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Bruno SM, Blaconà G, Lo Cicero S, Castelli G, Virgulti M, Testino G, Pierandrei S, Fuso A, Cimino G, Ferraguti G, Eramo A, Lucarelli M. Quantitative Evaluation of CFTR Gene Expression: A Comparison between Relative Quantification by Real-Time PCR and Absolute Quantification by Droplet Digital PCR. Genes (Basel) 2023; 14:1781. [PMID: 37761921 PMCID: PMC10531455 DOI: 10.3390/genes14091781] [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: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
In the precision medicine era of cystic fibrosis (CF), therapeutic interventions, by the so-called modulators, target the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The levels of targetable CFTR proteins are a main variable in the success of patient-specific therapy. In turn, the CFTR protein level depends, at least in part, on the level of CFTR mRNA. Many mechanisms can modulate the CFTR mRNA level, for example, transcriptional rate, stability of the mRNA, epigenetics, and pathogenic variants that can affect mRNA production and degradation. Independently from the causes of variable CFTR mRNA levels, their exact quantitative assessment is of great importance in CF. Methods with high analytical sensitivity, precision, and accuracy are mandatory for the quantitative evaluation aimed at the amelioration of the diagnostic, prognostic, and therapeutic aspects. This paper compares, for the first time, two CFTR gene expression quantification methods: a well-established method for the relative quantification of CFTR mRNA using a real-time PCR and an innovative method for its absolute quantification using a droplet digital PCR. No comprehensive methods for absolute CFTR quantification via droplet digital PCR have been published so far. The accurate quantification of CFTR expression at the mRNA level is a critical step for the personalized therapeutic approaches of CF.
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Affiliation(s)
- Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Germana Castelli
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Mariarita Virgulti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giancarlo Testino
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giuseppe Cimino
- Cystic Fibrosis Reference Center of Lazio Region, Policlinico Umberto I University Hospital, 00161 Rome, Italy;
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Adriana Eramo
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
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Lo Cicero S, Castelli G, Blaconà G, Bruno SM, Sette G, Pigliucci R, Villella VR, Esposito S, Zollo I, Spadaro F, Maria RD, Biffoni M, Cimino G, Amato F, Lucarelli M, Eramo A. L1077P CFTR pathogenic variant function rescue by Elexacaftor-Tezacaftor-Ivacaftor in cystic fibrosis patient-derived air-liquid interface (ALI) cultures and organoids: in vitro guided personalized therapy of non-F508del patients. Respir Res 2023; 24:217. [PMID: 37674160 PMCID: PMC10483775 DOI: 10.1186/s12931-023-02516-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
Cystic fibrosis (CF) is caused by defects of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR-modulating drugs may overcome specific defects, such as the case of Trikafta, which is a clinically approved triple combination of Elexacaftor, Tezacaftor and Ivacaftor (ETI) that exhibited a strong ability to rescue the function of the most frequent F508del pathogenic variant even in genotypes with the mutated allele in single copy. Nevertheless, most rare genotypes lacking the F508del allele are still not eligible for targeted therapies. Via the innovative approach of using nasal conditionally reprogrammed cell (CRC) cell-based models that mimic patient disease in vitro, which are obtainable from each patient due to the 100% efficiency of the cell culture establishment, we theratyped orphan CFTR mutation L1077P. Protein studies, Forskolin-induced organoid swelling, and Ussing chamber assays congruently proved the L1077P variant function rescue by ETI. Notably, this rescue takes place even in the context of a single-copy L1077P allele, which appears to enhance its expression. Thus, the possibility of single-allele treatment also arises for rare genotypes, with an allele-specific modulation as part of the mechanism. Of note, besides providing indication of drug efficacy with respect to specific CFTR pathogenic variants or genotypes, this approach allows the evaluation of the response of single-patient cells within their genetic background. In this view, our studies support in vitro guided personalized CF therapies also for rare patients who are nearly excluded from clinical trials.
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Affiliation(s)
- Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giovanni Sette
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Riccardo Pigliucci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Valeria Rachela Villella
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate S.c.a.r.l, Naples, Italy
| | - Speranza Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate S.c.a.r.l, Naples, Italy
| | - Immacolata Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate S.c.a.r.l, Naples, Italy
| | - Francesca Spadaro
- Confocal Microscopy Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario 'A. Gemelli'-IRCCS, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Reference Center of Lazio Region, AOU Policlinico Umberto I, Rome, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate S.c.a.r.l, Naples, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Adriana Eramo
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.
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Clinical and Genetic Characterisation of Cystic Fibrosis Patients in Latvia: A Twenty-Five-Year Experience. Diagnostics (Basel) 2022; 12:diagnostics12112893. [PMID: 36428953 PMCID: PMC9689702 DOI: 10.3390/diagnostics12112893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Cystic fibrosis (CF) is the most common life-limiting genetic disorder in European descent populations. It is caused by pathogenic variants in the CFTR gene, and inheritance is autosomal recessive. This study provides an up-to-date, comprehensive estimation of the distribution of CFTR pathogenic variants in Latvia and their phenotypic characteristics. It also reports the first results of the CF newborn screening programme following its implementation in 2019. We analysed the clinical and molecular data of CF patients treated at the only tertiary hospital in Latvia providing specialised healthcare for the disorder. Between 1997 and 2022, 66 CF patients from 62 families were diagnosed based on symptoms or a molecular confirmation (six patients were diagnosed through the CF newborn screening programme). F508del was identified in 70.5% of all CF chromosomes. Known variants were identified in more than one family: dele2,3, R1006H, L1335P, W57R, R553X, 2143delT and 3849+10kb C>T (legacy names used). Furthermore, two novel variants were identified, namely, c.503C>A p.(Ser168Ter) and c.(743+1_744-1)_(1584+1_1585-1)del p.(?). The available follow-up results indicated that Latvian CF patients demonstrated similar tendencies to CF patients worldwide. The oldest age at diagnosis prior to the implementation of the CF newborn screening programme was 14 years. We provide here, for the first time, a comprehensive description of Latvian CF patients. An improvement in the healthcare of CF patients over time, including access to diagnosis, is evident. Two novel CF-causing variants are reported, and F508del is the most frequently occurring variant in the population, thus suggesting that F508del screening should be followed by the testing of the full CFTR gene.
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Tosco A, Castaldo A, Colombo C, Claut L, Carnovale V, Iacotucci P, Lucarelli M, Cimino G, Fabrizzi B, Caporelli N, Majo F, Ciciriello F, Padoan R, Poli P, Taccetti G, Centrone C, Casciaro R, Castellani C, Salvatore D, Colangelo C, Bonomi P, Castaldo G, Terlizzi V. Clinical outcomes of a large cohort of individuals with the F508del/5T;TG12 CFTR genotype. J Cyst Fibros 2022; 21:850-855. [PMID: 35523714 DOI: 10.1016/j.jcf.2022.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND In recent years, patients with cystic fibrosis (CF) conductance regulator (CFTR) variant poly(T) sequences have been increasingly reported with a wide spectrum of clinical severity. We describe the long-term clinical outcomes and progression to a CF diagnosis over time in a large Italian cohort of patients carrying the CFTR F508del/5T;TG12 genotype. METHODS A retrospective analysis of subjects from 10 CF centres in Italy with the F508del/5T;TG12 genotype was performed. Demographic, clinical, microbiological, and biochemical data, as well as information about the follow-ups and complications of the enroled patients, were collected. RESULTS A total of 129 subjects (54 females; median age: 15.0 years, range: 0-58 years; 59 older than 18 years) were included. In terms of initial diagnoses, 30 were CF (23.3%), 41 were CFTR-related disorder (CFTR-RD) (31.7%), and 58 were CF transmembrane conductance regulator-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID) (45.0%). After a median follow-up of 6.7 years (range 0.2-25 years), 15 patients progressed to CF, bringing the total number of CF diagnoses to 45/129 (34.9%). Most of these patients had mild lung diseases with pancreatic sufficiency and a low prevalence of CF-related complications. CONCLUSIONS At the end of the study, 34.9% of subjects with the CFTR F508del/5T;TG12 genotype were diagnosed with CF. We suggest including patients with the F508del/5T;TG12 genotype in long-term follow-ups.
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Affiliation(s)
- Antonella Tosco
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Alice Castaldo
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Carla Colombo
- Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Laura Claut
- Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Vincenzo Carnovale
- Department of Translational Medical Science, Cystic Fibrosis Center, Adult Unit, University of Naples "Federico II", Italy
| | - Paola Iacotucci
- Department of Translational Medical Science, Cystic Fibrosis Center, Adult Unit, University of Naples "Federico II", Italy
| | - Marco Lucarelli
- Dept of Experimental Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Regional Reference Center, A.O.U. Policlinico Umberto I, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Fabio Majo
- Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabiana Ciciriello
- Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Padoan
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Piercarlo Poli
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Giovanni Taccetti
- Meyer Children's Hospital, Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Viale Gaetano Pieraccini 24, Florence, Italy
| | - Claudia Centrone
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | | | | | | | | | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples, Naples, Italy; CEINGE-Advanced Biotechnology, Naples, Italy
| | - Vito Terlizzi
- Meyer Children's Hospital, Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Viale Gaetano Pieraccini 24, Florence, Italy.
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Terlizzi V, Claut L, Colombo C, Tosco A, Castaldo A, Fabrizzi B, Lucarelli M, Cimino G, Carducci C, Dolce D, Biffi A, Bonomi P, Timpano S, Padoan R. Outcomes of early repeat sweat testing in infants with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome/CF screen-positive, inconclusive diagnosis. Pediatr Pulmonol 2021; 56:3785-3791. [PMID: 34549893 DOI: 10.1002/ppul.25683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Reaching early and definitive diagnosis in infants with cystic fibrosis (CF) transmembrane conductance regulator-related metabolic syndrome (CRMS)/CF screen-positive, inconclusive diagnosis (CFSPID) is a priority of all CF newborn screening programs. Currently, sweat testing (ST) is the gold standard for CF diagnosis or exclusion. We assessed outcomes in a cohort of Italian CRMS/CFSPID infants who underwent repeat ST in the 1st year of life. METHODS This multicentre, prospective study analysed clinical data and outcomes in CRMS/CFSPID infants born between September 1, 2018, and December 31, 2019, and followed until June 30, 2020. All subjects underwent CF transmembrane conductance regulator (CFTR) gene sequencing and the search for CFTR macrodeletions/macroduplications, and repeat ST in the 1st year of life. RESULTS Fifty subjects (median age at end of follow-up, 16 months [range, 7-21 months]) were enrolled. Forty-one (82%) had the first sweat chloride (SC) in the intermediate range. During follow up, 150 STs were performed (range, 1-7/infant). After a median follow-up of 8.5 months (range, 1-16.2 months), 11 (22%) subjects were definitively diagnosed as follows: CF (n = 2 [4%]) at 2 and 5 months, respectively; healthy carrier (n = 8 [16%]), at a median age of 4 months (range, 2-8 months); and healthy (n = 1 [2%]) at 2 months of age. Inconclusive diagnosis remained in 39 (78%) infants. CONCLUSIONS Early repeat ST in the 1st year of life can shorten the time to definitive diagnosis in screening positive subjects with initial SC levels in the intermediate range.
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Affiliation(s)
- Vito Terlizzi
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Anna Meyer Children's University, Florence, Italy
| | - Laura Claut
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Carla Colombo
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Antonella Tosco
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Alice Castaldo
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Benedetta Fabrizzi
- Mother - Child Department, Cystic Fibrosis Regional Reference Center, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Regional Reference Center, A.O.U. Policlinico Umberto I, Rome, Italy
| | - Carla Carducci
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Dolce
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Anna Meyer Children's University, Florence, Italy
| | - Arianna Biffi
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | | | - Silviana Timpano
- Department of Pediatrics, Cystic Fibrosis Regional Support Center, ASST Spedali Civili Brescia, University of Brescia, Brescia, Italy
| | - Rita Padoan
- Department of Pediatrics, Cystic Fibrosis Regional Support Center, ASST Spedali Civili Brescia, University of Brescia, Brescia, Italy
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Sette G, Lo Cicero S, Blaconà G, Pierandrei S, Bruno SM, Salvati V, Castelli G, Falchi M, Fabrizzi B, Cimino G, De Maria R, Biffoni M, Eramo A, Lucarelli M. Theratyping cystic fibrosis in vitro in ALI-culture and organoid models generated from patient-derived nasal epithelial Conditionally Reprogrammed Stem Cells. Eur Respir J 2021; 58:13993003.00908-2021. [PMID: 34413153 PMCID: PMC8675295 DOI: 10.1183/13993003.00908-2021] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/28/2021] [Indexed: 11/05/2022]
Abstract
QUESTION Cystic Fibrosis (CF) is due to pathogenic variants in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Recent improvement enabled pharmacologic therapy aiming at restoring mutated CFTR expression and function. CFTR "modulators" have revolutionised the CF therapeutic landscape, particularly the last approved Trikafta. This drug-combination is indicated by FDA and very recently by EMA for genotypes carrying at least one copy of CFTR with F508del pathogenic variant. However, several genotypes, are not eligible for Trikafta treatment, yet. MATERIALS/PATIENTS AND METHODS We exploited an innovative cellular approach allowing highly efficient in vitro-expansion of airway epithelial stem cells (AESC) through conditional reprogramming (CRC) from nasal brushing of CF patients. This approach, coupled to development of AESC-derived personalised disease models, as organoids and air liquid interface (ALI) cultures, revealed highly suitable for CFTR pharmacological-testing. RESULTS AND ANSWER TO THE QUESTION We fully validated the experimental models and implemented the CFTR functional assays and biochemical CFTR protein characterisation, that allowed to evaluate the efficacy of clinically available modulators in restoring CFTR maturation and function of each patient-derived "avatar" (theratyping). F508del homozygous genotypes, used as controls, confirmed the higher clinical activity of Trikafta in comparison with older modulators. Trikafta showed its efficacy also on three rare genotypes previously not eligible for modulators-treatment, opening the way to clinical translation. Finally, encouraging results for innovative drug combinations were also obtained.
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Affiliation(s)
- Giovanni Sette
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.,Co-first authors
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.,Co-first authors
| | - Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Valentina Salvati
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mario Falchi
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Reference Center of Lazio Region, AOU Policlinico Umberto I, Rome, Italy
| | - Ruggero De Maria
- U.O.C. Medical Oncology, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" - IRCCS, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Adriana Eramo
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy .,Co-last authors
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.,Co-last authors
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Quantitative Evaluation of CFTR Pre-mRNA Splicing Dependent on the (TG)mTn Poly-Variant Tract. Diagnostics (Basel) 2021; 11:diagnostics11020168. [PMID: 33504063 PMCID: PMC7911278 DOI: 10.3390/diagnostics11020168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/09/2021] [Accepted: 01/18/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic analysis in cystic fibrosis (CF) is a difficult task. Within the many causes of variability and uncertainty, a major determinant is poor knowledge of the functional effect of most DNA variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. In turn, knowledge of the effect of a CFTR variant has dramatic diagnostic, prognostic and, in the era of CF precision medicine, also therapeutic consequences. One of the most challenging CFTR variants is the (TG)mTn haplotype, which has variable functional effect and controversial clinical consequences. The exact quantification of the anomalous splicing of CFTR exon 10 (in the HGVS name; exon 9 in the legacy name) and, consequently, of the residual wild-type functional CFTR mRNA, should be mandatory in clinical assessment of patients with potentially pathological haplotype of this tract. Here, we present a real time-based assay for the quantification of the proportion of exon 10+/exon 10− CFTR mRNA, starting from nasal brushing. Our assay proved rapid, economic and easy to perform. Specific primers used for this assay are either disclosed or commercially available, allowing any laboratory to easily perform it. A simplified analysis of the data is provided, facilitating the interpretation of the results. This method helps to enhance the comprehension of the genotype–phenotype relationship in CF and CFTR-related disorders (CFTR-RD), crucial for the diagnosis, prognosis and personalized therapy of CF.
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8
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Pierandrei S, Blaconà G, Fabrizzi B, Cimino G, Cirilli N, Caporelli N, Angeloni A, Cipolli M, Lucarelli M. Two novel and correlated CF-causing insertions in the (TG)mTn tract of the CFTR gene. PLoS One 2019; 14:e0222838. [PMID: 31593572 PMCID: PMC6782095 DOI: 10.1371/journal.pone.0222838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023] Open
Abstract
Two novel and related pathogenic variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene were structurally and functionally characterized. These alterations have not been previously described in literature. Two patients with diagnosis of Cystic Fibrosis (CF) based on the presence of one mutated allele, p.Phe508del, pathological sweat test and clinical symptoms were studied. To complete the genotypes of both patients, an extensive genetic and functional analysis of the CFTR gene was performed. Extensive genetic characterization confirmed the presence of p.Phe508del pathogenic variant and revealed, in both patients, the presence of an insertion of part of intron 10 in intron 9 of the CFTR gene, within the (TG)m repeat, with a variable poly-T stretch. The molecular lesions resulted to be very similar in both patients, with only a difference in the number of T in the poly-T stretch. The functional characterization at RNA level revealed a complete anomalous splicing, without exon 10, from the allele with the insertion of both patients. Consequently, the alleles with the insertions are expected not to contribute to the formation of a functional CFTR protein. Molecular and functional features of these alterations are compatible with the definition of novel CF-causing variants of the CFTR gene. This also allowed the completion of the genetic characterization of both patients.
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Affiliation(s)
- Silvia Pierandrei
- Dept. of Mother-Child and Urologic Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Blaconà
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Care Center, Umberto I Hospital, Rome, Italy
| | - Natalia Cirilli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Antonio Angeloni
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Cipolli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
- * E-mail:
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9
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Terlizzi V, Lucarelli M, Salvatore D, Angioni A, Bisogno A, Braggion C, Buzzetti R, Carnovale V, Casciaro R, Castaldo G, Cirilli N, Collura M, Colombo C, Di Lullo AM, Elce A, Lucidi V, Madarena E, Padoan R, Quattrucci S, Raia V, Seia M, Termini L, Zarrilli F. Clinical expression of cystic fibrosis in a large cohort of Italian siblings. BMC Pulm Med 2018; 18:196. [PMID: 30577776 PMCID: PMC6303904 DOI: 10.1186/s12890-018-0766-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/12/2018] [Indexed: 02/10/2023] Open
Abstract
Background A clinical heterogeneity was reported in patients with Cystic Fibrosis (CF) with the same CFTR genotype and between siblings with CF. Methods We investigated all clinical aspects in a cohort of 101 pairs of siblings with CF (including 6 triplets) followed since diagnosis. Results Severe lung disease had a 22.2% concordance in sib-pairs, occurred early and the FEV1% at 12 years was predictive of the severity of lung disease in the adulthood. Similarly, CF liver disease occurred early (median: 15 years) and showed a concordance of 27.8% in sib-pairs suggesting a scarce contribution of genetic factors; in fact, only 2/15 patients with liver disease in discordant sib-pairs had a deficiency of alpha-1-antitrypsin (a known modifier gene of CF liver phenotype). CF related diabetes was found in 22 pairs (in 6 in both the siblings). It occurred later (median: 32.5 years) and is strongly associated with liver disease. Colonization by P. aeruginosa and nasal polyposis that required surgery had a concordance > 50% in sib-pairs and were poorly correlated to other clinical parameters. The pancreatic status was highly concordant in pairs of siblings (i.e., 95.1%) but a different pancreatic status was observed in patients with the same CFTR mutations. This suggests a close relationship of the pancreatic status with the “whole” CFTR genotype, including mutations in regulatory regions that may modulate the levels of CFTR expression. Finally, a severe course of CF was evident in a number of patients with pancreatic sufficiency. Conclusions Physicians involved in care of patients with CF and in genetic counseling must be aware of the clinical heterogeneity of CF even in sib-pairs that, at the state of the art, is difficult to explain. Electronic supplementary material The online version of this article (10.1186/s12890-018-0766-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vito Terlizzi
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy.
| | - Marco Lucarelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Donatello Salvatore
- Centro Regionale Fibrosi Cistica, Centro Pediatrico Bambino Gesù Basilicata, AOR San Carlo, Potenza, Italy
| | - Adriano Angioni
- Laboratorio di Genetica Medica, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Arianna Bisogno
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Cesare Braggion
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy
| | | | - Vincenzo Carnovale
- Centro Regionale Fibrosi Cistica Adulti, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Rosaria Casciaro
- Centro Regionale Fibrosi Cistica, U.O.C. Pneumologia, IRCCS G. Gaslini, Genua, Italy
| | - Giuseppe Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie avanzate, Naples, Italy
| | - Natalia Cirilli
- Centro Regionale Fibrosi Cistica, Dipartimento Materno-Infantile, Ospedali Riuniti Ancona, Ancona, Italy
| | - Mirella Collura
- CRR Fibrosi Cistica, Ospedale dei Bambini, ARNAS Civico, Palermo, Italy
| | - Carla Colombo
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Antonella Miriam Di Lullo
- Dipartimento di Neuroscienze, Scienze Riproduttive ed Odontostomatologica, Università di Napoli Federico II, Naples, Italy
| | | | - Vincenzina Lucidi
- Unità Regionale di Fibrosi Cistica, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Elisa Madarena
- Centro Regionale Fibrosi Cistica, Ospedale Giovanni Paolo II, Lamezia, Italy
| | - Rita Padoan
- Centro Regionale di supporto Fibrosi Cistica, Dipartimento di Pediatria, Università di Brescia, AO Spedali Civili, Brescia, Italy
| | - Serena Quattrucci
- Centro Fibrosi Cistica Regione Lazio, Dipartimento di Pediatria e Neuropsichiatria Infantile, Sapienza Università-Policlinico Umberto I, Rome, Italy
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Sezione Pediatrica, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Manuela Seia
- Laboratorio di Genetica Medica, Fondazione IRCCS Policlinico Ca' Granda Ospedale, Milan, Italy
| | - Lisa Termini
- Ospedale dei Bambini G. Di Cristina, Centro Regionale Fibrosi Cistica, Palermo, Italy
| | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
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10
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Chheda P, Dama T, Goradia D, Pande S, Vinarkar S. A novel CFTR gene variant - p.Tyr517* associated with cystic fibrosis: a case report. Fetal Pediatr Pathol 2018; 37:448-451. [PMID: 30588852 DOI: 10.1080/15513815.2018.1532473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease usually diagnosed by clinical findings and abnormal sweat chloride testing. CASE REPORT We report a case of an 18-month-old Indian female with clinical findings suggestive of CF referred for genetic confirmation. The CFTR gene was sequenced for 23 mutations as per American College of Medical Genetics (ACMG) guidelines for CF and showed presence of a known common heterozygous delF508 (c.1521_1523delCTT, p.Phe508 del) variant. In addition to delF508 variant, exon 10 of CFTR gene also showed a novel variant c.1551C > G, p.Tyr517*, which was classified as "likely pathogenic" based on recent ACMG variant classification guidelines. The presence of compound heterozygous pathogenic variants along with classical clinical findings, confirmed the diagnosis of CF in this patient. CONCLUSION The novel pathogenic variants (missense/nonsense/deletion/duplication) in CFTR gene are often identified and are associated with CF, thus highlighting the need of comprehensive complete CFTR gene analysis.
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Affiliation(s)
- Pratiksha Chheda
- a Department of Molecular Pathology , Metropolis Healthcare Ltd. , Mumbai , India
| | - Tavisha Dama
- a Department of Molecular Pathology , Metropolis Healthcare Ltd. , Mumbai , India
| | - Dollar Goradia
- a Department of Molecular Pathology , Metropolis Healthcare Ltd. , Mumbai , India
| | - Shailesh Pande
- b Department of Genetics , Metropolis Healthcare Ltd. , Mumbai , India
| | - Sushant Vinarkar
- a Department of Molecular Pathology , Metropolis Healthcare Ltd. , Mumbai , India
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11
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Elce A, Nigro E, Gelzo M, Iacotucci P, Carnovale V, Liguori R, Izzo V, Corso G, Castaldo G, Daniele A, Zarrilli F. Supervised physical exercise improves clinical, anthropometric and biochemical parameters in adult cystic fibrosis patients: A 2-year evaluation. CLINICAL RESPIRATORY JOURNAL 2018; 12:2228-2234. [PMID: 29601147 DOI: 10.1111/crj.12796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/02/2018] [Accepted: 03/19/2018] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Cystic fibrosis (CF) is the most common inherited, life limiting condition among Caucasians. No healing therapy is currently available for patients with CF. The aim of the study was to define clinical, anthropometric and biochemical effects of regular, supervised physical exercise in a large cohort of patients with CF. MATERIALS AND METHODS Fifty-nine adult patients with CF that performed regularly supervised physical exercise in the last 3 years in comparison to 59 sex and age matched sedentary patients with CF were included in the study. RESULTS Physical exercise had significantly beneficial effects on: (a) FEV1% decline; (b) anthropometric parameters (lower number of cases with altered BMI, waist and arm circumferences); (c) lipid and glucose metabolism; (d) vitamin D serum levels. Of course, some of this improvement may be because of the better adherence to therapy typical of patients with CF that perform physical activity. CONCLUSIONS Such clinical and metabolic effects make supervised physical activity one of the hubs in managing patients with CF.
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Affiliation(s)
- Ausilia Elce
- Dipartimento di Scienze Umanistiche, Università Telematica Pegaso, Naples 80132, Italy
| | - Ersilia Nigro
- Dipartimento di Medicina e Scienze, della Salute, Università del Molise, Campobasso, 86100, Italy.,CEINGE-Biotecnologie avanzate, Naples, Italy
| | - Monica Gelzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Paola Iacotucci
- Centro Regionale Fibrosi Cistica Adulti, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Vincenzo Carnovale
- Centro Regionale Fibrosi Cistica Adulti, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | | | - Viviana Izzo
- Dipartimento di Medicina, Chirurgia e Odontoiatria, Università degli Studi di Salerno, Baronissi, Italy
| | - Gaetano Corso
- Dipartimento di Medicina Clinica e Sperimentale, Università di Foggia, Foggia, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Aurora Daniele
- CEINGE-Biotecnologie avanzate, Naples, Italy.,Dipartimento di Scienze e Tecnologie Ambientali, Biologiche, Farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
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12
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Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology. J Mol Diagn 2017; 19:788-800. [PMID: 28736296 DOI: 10.1016/j.jmoldx.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University, Rome, Italy.
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alice Biffignandi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Giannone
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisella Alberti
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Carlo Corbetta
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Erminio Torresani
- Unit of Microbiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Centre, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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13
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Terlizzi V, Castaldo G, Salvatore D, Lucarelli M, Raia V, Angioni A, Carnovale V, Cirilli N, Casciaro R, Colombo C, Di Lullo AM, Elce A, Iacotucci P, Comegna M, Scorza M, Lucidi V, Perfetti A, Cimino R, Quattrucci S, Seia M, Sofia VM, Zarrilli F, Amato F. Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles. J Med Genet 2016; 54:224-235. [PMID: 27738188 DOI: 10.1136/jmedgenet-2016-103985] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND The effect of complex alleles in cystic fibrosis (CF) is poorly defined for the lack of functional studies. OBJECTIVES To describe the genotype-phenotype correlation and the results of either in vitro and ex vivo studies performed on nasal epithelial cells (NEC) in a cohort of patients with CF carrying cystic fibrosis transmembrane conductance regulator (CFTR) complex alleles. METHODS We studied 70 homozygous, compound heterozygous or heterozygous for CFTR mutations: p.[Arg74Trp;Val201Met;Asp1270Asn], n=8; p.[Ile148Thr;Ile1023_Val1024del], n=5; p.[Arg117Leu;Leu997Phe], n=6; c.[1210-34TG[12];1210-12T[5];2930C>T], n=3; p.[Arg74Trp;Asp1270Asn], n=4; p.Asp1270Asn, n=2; p.Ile148Thr, n=6; p.Leu997Phe, n=36. In 39 patients, we analysed the CFTR gating activity on NEC in comparison with patients with CF (n=8) and carriers (n=4). Finally, we analysed in vitro the p.[Arg74Trp;Val201Met;Asp1270Asn] complex allele. RESULTS The p.[Ile148Thr;Ile1023_Val1024del] caused severe CF in five compound heterozygous with a class I-II mutation. Their CFTR activity on NEC was comparable with patients with two class I-II mutations (mean 7.3% vs 6.9%). The p.[Arg74Trp;Asp1270Asn] and the p.Asp1270Asn have scarce functional effects, while p.[Arg74Trp;Val201Met;Asp1270Asn] caused mild CF in four of five subjects carrying a class I-II mutation in trans, or CFTR-related disorders (CFTR-RD) in three having in trans a class IV-V mutation. The p.[Arg74Trp;Val201Met;Asp1270Asn] causes significantly (p<0.001) higher CFTR activity compared with compound heterozygous for class I-II mutations. Furthermore, five of six compounds heterozygous with the p.[Arg117Leu;Leu997Phe] had mild CF, whereas the p.Leu997Phe, in trans with a class I-II CFTR mutation, caused CFTR-RD or a healthy status (CFTR activity: 21.3-36.9%). Finally, compounds heterozygous for the c.[1210-34TG[12];1210-12T[5];2930C>T] and a class I-II mutation had mild CF or CFTR-RD (gating activity: 18.5-19.0%). CONCLUSIONS The effect of complex alleles partially depends on the mutation in trans. Although larger studies are necessary, the CFTR activity on NEC is a rapid contributory tool to classify patients with CFTR dysfunction.
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Affiliation(s)
- Vito Terlizzi
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Florence, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | | | - Marco Lucarelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Sezione Pediatrica, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Adriano Angioni
- Laboratorio di Genetica Medica, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Vincenzo Carnovale
- Dipartimento di Scienze Mediche Traslazionali, Centro Regionale Fibrosi Cistica, Sezione Adulti, Università di Napoli Federico II, Naples, Italy
| | - Natalia Cirilli
- Dipartimento Materno-Infantile, Ospedali Riuniti Ancona, Centro Regionale Fibrosi Cistica, Ancona, Italy
| | - Rosaria Casciaro
- Dipartimento di Pediatria, Centro Regionale Fibrosi Cistica, IRCCS G. Gaslini, Genova, Italy
| | - Carla Colombo
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Antonella Miriam Di Lullo
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,Dipartimento di Neuroscienze, Sezione di ORL, Università di Napoli Federico II, Naples, Italy
| | | | - Paola Iacotucci
- Dipartimento di Scienze Mediche Traslazionali, Centro Regionale Fibrosi Cistica, Sezione Adulti, Università di Napoli Federico II, Naples, Italy
| | - Marika Comegna
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Manuela Scorza
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Biotecnologie e Bioscienze, Università di Milano Bicocca, Milan, Italy
| | - Vincenzina Lucidi
- Unità di Fibrosi Cistica, IRCCS Ospedale Pediatrico Bambin Gesù, Rome, Italy
| | | | - Roberta Cimino
- Dipartimento di Scienze Neurologiche, Riproduttive ed Odontostomatologiche, Università di Napoli Federico II, Naples, Italy
| | - Serena Quattrucci
- Centro Fibrosi Cistica, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Manuela Seia
- Laboratorio Genetica Medica, Ospedale Maggiore Policlinico, Milano, Italy
| | | | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
| | - Felice Amato
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
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14
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The Impact on Genetic Testing of Mutational Patterns of CFTR Gene in Different Clinical Macrocategories of Cystic Fibrosis. J Mol Diagn 2016; 18:554-65. [PMID: 27157324 DOI: 10.1016/j.jmoldx.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 01/29/2016] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
More than 2000 sequence variations of the cystic fibrosis transmembrane conductance regulator gene are known. The marked genetic heterogeneity, poor functional characterization of the vast majority of sequence variations, and an uncertain genotype-phenotype relationship complicate the definition of mutational search strategies. We studied the effect of the marked genetic heterogeneity detected in a case series comprising 610 patients of cystic fibrosis (CF), grouped in different clinical macrocategories, on the operative characteristics of the genetic test designed to fully characterize CF patients. The detection rate in each clinical macrocategory and at each mutational step was found to be influenced by genetic heterogeneity. The definition of a single mutational panel that is suitable for all clinical macrocategories proved impossible. Only for classic CF with pancreas insufficiency did a reduced number of mutations yield a detection rate of diagnostic value. All other clinical macrocategories required an extensive genetic search. The search for specific mutational classes appears to be useful only in specific CF clinical forms. A flowchart defining a mutational search that may be adopted for different CF clinical forms, optimized in respect to those already available, is proposed. The findings also have consequences for carrier screening strategies.
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15
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Lucarelli M, Bruno SM, Pierandrei S, Ferraguti G, Stamato A, Narzi F, Amato A, Cimino G, Bertasi S, Quattrucci S, Strom R. A Genotypic-Oriented View of CFTR Genetics Highlights Specific Mutational Patterns Underlying Clinical Macrocategories of Cystic Fibrosis. Mol Med 2015; 21:257-75. [PMID: 25910067 DOI: 10.2119/molmed.2014.00229] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/20/2015] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The genotype-phenotype relationship in this disease is still unclear, and diagnostic, prognostic and therapeutic challenges persist. We enrolled 610 patients with different forms of CF and studied them from a clinical, biochemical, microbiological and genetic point of view. Overall, there were 125 different mutated alleles (11 with novel mutations and 10 with complex mutations) and 225 genotypes. A strong correlation between mutational patterns at the genotypic level and phenotypic macrocategories emerged. This specificity appears to largely depend on rare and individual mutations, as well as on the varying prevalence of common alleles in different clinical macrocategories. However, 19 genotypes appeared to underlie different clinical forms of the disease. The dissection of the pathway from the CFTR mutated genotype to the clinical phenotype allowed to identify at least two components of the variability usually found in the genotype-phenotype relationship. One component seems to depend on the genetic variation of CFTR, the other component on the cumulative effect of variations in other genes and cellular pathways independent from CFTR. The experimental dissection of the overall biological CFTR pathway appears to be a powerful approach for a better comprehension of the genotype-phenotype relationship. However, a change from an allele-oriented to a genotypic-oriented view of CFTR genetics is mandatory, as well as a better assessment of sources of variability within the CFTR pathway.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy.,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.,Policlinico Umberto I Hospital, Rome, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Silvia Pierandrei
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy.,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Giampiero Ferraguti
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Antonella Stamato
- Policlinico Umberto I Hospital, Rome, Italy.,Department of Pediatrics, Sapienza University of Rome, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Fabiana Narzi
- Policlinico Umberto I Hospital, Rome, Italy.,Department of Pediatrics, Sapienza University of Rome, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Annalisa Amato
- Policlinico Umberto I Hospital, Rome, Italy.,Department of Pediatrics, Sapienza University of Rome, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Giuseppe Cimino
- Policlinico Umberto I Hospital, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Serenella Bertasi
- Policlinico Umberto I Hospital, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Serena Quattrucci
- Policlinico Umberto I Hospital, Rome, Italy.,Department of Pediatrics, Sapienza University of Rome, Rome, Italy.,Cystic Fibrosis Reference Center of Lazio Region, Rome, Italy
| | - Roberto Strom
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy.,Policlinico Umberto I Hospital, Rome, Italy
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16
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Schippa S, Iebba V, Santangelo F, Gagliardi A, De Biase RV, Stamato A, Bertasi S, Lucarelli M, Conte MP, Quattrucci S. Cystic fibrosis transmembrane conductance regulator (CFTR) allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients. PLoS One 2013; 8:e61176. [PMID: 23613805 PMCID: PMC3629184 DOI: 10.1371/journal.pone.0061176] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 03/05/2013] [Indexed: 12/12/2022] Open
Abstract
Introduction In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF). CFTR mutations (F508del is the most common) lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age. Methods Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure. Results Patients were classified by two different criteria: 1) presence/absence of F508del mutation; 2) disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme) were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum) were reduced. Conclusions This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a ‘systemic disease’, linking the lung and the gut in a joined axis.
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Affiliation(s)
- Serena Schippa
- Public Health and Infectious Diseases Department, Microbiology Unit, ‘Sapienza’ University of Rome, Rome, Italy
| | - Valerio Iebba
- Public Health and Infectious Diseases Department, Microbiology Unit, ‘Sapienza’ University of Rome, Rome, Italy
- * E-mail:
| | - Floriana Santangelo
- Public Health and Infectious Diseases Department, Microbiology Unit, ‘Sapienza’ University of Rome, Rome, Italy
| | - Antonella Gagliardi
- Public Health and Infectious Diseases Department, Microbiology Unit, ‘Sapienza’ University of Rome, Rome, Italy
| | - Riccardo Valerio De Biase
- Regional Cystic Fibrosis Centre, Paediatrics and Infant Neuropsychiatry Department, ‘Sapienza’ University of Rome, Rome, Italy
| | - Antonella Stamato
- Regional Cystic Fibrosis Centre, Paediatrics and Infant Neuropsychiatry Department, ‘Sapienza’ University of Rome, Rome, Italy
| | - Serenella Bertasi
- Regional Cystic Fibrosis Centre, Paediatrics and Infant Neuropsychiatry Department, ‘Sapienza’ University of Rome, Rome, Italy
| | - Marco Lucarelli
- Department of Haematology and Cellular Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Maria Pia Conte
- Public Health and Infectious Diseases Department, Microbiology Unit, ‘Sapienza’ University of Rome, Rome, Italy
| | - Serena Quattrucci
- Regional Cystic Fibrosis Centre, Paediatrics and Infant Neuropsychiatry Department, ‘Sapienza’ University of Rome, Rome, Italy
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Tang S, Moonnumakal SP, Stevens B, Douglas G, Mason S, Schmitt ES, Eng CM, Katz M, Fang P. Characterization of a recurrent 3.8kb deletion involving exons 17a and 17b within the CFTR gene. J Cyst Fibros 2012; 12:290-4. [PMID: 22998936 DOI: 10.1016/j.jcf.2012.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/29/2012] [Accepted: 08/29/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Large deletions within CFTR have been estimated to constitute 1-2% pathogenic alleles, but the occurrence could be much higher in classical cystic fibrosis (CF) patients with one mutation detectable by the routine screening/sequencing work-up. Currently, evaluation of major CFTR rearrangements is not included in the mutation analysis for the reproductive partner of a CF patient/carrier. METHODS Exon sequencing and Multiplex Ligation-dependent Amplification (MLPA) analyses were used to make a molecular diagnosis of two unrelated CF patients. Long PCR, restriction mapping, cloning, and hot start sequencing were employed to accurately annotate the rearrangement junctions. RESULTS Both patients had a heterozygous single amino acid deletion mutation identified by sequencing, and a heterozygous deletion of CFTR exons 17a and 17b detected by MLPA. Molecular characterization of the rearrangement breakpoints indicated that the two patients had an identical complex c.2988+1616_c.3367+356del3796ins62 change, flanked by a pair of perfectly inverted repeats of 32 nucleotides. CONCLUSIONS The c.2988+1616_c.3367+356del3796ins62 complex rearrangement is a recurrent mutation from patients of different ethnic backgrounds. This mutation can be detected through a simple PCR based analysis.
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Affiliation(s)
- Sha Tang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030, United States
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18
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Schrier SA, Bodurtha JN, Burton B, Chudley AE, Chiong MAD, D'avanzo MG, Lynch SA, Musio A, Nyazov DM, Sanchez-Lara PA, Shalev SA, Deardorff MA. The Coffin-Siris syndrome: a proposed diagnostic approach and assessment of 15 overlapping cases. Am J Med Genet A 2012; 158A:1865-76. [PMID: 22711679 DOI: 10.1002/ajmg.a.35415] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/15/2012] [Indexed: 11/10/2022]
Abstract
Coffin-Siris syndrome (CSS) is a rare, clinically heterogeneous disorder often considered in the setting of cognitive/developmental delay and 5th finger/nail hypoplasia. Due to the clinical variability of facial and other features, this diagnosis is often difficult to confirm clinically and the existence of this disorder as a specific diagnosis has been at times an issue of debate. In an effort to further delineate the spectrum and key phenotypic features, we reviewed 80 previously reported cases to define features in patients that most closely correlated with a convincing diagnosis. There appear to be two subtypes of CSS, one which displays the "classic" coarse facial features previously described; another displays "variant" facial features which are less striking. Using these features, we defined an algorithm to rank the confidence of diagnosis and applied it to 15 additional patients who had been previously characterized by chromosome microarray. This approach will also facilitate uniform categorization for whole-exome analysis.
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Affiliation(s)
- Samantha A Schrier
- Division of Human Genetics, The Children's Hospital of Philadelphia, and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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19
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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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20
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Abstract
Several diseases have been clinically or genetically related to cystic fibrosis (CF), but a consensus definition is lacking. Here, we present a proposal for consensus guidelines on cystic fibrosis transmembrane conductance regulator (CFTR)-related disorders (CFTR-RDs), reached after expert discussion and two dedicated workshops. A CFTR-RD may be defined as "a clinical entity associated with CFTR dysfunction that does not fulfil diagnostic criteria for CF". The utility of sweat testing, mutation analysis, nasal potential difference, and/or intestinal current measurement for the differential diagnosis of CF and CFTR-RD is discussed. Algorithms which use genetic and functional diagnostic tests to distinguish CF and CFTR-RDs are presented. According to present knowledge, congenital bilateral absence of vas deferens (CBAVD), acute recurrent or chronic pancreatitis and disseminated bronchiectasis, all with CFTR dysfunction, are CFTR-RDs.
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Earley MC, Laxova A, Farrell PM, Driscoll-Dunn R, Cordovado S, Mogayzel PJ, Konstan MW, Hannon WH. Implementation of the first worldwide quality assurance program for cystic fibrosis multiple mutation detection in population-based screening. Clin Chim Acta 2011; 412:1376-81. [PMID: 21514289 PMCID: PMC4086748 DOI: 10.1016/j.cca.2011.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 04/08/2011] [Accepted: 04/08/2011] [Indexed: 11/21/2022]
Abstract
BACKGROUND CDC's Newborn Screening Quality Assurance Program collaborated with several U.S. Cystic Fibrosis Care Centers to collect specimens for development of a molecular CFTR proficiency testing program using dried-blood spots for newborn screening laboratories. METHODS Adult and adolescent patients or carriers donated whole blood that was aliquoted onto filter paper cards. Five blind-coded specimens were sent to participating newborn screening laboratories quarterly. Proficiency testing results were evaluated based on presumptive clinical assessment. Individual evaluations and summary reports were sent to each participating laboratory and technical consultations were offered if incorrect assessments were reported. RESULTS The current CDC repository contains specimens with 39 different CFTR mutations. Up to 45 laboratories have participated in the program. Three years of data showed that correct assessments were reported 97.7% of the time overall when both mutations could be determined. Incorrect assessments that could have lead to a missed case occurred 0.9% of the time, and no information was reported 1.1% of the time due to sample failure. CONCLUSIONS Results show that laboratories using molecular assays to detect CFTR mutations are performing satisfactorily. The programmatic results presented demonstrate the importance and complexity of providing proficiency testing for DNA-based assays.
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Affiliation(s)
- Marie C Earley
- Centers for Disease Control and Prevention, Atlanta, Georgia 30341, USA.
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Ferraguti G, Pierandrei S, Bruno SM, Ceci F, Strom R, Lucarelli M. A template for mutational data analysis of the CFTR gene. Clin Chem Lab Med 2011; 49:1447-51. [PMID: 21627495 DOI: 10.1515/cclm.2011.604] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Automated DNA sequencing produces large amounts of data that need to be analyzed by appropriate software. Personalization of software can be a difficult and time-consuming task, especially if a large number of mutations have to be analyzed. METHODS The Applied BioSystems SeqScape software, based on the KB basecaller algorithm, is a versatile tool that can be used for mutational analysis and for data quality assessment of sequences belonging to any gene of interest. Using this software we analyzed over 1400 sequences of CFTR exons and adjacent intronic zones, representing over 500,000 bases. RESULTS We present an up to date specific template and a linked set of instructions for automated labeling of all point mutations and polymorphisms of the CFTR gene, whose mutations cause cystic fibrosis (the most common genetic disease among Caucasian individuals). We also describe our refined software settings for mutational analysis, in order to keep to a minimum the need of manual validation. CONCLUSIONS The use of our template greatly simplifies the mutational analysis of the CFTR gene, reducing human intervention. In our opinion, it might not only be useful to researchers that already perform CFTR mutational analysis by sequencing methods but it should also improve the approach in those laboratories that already use ABI PRISM instrumentation for a limited mutational analysis of the CFTR gene. Similar mutational templates can also be used for other disease causing genes, thus improving molecular genetics protocols.
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Affiliation(s)
- Giampiero Ferraguti
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
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23
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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: 37] [Impact Index Per Article: 2.8] [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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24
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Sheridan MB, Hefferon TW, Wang N, Merlo C, Milla C, Borowitz D, Green ED, Mogayzel PJ, Cutting GR. CFTR transcription defects in pancreatic sufficient cystic fibrosis patients with only one mutation in the coding region of CFTR. J Med Genet 2010; 48:235-41. [PMID: 21097845 DOI: 10.1136/jmg.2010.083287] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Patients with cystic fibrosis (CF) manifest a multisystem disease due to deleterious mutations in each gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). However, the role of dysfunctional CFTR is uncertain in individuals with mild forms of CF (ie, pancreatic sufficiency) and mutation in only one CFTR gene. METHODS Eleven pancreatic sufficient (PS) CF patients with only one CFTR mutation identified after mutation screening (three patients), mutation scanning (four patients) or DNA sequencing (four patients) were studied. Bi-directional sequencing of the coding region of CFTR was performed in patients who had mutation screening or scanning. If a second CFTR mutation was not identified, CFTR mRNA transcripts from nasal epithelial cells were analysed to determine if any PS-CF patients harboured a second CFTR mutation that altered RNA expression. RESULTS Sequencing of the coding regions of CFTR identified a second deleterious mutation in five of the seven patients who previously had mutation screening or mutation scanning. Five of the remaining six patients with only one deleterious mutation identified in the coding region of one CFTR gene had a pathologic reduction in the amount of RNA transcribed from their other CFTR gene (8.4-16% of wild type). CONCLUSIONS These results show that sequencing of the coding region of CFTR followed by analysis of CFTR transcription could be a useful diagnostic approach to confirm that patients with mild forms of CF harbour deleterious alterations in both CFTR genes.
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Affiliation(s)
- Molly B Sheridan
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
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25
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Auriche C, Di Domenico EG, Pierandrei S, Lucarelli M, Castellani S, Conese M, Melani R, Zegarra-Moran O, Ascenzioni F. CFTR expression and activity from the human CFTR locus in BAC vectors, with regulatory regions, isolated by a single-step procedure. Gene Ther 2010; 17:1341-54. [PMID: 20535216 DOI: 10.1038/gt.2010.89] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have assembled two BAC vectors containing a single fragment spanning the entire CFTR locus and including the upstream and downstream regions. The two vectors differ in size of the upstream region, and were recovered in Escherichia coli, with intact BAC DNAs prepared for structural and functional analyses. Sequence analysis allowed precise mapping of the inserts. We show that the CFTR gene was wild type and is categorized as the most frequent haplotype in Caucasian populations, identified by the following polymorphisms: (GATT)₇ in intron 6a; (TG)₁₁T₇ in intron 8; V470 at position 470. CFTR expression and activity were analyzed in model cells by RT-PCR, quantitative real-time PCR, western blotting, indirect immunofluorescence and electrophysiological methods, which show the presence of an active CFTR Cl ⁻ channel. Finally, and supporting the hypothesis that CFTR functions as a receptor for Pseudomonas aeruginosa, we show that CFTR-expressing cells internalized more bacteria than parental cells that do not express CFTR. Overall, these data demonstrate that the BAC vectors contain a functional CFTR fragment and have unique features, including derivation from a single fragment, availability of a detailed genomic map and the possibility to use standard extraction procedures for BAC DNA preparations.
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Affiliation(s)
- C Auriche
- Dipartimento di Biologia Cellulare e dello Sviluppo, Sapienza Università di Roma, Roma, Italy
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26
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Bickmann JK, Kamin W, Wiebel M, Häuser F, Wenzel JJ, Neukirch C, Stuhrmann M, Lackner KJ, Rossmann H. A Novel Approach to CFTR Mutation Testing by Pyrosequencing-Based Assay Panels Adapted to Ethnicities. Clin Chem 2009; 55:1083-91. [DOI: 10.1373/clinchem.2008.120220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Cystic fibrosis (CF) is a common autosomal recessive genetic disorder caused by a variety of sequence alterations in the CFTR gene [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)]. Because the relative prevalence of mutations strongly depends on the ethnic background, first-level testing of CF as defined by recent consensus recommendations ought to be adaptable to the ethnicity of patients.
Methods: We therefore developed and implemented a diagnostic approach to first-level testing for CF based on published mutation frequencies and Pyrosequencing (PSQ) technology that we complemented with standard procedures of mutation detection at the second level.
Results: The current test system of PSQ assays for 46 target CF mutations [including CFTRdele2,3 (21 kb) and 1342-6 (T)n (5T/7T/9T)] permits recombinations of single assays to optimize sensitivities for certain ethnicities. By easy expansion of the original mutation panel, the first-level test sensitivities with other ethnic groups would be increased, provided that the mutation frequencies are known. The test was validated with our local, ethnically mixed, but mainly German population (155 patients). The mutation-detection rate for the 92 patients whose CF was confirmed by the sweat test was 89.0% for the patients of German descent (73 of the 92 patients) and 73.7% for the patients of any other origin (19 of the 92 patients). Ethnicity-adapted testing panels for our foreign CF patients would increase the sensitivities for the respective groups by approximately 5%.
Conclusions: PSQ-based genotyping is a reliable, convenient, highly flexible, and inexpensive alternative to conventional methods for first-level testing of CFTR, facilitating flexible adaptation of the analyzed mutation panel to any local ethnic group.
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Affiliation(s)
| | - Wolfgang Kamin
- CF Center of the Children’s Hospital, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Matthias Wiebel
- Department of Pulmonology, Thorax Clinic of the University Clinic of Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Karl J Lackner
- Department of Clinical Chemistry and Laboratory Medicine, and
| | - Heidi Rossmann
- Department of Clinical Chemistry and Laboratory Medicine, and
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Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 2008; 7:179-96. [PMID: 18456578 DOI: 10.1016/j.jcf.2008.03.009] [Citation(s) in RCA: 381] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 03/14/2008] [Indexed: 02/06/2023]
Abstract
It is often challenging for the clinician interested in cystic fibrosis (CF) to interpret molecular genetic results, and to integrate them in the diagnostic process. The limitations of genotyping technology, the choice of mutations to be tested, and the clinical context in which the test is administered can all influence how genetic information is interpreted. This paper describes the conclusions of a consensus conference to address the use and interpretation of CF mutation analysis in clinical settings. Although the diagnosis of CF is usually straightforward, care needs to be exercised in the use and interpretation of genetic tests: genotype information is not the final arbiter of a clinical diagnosis of CF or CF transmembrane conductance regulator (CFTR) protein related disorders. The diagnosis of these conditions is primarily based on the clinical presentation, and is supported by evaluation of CFTR function (sweat testing, nasal potential difference) and genetic analysis. None of these features are sufficient on their own to make a diagnosis of CF or CFTR-related disorders. Broad genotype/phenotype associations are useful in epidemiological studies, but CFTR genotype does not accurately predict individual outcome. The use of CFTR genotype for prediction of prognosis in people with CF at the time of their diagnosis is not recommended. The importance of communication between clinicians and medical genetic laboratories is emphasized. The results of testing and their implications should be reported in a manner understandable to the clinicians caring for CF patients.
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29
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Bareil C, Guittard C, Altieri JP, Templin C, Claustres M, des Georges M. Comprehensive and rapid genotyping of mutations and haplotypes in congenital bilateral absence of the vas deferens and other cystic fibrosis transmembrane conductance regulator-related disorders. J Mol Diagn 2008; 9:582-8. [PMID: 17975025 DOI: 10.2353/jmoldx.2007.070040] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Available commercial kits only screen for the most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations causing classic cystic fibrosis and for the Tn variant in IVS8. However, full scanning of CFTR is needed for the diagnosis of patients with cystic fibrosis or CFTR-related disorders (including congenital bilateral absence of the vas deferens) bearing rare mutations. Standard strategies for detecting point mutations rely on extensive scanning of the gene by denaturing gradient gel electrophoresis or denaturing high performance liquid chromatography, which are time-consuming. Moreover, the haplotyping of IVS8-(TG)m and Tn tracts is still challenging despite several recent improvements. We have optimized both the detection of mutations and the haplotyping of IVS8 polyvariants in developing two methods: i) a rapid and robust direct sequence analysis of all exons/flanking introns of the CFTR gene based on single condition touchdown amplification/sequencing in 96-well plates, and ii) a fluorescent assay that allows haplotyping of IVS8-(TG)mTn even without family linkage study. Combined with search for rare large rearrangements, this strategy detected 87.9% of CFTR defects in congenital bilateral absence of the vas deferens patients, a proportion considerably higher than those usually reported. These highly efficient tests, scanning each sample in a few days, greatly improve the genotyping of patients with CFTR-related symptoms and may be particularly important in emergency situations such as fetus with hyperechogenic bowel suggestive of cystic fibrosis.
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Affiliation(s)
- Corinne Bareil
- Laboratoire de Génétique Moléculaire, Institut Universitaire de Recherche Clinique, 641 av du doyen Gaston Giraud, Montpellier cedex 5, France
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30
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Narzi L, Ferraguti G, Stamato A, Narzi F, Valentini SB, Lelli A, Delaroche I, Lucarelli M, Strom R, Quattrucci S. Does cystic fibrosis neonatal screening detect atypical CF forms? Extended genetic characterization and 4-year clinical follow-up. Clin Genet 2007; 72:39-46. [PMID: 17594398 DOI: 10.1111/j.1399-0004.2007.00825.x] [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: 11/30/2022]
Abstract
The neonatal screening protocol for cystic fibrosis (CF) is based on a first determination of blood immunoreactive trypsin (IRT1), followed by a first level genetic test that includes the 31 worldwide most common mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene (DNA31), and a second determination of blood immunoreactive trypsin (IRT2). This approach identifies, in addition to affected subjects, a high proportion of newborns with hypertrypsinaemia at birth, in whom only one mutation is identified and who have a negative or borderline sweat test and pancreatic sufficiency. Although it has been suggested that hypertrypsinaemia may be caused by a single CFTR mutation, whether such neonates should be merely considered as healthy carriers remains a matter of debate as hypertrypsinaemia at birth may be a biochemical marker of a CFTR malfunction because of a second mild mutation. We analyzed, by means of an extended sequencing protocol, 32 newborns who tested positive at an IRT1/DNA31/IRT2 screening protocol and in whom only one CFTR mutation was found. The results obtained demonstrate that 62.5% of these newborns were also carrying a second mild CFTR mutation. The high proportion of compound heterozygous subjects, combined with the results of a 4-year follow-up in nine of these subjects all of whom displaying initial CF clinical symptoms, suggest that it may be possible to use the IRT1/DNA31/IRT2 protocol of neonatal screening to identify newborns with atypical forms of CF. In view of these findings, an extended genetic search for subjects with compound heterozygosity and a periodic clinical assessment should be considered.
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Affiliation(s)
- L Narzi
- Department of Paediatrics, Cystic Fibrosis Centre, University of Rome La Sapienza, Rome, Italy
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