1
|
Aggarwal S, Vineeth VS, Padwal SS, Bhat SA, Singh A, Kulkarni A, Patil M, Tallapaka K, Pasumarthi D, Venkatapuram V, Thotakura PL, Dalal A, Bhandari R. SERPINA11 related novel serpinopathy - A perinatal lethal disorder. Clin Genet 2024; 106:367-373. [PMID: 38831697 DOI: 10.1111/cge.14564] [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: 03/02/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
SERPINA11 is a hitherto poorly characterised gene belonging to Clade A of the SERPIN superfamily, with unknown expression pattern and functional significance. We report a perinatal lethal phenotype in two foetuses from the same family associated with a biallelic loss of function variant in SERPINA11, and provide functional evidence to support its candidature as a Mendelian disorder. The SERPINA11 variant-associated foetal phenotype is characterised by gross and histopathological features of extracellular matrix disruption. Western blot and immunofluorescence analyses revealed SERPINA11 expression in multiple mouse tissues, with pronounced expression in the bronchiolar epithelium. We observed a significant decrease in SERPINA11 immunofluorescence in the affected foetal lung compared with a healthy gestation-matched foetus. Protein expression data from HEK293T cell lines following site-directed mutagenesis support the loss of function nature of the variant. Transcriptome analysis from the affected foetal liver indicated the possibility of reduced SERPINA11 transcript abundance. This novel serpinopathy appears to be a consequence of the loss of inhibition of serine proteases involved in extracellular matrix remodelling, revealing SERPINA11 as a protease inhibitor critical for embryonic development.
Collapse
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Venugopal Satidevi Vineeth
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrutika S Padwal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sameer Ahmed Bhat
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Aditya Kulkarni
- Department of Histopathology, Apollo Hospitals, Hyderabad, India
| | - Mallikarjun Patil
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | - Divya Pasumarthi
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vijayasree Venkatapuram
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Pragna Lakshmi Thotakura
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
2
|
Martín T, Guimarães C, Esquinas C, Torres-Duran M, Turner AM, Tanash H, Rodríguez-García C, Corsico A, López-Campos JL, Bartošovská E, Stæhr Jensen JU, Hernández-Pérez JM, Sucena M, Miravitlles M. Risk of lung disease in the PI*SS genotype of alpha-1 antitrypsin: an EARCO research project. Respir Res 2024; 25:260. [PMID: 38926693 PMCID: PMC11210092 DOI: 10.1186/s12931-024-02879-y] [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: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The PI*S variant is one of the most prevalent mutations within alpha-1 antitrypsin deficiency (AATD). The risk of developing AATD-related lung disease in individuals with the PI*SS genotype is poorly defined despite its substantial prevalence. Our study aimed to characterize this genotype and its risk for lung disease and compare it with the PI*ZZ and PI*SZ genotypes using data from the European Alpha-1 antitrypsin Deficiency Research Collaboration international registry. METHOD Demographic, clinical, functional, and quality of life (QoL) parameters were assessed to compare the PI*SS characteristics with the PI*SZ and PI*ZZ controls. A propensity score with 1:3 nearest-neighbour matching was performed for the most important confounding variables. RESULTS The study included 1007 individuals, with PI*SS (n = 56; 5.6%), PI*ZZ (n = 578; 57.4%) and PI*SZ (n = 373; 37.0%). The PI*SS population consisted of 58.9% men, with a mean age of 59.2 years and a mean FEV1(% predicted) of 83.4%. Compared to PI*ZZ individuals they had less frequent lung disease (71.4% vs. 82.2%, p = 0.037), COPD (41.4% vs. 60%, p = 0.002), and emphysema (23.2% vs. 51.9%, p < 0.001) and better preserved lung function, fewer exacerbations, lower level of dyspnoea, and better QoL. In contrast, no significant differences were found in the prevalence of lung diseases between PI*SS and PI*SZ, or lung function parameters, exacerbations, dyspnoea, or QoL. CONCLUSIONS We found that, as expected, the risk of lung disease associated with the PI*SS genotype is significantly lower compared with PI*ZZ, but does not differ from that observed in PI*SZ individuals, despite having higher serum AAT levels. TRIAL REGISTRATION www. CLINICALTRIALS gov (ID: NCT04180319).
Collapse
Affiliation(s)
- Teresa Martín
- Pneumology Department, Hospital Beatriz Ângelo, Av. Carlos Teixeira 3, Loures, 2674-514, Portugal.
| | - Catarina Guimarães
- Pneumology Department, Hospital Senhora da Oliveira, Guimarães, Portugal
| | - Cristina Esquinas
- Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Maria Torres-Duran
- Pneumology Department, NeumoVigo I+i Research Group, Hospital Álvaro Cunqueiro, IIS Galicia Sur, Vigo, Spain
| | - Alice M Turner
- Respiratory Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Hanan Tanash
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Carlota Rodríguez-García
- Pneumology Department, Complejo Hospitalario Clínico-Universitario de Santiago, Santiago de Compostela, Spain
| | - Angelo Corsico
- Pneumology Unit, IRCCS San Matteo Hospital Foundation, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - José Luis López-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS). Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Eva Bartošovská
- Department of Pneumology, Thomayer Hospital, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jens-Ulrik Stæhr Jensen
- Section of Respiratory Medicine, Department of Medicine, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - José María Hernández-Pérez
- Pneumology Department, Hospital Universitario Nuestra Señora de La Candelaria, Santa Cruz de Tenerife, Spain
| | - Maria Sucena
- Pneumology Department, Centro Hospitalar Universitário de Santo António, Porto, Portugal
| | - Marc Miravitlles
- Pneumology Department, Hospital Universitari Vall d'Hebron/Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus. CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| |
Collapse
|
3
|
Walsh C, Jin S. Induced Pluripotent Stem Cells and CRISPR-Cas9 Innovations for Treating Alpha-1 Antitrypsin Deficiency and Glycogen Storage Diseases. Cells 2024; 13:1052. [PMID: 38920680 PMCID: PMC11201389 DOI: 10.3390/cells13121052] [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: 05/24/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Human induced pluripotent stem cell (iPSC) and CRISPR-Cas9 gene-editing technologies have become powerful tools in disease modeling and treatment. By harnessing recent biotechnological advancements, this review aims to equip researchers and clinicians with a comprehensive and updated understanding of the evolving treatment landscape for metabolic and genetic disorders, highlighting how iPSCs provide a unique platform for detailed pathological modeling and pharmacological testing, driving forward precision medicine and drug discovery. Concurrently, CRISPR-Cas9 offers unprecedented precision in gene correction, presenting potential curative therapies that move beyond symptomatic treatment. Therefore, this review examines the transformative role of iPSC technology and CRISPR-Cas9 gene editing in addressing metabolic and genetic disorders such as alpha-1 antitrypsin deficiency (A1AD) and glycogen storage disease (GSD), which significantly impact liver and pulmonary health and pose substantial challenges in clinical management. In addition, this review discusses significant achievements alongside persistent challenges such as technical limitations, ethical concerns, and regulatory hurdles. Future directions, including innovations in gene-editing accuracy and therapeutic delivery systems, are emphasized for next-generation therapies that leverage the full potential of iPSC and CRISPR-Cas9 technologies.
Collapse
Affiliation(s)
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| |
Collapse
|
4
|
Janciauskiene S, Lechowicz U, Pelc M, Olejnicka B, Chorostowska-Wynimko J. Diagnostic and therapeutic value of human serpin family proteins. Biomed Pharmacother 2024; 175:116618. [PMID: 38678961 DOI: 10.1016/j.biopha.2024.116618] [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: 01/11/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SERPIN (serine proteinase inhibitors) is an acronym for the superfamily of structurally similar proteins found in animals, plants, bacteria, viruses, and archaea. Over 1500 SERPINs are known in nature, while only 37 SERPINs are found in humans, which participate in inflammation, coagulation, angiogenesis, cell viability, and other pathophysiological processes. Both qualitative or quantitative deficiencies or overexpression and/or abnormal accumulation of SERPIN can lead to diseases commonly referred to as "serpinopathies". Hence, strategies involving SERPIN supplementation, elimination, or correction are utilized and/or under consideration. In this review, we discuss relationships between certain SERPINs and diseases as well as putative strategies for the clinical explorations of SERPINs.
Collapse
Affiliation(s)
- Sabina Janciauskiene
- Department of Pulmonary and Infectious Diseases and BREATH German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany; Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St, Warsaw 01-138, Poland
| | - Urszula Lechowicz
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St, Warsaw 01-138, Poland
| | - Magdalena Pelc
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St, Warsaw 01-138, Poland
| | - Beata Olejnicka
- Department of Pulmonary and Infectious Diseases and BREATH German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St, Warsaw 01-138, Poland.
| |
Collapse
|
5
|
Sarrou S, Voulgaridi I, Fousika A, Dadouli K, Margaritopoulou O, Kakkas I, Hadjichristodoulou C, Kalala F, Speletas M. Heterozygous SERPINA1 Defects and Their Impact on Clinical Manifestations of Patients with Predominantly Antibody Deficiencies. Int J Mol Sci 2024; 25:5382. [PMID: 38791420 PMCID: PMC11120870 DOI: 10.3390/ijms25105382] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Patients with predominantly antibody deficiencies (PADs) display hypogammaglobulinemia with a high prevalence of infections, along with autoimmune manifestations, benign and malignant lymphoproliferation and granulomatous disease. It is noteworthy that PAD patients, even those with defects in the same causative genes, display a variable clinical phenotype, suggesting that additional genetic polymorphisms, located in either immune-related or non-immune-related genes, may affect their clinical and laboratory phenotype. In this context, we analyzed 80 PAD patients, including 70 with common variable immunodeficiency (CVID) for SERPINA1 defects, in order to investigate the possible contribution to PAD clinical phenotype. Ten CVID patients carried heterozygous pathogenic SERPINA1 defects with normal alpha-1 antitrypsin levels. Interestingly, the presence of the Z allele (rs28929474), which was found in three patients, was significantly associated with liver disease; hepatic complications were also observed in patients carrying the p.Leu23Gln (rs1379209512) and the p.Phe76del (rs775982338) alleles. Conversely, no correlation of SERPINA1 defective variants with respiratory complications was observed, although patients with pathogenic variants exhibit a reduced probability of developing autoimmune diseases. Therefore, we recommend SERPINA1 genetic analysis in PAD in order to identify patients with a higher risk for liver disease.
Collapse
Affiliation(s)
- Styliani Sarrou
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (S.S.); (A.F.); (O.M.); (F.K.)
| | - Ioanna Voulgaridi
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larissa, Greece; (I.V.); (K.D.); (C.H.)
| | - Athanasia Fousika
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (S.S.); (A.F.); (O.M.); (F.K.)
| | - Katerina Dadouli
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larissa, Greece; (I.V.); (K.D.); (C.H.)
| | - Olympia Margaritopoulou
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (S.S.); (A.F.); (O.M.); (F.K.)
| | - Ioannis Kakkas
- Department of Immunology and Histocompatibility, “Evaggelismos” General Hospital, 10676 Athens, Greece;
| | - Christos Hadjichristodoulou
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larissa, Greece; (I.V.); (K.D.); (C.H.)
| | - Fani Kalala
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (S.S.); (A.F.); (O.M.); (F.K.)
| | - Matthaios Speletas
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (S.S.); (A.F.); (O.M.); (F.K.)
| |
Collapse
|
6
|
Dasí F. Alpha-1 antitrypsin deficiency. Med Clin (Barc) 2024; 162:336-342. [PMID: 37993348 DOI: 10.1016/j.medcli.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
Alpha-1 antitrypsin deficiency (AATD) is a rare hereditary condition caused by decreased plasma and tissue levels of alpha-1 antitrypsin (AAT) that can lead to serious lung and liver disease in children and adults. AATD patients face challenges such as under diagnosis, clinical variability, and limited treatment options for liver disease. Early detection and biomarkers for predicting outcomes are needed to improve patient outcome. Currently, the only approved pharmacological therapy is augmentation therapy, which can delay the progression of emphysema. However, alternative strategies such as gene therapy, induced pluripotent stem cells, and prevention of AAT polymerization inside hepatocytes are being investigated. This review aims to summarize and update current knowledge on AATD, identify areas of controversy, and formulate questions for further research.
Collapse
Affiliation(s)
- Francisco Dasí
- Universitat de València, Facultad de Medicina, Departamento de Fisiología, IIS INCLIVA, Valencia, Spain.
| |
Collapse
|
7
|
Lechowicz U, Martinez-Delgado B, Liu B, Wrenger S, Rozy A, Zdral A, DeLuca DS, Welte T, Janciauskiene S, Chorostowska-Wynimko J. An association between plasma levels of α2-macroglobulin and α1-antitrypsin in PiMM and PiZZ individuals differing in COPD presentation. Clin Biochem 2024; 126:110736. [PMID: 38428450 DOI: 10.1016/j.clinbiochem.2024.110736] [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: 12/21/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
INTRODUCTION Compared to normal PiMM, individuals with severe α1-antitrypsin (AAT) PiZZ (Glu342Lys) genotype deficiency are at higher risk of developing early-onset chronic obstructive pulmonary disease (COPD)/emphysema associated with Z-AAT polymers and neutrophilic inflammation. We aimed to investigate putative differences in plasma levels of acute phase proteins (APP) between PiMM and PiZZ subjects and to determine plasma Z-AAT polymer levels in PiZZ subjects. MATERIALS AND METHODS Nephelometric analysis of seven plasma APPs was performed in 67 PiMM and 44 PiZZ subjects, of whom 43 and 42, respectively, had stable COPD. Of the PiZZ-COPD patients, 21 received and 23 did not receive intravenous therapy with human AAT preparations (IV-AAT). Plasma levels of Z-AAT polymers were determined by Western blotting using specific mouse monoclonal antibodies (2C1 and LG96). RESULTS In addition to lower plasma AAT, PiZZ patients had higher α2-macroglobulin (A2MG) levels than PiMM patients. In contrast, PiZZ who received IV-AAT had higher AAT values but lower A2MG values than PiZZ without IV-AAT. Regardless of the AAT genotype, AAT levels were inversely correlated with A2MG, and the AAT/A2MG ratio was correlated with lung diffusion capacity (DCLO%). All PiZZ patients had circulating Z-AAT polymer levels that correlated directly with A2MG. In PiZZ without IV-AAT therapy polymer levels correlated inversely with the ratio of forced expiratory volume in 1 s to forced vital capacity (FEV1/FVC). CONCLUSION Combined measurement of plasma AAT and A2MG levels may be of clinical value in assessing the progression of COPD and requires further attention.
Collapse
Affiliation(s)
- Urszula Lechowicz
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases Warsaw, Poland
| | - Beatriz Martinez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), CIBER of Rare Diseases, CIBERER, Madrid, Spain.
| | - Bin Liu
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover, Germany.
| | - Sabine Wrenger
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover, Germany.
| | - Adriana Rozy
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases Warsaw, Poland
| | - Aneta Zdral
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases Warsaw, Poland.
| | - David S DeLuca
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover, Germany.
| | - Tobias Welte
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover, Germany.
| | - Sabina Janciauskiene
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases Warsaw, Poland; Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover, Germany.
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases Warsaw, Poland
| |
Collapse
|
8
|
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.
Collapse
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.)
| |
Collapse
|
9
|
Kolagatla S, Gullapalli D, Vangara A, Chan R, Jernigan D, Moka N, Ganti SS. Characteristics of Patients With Alpha-1 Antitrypsin Deficiency From Rural Appalachia: A Retrospective Single-Center Study. Cureus 2024; 16:e56395. [PMID: 38633947 PMCID: PMC11023687 DOI: 10.7759/cureus.56395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Alpha-1 antitrypsin (AAT) deficiency, an autosomal co-dominant inherited condition, significantly impacts lung and liver functions, with mutations in the SERPINA1 gene, notably the Z allele, playing a pivotal role in disease susceptibility. This retrospective descriptive study from a rural Eastern Kentucky pulmonary clinic aimed to characterize patients with AAT deficiency, focusing on demographic, clinical, and laboratory parameters extracted from electronic health records (EHR) of Appalachian Regional Healthcare (ARH). Among 100 patient encounters, 56 were analyzed, revealing notable sex-based differences in smoking rates and co-existing conditions, with males showing higher rates of black lung and chronic obstructive pulmonary disease. In comparison, females exhibited higher rates of asthma, COVID-19, pneumothorax, and obstructive sleep apnea. The study emphasizes the importance of understanding genotype-phenotype correlations and demographic factors in assessing AAT deficiency, advocating for further research to refine management strategies and elucidate causal relationships.
Collapse
Affiliation(s)
| | | | - Avinash Vangara
- Internal Medicine, Appalachian Regional Healthcare, Harlan, USA
| | - Regina Chan
- Physical Medicine and Rehabilitation, Albany Medical College, Albany, USA
| | - Derek Jernigan
- Internal Medicine, Kettering Medical Center, Kettering, USA
| | - Nagabhishek Moka
- Oncology, Hematology, and Internal Medicine, Appalachian Regional Healthcare, Hazard, USA
| | | |
Collapse
|
10
|
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; 0:cclm-2023-1348. [PMID: 38407261 DOI: 10.1515/cclm-2023-1348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
11
|
Ferrarotti I, Wencker M, Chorostowska-Wynimko J. Rare variants in alpha 1 antitrypsin deficiency: a systematic literature review. Orphanet J Rare Dis 2024; 19:82. [PMID: 38388492 PMCID: PMC10885523 DOI: 10.1186/s13023-024-03069-1] [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: 10/10/2023] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Alpha 1 Antitrypsin Deficiency (AATD) is a largely underrecognized genetic condition characterized by low Alpha 1 Antitrypsin (AAT) serum levels, resulting from variations in SERPINA1. Many individuals affected by AATD are thought to be undiagnosed, leading to poor patient outcomes. The Z (c.1096G > A; p.Glu366Lys) and S (c.863A > T; p.Glu288Val) deficiency variants are the most frequently found variants in AATD, with the Z variant present in most individuals diagnosed with AATD. However, there are many other less frequent variants known to contribute to lung and/or liver disease in AATD. To identify the most common rare variants associated with AATD, we conducted a systematic literature review with the aim of assessing AATD variation patterns across the world. METHODS A systematic literature search was performed to identify published studies reporting AATD/SERPINA1 variants. Study eligibility was assessed for the potential to contain relevant information, with quality assessment and data extraction performed on studies meeting all eligibility criteria. AATD variants were grouped by variant type and linked to the geographical region identified from the reporting article. RESULTS Of the 4945 articles identified by the search string, 864 contained useful information for this study. Most articles came from the United States, followed by the United Kingdom, Germany, Spain, and Italy. Collectively, the articles identified a total of 7631 rare variants and 216 types of rare variant across 80 counties. The F (c.739C > T; p.Arg247Cys) variant was identified 1,281 times and was the most reported known rare variant worldwide, followed by the I (c.187C > T; p.Arg63Cys) variant. Worldwide, there were 1492 Null/rare variants that were unidentified at the time of source article publication and 75 rare novel variants reported only once. CONCLUSION AATD goes far beyond the Z and S variants, suggesting there may be widespread underdiagnosis of patients with the condition. Each geographical region has its own distinctive variety of AATD variants and, therefore, comprehensive testing is needed to fully understand the true number and type of variants that exist. Comprehensive testing is also needed to ensure accurate diagnosis, optimize treatment strategies, and improve outcomes for patients with AATD.
Collapse
Affiliation(s)
- Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumology Unit, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | | | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| |
Collapse
|
12
|
Karadoğan D, Şahin Ü, Dreger B, Grandoso L, Osaba L. Case report of a novel alpha1-antitrypsin null variant in Türkiye: Q0 RİZE. BMC Pulm Med 2024; 24:91. [PMID: 38383302 PMCID: PMC10882785 DOI: 10.1186/s12890-024-02900-6] [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] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Alpha1-antitrypsin (AAT) is a serine protease inhibitor that serves as a counterbalance to the activity of elastases, e.g., neutrophil elastase in lung tissue. AAT deficiency (AATD) is a rare disorder usually arising from mutations to the SERPINA1 gene that codes for AAT. The most common AATD alleles are S and Z which produce ~ 40% and ~ 90% reductions in serum AAT, respectively. Rare genetic variants (> 500 identified) can also be associated with mild to severe AATD. RESULTS This report describes a novel mutation of SERPINA1 producing AATD, which we have designated, Q0RİZE. This mutation was identified in a 44-year-old woman admitted with massive hemoptysis and treated with bronchial artery embolization. Computed tomography revealed centriacinar and panacinar emphysema with prominent air entrapment, atelectasis, and localized bronchiectasis. Serum AAT was < 0.27 g/L (below detection limit). Genetic analysis showed homozygous deletion of exons I to III. CONCLUSIONS Although many SERPINA1 variants have been identified, variants with large deletions and identified in a homozygous individual, as seen in this case with Q0RIZE, are uncommon. AATD is an underdiagnosed and undertreated disease. Wider screening of COPD patients could result in earlier diagnosis and treatment that could preserve lung function.
Collapse
Affiliation(s)
- Dilek Karadoğan
- School of Medicine, Department of Chest Diseases, Recep Tayyip Erdoğan University, Rize, Türkiye.
| | - Ünal Şahin
- School of Medicine, Department of Chest Diseases, Recep Tayyip Erdoğan University, Rize, Türkiye
| | - Bettina Dreger
- Pulmonology Medical Affairs, Grifols Deutschland GmbH, Frankfurt, Germany
| | | | - Lourdes Osaba
- Progenika Biopharma, a Grifols company, Derio, Spain
| |
Collapse
|
13
|
Annunziata A, Fiorentino G, Balestrino M, Rega R, Spinelli S, Atripaldi L, Sola A, Massaro F, Calabrese C. Alpha-1 Antitrypsin PI M Heterozygotes with Rare Variants: Do They Need a Clinical and Functional Follow-Up? J Clin Med 2024; 13:1084. [PMID: 38398397 PMCID: PMC10889345 DOI: 10.3390/jcm13041084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background: Few data are available on the risk of airway dysfunction in protease inhibitor (PI*) M heterozygotes carrying rare null or deficient allelic variants of the gene SERPINA-1 (PI*MR). (2) Methods: In this observational study, in a cohort of PI*MR heterozygotes, we evaluated respiratory functional parameters at baseline and at one-year follow-up. Moreover, we compared such parameters with those of the PI*MZ and PI*MS patients. (3) Results: A total of 60 patients were recruited; 35 PI*MR, 11 PI*MZ and 14 PI*MS. At the annual follow-up, the PI*MR and PI*MZ patients demonstrated a significantly higher FEV1 decline than the PI*MS group (p = 0.04 and p = 0.018, respectively). The PI*MR patients showed a significant increase in DLCO annual decline in comparison with the PI*MS group (p = 0.02). At baseline, the PI*MR smoking patients, compared with nonsmokers, showed statistically significant lower values of FEV1, FEV1/FVC and DLCO (p = 0.0004, p < 0.0001, p = 0.007, respectively) and, at the one-year follow-up, they displayed a significantly higher FEV1 and DLCO decline (p = 0.0022, p = 0.011, respectively). PI*MR heterozygotes with COPD showed a significantly higher FEV1, FEV1/FVC and DLCO annual decline in comparison with healthy PI*MR (p = 0.0083, p = 0.043, p = 0.041). (4) Conclusions: These results suggest that PI*MR heterozygotes, particularly smokers with COPD, have a greater annual decline in respiratory functional parameters and need to be monitored.
Collapse
Affiliation(s)
- Anna Annunziata
- Department of Intensive Care, Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Giuseppe Fiorentino
- Department of Intensive Care, Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Marco Balestrino
- Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli", Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Roberto Rega
- Department of Intensive Care, Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Sara Spinelli
- Department of Intensive Care, Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Lidia Atripaldi
- Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli", Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Alessio Sola
- Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli", Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Federica Massaro
- Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli", Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| | - Cecilia Calabrese
- Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli", Azienda Ospedaliera di Rilievo Nazionale dei Colli, 80131 Naples, Italy
| |
Collapse
|
14
|
Poole B, Oshins R, Huo Z, Aranyos A, West J, Duarte S, Clark VC, Beduschi T, Zarrinpar A, Brantly M, Khodayari N. Sirtuin3 promotes the degradation of hepatic Z alpha-1 antitrypsin through lipophagy. Hepatol Commun 2024; 8:e0370. [PMID: 38285890 PMCID: PMC10830086 DOI: 10.1097/hc9.0000000000000370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Alpha-1 antitrypsin deficiency (AATD) is a genetic disease caused by misfolding and accumulation of mutant alpha-1 antitrypsin (ZAAT) in the endoplasmic reticulum of hepatocytes. Hepatic ZAAT aggregates acquire a toxic gain-of-function that impacts the endoplasmic reticulum which is theorized to cause liver disease in individuals with AATD who present asymptomatic until late-stage cirrhosis. Currently, there is no treatment for AATD-mediated liver disease except liver transplantation. In our study of mitochondrial RNA, we identified that Sirtuin3 (SIRT3) plays a role in the hepatic phenotype of AATD. METHODS Utilizing RNA and protein analysis in an in vitro AATD model, we investigated the role of SIRT3 in the pathophysiology of AATD-mediated liver disease while also characterizing our novel, transgenic AATD mouse model. RESULTS We show lower expression of SIRT3 in ZAAT-expressing hepatocytes. In contrast, the overexpression of SIRT3 increases hepatic ZAAT degradation. ZAAT degradation mediated by SIRT3 appeared independent of proteasomal degradation and regular autophagy pathways. We observed that ZAAT-expressing hepatocytes have aberrant accumulation of lipid droplets, with ZAAT polymers localizing on the lipid droplet surface in a direct interaction with Perilipin2, which coats intracellular lipid droplets. SIRT3 overexpression also induced the degradation of lipid droplets in ZAAT-expressing hepatocytes. We observed that SIRT3 overexpression induces lipophagy by enhancing the interaction of Perilipin2 with HSC70. ZAAT polymers then degrade as a consequence of the mobilization of lipids through this process. CONCLUSIONS In this context, SIRT3 activation may eliminate the hepatic toxic gain-of-function associated with the polymerization of ZAAT, providing a rationale for a potential novel therapeutic approach to the treatment of AATD-mediated liver disease.
Collapse
Affiliation(s)
- Brittney Poole
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Regina Oshins
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Public Health, University of Florida, Gainesville, Florida, USA
| | - Alek Aranyos
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Jesse West
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Sergio Duarte
- Department of Surgery, Division of Transplantation and Hepatobiliary Surgery, University of Florida, Gainesville, Florida, USA
| | - Virginia C. Clark
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Florida, Gainesville, Florida, USA
| | - Thiago Beduschi
- Department of Surgery, Division of Transplantation and Hepatobiliary Surgery, University of Florida, Gainesville, Florida, USA
| | - Ali Zarrinpar
- Department of Surgery, Division of Transplantation and Hepatobiliary Surgery, University of Florida, Gainesville, Florida, USA
| | - Mark Brantly
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Nazli Khodayari
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
15
|
Orimoloye HT, He D, Li T, Janzen C, Barjaktarevic I, Wang X, Hansen J, Heck JE. Alpha-1 antitrypsin deficiency and pregnancy complications and birth outcomes: A population-based cohort study in Denmark. PLoS One 2024; 19:e0296434. [PMID: 38166066 PMCID: PMC10760838 DOI: 10.1371/journal.pone.0296434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/13/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Alpha-1 antitrypsin deficiency (AATD) is related to developing lung and liver disease, but no large-scale studies examine its association with birth outcomes. OBJECTIVE We investigated the risk of pregnancy complications and adverse birth outcomes in mothers and children with AATD. METHODS Using a large cohort data of Danish mothers and children with AATD from 1973 to 2013 (n = 2,027,229), with 559 cases (305 mothers and 254 children). We conducted Poisson regression to examine associations between alpha-1 antitrypsin deficiency, adverse birth outcomes, and pregnancy complications in mothers and children. RESULTS AATD was related to term low birth weight [<2500g; Risk Ratio(RR) = 2.04, 95% confidence interval (CI): 1.50-2.79], lowest quartile of abdominal circumference at birth in children of non-smoking mothers (RR = 1.55, 95% CI: 1.14-2.11), delivery via Cesarean-section (RR = 1.59, 95% CI: 1.05-2.40), preterm birth (RR = 1.54, 95% CI: 1.19-2.00) and preeclampsia (RR = 2.64, 95% CI: 1.76-3.94). CONCLUSIONS This emphasizes the need for mothers with AATD to be monitored closely during pregnancy to reduce the risk of adverse birth outcomes. Routine screening for alpha-1 antitrypsin in pregnancy may be considered among mothers with a pulmonary and liver disease history.
Collapse
Affiliation(s)
- Helen T. Orimoloye
- Department of Rehabilitation and Health Services, University of North Texas, Denton, Texas, United States of America
| | - Di He
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Tong Li
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Carla Janzen
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Igor Barjaktarevic
- Division of Pulmonary and Critical Care, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Xuexia Wang
- Department of Biostatistics, Florida International University, Miami, Florida, United States of America
| | | | - Julia E. Heck
- Department of Rehabilitation and Health Services, University of North Texas, Denton, Texas, United States of America
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|
16
|
Barzon V, Ferrarotti I, Ottaviani S. Sanger and Next-Generation Sequencing of AAT. Methods Mol Biol 2024; 2750:57-67. [PMID: 38108967 DOI: 10.1007/978-1-0716-3605-3_6] [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] [Indexed: 12/19/2023]
Abstract
Sequencing of DNA is normally the final procedure carried out to determine the actual pathogenic variants when the techniques used for genotyping are unable to provide complete identification of both AAT alleles. Gene sequencing of complete SERPINA1 gene by using the Sanger method or next-generation sequencing (NGS) is crucial to enable correct diagnosis in patients with alpha1-antitrypsin deficiency caused by uncommon AAT variants.This protocol explains how to correctly sequence SERPINA1 gene both with Sanger method and NGS.
Collapse
Affiliation(s)
- Valentina Barzon
- Department of Internal Medicine and Therapeutics, Pulmonology Unit, University of Pavia, Pavia, Italy
| | - Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Stefania Ottaviani
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, UOC Pulmonology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| |
Collapse
|
17
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
18
|
Gruntman AM, Xue W, Flotte TR. Alpha-1 Antitrypsin Deficiency. Methods Mol Biol 2024; 2750:1-7. [PMID: 38108962 DOI: 10.1007/978-1-0716-3605-3_1] [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] [Indexed: 12/19/2023]
Abstract
Alpha-1 antitrypsin (AAT) deficiency is a common monogenic disorder in which there is a strong founder effect of a single missense mutation in SERPINA1, the gene encoding this major circulating serum anti-protease that is normally expressed primarily in hepatocytes. These features make AAT deficiency particularly attractive as a target for therapeutic gene editing using a wide variety of approaches.
Collapse
Affiliation(s)
- Alisha M Gruntman
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Terence R Flotte
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| |
Collapse
|
19
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
20
|
Kemp J, Ladwig PM, Snyder MR. Alpha-1-Antitrypsin (A1AT) Proteotyping by LC-MS/MS. Methods Mol Biol 2024; 2750:95-106. [PMID: 38108970 DOI: 10.1007/978-1-0716-3605-3_9] [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] [Indexed: 12/19/2023]
Abstract
The diagnosis of alpha-1-antitrypsin (A1AT) deficiency is established by quantitation of protein concentration in serum (immunoassay) followed by determination of specific allelic variants by phenotyping (isoelectric focusing (IEF) gel electrophoresis) and/or allele-specific genotyping. Various phenotyping and genotyping methodologies are available, and each has their own advantages and disadvantages. As an alternative, mass spectrometry is emerging as a powerful tool in the identification and quantitation of proteins and peptides. The method described here, referred to as proteotyping, is a proteomic method using trypsin digestion and tandem mass spectrometry that detects the most common deficiency alleles, S and Z, associated with A1AT deficiency.This qualitative mass spectrometry method is based on the principle that the S and Z mutations lead to amino acid changes which result in a change in the mass of the A1AT protein. When the A1AT protein is proteolytically digested, multiple peptides are generated, two of which include the sites of the S and Z mutations, respectively. Peptides generated from wild-type A1AT (M alleles) differ in sequence and mass from peptides generated from the S and Z alleles at these two specific locations. The mass difference allows for differentiation of S and Z peptides, representing the deficiency alleles, from non-S and non-Z peptides, representing the wild-type alleles (M). Interpretation of the peptide patterns in conjunction with A1AT quantitation by immunoassay allows for an accurate assessment for the presence of deficiency alleles in the majority of patients.
Collapse
Affiliation(s)
- Jennifer Kemp
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paula M Ladwig
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melissa R Snyder
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
21
|
Marin-Hinojosa C, Fatela-Cantillo D, Lopez-Campos JL. Measuring of Alpha-1 Antitrypsin Concentration by Nephelometry or Turbidimetry. Methods Mol Biol 2024; 2750:123-133. [PMID: 38108973 DOI: 10.1007/978-1-0716-3605-3_12] [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] [Indexed: 12/19/2023]
Abstract
Most clinical laboratories quantify alpha-1 antitrypsin using either nephelometry or turbidimetry techniques because they are commercially available, amenable to automation, and precise. Both methods are based on light scatter. The foundation of both techniques is based on incubation of the specimen with anti-AAT polyclonal antibody solution, a polymer matrix between endogenous AAT and the reagent antibodies forms, leading to production of light-scattering large particles. Although these two terms are sometimes used synonymously, technically speaking they are not.Nephelometry measures the amount of turbidity or cloudiness of a solution by directly quantifying the intensity of the light scattered by insoluble particles in the sample. Therefore, this technique measures the light that passes through the sample, with the detector being placed at an angle from the sample. Turbidimetry is the process of measuring the loss of intensity of the light transmitted linearly through a sample caused by the scattering effect of insoluble particles. The decrease in light transmission is measured compared to a reference, and the absorbed light is quantified.Beyond specific technical differences between both techniques, there are two major differences between the two procedures that may influence the results. First, the concentration of the sample and the resulting intensity of scattered light relative to the intensity of the light source is one major factor. Second, the size of the scattering particles is also a key differentiating factor. This chapter describes the technical requirements, the different protocols, and the clinical applicability of these two techniques in the diagnosis of alpha-1 antitrypsin deficiency.
Collapse
Affiliation(s)
- Carmen Marin-Hinojosa
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Fatela-Cantillo
- Unidad de Gestión Clínica de Laboratorios, Servicio de Bioquímica Clínica, Sección de Inmunoproteínas y Marcadores Tumorales, Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
22
|
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.
Collapse
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.)
| |
Collapse
|
23
|
Gogate A, Belcourt J, Shah M, Wang AZ, Frankel A, Kolmel H, Chalon M, Stephen P, Kolli A, Tawfik SM, Jin J, Bahal R, Rasmussen TP, Manautou JE, Zhong XB. Targeting the Liver with Nucleic Acid Therapeutics for the Treatment of Systemic Diseases of Liver Origin. Pharmacol Rev 2023; 76:49-89. [PMID: 37696583 PMCID: PMC10753797 DOI: 10.1124/pharmrev.123.000815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Systemic diseases of liver origin (SDLO) are complex diseases in multiple organ systems, such as cardiovascular, musculoskeletal, endocrine, renal, respiratory, and sensory organ systems, caused by irregular liver metabolism and production of functional factors. Examples of such diseases discussed in this article include primary hyperoxaluria, familial hypercholesterolemia, acute hepatic porphyria, hereditary transthyretin amyloidosis, hemophilia, atherosclerotic cardiovascular diseases, α-1 antitrypsin deficiency-associated liver disease, and complement-mediated diseases. Nucleic acid therapeutics use nucleic acids and related compounds as therapeutic agents to alter gene expression for therapeutic purposes. The two most promising, fastest-growing classes of nucleic acid therapeutics are antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs). For each listed SDLO disease, this article discusses epidemiology, symptoms, genetic causes, current treatment options, and advantages and disadvantages of nucleic acid therapeutics by either ASO or siRNA drugs approved or under development. Furthermore, challenges and future perspectives on adverse drug reactions and toxicity of ASO and siRNA drugs for the treatment of SDLO diseases are also discussed. In summary, this review article will highlight the clinical advantages of nucleic acid therapeutics in targeting the liver for the treatment of SDLO diseases. SIGNIFICANCE STATEMENT: Systemic diseases of liver origin (SDLO) contain rare and common complex diseases caused by irregular functions of the liver. Nucleic acid therapeutics have shown promising clinical advantages to treat SDLO. This article aims to provide the most updated information on targeting the liver with antisense oligonucleotides and small interfering RNA drugs. The generated knowledge may stimulate further investigations in this growing field of new therapeutic entities for the treatment of SDLO, which currently have no or limited options for treatment.
Collapse
Affiliation(s)
- Anagha Gogate
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jordyn Belcourt
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Milan Shah
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alicia Zongxun Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alexis Frankel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Holly Kolmel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Matthew Chalon
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Prajith Stephen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Aarush Kolli
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Sherouk M Tawfik
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| |
Collapse
|
24
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
25
|
Kappe NN, Alagem N, Tov N, Stolk J. Governmental Non-Pharmaceutical Interventions during the COVID-19 Pandemic and the COPD Exacerbation and Respiratory Infection Rate in Patients with Alpha-1 Antitrypsin Deficiency. COPD 2023; 20:292-297. [PMID: 37665565 DOI: 10.1080/15412555.2023.2249108] [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: 06/13/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023]
Abstract
During the COVID-19 pandemic the number of hospital admissions due to chronic obstructive pulmonary disease (COPD) exacerbations was significantly reduced. The reason for this decline is not fully understood. Governmental non-pharmaceutical interventions (NPI's), an increase in community treated exacerbations, or healthcare avoidance by patients, are potential reasons. For the current study, the impact of Dutch governmental NPI's on the COPD exacerbations and respiratory infections rate in patients with severe alpha-1 antitrypsin deficiency (AATD) was analyzed. The patients participated in the NCT04204252 study, a randomized controlled trial evaluating the efficacy and safety of inhaled alpha-1 antitrypsin. Data collected in the time-period from March 2020 until February 2022 was analyzed. In this period the Dutch government imposed variable NPI's to contain the spread of SARS-CoV-2. Patients were required to document their daily symptoms in an electronic diary. The strictness of the governmental NPI's was measured by the COVID-19 Stringency Index. 19 patients participated in this study during the analysis period. A total of 40 respiratory infections and COPD exacerbations occurred. The Spearman's correlation coefficient of the monthly average COVID-19 Stringency Index and respiratory infections and COPD exacerbations rate was -0.316 (p = 0.132). When months known for a low respiratory infection rate were excluded, the correlation coefficient was -0.625 (p = 0.010). This study showed a significant negative correlation between the COPD exacerbations and respiratory infection rate and the COVID-19 Stringency Index in patients with AATD related COPD in the autumn-winter months.
Collapse
Affiliation(s)
- Naomi Nanke Kappe
- Department of Pulmonology, Leiden University Medical Center, Member of European Reference Network Lung, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Jan Stolk
- Department of Pulmonology, Leiden University Medical Center, Member of European Reference Network Lung, Leiden, The Netherlands
| |
Collapse
|
26
|
Tural Onur S, Natoli A, Dreger B, Arınç S, Sarıoğlu N, Çörtük M, Karadoğan D, Şenyiğit A, Yıldız BP, Köktürk N, Argun Barıs S, Kodalak Cengiz S, Polatli M. An Alpha-1 Antitrypsin Deficiency Screening Study in Patients with Chronic Obstructive Pulmonary Disease, Bronchiectasis, or Asthma in Turkey. Int J Chron Obstruct Pulmon Dis 2023; 18:2785-2794. [PMID: 38046982 PMCID: PMC10693271 DOI: 10.2147/copd.s425835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Purpose Alpha-1 antitrypsin deficiency (AATD) is a rare hereditary condition characterized by decreased serum alpha-1 antitrypsin (AAT) levels. We aim to identify AATD in patients with chronic obstructive pulmonary disease (COPD), bronchiectasis, or asthma and to report the frequency of AAT variants in Turkey. Patients and Methods This non-interventional, multicenter, prospective study was conducted between October 2021 and June 2022. Adult patients with COPD, bronchiectasis, asthma, liver symptoms, or family members with AATD were included. Demographic and clinical characteristics, pulmonary diagnosis, respiratory symptoms, and AAT serum levels were assessed. Whole blood samples were collected as dried blood spots, and the most common AATD mutations were simultaneously tested by allele-specific genotyping. Results A total of 1088 patients, mainly diagnosed with COPD (92.7%) and shortness of breath (78.7%), were assessed. Fifty-one (5%) were found to have AATD mutations. Fifteen (29.4%) patients had Pi*S or Pi*Z mutations, whereas 36 (70.6%) patients carried rare alleles Pi*M malton (n=18, 35.3% of mutations), Pi*I (n=8, 16%), Pi*P lowell (n=7, 14%), Pi*M heerlen (n=2, 4%), and Pi*S iiyama (n=1, 2%). The most common heterozygous combinations were Pi*M/Z (n=12, 24%), and Pi*M/M malton (n=11, 22%). Ten patients with severe AATD due to two deficiency alleles were identified, two with the Pi*Z/Z genotype, four with the genotype Pi*M malton/M malton, three with Pi*Z/M malton, and one with Pi*Z/M heerlen. Conclusion Our results identified AATD mutations as a genetic-based contributor to lung disease in patients with COPD or bronchiectasis and assessed their frequency in a population of Turkish patients.
Collapse
Affiliation(s)
- Seda Tural Onur
- Department of Pulmonology, Yedikule Chest Diseases and Thoracic Surgery Education and Research Hospital, University of Health Sciences, Istanbul, Türkiye
| | - Antonino Natoli
- Scientific and Medical Affairs, Scientific Innovation Office, Grifols, Frankfurt, Deutschland
| | - Bettina Dreger
- Scientific and Medical Affairs, Scientific Innovation Office, Grifols, Frankfurt, Deutschland
| | - Sibel Arınç
- Clinic of Chest Diseases, University of Health Sciences Turkey, S.B.Ü. Süreyyapaşa Chest Diseases and Thoracic Surgery Training and Research Hospital, İstanbul, Türkiye
| | - Nurhan Sarıoğlu
- Department of Pulmonology, Balıkesir University Faculty of Medicine, Pulmonology Clinic, Balıkesir, Türkiye
| | - Mustafa Çörtük
- Department of Pulmonology, Yedikule Chest Diseases and Thoracic Surgery Education and Research Hospital, University of Health Sciences, Istanbul, Türkiye
| | - Dilek Karadoğan
- Department of Chest Diseases, Recep Tayyip Erdoğan University, School of Medicine, Rize, Türkiye
| | - Abdurrahman Şenyiğit
- Department of Chest Diseases, Dicle University Faculty of Medicine Hospital, Diyarbakır, Türkiye
| | - Birsen Pınar Yıldız
- Department of Pulmonology, Yedikule Chest Diseases and Thoracic Surgery Education and Research Hospital, University of Health Sciences, Istanbul, Türkiye
| | - Nurdan Köktürk
- Department of Pulmonary Medicine, Gazi University, School of Medicine, Ankara, Türkiye
| | - Serap Argun Barıs
- Department of Pulmonary Diseases, Faculty of Medicine, Kocaeli University, Kocaeli, Türkiye
| | | | - Mehmet Polatli
- Faculty of Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| |
Collapse
|
27
|
Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [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: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
Collapse
Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Xiaoping Wu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Solé-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sara Elizabeth Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Carol A Wang
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Sundararajan Srinivasan
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | | | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
| | - Catherine Allard
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marika Groleau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Teemu Kuulasmaa
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Daniel J Leirer
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Haoxiang Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Cathrine Ebbing
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Herlev Hospital, Herlev, Denmark
| | - Christian Erikstrup
- Department Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marisa Estarlich
- Faculty of Nursing and Chiropody, Universitat de València, C/Menendez Pelayo, Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Stephen Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Eero Kajantie
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Camilla S Morgen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Ellen A Nohr
- Institute of Clinical research, University of Southern Denmark, Odense, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Beverley M Shields
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | | | - Marja Vaarasmaki
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Bjarni J Vilhjalmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Dorte Gybel-Brask
- Psychotherapeutic Outpatient Clinic, Mental Health Services, Capital Region, Copenhagen, Denmark
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rebecca M Reynolds
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
28
|
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.
| |
Collapse
|
29
|
Lunghi B, Ziliotto N, Balestra D, Rossi L, Della Valle P, Pignatelli P, Pinotti M, D’Angelo A, Marchetti G, Bernardi F. Whole-Exome Sequencing in a Family with an Unexplained Tendency for Venous Thromboembolism: Multicomponent Prediction of Low-Frequency Variant Deleteriousness and of Individual Protein Interaction. Int J Mol Sci 2023; 24:13809. [PMID: 37762110 PMCID: PMC10530467 DOI: 10.3390/ijms241813809] [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: 07/14/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Whole-exome sequencing (WES) in families with an unexplained tendency for venous thromboembolism (VTE) may favor detection of low-frequency variants in genes with known contribution to hemostasis or associated with VTE-related phenotypes. WES analysis in six family members, three of whom affected by documented VTE, filtered for MAF < 0.04 in 192 candidate genes, revealed 22 heterozygous (16 missense and six synonymous) variants in patients. Functional prediction by multi-component bioinformatics tools, implemented by a database/literature search, including ClinVar annotation and QTL analysis, prioritized 12 missense variants, three of which (CRP Leu61Pro, F2 Asn514Lys and NQO1 Arg139Trp) were present in all patients, and the frequent functional variants FGB Arg478Lys and IL1A Ala114Ser. Combinations of prioritized variants in each patient were used to infer functional protein interactions. Different interaction patterns, supported by high-quality evidence, included eight proteins intertwined in the "acute phase" (CRP, F2, SERPINA1 and IL1A) and/or in the "fibrinogen complex" (CRP, F2, PLAT, THBS1, VWF and FGB) significantly enriched terms. In a wide group of candidate genes, this approach highlighted six low-frequency variants (CRP Leu61Pro, F2 Asn514Lys, SERPINA1 Arg63Cys, THBS1 Asp901Glu, VWF Arg1399His and PLAT Arg164Trp), five of which were top ranked for predicted deleteriousness, which in different combinations may contribute to disease susceptibility in members of this family.
Collapse
Affiliation(s)
- Barbara Lunghi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Nicole Ziliotto
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy;
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Lucrezia Rossi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Patrizia Della Valle
- Unit of Coagulation Service and Thrombosis Research, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (P.D.V.); (A.D.)
| | - Pasquale Pignatelli
- Department of Clinical Internal, Anesthesiological, and Cardiovascular Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Armando D’Angelo
- Unit of Coagulation Service and Thrombosis Research, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (P.D.V.); (A.D.)
| | - Giovanna Marchetti
- Department of Neuroscience and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy;
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| |
Collapse
|
30
|
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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
31
|
Mornex JF, Traclet J, Guillaud O, Dechomet M, Lombard C, Ruiz M, Revel D, Reix P, Cottin V. Alpha1-antitrypsin deficiency: An updated review. Presse Med 2023; 52:104170. [PMID: 37517655 DOI: 10.1016/j.lpm.2023.104170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/07/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
Alpha1-antitrypsin deficiency (AATD) is a rare autosomal recessive disease associated with the homozygous Z variant of the SERPINA1 gene. Clinical expression of AATD, reported 60 years ago associate a severe deficiency, pulmonary emphysema and/or liver fibrosis. Pulmonary emphysema is due to the severe alpha1-antitrypsin deficiency of the ZZ homozygous status and is favored by smoking. Liver fibrosis is due to the ZZ homozygous status and is favored by obesity and excessive chronic alcohol intake, with a risk of liver cancer. Diagnosis is based on serum level and either isoelectric focusing determination of the biochemical phenotype or PCR detection of some variants. SERPINA1 gene sequencing is necessary in case of discrepancies between the results of these tests. No treatment is available for the liver disease in AATD. Although no specific trial has been performed, COPD in AATD should be treated as per COPD recommendations. Based on a randomized clinical trial, augmentation therapy is indicated in non-smoking adults less than 70 years of age with emphysema at chest CT, confirmed homozygous AATD, and FEV1 between 35% and 70% of predicted. In contrast Z heterozygosis (MZ or SZ) brings a risk of lung or liver disease only in association with further risk factors. Early detection, in all patients with COPD and chronic liver disease, is critical for the correct information of Z variant carriers. News ways of correcting the liver production of alpha1-antitrypsin will modify the care of AATD patients.
Collapse
Affiliation(s)
- Jean-François Mornex
- Université de Lyon, université Lyon 1, INRAE, EPHE, UMR754, IVPC, F-69007 Lyon, France; Centre de référence des maladies pulmonaires rares, Orphalung, RESPIFIL, ERN-LUNG, F-69500 Bron, France; Hospices civils de Lyon, hôpital Louis-Pradel, service de pneumologie, F-69500 Bron, France; Inserm, hospices civils de Lyon, CIC 1407, F-69500 Bron, France.
| | - Julie Traclet
- Centre de référence des maladies pulmonaires rares, Orphalung, RESPIFIL, ERN-LUNG, F-69500 Bron, France; Hospices civils de Lyon, hôpital Louis-Pradel, service de pneumologie, F-69500 Bron, France
| | - Olivier Guillaud
- Ramsay générale de santé, clinique de la Sauvegarde, F-69009 Lyon, France; Hospices civils de Lyon, hôpital Edouard Herriot, Fédération des spécialités digestives, F-69003 Lyon, France
| | - Magali Dechomet
- Hospices civils de Lyon, hôpital Lyon sud, service d'immunologie biologique, F-69495 Pierre Bénite, France
| | - Christine Lombard
- Hospices civils de Lyon, hôpital Lyon sud, service d'immunologie biologique, F-69495 Pierre Bénite, France
| | - Mathias Ruiz
- Centre de référence de l'atrésie des voies biliaires et des cholestases génétiques, FILFOIE, F-69500 Bron, France; Hospices civils de Lyon, hôpital femme mère enfant, service d'hépatologie, gastroentérologie et nutrition pédiatrique, F-69500 Bron, France
| | - Didier Revel
- Hospices civils de Lyon, hôpital Louis Pradel, service d'imagerie, F-69500 Bron, France
| | - Philippe Reix
- Service de pneumologie, allergologie pédiatrique. Hôpital Femme Mère Enfant. Hospices civils de Lyon, F-69500 Bron, France; Université de Lyon, université Lyon, CNRS, UMR 5558, équipe EMET, F-69100 Villeurbanne, France
| | - Vincent Cottin
- Université de Lyon, université Lyon 1, INRAE, EPHE, UMR754, IVPC, F-69007 Lyon, France; Centre de référence des maladies pulmonaires rares, Orphalung, RESPIFIL, ERN-LUNG, F-69500 Bron, France; Hospices civils de Lyon, hôpital Louis-Pradel, service de pneumologie, F-69500 Bron, France
| |
Collapse
|
32
|
Pérez-Luz S, Lalchandani J, Matamala N, Barrero MJ, Gil-Martín S, Saz SRD, Varona S, Monzón S, Cuesta I, Justo I, Marcacuzco A, Hierro L, Garfia C, Gomez-Mariano G, Janciauskiene S, Martínez-Delgado B. Quantitative Lipid Profiling Reveals Major Differences between Liver Organoids with Normal Pi*M and Deficient Pi*Z Variants of Alpha-1-antitrypsin. Int J Mol Sci 2023; 24:12472. [PMID: 37569847 PMCID: PMC10419530 DOI: 10.3390/ijms241512472] [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: 06/29/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Different mutations in the SERPINA1 gene result in alpha-1 antitrypsin (AAT) deficiency and in an increased risk for the development of liver diseases. More than 90% of severe deficiency patients are homozygous for Z (Glu342Lys) mutation. This mutation causes Z-AAT polymerization and intrahepatic accumulation which can result in hepatic alterations leading to steatosis, fibrosis, cirrhosis, and/or hepatocarcinoma. We aimed to investigate lipid status in hepatocytes carrying Z and normal M alleles of the SERPINA1 gene. Hepatic organoids were developed to investigate lipid alterations. Lipid accumulation in HepG2 cells overexpressing Z-AAT, as well as in patient-derived hepatic organoids from Pi*MZ and Pi*ZZ individuals, was evaluated by Oil-Red staining in comparison to HepG2 cells expressing M-AAT and liver organoids from Pi*MM controls. Furthermore, mass spectrometry-based lipidomics analysis and transcriptomic profiling were assessed in Pi*MZ and Pi*ZZ organoids. HepG2 cells expressing Z-AAT and liver organoids from Pi*MZ and Pi*ZZ patients showed intracellular accumulation of AAT and high numbers of lipid droplets. These latter paralleled with augmented intrahepatic lipids, and in particular altered proportion of triglycerides, cholesterol esters, and cardiolipins. According to transcriptomic analysis, Pi*ZZ organoids possess many alterations in genes and cellular processes of lipid metabolism with a specific impact on the endoplasmic reticulum, mitochondria, and peroxisome dysfunction. Our data reveal a relationship between intrahepatic accumulation of Z-AAT and alterations in lipid homeostasis, which implies that liver organoids provide an excellent model to study liver diseases related to the mutation of the SERPINA1 gene.
Collapse
Affiliation(s)
- Sara Pérez-Luz
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
| | - Jaanam Lalchandani
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
| | - Nerea Matamala
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
| | - Maria Jose Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain;
| | - Sara Gil-Martín
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER U758, 28029 Madrid, Spain
| | - Sheila Ramos-Del Saz
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
| | - Sarai Varona
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.V.); (S.M.); (I.C.)
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.V.); (S.M.); (I.C.)
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.V.); (S.M.); (I.C.)
| | - Iago Justo
- General and Digestive Surgery Department, Hospital 12 de Octubre, 28041 Madrid, Spain; (I.J.); (A.M.)
| | - Alberto Marcacuzco
- General and Digestive Surgery Department, Hospital 12 de Octubre, 28041 Madrid, Spain; (I.J.); (A.M.)
| | - Loreto Hierro
- Paediatric Hepatology Service, Research Institute of University Hospital La Paz, (IdiPAZ), 28046 Madrid, Spain;
| | - Cristina Garfia
- Digestive Department, Hospital 12 de Octubre, 28041 Madrid, Spain;
| | - Gema Gomez-Mariano
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover Medical School, 30625 Hannover, Germany;
| | - Beatriz Martínez-Delgado
- Molecular Genetics and Genetic Diagnostic Units, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain; (S.P.-L.); (J.L.); (N.M.); (S.G.-M.); (S.R.-D.S.); (G.G.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER U758, 28029 Madrid, Spain
| |
Collapse
|
33
|
Feitosa PH. Diagnosis and augmentation therapy for alpha-1 antitrypsin deficiency: current knowledge and future potential. Drugs Context 2023; 12:2023-3-1. [PMID: 37521109 PMCID: PMC10379007 DOI: 10.7573/dic.2023-3-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
The underdiagnosis of alpha-1 antitrypsin (AAT) deficiency (AATD) has been recognized for many years, yet little progress has been made in treatment of the disease. In this review, we summarize the AATD disease process as well as its diagnosis and treatment by AAT augmentation therapy. AATD is a rare autosomal disease that primarily affects the lungs and liver. AATD is associated with an increased susceptibility to developing pulmonary emphysema. The specific pharmacological treatment for AATD is intravenous administration of exogenous AAT. Augmentation therapy with AAT increases serum and pulmonary epithelial AAT levels, restores anti-elastase capacity, and decreases inflammatory mediators in the lung. Augmentation therapy reduces the loss of lung density over time, thus slowing progression of the disease. The effects of augmentation therapy on outcomes, such as frequency/duration of flare-ups, quality of life, lung function decline and mortality, are assessed. Wider testing for AATD, potentially through primary care physicians, could result in earlier treatment and better outcomes for individuals with AATD-induced lung respiratory disease.
Collapse
|
34
|
Perez-Luz S, Matamala N, Gomez-Mariano G, Janciauskiene S, Martínez-Delgado B. NAFLD and AATD Are Two Diseases with Unbalanced Lipid Metabolism: Similarities and Differences. Biomedicines 2023; 11:1961. [PMID: 37509601 PMCID: PMC10377048 DOI: 10.3390/biomedicines11071961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a type of steatosis commonly associated with obesity, dyslipidemia, hypertension, and diabetes. Other diseases such as inherited alpha-1 antitrypsin deficiency (AATD) have also been related to the development of liver steatosis. The primary reasons leading to hepatic lipid deposits can be genetic and epigenetic, and the outcomes range from benign steatosis to liver failure, as well as to extrahepatic diseases. Progressive hepatocellular damage and dysregulated systemic immune responses can affect extrahepatic organs, specifically the heart and lungs. In this review, we discuss the similarities and differences between the molecular pathways of NAFLD and AATD, and the putative value of hepatic organoids as novel models to investigate the physio pathological mechanisms of liver steatosis.
Collapse
Affiliation(s)
- Sara Perez-Luz
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
| | - Nerea Matamala
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
| | - Gema Gomez-Mariano
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
| | - Sabina Janciauskiene
- Department of Respiratory Medicine and Infectious Diseases, Biomedical Research in Endstage and Obstructive Lung Disease Hannover BREATH, Member of the German Center for Lung Research DZL, Hannover Medical School, 30625 Hannover, Germany
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, CIBERER U758, 28029 Madrid, Spain
| |
Collapse
|
35
|
Lopez-Campos JL, Rapun N, Czischke K, Jardim JR, Acquier MF, Munive AA, Günen H, Drobnic E, Miravitlles M, Osaba L. Distribution of alpha1 antitrypsin rare alleles in six countries: Results from the Progenika diagnostic network. Hum Genomics 2023; 17:48. [PMID: 37277845 DOI: 10.1186/s40246-023-00497-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Knowledge of the frequency of rare SERPINA1 mutations could help in the management of alpha1 antitrypsin deficiency (AATD). The present study aims to assess the frequencies of rare and null alleles and their respiratory and hepatic pathogenicity. METHODS This is a secondary analysis of a study that evaluated the viability of the Progenika diagnostic genotyping system in six different countries by analyzing 30,827 samples from cases of suspected AATD. Allele-specific genotyping was carried out with the Progenika A1AT Genotyping Test which analyses 14 mutations in buccal swabs or dried blood spots samples. SERPINA1 gene sequencing was performed for serum AAT-genotype discrepancies or by request of the clinician. Only cases with rare mutations were included in this analysis. RESULTS There were 818 cases (2.6%) carrying a rare allele, excluding newly identified mutations. All were heterozygous except for 20 that were homozygous. The most frequent alleles were the M-like alleles, PI*Mmalton and PI*Mheerlen. Of the 14 mutations included in the Progenika panel, there were no cases detected of PI*Siiyama, PI*Q0granite falls and PI*Q0west. Other alleles not included in the 14-mutation panel and identified by gene sequencing included PI*Mwürzburg, PI*Zbristol, and PI*Zwrexham, and the null alleles PI*Q0porto, PI*Q0madrid, PI*Q0brescia, and PI*Q0kayseri. CONCLUSIONS The Progenika diagnostic network has allowed the identification of several rare alleles, some unexpected and not included in the initial diagnostic panel. This establishes a new perspective on the distribution of these alleles in different countries. These findings may help prioritize allele selection for routine testing and highlights the need for further research into their pathogenetic role.
Collapse
Affiliation(s)
- José Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Avda. Manuel Siurot, S/N, 41013, Seville, Spain.
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
| | - Noelia Rapun
- Progenika Biopharma, a Grifols Company. Derio, Vizcaya, Spain
| | - Karen Czischke
- Departamento de Neumología, Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - José R Jardim
- Centro de Reabilitação Pulmonar da Escola Paulista de Medicina da Universidade Federal de São Paulo (EPM/Unifesp), São Paulo, Brazil
| | | | - Abraham Ali Munive
- Departamento Médico, Fundación Neumológica Colombiana, Bogotá, D.C., Colombia
| | - Hakan Günen
- University of Health Sciences, Süreyyapaşa Research and Training Center for Chest Diseases and Thoracic Surgery, Istanbul, Turkey
| | | | - Marc Miravitlles
- Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Lourdes Osaba
- Progenika Biopharma, a Grifols Company. Derio, Vizcaya, Spain
| |
Collapse
|
36
|
Martín-González E, Hernández-Pérez JM, Pérez JAP, Pérez-García J, Herrera-Luis E, González-Pérez R, González-González O, Mederos-Luis E, Sánchez-Machín I, Poza-Guedes P, Sardón O, Corcuera P, Cruz MJ, González-Barcala FJ, Martínez-Rivera C, Mullol J, Muñoz X, Olaguibel JM, Plaza V, Quirce S, Valero A, Sastre J, Korta-Murua J, Del Pozo V, Lorenzo-Díaz F, Villar J, Pino-Yanes M, González-Carracedo MA. Alpha-1 antitrypsin deficiency and Pi*S and Pi*Z SERPINA1 variants are associated with asthma exacerbations. Pulmonology 2023:S2531-0437(23)00091-0. [PMID: 37236906 DOI: 10.1016/j.pulmoe.2023.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION AND OBJECTIVES Asthma is a chronic inflammatory disease of the airways. Asthma patients may experience potentially life-threatening episodic flare-ups, known as exacerbations, which may significantly contribute to the asthma burden. The Pi*S and Pi*Z variants of the SERPINA1 gene, which usually involve alpha-1 antitrypsin (AAT) deficiency, had previously been associated with asthma. The link between AAT deficiency and asthma might be represented by the elastase/antielastase imbalance. However, their role in asthma exacerbations remains unknown. Our objective was to assess whether SERPINA1 genetic variants and reduced AAT protein levels are associated with asthma exacerbations. MATERIALS AND METHODS In the discovery analysis, SERPINA1 Pi*S and Pi*Z variants and serum AAT levels were analyzed in 369 subjects from La Palma (Canary Islands, Spain). As replication, genomic data from two studies focused on 525 Spaniards and publicly available data from UK Biobank, FinnGen, and GWAS Catalog (Open Targets Genetics) were analyzed. The associations between SERPINA1 Pi*S and Pi*Z variants and AAT deficiency with asthma exacerbations were analyzed with logistic regression models, including age, sex, and genotype principal components as covariates. RESULTS In the discovery, a significant association with asthma exacerbations was found for both Pi*S (odds ratio [OR]=2.38, 95% confidence interval [CI]= 1.40-4.04, p-value=0.001) and Pi*Z (OR=3.49, 95%CI=1.55-7.85, p-value=0.003)Likewise, AAT deficiency was associated with a higher risk for asthma exacerbations (OR=5.18, 95%CI=1.58-16.92, p-value=0.007) as well as AAT protein levels (OR= 0.72, 95%CI=0.57-0.91, p-value=0.005). The Pi*Z association with exacerbations was replicated in samples from Spaniards with two generations of Canary Islander origin (OR=3.79, p-value=0.028), and a significant association with asthma hospitalizations was found in the Finnish population (OR=1.12, p-value=0.007). CONCLUSIONS AAT deficiency could be a potential therapeutic target for asthma exacerbations in specific populations.
Collapse
Affiliation(s)
- Elena Martín-González
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain
| | - José M Hernández-Pérez
- Department of Respiratory Medicine, Hospital Universitario de N.S de Candelaria, 38010 Santa Cruz de Tenerife, Spain; Respiratory Medicine, Hospital Universitario de La Palma, 38713 Breña Alta, Santa Cruz de Tenerife, Spain
| | - José A Pérez Pérez
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
| | - Javier Pérez-García
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain
| | - Ruperto González-Pérez
- Allergy Department, Hospital Universitario de Canarias, 38320 La Laguna, Tenerife, Spain; Severe Asthma Unit, Allergy Department, Hospital Universitario de Canarias, 38320 La Laguna, Spain
| | | | - Elena Mederos-Luis
- Allergy Department, Hospital Universitario de Canarias, 38320 La Laguna, Tenerife, Spain
| | | | - Paloma Poza-Guedes
- Allergy Department, Hospital Universitario de Canarias, 38320 La Laguna, Tenerife, Spain; Severe Asthma Unit, Allergy Department, Hospital Universitario de Canarias, 38320 La Laguna, Spain
| | - Olaia Sardón
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain; Department of Pediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
| | - María J Cruz
- Department of Respiratory Medicine, Hospital Vall d'Hebron, Barcelona, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco J González-Barcala
- Department of Respiratory Medicine, Complejo Hospitalario Universitario de Santiago, Santiago de Compostela, La Coruña, Spain
| | - Carlos Martínez-Rivera
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Respiratory Medicine, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Joaquim Mullol
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Rhinology Unit & Smell Clinic, ENT Department, Clinical and Experimental Respiratory Immunoallergy (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Xavier Muñoz
- Department of Respiratory Medicine, Hospital Vall d'Hebron, Barcelona, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - José M Olaguibel
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Allergy, Hospital Universitario de Navarra, Pamplona, Navarra, Spain
| | - Vicente Plaza
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Respiratory Medicine, Hospital de la Santa Creu i Sant Pau, Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Santiago Quirce
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Allergy, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Antonio Valero
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Allergy Unit & Severe Asthma Unit, Pneumonology and Allergy Department, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Joaquín Sastre
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Allergy, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Javier Korta-Murua
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
| | - Victoria Del Pozo
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Fabián Lorenzo-Díaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - María Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain.
| | - Mario A González-Carracedo
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), 38200 La Laguna, Tenerife, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain.
| |
Collapse
|
37
|
Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
Collapse
Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| |
Collapse
|
38
|
[Alpha-1 antitrypsin deficiency]. Med Clin (Barc) 2023; 160:203-205. [PMID: 36253208 DOI: 10.1016/j.medcli.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
|
39
|
Hernández-Pérez JM, Martín-González E, González-Carracedo MA. Alpha-1 Antitrypsin Deficiency and SERPINA1 Variants Could Play a Role in Asthma Exacerbations. Arch Bronconeumol 2023:S0300-2896(23)00038-8. [PMID: 36948995 DOI: 10.1016/j.arbres.2023.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023]
Affiliation(s)
- José M Hernández-Pérez
- Department of Respiratory Medicine, Hospital Universitario de N.S de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.
| | - Elena Martín-González
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
| | - Mario A González-Carracedo
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Guillaud O, Dumortier J, Couchonnal-Bedoya E, Ruiz M. Wilson Disease and Alpha1-Antitrypsin Deficiency: A Review of Non-Invasive Diagnostic Tests. Diagnostics (Basel) 2023; 13:diagnostics13020256. [PMID: 36673066 PMCID: PMC9857715 DOI: 10.3390/diagnostics13020256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
Wilson disease and alpha1-antitrypsin deficiency are two rare genetic diseases that may impact predominantly the liver and/or the brain, and the liver and/or the lung, respectively. The early diagnosis of these diseases is important in order to initiate a specific treatment, when available, ideally before irreversible organ damage, but also to initiate family screening. This review focuses on the non-invasive diagnostic tests available for clinicians in both diseases. These tests are crucial at diagnosis to reduce the potential diagnostic delay and assess organ involvement. They also play a pivotal role during follow-up to monitor disease progression and evaluate treatment efficacy of current or emerging therapies.
Collapse
Affiliation(s)
- Olivier Guillaud
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Centre National de Référence pour la Maladie de Wilson, 69500 Bron, France
- Ramsay Générale de Santé, Clinique de la Sauvegarde, 69009 Lyon, France
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Fédération des Spécialités Digestives, 69003 Lyon, France
- Correspondence: ; Tel.: +33-4-72-11-95-19
| | - Jérôme Dumortier
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Centre National de Référence pour la Maladie de Wilson, 69500 Bron, France
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Fédération des Spécialités Digestives, 69003 Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, 69003 Lyon, France
| | - Eduardo Couchonnal-Bedoya
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Centre National de Référence pour la Maladie de Wilson, 69500 Bron, France
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Service d’Hépatogastroentérologie et Nutrition Pédiatrique, 69500 Bron, France
| | - Mathias Ruiz
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Service d’Hépatogastroentérologie et Nutrition Pédiatrique, 69500 Bron, France
- Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, Centre National de Référence pour l’Atrésie des Voies Biliaires et les Cholestases Génétiques, 69500 Bron, France
| |
Collapse
|
42
|
Improving the Laboratory Diagnosis of M-like Variants Related to Alpha1-Antitrypsin Deficiency. Int J Mol Sci 2022; 23:ijms23179859. [PMID: 36077263 PMCID: PMC9456480 DOI: 10.3390/ijms23179859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/26/2022] Open
Abstract
Alpha1-antitrypsin (AAT) is a serine protease inhibitor that is encoded by the highly polymorphic SERPINA1 gene. Mutations in this gene can lead to AAT deficiency (AATD), which is associated with an increased risk of lung and/or liver disease. On the basis of electrophoretic migration, AAT variants are named with capital letters; M (medium) signifies the normal protein. Among pathological variants, the M-like ones represent a heterogeneous group of rare allelic variants that exhibit the same electrophoretic pattern as the M wild-type protein, which makes them difficult to detect with routine methods. In order to avoid their misdiagnosis, the present study defines and validates effective methods for the detection of two pathogenic M-like variants, Mwurzburg and Mwhitstable. Comparison of protein phenotypes using isoelectric focusing of samples that presented the Mwurzburg variant, as revealed by exons 5 sequencing, identified a particular electrophoretic pattern amenable to the Mwurzburg protein. The specific phenotyping pattern was retrospectively validated, thus enabling the detection of 16 patients with Mwurzburg variant among the subjects already tested but not sequenced according to our diagnostic algorithm. The Mwhitstable allele was detected by intron 4 sequencing of SERPINA1 gene. Mwurzburg and Mwhitstable are often misdiagnosed and the introduction of diagnostic improvements can help the clinical management, especially in patients with established lung disease without any other reported risk factors.
Collapse
|
43
|
COVID-19 Survivor Patients Carrying the Rs35705950 Risk Allele in MUC5B Have Higher Plasma Levels of Mucin 5B. Curr Issues Mol Biol 2022; 44:3283-3290. [PMID: 35892712 PMCID: PMC9329856 DOI: 10.3390/cimb44080226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Genetic susceptibility to infectious diseases is partly due to the variation in the human genome, and COVID-19 is not the exception. This study aimed to identify whether risk alleles of known genes linked with emphysema (SERPINA1) and pulmonary fibrosis (MUC5B) are associated with severe COVID-19, and whether plasma mucin 5B differs according to patients' outcomes. MATERIALS AND METHODS We included 1258 Mexican subjects diagnosed with COVID-19. We genotyped rs2892474 and rs17580 of the SERPINA1 gene and rs35705950 of MUC5B. Based on the rs35705950 genotypes, mucin 5B plasma protein levels were quantified. RESULTS Homozygous for the risk alleles of the three polymorphisms were found in less than 5% of the study population, but no statistically significant difference in the genotype or allele association analysis. At the protein level, non-survivors carrying one or two copies of the risk allele rs35705950 in MUC5B (GT + TT) had lower levels of mucin 5B compared to the survivors (0.0 vs. 0.17 ng/mL, p = 0.0013). CONCLUSION The polymorphisms rs28929474 and rs17580 of SERPINA1 and rs35705950 of MUC5B are not associated with the risk of severe COVID-19 in the Mexican population. COVID-19 survivor patients bearing one or two copies of the rs35705950 risk allele have higher plasma levels of mucin 5B.
Collapse
|
44
|
Mornex JF, Balduyck M, Cuvelier A, Cottin V, Mal H. [Alpha1-antitrypsin deficiency: French guidelines… at last !]. Rev Mal Respir 2022; 39:575-577. [PMID: 35792000 DOI: 10.1016/j.rmr.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- J-F Mornex
- Université de Lyon, université Lyon 1, INRAE, EPHE, UMR754, IVPC, F-69007 ; Lyon, France ; Centre de référence coordonnateur des maladies pulmonaires rares; Hospices civils de Lyon, service de pneumologie, hôpital Louis Pradel, 69500 Bron, France.
| | - M Balduyck
- CHU de Lille, centre de biologie pathologie, laboratoire de biochimie et biologie moléculaire HMNO ; faculté de pharmacie et EA 7364 RADEME, université de Lille, service de biochimie et biologie moléculaire, Lille, France
| | - A Cuvelier
- Service de pneumologie, oncologie thoracique et soins intensifs respiratoires, CHU de Rouen, Rouen ; Groupe de recherche sur le handicap ventilatoire et neurologique (GRHVN), université Normandie Rouen, Rouen, France
| | - V Cottin
- Université de Lyon, université Lyon 1, INRAE, EPHE, UMR754, IVPC, F-69007 ; Lyon, France ; Centre de référence coordonnateur des maladies pulmonaires rares; Hospices civils de Lyon, service de pneumologie, hôpital Louis Pradel, 69500 Bron, France
| | - H Mal
- Service de pneumologie B, hôpital Bichat - Claude-Bernard, AP-HP Nord- Université Paris Cité ; Inserm U1152, Paris, France
| |
Collapse
|
45
|
Lopez-Campos JL, Osaba L, Czischke K, Jardim JR, Fernandez Acquier M, Ali A, Günen H, Rapun N, Drobnic E, Miravitlles M. Feasibility of a genotyping system for the diagnosis of alpha1 antitrypsin deficiency: a multinational cross-sectional analysis. Respir Res 2022; 23:152. [PMID: 35689213 PMCID: PMC9184812 DOI: 10.1186/s12931-022-02074-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/29/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Currently, strategies for improving alpha1 antitrypsin deficiency (AATD) diagnosis are needed. Here we report the performance of a multinational multiplex-based genotyping test on dried blood spots and buccal swabs sent by post or courier and with web registration for subjects with suspected AATD in Argentina, Brazil, Chile, Colombia, Spain, and Turkey.
Methods This was an observational, cross-sectional analysis of samples from patients with suspected AATD from March 2018 to January 2022. Samples were coded on a web platform and sent by post or courier to the central laboratory in Northern Spain. Allele-specific genotyping for the 14 most common mutations was carried out with the A1AT Genotyping Test (Progenika-Grifols, Spain). SERPINA1 gene sequencing was performed if none of the mutations were found or one variant was detected in heterozygous status and the AAT serum level was < 60 mg/dl, or if requested by the clinician in charge. Results The study included 30,827 samples: 30,458 (94.7%) with final results after direct genotyping and 369 (1.1%) with additional gene sequencing. Only 0.3% of the samples were not processed due to their poor quality. The prevalence of the most frequent allele combinations was MS 14.7%, MZ 8.6%, SS 1.9%, SZ 1.9%, and ZZ 0.9%. Additionally, 70 cases with new mutations were identified. Family screening was conducted in 2.5% of the samples. Samples from patients with respiratory diseases other than COPD, including poorly controlled asthma or bronchiectasis, also presented AATD mutations. Conclusions Our results confirm the viability of this diagnostic system for genotyping AATD conducted simultaneously in different countries. The system has proved satisfactory and can improve the timely diagnosis of AATD. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02074-x.
Collapse
Affiliation(s)
- José Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Avda. Manuel Siurot, s/n, 41013, Seville, Spain. .,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
| | - Lourdes Osaba
- Progenika Biopharma, a Grifols Company, Derio, Vizcaya, Spain
| | - Karen Czischke
- Departamento de Neumología, Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - José R Jardim
- Centro de Reabilitação Pulmonar da Escola Paulista de Medicina da Universidade Federal de São Paulo (EPM/Unifesp), São Paulo, Brazil
| | | | - Abraham Ali
- Departamento Médico, Fundación Neumológica Colombiana, Bogotá, D.C., Colombia
| | - Hakan Günen
- Süreyyapaşa Research and Training Center for Chest Diseases and Thoracic Surgery, University of Health Sciences, Istanbul, Turkey
| | - Noelia Rapun
- Progenika Biopharma, a Grifols Company, Derio, Vizcaya, Spain
| | | | - Marc Miravitlles
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Neumología, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| |
Collapse
|
46
|
Yang Z, Macdonald-Dunlop E, Chen J, Zhai R, Li T, Richmond A, Klarić L, Pirastu N, Ning Z, Zheng C, Wang Y, Huang T, He Y, Guo H, Ying K, Gustafsson S, Prins B, Ramisch A, Dermitzakis ET, Png G, Eriksson N, Haessler J, Hu X, Zanetti D, Boutin T, Hwang SJ, Wheeler E, Pietzner M, Raffield LM, Kalnapenkis A, Peters JE, Viñuela A, Gilly A, Elmståhl S, Dedoussis G, Petrie JR, Polašek O, Folkersen L, Chen Y, Yao C, Võsa U, Pairo-Castineira E, Clohisey S, Bretherick AD, Rawlik K, Esko T, Enroth S, Johansson Å, Gyllensten U, Langenberg C, Levy D, Hayward C, Assimes TL, Kooperberg C, Manichaikul AW, Siegbahn A, Wallentin L, Lind L, Zeggini E, Schwenk JM, Butterworth AS, Michaëlsson K, Pawitan Y, Joshi PK, Baillie JK, Mälarstig A, Reiner AP, Wilson JF, Shen X. Genetic Landscape of the ACE2 Coronavirus Receptor. Circulation 2022; 145:1398-1411. [PMID: 35387486 PMCID: PMC9047645 DOI: 10.1161/circulationaha.121.057888] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood. METHODS We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data. RESULTS We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells. CONCLUSIONS Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.
Collapse
Affiliation(s)
- Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - Jiantao Chen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ting Li
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Lucija Klarić
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Human Technopole Viale Rita Levi-Montalcini, Milan, Italy (N.P.)
| | - Zheng Ning
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Yipeng Wang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Tingting Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Yazhou He
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu (Y.H.)
| | - Huiming Guo
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences, Guangzhou, China (H.G.)
| | - Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA (K.Y.)
- T.H. Chan School of Public Health, Harvard University, Boston, MA (K.Y.)
| | - Stefan Gustafsson
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Bram Prins
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Anna Ramisch
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Technical University of Munich (TUM), School of Medicine, Germany (G.P.)
| | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Shih-Jen Hwang
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill (L.M.R.)
| | - Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
- Institute of Molecular and Cell Biology, University of Tartu, Estonia (A.K.)
| | - James E. Peters
- Department of Immunology and Inflammation, Imperial College London, UK (J.E.P.)
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK (A.V.)
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
| | - Sölve Elmståhl
- Faculty of Medicine, Lund University, Sweden (S. Elmståhl)
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Greece (G.D.)
| | - John R. Petrie
- Institute of Cardiovascular & Medical Sciences, University of Glasgow, UK (J. Petrie)
| | - Ozren Polašek
- University of Split School of Medicine, Croatia (O.P.)
- Algebra University College, Ilica, Zagreb, Croatia (O.P.)
| | | | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chen Yao
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | | | | | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Daniel Levy
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Themistocles L. Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Agneta Siegbahn
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Wallentin
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Germany (E.Z.)
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden (J.M.S.)
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
- British Heart Foundation Centre of Research Excellence, University of Cambridge, UK (A.S.B.)
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, UK (A.S.B.)
| | - Karl Michaëlsson
- Department of Surgical Sciences, Uppsala University, Sweden (K.M.)
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
- Intensive Care Unit, Royal Infirmary of Edinburgh, UK (J.K.B.)
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden (A.M.)
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China (X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| |
Collapse
|
47
|
Grover SP, Mackman N. Anticoagulant SERPINs: Endogenous Regulators of Hemostasis and Thrombosis. Front Cardiovasc Med 2022; 9:878199. [PMID: 35592395 PMCID: PMC9110684 DOI: 10.3389/fcvm.2022.878199] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 12/17/2022] Open
Abstract
Appropriate activation of coagulation requires a balance between procoagulant and anticoagulant proteins in blood. Loss in this balance leads to hemorrhage and thrombosis. A number of endogenous anticoagulant proteins, such as antithrombin and heparin cofactor II, are members of the serine protease inhibitor (SERPIN) family. These SERPIN anticoagulants function by forming irreversible inhibitory complexes with target coagulation proteases. Mutations in SERPIN family members, such as antithrombin, can cause hereditary thrombophilias. In addition, low plasma levels of SERPINs have been associated with an increased risk of thrombosis. Here, we review the biological activities of the different anticoagulant SERPINs. We further consider the clinical consequences of SERPIN deficiencies and insights gained from preclinical disease models. Finally, we discuss the potential utility of engineered SERPINs as novel therapies for the treatment of thrombotic pathologies.
Collapse
|
48
|
Tiensuu H, Haapalainen AM, Tissarinen P, Pasanen A, Määttä TA, Huusko JM, Ohlmeier S, Bergmann U, Ojaniemi M, Muglia LJ, Hallman M, Rämet M. Human placental proteomics and exon variant studies link AAT/SERPINA1 with spontaneous preterm birth. BMC Med 2022; 20:141. [PMID: 35477570 PMCID: PMC9047282 DOI: 10.1186/s12916-022-02339-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Preterm birth is defined as live birth before 37 completed weeks of pregnancy, and it is a major problem worldwide. The molecular mechanisms that lead to onset of spontaneous preterm birth are incompletely understood. Prediction and evaluation of the risk of preterm birth is challenging as there is a lack of accurate biomarkers. In this study, our aim was to identify placental proteins that associate with spontaneous preterm birth. METHODS We analyzed the proteomes from placentas to identify proteins that associate with both gestational age and spontaneous labor. Next, rare and potentially damaging gene variants of the identified protein candidates were sought for from our whole exome sequencing data. Further experiments we performed on placental samples and placenta-associated cells to explore the location and function of the spontaneous preterm labor-associated proteins in placentas. RESULTS Exome sequencing data revealed rare damaging variants in SERPINA1 in families with recurrent spontaneous preterm deliveries. Protein and mRNA levels of alpha-1 antitrypsin/SERPINA1 from the maternal side of the placenta were downregulated in spontaneous preterm births. Alpha-1 antitrypsin was expressed by villous trophoblasts in the placenta, and immunoelectron microscopy showed localization in decidual fibrinoid deposits in association with specific extracellular proteins. siRNA knockdown in trophoblast-derived HTR8/SVneo cells revealed that SERPINA1 had a marked effect on regulation of the actin cytoskeleton pathway, Slit-Robo signaling, and extracellular matrix organization. CONCLUSIONS Alpha-1 antitrypsin is a protease inhibitor. We propose that loss of the protease inhibition effects of alpha-1 antitrypsin renders structures critical to maintaining pregnancy susceptible to proteases and inflammatory activation. This may lead to spontaneous premature birth.
Collapse
Affiliation(s)
- Heli Tiensuu
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Antti M Haapalainen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Pinja Tissarinen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Anu Pasanen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Tomi A Määttä
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Johanna M Huusko
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland.,Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA
| | - Steffen Ohlmeier
- Proteomics and Mass Spectrometry Core Facilities, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014, Oulu, Finland
| | - Ulrich Bergmann
- Proteomics and Mass Spectrometry Core Facilities, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014, Oulu, Finland
| | - Marja Ojaniemi
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland
| | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA.,Burroughs Wellcome Fund, Research Triangle Park, North Carolina, 27709, USA
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland. .,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland.
| | - Mika Rämet
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland. .,Department of Children and Adolescents, Oulu University Hospital, 90014, Oulu, Finland. .,Faculty of Medicine and Health Technology, Tampere University, 33014, Tampere, Finland.
| |
Collapse
|
49
|
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
Collapse
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
| |
Collapse
|
50
|
Maslakova AA, Didych DA, Golyshev SA, Katrukha IA, Viushkov VS, Zamalutdinov AV, Potashnikova DM, Rubtsov MA, Smirnova OV, Orlovsky IV. Towards unveiling the nature of short SERPINA1 transcripts: Avoiding the main ORF control to translate alpha1-antitrypsin C-terminal peptides. Int J Biol Macromol 2022; 203:703-717. [PMID: 35090941 DOI: 10.1016/j.ijbiomac.2022.01.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
Alternative ORFs in-frame with the known genes are challenging to reveal. Yet they may contribute significantly to proteome diversity. Here we focused on the individual expression of the SERPINA1 gene exon 5 leading to direct translation of alpha1-antitrypsin (AAT) C-terminal peptides. The discovery of alternative ways for their production may expand the current understanding of the serpin gene's functioning. We detected short transcripts expressed primarily in hepatocytes. We identified four variants of hepatocyte-specific SERPINA1 short transcripts and individually probed their potential to be translated in living cells. The long mRNA gave the full-length AAT-eGFP fusion, while in case of short transcripts we deduced four active SERPINA1 in-frame alternative ORFs encoding 10, 21, 153 and 169 amino acids AAT C-terminal oligo- and polypeptides. Unlike secretory AAT-eGFP fusion exhibiting classical AAT behavior, truncated AAT-fusions differ by intracellular retention and nuclear enrichment. Immunofluorescence on the endogenous AAT C-terminal epitope showed its accumulation in the cell nucleoli, indicating that short transcripts may be translated in vivo. FANTOM5 CAGE data on SERPINA1 suggest that short transcripts originate from the post-transcriptional cleavage of the spliced mRNA, initiated mainly from the hepatocyte-specific promoter. CONCLUSION: Short SERPINA1 transcripts may represent a source for the direct synthesis of AAT C-terminal peptides with properties uncommon to AAT.
Collapse
Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya, Moscow 117997, Russia
| | - S A Golyshev
- A.N. Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - I A Katrukha
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; HyTest Ltd., Joukahaisenkatu, Turku 20520, Finland
| | - V S Viushkov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A V Zamalutdinov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- A.N. Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| |
Collapse
|