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Balderacchi AM, Bignotti M, Ottaviani S, Denardo A, Barzon V, Ben Khlifa E, Vailati G, Piloni D, Benini F, Corda L, Corsico AG, Ferrarotti I, Fra A. Quantification of circulating alpha-1-antitrypsin polymers associated with different SERPINA1 genotypes. Clin Chem Lab Med 2024; 62:1980-1990. [PMID: 38407261 DOI: 10.1515/cclm-2023-1348] [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: 11/24/2023] [Accepted: 02/15/2024] [Indexed: 02/27/2024]
Abstract
OBJECTIVES Alpha-1-antitrypsin deficiency is a genetic disorder caused by mutations in the SERPINA1 gene encoding alpha-1-antitrypsin (AAT), the major serine protease inhibitor in plasma. Reduced AAT levels are associated with elevated risk of developing emphysema mainly due to uncontrolled activity of neutrophil elastase in the lungs. The prevalent Z-AAT mutant and many rare pathogenic AAT variants also predispose to liver disease due to their accumulation as polymeric chains in hepatocytes. Part of these polymers are secreted into the bloodstream and could represent biomarkers of intra-hepatic accumulation. Moreover, being inactive, they further lower lung protection against proteases. Aim of our study is to accurately quantify the percentage of circulating polymers (CP) in a cohort of subjects with different SERPINA1 genotypes. METHODS CP concentration was measured in plasma or Dried Blood Spot (DBS) by a sensitive sandwich ELISA based on capture by the polymer-specific 2C1 monoclonal antibody. RESULTS CP were significantly elevated in patients with the prevalent PI*SZ and PI*ZZ genotypes, with considerable intra-genotype variability. Notably, higher percentage of polymers was observed in association with elevated C-reactive protein. CP levels were also increased in carriers of the Mmalton variant, and of Mprocida, I, Plowell and Mherleen in heterozygosity with Z-AAT. CONCLUSIONS These findings highlight the importance of implementing CP quantification in a clinical laboratory. Indeed, the variable amount of CP in patients with the same genotype may correlate with the variable severity of the associated lung and liver diseases. Moreover, CP can reveal the polymerogenic potential of newly discovered ultrarare AAT variants.
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Affiliation(s)
- Alice M Balderacchi
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, 18631Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mattia Bignotti
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 9297University of Brescia, Brescia, Italy
| | - Stefania Ottaviani
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, 18631Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Andrea Denardo
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 9297University of Brescia, Brescia, Italy
| | - Valentina Barzon
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, 19001University of Pavia, Pavia, Italy
| | - Emna Ben Khlifa
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 9297University of Brescia, Brescia, Italy
| | - Guido Vailati
- Referral Centre for Alpha-1 Antitrypsin Deficiency, 18515 Spedali Civili , Brescia, Italy
| | - Davide Piloni
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, 18631Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Benini
- Referral Centre for Alpha-1 Antitrypsin Deficiency, 18515 Spedali Civili , Brescia, Italy
| | - Luciano Corda
- Referral Centre for Alpha-1 Antitrypsin Deficiency, 18515 Spedali Civili , Brescia, Italy
| | - Angelo G Corsico
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, 18631Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, 19001University of Pavia, Pavia, Italy
| | - Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, 18631Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, 19001University of Pavia, Pavia, Italy
| | - Annamaria Fra
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 9297University of Brescia, Brescia, Italy
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2
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González-Carracedo MA, Herrera-Luis E, Marco-Simancas M, Escuela-Escobar A, Martín-González E, Sardón-Prado O, Corcuera P, Hernández-Pérez JM, Lorenzo-Díaz F, Pérez-Pérez JA. Haplotype-Aware Detection of SERPINA1 Variants by Nanopore Sequencing. J Mol Diagn 2024:S1525-1578(24)00195-8. [PMID: 39276924 DOI: 10.1016/j.jmoldx.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 09/17/2024] Open
Abstract
α-1 Antitrypsin (AAT) is an acute-phase reactant with immunomodulatory properties that mainly inhibits neutrophil elastase. Low serum levels cause AAT deficiency (AATD), an underdiagnosed condition that predisposes to pulmonary and hepatic diseases. The SERPINA1 gene, which encodes AAT, contains >500 variants. PI∗Z and PI∗S alleles are the most diagnosed causes of AATD, but the role of the SERPINA1 haplotypes in AAT function remains unknown. SERPINA1 gene was PCR amplified from 94 patients with asthma, using primers with tails for indexing. Sequencing libraries were loaded into a MinION-Mk1C, and MinKNOW was used for basecalling and demultiplexing. Nanofilt and Minimap2 were used for filtering and mapping/alignment. Variant calling/phasing were performed with PEPPER-Margin-DeepVariant. SERPINA1 gene was 100% covered for all samples, with a minimum sequencing depth of 500×. A total of 75 single-nucleotide variants (SNVs) and 4 insertions/deletions were detected, with 45 and 2 of them highly polymorphic (minor allele frequency >0.1), respectively. Nine of the SNVs showed differences in allele frequencies when compared with the overall Spanish population. More than 90% of heterozygous SNVs were phased, yielding 91 and 58 different haplotypes for each SERPINA1 amplified region. Haplotype-based linkage disequilibrium analysis suggests that a recombination hotspot could generate variation in the SERPINA1 gene. The proposed workflow enables haplotype-aware genotyping of the SERPINA1 gene by nanopore sequencing, which will allow the development of novel AATD diagnostic strategies.
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Affiliation(s)
- Mario A González-Carracedo
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - Esther Herrera-Luis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - María Marco-Simancas
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - Ainhoa Escuela-Escobar
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain
| | - Elena Martín-González
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - Olaia Sardón-Prado
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain; Department of Pediatrics, University of the Basque Country, San Sebastián, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
| | - Jose M Hernández-Pérez
- Department of Respiratory Medicine, Hospital Universitario de N.S. de Candelaria, Tenerife, Spain
| | - Fabián Lorenzo-Díaz
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain
| | - José A Pérez-Pérez
- Genetics Laboratory, Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Tenerife, Spain; Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Spain.
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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Mróz J, Pelc M, Mitusińska K, Chorostowska-Wynimko J, Jezela-Stanek A. Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT). Genes (Basel) 2024; 15:340. [PMID: 38540399 PMCID: PMC10970068 DOI: 10.3390/genes15030340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 06/14/2024] Open
Abstract
In the rapidly advancing field of bioinformatics, the development and application of computational tools to predict the effects of single nucleotide variants (SNVs) are shedding light on the molecular mechanisms underlying disorders. Also, they hold promise for guiding therapeutic interventions and personalized medicine strategies in the future. A comprehensive understanding of the impact of SNVs in the SERPINA1 gene on alpha-1 antitrypsin (AAT) protein structure and function requires integrating bioinformatic approaches. Here, we provide a guide for clinicians to navigate through the field of computational analyses which can be applied to describe a novel genetic variant. Predicting the clinical significance of SERPINA1 variation allows clinicians to tailor treatment options for individuals with alpha-1 antitrypsin deficiency (AATD) and related conditions, ultimately improving the patient's outcome and quality of life. This paper explores the various bioinformatic methodologies and cutting-edge approaches dedicated to the assessment of molecular variants of genes and their product proteins using SERPINA1 and AAT as an example.
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Affiliation(s)
- Jakub Mróz
- Tunneling Group, Biotechnology Center, Silesian University of Technology, Krzywoustego St. 8, 44-100 Gliwice, Poland;
| | - Magdalena Pelc
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Center, Silesian University of Technology, Krzywoustego St. 8, 44-100 Gliwice, Poland;
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01-138 Warsaw, Poland; (M.P.); (J.C.-W.)
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5
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Piloni D, Ottaviani S, Saderi L, Corda L, Baderna P, Barzon V, Balderacchi AM, Seebacher C, Balbi B, Albicini F, Corino A, Mennitti MC, Tirelli C, Spreafico F, Bosio M, Mariani F, Sotgiu G, Corsico AG, Ferrarotti I. Comparison among populations with severe and intermediate alpha1-antitrypsin deficiency and chronic obstructive pulmonary disease. Minerva Med 2024; 115:23-31. [PMID: 37021471 DOI: 10.23736/s0026-4806.22.08266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
BACKGROUND Severe alpha1-antitrypsin (AAT) deficiency (AATD) is associated with a high risk of airflow obstruction and emphysema. The risk of lung disease in those with intermediate AAT deficiency is unclear. Our aims were to compare pulmonary function, time of onset of symptoms, and indicators of quality of life among patients with severe AATD (PI*ZZ), patients with intermediate AATD (PI*MZ) from the Italian Registry of AATD with a chronic obstructive pulmonary disease (COPD) cohort of patients without AATD (PI*MM). METHODS We considered a total of 613 patients: 330 with the PI*ZZ genotype, 183 with the PI*MZ genotype and 100 with the PI*MM genotype. Radiological exams, pulmonary function test, and measurement of quality of life have been performed on all cohorts of patients. RESULTS The three populations differ significantly in terms of age at COPD/AATD diagnosis (P=0.00001), respiratory function (FEV1, FVC, DLCO P<0.001), quality of life (P=0.0001) and smoking history (P<0.0001). PI*ZZ genotype had 24.9 times a higher likelihood of developing airflow obstruction. The MZ genotype is not associated with a significant early risk of airflow obstruction. CONCLUSIONS The comparison of populations with PI*ZZ, MZ and MM genotypes allows to delineate the role of alpha1-antitrypsin deficiency on respiratory function and on the impact on quality of life, in relation to other risk factors. These results highlight the crucial role of primary and secondary prevention on smoking habits in PI*MZ subjects and the importance of an early diagnosis.
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Affiliation(s)
- Davide Piloni
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
| | - Stefania Ottaviani
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
| | - Laura Saderi
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Luciano Corda
- First Division of Medicine, ASST Spedali Civili, Brescia, Italy
| | | | - Valentina Barzon
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
| | - Alice M Balderacchi
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
| | | | - Bruno Balbi
- Division of Pneumology, IRCCS Maugeri Scientific Clinical Institutes, Veruno, Novara, Italy
| | - Federica Albicini
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
| | - Alessandra Corino
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
| | - Maria C Mennitti
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
| | - Claudio Tirelli
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
| | - Fabio Spreafico
- First Division of Medicine, ASST Spedali Civili, Brescia, Italy
| | - Matteo Bosio
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
| | - Francesca Mariani
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
| | - Giovanni Sotgiu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Angelo G Corsico
- Section of Pneumology, IRCCS San Matteo Polyclinic Foundation, Pavia, Italy
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy
- AATD Core Network of European Reference Network LUNG, Frankfurt am Main, Germany
| | - Ilaria Ferrarotti
- Department of Internal Medicine, and Therapeutics, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Polyclinic Foundation, University of Pavia, Pavia, Italy -
- AATD Core Network of European Reference Network LUNG, Frankfurt am Main, Germany
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Papiris SA, Veith M, Papaioannou AI, Apollonatou V, Ferrarotti I, Ottaviani S, Tzouvelekis A, Tzilas V, Rovina N, Stratakos G, Gerogianni I, Daniil Z, Kolilekas L, Dimakou K, Pitsidianakis G, Tzanakis N, Tryfon S, Fragopoulos F, Antonogiannaki EM, Lazaratou A, Fouka E, Papakosta D, Emmanouil P, Anagnostopoulos N, Karampitsakos T, Vlami K, Kallieri M, Lyberopoulos P, Loukides S, Bouros D, Bush A, Balduyck M, Lombard C, Cottin V, Mornex JF, Vogelmeier CF, Greulich T, Manali ED. Alpha1-antitrypsin deficiency in Greece: Focus on rare variants. Pulmonology 2024; 30:43-52. [PMID: 36797151 DOI: 10.1016/j.pulmoe.2022.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 02/16/2023] Open
Abstract
PURPOSE A1Antitrypsin deficiency (AATD) pathogenic mutations are expanding beyond the PI*Z and PI*S to a multitude of rare variants. AIM to investigate genotype and clinical profile of Greeks with AATD. METHODS Symptomatic adult-patients with early-emphysema defined by fixed airway obstruction and computerized-tomography scan and lower than normal serum AAT levels were enrolled from reference centers all over Greece. Samples were analyzed in the AAT Laboratory, University of Marburg-Germany. RESULTS Included are 45 adults, 38 homozygous or compound heterozygous for pathogenic variants and 7 heterozygous. Homozygous were 57.9% male, 65.8% ever-smokers, median (IQR) age 49.0(42.5-58.5) years, AAT-levels 0.20(0.08-0.26) g/L, FEV1(%predicted) 41.5(28.8-64.5). PI*Z, PI*Q0, and rare deficient allele's frequency was 51.3%, 32.9%,15.8%, respectively. PI*ZZ genotype was 36.8%, PI*Q0Q0 21.1%, PI*MdeficientMdeficient 7.9%, PI*ZQ0 18.4%, PI*Q0Mdeficient 5.3% and PI*Zrare-deficient 10.5%. Genotyping by Luminex detected: p.(Pro393Leu) associated with MHeerlen (M1Ala/M1Val); p.(Leu65Pro) with MProcida; p.(Lys241Ter) with Q0Bellingham; p.(Leu377Phefs*24) with Q0Mattawa (M1Val) and Q0Ourem (M3); p.(Phe76del) with MMalton (M2), MPalermo (M1Val), MNichinan (V) and Q0LaPalma (S); p.(Asp280Val) with PLowell (M1Val); PDuarte (M4), YBarcelona (p.Pro39His). Gene-sequencing (46.7%) detected Q0GraniteFalls, Q0Saint-Etienne, Q0Amersfoort(M1Ala), MWürzburg, NHartfordcity and one novel-variant (c.1A>G) named Q0Attikon.Heterozygous included PI*MQ0Amersfoort(M1Ala), PI*MMProcida, PI*Mp.(Asp280Val), PI*MOFeyzin. AAT-levels were significantly different between genotypes (p = 0.002). CONCLUSION Genotyping AATD in Greece, a multiplicity of rare variants and a diversity of rare combinations, including unique ones were observed in two thirds of patients, expanding knowledge regarding European geographical trend in rare variants. Gene sequencing was necessary for genetic diagnosis. In the future the detection of rare genotypes may add to personalize preventive and therapeutic measures.
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Affiliation(s)
- S A Papiris
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece.
| | - M Veith
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - A I Papaioannou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - V Apollonatou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - I Ferrarotti
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumonology Unit, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy
| | - S Ottaviani
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumonology Unit, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy
| | - A Tzouvelekis
- Department of Respiratory Medicine, General Hospital of Patras, University of Patras, Greece
| | - V Tzilas
- 5th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - N Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, Medical School, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - G Stratakos
- 1st Respiratory Medicine Department of the National, Kapodistrian University of Athens, Athens, Greece
| | - I Gerogianni
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa Greece
| | - Z Daniil
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa Greece
| | - L Kolilekas
- 7thPulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - K Dimakou
- 5th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - G Pitsidianakis
- Department of Thoracic Medicine, University Hospital, University of Crete, Heraklion, Crete 71110, Greece
| | - N Tzanakis
- Department of Thoracic Medicine, University Hospital, University of Crete, Heraklion, Crete 71110, Greece
| | - S Tryfon
- General Hospital "G. Papanikolaou", Thessaloniki, Greece
| | - F Fragopoulos
- Pulmonary Department, General Hospital of Nicosia, Cyprus
| | - E M Antonogiannaki
- 4th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - A Lazaratou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - E Fouka
- A Department of Pulmonary Medicine, Aristotle University of Thessaloniki, "G. Papanikolaou" Hospital, Exochi, Thessaloniki, Greece
| | - D Papakosta
- A Department of Pulmonary Medicine, Aristotle University of Thessaloniki, "G. Papanikolaou" Hospital, Exochi, Thessaloniki, Greece
| | | | - N Anagnostopoulos
- 1st Respiratory Medicine Department of the National, Kapodistrian University of Athens, Athens, Greece
| | - T Karampitsakos
- Department of Respiratory Medicine, General Hospital of Patras, University of Patras, Greece
| | - K Vlami
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - M Kallieri
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - P Lyberopoulos
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - S Loukides
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - D Bouros
- Iatriko Medical Center, Athens, Greece; School of Medicine, National and Kapodistrian University of Athens, Athens Greece
| | - A Bush
- Paediatrics and Paediatric Respirology, Imperial College, Imperial Centre for Paediatrics and Child Health, Royal Brompton Harefield NHS Foundation Trust, London, United Kingdom
| | - M Balduyck
- laboratoire de Biochimie et Biologie Moléculaire (HMNO), Centre de Biologie Pathologie, Faculté de pharmacie et EA 7364 RADEME, Laboratoire de Biochimie et Biologie Moléculaire, CHU de Lille, Université de Lille, Lille, France
| | - C Lombard
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon and Université Claude Bernard-Lyon 1, Lyon, France
| | - V Cottin
- Service de pneumologie, Centre National Coordinateur de Référence des Maladies Pulmonaires Rares, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France
| | - J F Mornex
- Service de pneumologie, Centre National Coordinateur de Référence des Maladies Pulmonaires Rares, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France
| | - C F Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - T Greulich
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - E D Manali
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
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7
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Denardo A, Ben Khlifa E, Bignotti M, Fra A. Characterization of Novel Alpha-1-Antitrypsin Coding Variants in a Mammalian Cellular Model. Methods Mol Biol 2024; 2750:79-93. [PMID: 38108969 DOI: 10.1007/978-1-0716-3605-3_8] [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] [Indexed: 12/19/2023]
Abstract
Advances in genetic screening technologies have considerably accelerated the discovery of rare alpha-1-antitrypsin (AAT) variants. Expression in cellular models is an effective approach to evaluate the pathogenic potential of these new AAT variants, whose clinical significance would otherwise remain uncertain. Here we provide a detailed description of established methods for in vitro characterization of AAT coding variants expressed in HEK293T/17 cells. The protocols include determination of secretion efficiency, the tendency to form polymeric chains and the anti-elastase inhibitory activity.
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Affiliation(s)
- Andrea Denardo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emna Ben Khlifa
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Mattia Bignotti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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8
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Lafortune P, Zahid K, Ploszaj M, Awadalla E, Carroll TP, Geraghty P. Testing Alpha-1 Antitrypsin Deficiency in Black Populations. Adv Respir Med 2023; 92:1-12. [PMID: 38392031 PMCID: PMC10886060 DOI: 10.3390/arm92010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 02/24/2024]
Abstract
Alpha-1 antitrypsin (AAT) deficiency (AATD) is an under-recognized hereditary disorder and a significant cause of chronic obstructive pulmonary disease (COPD), a disease that contributes to global mortality. AAT is encoded by the SERPINA1 gene, and severe mutation variants of this gene increase the risk of developing COPD. AATD is more frequently screened for in non-Hispanic White populations. However, AATD is also observed in other ethnic groups and very few studies have documented the mutation frequency in these other ethnic populations. Here, we review the current literature on AATD and allele frequency primarily in Black populations and discuss the possible clinical outcomes of low screening rates in a population that experiences poor health outcomes and whether the low frequency of AATD is related to a lack of screening in this population or a truly low frequency of mutations causing AATD. This review also outlines the harmful SERPINA1 variants, the current epidemiology knowledge of AATD, health inequity in Black populations, AATD prevalence in Black populations, the clinical implications of low screening of AATD in this population, and the possible dangers of not diagnosing or treating AATD.
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Affiliation(s)
- Pascale Lafortune
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Kanza Zahid
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Magdalena Ploszaj
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Emilio Awadalla
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
| | - Tomás P. Carroll
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
- Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Patrick Geraghty
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA; (P.L.); (K.Z.); (M.P.); (E.A.)
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9
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Denardo A, Ben Khlifa E, Bignotti M, Giuliani R, D'Acunto E, Miranda E, Irving JA, Fra A. Probing of the reactive center loop region of alpha-1-antitrypsin by mutagenesis predicts new type-2 dysfunctional variants. Cell Mol Life Sci 2023; 81:6. [PMID: 38087060 PMCID: PMC11073084 DOI: 10.1007/s00018-023-05059-1] [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: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Lung disease in alpha-1-antitrypsin deficiency (AATD) mainly results from insufficient control of the serine proteases neutrophil elastase (NE) and proteinase-3 due to reduced plasma levels of alpha-1-antitrypsin (AAT) variants. Mutations in the specificity-determining reactive center loop (RCL) of AAT would be predicted to minimally affect protein folding and secretion by hepatocytes but can impair anti-protease activity or alter the target protease. These properly secreted but dysfunctional 'type-2' variants would not be identified by common diagnostic protocols that are predicated on a reduction in circulating AAT. This has potential clinical relevance: in addition to the dysfunctional Pittsburgh and Iners variants reported previously, several uncharacterized RCL variants are present in genome variation databases. To prospectively evaluate the impact of RCL variations on secretion and anti-protease activity, here we performed a systematic screening of amino acid substitutions occurring at the AAT-NE interface. Twenty-three AAT variants that can result from single nucleotide polymorphisms in this region, including 11 present in sequence variation databases, were expressed in a mammalian cell model. All demonstrated unaltered protein folding and secretion. However, when their ability to form stable complexes with NE was evaluated by western blot, enzymatic assays, and a novel ELISA developed to quantify AAT-NE complexes, substrate-like and NE-binding deficient dysfunctional variants were identified. This emphasizes the ability of the RCL to accommodate inactivating substitutions without impacting the integrity of the native molecule and demonstrates that this class of molecule violates a generally accepted paradigm that equates circulating levels with functional protection of lung tissue.
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Affiliation(s)
- Andrea Denardo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emna Ben Khlifa
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Mattia Bignotti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Roberta Giuliani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emanuela D'Acunto
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, UK
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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10
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Papiris SA, Veith M, Lazaratou A, Balduyck M, Lombard C, Dechomet M, Odou MF, Entrena E, Osaba L, Kallieri M, Apollonatou V, Prountzos S, Kontopoulou C, Kolilekas L, Ferrarotti I, Mornex JF, Vogelmeier CF, Greulich T, Manali ED. PI*ZQ0 Attikon genotype discovery in severe alpha-1 antitrypsin deficiency. Pulmonology 2023; 29:564-567. [PMID: 37263862 DOI: 10.1016/j.pulmoe.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- S A Papiris
- 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - M Veith
- Department of Medicine, Pulmonary and Critical Care Medicine, UKGM, Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - A Lazaratou
- 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - M Balduyck
- CHU de Lille, laboratoire de biochimie et biologie moléculaire (HMNO), centre de biologie pathologie, Faculté de pharmacie et EA 7364 RADEME, laboratoire de biochimie et biologie moléculaire, Université de Lille, Lille, France
| | - C Lombard
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon & Université Claude Bernard-Lyon 1, Lyon, France
| | - M Dechomet
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon & Université Claude Bernard-Lyon 1, Lyon, France
| | - M-F Odou
- CHU Lille, Service de Biochimie et Biologie moléculaire 'Hormonologie, Métabolisme-Nutrition, Oncologie', Univ. Lille, Inserm, U1286 - Infinite, F-59000 Lille, France
| | - E Entrena
- Progenika Biopharma, a Grifols Company, Derio, Vizcaya, Spain
| | - L Osaba
- Progenika Biopharma, a Grifols Company, Derio, Vizcaya, Spain
| | - M Kallieri
- 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - V Apollonatou
- 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - S Prountzos
- 2nd Department of Radiology, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - C Kontopoulou
- 2nd Department of Radiology, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece
| | - L Kolilekas
- 7thPulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - I Ferrarotti
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumonology Unit, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy
| | - J-F Mornex
- Service de pneumologie, Centre national coordinateur de référence des maladies pulmonaires rares, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France
| | - C-F Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, UKGM, Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - T Greulich
- Department of Medicine, Pulmonary and Critical Care Medicine, UKGM, Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - E D Manali
- 2nd Pulmonary Medicine Department, General University Hospital "Attikon", Medical School, National and Kapodistrian University of Athens, Greece.
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11
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Ottaviani S, Bartoli G, Carroll TP, Gangemi F, Balderacchi AM, Barzon V, Corino A, Piloni D, McElvaney NG, Corsico AG, Irving JA, Fra A, Ferrarotti I. Comprehensive Clinical Diagnostic Pipelines Reveal New Variants in Alpha-1 Antitrypsin Deficiency. Am J Respir Cell Mol Biol 2023; 69:355-366. [PMID: 37071847 DOI: 10.1165/rcmb.2022-0470oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/18/2023] [Indexed: 04/20/2023] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is an underdiagnosed disorder associated with mutations in the SERPINA1 gene encoding alpha-1 antitrypsin (AAT). Severe AATD can manifest as pulmonary emphysema and progressive liver disease. Besides the most common pathogenic variants S (E264V) and Z (E342K), many rarer genetic variants of AAT have been found in patients and in the general population. Here we report a panel of new SERPINA1 variants, including 4 null and 16 missense alleles, identified among a cohort of individuals with suspected AATD whose phenotypic follow-up showed inconclusive or atypical results. Because the pathogenic significance of the missense variants was unclear purely on the basis of clinical data, the integration of computational, biochemical, and cellular studies was used to define the associated risk of disease. Established pathogenicity predictors and structural analysis identified a panel of candidate damaging mutations that were characterized by expression in mammalian cell models. Polymer formation, intracellular accumulation, and secretory efficiency were evaluated experimentally. Our results identified two AAT mutants with a Z-like polymerogenic severe deficiency profile (Smilano and Mcampolongo) and three milder variants (Xsarezzo, Pdublin, and Ctiberias). Overall, the experimentally determined behavior of the variants was in agreement with the pathogenicity scores of the REVEL (an ensemble method for predicting the pathogenicity of rare missense variants) predictor, supporting the utility of this bioinformatic tool in the initial assessment of newly identified amino acid substitutions of AAT. Our study, in addition to describing 20 new SERPINA1 variants, provides a model for a multidisciplinary approach to classification of rare AAT variants and their clinical impact on individuals with rare AATD genotypes.
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Affiliation(s)
- Stefania Ottaviani
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Giulia Bartoli
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Tomás P Carroll
- α-1 Foundation Ireland, Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Fabrizio Gangemi
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alice M Balderacchi
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Valentina Barzon
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, University of Pavia, Pavia, Italy
| | - Alessandra Corino
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Davide Piloni
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Noel G McElvaney
- α-1 Foundation Ireland, Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Angelo G Corsico
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, University of Pavia, Pavia, Italy
- European Reference Network on Rare Respiratory Diseases (ERN-LUNG); and
| | - James A Irving
- University College London Respiratory, Rayne Institute and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Annamaria Fra
- Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Unità Operativa Complessa Pneumologia, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, University of Pavia, Pavia, Italy
- European Reference Network on Rare Respiratory Diseases (ERN-LUNG); and
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12
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Höger P, Veith M, Greulich T, Limen E, Brock J, Schlamp K, Buschulte K, Presotto MA, Schäfer JC, Herth F, Trudzinski FC. Characterization of three new SERPINA1 variants PiQ0Heidelberg II, PiQ0Heidelberg III and PiQ0Heidelberg IV in patients with severe alpha-1 antitrypsin deficiency. Respir Med Case Rep 2023; 43:101838. [PMID: 37021142 PMCID: PMC10068255 DOI: 10.1016/j.rmcr.2023.101838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
Background The clinical and molecular characteristics of three patients with previously unreported SERPINA1 mutations associated with severe alpha-1 antitrypsin deficiency (AATD) are described. The pathophysiology of the chronic obstructive pulmonary disease (COPD) present in these patients was characterized through clinical, biochemical, and genetic examinations. Case presentations Case 1: A 73-year-old male with bilateral centri-to panlobular emphysema and multiple increasing ventrobasal bullae and incomplete fissures, COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) grade III B), progressive dyspnea on exertion (DOE), AAT level of 0.1-0.2 g/L. Genetic testing revealed a unique SERPINA1 mutation: Pi*Z/c.1072C > T. This allele was designated PiQ0Heidelberg II. Case 2: A 47-year-old male with severely heterogenous centri-to panlobular emphysema concentrated in the lower lobes, COPD GOLD IV D with progressive DOE, AAT <0.1 g/L. He also had a unique Pi*Z/c.10del mutation in SERPINA1. This allele was named PiQ0Heidelberg III. Case 3: A 58-year-old female with basally accentuated panlobular emphysema, GOLD II B COPD, progressive DOE. AAT 0.1 g/L. Genetic analysis revealed Pi*Z/c.-5+1G > A and c.-472G > A mutations in SERPINA1. This variant allele was named PiQ0Heidelberg IV. Conclusions Each of these patients had a unique and previously unreported SERPINA1 mutation. In two cases, AATD and a history of smoking led to severe lung disease. In the third case, timely diagnosis, and institution of AAT replacement stabilized lung function. Wider screening of COPD patients for AATD could lead to faster diagnosis and earlier treatment of AATD patients with AATD which could slow or prevent progression of their disease.
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13
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Sun S, Wang C, Zhao P, Kline GM, Grandjean JMD, Jiang X, Labaudiniere R, Wiseman RL, Kelly JW, Balch WE. Capturing the conversion of the pathogenic alpha-1-antitrypsin fold by ATF6 enhanced proteostasis. Cell Chem Biol 2023; 30:22-42.e5. [PMID: 36630963 PMCID: PMC9930901 DOI: 10.1016/j.chembiol.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/07/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023]
Abstract
Genetic variation in alpha-1 antitrypsin (AAT) causes AAT deficiency (AATD) through liver aggregation-associated gain-of-toxic pathology and/or insufficient AAT activity in the lung manifesting as chronic obstructive pulmonary disease (COPD). Here, we utilize 71 AATD-associated variants as input through Gaussian process (GP)-based machine learning to study the correction of AAT folding and function at a residue-by-residue level by pharmacological activation of the ATF6 arm of the unfolded protein response (UPR). We show that ATF6 activators increase AAT neutrophil elastase (NE) inhibitory activity, while reducing polymer accumulation for the majority of AATD variants, including the prominent Z variant. GP-based profiling of the residue-by-residue response to ATF6 activators captures an unexpected role of the "gate" area in managing AAT-specific activity. Our work establishes a new spatial covariant (SCV) understanding of the convertible state of the protein fold in response to genetic perturbation and active environmental management by proteostasis enhancement for precision medicine.
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Affiliation(s)
- Shuhong Sun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Pei Zhao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabe M Kline
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Xin Jiang
- Protego Biopharma, 10945 Vista Sorrento Parkway, San Diego, CA, USA
| | | | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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14
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Aiello M, Marchi L, Ferrarotti I, Frizzelli A, Pisi R, Calzetta L, Manari G, Pelà G, Russo A, Minerba R, Aloe R, Ranzieri S, Corradi M, Chetta A. Distribution of the Clinical Manifestations of Alpha 1 Antitrypsin Deficiency in Respiratory Outpatients from an Area of Northern Italy. Respiration 2022; 101:851-858. [PMID: 35793662 DOI: 10.1159/000525549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Alpha 1 antitrypsin deficiency (AATD) is an autosomal codominant genetic condition that affects Caucasians of the European population due to the presence of a deficient allele of the SERPINA1 gene. A frequency of about 1/5,000 individuals has been estimated in Italy. OBJECTIVES The aim of the study was to evaluate the distribution of the clinical manifestations of severe and intermediate genetic AATD in the geographic area around Parma in Northern Italy. METHOD 238 subjects were submitted to molecular analysis of the SERPINA1 gene, and data on anthropometric variables, smoking habits, number of packs per year, AAT serum concentration, and clinical manifestations were recorded and presented as mean ± SD or median values (1st quartile; 3rd quartile). RESULTS The results show a distribution of genetic AATD of 4.1% of the screened population in the area encompassing the city of Parma. PI*MS and PI*MZ were the most common genotypes at 40.9% and 28.2% of the population with genetic AATD, and asthma and emphysema were the most represented clinical manifestations. CONCLUSION Our study allowed to increase the knowledge of the distribution of genetic AATD in Northern Italy providing information regarding frequencies of genotypes and clinical manifestations of the disorder.
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Affiliation(s)
- Marina Aiello
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Laura Marchi
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Ilaria Ferrarotti
- Center for the Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumology Unit, University of Pavia, Pavia, Italy
| | - Annalisa Frizzelli
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Roberta Pisi
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Luigino Calzetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Gaia Manari
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Giovanna Pelà
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Department of General and Specialistic Medicine, University-Hospital of Parma, Parma, Italy
| | - Annalisa Russo
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Parma, Parma, Italy
| | - Roberta Minerba
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Parma, Parma, Italy
| | - Rosalia Aloe
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Parma, Parma, Italy
| | - Silvia Ranzieri
- Department of Medicine and Surgery, Occupational Medicine Unit, University of Parma, Parma, Italy
| | - Massimo Corradi
- Department of Medicine and Surgery, Occupational Medicine Unit, University of Parma, Parma, Italy
| | - Alfredo Chetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
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15
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Im H, Lim J. Antioxidant Responses are Crucial for Defense against Misfolded Human
Z-Type α1-Antitrypsin. Protein Pept Lett 2022; 29:384-391. [DOI: 10.2174/0929866529666220321151913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/18/2021] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
Abstract
Backgrounds:
The Z-type variant of human α1-antitrypsin is involved in liver cirrhosis
and pulmonary emphysema. Due to its slow folding characteristics, this variant accumulates folding
intermediates and forms protein aggregates within hepatocytes. Misfolded proteins may induce
oxidative stress and subsequent cell death.
Objective:
The potential application of antioxidant response signaling pathway and antioxidants to
cope with Z-type α1-antitrypsin-induced oxidative stress was evaluated.
Methods:
Overexpression of Z-type α1-antitrypsin in Saccharomyces cerevisiae provoked oxidative
stress and increased susceptibility to oxidative challenges such as hydrogen peroxide treatment.
Deletion of antioxidant-response genes, including yap1, skn7, sod2, tsa1, and pst2, exacerbated the
slow growth phenotype of Z-type α1-antitrypsin-expressing cells. Antioxidant treatment alleviated
oxidative stress and cytotoxicity induced by Z-type α1-antitrypsin.
Results:
Our results show that cellular antioxidant capacity is crucial to protection against
misfolded Z-type α1-antitrypsin.
Conclusion:
The information obtained here may be used to prevent oxidative stress caused by
misfolded proteins, which are associated with several degenerative diseases, including amyotrophic
lateral sclerosis and Parkinson’s disease.
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Affiliation(s)
- Hana Im
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea
| | - Jaeyeon Lim
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea
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16
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Aiello M, Frizzelli A, Marchi L, Ferrarotti I, Piloni D, Pelà G, De Simoni A, D'Aloisio L, Calzetta L, Chetta A. Clinical manifestations of a new alpha‐1 antitrypsin genetic variant:
Q0parma
. Respirol Case Rep 2022; 10:e0936. [PMID: 35433011 PMCID: PMC9008433 DOI: 10.1002/rcr2.936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/13/2022] [Indexed: 11/12/2022] Open
Abstract
Alpha‐1 antitrypsin deficiency is an autosomal, codominant disorder caused by mutations of the SERPINA1 gene. Several mutations of SERPINA1 have been described associated with the development of pulmonary emphysema and/or chronic liver disease and cirrhosis. Here, we report a very rare PI*Q0parma variant identified for the first time in an Italian family originally from the city of Parma in Northern Italy
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Affiliation(s)
- Marina Aiello
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
| | - Annalisa Frizzelli
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
| | - Laura Marchi
- Department of Food and Drug University of Parma Parma Italy
| | - Ilaria Ferrarotti
- Center for the Diagnosis of Inherited Alpha1‐Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumology Unit University of Pavia Pavia Italy
| | - Davide Piloni
- Unit of Respiratory Diseases, Department of Medical Sciences and Infective Diseases IRCCS Policlinico San Matteo Foundation Pavia Italy
| | - Giovanna Pelà
- Department of Medicine and Surgery University of Parma Parma Italy
- Department of General and Specialistic Medicine University‐Hospital of Parma Parma Italy
| | - Alessandro De Simoni
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
| | - Lorenzo D'Aloisio
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
| | - Luigino Calzetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
| | - Alfredo Chetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit University of Parma Parma Italy
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17
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D'Acunto E, Fra A, Visentin C, Manno M, Ricagno S, Galliciotti G, Miranda E. Neuroserpin: structure, function, physiology and pathology. Cell Mol Life Sci 2021; 78:6409-6430. [PMID: 34405255 PMCID: PMC8558161 DOI: 10.1007/s00018-021-03907-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022]
Abstract
Neuroserpin is a serine protease inhibitor identified in a search for proteins implicated in neuronal axon growth and synapse formation. Since its discovery over 30 years ago, it has been the focus of active research. Many efforts have concentrated in elucidating its neuroprotective role in brain ischemic lesions, the structural bases of neuroserpin conformational change and the effects of neuroserpin polymers that underlie the neurodegenerative disease FENIB (familial encephalopathy with neuroserpin inclusion bodies), but the investigation of the physiological roles of neuroserpin has increased over the last years. In this review, we present an updated and critical revision of the current literature dealing with neuroserpin, covering all aspects of research including the expression and physiological roles of neuroserpin, both inside and outside the nervous system; its inhibitory and non-inhibitory mechanisms of action; the molecular structure of the monomeric and polymeric conformations of neuroserpin, including a detailed description of the polymerisation mechanism; and the involvement of neuroserpin in human disease, with particular emphasis on FENIB. Finally, we briefly discuss the identification by genome-wide screening of novel neuroserpin variants and their possible pathogenicity.
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Affiliation(s)
- Emanuela D'Acunto
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristina Visentin
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Molecular and Translational Cardiology, I.R.C.C.S. Policlinico San Donato, Milan, Italy
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | - Stefano Ricagno
- Department of Biosciences, University of Milan, Milan, Italy
| | - Giovanna Galliciotti
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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18
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Foil KE. Variants of SERPINA1 and the increasing complexity of testing for alpha-1 antitrypsin deficiency. Ther Adv Chronic Dis 2021; 12_suppl:20406223211015954. [PMID: 34408833 PMCID: PMC8367212 DOI: 10.1177/20406223211015954] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is caused by mutations in the SERPINA1 gene, which encodes the alpha-1 antitrypsin (AAT) protein. Currently, over 200 SERPINA1 variants have been identified, many of which cause the quantitative and/or qualitative changes in AAT responsible for AATD-associated lung and liver disease. The types of these pathogenic mutations are varied, often resulting in misfolding, or truncating of the AAT amino acid sequence, and improvements in sequencing technology are helping to identify known and novel genetic variants. However, due to the diversity and novelty of rare variants, the clinical significance of many is largely unknown. There is, therefore, a lack of guidance on how patients should be monitored and treated when the clinical significance of their variant combination is unclear or variable. Nevertheless, it is important that physicians understand the advantages and disadvantages of the different testing methodologies available to diagnose AATD. Owing to the autosomal inheritance of the genetic mutations responsible for AATD, genetic testing should be offered not only to patients at increased AATD risk (e.g. patients with chronic obstructive pulmonary disease), but also to relatives of those with an abnormal result. Genetic counseling may help patients and family members understand the possible outcomes of testing and the implications for the family. While stress/anxiety can arise from genetic diagnosis or confirmation of carrier status, there can be positive consequences to genetic testing, including improved lifestyle choices, directed medical care, and empowered family planning. As genetic testing technology grows and becomes more popular, testing without physician referral is becoming more prevalent, irrespective of the availability of genetic counseling. Therefore, the Alpha-1 Foundation offers genetic counseling, as well as other support and educational material, for patients with AATD, as well as their families and physicians, to help improve the understanding of potential benefits and consequences of genetic testing.
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Affiliation(s)
- Kimberly E Foil
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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19
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Lim J, Lee K, Im H. Reinforcement of the Unfolded Protein Response Mitigates Cytotoxicity Induced by Human Z‐Type α
1
‐Antitrypsin. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jaeyeon Lim
- Department of Integrative Bioscience and Biotechnology Sejong University Seoul 05006 South Korea
| | - Kyunghee Lee
- Department of Chemistry Sejong University Seoul 05006 South Korea
| | - Hana Im
- Department of Integrative Bioscience and Biotechnology Sejong University Seoul 05006 South Korea
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20
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Ronzoni R, Ferrarotti I, D’Acunto E, Balderacchi AM, Ottaviani S, Lomas DA, Irving JA, Miranda E, Fra A. The Importance of N186 in the Alpha-1-Antitrypsin Shutter Region Is Revealed by the Novel Bologna Deficiency Variant. Int J Mol Sci 2021; 22:5668. [PMID: 34073489 PMCID: PMC8198886 DOI: 10.3390/ijms22115668] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Alpha-1-antitrypsin (AAT) deficiency causes pulmonary disease due to decreased levels of circulating AAT and consequently unbalanced protease activity in the lungs. Deposition of specific AAT variants, such as the common Z AAT, within hepatocytes may also result in liver disease. These deposits are comprised of ordered polymers of AAT formed by an inter-molecular domain swap. The discovery and characterization of rare variants of AAT and other serpins have historically played a crucial role in the dissection of the structural mechanisms leading to AAT polymer formation. Here, we report a severely deficient shutter region variant, Bologna AAT (N186Y), which was identified in five unrelated subjects with different geographical origins. We characterized the new variant by expression in cellular models in comparison with known polymerogenic AAT variants. Bologna AAT showed secretion deficiency and intracellular accumulation as detergent-insoluble polymers. Extracellular polymers were detected in both the culture media of cells expressing Bologna AAT and in the plasma of a patient homozygous for this variant. Structural modelling revealed that the mutation disrupts the hydrogen bonding network in the AAT shutter region. These data support a crucial coordinating role for asparagine 186 and the importance of this network in promoting formation of the native structure.
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Affiliation(s)
- Riccardo Ronzoni
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - Ilaria Ferrarotti
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - Emanuela D’Acunto
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy; (E.D.); (E.M.)
| | - Alice M. Balderacchi
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - Stefania Ottaviani
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - David A. Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - James A. Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - Elena Miranda
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy; (E.D.); (E.M.)
- Italian Pasteur Institute—Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
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21
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Annunziata A, Ferrarotti I, Coppola A, Lanza M, Imitazione P, Spinelli S, Micco PD, Fiorentino G. Alpha-1 Antitrypsin Screening in a Selected Cohort of Patients Affected by Chronic Pulmonary Diseases in Naples, Italy. J Clin Med 2021; 10:jcm10081546. [PMID: 33916947 PMCID: PMC8067626 DOI: 10.3390/jcm10081546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Alpha-1 antitrypsin deficiency (AATD) is a genetic condition associated with several respiratory diseases in patients with severe protein deficiency. AATD is often late diagnosed or underdiagnosed. Diagnosis frequently occurs in patients with chronic obstructive pulmonary disease and emphysema characterized by frequent exacerbations and over ten years' duration. The purpose of this study was to evaluate the incidence of alpha-1 antitrypsin deficiency in patients with the chronic pulmonary disease after a thorough screening in the city of Naples in southern Italy. MATERIALS AND METHODS Two hundred patients suffering from respiratory pathology (chronic obstructive pulmonary disease (COPD), emphysema, asthma, or bronchiectasis) were examined and evaluated in our outpatients' clinic and tested for serum levels of AAT. Patients who had a respiratory disease suspected of AATD and/or serum AAT < 120 mg/dL underwent genetic testing. Genetic screening was performed on samples from 141 patients. RESULTS A total of 36 patients had an intermediate deficiency of AAT levels. Among them, 8 were PI*MZ, 6 were PI*MS and 22 had rare pathological mutations. Five patients had a severe AATD, all were composite heterozygous with S or Z allele, while the other allele had a rare pathological mutation. CONCLUSIONS The incidence of genetic defects as AATD in the population of patients affected by chronic respiratory disorders is always a matter of discussion because of the frequent interaction between genes and environmental causes. In our series, numerous rare variants and compound heterozygosity have been described. No homozygous patients have been described. The present is one of few studies available on the incidence of rare variants in the geographic area of the city of Naples. So, our results could be considered interesting not only to know the incidence of AATD and its related rare mutations but also to support early diagnosis and treatments for patients with chronic pulmonary disease and frequent exacerbation and to fight the association with environmental causes of pulmonary damages as smoking.
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Affiliation(s)
- Anna Annunziata
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
- Correspondence:
| | - Ilaria Ferrarotti
- Center for Diagnosis of Inherited Alpha1-Antitrypsin Deficiency, Pneumology Unit, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy;
| | - Antonietta Coppola
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
| | - Maurizia Lanza
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
| | - Pasquale Imitazione
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
| | - Sara Spinelli
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
| | - Pierpaolo Di Micco
- Department of Medicine, Buon Consiglio Fatebenefratelli Hospital of Naples, 80128 Naples, Italy;
| | - Giuseppe Fiorentino
- Unit of Respiratory Physiopathology, Department of Critic Area, Monaldi Hospital, 80131 Naples, Italy; (A.C.); (M.L.); (P.I.); (S.S.); (G.F.)
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22
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Seixas S, Marques PI. Known Mutations at the Cause of Alpha-1 Antitrypsin Deficiency an Updated Overview of SERPINA1 Variation Spectrum. APPLICATION OF CLINICAL GENETICS 2021; 14:173-194. [PMID: 33790624 PMCID: PMC7997584 DOI: 10.2147/tacg.s257511] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Alpha-1-Antitrypsin deficiency (AATD), caused by SERPINA1 mutations, is one of the most prevalent Mendelian disorders among individuals of European descend. However, this condition, which is characterized by reduced serum levels of alpha-1-antitrypsin (AAT) and associated with increased risks of pulmonary emphysema and liver disease in both children and adults, remains frequently underdiagnosed. AATD clinical manifestations are often correlated with two pathogenic variants, the Z allele (p.Glu342Lys) and the S allele (p.Glu264Val), which can be combined in severe ZZ or moderate SZ risk genotypes. Yet, screenings of AATD cases and large sequencing efforts carried out in both control and disease populations are disclosing outstanding numbers of rare SERPINA1 variants (>500), including many pathogenic and other likely deleterious mutations. Generally speaking, pathogenic variants can be subdivided into either loss- or gain-of-function according to their pathophysiological effects. In AATD, the loss-of-function is correlated with an uncontrolled activity of elastase by its natural inhibitor, the AAT. This phenomenon can result from the absence of circulating AAT (null alleles), poor AAT secretion from hepatocytes (deficiency alleles) or even from a modified inhibitory activity (dysfunctional alleles). On the other hand, the gain-of-function is connected with the formation of AAT polymers and their switching on of cellular stress and inflammatory responses (deficiency alleles). Less frequently, the gain-of-function is related to a modified protease affinity (dysfunctional alleles). Here, we revisit SERPINA1 mutation spectrum, its origins and population history with a greater emphasis on variants fitting the aforementioned processes of AATD pathogenesis. Those were selected based on their clinical significance and wider geographic distribution. Moreover, we also provide some directions for future studies of AATD clinically heterogeneity and comprehensive diagnosis.
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Affiliation(s)
- Susana Seixas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Patricia Isabel Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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23
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Balderacchi AM, Barzon V, Ottaviani S, Corino A, Zorzetto M, Wencker M, Corsico AG, Ferrarotti I. Comparison of different algorithms in laboratory diagnosis of alpha1-antitrypsin deficiency. Clin Chem Lab Med 2021; 59:1384-1391. [PMID: 33675199 DOI: 10.1515/cclm-2020-1881] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Alpha1-antitrypsin deficiency (AATD) is an inherited condition that predisposes individuals to an increased risk of developing lung and liver disease. Even though AATD is one of the most widespread inherited diseases in Caucasian populations, only a minority of affected individuals has been detected. Whereas methods have been validated for AATD testing, there is no universally-established algorithm for the detection and diagnosis of the disorder. In order to compare different methods for diagnosing AATD, we carried out a systematic review of the literature on AATD diagnostic algorithms. METHODS Complete biochemical and molecular analyses of 5,352 samples processed in our laboratory were retrospectively studied using each of the selected algorithms. RESULTS When applying the diagnostic algorithms to the same samples, the frequency of False Negatives varied from 1.94 to 12.9%, the frequency of True Negatives was 62.91% for each algorithm and the frequency of True Positives ranged from 24.19 to 35.15%. We, therefore, highlighted some differences among Negative Predictive Values, ranging from 0.83 to 0.97. Accordingly, the sensitivity of each algorithm ranged between 0.61 and 0.95. We also postulated 1.108 g/L as optimal AAT cut-off value, in absence of inflammatory status, which points to the possible presence of genetic AATD. CONCLUSIONS The choice of the diagnostic algorithm has a significant impact on the correct diagnosis of AATD, which is essential for appropriate treatment and medical care. The fairly large number of possible false negative diagnoses revealed by the present paper should also warn clinicians of negative results in patients with clinically-suspected AATD.
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Affiliation(s)
- Alice M Balderacchi
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentina Barzon
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefania Ottaviani
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alessandra Corino
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Michele Zorzetto
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Angelo G Corsico
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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24
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McNulty MJ, Silberstein DZ, Kuhn BT, Padgett HS, Nandi S, McDonald KA, Cross CE. Alpha-1 antitrypsin deficiency and recombinant protein sources with focus on plant sources: Updates, challenges and perspectives. Free Radic Biol Med 2021; 163:10-30. [PMID: 33279618 DOI: 10.1016/j.freeradbiomed.2020.11.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Alpha-1 antitrypsin deficiency (A1ATD) is an autosomal recessive disease characterized by low plasma levels of A1AT, a serine protease inhibitor representing the most abundant circulating antiprotease normally present at plasma levels of 1-2 g/L. The dominant clinical manifestations include predispositions to early onset emphysema due to protease/antiprotease imbalance in distal lung parenchyma and liver disease largely due to unsecreted polymerized accumulations of misfolded mutant A1AT within the endoplasmic reticulum of hepatocytes. Since 1987, the only FDA licensed specific therapy for the emphysema component has been infusions of A1AT purified from pooled human plasma at the 2020 cost of up to US $200,000/year with the risk of intermittent shortages. In the past three decades various, potentially less expensive, recombinant forms of human A1AT have reached early stages of development, one of which is just reaching the stage of human clinical trials. The focus of this review is to update strategies for the treatment of the pulmonary component of A1ATD with some focus on perspectives for therapeutic production and regulatory approval of a recombinant product from plants. We review other competitive technologies for treating the lung disease manifestations of A1ATD, highlight strategies for the generation of data potentially helpful for securing FDA Investigational New Drug (IND) approval and present challenges in the selection of clinical trial strategies required for FDA licensing of a New Drug Approval (NDA) for this disease.
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Affiliation(s)
- Matthew J McNulty
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - David Z Silberstein
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - Brooks T Kuhn
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA
| | | | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Karen A McDonald
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Carroll E Cross
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA; Department of Physiology and Membrane Biology, University of California, Davis, CA, USA.
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25
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Kueppers F. Clinical presentations of four patients with rare Alpha 1 Antitrypsin variants identified in a single US center. Respir Med Case Rep 2021; 32:101345. [PMID: 33552892 PMCID: PMC7848626 DOI: 10.1016/j.rmcr.2021.101345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Alpha 1 Antitrypsin Deficiency (AATD) is a rare condition primarily associated with lung complications and liver disease. As disease symptoms are similar to those in other respiratory conditions, patients generally experience long delays before receiving an accurate diagnosis and treatment. AATD results from mutations in the SERPINA1 gene that encodes Alpha 1 Antitrypsin (AAT). Over 500 single-nucleotide variants have been reported in mutation databases; however, there is increasing interest in the clinical significance of rare and novel SERPINA1 variants. In this case series of four patients from a single US center, next-generation sequencing (NGS) was used to guide AATD diagnosis. Four distinct rare variants of SERPINA1 (P289S; I50N; E204K; H262Y) were identified, three of which were found in patients with advanced chronic obstructive pulmonary disease (COPD)/emphysema. Computational modeling predicted these mutations to have potentially deleterious effects, a finding supported by AAT levels that were comparable with those seen in individuals heterozygous for the most common deficiency allele (PI*MZ). The remaining mutation (E204K) was found in a patient with a cerebral aneurysm; potential links between SERPINA1 variants and neurological conditions, such as cerebral aneurysm and arterial dissections, have been previously reported in individuals with heterozygous AATD phenotypes (PI*MS and PI*MZ). Novel and rare variants, often not detected by basic AATD diagnostic tests, have the potential to contribute to the development of COPD and emphysema. Detection of these variants can be enhanced by NGS, and modeling techniques can help determine if variants are pathogenic, thereby enabling a quicker, more accurate AATD diagnosis.
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Key Words
- AAT, Alpha 1 Antitrypsin
- AATD, Alpha 1 Antitrypsin Deficiency
- Alpha 1 Antitrypsin
- Alpha 1 Antitrypsin Deficiency
- CIDP, chronic inflammatory demyelinating polyneuropathy
- COPD, chronic obstructive pulmonary disease
- CT, computed tomography
- Diagnostic tests
- FEV1, forced expiratory volume in 1 s
- FVC, forced vital capacity
- IEF, isoelectric focusing
- Mutation
- NGS, next-generation sequencing
- Novel variants
- PCR, polymerase chain reaction
- SERPINA1
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26
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Milne S, Sin DD. Biomarkers in Chronic Obstructive Pulmonary Disease: The Gateway to Precision Medicine. Clin Chest Med 2020; 41:383-394. [PMID: 32800193 DOI: 10.1016/j.ccm.2020.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a highly heterogeneous disease with limited adequate treatments. Biomarkers-which may relate to disease susceptibility, diagnosis, prognosis, or treatment response-are ideally suited to dissecting such a complex disease and form a critical component of the precision medicine paradigm. Not all potential candidates, however, make good biomarkers. To date, only plasma fibrinogen has been approved by regulatory bodies as a biomarker of exacerbation risk for clinical trial enrichment. This review outlines some of the challenges of biomarker research in COPD and highlights novel and promising biomarker candidates.
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Affiliation(s)
- Stephen Milne
- Centre for Heart Lung Innovation and Division of Respiratory Medicine, University of British Columbia, Room 166, St Paul's Hospital, 1081 Burrard St, Vancouver, British Columbia V6Z 1Y6, Canada; Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales 2006, Australia.
| | - Don D Sin
- Centre for Heart Lung Innovation and Division of Respiratory Medicine, University of British Columbia, Room 166, St Paul's Hospital, 1081 Burrard St, Vancouver, British Columbia V6Z 1Y6, Canada
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27
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Quinn M, Turner AM. Modernising case finding for α 1-antitrypsin deficiency by DNA sequencing of COPD patients. Eur Respir J 2020; 56:56/4/2002628. [DOI: 10.1183/13993003.02628-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 11/05/2022]
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28
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Ottaviani S, Barzon V, Buxens A, Gorrini M, Larruskain A, El Hamss R, Balderacchi AM, Corsico AG, Ferrarotti I. Molecular diagnosis of alpha1-antitrypsin deficiency: A new method based on Luminex technology. J Clin Lab Anal 2020; 34:e23279. [PMID: 32181528 PMCID: PMC7370739 DOI: 10.1002/jcla.23279] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/17/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Alpha1‐antitrypsin deficiency (AATD) is an under‐diagnosed hereditary disorder characterized by reduced serum levels of alpha1‐antitrypsin (AAT) and increased risk to develop lung and liver diseases at an early age. AAT is encoded by the highly polymorphic SERPINA1 gene. The most common deficiency alleles are S and Z, but more than 150 rare variants lead to low levels of the protein. To identify these pathological allelic variants, sequencing is required. Since traditional sequencing is expensive and time‐consuming, we evaluated the accuracy of A1AT Genotyping Test, a new diagnostic genotyping kit which allows to simultaneously identify and genotype 14 deficiency variants of the SERPINA1 gene based on Luminex technology. Methods A total of 418 consecutive samples with AATD suspicion and submitted to the Italian Reference laboratory between January and April 2016 were analyzed both by applying the diagnostic algorithm currently in use, and by applying A1AT Genotyping Test. Results The assay gave the following results: 101 samples (24.2%) were positive for at least one of the 14 deficiency variants, 316 (75.6%) were negative for all the variants analyzed. The identified mutations showed a 100% correlation with the results obtained with our diagnostic algorithm. Seventeen samples (4%) resulted negative for the assay but sequencing identified other rare pathological variants in SERPINA1 gene. Conclusion The A1AT Genotyping Test assay was highly reliable and robust and allowed shorter diagnostic times. In few cases, it has been necessary to sequence the SERPINA1 gene to identify other rare mutations not included in the kit.
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Affiliation(s)
- Stefania Ottaviani
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentina Barzon
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Amaya Buxens
- Progenika Biopharma, A Grifols Company, Derio, Spain
| | - Marina Gorrini
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | | | - Alice M Balderacchi
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Angelo G Corsico
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Ilaria Ferrarotti
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Laboratory of Biochemistry and Genetics, Institute for Respiratory Disease, Department of Internal Medicine and Therapeutics, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Wang C, Zhao P, Sun S, Teckman J, Balch WE. Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2020; 7:224-246. [PMID: 32726074 DOI: 10.15326/jcopdf.7.3.2019.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep medicine is rapidly moving towards a high-definition approach for therapeutic management of the patient as an individual given the rapid progress of genome sequencing technologies and machine learning algorithms. While considered a monogenic disease, alpha-1 antitrypsin (AAT) deficiency (AATD) patients present with complex and variable phenotypes we refer to as the "hallmarks of AATD" that involve distinct molecular mechanisms in the liver, plasma and lung tissues, likely due to both coding and non-coding variation as well as genetic and environmental modifiers in different individuals. Herein, we briefly review the current therapeutic strategies for the management of AATD. To embrace genetic diversity in the management of AATD, we provide an overview of the disease phenotypes of AATD patients harboring different AAT variants. Linking genotypic diversity to phenotypic diversity illustrates the potential for sequence-specific regions of AAT protein fold design to play very different roles during nascent synthesis in the liver and/or function in post-liver plasma and lung environments. We illustrate how to manage diversity with recently developed machine learning (ML) approaches that bridge sequence-to-function-to-structure knowledge gaps based on the principle of spatial covariance (SCV). SCV relationships provide a deep understanding of the genotype to phenotype transformation initiated by AAT variation in the population to address the role of genetic and environmental modifiers in the individual. Embracing the complexity of AATD in the population is critical for risk management and therapeutic intervention to generate a high definition medicine approach for the patient.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Jeffrey Teckman
- Pediatrics and Biochemistry, Saint Louis University, and Cardinal Glennon Children's Medical Center, St. Louis, Missouri
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California
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30
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Gómez-Mariano G, Matamala N, Martínez S, Justo I, Marcacuzco A, Jimenez C, Monzón S, Cuesta I, Garfia C, Martínez MT, Huch M, Pérez de Castro I, Posada M, Janciauskiene S, Martínez-Delgado B. Liver organoids reproduce alpha-1 antitrypsin deficiency-related liver disease. Hepatol Int 2019; 14:127-137. [PMID: 31832977 PMCID: PMC6994530 DOI: 10.1007/s12072-019-10007-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/26/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND AIMS Alpha-1 antitrypsin (AAT) is a product of SERPINA1 gene mainly expressed by hepatocytes. Clinically relevant mutations in the SERPINA1 gene, such as Z (Glu342Lys), results in an expression of misfolded AAT protein having high propensity to polymerize, accumulate in hepatocytes and thus to enhance a risk for hepatocyte damage and subsequent liver disease. So far, the relationship between the Z-AAT accumulation and liver cell damage remains not completely understood. We present three-dimensional organoid culture systems, as a novel tool for modeling Z-AAT-related liver diseases. METHODS We have established liver organoids from liver biopsies of patients with homozygous (ZZ) and heterozygous (MZ) deficiency and normal (MM) genotypes of AAT. The features of these organoid models were characterized by analyzing AAT protein secretion and intracellular aggregation in MZ and ZZ genotypes as well as SERPINA1 expression in differentiated cultures. RESULTS Transcriptional analysis of differentiated organoid cultures by RNA-Seq showed hepatocyte-specific gene expression profile. Genes, such as ALB, APOB, CYP3A4 and SERPINA1, were validated and confirmed through quantitative-PCR analysis. The organoids from MZ and ZZ cases showed intracellular aggregation and lower secretion of AAT protein, and lower expression of ALB and APOB, as typically seen in hepatocytes from Z-AAT deficiency patients. Furthermore, organoids responded to external stimulus. Treatment with oncostatin M, a well-known inducer of SERPINA1, increased expression of the full-length transcripts (AAT-1C) as well as the short transcript of AAT (AAT-ST1C4). CONCLUSIONS Liver organoid model recapitulates the key features of Z-AAT deficiency and provides a useful tool for disease modeling.
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Affiliation(s)
- Gema Gómez-Mariano
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Nerea Matamala
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Selene Martínez
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Iago Justo
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Alberto Marcacuzco
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Carlos Jimenez
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Garfia
- Digestive Department, Hospital Doce de Octubre, Madrid, Spain
| | | | - Meritxell Huch
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ignacio Pérez de Castro
- Gene Therapy Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Manuel Posada
- Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Centre for Biomedical Network Research on Rare Diseases, CIBERER, Madrid, Spain
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, German Centre for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
- Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Centre for Biomedical Network Research on Rare Diseases, CIBERER, Madrid, Spain
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31
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Franciosi AN, Carroll TP, McElvaney NG. Pitfalls and caveats in α1-antitrypsin deficiency testing: a guide for clinicians. THE LANCET RESPIRATORY MEDICINE 2019; 7:1059-1067. [PMID: 31324540 DOI: 10.1016/s2213-2600(19)30141-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/05/2019] [Accepted: 03/11/2019] [Indexed: 01/04/2023]
Abstract
α1-antitrypsin deficiency (AATD) remains the only readily identified genetic cause of chronic obstructive pulmonary disease (COPD). Furthermore, there is growing evidence that even a moderate deficiency increases the risk of lung disease among smokers. Despite these facts, the uptake of testing for AATD in at-risk populations remains low for many reasons, and a lack of clarity among clinicians regarding the most appropriate diagnostic techniques presents a major deterrent. This Personal View addresses the benefits of diagnosis, the technical basis of the available diagnostic methods, and possible clinical confounders for each test. We include a series of unusual cases encountered at our National Centre of Expertise to provide context. The topics covered should equip clinicians with the core knowledge required to confidently assess patients for AATD.
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Affiliation(s)
- Alessandro N Franciosi
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Medicine, Beaumont Hospital, Dublin, Ireland.
| | - Tomás P Carroll
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland; Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Noel G McElvaney
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Medicine, Beaumont Hospital, Dublin, Ireland
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32
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Kueppers F, Andrake MD, Xu Q, Dunbrack RL, Kim J, Sanders CL. Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency. BMC MEDICAL GENETICS 2019; 20:125. [PMID: 31307431 PMCID: PMC6631921 DOI: 10.1186/s12881-019-0852-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/24/2019] [Indexed: 12/22/2022]
Abstract
Background Alpha 1 Antitrypsin (AAT) is a key serum proteinase inhibitor encoded by SERPINA1. Sequence variants of the gene can cause Alpha 1 Antitrypsin Deficiency (AATD), a condition associated with lung and liver disease. The majority of AATD cases are caused by the ‘Z’ and ‘S’ variants – single-nucleotide variations (SNVs) that result in amino acid substitutions of E342K and E264V. However, SERPINA1 is highly polymorphic, with numerous potentially clinically relevant variants reported. Novel variants continue to be discovered, and without reports of pathogenicity, it can be difficult for clinicians to determine the best course of treatment. Methods We assessed the utility of next-generation sequencing (NGS) and predictive computational analysis to guide the diagnosis of patients suspected of having AATD. Blood samples on serum separator cards were submitted to the DNA1 Advanced Screening Program (Biocerna LLC, Fulton, Maryland, USA) by physicians whose patients were suspected of having AATD. Laboratory analyses included quantification of serum AAT levels, qualitative analysis by isoelectric focusing, and targeted genotyping and NGS of the SERPINA1 gene. Molecular modeling software UCSF Chimera (University College of San Francisco, CA) was used to visualize the positions of amino acid changes as a result of rare/novel SNVs. Predictive software was used to assess the potential pathogenicity of these variants; methods included a support vector machine (SVM) program, PolyPhen-2 (Harvard University, Cambridge, MA), and FoldX (Centre for Genomic Regulation, Barcelona, Spain). Results Samples from 23 patients were analyzed; 21 rare/novel sequence variants were identified by NGS, including splice variants (n = 2), base pair deletions (n = 1), stop codon insertions (n = 2), and SNVs (n = 16). Computational modeling of protein structures caused by the novel SNVs showed that 8 were probably deleterious, and two were possibly deleterious. For the majority of probably/possibly deleterious SNVs (I50N, P289S, M385T, M221T, D341V, V210E, P369H, V333M and A142D), the mechanism is probably via disruption of the packed hydrophobic core of AAT. Several deleterious variants occurred in combination with more common deficiency alleles, resulting in very low AAT levels. Conclusions NGS and computational modeling are useful tools that can facilitate earlier, more precise diagnosis, and consideration for AAT therapy in AATD. Electronic supplementary material The online version of this article (10.1186/s12881-019-0852-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Friedrich Kueppers
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Mark D Andrake
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Qifang Xu
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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33
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Trehalose: is it a potential inhibitor of antithrombin polymerization? Biosci Rep 2019; 39:BSR20190567. [PMID: 31147454 PMCID: PMC6579975 DOI: 10.1042/bsr20190567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
SERine Protease INhibitorS (Serpins) are a superfamily of proteins that are characterized by having a similar three-dimensional structure. The native conformation is not most thermodynamically stable, so polymerization is the main consequence when its stability is altered as a result of certain mutations. The polymerization of serpins has been a research topic for many years. Different mechanisms have been proposed and in the same way different compounds or strategies have been studied to prevent polymerization. A recent paper published in Bioscience Reports by Naseem et al. [Biosci. Rep. (2019) 5, 39] studies the role of trehalose in the prevention of the polymerization of antithrombin, which belongs to the serpin superfamily. The main consequence of the antithrombin polymerization is the increased thrombotic risk, since antithrombin is the main inhibitor of the coagulation cascade. The authors demonstrate that trehalose is able to prevent the in vitro polymerization of antithrombin, under conditions in which it usually tends to polymerize, and demonstrate it by using different techniques. However, the binding site of trehalose in antithrombin should be defined by site-directed mutagenesis. On the other hand, it is not clear if all serpins polymerize in vivo through the same mechanism and it is also not clear if the same serpin can even polymerize through different mechanisms. Therefore, there are still doubts about the potential of trehalose or its derivatives to prevent in vivo antithrombin polymerization and, therefore, reduce thrombotic risk, as well as whether trehalose would be able to reduce polymerization in other serpins.
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34
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Trinh HN, Jang SH, Lee C. Functional characterization of a SNP (F51S) found in human alpha 1-antitrypsin. Mol Genet Genomic Med 2019; 7:e819. [PMID: 31251477 PMCID: PMC6687665 DOI: 10.1002/mgg3.819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/16/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Alpha 1-antitrypsin (A1AT) deficiency is related to lung and liver diseases, including pulmonary emphysema and liver cirrhosis in humans. Genetic variations including single nucleotide polymorphisms (SNPs) of SERPINA1 are responsible for A1AT deficiency, but the characteristics of the SNPs are not well-understood. Here, we investigated the features of a rare SNP (F51S) of A1AT, which introduces an additional N-glycosylation site in the N-terminal region of A1AT. METHODS We evaluated the F51S variant compared with the wild-type (WT) A1AT with regard to expression in CHO-K1 cells, trypsin inhibitory activity, polymerization, and thermal stability. RESULTS The recombinant F51S protein expressed in CHO-K1 cells was mostly retained inside cells. The F51S variant had trypsin inhibitory activity, but reduced thermal stability compared with the WT A1AT. The native acrylamide gel data showed that F51S tended to prevent polymerization of A1AT. CONCLUSION The results of this study indicate that Phe51 and the surrounding hydrophobic residue cluster plays an important role in the conformation and secretion of A1AT and suggest the harmful effects of a rare F51S SNP in human health.
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Affiliation(s)
- Hong-Nhung Trinh
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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35
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Laffranchi M, Elliston ELK, Gangemi F, Berardelli R, Lomas DA, Irving JA, Fra A. Characterisation of a type II functionally-deficient variant of alpha-1-antitrypsin discovered in the general population. PLoS One 2019; 14:e0206955. [PMID: 30633749 PMCID: PMC6329500 DOI: 10.1371/journal.pone.0206955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/02/2019] [Indexed: 11/23/2022] Open
Abstract
Lung disease in alpha-1-antitrypsin deficiency (AATD) results from dysregulated proteolytic activity, mainly by neutrophil elastase (HNE), in the lung parenchyma. This is the result of a substantial reduction of circulating alpha-1-antitrypsin (AAT) and the presence in the plasma of inactive polymers of AAT. Moreover, some AAT mutants have reduced intrinsic activity toward HNE, as demonstrated for the common Z mutant, as well as for other rarer variants. Here we report the identification and characterisation of the novel AAT reactive centre loop variant Gly349Arg (p.G373R) present in the ExAC database. This AAT variant is secreted at normal levels in cellular models of AATD but shows a severe reduction in anti-HNE activity. Biochemical and molecular dynamics studies suggest it exhibits unfavourable RCL presentation to cognate proteases and compromised insertion of the RCL into β-sheet A. Identification of a fully dysfunctional AAT mutant that does not show a secretory defect underlines the importance of accurate genotyping of patients with pulmonary AATD manifestations regardless of the presence of normal levels of AAT in the circulation. This subtype of disease is reminiscent of dysfunctional phenotypes in anti-thrombin and C1-inibitor deficiencies so, accordingly, we classify this variant as the first pure functionally-deficient (type II) AATD mutant.
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Affiliation(s)
- Mattia Laffranchi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emma L K Elliston
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Fabrizio Gangemi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Romina Berardelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - David A Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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36
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Renoux C, Odou MF, Tosato G, Teoli J, Abbou N, Lombard C, Zerimech F, Porchet N, Chapuis Cellier C, Balduyck M, Joly P. Description of 22 new alpha-1 antitrypsin genetic variants. Orphanet J Rare Dis 2018; 13:161. [PMID: 30223862 PMCID: PMC6142351 DOI: 10.1186/s13023-018-0897-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/23/2018] [Indexed: 11/15/2022] Open
Abstract
Alpha-1 antitrypsin deficiency is an autosomal co-dominant disorder caused by mutations of the highly polymorphic SERPINA1 gene. This genetic disorder still remains largely under-recognized and can be associated with lung and/or liver injury. The laboratory testing for this deficiency typically comprises serum alpha-1 antitrypsin quantification, phenotyping according to the isoelectric focusing pattern and genotyping if necessary. To date, more than 100 SERPINA1 variants have been described and new genetic variants are frequently discovered. Over the past 10 years, 22 new genetic variants of the SERPINA1 gene were identified in the daily practice of the University Medical laboratories of Lille and Lyon (France). Among these 22 variants, seven were Null alleles and one with a M1 migration pattern (M1Cremeaux) was considered as deficient according to the clinical and biological data and to the American College of Medical Genetics and Genomics (ACMG) criteria. Three other variants were classified as likely pathogenic, three as variants of uncertain significance while the remaining ones were assumed to be neutral. Moreover, we also identified in this study two recently described SERPINA1 deficient variants: Trento (p.Glu99Val) and SDonosti (p.Ser38Phe). The current data, together with a recent published meta-analysis, represent the most up-to-date list of SERPINA1 variants available so far.
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Affiliation(s)
- Céline Renoux
- Laboratoire de Biochimie et Biologie moléculaire Grand Est, UF "Biochimie des pathologies érythrocytaires", Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France.,Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Team "Vascular Biology and Red Blood Cell", Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Marie-Françoise Odou
- Service de Biochimie et Biologie moléculaire "Hormonologie, Métabolisme-Nutrition, Oncologie", CHU Lille, F-59000, Lille, France. .,Faculty of Pharmaceutical and Biological Sciences, UMR995, LIRIC (Lille Inflammation Research International Center), University of Lille, F-59000, Lille, France.
| | - Guillaume Tosato
- Service de Biochimie et Biologie moléculaire "Hormonologie, Métabolisme-Nutrition, Oncologie", CHU Lille, F-59000, Lille, France
| | - Jordan Teoli
- Laboratoire de Biochimie et Biologie moléculaire Grand Est, UF "Biochimie des pathologies érythrocytaires", Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Norman Abbou
- Laboratoire de Biochimie et Biologie moléculaire Grand Est, UF "Biochimie des pathologies érythrocytaires", Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Christine Lombard
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon & Université Claude Bernard-Lyon 1, Lyon, France
| | - Farid Zerimech
- Service de Biochimie et Biologie moléculaire "Hormonologie, Métabolisme-Nutrition, Oncologie", CHU Lille, F-59000, Lille, France.,EA4483, IMPECS, Institut Pasteur de Lille, University of Lille, F-59000, Lille, France
| | - Nicole Porchet
- Service de Biochimie et Biologie moléculaire "Hormonologie, Métabolisme-Nutrition, Oncologie", CHU Lille, F-59000, Lille, France
| | - Colette Chapuis Cellier
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon & Université Claude Bernard-Lyon 1, Lyon, France
| | - Malika Balduyck
- Service de Biochimie et Biologie moléculaire "Hormonologie, Métabolisme-Nutrition, Oncologie", CHU Lille, F-59000, Lille, France.,Faculty of Pharmaceutical and Biological Sciences, EA7364, RADEME (Research team on rare developmental and metabolic diseases), University of Lille, F-59000, Lille, France
| | - Philippe Joly
- Laboratoire de Biochimie et Biologie moléculaire Grand Est, UF "Biochimie des pathologies érythrocytaires", Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France.,Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Team "Vascular Biology and Red Blood Cell", Université Claude Bernard Lyon 1, Villeurbanne, France
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