1
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Hong JS, Tindall JM, Tindall SR, Sorscher EJ. Mutation accumulation in H. sapiens F508del CFTR countermands dN/dS type genomic analysis. PLoS One 2024; 19:e0305832. [PMID: 39024311 PMCID: PMC11257350 DOI: 10.1371/journal.pone.0305832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Understanding the mechanisms that underlie de novo mutations (DNMs) can be essential for interpreting human evolution, including aspects such as rapidly diverging genes, conservation of non-coding regulatory elements, and somatic DNA adaptation, among others. DNM accumulation in Homo sapiens is often limited to evaluation of human trios or quads across a single generation. Moreover, human SNPs in exons, pseudogenes, or other non-coding elements can be ancient and difficult to date, including polymorphisms attributable to founder effects and identity by descent. In this report, we describe multigenerational evolution of a human coding locus devoid of natural selection, and delineate patterns and principles by which DNMs have accumulated over the past few thousand years. We apply a data set comprising cystic fibrosis transmembrane conductance regulator (CFTR) alleles from 2,393 individuals homozygous for the F508del defect. Additional polymorphism on the F508del background diversified subsequent to a single mutational event during recent human history. Because F508del CFTR is without function, SNPs observed on this haplotype are effectively attributable to factors that govern accumulating de novo mutations. We show profound enhancement of transition, synonymous, and positionally repetitive polymorphisms, indicating appearance of DNMs in a manner evolutionarily designed to protect protein coding DNA against mutational attrition while promoting diversity.
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Affiliation(s)
- Jeong S. Hong
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Janice M. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Samuel R. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eric J. Sorscher
- Emory University School of Medicine, Atlanta, Georgia, United States of America
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2
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Pellen N, Reste JYL, Argouarc'h J. Modelling the spread of cystic fibrosis in Brittany using genealogical data over five centuries. J Cyst Fibros 2024; 23:341-348. [PMID: 37985320 DOI: 10.1016/j.jcf.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The French region of Brittany presents one of the highest cystic fibrosis (CF)-causing allele frequency in Europe. Here, we tested two hypotheses: i) CF-causing allele carriers arrived by sea in the middle of the 1st millennium AD, and ii) a selective advantage for healthy carriers explains this high rate. METHODS From the census of cystic fibrosis patients, frequency maps of the most widespread alleles were established. A mathematical model was developed, based on birth date and place of the ancestors of these patients over 5 centuries, to determine the distribution of local migrations and their parameters for inter-generational intervals of 32 years. This model was applied to simulate the spread of CF-causing variant carriers, according to different scenarios that corresponded to the immigration of a given number of variant carriers at different times (year) and places, and to compare their results to current frequency maps. RESULTS Migrants carrying a CFTR variant settled in several locations, around which they spread, notably in Central Brittany (F508del variant), Léon (G551D variant) and Cornouaille (1078delT variant). Until the end of the 18th century, the spreading of disease-causing allele carriers was relatively slow, and allele frequencies progressively increased. Then, the mean migration distances increased rapidly, leading to a decline in local frequencies. CONCLUSIONS The main CFTR variants could only have reached their current frequencies through a selective advantage for healthy carriers of the order of 4-6 % at each generation. For the most widespread variant (F508del), the model supports the hypothesis that it appeared around 190 generations ago.
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Affiliation(s)
- Nadine Pellen
- ER 7479 SPURBO, University of Western Brittany, 22, av. Camille Desmoulins, Brest, FR 29238, France.
| | - Jean-Yves Le Reste
- ER 7479 SPURBO, University of Western Brittany, 22, av. Camille Desmoulins, Brest, FR 29238, France
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3
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Krasnova M, Efremova A, Mokrousova D, Bukharova T, Kashirskaya N, Kutsev S, Kondratyeva E, Goldshtein D. Advances in the Study of Common and Rare CFTR Complex Alleles Using Intestinal Organoids. J Pers Med 2024; 14:129. [PMID: 38392563 PMCID: PMC10890655 DOI: 10.3390/jpm14020129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Complex alleles (CAs) arise when two or more nucleotide variants are present on a single allele. CAs of the CFTR gene complicate the cystic fibrosis diagnosis process, classification of pathogenic variants, and determination of the clinical picture of the disease and increase the need for additional studies to determine their pathogenicity and modulatory effect in response to targeted therapy. For several different populations around the world, characteristic CAs of the CFTR gene have been discovered, although in general the prevalence and pathogenicity of CAs have not been sufficiently studied. This review presents examples of using intestinal organoid models for assessments of the two most common and two rare CFTR CAs in individuals with cystic fibrosis in Russia.
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Affiliation(s)
- Maria Krasnova
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | - Anna Efremova
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | | | | | - Nataliya Kashirskaya
- Research Centre for Medical Genetics, Moscow 115522, Russia
- Moscow Regional Research and Clinical Institute ("MONIKI"), Schepkina Street, 61/2, 1, Moscow 129110, Russia
| | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow 115522, Russia
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4
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Hosseini Nami A, Kabiri M, Zafarghandi Motlagh F, Shirzadeh T, Bagherian H, Zeinali R, Karimi A, Zeinali S. Identification and in silico structural analysis for the first de novo mutation in the cystic fibrosis transmembrane conductance regulator protein in Iran: case report and developmental insight using microsatellite markers. Ther Adv Respir Dis 2024; 18:17534666241253990. [PMID: 38904297 PMCID: PMC11193346 DOI: 10.1177/17534666241253990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/19/2024] [Indexed: 06/22/2024] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by the inheritance of two mutant cystic fibrosis transmembrane conductance regulator (CFTR) alleles, one from each parent. Autosomal recessive disorders are rarely associated with germline mutations or mosaicism. Here, we propose a case of paternal germline mutation causing CF. The subject also had an identifiable maternal mutant allele. We identified the compound heterozygous variants in the proband through Sanger sequencing, and in silico studies predicted functional effects on the protein. Also, short tandem repeat markers revealed the de novo nature of the mutation. The maternal mutation in the CFTR gene was c.1000C > T. The de novo mutation was c.178G > A, p.Glu60Lys. This mutation is located in the lasso motif of the CFTR protein and, according to in silico structural analysis, disrupts the interaction of the lasso motif and R-domain, thus influencing protein function. This first reported case of de novo mutation in Asia has notable implications for molecular diagnostics, genetic counseling, and understanding the genetic etiology of recessive disorders in the Iranian population.
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Affiliation(s)
- Amin Hosseini Nami
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Tina Shirzadeh
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Hamideh Bagherian
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Razie Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Karimi
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Sirous Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), No. 41, Irna St., Valiasr St., Tehran, Iran
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Krasnova M, Efremova A, Bukhonin A, Zhekaite E, Bukharova T, Melyanovskaya Y, Goldshtein D, Kondratyeva E. The Effect of Complex Alleles of the CFTR Gene on the Clinical Manifestations of Cystic Fibrosis and the Effectiveness of Targeted Therapy. Int J Mol Sci 2023; 25:114. [PMID: 38203285 PMCID: PMC10779438 DOI: 10.3390/ijms25010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
The authors of this article analyzed the available literature with the results of studying the prevalence of complex alleles of the CFTR gene among patients with cystic fibrosis, and their pathogenicity and influence on targeted therapy with CFTR modulators. Cystic fibrosis (CF) is a multisystemic autosomal recessive disease caused by a defect in the expression of the CFTR protein, and more than 2000 genetic variants are known. Clinically significant variants are divided into seven classes. Information about the frequency of complex alleles appears in a number of registers, along with the traditional presentation of data on genetic variants. Complex alleles (those with the presence of more than two nucleotide variants on one allele) can complicate the diagnosis of the disease, and change the clinical manifestations of cystic fibrosis and the response to treatment, since each variant in the complex allele can contribute to the functional activity of the CFTR protein, changing it both in terms of increasing and decreasing function. The role of complex alleles is often underestimated, and their frequency has not been studied. At the moment, characteristic frequently encountered complex alleles have been found for several populations of patients with cystic fibrosis, but the prevalence and pathogenicity of newly detected complex alleles require additional research. In this review, more than 35 complex alleles of the CFTR gene from existing research studies were analyzed, and an analysis of their influence on the manifestations of the disease and the effectiveness of CFTR modulators was also described.
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Affiliation(s)
| | - Anna Efremova
- Research Centre for Medical Genetics, Moscow 115522, Russia; (M.K.); (A.B.); (E.Z.); (T.B.); (Y.M.); (D.G.); (E.K.)
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6
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Terlizzi V, Centrone C, Ferrari B, Castellani C, Gunawardena TNA, Taccetti G, Laselva O. Modulator Therapy in Cystic Fibrosis Patients with cis Variants in F508del Complex Allele: A Short-Term Observational Case Series. J Pers Med 2022; 12:jpm12091421. [PMID: 36143206 PMCID: PMC9504164 DOI: 10.3390/jpm12091421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Previous studies reported the influence of cis variants in F508del cystic fibrosis (CF) patients in their responses to CFTR modulators. The current study is a prospective, observational study involving three patients with CF and pancreatic insufficiency, carrying a complex allele including F508del with A238V, I1027T, or L467F. We report clinical data before and after 4 weeks of treatment with tezacaftor (TEZ)/ivacaftor (IVA), elexacaftor (ELX)/TEZ/IVA, and lumacaftor (LUM)/IVA for patients with complex alleles A238V, I1027T, and L467F, respectively. The 50-year-old patient bearing F508del;A238V/D1152H showed a normal sweat test (13 mEq/L) and improvements in forced expiratory volume in the first second (FEV1) (+7 points), body mass index (BMI) (+0.85), and respiratory CF Questionnaire-Revised (CFQ-R) domain (+22.2 points). The 12-year-old patient bearing F508del;I1027T/R709X showed an improvement in a sweat test (−40 mEq/l), FEV1 (+9 points) and the respiratory CFQ-R domain (+16.7 points). No changes in outcomes were observed for the 6-year-old patient F508del;L467F/F508del. Our data highlight that the reported variants do not modify the phenotypic expression of F508del. Searching L467F is crucial in CF patients with F508del nonresponsive to ELX/TEZ/IVA. Further data are needed to evaluate the clinical effect of these variants after a longer follow up.
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Affiliation(s)
- Vito Terlizzi
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Meyer Children’s Hospital, 50139 Florence, Italy
- Correspondence: (V.T.); (O.L.); Tel.: +39-0881588074 (O.L.)
| | - Claudia Centrone
- Diagnostic Genetics Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Beatrice Ferrari
- Rehabilitation Unit, Meyer Children’s Hospital, 50139 Florence, Italy
| | - Chiara Castellani
- Department of Radiology, Meyer Children’s Hospital, 50139 Florence, Italy
| | - Tarini N. A. Gunawardena
- Programme in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 8X4, Canada
- Programme in Translational Medicine, The Hospital for Sick Children, Toronto, ON M5G 8X4, Canada
| | - Giovanni Taccetti
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Meyer Children’s Hospital, 50139 Florence, Italy
| | - Onofrio Laselva
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
- Correspondence: (V.T.); (O.L.); Tel.: +39-0881588074 (O.L.)
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7
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Petrova NV, Kashirskaya NY, Vasilyeva TA, Balinova NV, Marakhonov AV, Kondratyeva EI, Zhekaite EK, Voronkova AY, Kutsev SI, Zinchenko RA. High frequency of complex CFTR alleles associated with c.1521_1523delCTT (F508del) in Russian cystic fibrosis patients. BMC Genomics 2022; 23:252. [PMID: 35365085 PMCID: PMC8973895 DOI: 10.1186/s12864-022-08466-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis (CF, MIM# 219,700) is an autosomal recessive disease caused by pathogenic variants within the CFTR gene. It was shown that genetic variants located in cis can affect disease severity or treatment response because of additive or epistatic effects. Studies on the prevalence of complex alleles in Russian CF patients have just begun. Aim To evaluate frequencies and genetic background of complex alleles carrying c.1521_1523delCTT (F508del) and c.1399C>T (L467F), c.2562T>G (T854=) or c.4389G>A (Q1463=) in cis; to determine clinical consequences of complex allele c.[1399C>T;1521_1523delCTT] ([L467;F508del]) in Russian CF patients. Methods Sequencing of coding regions of CFTR gene and analysis of polymorphic markers in CF patients carrying F508del variant. Comparing of clinical features in two groups patients having genotypes [L467F;F508del];[F508del] (group 1) and [F508del];[F508del] (group 2). Results Frequency of [L467F;F508del] allele linked to 2–2–21–6–17–13 haplotype was 4.42%, of [F508del;T854=;Q1463=] allele linked to haplotype 1–2–21–6–17–13 – 2.2% in F508del chromosomes. No differences in disease severity in patients carrying complex allele [L467F;F508del] and patients homozygous for F508del was found. Conclusion The frequency of complex alleles associated with F508del was at least 6.6% in Russian CF patients, which should be taken into account for the decision on optimal treatment options with CFTR modulators.
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Affiliation(s)
- Nika V Petrova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | | | | | | | - Andrey V Marakhonov
- Research Centre for Medical Genetics, Moscow, Russian Federation. .,Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics, Moskvorechie St., 1, 115522, Moscow, Russian Federation.
| | | | - Elena K Zhekaite
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Anna Y Voronkova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Sergey I Kutsev
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Rena A Zinchenko
- Research Centre for Medical Genetics, Moscow, Russian Federation.,N.A. Semashko National Research Institute of Public Health, Moscow, Russian Federation
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8
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Chevalier B, Hinzpeter A. The influence of CFTR complex alleles on precision therapy of cystic fibrosis. J Cyst Fibros 2019; 19 Suppl 1:S15-S18. [PMID: 31883651 DOI: 10.1016/j.jcf.2019.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/14/2019] [Accepted: 12/14/2019] [Indexed: 10/25/2022]
Abstract
CFTR is an extensively studied gene and multiple sequence variants have been identified, many of which still need to be defined as neutral or disease causing. Complex alleles are defined when at least two variants are identified on the same allele. Each pathogenic variant can affect distinct steps of the CFTR biogenesis. As CFTR modulators are being developed to alleviate specific defects, pathogenic variants need to be characterized to propose adequate treatments. Conversely, cis-variants can affect treatment response when defects are additive or if they alter the binding or efficacy of the modulator. Hence, complex alleles increase the complexity of CFTR variant classification and need to be assigned as neutral, disease causing or modulating treatment efficacy. This review was based on a symposium session presented at the 16th ECFS Basic Science Conference, Dubrovnik, Croatia, 27 to 30 March, 2019.
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Affiliation(s)
- Benoit Chevalier
- INSERM U1151, Institut Necker Enfants Malades, Paris, France; Université Paris Descartes, Paris, France.
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, Paris, France; Université Paris Descartes, Paris, France.
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Farrell P, Férec C, Macek M, Frischer T, Renner S, Riss K, Barton D, Repetto T, Tzetis M, Giteau K, Duno M, Rogers M, Levy H, Sahbatou M, Fichou Y, Le Maréchal C, Génin E. Estimating the age of p.(Phe508del) with family studies of geographically distinct European populations and the early spread of cystic fibrosis. Eur J Hum Genet 2018; 26:1832-1839. [PMID: 30089827 DOI: 10.1038/s41431-018-0234-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 01/25/2023] Open
Abstract
The high incidence of cystic fibrosis (CF) is due to the frequency of the c.1521_1523delCTT variant in the cystic fibrosis transmembrane conductance regulator (CFTR), but its age and origin are uncertain. This gap limits attempts to shed light on the presumed heterozygote selective advantage that accounts for the variant's high prevalence among Caucasian Europeans and Europe-derived populations. In addition, explaining the nature of heterozygosity to screened individuals with one c.1521_1523delCTT variant is challenging when families raise questions about these issues. To address this gap, we obtained DNA samples from 190 patients bearing c.1521_1523delCTT and their parents residing in geographically distinct European populations plus a Germany-derived population in the USA. We identified microsatellites spanning CFTR and reconstructed haplotypes at 10 loci to estimate the time/age of the most recent common ancestor (tMRCA) with the Estiage program. We found that the age estimates differ between northwestern populations, where the mean tMRCA values vary between 4600 and 4725 years, and the southeastern populations where c.1521_1523delCTT seems to have been introduced only about 1000 years ago. The tMRCA values of Central Europeans were intermediate. Thus, our data resolve a controversy by establishing an early Bronze Age origin of the c.1521_1523delCTT allele and demonstrating its likely spread from northwest to southeast during ancient migrations. Moreover, taking the archeological record into account, our results introduce a novel concept by suggesting that Bell Beaker folk were the probable migrating population responsible for the early dissemination of c.1521_1523delCTT in prehistoric Europe.
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Affiliation(s)
- Philip Farrell
- Pediatrics and Population Health Sciences, University of Wisconsin, Madison, WI, USA.
| | - Claude Férec
- UMR 1078 Génétique, Génomique fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, CHU Brest, Brest, France.,Laboratoire de Génétique, CHU Brest, Brest, France
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University- 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Thomas Frischer
- Paediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | - Sabine Renner
- Paediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | - Katharina Riss
- Paediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | - David Barton
- School of Medicine, University College Dublin, Dublin, Ireland.,Department of Clinical Genetics, Our Lady's Children's Hospital, Dublin, Ireland
| | - Teresa Repetto
- Meyer Children Hospital, Cystic Fibrosis Center, Florence University, Florence, Italy
| | - Maria Tzetis
- Department of Medical Genetics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Morten Duno
- Department of Clinical Genetics, University Hospital, Copenhagen, Copenhagen, Denmark
| | - Melissa Rogers
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Hara Levy
- Northwestern University Feinberg School of Medicine and the Ann & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | | | - Yann Fichou
- UMR 1078 Génétique, Génomique fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, CHU Brest, Brest, France
| | - Cédric Le Maréchal
- UMR 1078 Génétique, Génomique fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, CHU Brest, Brest, France.,Laboratoire de Génétique, CHU Brest, Brest, France
| | - Emmanuelle Génin
- UMR 1078 Génétique, Génomique fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, CHU Brest, Brest, France
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10
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Baatallah N, Bitam S, Martin N, Servel N, Costes B, Mekki C, Chevalier B, Pranke I, Simonin J, Girodon E, Hoffmann B, Mornon JP, Callebaut I, Sermet-Gaudelus I, Fanen P, Edelman A, Hinzpeter A. Cis variants identified in F508del complex alleles modulate CFTR channel rescue by small molecules. Hum Mutat 2018; 39:506-514. [PMID: 29271547 DOI: 10.1002/humu.23389] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/17/2022]
Abstract
Molecules correcting the trafficking (correctors) and gating defects (potentiators) of the cystic fibrosis causing mutation c.1521_1523delCTT (p.Phe508del) begin to be a useful treatment for CF patients bearing p.Phe508del. This mutation has been identified in different genetic contexts, alone or in combination with variants in cis. Until now, 21 exonic variants in cis of p.Phe508del have been identified, albeit at a low frequency. The aim of this study was to evaluate their impact on the efficacy of CFTR-directed corrector/potentiator therapy (Orkambi). The analysis by minigene showed that two out of 15 cis variants tested increased exon skipping (c.609C > T and c.2770G > A). Four cis variants were studied functionally in the absence of p.Phe508del, one of which was found to be deleterious for protein maturation c.1399C > T (p.Leu467Phe). In the presence of p.Phe508del, this variant was the only to prevent the response to Orkambi treatment. This study showed that some patients carrying p.Phe508del complex alleles are predicted to poorly respond to corrector/potentiator treatments. Our results underline the importance to validate treatment efficacy in the context of complex alleles.
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Affiliation(s)
- Nesrine Baatallah
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Sara Bitam
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Natacha Martin
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France
| | - Nathalie Servel
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Bruno Costes
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France.,Université Paris-Est, Créteil, France
| | - Chadia Mekki
- Department of Genetics, GH Henri Mondor, APHP, Créteil, France
| | - Benoit Chevalier
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Iwona Pranke
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Juliette Simonin
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Emmanuelle Girodon
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Laboratoire de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, AP-HP, Paris, France
| | - Brice Hoffmann
- CNRS UMR7590, Sorbonne Universités, Université Pierre et Marie Curie-Paris6-MNHN-IRD-IUC, Paris, France
| | - Jean-Paul Mornon
- CNRS UMR7590, Sorbonne Universités, Université Pierre et Marie Curie-Paris6-MNHN-IRD-IUC, Paris, France
| | - Isabelle Callebaut
- CNRS UMR7590, Sorbonne Universités, Université Pierre et Marie Curie-Paris6-MNHN-IRD-IUC, Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Pascale Fanen
- INSERM, U955, Institut de Recherche Henri Mondor, IMRB, Créteil, France.,Université Paris-Est, Créteil, France.,Department of Genetics, GH Henri Mondor, APHP, Créteil, France
| | - Aleksander Edelman
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, INEM, Paris, France.,Université Paris Descartes, Paris, France
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Vecchio-Pagán B, Blackman SM, Lee M, Atalar M, Pellicore MJ, Pace RG, Franca AL, Raraigh KS, Sharma N, Knowles MR, Cutting GR. Deep resequencing of CFTR in 762 F508del homozygotes reveals clusters of non-coding variants associated with cystic fibrosis disease traits. Hum Genome Var 2016; 3:16038. [PMID: 27917292 PMCID: PMC5121184 DOI: 10.1038/hgv.2016.38] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/09/2023] Open
Abstract
Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5' and 5 kb 3' of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration. In phase 2, a 510 kb region, which included the entire topologically associated domain of CFTR, was sequenced in 276 F508del homozygotes drawn from extremes of lung function. An additional 163 individuals who carried F508del and a different CF-causing variant were sequenced to inform haplotype construction. Region-based burden testing of both common and rare variants revealed seven regions of significance (α=0.01), five of which overlapped known regulatory elements or chromatin interactions. Notably, the -80 kb locus known to interact with the CFTR promoter was associated with variation in both CF traits. Haplotype analysis revealed a single rare recombination event (1.9% frequency) in intron 15 of CFTR bearing the F508del variant. Otherwise, the majority of F508del chromosomes were markedly similar, consistent with a single origin of the F508del allele. Together, these high-resolution variant analyses of the CFTR locus suggest a role for non-coding regulatory motifs in trait variation among individuals carrying the common CF allele.
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Affiliation(s)
- Briana Vecchio-Pagán
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Scott M Blackman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melis Atalar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew J Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rhonda G Pace
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arianna L Franca
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen S Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael R Knowles
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Fichou Y, Férec C. Molecular RHD-RHCE Analysis by Multiplex PCR of Short Fluorescent Fragments. Methods Mol Biol 2016; 1310:97-104. [PMID: 26024628 DOI: 10.1007/978-1-4939-2690-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several hundred variant alleles have been reported within the homologous RHD and RHCE genes that encode the antigens involved in the human Rh blood group system, which is of the main interest in the field of both transfusion and obstetrical medicine. Although these variants can be mostly characterized at the molecular level by sequence-specific primer polymerase chain reaction (SSP-PCR) and/or direct sequencing, some allelic combinations remain unresolved by conventional methods. Typically exon deletion or hybrid genes may be difficult to assess in a heterozygous context. Here we describe a qualitative and quantitative method to resolve copy number variations in the RH gene exons by quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF).
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Affiliation(s)
- Yann Fichou
- Etablissement Français du Sang (EFS) - Bretagne, 46 rue Félix Le Dantec, 29218, Brest, France,
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13
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The novel complex allele [A238V;F508del] of the CFTR gene: clinical phenotype and possible implications for cystic fibrosis etiological therapies. J Hum Genet 2016; 61:473-81. [PMID: 26911355 DOI: 10.1038/jhg.2016.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 02/08/2023]
Abstract
Few mutations in cis have been annotated for F508del homozygous patients. Southern Italy patients who at a first analysis appeared homozygous for the F508del mutation (n=63) or compound heterozygous for the F508del and another mutation in the cystic fibrosis transmembrane conductance regulator gene (n=155) were searched for the A238V mutation in exon 6. The allelic frequency of the complex allele [A238V;F508del] was 0.04. When the whole data set was used (comprised also of 56 F508del/F508del and 34 F508del/other mutation controls), no differences reached the statistical significance in the clinical parameters, except chloride concentrations which were lower in [A238V;F508del]/other mutation compared with F508del/other mutation (P=0.03). The two study groups presented less complications than the control groups. Within the minimal data set (34 F508del/F508del, 27 F508del/other mutation, 4 [A238V;F508del]/F508del cases and 5 [A238V;F508del]/other mutation cases); that is, presenting all the variables in each patient, forced expiratory volume in 1 s and forced vital capacity presented a trend to lower levels in the study groups in comparison with the F508del/F508del group, and C-reactive protein approximated statistically significant higher levels in the [A238V;F508del]/other mutation as compared with F508del/F508del patients (P=0.09). The analysis of statistical dependence among the variables showed a significant anticorrelation between chloride and body mass index in the [A238V;F508del]/other mutation group. In conclusion, the complex allele [A238V;F508del] seems to be associated with less general complications than in the control groups, on the other hand possibly giving a worse pulmonary phenotype and higher systemic/local inflammatory response. These findings have implications for the correct recruitment and clinical response of F508del patients in the clinical trials testing the new etiological drugs for cystic fibrosis.
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14
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Fichou Y, Le Maréchal C, Bryckaert L, Dupont I, Jamet D, Chen JM, Férec C. A convenient qualitative and quantitative method to investigate RHD-RHCE hybrid genes. Transfusion 2013; 53:2974-82. [PMID: 23550903 DOI: 10.1111/trf.12179] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/24/2013] [Accepted: 02/10/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular biology techniques, such as single specific-primer polymerase chain reaction (PCR), denaturing-high performance liquid chromatography, direct sequencing, next-generation sequencing, and microarray platforms, contribute to the efficient genotyping of the human blood group RHD gene. However, some alleles remain undetermined in rare cases in DNA samples carrying two copies of the RHD gene, which challenge the identification of D-CE hybrid genes. STUDY DESIGN AND METHODS We set up, in a single-tube format, a qualitative and quantitative assay based on multiplex PCR of short fluorescent fragments (QMPSF) to simultaneously amplify all 10 RHD exons on the one hand and all 10 RHCE exons on the other hand. RESULTS The test proved to be useful to rapidly identify hybrid genes in hemizygous RHD samples carrying a hybrid D-CE gene and to resolve unknown genotypes by quantifying individual exons in compound heterozygous samples, but also unexpectedly helped to redefine the RHDΨ haplotype. While validating the test, two novel single-point variants, c.648G>C (p.L216F) and c.1048G>C (p.D350H), were found. CONCLUSION For the first time, a QMPSF-based method is reliable to individually quantify the exons of both RH genes, including hybrid D-CE genes in compound heterozygous samples and may help to investigate samples with unknown RHD and/or RHCE status.
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Affiliation(s)
- Yann Fichou
- Etablissement Français du Sang (EFS)-Bretagne, Brest, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France; Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France; Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan, Brest, France
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15
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Cordovado S, Hendrix M, Greene C, Mochal S, Earley M, Farrell P, Kharrazi M, Hannon W, Mueller P. CFTR mutation analysis and haplotype associations in CF patients. Mol Genet Metab 2012; 105:249-54. [PMID: 22137130 PMCID: PMC3551260 DOI: 10.1016/j.ymgme.2011.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/20/2011] [Accepted: 10/20/2011] [Indexed: 11/24/2022]
Abstract
Most newborn screening (NBS) laboratories use second-tier molecular tests for cystic fibrosis (CF) using dried blood spots (DBS). The Centers for Disease Control and Prevention's NBS Quality Assurance Program offers proficiency testing (PT) in DBS for CF transmembrane conductance regulator (CFTR) gene mutation detection. Extensive molecular characterization on 76 CF patients, family members or screen positive newborns was performed for quality assurance. The coding, regulatory regions and portions of all introns were sequenced and large insertions/deletions were characterized as well as two intronic di-nucleotide microsatellites. For CF patient samples, at least two mutations were identified/verified and four specimens contained three likely CF-associated mutations. Thirty-four sequence variations in 152 chromosomes were identified, five of which were not previously reported. Twenty-seven of these variants were used to predict haplotypes from the major haplotype block defined by HapMap data that spans the promoter through intron 19. Chromosomes containing the F508del (p.Phe508del), G542X (p.Gly542X) and N1303K (p.Asn1303Lys) mutations shared a common haplotype subgroup, consistent with a common ancient European founder. Understanding the haplotype background of CF-associated mutations in the U.S. population provides a framework for future phenotype/genotype studies and will assist in determining a likely cis/trans phase of the mutations without need for parent studies.
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Affiliation(s)
- S.K. Cordovado
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
- Corresponding author. Fax: +1 770 488 4005, (S.K. Cordovado)
| | - M. Hendrix
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - C.N. Greene
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - S. Mochal
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - M.C. Earley
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - P.M. Farrell
- University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, Madison, WI, USA
| | - M. Kharrazi
- California Department of Public Health, Richmond, CA 94804, USA
| | - W.H. Hannon
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
| | - P.W. Mueller
- Centers for Disease Control and Prevention, 4770 Buford Highway MS F24, Atlanta, GA, USA
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Lucarelli M, Narzi L, Pierandrei S, Bruno SM, Stamato A, d'Avanzo M, Strom R, Quattrucci S. A new complex allele of the CFTR gene partially explains the variable phenotype of the L997F mutation. Genet Med 2011; 12:548-55. [PMID: 20706124 DOI: 10.1097/gim.0b013e3181ead634] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE To evaluate the role of complex alleles, with two or more mutations in cis position, of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in the definition of the genotype-phenotype relationship in cystic fibrosis (CF), and to evaluate the functional significance of the highly controversial L997F CFTR mutation. METHODS We evaluated the diagnosis of CF or CFTR-related disorders in 12 unrelated subjects with highly variable phenotypes. According to a first CFTR mutational analysis, subjects appeared to be compound heterozygotes for a classic mutation and the L997F mutation. A further CFTR mutational analysis was conducted by means of a protocol of extended sequencing, particularly suited to the detection of complex alleles. RESULTS We detected a new [R117L; L997F] CFTR complex allele in the four subjects with the highest sweat test values and CF. The eight subjects without the complex allele showed the most varied biochemical and clinical outcome and were diagnosed as having mild CF, CFTR-related disorders, or even no disease. CONCLUSIONS The new complex allele partially explains the variable phenotype in CF subjects with the L997F mutation. CFTR complex alleles are likely to have a role in the definition of the genotype-phenotype relationship in CF. Whenever apparently identical CFTR-mutated genotypes are found in subjects with divergent phenotypes, an extensive mutational search is mandatory.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy.
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Gal SL, Héry-Arnaud G, Ramel S, Virmaux M, Damiani C, Totet A, Nevez G. Pneumocystis jirovecii and cystic fibrosis in France. ACTA ACUST UNITED AC 2010; 42:225-7. [DOI: 10.3109/00365540903447000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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