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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: 1] [Impact Index Per Article: 1.0] [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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2
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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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3
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Guo W, Ji P, Xie Y. Genetic diagnosis and treatment of hereditary renal tubular disease with hypokalemia and alkalosis. J Nephrol 2023; 36:575-591. [PMID: 35994232 DOI: 10.1007/s40620-022-01428-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Renal tubules play an important role in maintaining water, electrolyte, and acid-base balance. Renal tubule dysfunction can cause electrolyte disorders and acid-base imbalance. Clinically, hypokalemic renal tubular disease is the most common tubule disorder. With the development of molecular genetics and gene sequencing technology, hereditary renal tubular diseases have attracted attention, and an increasing number of pathogenic genes related to renal tubular diseases have been discovered and reported. Inherited renal tubular diseases mainly occur due to mutations in genes encoding various specific transporters or ion channels expressed on the tubular epithelial membrane, leading to dysfunctional renal tubular reabsorption, secretion, and excretion. An in-depth understanding of the molecular genetic basis of hereditary renal tubular disease will help to understand the physiological function of renal tubules, the mechanism by which the kidney maintains water, electrolyte, and acid-base balance, and the relationship between the kidney and other systems in the body. Meanwhile, understanding these diseases also improves our understanding of the pathogenesis of hypokalemia, alkalosis and other related diseases and ultimately promotes accurate diagnostics and effective disease treatment. The present review summarizes the most common hereditary renal tubular diseases (Bartter syndrome, Gitelman syndrome, EAST syndrome and Liddle syndrome) characterized by hypokalemia and alkalosis. Further detailed explanations are provided for pathogenic genes and functional proteins, clinical manifestations, intrinsic relationship between genotype and clinical phenotype, diagnostic clues, differential diagnosis, and treatment strategies for these diseases.
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Affiliation(s)
- Wenkai Guo
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, People's Republic of China
- School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China
| | - Pengcheng Ji
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, People's Republic of China
| | - Yuansheng Xie
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, People's Republic of China.
- School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China.
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Blaconà G, Raso R, Castellani S, Pierandrei S, Del Porto P, Ferraguti G, Ascenzioni F, Conese M, Lucarelli M. Downregulation of epithelial sodium channel (ENaC) activity in cystic fibrosis cells by epigenetic targeting. Cell Mol Life Sci 2022; 79:257. [PMID: 35462606 PMCID: PMC9035428 DOI: 10.1007/s00018-022-04190-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 12/31/2022]
Abstract
The pathogenic mechanism of cystic fibrosis (CF) includes the functional interaction of the cystic fibrosis transmembrane conductance regulator (CFTR) protein with the epithelial sodium channel (ENaC). The reduction of ENaC activity may constitute a therapeutic option for CF. This hypothesis was evaluated using drugs that target the protease-dependent activation of the ENaC channel and the transcriptional activity of its coding genes. To this aim we used: camostat, a protease inhibitor; S-adenosyl methionine (SAM), showed to induce DNA hypermethylation; curcumin, known to produce chromatin condensation. SAM and camostat are drugs already clinically used in other pathologies, while curcumin is a common dietary compound. The experimental systems used were CF and non-CF immortalized human bronchial epithelial cell lines as well as human bronchial primary epithelial cells. ENaC activity and SCNN1A, SCNN1B and SCNN1G gene expression were analyzed, in addition to SCNN1B promoter methylation. In both immortalized and primary cells, the inhibition of extracellular peptidases and the epigenetic manipulations reduced ENaC activity. Notably, the reduction in primary cells was much more effective. The SCNN1B appeared to be the best target to reduce ENaC activity, in respect to SCNN1A and SCNN1G. Indeed, SAM treatment resulted to be effective in inducing hypermethylation of SCNN1B gene promoter and in lowering its expression. Importantly, CFTR expression was unaffected, or even upregulated, after treatments. These results open the possibility of CF patients’ treatment by epigenetic targeting.
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Affiliation(s)
- Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Roberto Raso
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Paola Del Porto
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy. .,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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Farra C, Awwad J, Hamadeh L, Khoueiry P, Halawi Z, Yazbeck N, Daher R, Souaid M, Hamdar L, Yammine T, Yunis K. CFTR mutational screening by next-generation sequencing reveals novel variants and a high carrier rate in a Middle Eastern population. Ann Hum Genet 2021; 86:80-86. [PMID: 34888852 DOI: 10.1111/ahg.12450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
Cystic fibrosis is the most common life-limiting autosomal recessive disease in western countries with an incidence of 1:2500 in United States and 1:1000 in some European countries. Similar incidences were noted for the Middle East with variations from 1 in 2560 to 1 in 15,876 according to the degree of consanguinity. This is a preliminary systematic study that aims to assess the incidence and carrier rate of cystic fibrosis in the Middle Eastern Lebanese population; known for a high frequency of consanguinity. One hundred thirteen DNA samples were collected from neonatal blood cards obtained from newborns to healthy unrelated families with no previous history of Cystic fibrosis. Screening for Cystic Fibrosis-causing pathogenic variants was performed using next generation sequencing, and 17 different single nucleotide variants were detected, including six pathogenic and likely pathogenic. 5.5%-7% newborns were found to be carriers of a variant strongly suggestive of pathogenicity and comparable to published literature worldwide. This pilot analysis highlights the challenging interpretation of CFTR variants in a country underrepresented by large ethnic population analyses, and stresses the importance of premarital screening programs for Cystic fibrosis.
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Affiliation(s)
- Chantal Farra
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Johnny Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lama Hamadeh
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Zeina Halawi
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nadine Yazbeck
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rose Daher
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mirna Souaid
- Medical Genetics Unit, Department of pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Layal Hamdar
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Tony Yammine
- Medical Genetics Unit, Saint Joseph University, Beirut, Lebanon
| | - Khalid Yunis
- Department of Pediatrics, American University of Beirut Medical Center, Beirut, Lebanon
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Cantú-Reyna C, Galindo-Ramírez R, Vázquez-Cantú M, Haddad-Talancón L, García-Muñoz W. Frequency of allele variations in the CFTR gene in a Mexican population. BMC Med Genomics 2021; 14:262. [PMID: 34740355 PMCID: PMC8569977 DOI: 10.1186/s12920-021-01111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
Background Cystic fibrosis (CF) is an autosomal recessive disorder caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CF variants incidence is highly variable and even undetermined in some countries like Mexico. Methods In this study, the allele frequencies of 361 variants in the CFTR gene were investigated in 1455 Mexicans without a CF or CFTR-related disorders (CFTR-RD) diagnosis. We also performed a statistical comparative analysis against allele frequencies of different populations to measure genetic differences in the prevalence of CFTR variants. Results In the vast majority of cases, the allele frequencies of this cohort were comparable to those found in other populations. However, some variants displayed significant differences in their allele frequencies when compared with European and African populations. Conclusions This study provides information about CFTR variants to predict the prevalence of CF in Mexico and uncover other unknown but frequent pathogenic variants in the country. Additionally, other CFTR-RD variants have also been studied using population data of the same CFTR variants. Studies like this could help develop a regional molecular diagnostic screen to optimize the medical care of CF patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01111-w.
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Affiliation(s)
- Consuelo Cantú-Reyna
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Roberto Galindo-Ramírez
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico
| | - Mercedes Vázquez-Cantú
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Lorenza Haddad-Talancón
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico
| | - Willebaldo García-Muñoz
- Laboratorio de genética humana, Código 46, S.A de C.V, Camelias 3-Int 10, Los Tabachines, C.P. 62498, Cuernavaca Morelos, Mexico.
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7
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Terlizzi V, Claut L, Tosco A, Colombo C, Raia V, Fabrizzi B, Lucarelli M, Angeloni A, Cimino G, Castaldo A, Marsiglio L, Timpano S, Cirilli N, Moroni L, Festini F, Piccinini P, Zavataro L, Bonomi P, Taccetti G, Southern KW, Padoan R. A survey of the prevalence, management and outcome of infants with an inconclusive diagnosis following newborn bloodspot screening for cystic fibrosis (CRMS/CFSPID) in six Italian centres. J Cyst Fibros 2021; 20:828-834. [PMID: 33883100 DOI: 10.1016/j.jcf.2021.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVE We evaluated the prevalence, Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene profile, clinical data, management and outcome for infants with a CFTR-related metabolic syndrome/CF Screen Positive, Inconclusive Diagnosis (CRMS/CFSPID) designation from six Italian centres. METHODS All newborn bloodspot screening (NBS) positive infants born from January 2011 to August 2018 with a CF diagnosis or a CRMS/CFSPID designation were enrolled. Data on sweat testing, genetics, clinical course and management were collected. RESULTS We enrolled 257 CF patientsand 336 infants with a CRMS/CFSPID designation (CF: CRMS/CFSPID ratio of 1:1.30).Blood immuno-reactive trypsinogen (IRT) was significantly lower in CRMS/CFSPID infants and the F508del variant accounted for only 20% of alleles. Children with CRMS/CFSPID showed a milder clinical course, pancreatic sufficiency compared to CF infants. Varied practice across centres was identified regarding sweat testing, chest radiograph (8-100%) and salt supplementation (11-90%). Eighteen (5.3%) CRMS/CFSPID infants converted or were reclassified to diagnosis of CF. Four infants (1.3%) developed a clinical feature consistent with a CFTR-related disorder (1.2%). Twenty-seven were re-classified as healthy carriers (8.0%) and 16 as healthy infants (4.8%). CONCLUSIONS We have identified considerable variability in the evaluation and management of infants with an inconclusive diagnosis following NBS across six Italian centres. CRMS/CFSPID is more regularly seen in this population compared to countries with higher prevalence of F508del.Conversion to a CF diagnosis was recorded in 18 (5.3%) of CRMS/CFSPID infants and in 16 was as a result of increasing sweat chloride concentration.
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Affiliation(s)
- Vito Terlizzi
- Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Anna Meyer Children's University, Florence, 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
| | - Antonella Tosco
- 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
| | - Valeria Raia
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Regional Reference Center, A.O.U. Policlinico Umberto I, Rome, Italy
| | - Alice Castaldo
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Laura Marsiglio
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Silviana Timpano
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Natalia Cirilli
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Laura Moroni
- Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Filippo Festini
- Department of Health Sciences, University of Florence, Florence, Italy
| | | | - Lucia Zavataro
- Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Anna Meyer Children's University, Florence, Italy
| | | | - Giovanni Taccetti
- Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Anna Meyer Children's University, Florence, Italy
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, Institute in the Park, Alder Hey Children's Hospital, Liverpool, United Kingdom
| | - Rita Padoan
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
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8
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Pierandrei S, Truglio G, Ceci F, Del Porto P, Bruno SM, Castellani S, Conese M, Ascenzioni F, Lucarelli M. DNA Methylation Patterns Correlate with the Expression of SCNN1A, SCNN1B, and SCNN1G (Epithelial Sodium Channel, ENaC) Genes. Int J Mol Sci 2021; 22:ijms22073754. [PMID: 33916525 PMCID: PMC8038451 DOI: 10.3390/ijms22073754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
The interplay between the cystic fibrosis transmembrane conductance regulator (CFTR) and the epithelial sodium channel (ENaC) in respiratory epithelia has a crucial role in the pathogenesis of cystic fibrosis (CF). The comprehension of the mechanisms of transcriptional regulation of ENaC genes is pivotal to better detail the pathogenic mechanism and the genotype-phenotype relationship in CF, as well as to realize therapeutic approaches based on the transcriptional downregulation of ENaC genes. Since we aimed to study the epigenetic transcriptional control of ENaC genes, an assessment of their expression and DNA methylation patterns in different human cell lines, nasal brushing samples, and leucocytes was performed. The mRNA expression of CFTR and ENaC subunits α, β and γ (respectively SCNN1A, SCNN1B, and SCNN1G genes) was studied by real time PCR. DNA methylation of 5'-flanking region of SCNN1A, SCNN1B, and SCNN1G genes was studied by HpaII/PCR. The levels of expression and DNA methylation of ENaC genes in the different cell lines, brushing samples, and leukocytes were very variable. The DNA regions studied of each ENaC gene showed different methylation patterns. A general inverse correlation between expression and DNA methylation was evidenced. Leukocytes showed very low expression of all the 3 ENaC genes corresponding to a DNA methylated pattern. The SCNN1A gene resulted to be the most expressed in some cell lines that, accordingly, showed a completely demethylated pattern. Coherently, a heavy and moderate methylated pattern of, respectively, SCNN1B and SCNN1G genes corresponded to low levels of expression. As exceptions, we found that dexamethasone treatment appeared to stimulate the expression of all the 3 ENaC genes, without an evident modulation of the DNA methylation pattern, and that in nasal brushing a considerable expression of all the 3 ENaC genes were found despite an apparent methylated pattern. At least part of the expression modulation of ENaC genes seems to depend on the DNA methylation patterns of specific DNA regions. This points to epigenetics as a controlling mechanism of ENaC function and as a possible therapeutic approach for CF.
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Affiliation(s)
- Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Gessica Truglio
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Fabrizio Ceci
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
| | - Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Via Napoli 121, 71122 Foggia, Italy;
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
- Correspondence: (F.A.); (M.L.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Viale Regina Elena 291, 00161 Roma, Italy
- Correspondence: (F.A.); (M.L.)
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9
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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10
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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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11
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Carriers of cystic fibrosis among sperm donors: complete CFTR gene analysis versus CFTR genotyping. Fertil Steril 2020; 114:524-534. [PMID: 32773111 DOI: 10.1016/j.fertnstert.2020.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine the frequency of cystic fibrosis (CF) carriers among sperm donors in Spain studied through a complete analysis of the CFTR gene and to compare the results with those that would have been obtained by the 4 genotyping panels of the CFTR gene most commonly used as a carrier test in the context of assisted reproduction in our country. DESIGN Descriptive observational study. SETTING Private center. PATIENTS Nine hundred thirty-five sperm donors, from January 2014 to June 2019. INTERVENTION None. MAIN OUTCOME MEASURE Presence of pathogenic variants in the CFTR gene. RESULTS 17% of the donors were carriers of at least 1 pathogenic variant in CFTR, with 39 different pathogenic variants detected. Only 4 of these 39 variants (10.27%) would have been detected by the 4 genotyping tests considered, and 22 variants (56.41%) would not have been detected by any of the genotyping tests. The pathogenic variants of the CFTR gene included in the different genotyping tests analyzed vary widely, and <50% are common to all of them. CONCLUSIONS Although the was not based in the general population, these results show that the use of genotyping tests is associated with a high reproductive risk, because the rate of detection of CF carriers was lower when these panels were applied, in comparison with the complete study of the CFTR gene. We recommend that complete sequencing of the CFTR gene by next-generation sequencing be performed as a screening method for CF in sperm donors.
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12
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Nappo S, Mannucci L, Novelli G, Sangiuolo F, D'Apice MR, Botta A. Carrier frequency of CFTR variants in the non-Caucasian populations by genome aggregation database (gnomAD)-based analysis. Ann Hum Genet 2020; 84:463-468. [PMID: 32484936 DOI: 10.1111/ahg.12396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 11/30/2022]
Abstract
The complexity in the molecular diagnosis of Cystic Fibrosis (CF) also depends on the variable prevalence/incidence of the disease associated with the wide CFTR allelic heterogeneity among different populations. In fact, CF incidence in Asian and African countries is underestimated and the few patients reported so far have rare or unique CFTR pathogenic variants. To obtain insights into CF variants profile and frequency, we used the large population sequencing data in the Genome Aggregation Database (gnomAD). We selected 207 CF-causing/varying clinical consequence variants from CFTR2 database and additional 15 variants submitted to the ClinVar database. Only 14 of these variants were found in the East-Asian population, while for South-Asian and African populations we identified 43 and 52 variants, respectively, confirming the peculiarity of the CFTR allelic spectrum with only few population-specific variants. These data could be used to optimize CFTR carrier screening in non-Caucasian subjects, choosing between the full gene sequencing and cost and time-effective targeted panels.
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Affiliation(s)
| | | | - Giuseppe Novelli
- Medical Genetics Unit, Policlinico Tor Vergata, Rome, Italy.,Neuromed IRCCS Institute, Pozzilli, IS, Italy.,Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome Tor Vergata, Rome, Italy
| | - Federica Sangiuolo
- Medical Genetics Unit, Policlinico Tor Vergata, Rome, Italy.,Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome Tor Vergata, Rome, Italy
| | | | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome Tor Vergata, Rome, Italy
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13
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Abstract
Next generation DNA sequencing (NGS) has the potential to improve the diagnostic and prognostic utility of newborn screening programmes. This study assesses the feasibility of automating NGS on dried blood spot (DBS) DNA in a United Kingdom National Health Service (UK NHS) laboratory. An NGS panel targeting the entire coding sequence of five genes relevant to disorders currently screened for in newborns in the UK was validated on DBS DNA. An automated process for DNA extraction, NGS and bioinformatics analysis was developed. The process was tested on DBS to determine feasibility, turnaround time and cost. The analytical sensitivity of the assay was 100% and analytical specificity was 99.96%, with a mean 99.5% concordance of variant calls between DBS and venous blood samples in regions with ≥30× coverage (96.8% across all regions; all variant calls were single nucleotide variants (SNVs), with indel performance not assessed). The pipeline enabled processing of up to 1000 samples a week with a turnaround time of four days from receipt of sample to reporting. This study concluded that it is feasible to automate targeted NGS on routine DBS samples in a UK NHS laboratory setting, but it may not currently be cost effective as a first line test.
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14
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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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15
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Martínez-Hernández A, Larrosa J, Barajas-Olmos F, García-Ortíz H, Mendoza-Caamal EC, Contreras-Cubas C, Mirzaeicheshmeh E, Lezana JL, Orozco L. Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report. BMC Med Genomics 2019; 12:68. [PMID: 31118044 PMCID: PMC6532186 DOI: 10.1186/s12920-019-0528-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/13/2019] [Indexed: 01/18/2023] Open
Abstract
Background Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF). Case presentation Here, we report the first case of a novel/de novo variant in a Mexican patient with CF. Our patient was an 8-year-old male who had exhibited the clinical onset of CF at one month of age, with steatorrhea, malabsorption, poor weight gain, anemia, and recurrent respiratory tract infections. Complete sequencing of the CFTR gene by next generation sequencing (NGS) revealed two different variants in trans, including the previously reported CF-causing variant c.3266G > A (p.Trp1089*, W1089*), that was inherited from the mother, and the novel/de novo CFTR variant c.1762G > T (p.Glu588*). Conclusion Our results demonstrate the efficiency of targeted NGS for making a rapid and precise diagnosis in patients with clinically suspected CF. This method can enable the provision of accurate genetic counselling, and improve our understanding of the molecular basis of genetic diseases.
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Affiliation(s)
- Angélica Martínez-Hernández
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Julieta Larrosa
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico y Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Humberto García-Ortíz
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | | | - Cecilia Contreras-Cubas
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Elaheh Mirzaeicheshmeh
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - José Luis Lezana
- Clinica de Fibrosis Quística y Laboratorio de Fisiologia Pulmonar Hospital Infantil de México Federico Gómez. Asociación Mexicana de Fibrosis Quística, A. C, CDMX, Mexico City, Mexico
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico.
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16
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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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Raraigh KS, Pastore MT, Greene L, Karczeski BA, Fisher LK, Ramsey BW, Langfelder-Schwind E. Diagnosis and Treatment of Cystic Fibrosis: A (Not-so) Simple Recessive Condition. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Lucarelli M. New era of cystic fibrosis: Full mutational analysis and personalized therapy. World J Med Genet 2017; 7:1-9. [DOI: 10.5496/wjmg.v7.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/19/2016] [Accepted: 02/21/2017] [Indexed: 02/07/2023] Open
Abstract
Despite its apparently simple genetics, cystic fibrosis (CF) is a rather complex genetic disease. A lot of variability in the steps of the path from the cystic fibrosis transmembrane conductance regulator (CFTR) gene to the clinical manifestations originates an uncertain genotype - phenotype relationship. A major determinant of this uncertainty is the incomplete knowledge of the CFTR mutated genotypes, due to the high number of CFTR mutations and to the higher number of their combinations in trans and in cis. Also the very limited knowledge of functional effects of CFTR mutated alleles severely impairs our diagnostic and prognostic ability. The final phenotypic modulation exerted by CFTR modifier genes and interactome further complicates the framework. The next generation sequencing approach is a rapid, low-cost and high-throughput tool that allows a near complete structural characterization of CFTR mutated genotypes, as well as of genotypes of several other genes cooperating to the final CF clinical manifestations. This powerful method perfectly complements the new personalized therapeutic approach for CF. Drugs active on specific CFTR mutational classes are already available for CF patients or are in phase 3 trials. A complete genetic characterization has been becoming crucial for a correct personalized therapy. However, the need of a functional classification of each CFTR mutation potently arises. Future big efforts towards an ever more detailed knowledge of both structural and functional CFTR defects, coupled to parallel personalized therapeutic interventions decisive for CF cure can be foreseen.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00161 Rome, Italy
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