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Wu M, Davis JD, Zhao C, Daley T, Oliver KE. Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment. J Clin Transl Endocrinol 2024; 36:100344. [PMID: 38765466 PMCID: PMC11099334 DOI: 10.1016/j.jcte.2024.100344] [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: 12/14/2023] [Revised: 02/21/2024] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Cystic fibrosis (CF) has been traditionally viewed as a disease that affects White individuals. However, CF occurs among all races, ethnicities, and geographic ancestries. The disorder results from mutations in the CF transmembrane conductance regulator (CFTR). Varying incidence of CF is reported among Black, Indigenous, and People of Color (BIPOC), who typically exhibit worse clinical outcomes. These populations are more likely to carry rare CFTR variants omitted from newborn screening panels, leading to disparities in care such as delayed diagnosis and treatment. In this study, we present a case-in-point describing an individual of Gambian descent identified with CF. Patient genotype includes a premature termination codon (PTC) (c.2353C>T) and previously undescribed single nucleotide deletion (c.1970delG), arguing against effectiveness of currently available CFTR modulator-based interventions. Strategies for overcoming these two variants will likely include combinations of PTC suppressors, nonsense mediated decay inhibitors, and/or alternative approaches (e.g. gene therapy). Investigations such as the present study establish a foundation from which therapeutic treatments may be developed. Importantly, c.2353C>T and c.1970delG were not detected in the patient by traditional CFTR screening panels, which include an implicit racial and ethnic diagnostic bias as these tests are comprised of mutations largely observed in people of European ancestry. We suggest that next-generation sequencing of CFTR should be utilized to confirm or exclude a CF diagnosis, in order to equitably serve BIPOC individuals. Additional epidemiologic data, basic science investigations, and translational work are imperative for improving understanding of disease prevalence and progression, CFTR variant frequency, genotype-phenotype correlation, pharmacologic responsiveness, and personalized medicine approaches for patients with African ancestry and other historically understudied geographic lineages.
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Affiliation(s)
- Malinda Wu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Jacob D. Davis
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Conan Zhao
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tanicia Daley
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
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2
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Kandel R, Jung J, Neal S. Proteotoxic stress and the ubiquitin proteasome system. Semin Cell Dev Biol 2024; 156:107-120. [PMID: 37734998 PMCID: PMC10807858 DOI: 10.1016/j.semcdb.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.
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Affiliation(s)
- Rachel Kandel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Jasmine Jung
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Sonya Neal
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Ludwig N, Thörner-van Almsick J, Mersmann S, Bardel B, Niemann S, Chasan AI, Schäfers M, Margraf A, Rossaint J, Kahl BC, Zarbock A, Block H. Nuclease activity and protein A release of Staphylococcus aureus clinical isolates determine the virulence in a murine model of acute lung infection. Front Immunol 2023; 14:1259004. [PMID: 37849760 PMCID: PMC10577289 DOI: 10.3389/fimmu.2023.1259004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023] Open
Abstract
Staphylococcus aureus is a common cause of hospital-acquired pneumonia associated with high mortality. Adequate clinical treatment is impeded by increasing occurrence of antibiotic resistances. Understanding the underlying mechanisms of its virulence during infections is a prerequisite to finding alternative treatments. Here, we demonstrated that an increased nuclease activity of a S. aureus isolate from a person with cystic fibrosis confers a growth advantage in a model of acute lung infection compared to the isogenic strain with low nuclease activity. Comparing these CF-isolates with a common MRSA-USA300 strain with similarly high nuclease activity but significantly elevated levels of Staphylococcal Protein A (SpA) revealed that infection with USA300 resulted in a significantly increased bacterial burden in a model of murine lung infection. Replenishment with the cell wall-bound SpA of S. aureus, which can also be secreted into the environment and binds to tumor necrosis factor receptor -1 (TNFR-1) to the CF-isolates abrogated these differences. In vitro experiments confirmed significant differences in spa-expression between USA300 compared to CF-isolates, thereby influencing TNFR-1 shedding, L-selectin shedding, and production of reactive oxygen species through activation of ADAM17.
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Affiliation(s)
- Nadine Ludwig
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Julia Thörner-van Almsick
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Sina Mersmann
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Bernadette Bardel
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Silke Niemann
- Institute for Medical Microbiology, University Hospital Muenster, Muenster, Germany
| | - Achmet Imam Chasan
- Institute of Immunology, University Hospital Muenster, Muenster, Germany
| | - Michael Schäfers
- European Institute for Molecular Imaging (EIMI), University of Muenster, Muenster, Germany
| | - Andreas Margraf
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Jan Rossaint
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Barbara C. Kahl
- Institute for Medical Microbiology, University Hospital Muenster, Muenster, Germany
| | - Alexander Zarbock
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
| | - Helena Block
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Muenster, Germany
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4
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Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat Methods 2023; 20:898-907. [PMID: 37156841 DOI: 10.1038/s41592-023-01859-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/17/2023] [Indexed: 05/10/2023]
Abstract
Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.
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Affiliation(s)
- Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sneha Suresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Pranam Chatterjee
- Wyss Institute, Harvard Medical School, Boston, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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5
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Leroy C, Spelier S, Essonghe NC, Poix V, Kong R, Gizzi P, Bourban C, Amand S, Bailly C, Guilbert R, Hannebique D, Persoons P, Arhant G, Prévotat A, Reix P, Hubert D, Gérardin M, Chamaillard M, Prevarskaya N, Rebuffat S, Shapovalov G, Beekman J, Lejeune F. Use of 2,6-diaminopurine as a potent suppressor of UGA premature stop codons in cystic fibrosis. Mol Ther 2023; 31:970-985. [PMID: 36641622 PMCID: PMC10124085 DOI: 10.1016/j.ymthe.2023.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/10/2022] [Accepted: 01/12/2023] [Indexed: 01/16/2023] Open
Abstract
Nonsense mutations are responsible for around 10% of cases of genetic diseases, including cystic fibrosis. 2,6-diaminopurine (DAP) has recently been shown to promote efficient readthrough of UGA premature stop codons. In this study, we show that DAP can correct a nonsense mutation in the Cftr gene in vivo in a new CF mouse model, in utero, and through breastfeeding, thanks, notably, to adequate pharmacokinetic properties. DAP turns out to be very stable in plasma and is distributed throughout the body. The ability of DAP to correct various endogenous UGA nonsense mutations in the CFTR gene and to restore its function in mice, in organoids derived from murine or patient cells, and in cells from patients with cystic fibrosis reveals the potential of such readthrough-stimulating molecules in developing a therapeutic approach. The fact that correction by DAP of certain nonsense mutations reaches a clinically relevant level, as judged from previous studies, makes the use of this compound all the more attractive.
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Affiliation(s)
- Catherine Leroy
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Sacha Spelier
- Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands; Center for Living Technologies, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Nadège Charlene Essonghe
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Virginie Poix
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Rebekah Kong
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Patrick Gizzi
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR 3286 CNRS-Université de Strasbourg, 67404 Illkirch, France
| | - Claire Bourban
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR 3286 CNRS-Université de Strasbourg, 67404 Illkirch, France
| | - Séverine Amand
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Christine Bailly
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Romain Guilbert
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - David Hannebique
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - Philippe Persoons
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - Gwenaëlle Arhant
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Anne Prévotat
- University Lille, Clinique des Maladies Respiratoires, CRCM Hôpital Calmette, CHRU Lille, 59000 Lille, France
| | - Philippe Reix
- CRCM Pédiatrique Lyon, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, UMR 5558 (EMET), CNRS, LBBE, Université de Lyon, 69622 Villeurbanne, France
| | - Dominique Hubert
- Pulmonary Department and Adult CF Centre, Cochin Hospital, AP-HP, Paris, France
| | - Michèle Gérardin
- CF Pediatric Centre, Robert Debré Hospital, AP-HP, 75019 Paris, France
| | - Mathias Chamaillard
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France
| | - Natalia Prevarskaya
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - George Shapovalov
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Jeffrey Beekman
- Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands; Center for Living Technologies, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Fabrice Lejeune
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France.
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Behroozian S, Zlosnik JEA, Xu W, Li LY, Davies JE. Antibacterial Activity of a Natural Clay Mineral against Burkholderia cepacia Complex and Other Bacterial Pathogens Isolated from People with Cystic Fibrosis. Microorganisms 2023; 11:microorganisms11010150. [PMID: 36677442 PMCID: PMC9862493 DOI: 10.3390/microorganisms11010150] [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] [Received: 11/14/2022] [Revised: 12/15/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
There is an impending crisis in healthcare brought about by a new era of untreatable infections caused by bacteria resistant to all available antibiotics. Thus, there is an urgent need to identify novel antimicrobial agents to counter the continuing threat posed by formerly treatable infections. We previously reported that a natural mineral clay known as Kisameet clay (KC) is a potent inhibitor of the organisms responsible for acute infections. Chronic bacterial infections present another major challenge to treatment by antimicrobials, due to their prolonged nature, which results in repeated exposure to antibiotics and a constant selection for antimicrobial resistance. A prime example is bacteria belonging to the Burkholderia cepacia complex (Bcc), which particularly causes some of the most serious chronic lung infections in patients with cystic fibrosis (CF) associated with unpredictable clinical outcomes, poor prognosis, and high mortality rates. Eradication of these organisms from CF patients with limited effective antimicrobial options is a major challenge. Novel therapeutic approaches are urgently required. Here, we report the in vitro antibacterial activity of KC aqueous suspensions (1-10% w/v) and its aqueous extract (L100) against a collection of extensively and multi-drug resistant clinical isolates of Bcc, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia isolated from patients with CF. These findings present a potential novel therapy for further investigation in the clinic.
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Affiliation(s)
- Shekooh Behroozian
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 E Mall, Vancouver, BC V6T 1Z3, Canada
- Correspondence: (S.B.); (J.E.D.)
| | - James E. A. Zlosnik
- Centre for Understanding and Preventing Infection in Children, Division of Infectious Diseases, Department of Pediatrics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Wanjing Xu
- Department of Civil Engineering, University of British Columbia, 6250 Applied Science Ln, Vancouver, BC V6T 1Z3, Canada
| | - Loretta Y. Li
- Department of Civil Engineering, University of British Columbia, 6250 Applied Science Ln, Vancouver, BC V6T 1Z3, Canada
| | - Julian E. Davies
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Correspondence: (S.B.); (J.E.D.)
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7
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Fairweather N, Jones FW. Facilitators and barriers to empowerment in children and young people with cystic fibrosis: a meta-synthesis of the qualitative literature. Disabil Rehabil 2022; 44:7767-7780. [PMID: 34802345 DOI: 10.1080/09638288.2021.2003876] [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: 01/18/2023]
Abstract
PURPOSE Patient empowerment may be particularly important in children and young people (CYP) with CF, due to high treatment burden and limited peer support opportunities. This review aimed to meta-synthesize the qualitative literature pertaining to empowerment in CYP with CF. MATERIALS AND METHODS This work was guided by the ENTREQ framework, with a search strategy based on the SPIDER framework. A systematic search of PsycInfo, Medline, CINAHL and ASSIA databases was conducted. Identified studies were quality assessed and data analysed using thematic synthesis. PROSPERO registration: CRD42019154014. RESULTS Seventeen studies met inclusion criteria, though none explicitly explored empowerment. Thematic synthesis identified six analytic themes: relational support, information and understanding and feeling heard and respected appeared to facilitate empowerment, while prejudices and assumptions were identified as potential barriers. Mastery and competence and Navigating being different appeared to be components of empowerment. CONCLUSIONS The findings provide an initial understanding of patient empowerment in CYP with CF. Potential clinical implications include the need for more CYP-friendly information, more shared decision making and more opportunities to experience mastery. The need for further research is highlighted, particularly relating to developmental influences and factors unique to CF, which are not adequately addressed in existing patient empowerment models.Implications for rehabilitationEmpowerment in children and young people with cystic fibrosis can be facilitated by supportive and respectful relationships with family, friends and clinical teams, that enable them to feel heard and understood.It can be further supported by providing developmentally appropriate information and opportunities for children and young people to experience mastery and competency in typical childhood activities.Prejudices and assumptions about the capabilities of children and young people with CF, even when based in good intentions, can act as a barrier to empowerment.Empowerment can shape (and be shaped by) the way the children and young people navigate differences associated with living with CF.
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Affiliation(s)
- Naomi Fairweather
- Salomons Institute for Applied Psychology, Canterbury Christ Church University, Tunbridge Wells, Kent, UK
| | - Fergal W Jones
- Salomons Institute for Applied Psychology, Canterbury Christ Church University, Tunbridge Wells, Kent, UK
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8
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Cingolani P. Variant Annotation and Functional Prediction: SnpEff. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2493:289-314. [PMID: 35751823 DOI: 10.1007/978-1-0716-2293-3_19] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Variant annotations, in general, refer to the process of information enrichment of genomic variants from a sequencing experiment. Typically these annotations include functional predictions, such as predicting the amino acid sequence changes from the DNA variant, predicting whether the variant will induce a splice anomaly, or predicting nonsense mediated decay. But other annotations also include combining with genomic databases, adding conservation scores, or comparing to allele frequencies from large population databases. Finally, all these annotations are combined to prioritize and filter variants into a reduced set of highly relevant variants for the study or clinical assay.
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9
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Fairweather NH, Jones FW, Harris SA, Deiros Collado M, Shayle A. Thriving alongside cystic fibrosis: Developing a grounded theory of empowerment in children and young people with cystic fibrosis during key life transitions. Child Care Health Dev 2021; 47:484-493. [PMID: 33638555 DOI: 10.1111/cch.12860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/21/2020] [Accepted: 02/21/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Although the importance of patient empowerment is increasingly recognized, little is known about empowerment in children and young people (CYP) with long-term conditions. Empowerment may be particularly important in CYP with cystic fibrosis (CF) due to high treatment burden and limited opportunities for peer support. METHODS A Grounded Theory method was employed to develop a preliminary theory of empowerment in CYP with CF. Seven CYP with CF, five parents and four professionals were interviewed. RESULTS AND CONCLUSIONS The emerging model suggests that 'thriving alongside CF' may be supported by interactions between 'having a team' and 'taking charge and having a voice', leading to 'being able to just be a child', that 'concealing self' may get in the way of 'thriving alongside CF' and that these processes occur within wider medical and developmental contexts. Study limitations, clinical and research implications are discussed.
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Affiliation(s)
- Naomi H Fairweather
- Salomons Institute for Applied Psychology, Canterbury Christ Church University, Kent, UK.,Sussex Partnership NHS Foundation Trust, Sussex, UK
| | - Fergal W Jones
- Salomons Institute for Applied Psychology, Canterbury Christ Church University, Kent, UK.,Sussex Partnership NHS Foundation Trust, Sussex, UK
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10
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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11
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Gál E, Dolenšek J, Stožer A, Czakó L, Ébert A, Venglovecz V. Mechanisms of Post-Pancreatitis Diabetes Mellitus and Cystic Fibrosis-Related Diabetes: A Review of Preclinical Studies. Front Endocrinol (Lausanne) 2021; 12:715043. [PMID: 34566890 PMCID: PMC8461102 DOI: 10.3389/fendo.2021.715043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Anatomical proximity and functional correlations between the exocrine and endocrine pancreas warrant reciprocal effects between the two parts. Inflammatory diseases of the exocrine pancreas, such as acute or chronic pancreatitis, or the presence of cystic fibrosis disrupt endocrine function, resulting in diabetes of the exocrine pancreas. Although novel mechanisms are being increasingly identified, the intra- and intercellular pathways regulating exocrine-endocrine interactions are still not fully understood, making the development of new and more effective therapies difficult. Therefore, this review sought to accumulate current knowledge regarding the pathogenesis of diabetes in acute and chronic pancreatitis, as well as cystic fibrosis.
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Affiliation(s)
- Eleonóra Gál
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - Jurij Dolenšek
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Andraž Stožer
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - László Czakó
- First Department of Medicine, University of Szeged, Szeged, Hungary
| | - Attila Ébert
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
| | - Viktória Venglovecz
- Department of Pharmacology and Pharmacotherapy, University of Szeged, Szeged, Hungary
- *Correspondence: Viktória Venglovecz,
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12
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The Effect of Synonymous Single-Nucleotide Polymorphisms on an Atypical Cystic Fibrosis Clinical Presentation. Life (Basel) 2020; 11:life11010014. [PMID: 33375403 PMCID: PMC7824434 DOI: 10.3390/life11010014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
Synonymous single nucleotide polymorphisms (sSNPs), which change a nucleotide, but not the encoded amino acid, are perceived as neutral to protein function and thus, classified as benign. We report a patient who was diagnosed with cystic fibrosis (CF) at an advanced age and presented very mild CF symptoms. The sequencing of the whole cystic fibrosis transmembrane conductance regulator (CFTR) gene locus revealed that the patient lacks known CF-causing mutations. We found a homozygous sSNP (c.1584G>A) at the end of exon 11 in the CFTR gene. Using sensitive molecular methods, we report that the c.1584G>A sSNP causes cognate exon skipping and retention of a sequence from the downstream intron, both of which, however, occur at a relatively low frequency. In addition, we found two other sSNPs (c.2562T>G (p.Thr854=) and c.4389G>A (p.Gln1463=)), for which the patient is also homozygous. These two sSNPs stabilize the CFTR protein expression, compensating, at least in part, for the c.1584G>A-triggered inefficient splicing. Our data highlight the importance of considering sSNPs when assessing the effect(s) of complex CFTR alleles. sSNPs may epistatically modulate mRNA and protein expression levels and consequently influence disease phenotype and progression.
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13
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Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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14
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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De Boeck K. Cystic fibrosis in the year 2020: A disease with a new face. Acta Paediatr 2020; 109:893-899. [PMID: 31899933 DOI: 10.1111/apa.15155] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 12/14/2022]
Abstract
The autosomal recessive disease cystic fibrosis (CF) was once untreatable and deadly in childhood, but now most patients survive to adulthood. Many countries have instituted CF newborn screening because early diagnosis improves outcome. CF research has greatly intensified following the discovery of the CF transmembrane conductance regulator (CFTR) gene, which has more than 2000 different mutations. For patients with common mutations like F508del, CFTR modulators are life transforming and may even prevent major complications if started early in childhood. For some patients with rare CFTR mutations, a treatment path still needs to be developed. Conclusion: This review provides a general update on CF, including screening and current and future treatment.
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Affiliation(s)
- Kris De Boeck
- Pediatric Pulmonology University Hospitals of Leuven University of Leuven Leuven Belgium
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16
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Regulation of CFTR Biogenesis by the Proteostatic Network and Pharmacological Modulators. Int J Mol Sci 2020; 21:ijms21020452. [PMID: 31936842 PMCID: PMC7013518 DOI: 10.3390/ijms21020452] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal inherited disease among Caucasians in North America and a significant portion of Europe. The disease arises from one of many mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator, or CFTR. The most common disease-associated allele, F508del, along with several other mutations affect the folding, transport, and stability of CFTR as it transits from the endoplasmic reticulum (ER) to the plasma membrane, where it functions primarily as a chloride channel. Early data demonstrated that F508del CFTR is selected for ER associated degradation (ERAD), a pathway in which misfolded proteins are recognized by ER-associated molecular chaperones, ubiquitinated, and delivered to the proteasome for degradation. Later studies showed that F508del CFTR that is rescued from ERAD and folds can alternatively be selected for enhanced endocytosis and lysosomal degradation. A number of other disease-causing mutations in CFTR also undergo these events. Fortunately, pharmacological modulators of CFTR biogenesis can repair CFTR, permitting its folding, escape from ERAD, and function at the cell surface. In this article, we review the many cellular checkpoints that monitor CFTR biogenesis, discuss the emergence of effective treatments for CF, and highlight future areas of research on the proteostatic control of CFTR.
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17
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Banjar HH, Tuleimat L, El Seoudi AAA, Mogarri I, Alhaider S, Nizami IY, AlMaghamsi T, Alkaf SA, Moghrabi N. Genotype patterns for mutations of the cystic fibrosis transmembrane conductance regulator gene: a retrospective descriptive study from Saudi Arabia. Ann Saudi Med 2020; 40:15-24. [PMID: 32026723 PMCID: PMC7012030 DOI: 10.5144/0256-4947.2020.15] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 07/20/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) occurs in populations in Saudi Arabia and the Gulf area. Approximately 2000 known variants have been identified for the CF transmembrane conductance regulator (CTFR) gene. Screening for ten of the most common variants can detect 80% of alleles. OBJECTIVE Determine the pattern of CFTR variants in the CF population of Saudi Arabia. DESIGN A retrospective, descriptive. SETTING Tertiary care center. PATIENTS AND METHODS We examined the medical records of 396 confirmed CF patients of all age groups that were positive for a CFTR variant from the period of 1 January 1998 to 1 December 2017. MAIN OUTCOME MEASURES Zygosity, morbidity and mortality patterns of different types of CFTR variants. SAMPLE SIZE 312 families that included 396 patients. RESULTS Of 48 variants identified, 6 were novel, having not been described in the medical literature. A homozygous state was found in 283 families (90.7%) and compound heterozygosity in 23 (7.4%). Six families were heterozygous (1.9%). Median age (interquartile range) was 10.2 months (4.4 months to 5.7 years) at diagnosis and 9.7 (5.4-16.5) years at follow up. Of 396 patients, 378 patients (95.5%) survived and 18 (4.5%) died. The ten most common variants identified in descending frequency were: p.Gly473GlufsX54 in 98 alleles (16%), p.Ile1234Val in 66 alleles (11%), F508del in 64 alleles (11%), 711+1G>T in 62 alleles (10%), 3120+1G>A in 62 alleles (11%), p.His139Leuin 38 alleles (6.4%), p.Gln637Hisfs in 30 alleles (5.2%), p.Ser549Arg in 27 alleles (4.5%), p.Asn1303Lys in 14 alleles (2.3%), delExon19-21in 10 alleles (1.6%). This analysis identified 79.2% of our CFTR variants. CONCLUSION CFTR mutational patterns in our CF population are characterized by a high allelic heterogeneity. The high prevalence of homozygous variants reflects the high level of consanguinity between parents. LIMITATIONS Our CFTR screening reflected only about 80% of CF patients in Saudi Arabia. CONFLICT OF INTEREST None.
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Affiliation(s)
- Hanaa Hasan Banjar
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lin Tuleimat
- From the Department of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | | | - Ibrahim Mogarri
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sami Alhaider
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Imran Yaqoob Nizami
- From the Organ Transplant Center, King Faisal Specialist and Research Center, Riyadh, Saudi Arabia
| | - Talal AlMaghamsi
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sara Andulrahman Alkaf
- From the Biostatistic Epidemiology and Scientific Computing Department, King Faisal Center for Research and Islamic Studies, Riyadh, Saudi Arabia
| | - Nabil Moghrabi
- From the Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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18
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Banjar H, Al-Mogarri I, Nizami I, Al-Haider S, AlMaghamsi T, Alkaf S, Al-Enazi A, Moghrabi N. Geographic distribution of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Saudi Arabia. Int J Pediatr Adolesc Med 2019; 8:25-28. [PMID: 33718573 PMCID: PMC7922840 DOI: 10.1016/j.ijpam.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/18/2019] [Accepted: 12/03/2019] [Indexed: 01/17/2023]
Abstract
Introduction Cystic fibrosis (CF) has been reported before in Saudi Arabia and the Gulf area. It has been found that screening for 10 most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations can detect 80% of positive CFTR cases. Objectives To determine the geographic distribution of the most common CFTR variants in 5 regions of Saudi Arabia. Methodology A retrospective chart review of all CFTR variants conducted from January 1, 1992 to December 1, 2017. Results The ten most common CFTR mutations in the Saudi population were as follows: p.Gly473GlufsX54 (17%), p.Phe508del (12%), p.Ile1234Val (12%), 3120+1G > A (11%), 711+1G > T (9%), p.His139Leu (6%), p.Gln637Hisfs (5%), p.Ser549Arg (3%), p.N1303K (3%), and delExon19-21 (2%) along with other variants 79 (20%). In terms of the highest frequency, the c.2988+1G > A (3120+1G > A) variant was found in the eastern province (7.3%) of Saudi Arabia, the c.1418delG (p.Gly473GlufsX54) variant in the northern province (6.8%), the c.579+1G > T (711+1G > T) variant in the southern province (4.8%), the c.3700A > G (p.Ile1234Val) variant in the central province (4.8%), and c.1521_1523delCTT (p.Phe508del) variant in the western province (4.3%). Conclusion The eastern and the northern provinces have the highest prevalence of CF, with the c.2988+1G > A (3120+1G > A) and c.1418delG (p.Gly473GlufsX54) variants showing the highest distribution in the Saudi CF population, which may reflect the effect of consanguinity within the same tribe. Proper family screening and counseling should be emphasized.
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Affiliation(s)
- Hanaa Banjar
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Ibrahim Al-Mogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Imran Nizami
- Organ Transplant Center, (King Faisal Specialist Hospital and Research Center), Riyadh, Saudi Arabia
| | - Sami Al-Haider
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Talal AlMaghamsi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Jeddah, Saudi Arabia
| | - Sara Alkaf
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Abdulaziz Al-Enazi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Nabil Moghrabi
- Department of Genetics, Molecular Diagnostic Laboratory, The Research Center, KFSHRC, Riyadh, Saudi Arabia
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Zainal Abidin N, Haq IJ, Gardner AI, Brodlie M. Ataluren in cystic fibrosis: development, clinical studies and where are we now? Expert Opin Pharmacother 2017; 18:1363-1371. [DOI: 10.1080/14656566.2017.1359255] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Noreen Zainal Abidin
- Paediatric Respiratory Medicine, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust , Newcastle upon Tyne, UK
| | - Iram J. Haq
- Paediatric Respiratory Medicine, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust , Newcastle upon Tyne, UK
- Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne, UK
| | - Aaron I. Gardner
- Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne, UK
| | - Malcolm Brodlie
- Paediatric Respiratory Medicine, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust , Newcastle upon Tyne, UK
- Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne, UK
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20
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Straniero L, Soldà G, Costantino L, Seia M, Melotti P, Colombo C, Asselta R, Duga S. Whole-gene CFTR sequencing combined with digital RT-PCR improves genetic diagnosis of cystic fibrosis. J Hum Genet 2016; 61:977-984. [PMID: 27488443 DOI: 10.1038/jhg.2016.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/31/2016] [Accepted: 07/07/2016] [Indexed: 11/09/2022]
Abstract
Despite extensive screening, 1-5% of cystic fibrosis (CF) patients lack a definite molecular diagnosis. Next-generation sequencing (NGS) is making affordable genetic testing based on the identification of variants in extended genomic regions. In this frame, we analyzed 23 CF patients and one carrier by whole-gene CFTR resequencing: 4 were previously characterized and served as controls; 17 were cases lacking a complete diagnosis after a full conventional CFTR screening; 3 were consecutive subjects referring to our centers, not previously submitted to any screening. We also included in the custom NGS design the coding portions of the SCNN1A, SCNN1B and SCNN1G genes, encoding the subunits of the sodium channel ENaC, which were found to be mutated in CF-like patients. Besides 2 novel SCNN1B missense mutations, we identified 22 previously-known CFTR mutations, including 2 large deletions (whose breakpoints were precisely mapped), and novel deep-intronic variants, whose role on splicing was excluded by ex-vivo analyses. Finally, for 2 patients, compound heterozygotes for a CFTR mutation and the intron-9c.1210-34TG[11-12]T5 allele-known to be associated with decreased CFTR mRNA levels-the molecular diagnosis was implemented by measuring the residual level of wild-type transcript by digital reverse transcription polymerase chain reaction performed on RNA extracted from nasal brushing.
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Affiliation(s)
- Letizia Straniero
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Carla Colombo
- Cystic Fibrosis Center of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
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21
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Lannon CL, Hinchliffe SA, Pope JD, Ball LM, Van Velzen D. Ulceration of the Small and Large Bowel Mucosain Resection Specimens of Cystic Fibrosis Patients with Fibrosing Colonopathy. Int J Toxicol 2016. [DOI: 10.1080/109158198226765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fibrosing colonopathy (FC), observed in cystic fibrosis patients taking high-strength pancreatic enzyme preparations, is characterized by progressive obstruction of the ascending colon, with long-segment fusiform stenosis due to the deposition of submucosal fibrous tissue. The pathogenesis is uncertain, although direct toxic damage to the colonic mucosa by a constituent of such preparations has been proposed as an explanation. Mucosal defects and rectal bleeding have been observed by colonoscopy in cystic fibrosis patients at risk for and with evident FC. In a quantitative, observational study, mucosal defects were studied in six ileo-cecal resection specimens with FC confirmed by three independent pathologists' review. Representative areas (2.5-cm-long segments) were taken of terminal ileum, cecal colon, and ascending colon both at the site of most severe stenosis and at the most distal ascending colon site available; after processing with paraffin, the areas were serially sectioned at 500-μm intervals for the preparation of 5-μm sections for microscopical assessment. Marking in each section the area affected by (repairing) ulceration, and using three-dimensional reconstructions of the bowel lining, individual mucosal lesions were reconstructed. Using the reconstructed bowels, point scoring analysis of the area fraction affected by ulceration as well as the area of individual lesions was carried out. Lesions of variable age were found in the terminal
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Affiliation(s)
- C. L. Lannon
- Department of Pathology, Dalhousie University, IWK Grace Health Centre, Halifax, Nova Scotia, Canada
| | - S. A. Hinchliffe
- Department of Pathology, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne, United Kingdom
| | - J. D. Pope
- MRC Research Centre, University of Oxford, Oxford, United Kingdom
| | - L. M. Ball
- Department of Pathology, Dalhousie University, IWK Grace Health Centre, Halifax, Nova Scotia, Canada
| | - D. Van Velzen
- Department of Pathology, Dalhousie University, IWK Grace Health Centre, Halifax, Nova Scotia, Canada
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22
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Characterizing diverse orthologues of the cystic fibrosis transmembrane conductance regulator protein for structural studies. Biochem Soc Trans 2015; 43:894-900. [DOI: 10.1042/bst20150081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an ion channel, the cystic fibrosis transmembrane conductance regulator (CFTR) protein occupies a unique niche within the ABC family. Orthologues of CFTR are extant throughout the animal kingdom from sharks to platypods to sheep, where the osmoregulatory function of the protein has been applied to differing lifestyles and diverse organ systems. In humans, loss-of-function mutations to CFTR cause the disease cystic fibrosis, which is a significant health burden in populations of white European descent. Orthologue screening has proved fruitful in the pursuit of high-resolution structural data for several membrane proteins, and we have applied some of the princples developed in previous studies to the expression and purification of CFTR. We have overexpressed this protein, along with evolutionarily diverse orthologues, in Saccharomyces cerevisiae and developed a purification to isolate it in quantities sufficient for structural and functional studies.
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Micoud J, Chauvet S, Scheckenbach KEL, Alfaidy N, Chanson M, Benharouga M. Involvement of the heterodimeric interface region of the nucleotide binding domain-2 (NBD2) in the CFTR quaternary structure and membrane stability. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2420-31. [PMID: 26083625 DOI: 10.1016/j.bbamcr.2015.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 11/27/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is the only member of the ATP-binding cassette (ABC) superfamily that functions as a chloride channel. The predicted structure of CFTR protein contains two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD1 and NBD2). The opening of the Cl- channel is directly linked to ATP-driven tight dimerization of CFTR's NBD1 and NBD2 domains. The presence of a heterodimeric interfaces (HI) region in NBD1 and NBD2 generated a head to tail orientation necessary for channel activity. This process was also suggested to promote important conformational changes in the associated transmembrane domains of CFTR, which may impact the CFTR plasma membrane stability. To better understand the role of the individual HI region in this process, we generated recombinant CFTR protein with suppressed HI-NBD1 and HI-NBD2. Our results indicate that HI-NBD2 deletion leads to the loss of the dimerization profile of CFTR that affect its plasma membrane stability. We conclude that, in addition to its role in Cl- transport, HI-NBD2 domain confers membrane stability of CFTR by consolidating its quaternary structure through interactions with HI-NBD1 region.
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Affiliation(s)
- Julien Micoud
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | - Sylvain Chauvet
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France
| | | | - Nadia Alfaidy
- Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1036 Grenoble, France
| | - Marc Chanson
- Laboratory of Clinical Investigation III, Geneva University Hospitals and University of Geneva, 1211 Geneva, Switzerland
| | - Mohamed Benharouga
- Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, Grenoble, France; Commissariat à l'Energie Atomique (CEA), DSV-iRTSV, Grenoble, France; Grenoble Alpes Université (GAU), Grenoble 1, France.
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Abstract
Despite remarkable progress in the identification of mutations that drive genetic disorders, progress in understanding the effect of genetic background on the penetrance and expressivity of causal alleles has been modest, in part because of the methodological challenges in identifying genetic modifiers. Nonetheless, the progressive discovery of modifier alleles has improved both our interpretative ability and our analytical tools to dissect such phenomena. In this review, we analyze the genetic properties and behaviors of modifiers as derived from studies in patient populations and model organisms and we highlight conceptual and technological tools used to overcome some of the challenges inherent in modifier mapping and cloning. Finally, we discuss how the identification of these modifiers has facilitated the elucidation of biological pathways and holds the potential to improve the clinical predictive value of primary causal mutations and to develop novel drug targets.
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Affiliation(s)
- Maria Kousi
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710
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Crane AM, Kramer P, Bui JH, Chung WJ, Li XS, Gonzalez-Garay ML, Hawkins F, Liao W, Mora D, Choi S, Wang J, Sun HC, Paschon DE, Guschin DY, Gregory PD, Kotton DN, Holmes MC, Sorscher EJ, Davis BR. Targeted correction and restored function of the CFTR gene in cystic fibrosis induced pluripotent stem cells. Stem Cell Reports 2015; 4:569-77. [PMID: 25772471 PMCID: PMC4400651 DOI: 10.1016/j.stemcr.2015.02.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/13/2022] Open
Abstract
Recently developed reprogramming and genome editing technologies make possible the derivation of corrected patient-specific pluripotent stem cell sources-potentially useful for the development of new therapeutic approaches. Starting with skin fibroblasts from patients diagnosed with cystic fibrosis, we derived and characterized induced pluripotent stem cell (iPSC) lines. We then utilized zinc-finger nucleases (ZFNs), designed to target the endogenous CFTR gene, to mediate correction of the inherited genetic mutation in these patient-derived lines via homology-directed repair (HDR). We observed an exquisitely sensitive, homology-dependent preference for targeting one CFTR allele versus the other. The corrected cystic fibrosis iPSCs, when induced to differentiate in vitro, expressed the corrected CFTR gene; importantly, CFTR correction resulted in restored expression of the mature CFTR glycoprotein and restoration of CFTR chloride channel function in iPSC-derived epithelial cells.
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Affiliation(s)
- Ana M Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Philipp Kramer
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jacquelin H Bui
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Wook Joon Chung
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, AL 35294, USA
| | - Xuan Shirley Li
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Manuel L Gonzalez-Garay
- Center for Molecular Imaging, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Finn Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Wei Liao
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Daniela Mora
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Sangbum Choi
- Division of Clinical and Translational Sciences, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jianbin Wang
- Sangamo BioSciences, Inc., Richmond, CA 94804, USA
| | - Helena C Sun
- Sangamo BioSciences, Inc., Richmond, CA 94804, USA
| | | | | | | | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | - Eric J Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, AL 35294, USA
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA.
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Abstract
OBJECTIVE Mutations in the cationic trypsinogen (PRSS1), cystic fibrosis transmembrane conductance regulator (CFTR), serine protease inhibitor Kazal type 1 (SPINK1), and chymotrypsin C (CTRC) genes are associated with an elevated risk for chronic pancreatitis, which is a known risk factor for pancreatic cancer (PC). Therefore, we analyzed whether PRSS1, CFTR, SPINK1, and/or CTRC mutations are associated with pancreatic adenocarcinoma. METHODS The study cohort was composed of 121 PC patients, of whom 74 were classified as having chronic pancreatitis, 102 patients with idiopathic chronic pancreatitis, and 130 as healthy controls. Mutation analyses for the CFTR, SPINK1, PRSS1, and CTRC genes were performed for the presence of the most common mutations. RESULTS The frequency of CFTR mutations in patients with PC was not significantly different in comparison with healthy controls and controls with pancreatitis. The SPINK1 mutation frequency was significantly decreased in patients with PC in comparison with patients with idiopathic pancreatitis but varied not significantly in comparison with healthy controls. None of the selected 121 PC samples showed a pancreatitis-predisposing mutation in the PRSS1 or CTRC gene. CONCLUSIONS Mutations in the genes CFTR, SPINK1, PRSS1, and CTRC do not seem to significantly increase the risk for pancreatic adenocarcinoma.
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27
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Complement yourself: Transcomplementation rescues partially folded mutant proteins. Biophys Rev 2014; 6:169-180. [PMID: 24949105 DOI: 10.1007/s12551-014-0137-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cystic Fibrosis (CF) is an autosomal disease associated with malfunction in fluid and electrolyte transport across several mucosal membranes. The most common mutation in CF is an in-frame three-base pair deletion that removes a phenylalanine at position 508 in the first nucleotide-binding domain of the cystic fibrosis conductance regulator (CFTR) chloride channel. This mutation has been studied extensively and leads to biosynthetic arrest of the protein in the endoplasmic reticulum and severely reduced channel activity. This review discusses a novel method of rescuing ΔF508 with transcomplementation, which occurs when smaller fragments of CFTR containing the wild-type nucleotide binding domain are co-expressed with the ΔF508 deletion mutant. Transcomplementation rescues the processing and channel activity of ΔF508 and reduces its rate of degradation in airway epithelial cells. To apply transcomplementation as a therapy would require that the cDNA encoding the truncated CFTR be delivered to cells. We also discuss a gene therapeutic approach based on delivery of a truncated form of CFTR to airway cells using adeno-associated viral vectors.
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Muthuswamy S, Agarwal S, Awasthi S, Singh S, Dixit P, Maurya N, Choudhuri G. Spectrum and distribution of CFTR gene mutations in asthma and chronic pancreatitis cases of North Indian population. Gene 2014; 539:125-31. [PMID: 24440239 DOI: 10.1016/j.gene.2014.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 01/01/2014] [Accepted: 01/03/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Cystic fibrosis transmembrane conductance regulator (CFTR) gene accounts for an autosomal recessive condition called cystic fibrosis (CF). In the Indian subcontinent, CF and its related diseases are under-diagnosed by the medical community due to poor knowledge of the disease and its confounding diagnosis, and also due to poor medical facilities available for these patients, thus causing an increased infant mortality rate with a low life expectancy in general. The aim of the study was to document the spectrum and distribution of CFTR mutations in controls, asthma and chronic pancreatitis cases of North India. METHODS A total of 800 subjects including 400 controls, 250 asthma cases and150 chronic pancreatitis cases were analyzed for 6 mutations (F508del, G542X, G551D, R117H, W1282X, and S549N) and IVS8 Tn polymorphism. RESULTS Out of 800 subjects, 18% [asthma - 24% (n=250), CP - 29.33% (n=150) cases and controls - 9.3% (n=400)] were positive for heterozygous mutation, 0.8% of the (n=250) asthmatic cases (n=250) were homozygous for IVS8 T5 polymorphism while no subjects were found positive for W1282X mutation. T5 polymorphism was more common in asthmatic cases while F508del mutation in chronic pancreatitis cases. The carrier frequency of F508del, G542X, G551D, R117H, S549N and T5 was 0.015, 0.025, 0.02, 0.005, 0.005, and 0.022 respectively. The cumulative carrier frequency was 0.093. CONCLUSION CFTR mutations were underestimated in Indian population. The present study will serve in establishment of genetic screening and prenatal setup for Indian population.
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Affiliation(s)
| | - Sarita Agarwal
- Deptarment of Medical Genetics, SGPGIMS, Lucknow 226014, India.
| | | | - Shweta Singh
- Deptarment of Medical Genetics, SGPGIMS, Lucknow 226014, India
| | | | - Nutan Maurya
- Department of Pediatrics, KGMU, Lucknow 226003, India
| | - Gourdas Choudhuri
- Institute of Digestive and Hepatobiliary Sciences, Medanta Medcity, New Delhi, India
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Abou Alaiwa MH, Beer AM, Pezzulo AA, Launspach JL, Horan RA, Stoltz DA, Starner TD, Welsh MJ, Zabner J. Neonates with cystic fibrosis have a reduced nasal liquid pH; a small pilot study. J Cyst Fibros 2014; 13:373-7. [PMID: 24418186 DOI: 10.1016/j.jcf.2013.12.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Disrupted HCO3(-) transport and reduced airway surface liquid (ASL) pH in cystic fibrosis (CF) may initiate airway disease. We hypothesized that ASL pH is reduced in neonates with CF. METHODS In neonates with and without CF, we measured pH of nasal ASL. We also measured nasal pH in older children and adults. RESULTS In neonates with CF, nasal ASL (pH5.2 ± 0.3) was more acidic than in non-CF neonates (pH6.4 ± 0.2). In contrast, nasal pH of CF children and adults was similar to values measured in people without CF. CONCLUSIONS At an age when infection, inflammation and airway wall remodeling are minimal, neonates with CF had an acidic nasal ASL compared to babies without CF. The CF:non-CF pH difference disappeared in older individuals, perhaps because secondary manifestations of disease increase ASL pH. These results aid understanding of CF pathogenesis and suggest opportunities for therapeutic intervention and monitoring of disease.
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Affiliation(s)
- Mahmoud H Abou Alaiwa
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alison M Beer
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alejandro A Pezzulo
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Janice L Launspach
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Rebecca A Horan
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - David A Stoltz
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Timothy D Starner
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Michael J Welsh
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Howard Hughes Medical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Joseph Zabner
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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30
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Dekkers JF, Wiegerinck CL, de Jonge HR, Bronsveld I, Janssens HM, de Winter-de Groot KM, Brandsma AM, de Jong NWM, Bijvelds MJC, Scholte BJ, Nieuwenhuis EES, van den Brink S, Clevers H, van der Ent CK, Middendorp S, Beekman JM. A functional CFTR assay using primary cystic fibrosis intestinal organoids. Nat Med 2013; 19:939-45. [PMID: 23727931 DOI: 10.1038/nm.3201] [Citation(s) in RCA: 711] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 12/20/2012] [Indexed: 01/02/2023]
Abstract
We recently established conditions allowing for long-term expansion of epithelial organoids from intestine, recapitulating essential features of the in vivo tissue architecture. Here we apply this technology to study primary intestinal organoids of people suffering from cystic fibrosis, a disease caused by mutations in CFTR, encoding cystic fibrosis transmembrane conductance regulator. Forskolin induces rapid swelling of organoids derived from healthy controls or wild-type mice, but this effect is strongly reduced in organoids of subjects with cystic fibrosis or in mice carrying the Cftr F508del mutation and is absent in Cftr-deficient organoids. This pattern is phenocopied by CFTR-specific inhibitors. Forskolin-induced swelling of in vitro-expanded human control and cystic fibrosis organoids corresponds quantitatively with forskolin-induced anion currents in freshly excised ex vivo rectal biopsies. Function of the CFTR F508del mutant protein is restored by incubation at low temperature, as well as by CFTR-restoring compounds. This relatively simple and robust assay will facilitate diagnosis, functional studies, drug development and personalized medicine approaches in cystic fibrosis.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
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Cotten SW, Bender LM, Willis MS. Multiple Positive Sweat Chloride Tests in an Infant Asymptomatic for Cystic Fibrosis. Lab Med 2012. [DOI: 10.1309/lm19fqyqefowut9x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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32
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Pagano MA, Marin O, Cozza G, Sarno S, Meggio F, Treharne KJ, Mehta A, Pinna LA. Cystic fibrosis transmembrane regulator fragments with the Phe508 deletion exert a dual allosteric control over the master kinase CK2. Biochem J 2010; 426:19-29. [PMID: 19925455 PMCID: PMC3026963 DOI: 10.1042/bj20090813] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cystic fibrosis mostly follows a single Phe508 deletion in CFTR (cystic fibrosis transmembrane regulator) (CFTRDeltaF508), thereby causing premature fragmentation of the nascent protein with concomitant alterations of diverse cellular functions. We show that CK2, the most pleiotropic protein kinase, undergoes allosteric control of its different cellular forms in the presence of short CFTR peptides encompassing the Phe508 deletion: these CFTRDeltaF508 peptides drastically inhibit the isolated catalytic subunit (alpha) of the kinase and yet up-regulate the holoenzyme, composed of two catalytic and two non-catalytic (beta) subunits. Remarkable agreement between in silico docking and our biochemical data point to different sites for the CFTRDeltaF508 peptide binding on isolated CK2alpha and on CK2beta assembled into the holoenzyme, suggesting that CK2 targeting may be perturbed in cells expressing CFTRDeltaF508; this could shed light on some pleiotropic aspects of cystic fibrosis disease.
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Affiliation(s)
- Mario A. Pagano
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
- Venetian Institute for Molecular Medicine (VIMM), via Orus 2, 35129 Padova, Italy
| | - Oriano Marin
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
- Venetian Institute for Molecular Medicine (VIMM), via Orus 2, 35129 Padova, Italy
| | - Giorgio Cozza
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Stefania Sarno
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
- Venetian Institute for Molecular Medicine (VIMM), via Orus 2, 35129 Padova, Italy
| | - Flavio Meggio
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Kate J. Treharne
- Division of Medical Sciences, Centre for Cardiovascular and Lung Biology, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, Scotland, U.K
| | - Anil Mehta
- Division of Medical Sciences, Centre for Cardiovascular and Lung Biology, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, Scotland, U.K
| | - Lorenzo A. Pinna
- Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, viale G. Colombo 3, 35131 Padova, Italy
- Venetian Institute for Molecular Medicine (VIMM), via Orus 2, 35129 Padova, Italy
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Sharma N, Acharya N, Singh S, Singh M, Sharma U, Prasad R. Heterogenous spectrum of CFTR gene mutations in Indian patients with congenital absence of vas deferens. Hum Reprod 2009; 24:1229-36. [DOI: 10.1093/humrep/den500] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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35
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Abstract
PURPOSE Congenital bilateral absence of the vas deferens is a pathologic condition associated with normal spermatogenesis, azoospermia, and lack of both vasa deferentia. A significant association between mutations in the cystic fibrosis transmembrane conductance regulator gene among men with congenital bilateral absence of the vas deferens has been established. The objective of this study was to determine whether the F508C variant in the cystic fibrosis transmembrane conductance regulator gene has a significant effect on congenital bilateral absence of the vas deferens prevalence, when present in conjunction with a second cystic fibrosis transmembrane conductance regulator disease causing mutation. METHODS AND RESULTS We compared the frequency of F508C in male subjects submitted for diagnostic testing on suspicion of cystic fibrosis or during cystic fibrosis carrier screening, to men with a clinical diagnosis of congenital bilateral absence of the vas deferens. Although frequencies of F508C did not vary significantly between 850 individuals undergoing cystic fibrosis carrier screening and those submitted for diagnostic testing on suspicion of cystic fibrosis, the frequency of F508C in the congenital bilateral absence of the vas deferens population was significantly higher than expected (chi2 = 6.95, corrected P = 0.0486). CONCLUSION We conclude that the F508C variant in cystic fibrosis transmembrane conductance regulator may represent a pathogenic defect and lead to congenital bilateral absence of the vas deferens when combined with a second cystic fibrosis transmembrane conductance regulator mutation.
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Implication of the cystic fibrosis transmembrane conductance regulator gene in infertile family members of Indian CF patients. Biochem Genet 2008; 46:847-56. [PMID: 18810634 DOI: 10.1007/s10528-008-9199-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 07/15/2008] [Indexed: 10/21/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. Among males with CF, 95% are infertile due to congenital absence of the vas deferens. We investigated the role of family history of infertility among CF subjects and characterized mutations in them. Among 50 CF subjects, four had a family history of infertility. A homozygous c.1521_1523delCTT mutation was detected in one, two had a compound heterozygous genotype (c.1521_1523delCTT/c.3717 + 10 kbC>T), and c.1521_1523delCTT mutation was identified on one allele of fourth CF subject. Genetic analysis of each infertile family members of CF subjects revealed the c.1521_1523delCTT mutation on one allele; however, no mutation could be identified on other allele. Haplotype analysis of the infertile family members showed that at least one of the alleles shared the same haplotype as that of the index case. It is suggested that the CFTR gene is implicated in the infertile members of the CF families. Failure to detect mutations on the other allele by SSCP analysis demands direct gene sequencing to detect mutations in the intronic or promoter region.
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37
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Sharma N, Singh M, Kaur G, Thapa BR, Prasad R. Identification and characterization of CFTR gene mutations in Indian CF patients. Ann Hum Genet 2008; 73:26-33. [PMID: 18782298 DOI: 10.1111/j.1469-1809.2008.00477.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study was performed on Indian CF patients (n = 50) to investigate the spectrum of mutations in the CFTR gene and their association with intragenic and extragenic marker haplotypes. We report identification of 14 previously known and eight novel mutations, namely 3986-3987delC, 876-6del4, 1792InsA, L69H, S158N, Q493L, I530L and E1329Q. The frequency of delta F508 was found to be 27%. Absolute linkage between delta F508 and the KM.19-GATT-TUB9-M470V-T854T haplotype (2-2-1-1-1) predicts a relatively recent appearance of delta F508 in Indian CF patients. Low frequency of delta F508 mutation and detection of eight novel and thirteen rare mutations reflect a heterogeneous spectrum of mutations in Indian CF patients. Failure to detect mutations in 34% of alleles indicates the possible presence of gross deletions involving one or more exons or may indicate the location of the molecular defects in either the noncoding parts of the gene or in the promoter region, which warrants analysis of those regions.
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Affiliation(s)
- N Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India-160012
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Frenţescu L, Brownsell E, Hinks J, Malone G, Shaw H, Budişan L, Bulman M, Schwarz M, Pop L, Filip M, Tomescu E, Moşescu S, Popa I, Benga G. The study of cystic fibrosis transmembrane conductance regulator gene mutations in a group of patients from Romania. J Cyst Fibros 2008; 7:423-8. [DOI: 10.1016/j.jcf.2008.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/28/2008] [Accepted: 03/11/2008] [Indexed: 11/16/2022]
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39
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Horvatovich K, Örkényi M, Bíró É, Pongrácz K, Kisfali P, Talián G, Csöngei V, Járomi L, Sáfrány E, Harangi F, Sulyok E, Melegh B. Pseudo-Bartter syndrome in a case of cystic fibrosis caused by C1529G and G3978A compound heterozygosity. Orv Hetil 2008; 149:325-8. [DOI: 10.1556/oh.2008.28239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A beteg nyolc hónapos életkorban került vizsgálatra pár napja észlelt étvágytalanság és mérsékelt elesettség miatt. Laboratóriumi eredményei súlyos hypokalaemiát, hyponatraemiát és hypochloraemiás alkalosist mutattak. Mivel az alacsony szérumelektrolit-értékeknek megfelelően alacsony vizeletelektrolit-ürítés és emelkedett renin-, aldoszteronszint volt észlelhető, az állapot pszeudo-Bartter-szindrómának felelt meg. Felvetődött a mucoviscidosis diagnózisa, ezt az emelkedett verejtékkloridszint igazolta. A cisztás fibrosis transzmembrán regulátor gén 27 exonjának szekvenálása során a szerzők két, ritkán előforduló mutációt detektáltak kevert heterozigóta formában, az egyik a 10. exonban talált C1529G-, a másik a 20. exonban azonosított G3978A-mutáció. Ezek a cserék a mutáció helyén stopkodon létrejöttéhez vezetnek mindkét allélon (S466X és W1282X). A mutációk közül az első hordozását az egyébként tünetmentes anyában, az utóbbiét a szintén panaszmentes apában sikerült kimutatni. A gyermekben és az anyában a fentiek mellett a 17-es exonban még egy G3341A-mutációt is találtak, ami elméletileg R1070Q-aminosav-cserével is jár. A gyakorlatban azonban ez nem következhet be a gyermekben a C1529G-mutációval társuló stopkodon kialakulása miatt, így következménnyel sem kell számolni. Ezek az eltérések ΔF508-mutációval kombinálva eltérő súlyosságú tüneteket okoznak a különböző betegekben; együttes előfordulásukról azonban a szerzőknek nincs ismeretük. A beteg másfél éves nyomon követése során a kórlefolyás benignusnak tűnt.
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Affiliation(s)
- Katalin Horvatovich
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | - Mária Örkényi
- 2 Baranya Megyei Kerpel-Fronius Ödön Gyermekkórház Pécs
| | - Éva Bíró
- 2 Baranya Megyei Kerpel-Fronius Ödön Gyermekkórház Pécs
| | - Kálmán Pongrácz
- 3 Vas Megyei Markusovszky Lajos Kórház, Egyetemi Oktatókórház Szombathely
| | - Péter Kisfali
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | - Gábor Talián
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | - Veronika Csöngei
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | - Luca Járomi
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | - Enikő Sáfrány
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
| | | | - Endre Sulyok
- 2 Baranya Megyei Kerpel-Fronius Ödön Gyermekkórház Pécs
| | - Béla Melegh
- 1 Pécsi Tudományegyetem, Általános Orvostudományi Kar Orvosi Genetikai és Gyermekfejlődéstani Intézet Pécs Szigeti u. 12. 7624
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Socher E, Jarikote DV, Knoll A, Röglin L, Burmeister J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 2008; 375:318-30. [PMID: 18249184 DOI: 10.1016/j.ab.2008.01.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/08/2008] [Accepted: 01/08/2008] [Indexed: 11/19/2022]
Abstract
The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.
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Affiliation(s)
- Elke Socher
- Institut für Chemie, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany
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Bompadre SG, Li M, Hwang TC. Mechanism of G551D-CFTR (cystic fibrosis transmembrane conductance regulator) potentiation by a high affinity ATP analog. J Biol Chem 2007; 283:5364-9. [PMID: 18167357 DOI: 10.1074/jbc.m709417200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel gated by ATP binding and hydrolysis at its nucleotide binding domains (NBD). The NBDs dimerize in a head-to-tail configuration, forming two ATP binding pockets (ABP) with the ATP molecules buried at the dimer interface. Previous studies have indicated that ABP2, formed by the Walker A and B motifs of NBD2 and the signature sequence of NBD1, is the site critical for the ATP-dependent opening of CFTR. The G551D mutation in ABP2, the third most common cystic fibrosis-associated mutation, abolishes ATP-dependent gating, resulting in an open probability that is approximately 100-fold lower than that of wild-type channels. Interestingly, we found that the ATP analog N6-(2-phenylethyl)-ATP (P-ATP) increases G551D currents mainly by increasing the open time of the channel. This effect is reduced when P-ATP is applied together with ATP, suggesting a competition between ATP and P-ATP for a common binding site. Introducing mutations that lower the nucleotide binding affinity at ABP2 did not alter significantly the effects of P-ATP on G551D-CFTR, whereas an equivalent mutation at ABP1 (consisting of the Walker A and B motifs of NBD1 and the signature sequence of NBD2) dramatically decreased the potency of P-ATP, indicating that ABP1 is the site where P-ATP binds to increase the activity of G551D-CFTR. These results substantiate the idea that nucleotide binding at ABP1 stabilizes the open channel conformation. Our observation that P-ATP enhances the G551D activity by binding at ABP1 implicates that ABP1 can potentially be a target for drugs to bind and increase the channel activity.
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Affiliation(s)
- Silvia G Bompadre
- Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
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Ban H, Inoue M, Griesenbach U, Munkonge F, Chan M, Iida A, Alton EWFW, Hasegawa M. Expression and maturation of Sendai virus vector-derived CFTR protein: functional and biochemical evidence using a GFP-CFTR fusion protein. Gene Ther 2007; 14:1688-94. [PMID: 17898794 DOI: 10.1038/sj.gt.3303032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sendai virus (SeV) vector has been shown to efficiently transduce airway epithelial cells. As a precursor to the potential use of this vector for cystic fibrosis (CF) gene therapy, the correct maturation of the SeV vector-derived CF transmembrane conductance regulator (CFTR) protein was examined using biochemical and functional analyses. We constructed a recombinant SeV vector, based on the fusion (F) gene-deleted non-transmissible SeV vector, carrying the GFP-CFTR gene in which the N terminus of CFTR was fused to green fluorescence protein (GFP). This vector was recovered and propagated to high titers in the packaging cell line. Western blotting using an anti-GFP antibody detected both the fully glycosylated (mature) and the core-glycosylated (immature) proteins, indicating that SeV vector-derived GFP-CFTR was similar to endogenous CFTR. We also confirmed the functional channel activity of GFP-CFTR in an iodide efflux assay. The efficient expression of GFP-CFTR, and its apical surface localization, were observed in both MDCK cells in vitro, and in the nasal epithelium of mice in vivo. We concluded that recombinant SeV vector, a cytoplasmically maintained RNA vector, is able to direct production of a correctly localized, mature form of CFTR, suggesting the value of this vector for studies of CF gene therapy.
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Affiliation(s)
- H Ban
- DNAVEC Corporation, Tsukuba-shi, Ibaraki, Japan
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Luder AS, Mandel H, Khayat M, Gurevich I, Frankel P, Rivlin J, Falik-Zaccai TC. Chronic lung disease and cystic fibrosis phenotype in prolidase deficiency: a newly recognized association. J Pediatr 2007; 150:656-8, 658.e1. [PMID: 17517257 DOI: 10.1016/j.jpeds.2007.03.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 02/02/2007] [Accepted: 03/16/2007] [Indexed: 10/23/2022]
Abstract
Six families with prolidase deficiency (PD) and chronic lung disease are reported, a previously unrecognized association. In one family with a classic cystic fibrosis (CF) phenotype, no evidence for CF Transmembrane Conductance Regulator (CFTR)-related mutations could be found. Chronic lung disease and CFTR-mutation negative CF may be associated with PD.
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Affiliation(s)
- A S Luder
- Department of Pediatrics and Genetics, Ziv Medical Center, Safed, Israel.
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Bompadre SG, Sohma Y, Li M, Hwang TC. G551D and G1349D, two CF-associated mutations in the signature sequences of CFTR, exhibit distinct gating defects. J Gen Physiol 2007; 129:285-98. [PMID: 17353351 PMCID: PMC2151620 DOI: 10.1085/jgp.200609667] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 02/21/2007] [Indexed: 11/21/2022] Open
Abstract
Mutations in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR) result in cystic fibrosis (CF). CFTR is a chloride channel that is regulated by phosphorylation and gated by ATP binding and hydrolysis at its nucleotide binding domains (NBDs). G551D-CFTR, the third most common CF-associated mutation, has been characterized as having a lower open probability (Po) than wild-type (WT) channels. Patients carrying the G551D mutation present a severe clinical phenotype. On the other hand, G1349D, also a mutant with gating dysfunction, is associated with a milder clinical phenotype. Residues G551 and G1349 are located at equivalent positions in the highly conserved signature sequence of each NBD. The physiological importance of these residues lies in the fact that the signature sequence of one NBD and the Walker A and B motifs from the other NBD form the ATP-binding pocket (ABP1 and ABP2, named after the location of the Walker A motif) once the two NBDs dimerize. Our studies show distinct gating characteristics for these mutants. The G551D mutation completely eliminates the ability of ATP to increase the channel activity, and the observed activity is approximately 100-fold smaller than WT-CFTR. G551D-CFTR does not respond to ADP, AMP-PNP, or changes in [Mg(2+)]. The low activity of G551D-CFTR likely represents the rare ATP-independent gating events seen with WT channels long after the removal of ATP. G1349D-CFTR maintains ATP dependence, albeit with a Po approximately 10-fold lower than WT. Interestingly, compared to WT results, the ATP dose-response relationship of G1349D-CFTR is less steep and shows a higher apparent affinity for ATP. G1349D data could be well described by a gating model that predicts that binding of ATP at ABP1 hinders channel opening. Thus, our data provide a quantitative explanation at the single-channel level for different phenotypes presented by patients carrying these two mutations. In addition, these results support the idea that CFTR's two ABPs play distinct functional roles in gating.
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Affiliation(s)
- Silvia G Bompadre
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO 65211, USA
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Ciminelli BM, Bonizzato A, Bombieri C, Pompei F, Gabaldo M, Ciccacci C, Begnini A, Holubova A, Zorzi P, Piskackova T, Macek M, Castellani C, Modiano G, Pignatti PF. Highly preferential association of NonF508del CF mutations with the M470 allele. J Cyst Fibros 2007; 6:15-22. [PMID: 16784904 DOI: 10.1016/j.jcf.2006.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 04/27/2006] [Accepted: 04/28/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND On the basis of previous findings on random individuals, we hypothesized a preferential association of CF causing mutations with the M allele of the M470V polymorphic site of the CFTR gene. METHODS We have determined the M/V-CF mutation haplotype in a series of 201 North East Italian and 73 Czech CF patients who were not F508del homozygotes, as F508del was already known to be fully associated with the M allele. RESULTS Out of 358 not F508del CF genes, 84 carried the V allele and 274 the less common M allele. In the N-E Italian population, MM subjects have a risk of carrying a CF causing mutation 6.9x greater than VV subjects when F508del is excluded and 15.4x when F508del is included. In the Czech population a similar, although less pronounced, association is observed. CONCLUSIONS Besides the possible biological significance of this association, the possibility of exploiting it for a pilot screening program has been explored in a local North East Italian population for which CF patients were characterized for their CF mutation. General M470V genotyping followed by common CF mutation screening limited to couples in which each partner carries at least one M allele would need testing only 39% of the couples, which contribute 89% of the total risk, with a cost benefit.
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Affiliation(s)
- B M Ciminelli
- Department of Biology, University of Roma-Tor Vergata, Via della Ricerca Scientifica, s.n.c. 00133 Rome, and Cystic Fibrosis Centre, Hospital of Verona, Italy.
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Reboul MP, Tandonnet O, Biteau N, Belet-de Putter C, Rebouissoux L, Moradkhani K, Vu PY, Saura R, Arveiler B, Lacombe D, Taine L, Iron A. Mosaic maternal uniparental isodisomy for chromosome 7q21-qter. Clin Genet 2006; 70:207-13. [PMID: 16922723 DOI: 10.1111/j.1399-0004.2006.00664.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uniparental disomy (UPD) for several human chromosomes is associated with clinical abnormalities. We report the case of a 2-year-old boy with severe intrauterine and post-natal growth retardation (IUGR/PNGR) and highly variable sweat chloride concentrations. The patient was identified as heterozygous for the F508del mutation of the CFTR (cystic fibrosis transmembrane conductance regulator) gene. Unexpectedly, the signal corresponding to the maternally inherited F508del allele appeared much more intense than the paternally derived wild allele. Molecular analysis including polymorphic marker studies, microsatellites and single-nucleotide polymorphisms subsequently showed that the boy was a carrier of a de novo mosaic maternal isodisomy of a chromosome 7 segment while there was a biparental inheritance of the rest of the chromosome. This is the first report of a mosaic partial UPD7. The matUPD7 segment at 7q21-qter extends for 72.7 Mb. The karyotype (550 bands) of our patient was normal, and fluorescence in situ hybridization with probes mapping around the CFTR gene allowed us to rule out a partial duplication. The detection of this chromosomal rearrangement confirms the hypothesis that the 7q31-qter segment is a candidate for the localization of human imprinted genes involved in the control of IUGR and PNGR. It also emphasizes the importance of searching for UPD7 in severe, isolated and unexplained IUGR and PNGR.
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Affiliation(s)
- M-P Reboul
- Service de Génétique Médicale, Hopital Pellegrin, Laboratoire de Génétique Humaine, Développement et Cancer, Université Victor Segalen Bordeaux 2, France.
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Dawson RJP, Locher KP. Structure of a bacterial multidrug ABC transporter. Nature 2006; 443:180-5. [PMID: 16943773 DOI: 10.1038/nature05155] [Citation(s) in RCA: 972] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 08/11/2006] [Indexed: 01/30/2023]
Abstract
Multidrug transporters of the ABC family facilitate the export of diverse cytotoxic drugs across cell membranes. This is clinically relevant, as tumour cells may become resistant to agents used in chemotherapy. To understand the molecular basis of this process, we have determined the 3.0 A crystal structure of a bacterial ABC transporter (Sav1866) from Staphylococcus aureus. The homodimeric protein consists of 12 transmembrane helices in an arrangement that is consistent with cross-linking studies and electron microscopic imaging of the human multidrug resistance protein MDR1, but critically different from that reported for the bacterial lipid flippase MsbA. The observed, outward-facing conformation reflects the ATP-bound state, with the two nucleotide-binding domains in close contact and the two transmembrane domains forming a central cavity--presumably the drug translocation pathway--that is shielded from the inner leaflet of the lipid bilayer and from the cytoplasm, but exposed to the outer leaflet and the extracellular space.
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Affiliation(s)
- Roger J P Dawson
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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49
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Schrijver I, Ramalingam S, Sankaran R, Swanson S, Dunlop CLM, Keiles S, Moss RB, Oehlert J, Gardner P, Wassman ER, Kammesheidt A. Diagnostic testing by CFTR gene mutation analysis in a large group of Hispanics: novel mutations and assessment of a population-specific mutation spectrum. J Mol Diagn 2005; 7:289-99. [PMID: 15858154 PMCID: PMC1867528 DOI: 10.1016/s1525-1578(10)60557-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Characterization of CFTR mutations in the U.S. Hispanic population is vital to early diagnosis, genetic counseling, patient-specific treatment, and the understanding of cystic fibrosis (CF) pathogenesis. The mutation spectrum in Hispanics, however, remains poorly defined. A group of 257 self-identified Hispanics with clinical manifestations consistent with CF were studied by temporal temperature gradient electrophoresis and/or DNA sequencing. A total of 183 mutations were identified, including 14 different amino acid-changing novel variants. A significant proportion (78/85) of the different mutations identified would not have been detected by the ACMG/ACOG-recommended 25-mutation screening panel. Over one third of the mutations (27/85) occurred with a relative frequency >1%, which illustrates that the identified mutations are not all rare. This is supported by a comparison with other large CFTR studies. These results underscore the disparity in mutation identification between Caucasians and Hispanics and show utility for comprehensive diagnostic CFTR mutation analysis in this population.
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Affiliation(s)
- Iris Schrijver
- Department of Pathology, L235, Stanford University Medical Center, Stanford, CA 94305, USA.
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May JP, Brown LJ, van Delft I, Thelwell N, Harley K, Brown T. Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR. Org Biomol Chem 2005; 3:2534-42. [PMID: 15999185 DOI: 10.1039/b504759e] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A non-fluorescent quencher, based on the diaminoanthraquinone Disperse Blue 3, has been incorporated into oligonucleotides at the 5'-end, the 3'-end and internally as a thymidine derivative. Fluorimetry and fluorogenic real-time PCR experiments demonstrate that the quencher is effective with a wide range of fluorescent dyes. The anthraquinone moiety increases the melting temperature of DNA duplexes, thus allowing shorter, more discriminatory probes to be used. The quencher has been used in Scorpion primers and TaqMan probes for human DNA sequence recognition and mutation detection.
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Affiliation(s)
- Jonathan P May
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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