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Wang C, Zhao P, Sun S, Teckman J, Balch WE. Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2020; 7:224-246. [PMID: 32726074 DOI: 10.15326/jcopdf.7.3.2019.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep medicine is rapidly moving towards a high-definition approach for therapeutic management of the patient as an individual given the rapid progress of genome sequencing technologies and machine learning algorithms. While considered a monogenic disease, alpha-1 antitrypsin (AAT) deficiency (AATD) patients present with complex and variable phenotypes we refer to as the "hallmarks of AATD" that involve distinct molecular mechanisms in the liver, plasma and lung tissues, likely due to both coding and non-coding variation as well as genetic and environmental modifiers in different individuals. Herein, we briefly review the current therapeutic strategies for the management of AATD. To embrace genetic diversity in the management of AATD, we provide an overview of the disease phenotypes of AATD patients harboring different AAT variants. Linking genotypic diversity to phenotypic diversity illustrates the potential for sequence-specific regions of AAT protein fold design to play very different roles during nascent synthesis in the liver and/or function in post-liver plasma and lung environments. We illustrate how to manage diversity with recently developed machine learning (ML) approaches that bridge sequence-to-function-to-structure knowledge gaps based on the principle of spatial covariance (SCV). SCV relationships provide a deep understanding of the genotype to phenotype transformation initiated by AAT variation in the population to address the role of genetic and environmental modifiers in the individual. Embracing the complexity of AATD in the population is critical for risk management and therapeutic intervention to generate a high definition medicine approach for the patient.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Jeffrey Teckman
- Pediatrics and Biochemistry, Saint Louis University, and Cardinal Glennon Children's Medical Center, St. Louis, Missouri
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California
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Joly P, Lachaux A, Ruiz M, Restier L, Belmalih A, Chapuis-Cellier C, Francina A, Renoux C, Bouchecareilh M. SERPINA1 and MAN1B1 polymorphisms are not linked to severe liver disease in a French cohort of alpha-1 antitrypsin deficiency children. Liver Int 2017; 37:1608-1611. [PMID: 28887821 DOI: 10.1111/liv.13586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/30/2017] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Fifteen to twenty percent of alpha-1 antitrypsin deficiency patients (A1ATD) have a severe liver outcome (portal hypertension - PHT) during childhood. Since they all share the same ZZSERPINA1 genotype and that environmental factors such as alcohol cannot be advanced, the presence of modifier genes is now well recognized. SNPs located on the SERPINA1 and MAN1B1 genes have already been tested in very few studies with contradictory or not replicated results. METHODS Our genotype-phenotype correlation study, performed on 92 ZZ children, aimed at determining once and for all if SERPINA1 and MAN1B1 polymorphisms may be implied in the onset of PHT. To do so, we also performed for the first time a complete haplotype reconstruction for data analysis. RESULTS The two genetic associations with severe liver disease that had been suspected previously (one SNP for SERPINA1 and another for MAN1B1) were not confirmed in our cohort. Moreover, the haplotype analysis identified only one major genetic background for the SERPINA1 Z-allele, allowing us to exclude the presence of a frequent modifier SNP within. For MAN1B1, four major haplotypes were identified but the prevalence of PHT did not significantly differ between them. CONCLUSION We conclude that genetic polymorphisms in these two genes probably do not influence the onset of severe liver disease in A1ATD.
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Affiliation(s)
- Philippe Joly
- Laboratoire de Biochimie et Biologie Moléculaire Grand-Est, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Inter-University Laboratory of Human Movement Science, Univ Lyon - University Claude Bernard Lyon 1 - EA 7424, Villeurbanne, France
| | - Alain Lachaux
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Mathias Ruiz
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Lioara Restier
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Abdelhouaed Belmalih
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Colette Chapuis-Cellier
- Laboratoire d'immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon & Université Claude Bernard-Lyon 1, Lyon, France
| | - Alain Francina
- Laboratoire de Biochimie et Biologie Moléculaire Grand-Est, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Céline Renoux
- Laboratoire de Biochimie et Biologie Moléculaire Grand-Est, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Inter-University Laboratory of Human Movement Science, Univ Lyon - University Claude Bernard Lyon 1 - EA 7424, Villeurbanne, France
| | - Marion Bouchecareilh
- Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, Bordeaux, France.,France CNRS-UMR5095 Bordeaux, Bordeaux Cedex, France.,INSERM, UMR1053 Bordeaux Research In Translational Oncology, Univ. Bordeaux, BaRITOn, Bordeaux, France
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Joly P, Vignaud H, Di Martino J, Ruiz M, Garin R, Restier L, Belmalih A, Marchal C, Cullin C, Arveiler B, Fergelot P, Gitler AD, Lachaux A, Couthouis J, Bouchecareilh M. ERAD defects and the HFE-H63D variant are associated with increased risk of liver damages in Alpha 1-Antitrypsin Deficiency. PLoS One 2017; 12:e0179369. [PMID: 28617828 PMCID: PMC5472284 DOI: 10.1371/journal.pone.0179369] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The most common and severe disease causing allele of Alpha 1-Antitrypsin Deficiency (1ATD) is Z-1AT. This protein aggregates in the endoplasmic reticulum, which is the main cause of liver disease in childhood. Based on recent evidences and on the frequency of liver disease occurrence in Z-1AT patients, it seems that liver disease progression is linked to still unknown genetic factors. METHODS We used an innovative approach combining yeast genetic screens with next generation exome sequencing to identify and functionally characterize the genes involved in 1ATD associated liver disease. RESULTS Using yeast genetic screens, we identified HRD1, an Endoplasmic Reticulum Associated Degradation (ERAD) associated protein, as an inducer of Z-mediated toxicity. Whole exome sequencing of 1ATD patients resulted in the identification of two variants associated with liver damages in Z-1AT homozygous cases: HFE H63D and HERPUD1 R50H. Functional characterization in Z-1AT model cell lines demonstrated that impairment of the ERAD machinery combined with the HFE H63D variant expression decreased both cell proliferation and cell viability, while Unfolded Protein Response (UPR)-mediated cell death was hyperstimulated. CONCLUSION This powerful experimental pipeline allowed us to identify and functionally validate two genes involved in Z-1AT-mediated severe liver toxicity. This pilot study moves forward our understanding on genetic modifiers involved in 1ATD and highlights the UPR pathway as a target for the treatment of liver diseases associated with 1ATD. Finally, these findings support a larger scale screening for HERPUD1 R50H and HFE H63D variants in the sub-group of 1ATD patients developing significant chronic hepatic injuries (hepatomegaly, chronic cholestasis, elevated liver enzymes) and at risk developing liver cirrhosis.
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Affiliation(s)
- Philippe Joly
- University Lyon - University Claude Bernard Lyon 1 - EA 7424 – Inter-university Laboratory of Human Movement Science, Villeurbanne, France
- Laboratoire de Biochimie et biologie moléculaire Grand-Est, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Hélène Vignaud
- CNRS, University Bordeaux, UMR5095 Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Julie Di Martino
- CNRS, University Bordeaux, UMR5095 Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
- INSERM, University Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, Bordeaux, France
| | - Mathias Ruiz
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Roman Garin
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Lioara Restier
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Abdelouahed Belmalih
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Christelle Marchal
- CNRS, University Bordeaux, UMR5095 Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Christophe Cullin
- CNRS, University Bordeaux, UMR5095 Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Benoit Arveiler
- University Bordeaux, INSERM U1211, Laboratoire Maladies Rares, Génétique et Métabolisme (MRGM), Bordeaux, France
| | - Patricia Fergelot
- University Bordeaux, INSERM U1211, Laboratoire Maladies Rares, Génétique et Métabolisme (MRGM), Bordeaux, France
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alain Lachaux
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Lyon, Lyon, France
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marion Bouchecareilh
- CNRS, University Bordeaux, UMR5095 Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
- INSERM, University Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, Bordeaux, France
- * E-mail:
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Perlmutter DH. α1-antitrypsin Deficiency: A Misfolded Secretory Protein Variant with Unique Effects on the Endoplasmic Reticulum. ENDOPLASMIC RETICULUM STRESS IN DISEASES 2016; 3:63-72. [PMID: 28217691 PMCID: PMC5310618 DOI: 10.1515/ersc-2016-0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In the classical form of α1-antitrypsin deficiency (ATD) a point mutation leads to accumulation of a misfolded secretory glycoprotein in the endoplasmic reticulum (ER) of liver cells and so ATD has come to be considered a prototypical ER storage disease. It is associated with two major types of clinical disorders, chronic obstructive pulmonary disease (COPD) by loss-of-function mechanisms and hepatic cirrhosis and carcinogenesis by gain-of-function mechanisms. The lung disease predominantly results from proteolytic damage to the pulmonary connective tissue matrix because of reduced levels of protease inhibitor activity of α1-anitrypsin (AT) in the circulating blood and body fluids. Cigarette smoking is a powerful disease-promoting modifier but other modifiers are known to exist because variation in the lung disease phenotype is still found in smoking and non-smoking homozygotes. The liver disease is highly likely to be caused by the proteotoxic effects of intracellular misfolded protein accumulation and a high degree of variation in the hepatic phenotype among affected homozygotes has been hypothetically attributed to genetic and environmental modifiers that alter proteostasis responses. Liver biopsies of homozygotes show intrahepatocytic inclusions with dilation and expansion of the ER and recent studies of iPS-derived hepatocyte-like cells from individuals with ATD indicate that the changes in the ER directly vary with the hepatic phenotype i.e there is much lesser alteration in the ER in cells derived from homozygotes that do not have clinically significant liver disease. From a signaling perspective, studies in mammalian cell line and animal models expressing the classical α1-antitrypsin Z variant (ATZ) have found that ER signaling is perturbed in a relatively unique way with powerful activation of autophagy and the NFκB pathway but relatively limited, if any, UPR signaling. It is still not known how much these unique structural and functional changes and the variation among affected homozygotes relate to the tendency of this variant to polymerize and aggregate and/or to the repertoire of proteostasis mechanisms that are activated.
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Affiliation(s)
- David H Perlmutter
- Corresponding author: David H Perlmutter, School of Medicine, Washington University in St Louis, 660 South Euclid Boulevard, St Louis, Missouri 63130, 314-362-6827,
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Joly P, Restier L, Bouchecareilh M, Lacan P, Cabet F, Chapuis-Cellier C, Francina A, Lachaux A. Cohorte DEFI-ALPHA et projet hospitalier de recherche clinique POLYGEN DEFI-ALPHA. Étude des facteurs cliniques, biologiques et génétiques associés à l’apparition et à l’évolution de complications hépatiques chez les enfants présentant un déficit en alpha-1 antitrypsine. Rev Mal Respir 2015; 32:759-67. [DOI: 10.1016/j.rmr.2015.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/02/2014] [Indexed: 10/23/2022]
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Silverman GA, Pak SC, Perlmutter DH. Disorders of protein misfolding: alpha-1-antitrypsin deficiency as prototype. J Pediatr 2013; 163:320-6. [PMID: 23664631 PMCID: PMC3725216 DOI: 10.1016/j.jpeds.2013.03.077] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/06/2013] [Accepted: 03/27/2013] [Indexed: 02/06/2023]
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The endosomal protein-sorting receptor sortilin has a role in trafficking α-1 antitrypsin. Genetics 2012; 192:889-903. [PMID: 22923381 DOI: 10.1534/genetics.112.143487] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Up to 1 in 3000 individuals in the United States have α-1 antitrypsin deficiency, and the most common cause of this disease is homozygosity for the antitrypsin-Z variant (ATZ). ATZ is inefficiently secreted, resulting in protein deficiency in the lungs and toxic polymer accumulation in the liver. However, only a subset of patients suffer from liver disease, suggesting that genetic factors predispose individuals to liver disease. To identify candidate factors, we developed a yeast ATZ expression system that recapitulates key features of the disease-causing protein. We then adapted this system to screen the yeast deletion mutant collection to identify conserved genes that affect ATZ secretion and thus may modify the risk for developing liver disease. The results of the screen and associated assays indicate that ATZ is degraded in the vacuole after being routed from the Golgi. In fact, one of the strongest hits from our screen was Vps10, which can serve as a receptor for the delivery of aberrant proteins to the vacuole. Because genome-wide association studies implicate the human Vps10 homolog, sortilin, in cardiovascular disease, and because hepatic cell lines that stably express wild-type or mutant sortilin were recently established, we examined whether ATZ levels and secretion are affected by sortilin. As hypothesized, sortilin function impacts the levels of secreted ATZ in mammalian cells. This study represents the first genome-wide screen for factors that modulate ATZ secretion and has led to the identification of a gene that may modify disease severity or presentation in individuals with ATZ-associated liver disease.
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