidence to determine effects on lung function. No placebo-controlled monotherapy RCT demonstrated differences in mild, moderate or severe adverse effects (AEs); the clinical relevance of these events is difficult to assess due to their variety and few participants (all F508del/F508del). Dual therapy In a tezacaftor-ivacaftor group there was one death (deemed unrelated to the study drug). QoL scores (respiratory domain) favoured both lumacaftor-ivacaftor and tezacaftor-ivacaftor therapy compared to placebo at all time points (moderate-certainty evidence). At six months, relative change in forced expiratory volume in one second (FEV1) % predicted improved with all dual combination therapies compared to placebo (high- to moderate-certainty evidence). More pwCF reported early transient breathlessness with lumacaftor-ivacaftor (odds ratio (OR) 2.05, 99% confidence interval (CI) 1.10 to 3.83; I2 = 0%; 2 studies, 739 participants; high-certainty evidence). Over 120 weeks (initial study period and follow-up), systolic blood pressure rose by 5.1 mmHg and diastolic blood pressure by 4.1 mmHg with twice-daily 400 mg lumacaftor-ivacaftor (80 participants). The tezacaftor-ivacaftor RCTs did not report these adverse effects. Pulmonary exacerbation rates decreased in pwCF receiving additional therapies to ivacaftor compared to placebo (all moderate-certainty evidence): lumacaftor 600 mg (hazard ratio (HR) 0.70, 95% CI 0.57 to 0.87; I2 = 0%; 2 studies, 739 participants); lumacaftor 400 mg (HR 0.61, 95% CI 0.49 to 0.76; I2 = 0%; 2 studies, 740 participants); and tezacaftor (HR 0.64, 95% CI 0.46 to 0.89; 1 study, 506 participants). Triple therapy No study reported any deaths (high-certainty evidence). All other evidence was low- to moderate-certainty. QoL respiratory domain scores probably improved with triple therapy compared to control at six months (six studies). There was probably a greater relative and absolute change in FEV1 % predicted with triple therapy (four studies each across all combinations). The absolute change in FEV1 % predicted was probably greater for F508del/MF participants taking elexacaftor-tezacaftor-ivacaftor compared to placebo (mean difference 14.30, 95% CI 12.76 to 15.84; 1 study, 403 participants; moderate-certainty evidence), with similar results for other drug combinations and genotypes. There was little or no difference in adverse events between triple therapy and control (10 studies). No study reported time to next pulmonary exacerbation, but fewer F508del/F508del participants experienced a pulmonary exacerbation with elexacaftor-tezacaftor-ivacaftor at four weeks (OR 0.17, 99% CI 0.06 to 0.45; 1 study, 175 participants) and 24 weeks (OR 0.29, 95% CI 0.14 to 0.60; 1 study, 405 participants); similar results were seen across other triple therapy and genotype combinations. AUTHORS' CONCLUSIONS There is insufficient evidence of clinically important effects from corrector monotherapy in pwCF with F508del/F508del. Additional data in this review reduced the evidence for efficacy of dual therapy; these agents can no longer be considered as standard therapy. Their use may be appropriate in exceptional circumstances (e.g. if triple therapy is not tolerated or due to age). Both dual therapies (lumacaftor-ivacaftor, tezacaftor-ivacaftor) result in similar small improvements in QoL and respiratory function with lower pulmonary exacerbation rates. While the effect sizes for QoL and FEV1 still favour treatment, they have reduced compared to our previous findings. Lumacaftor-ivacaftor was associated with an increase in early transient shortness of breath and longer-term increases in blood pressure (not observed for tezacaftor-ivacaftor). Tezacaftor-ivacaftor has a better safety profile, although data are lacking in children under 12 years. In this population, lumacaftor-ivacaftor had an important impact on respiratory function with no apparent immediate safety concerns, but this should be balanced against the blood pressure increase and shortness of breath seen in longer-term adult data when considering lumacaftor-ivacaftor. Data from triple therapy trials demonstrate improvements in several key outcomes, including FEV1 and QoL. There is probably little or no difference in adverse events for triple therapy (elexacaftor-tezacaftor-ivacaftor/deutivacaftor; VX-659-tezacaftor-ivacaftor/deutivacaftor; VX-440-tezacaftor-ivacaftor; VX-152-tezacaftor-ivacaftor) in pwCF with one or two F508del variants aged 12 years or older (moderate-certainty evidence). Further RCTs are required in children under 12 years and those with more severe lung disease.
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Affiliation(s)
- Matthew Heneghan
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | | | - Ian P Sinha
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Sarah J Nevitt
- Department of Health Data Science, University of Liverpool, Liverpool, UK
- Centre for Reviews and Dissemination, University of York, York, UK
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22
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Taylor-Cousar JL, Robinson PD, Shteinberg M, Downey DG. CFTR modulator therapy: transforming the landscape of clinical care in cystic fibrosis. Lancet 2023; 402:1171-1184. [PMID: 37699418 DOI: 10.1016/s0140-6736(23)01609-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Following discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989 and subsequent elucidation of the varied CFTR protein abnormalities that result, a new era of cystic fibrosis management has emerged-one in which scientific principles translated from the bench to the bedside have enabled us to potentially treat the basic defect in the majority of children and adults with cystic fibrosis, with a resultant burgeoning adult cystic fibrosis population. However, the long-term effects of these therapies on the multiple manifestations of cystic fibrosis are still under investigation. Understanding the effects of modulators in populations excluded from clinical trials is also crucial. Furthermore, establishing appropriate disease measures to assess efficacy in the youngest potential trial participants and in those whose post-modulator lung function is in the typical range for people without chronic lung disease is essential for continued drug development. Finally, recognising that a health outcome gap has been created for some people and widened for others who are not eligible for, cannot tolerate, or do not have access to modulators is important.
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Affiliation(s)
- Jennifer L Taylor-Cousar
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA; Division of Pediatric Pulmonary Medicine, National Jewish Health, Denver, CO, USA; Division of Pulmonary Sciences and Critical Care Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA.
| | - Paul D Robinson
- Department of Respiratory Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia; Children's Health and Environment Program, Child Health Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel; B Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Damian G Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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23
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.556420. [PMID: 37745470 PMCID: PMC10515913 DOI: 10.1101/2023.09.15.556420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase, demonstrating that CFTR-F508del ERAD is highly buffered. Gene-drug interaction experiments demonstrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA, USA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA, USA 94305
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24
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Vena F, Mazza A, Bartolone M, Vasta A, D'Alberti E, Di Mascio D, D'Ambrosio V, Volpe G, Signore F, Pizzuti A, Giancotti A. Hyperechogenic fetal bowel: Current evidence-based prenatal diagnosis and management. JOURNAL OF CLINICAL ULTRASOUND : JCU 2023; 51:1172-1178. [PMID: 37553773 DOI: 10.1002/jcu.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 08/10/2023]
Abstract
Echogenic fetal bowel (EB) is a prenatal ultrasound finding (0.2%-1.4% of all pregnancies) defined as bowel of similar or greater echogenicity than surrounding bone. In fact, the ultrasound assessment is strongly subjective with inter-observer variability. The pathophysiology depends on the underlying condition, apparently related with meconium stasis and hypercellularity. It is often an isolated finding, with possible association with other structural anomalies. About the origin, it was observed in fetuses with cystic fibrosis, congenital infections, thalassemia, intraamniotic bleeding, fetal growth restriction. Fetuses with EB are at increased risk of adverse perinatal outcome, such as intrauterine growth restriction, placental dysfunction and perinatal death, highlighting the need for a thorough antenatal management and post-natal follow-up. It seems to be associated with a plenty of conditions, such as a poor fetal outcome, fetal growth restriction and placental dysfunction. Therefore management requires a multidisciplinary approach with different specialties' involvement and the prognosis is influenced by the underlying pathophysiology. In this complex scenario, the present review aims to define the clinical pathway which should be offered to pregnant women in case of finding of fetal EB ultrasound marker, to rule out any suspected pathological cause.
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Affiliation(s)
- Flaminia Vena
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandra Mazza
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Martina Bartolone
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Adele Vasta
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Elena D'Alberti
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Daniele Di Mascio
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Valentina D'Ambrosio
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Fabrizio Signore
- Obstetrics and Gynecology Department, USL Roma 2, Sant'Eugenio Hospital, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonella Giancotti
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Rome, Italy
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25
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Huang W, Smith AT, Korotun M, Iacono A, Wang J. Lung Transplantation in a New Era in the Field of Cystic Fibrosis. Life (Basel) 2023; 13:1600. [PMID: 37511977 PMCID: PMC10381966 DOI: 10.3390/life13071600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/08/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Lung transplantation for people with cystic fibrosis (PwCF) is a critical therapeutic option, in a disease without a cure to this day, and its overall success in this population is evident. The medical advancements in knowledge, treatment, and clinical care in the field of cystic fibrosis (CF) rapidly expanded and improved over the last several decades, starting from early pathology reports of CF organ involvement in 1938, to the identification of the CF gene in 1989. Lung transplantation for CF has been performed since 1983, and CF now accounts for about 17% of pre-transplantation diagnoses in lung transplantation recipients. Cystic fibrosis transmembrane conductance regulator (CFTR) modulators have been the latest new therapeutic modality addressing the underlying CF protein defect with the first modulator, ivacaftor, approved in 2012. Fast forward to today, and we now have a growing CF population. More than half of PwCF are now adults, and younger patients face a better life expectancy than they ever did before. Unfortunately, CFTR modulator therapy is not effective in all patients, and efficacy varies among patients; it is not a cure, and CF remains a progressive disease that leads predominantly to respiratory failure. Lung transplantation remains a lifesaving treatment for this disease. Here, we reviewed the current knowledge of lung transplantation in PwCF, the challenges associated with its implementation, and the ongoing changes to the field as we enter a new era in the care of PwCF. Improved life expectancy in PwCF will surely influence the role of transplantation in patient care and may even lead to a change in the demographics of which people benefit most from transplantation.
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Affiliation(s)
- Wei Huang
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Alexander T Smith
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Maksim Korotun
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Aldo Iacono
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Janice Wang
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Institute of Health System Science, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA
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26
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Li JQ, Wang HJ. [Research advances in pharmacotherapy for rare diseases in children]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2023; 25:759-766. [PMID: 37529960 PMCID: PMC10414178 DOI: 10.7499/j.issn.1008-8830.2302048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 08/03/2023]
Abstract
There are more than 7 000 rare diseases and approximately 475 million individuals with rare diseases globally, with children accounting for two-thirds of this population. Due to a relatively small patient population and limited financial resources allocated for drug research and development in pharmaceutical enterprises, there are still no drugs approved for the treatment of several thousands of these rare diseases. At present, there are no drugs for 95% of the patients with rare diseases, and consequently, the therapeutic drugs for rare diseases have been designated as orphan drugs. In order to guide pharmaceutical enterprises to strengthen the research and development of orphan drugs, various nations have enacted the acts for rare disease drugs, promoted and simplified the patent application process for orphan drugs, and provided scientific recommendations and guidance for the research and development of orphan drugs. Since there is a relatively high incidence rate of rare diseases in children, this article reviews the latest research on pharmacotherapy for children with rare diseases.
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Affiliation(s)
- Jia-Qi Li
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hui-Jun Wang
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China
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27
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Salazar-Barragan M, Taub DR. The Effects of Elexacaftor, Tezacaftor, and Ivacaftor (ETI) on Blood Glucose in Patients With Cystic Fibrosis: A Systematic Review. Cureus 2023; 15:e41697. [PMID: 37575762 PMCID: PMC10413995 DOI: 10.7759/cureus.41697] [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: 07/09/2023] [Indexed: 08/15/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder resulting from defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, which in turn results in a multi-systemic disorder. There are numerous known CF alleles associated with different mutations of the CFTR gene, with the most common CF allele being a three-base-pair deletion known as ΔF508. One common manifestation of CF is glycemic dysregulation associated with decreased insulin secretion, often progressing into a distinct form of diabetes known as cystic fibrosis-related diabetes (CFRD). In the past decade, a class of drugs known as CFTR modulators has entered clinical practice. These drugs interact with the CFTR protein to restore its function, with different modulators (or combinations of modulators) suitable for patients with different CFTR mutations. Previous research has established that the modulator ivacaftor is effective in decreasing blood glucose and sometimes resolving CFRD in patients with certain CFTR mutations (class III mutations). However, early modulator therapies for individuals with the common ΔF508 mutation (e.g., a combination of the modulators lumacaftor and ivacaftor) have largely proven ineffective in improving glucose regulation. More recently, a combination therapy of three modulators, namely elexacaftor, tezacaftor, and ivacaftor (ETI), has entered clinical practice for patients with the ΔF508 mutation. However, it is not clear whether this therapy is effective in treating dysglycemia. We searched for studies of any design that examined the effects of ETI on measures of blood glucose. All available studies were observational studies comparing patients before and after initiating ETI therapy. Measures of daily-life blood glucose (those obtained with continuous glucose monitoring systems or by measuring glycated hemoglobin (HbA1c)) and post-prandial glucose spikes from oral glucose tolerance tests showed significant improvements in at least some studies. The majority of studies showed significant improvements from pre- to post-ETI in one or more blood glucose measures. While the interpretation of this evidence is complicated by the lack of randomized controlled trials, it appears that ETI therapy is associated with improved glucose regulation for at least some patients with the ΔF508 mutation.
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Affiliation(s)
| | - Daniel R Taub
- Biology, Southwestern University, Georgetown, TX, USA
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28
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Abstract
BACKGROUND Hypertonic saline enhances mucociliary clearance and may lessen the destructive inflammatory process in the airways. This is an update of a previously published review. OBJECTIVES To investigate efficacy and tolerability of nebulised hypertonic saline treatment in people with cystic fibrosis (CF) compared to placebo or other treatments that enhance mucociliary clearance. SEARCH METHODS We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Cystic Fibrosis Trials Register, comprising references identified from comprehensive electronic database searches, handsearches of relevant journals and abstract books of conference proceedings. We also searched ongoing trials databases. Most recent search: 25 April 2022. SELECTION CRITERIA We included randomised and quasi-randomised controlled trials assessing hypertonic saline compared to placebo or other mucolytic therapy, for any duration or dose regimen in people with CF (any age or disease severity). DATA COLLECTION AND ANALYSIS Two authors independently reviewed all identified trials and data, and assessed trial quality. We assessed the certainty of the evidence using GRADE. For cross-over trials we stipulated a one-week washout period. We planned to use results from a paired analysis in the review, but this was only possible in one trial. For other cross-over trials, we chose to treat the trials as if they were parallel. MAIN RESULTS We included 24 trials (1318 participants, aged one month to 56 years); we excluded 29 trials, two trials are ongoing and six are awaiting classification. We judged 15 of the 24 included trials to have a high risk of bias due to participants' ability to discern the taste of the solutions. Hypertonic saline 3% to 7% versus placebo (stable disease) We are uncertain whether the regular use of nebulised hypertonic saline in stable lung disease leads to an improvement in forced expiratory volume in one second (FEV1) % predicted at four weeks, (mean difference (MD) 3.30%, 95% confidence interval (CI) 0.71 to 5.89; 4 trials, 246 participants; very low-certainty evidence). In preschool children we found no difference in lung clearance index (LCI) at four weeks, but a small improvement after 48 weeks of treatment with hypertonic saline compared to isotonic saline (MD -0.60, 95% CI -1.00 to -0.19; 2 trials, 192 participants). We are also uncertain whether hypertonic saline made a difference to mucociliary clearance, pulmonary exacerbations or adverse events compared to placebo. Hypertonic saline versus control (acute exacerbation) Two trials compared hypertonic saline to control, but only one provided data. There may be little or no difference in lung function measured by FEV1 % predicted after hypertonic saline compared to isotonic saline (MD 5.10%, 95% CI -14.67 to 24.87; 1 trial, 130 participants). Neither trial reported any deaths or measures of sputum clearance. There were no serious adverse events. Hypertonic saline versus rhDNase Three trials compared a similar dose of hypertonic saline to recombinant deoxyribonuclease (rhDNase); two trials (61 participants) provided data for inclusion in the review. We are uncertain whether there was an effect of hypertonic saline on FEV1 % predicted after three weeks (MD 1.60%, 95% CI -7.96 to 11.16; 1 trial, 14 participants; very low-certainty evidence). At three months, rhDNase may lead to a greater increase in FEV1 % predicted than hypertonic saline (5 mL twice daily) at 12 weeks in participants with moderate to severe lung disease (MD 8.00%, 95% CI 2.00 to 14.00; low-certainty evidence). We are uncertain whether adverse events differed between the two treatments. No deaths were reported. Hypertonic saline versus amiloride One trial (12 participants) compared hypertonic saline to amiloride but did not report on most of our outcomes. The trial found that there was no difference between treatments in measures of sputum clearance (very low-certainty evidence). Hypertonic saline compared with sodium-2-mercaptoethane sulphonate (Mistabron®) One trial (29 participants) compared hypertonic saline to sodium-2-mercaptoethane sulphonate. The trial did not measure our primary outcomes. There was no difference between treatments in any measures of sputum clearance, courses of antibiotics or adverse events (very low-certainty evidence). Hypertonic saline versus mannitol One trial (12 participants) compared hypertonic saline to mannitol, but did not report lung function at relevant time points for this review; there were no differences in sputum clearance, but mannitol was reported to be more 'irritating' (very low-certainty evidence). Hypertonic saline versus xylitol Two trials compared hypertonic saline to xylitol, but we are uncertain whether there is any difference in FEV1 % predicted or median time to exacerbation between groups (very low-certainty evidence). No other outcomes were reported in the review. Hypertonic saline 7% versus hypertonic saline 3% We are uncertain whether there was an improvement in FEV1 % predicted after treatment with 7% hypertonic saline compared with 3% (very low-certainty evidence). AUTHORS' CONCLUSIONS We are very uncertain if regular use of nebulised hypertonic saline by adults and children over the age of 12 years with CF results in an improvement in lung function after four weeks (three trials; very low-certainty evidence); there was no difference seen at 48 weeks (one trial; low-certainty evidence). Hypertonic saline improved LCI modestly in children under the age of six years. Evidence from one small cross-over trial in children indicates that rhDNase may lead to better lung function than hypertonic saline at three months; qualifying this, we highlight that while the study did demonstrate that the improvement in FEV1 was greater with daily rhDNase, there were no differences seen in any of the secondary outcomes. Hypertonic saline does appear to be an effective adjunct to physiotherapy during acute exacerbations of lung disease in adults. However, for the outcomes assessed, the certainty of the evidence ranged from very low to low at best, according to the GRADE criteria. The role of hypertonic saline in conjunction with cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy now needs to be considered, and future research needs to focus on this aspect.
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Affiliation(s)
- Peter Wark
- Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton, Australia
| | - Vanessa M McDonald
- Centre of Excellence in Severe Asthma and Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, Australia
| | - Sherie Smith
- Division of Child Health, Obstetrics & Gynaecology (COG), School of Medicine, University of Nottingham, Nottingham, UK
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29
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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30
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Hosseini Nami A, Kabiri M, Zafarghandi Motlagh F, Shirzadeh T, Fakhari N, Karimi A, Bagherian H, Jamali M, Younesikhah S, Shadman S, Zeinali R, Zeinali S. Genetic attributes of Iranian cystic fibrosis patients: the diagnostic efficiency of CFTR mutations in over a decade. Front Genet 2023; 14:1140034. [PMID: 37274793 PMCID: PMC10234504 DOI: 10.3389/fgene.2023.1140034] [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: 01/08/2023] [Accepted: 04/10/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives: Cystic fibrosis (CF) is the most prevalent autosomal recessive disorder among Caucasians. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause this pathology. We, therefore, aimed to describe the CFTR mutations and their geographical distribution in Iran. Method: The mutation spectrum for 87 families from all Iranian ethnicities was collected using ARMS PCR, Sanger sequencing, and MLPA. Results: Mutations were identified in 95.8% of cases. This dataset revealed that the most frequent mutations in the Iranian population were F508del, c.1000C>T, c.1397C>G, c.1911delG, and c.1393-1G>A. In addition, we found weak evidence for Turkey being the possible geographical pathway for introducing CFTR mutations into Iran by mapping the frequency of CFTR mutations. Conclusion: Our descriptive results will facilitate the genetic detection and prenatal diagnosis of cystic fibrosis within the Iranian population.
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Affiliation(s)
- Amin Hosseini Nami
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Tina Shirzadeh
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Negar Fakhari
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Ali Karimi
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Hamideh Bagherian
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mojdeh Jamali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Shahrzad Younesikhah
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Sara Shadman
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Razie Zeinali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sirous Zeinali
- Dr. Zeinali’s Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
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31
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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Genome-engineering technologies for modeling and treatment of cystic fibrosis. Adv Med Sci 2023; 68:111-120. [PMID: 36917892 DOI: 10.1016/j.advms.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by defects in the CF transmembrane conductance regulator (CFTR) protein. Due to the genetic nature of the disease, interventions in the genome can target any underlying alterations and potentially provide permanent disease resolution. The current development of gene-editing tools, such as designer nuclease technology capable of genome correction, holds great promise for both CF and other genetic diseases. In recent years, Cas9-based technologies have enabled the generation of genetically defined human stem cell and disease models based on induced pluripotent stem cells (iPSC). In this article, we outline the potential and possibilities of using CRISPR/Cas9-based gene-editing technology in CF modeling.
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Noni M, Katelari A, Poulou M, Ioannidis D, Kapasouri EM, Tzetis M, Doudounakis SE, Kanaka-Gantenbein C, Spoulou V. Frequencies of pathogenic CFTR variants in Greek cystic fibrosis patients with allergic bronchopulmonary aspergillosis and Aspergillus fumigatus chronic colonization: A retrospective cohort study. J Mycol Med 2023; 33:101326. [PMID: 36272381 DOI: 10.1016/j.mycmed.2022.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION The clinical spectrum of Aspergillus fumigatus diseases in cystic fibrosis (CF) patients, including allergic bronchopulmonary aspergillosis (ABPA) and Aspergillus fumigatus chronic colonization, has recently gained attention due to its association with the progression of lung disease. Our aim was to examine whether there is a difference on pathogenic variant frequencies of the CFTR gene between CF patients with ABPA and those with A. fumigatus chronic colonization. MATERIAL AND METHODS Greek CF patients diagnosed with ABPA and/or A. fumigatus chronic colonization were grouped according to their CFTR genotype. Patients with "minimal" CFTR function were defined as carrying a combination of class I or II pathogenic variants, while patients with "residual" function as carrying at least one class III, IV, V or VI pathogenic variant. RESULTS Fifty-four CF patients were included and all except one were defined as having "minimal" CFTR function. Among the 108 CFTR alleles, 69 (63.9%) of pathogenic variants belonged to class II, and 32 (29.6%) to class I. Five patients had a history of both ABPA and A. fumigatus chronic colonization. No significant difference was detected among patients diagnosed only with ABPA (n = 29) and those who had only a positive history of A. fumigatus chronic colonization (n = 20). The median age of ABPA diagnosis was significantly lower than the median age of A. fumigatus chronic colonization (P = 0.011), while no significant difference was detected on median FEV1% predicted. DISCUSSION No significant differences were detected in the type of CFTR pathogenic variants among patients with ABPA and those with A. fumigatus colonization. Similar studies should be performed in larger CF populations of different ethnic origin to further confirm our results.
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Affiliation(s)
- Maria Noni
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece.
| | - Anna Katelari
- Institute of Child Health, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Myrto Poulou
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Diomidis Ioannidis
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Efthymia-Maria Kapasouri
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Christina Kanaka-Gantenbein
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Vana Spoulou
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Division of Infectious Diseases, "Aghia Sophia" Children's Hospital, Athens, Greece
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Rehani MR, Marcus MS, Harris AB, Farrell PM, Ren CL. Variation in cystic fibrosis newborn screening algorithms in the United States. Pediatr Pulmonol 2023; 58:927-933. [PMID: 36507555 DOI: 10.1002/ppul.26279] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
RATIONALE Cystic fibrosis (CF) newborn screening (NBS) algorithms in the United States vary by state. Differences in CF NBS algorithms could potentially affect the detection rate of CF newborns and lead to disparities in CF diagnosis amongst different racial and ethnic groups. OBJECTIVES Generate a database of CF NBS algorithms in the United States and identify processes that may potentially lead to missed diagnoses or lead to healthcare disparities. METHODS We sent an online survey to state and regional CF and NBS leaders about the type and threshold of immunoreactive trypsinogen (IRT) cutoff used and methods used for CFTR gene variant analysis. Follow-up by email and phone was done to ensure a response from every state, clarify responses, and resolve discordances. RESULTS There is wide variation in the NBS algorithms employed by different states. Approximately half the states use a floating IRT cutoff, and half use a fixed IRT cutoff. CFTR variant analysis also varies widely, with two states analyzing only for the F508del variant and four states incorporating CFTR gene sequencing. The other states use CFTR variant panels ranging from 23 to 365 CFTR variants. CONCLUSIONS CF NBS algorithms vary widely amongst the different states in the United States, which affects the ability of CF NBS to diagnose newborn infants with CF consistently and uniformly across the country and potentially may miss more infants with CF from minority populations. Our results identify an important area for quality improvement in CF NBS.
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Affiliation(s)
- Maryann R Rehani
- Milken Institute of Public Health, George Washington University, Washington, District of Columbia, USA.,Madison Waisman Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Mary S Marcus
- Madison Waisman Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Anne B Harris
- Madison Waisman Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Philip M Farrell
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Clement L Ren
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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35
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Massie J. Overcoming the burden of cystic fibrosis. Med J Aust 2023; 218:118-119. [PMID: 36641140 DOI: 10.5694/mja2.51837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023]
Affiliation(s)
- John Massie
- Royal Children's Hospital Melbourne, Melbourne, VIC
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36
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Hayes D, Dani A, Guzman-Gomez A, Zafar F, Morales DLS, Ziady AG. Changing racial and ethnic differences for lung transplantation in cystic fibrosis. Pediatr Transplant 2023; 27:e14404. [PMID: 36206358 PMCID: PMC9839480 DOI: 10.1111/petr.14404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/05/2022] [Accepted: 09/18/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND CFTR modulators, especially (elexacaftor/tezacaftor/ivacaftor), have positively impacted the CF population and quickly decreased LTx numbers. However, no study has investigated if this reduction is universal across all races/ethnicities. METHODS Using the UNOS Registry, we explored the frequency/proportions of LTx in WNH and NW (Black, non-Hispanic/Hispanic-Latino/Asian-non Hispanic/American Indian-Alaskan Native-non-Hispanic/Native Hawaiian/Other Pacific Islander-non-Hispanic/Multiracial) in children and adults with CF in the US. RESULTS Between 1990 and 2019, the annual mean (±SD) number of LTxs for children with CF was 23.2 (±7.7) compared to 5 in 2020 (p < .001) and in 2021 (p < .001). In adults from 1990 to 2019, the mean (±SD) number of LTxs performed was 144.9 (±73.5), which was significantly higher than 2020 (n = 73; p < .001) and 2021 (n = 45; p < .001). Comparing 1990-2019 to post-2019, the proportion of LTxs performed in both children and adults with CF has decreased from 50.5% (696/1378) to 16.4% (9/55) and from 12.1% (4773/39542) to 2.4% (118/5004), respectively. In WNH pediatric patients, the difference in the percentage of all LTx made up by CF patients between the two eras was 41.2% compared to NW patients where the difference was 11%. Similarly in adults, the difference between the two eras was 10.4% in WNH and 2.4% in NW patients. CONCLUSIONS The recent reduction in LTx for the CF population has had less impact on the NW population in the US, so the continuation of optimal referrals for this group is needed.
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Affiliation(s)
- Don Hayes
- Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Alia Dani
- Department of Cardiothoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Amalia Guzman-Gomez
- Department of Cardiothoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Farhan Zafar
- Department of Cardiothoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - David L. S. Morales
- Department of Cardiothoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Assem G. Ziady
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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Akça ÖF, Uzun N, Pekcan S, Akkuş E, Güleç K. Caregiver burden and related factors in mothers of children and adolescents with cystic fibrosis. Minerva Pediatr (Torino) 2023; 75:144-146. [PMID: 33858133 DOI: 10.23736/s2724-5276.21.06215-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ömer F Akça
- Department of Child and Adolescent Psychiatry, Meram School of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Necati Uzun
- Department of Child and Adolescent Psychiatry, Meram School of Medicine, Necmettin Erbakan University, Konya, Turkey -
| | - Sevgi Pekcan
- Department of Pediatrics, Meram School of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Erkan Akkuş
- Department of Pediatric Gastroenterology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Kemal Güleç
- Department of Pediatrics, Reyhahli State Hospital, Hatay, Turkey
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Ravatin M, Odolczyk N, Servel N, Guijarro JI, Tagat E, Chevalier B, Baatallah N, Corringer PJ, Lukács GL, Edelman A, Zielenkiewicz P, Chambard JM, Hinzpeter A, Faure G. Design of Crotoxin-Based Peptides with Potentiator Activity Targeting the ΔF508NBD1 Cystic Fibrosis Transmembrane Conductance Regulator. J Mol Biol 2023; 435:167929. [PMID: 36566799 DOI: 10.1016/j.jmb.2022.167929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
We have previously shown that the CBb subunit of crotoxin, a β-neurotoxin with phospholipase A2 (PLA2) activity, targets the human ΔF508CFTR chloride channel implicated in cystic fibrosis (CF). By direct binding to the nucleotide binding domain 1 (NBD1) of ΔF508CFTR, this neurotoxic PLA2 acts as a potentiator increasing chloride channel current and corrects the trafficking defect of misfolded ΔF508CFTR inside the cell. Here, for a therapeutics development of new anti-cystic fibrosis agents, we use a structure-based in silico approach to design peptides mimicking the CBb-ΔF508NBD1 interface. Combining biophysical and electrophysiological methods, we identify several peptides that interact with the ΔF508NBD1 domain and reveal their effects as potentiators on phosphorylated ΔF508CFTR. Moreover, protein-peptide interactions and electrophysiological studies allowed us to identify key residues of ΔF508NBD1 governing the interactions with the novel potentiators. The designed peptides bind to the same region as CBb phospholipase A2 on ΔF508NBD1 and potentiate chloride channel activity. Certain peptides also show an additive effect towards the clinically approved VX-770 potentiator. The identified CF therapeutics peptides represent a novel class of CFTR potentiators and illustrate a strategy leading to reproducing the effect of specific protein-protein interactions.
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Affiliation(s)
- Marc Ravatin
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3571, Récepteurs-Canaux, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; Sanofi, R&D, Integrated Drug Discovery, In Vitro Biology, Vitry-sur-Seine, France
| | - Norbert Odolczyk
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3571, Récepteurs-Canaux, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Nathalie Servel
- INSERM, U1151, Université de Paris Cité, Institut Necker Enfants Malades (INEM), CNRS, UMR 8253, 160 rue de Vaugirard, F-75015 Paris, France
| | - J Iñaki Guijarro
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3528, Biological NMR and HDX-MS Technological Platform, 28 rue du Dr. Roux, F-75015 Paris, France
| | - Eric Tagat
- Sanofi, R&D, Integrated Drug Discovery, In Vitro Biology, Vitry-sur-Seine, France
| | - Benoit Chevalier
- INSERM, U1151, Université de Paris Cité, Institut Necker Enfants Malades (INEM), CNRS, UMR 8253, 160 rue de Vaugirard, F-75015 Paris, France
| | - Nesrine Baatallah
- INSERM, U1151, Université de Paris Cité, Institut Necker Enfants Malades (INEM), CNRS, UMR 8253, 160 rue de Vaugirard, F-75015 Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3571, Récepteurs-Canaux, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France
| | - Gergely L Lukács
- Department of Physiology and Biochemistry, McGill University, Montréal, Quebec, Canada
| | - Aleksander Edelman
- INSERM, U1151, Université de Paris Cité, Institut Necker Enfants Malades (INEM), CNRS, UMR 8253, 160 rue de Vaugirard, F-75015 Paris, France
| | - Piotr Zielenkiewicz
- Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jean-Marie Chambard
- Sanofi, R&D, Integrated Drug Discovery, In Vitro Biology, Vitry-sur-Seine, France
| | - Alexandre Hinzpeter
- INSERM, U1151, Université de Paris Cité, Institut Necker Enfants Malades (INEM), CNRS, UMR 8253, 160 rue de Vaugirard, F-75015 Paris, France.
| | - Grazyna Faure
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3571, Récepteurs-Canaux, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France.
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Abstract
Cystic fibrosis (CF) is an inherited multisystemic disease that can cause progressive bronchiectasis, pancreatic endocrine and exocrine insufficiency, distal intestinal obstruction syndrome, liver dysfunction, and other disorders. Traditional therapies focused on the treatment or prevention of damage to each organ system with incremental modalities such as nebulized medications for the lungs, insulin for diabetes, and supplementation with pancreatic enzymes. However, the advent of highly effective modulator therapies that target specific cystic fibrosis transmembrane conductance regulator protein malformations resulting from individual genetic mutations has transformed the lives and prognosis for persons with CF.
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Affiliation(s)
- Shijing Jia
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA;
| | - Jennifer L Taylor-Cousar
- Divisions of Pulmonary Sciences and Critical Care Medicine and Pediatric Pulmonology, National Jewish Health, Denver, Colorado, USA;
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40
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Song J, Dong L, Sun H, Luo N, Huang Q, Li K, Shen X, Jiang Z, Lv Z, Peng L, Zhang M, Wang K, Liu K, Hong J, Yi C. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol Cell 2023; 83:139-155.e9. [PMID: 36521489 DOI: 10.1016/j.molcel.2022.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
Nonsense mutations, accounting for >20% of disease-associated mutations, lead to premature translation termination. Replacing uridine with pseudouridine in stop codons suppresses translation termination, which could be harnessed to mediate readthrough of premature termination codons (PTCs). Here, we present RESTART, a programmable RNA base editor, to revert PTC-induced translation termination in mammalian cells. RESTART utilizes an engineered guide snoRNA (gsnoRNA) and the endogenous H/ACA box snoRNP machinery to achieve precise pseudouridylation. We also identified and optimized gsnoRNA scaffolds to increase the editing efficiency. Unexpectedly, we found that a minor isoform of pseudouridine synthase DKC1, lacking a C-terminal nuclear localization signal, greatly improved the PTC-readthrough efficiency. Although RESTART induced restricted off-target pseudouridylation, they did not change the coding information nor the expression level of off-targets. Finally, RESTART enables robust pseudouridylation in primary cells and achieves functional PTC readthrough in disease-relevant contexts. Collectively, RESTART is a promising RNA-editing tool for research and therapeutics.
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Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Nan Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Qiang Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, PRC
| | - Xiaowen Shen
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC
| | - Zhe Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Zhicong Lv
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Luxin Peng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, PRC
| | | | - Kun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Ke Liu
- Department of Otolaryngology Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, PRC
| | - Jiaxu Hong
- Department of Ophthalmology, Eye and Ear, Nose, Throat Hospital of Fudan University, Shanghai, PRC
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, PRC.
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41
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Lindgren NR, McDaniel MS, Novak L, Swords WE. Acute polymicrobial airway infections: analysis in cystic fibrosis mice. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001290. [PMID: 36748431 PMCID: PMC9993112 DOI: 10.1099/mic.0.001290] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cystic fibrosis (CF) is a genetic disorder affecting epithelial ion transport, which among other impacts results in defective mucociliary clearance and innate defenses in the respiratory tract. Consequently, people with CF experience lifelong infections of the respiratory mucosa that are chronic and polymicrobial in nature. Young children with CF are initially colonized by opportunists like nontypeable Haemophilus influenzae (NTHi), which normally resides within the microbiome of the nasopharynx and upper airways and can also cause infections of the respiratory mucosa that include bronchitis and otitis media. NTHi is typically supplanted by other microbes as patients age; for example, people with CF are often chronically infected with mucoid strains of Pseudomonas aeruginosa, which prior work in our laboratory has shown to promote colonization and persistence by other opportunists that include Stenotrophomonas maltophilia. Our previous work has shown that polymicrobial infection impacts host colonization and persistence of incoming microbes via diverse mechanisms that include priming of host immunity that can promote microbial clearance, and cooperativity within polymicrobial biofilms, which can promote persistence. In infection studies with BALB/c Cftrtm1UNC mice, results showed, as previously observed for WT BALB/c mice, preceding infection with NTHi decreased colonization and persistence by P. aeruginosa. Likewise, polymicrobial infection of BALB/c Cftrtm1UNC and C57BL/6 Cftrtm1UncTg(FABPhCFTR)1Jaw/J mice showed correlation between S. maltophilia and P. aeruginosa, with increased bacterial colonization and lung pathology. Based on these results, we conclude that our previous observations regarding polymicrobial infections with CF opportunists in WT mice are also validated using CF mice.
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Affiliation(s)
- Natalie R Lindgren
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
| | - Melissa S McDaniel
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
| | - Lea Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, USA
| | - W Edward Swords
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
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42
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Vega C, Espínola D, Ascurra M, Fraenkel S, Valenzuela A, Ortíz L. Frequency of F508del Variant in Patients with Cystic Fibrosis from Paraguay. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2023. [DOI: 10.1590/2326-4594-jiems-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Affiliation(s)
- Celeste Vega
- Centro para el Desarrollo de la Investigación Científica, Paraguay
| | - Dahiana Espínola
- Centro para el Desarrollo de la Investigación Científica, Paraguay
| | - Marta Ascurra
- Ministerio de Salud Pública y Bienestar Social, Paraguay
| | | | | | - Lourdes Ortíz
- Ministerio de Salud Pública y Bienestar Social, Paraguay
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43
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Muacevic A, Adler JR, Elnazir B. Beyond the Local Basic Panel: Full CFTR Gene Analysis Identifies Novel CF Mutation Missed on Standard Testing in an Arabic Child. Cureus 2023; 15:e33337. [PMID: 36741604 PMCID: PMC9896132 DOI: 10.7759/cureus.33337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by different mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It is the most common inherited disorder in the Caucasian population, with around 2000 mutations identified for the CFTR gene. The precise prevalence of CF in Arab countries remains unknown, with the prevalence of F508 del found to be a common type with other endemic mutations. We describe the case of a CF patient who was diagnosed at the age of seven years. She presented post-cardiac surgery for further evaluation for a recurrent chest infection and subtle dysmorphic features. CF genetic testing for the most common 31 mutations (CF panel) was negative, and a novel mutation was identified on CFTR gene sequencing.
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44
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Moni SS, Al Basheer A. Molecular targets for cystic fibrosis and therapeutic potential of monoclonal antibodies. Saudi Pharm J 2022; 30:1736-1747. [PMID: 36601503 PMCID: PMC9805982 DOI: 10.1016/j.jsps.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease that affects the exocrine glands and is caused by cystic fibrosis transmembrane conductance regulator gene (CFTR) mutations. Lung disease is the leading cause of morbidity in patients. Target-specific treatment of CF has been achieved using monoclonal antibodies (mAbs). The purpose of this article is to discuss the possibility of treating CF with mAbs through their significant target specificity. We searched electronic databases in Web of Science, PubMed, EMBASE, Scopus, and Google Scholar from 1984 to 2021. We discussed the critical role of targeted therapy in cystic fibrosis, as it will be more effective at suppressing the molecular networks. After conducting a critical review of the available literature, we concluded that it is critical to understand the fundamental molecular mechanisms underlying CF prior to incorporating biologics into the therapy regimen. Omalizumab, Mepolizumab, Benralizumab, Dupilumab and KB001-A have been successfully screened for asthma-complicated CF, and their efficacies have been well reported. Despite the availability of effective targeted biologics, treating CF has remained a difficult task, particularly when it comes to reduction of secondary inflammatory mediators. This review emphasizes the overall views on CF, the immunological mechanism of CF, and the prospective therapeutic use of mAbs as potential targeted biologics for enhancing the overall status of human health.
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45
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Toward a Broader Understanding of Cystic Fibrosis Epidemiology and Its Impact on Clinical Manifestations. Clin Chest Med 2022; 43:579-590. [PMID: 36344067 DOI: 10.1016/j.ccm.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The incidence of cystic fibrosis remains constant in North America and Western Europe is 1 in 3500 live births, but survival and quality of life have improved. The cystic fibrosis population has shifted toward the adult age range with a concomitant shift in the spectrum of complications. Survival increased because of aggressive symptomatic therapy, earlier diagnosis by newborn screening, and the introduction of modulators of the cystic fibrosis transmembrane conductance regulator, so that predicted median survival age is now about 50 years. In the United States, members of low socioeconomic status populations or members of racial or ethnic minorities have benefitted less from these advances.
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46
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Clinical and Genetic Characterisation of Cystic Fibrosis Patients in Latvia: A Twenty-Five-Year Experience. Diagnostics (Basel) 2022; 12:diagnostics12112893. [PMID: 36428953 PMCID: PMC9689702 DOI: 10.3390/diagnostics12112893] [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: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Cystic fibrosis (CF) is the most common life-limiting genetic disorder in European descent populations. It is caused by pathogenic variants in the CFTR gene, and inheritance is autosomal recessive. This study provides an up-to-date, comprehensive estimation of the distribution of CFTR pathogenic variants in Latvia and their phenotypic characteristics. It also reports the first results of the CF newborn screening programme following its implementation in 2019. We analysed the clinical and molecular data of CF patients treated at the only tertiary hospital in Latvia providing specialised healthcare for the disorder. Between 1997 and 2022, 66 CF patients from 62 families were diagnosed based on symptoms or a molecular confirmation (six patients were diagnosed through the CF newborn screening programme). F508del was identified in 70.5% of all CF chromosomes. Known variants were identified in more than one family: dele2,3, R1006H, L1335P, W57R, R553X, 2143delT and 3849+10kb C>T (legacy names used). Furthermore, two novel variants were identified, namely, c.503C>A p.(Ser168Ter) and c.(743+1_744-1)_(1584+1_1585-1)del p.(?). The available follow-up results indicated that Latvian CF patients demonstrated similar tendencies to CF patients worldwide. The oldest age at diagnosis prior to the implementation of the CF newborn screening programme was 14 years. We provide here, for the first time, a comprehensive description of Latvian CF patients. An improvement in the healthcare of CF patients over time, including access to diagnosis, is evident. Two novel CF-causing variants are reported, and F508del is the most frequently occurring variant in the population, thus suggesting that F508del screening should be followed by the testing of the full CFTR gene.
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47
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Wei J, Zhang W, Li J, Jin Y, Qiu Z. Application of the transgenic pig model in biomedical research: A review. Front Cell Dev Biol 2022; 10:1031812. [PMID: 36325365 PMCID: PMC9618879 DOI: 10.3389/fcell.2022.1031812] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
The large animal model has gradually become an essential part of preclinical research studies, relating to exploring the disease pathological mechanism, genic function, pharmacy, and other subjects. Although the mouse model has already been widely accepted in clinical experiments, the need for finding an animal model with high similarity compared with a human model is urgent due to the different body functions and systems between mice and humans. The pig is an optimal choice for replacement. Therefore, enhancing the production of pigs used for models is an important part of the large animal model as well. Transgenic pigs show superiority in pig model creation because of the progress in genetic engineering. Successful cases of transgenic pig models occur in the clinical field of metabolic diseases, neurodegenerative diseases, and genetic diseases. In addition, the choice of pig breed influences the effort and efficiency of reproduction, and the mini pig has relative obvious advantages in pig model production. Indeed, pig models in these diseases provide great value in studies of their causes and treatments, especially at the genetic level. This review briefly outlines the method used to create transgenic pigs and species of producing transgenic pigs and provides an overview of their applications on different diseases and limitations for present pig model developments.
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Affiliation(s)
| | | | | | - Ye Jin
- *Correspondence: Ye Jin, ; Zhidong Qiu,
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48
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Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis. Int J Mol Sci 2022; 23:ijms232012351. [PMID: 36293229 PMCID: PMC9604016 DOI: 10.3390/ijms232012351] [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: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Cystic fibrosis is a genetic disease caused by mutation of the CFTR gene, which encodes a chloride and bicarbonate transporter in epithelial cells. Due to the vast range of geno- and phenotypes, it is difficult to find causative treatments; however, small-molecule therapeutics have been clinically approved in the last decade. Still, the search for novel therapeutics is ongoing, and thousands of compounds are being tested in different assays, often leaving their mechanism of action unknown. Here, we bring together a CFTR-specific compound database (CandActCFTR) and systems biology model (CFTR Lifecycle Map) to identify the targets of the most promising compounds. We use a dual inverse screening approach, where we employ target- and ligand-based methods to suggest targets of 309 active compounds in the database amongst 90 protein targets from the systems biology model. Overall, we identified 1038 potential target–compound pairings and were able to suggest targets for all 309 active compounds in the database.
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49
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Recovery of ΔF508-CFTR Function by Citrate. Nutrients 2022; 14:nu14204283. [PMID: 36296967 PMCID: PMC9610893 DOI: 10.3390/nu14204283] [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: 09/26/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Treatment of cystic fibrosis relies so far on expensive and sophisticated drugs. A logical approach to rescuing the defective ΔF508-CFTR protein has not yet been published. Therefore, virtual docking of ATP and CFTR activators to the open conformation of the CFTR protein was performed. A new ATP binding site outside of the two known locations was identified. It was located in the cleft between the nucleotide binding domains NBD1 and NBD2 and comprised six basic amino acids in close proximity. Citrate and isocitrate were also bound to this site. Citrate was evaluated for its action on epithelial cells with intact CFTR and defective ΔF508-CFTR. It activated hyaluronan export from human breast carcinoma cells and iodide efflux, and recovered ΔF508-CFTR from premature intracellular degradation. In conclusion, citrate is an activator for ΔF508-CFTR and increases export by defective ΔF508-CFTR into the extracellular matrix of epithelial cells.
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50
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Sui H, Xu X, Su Y, Gong Z, Yao M, Liu X, Zhang T, Jiang Z, Bai T, Wang J, Zhang J, Xu C, Luo M. Gene therapy for cystic fibrosis: Challenges and prospects. Front Pharmacol 2022; 13:1015926. [PMID: 36304167 PMCID: PMC9592762 DOI: 10.3389/fphar.2022.1015926] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Cystic fibrosis (CF) is a life-threatening autosomal-recessive disease caused by mutations in a single gene encoding cystic fibrosis transmembrane conductance regulator (CFTR). CF effects multiple organs, and lung disease is the primary cause of mortality. The median age at death from CF is in the early forties. CF was one of the first diseases to be considered for gene therapy, and efforts focused on treating CF lung disease began shortly after the CFTR gene was identified in 1989. However, despite the quickly established proof-of-concept for CFTR gene transfer in vitro and in clinical trials in 1990s, to date, 36 CF gene therapy clinical trials involving ∼600 patients with CF have yet to achieve their desired outcomes. The long journey to pursue gene therapy as a cure for CF encountered more difficulties than originally anticipated, but immense progress has been made in the past decade in the developments of next generation airway transduction viral vectors and CF animal models that reproduced human CF disease phenotypes. In this review, we look back at the history for the lessons learned from previous clinical trials and summarize the recent advances in the research for CF gene therapy, including the emerging CRISPR-based gene editing strategies. We also discuss the airway transduction vectors, large animal CF models, the complexity of CF pathogenesis and heterogeneity of CFTR expression in airway epithelium, which are the major challenges to the implementation of a successful CF gene therapy, and highlight the future opportunities and prospects.
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Affiliation(s)
- Hongshu Sui
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
| | - Xinghua Xu
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Yanping Su
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Zhaoqing Gong
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Minhua Yao
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Xiaocui Liu
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Ting Zhang
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Ziyao Jiang
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Tianhao Bai
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Junzuo Wang
- The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an, Shandong, China
| | - Jingjun Zhang
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, China
| | - Changlong Xu
- The Reproductive Medical Center of Nanning Second People’s Hospital, Nanning, China
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
| | - Mingjiu Luo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
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