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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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Sun S, Wang C, Zhao P, Kline GM, Grandjean JMD, Jiang X, Labaudiniere R, Wiseman RL, Kelly JW, Balch WE. Capturing the conversion of the pathogenic alpha-1-antitrypsin fold by ATF6 enhanced proteostasis. Cell Chem Biol 2023; 30:22-42.e5. [PMID: 36630963 PMCID: PMC9930901 DOI: 10.1016/j.chembiol.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/07/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023]
Abstract
Genetic variation in alpha-1 antitrypsin (AAT) causes AAT deficiency (AATD) through liver aggregation-associated gain-of-toxic pathology and/or insufficient AAT activity in the lung manifesting as chronic obstructive pulmonary disease (COPD). Here, we utilize 71 AATD-associated variants as input through Gaussian process (GP)-based machine learning to study the correction of AAT folding and function at a residue-by-residue level by pharmacological activation of the ATF6 arm of the unfolded protein response (UPR). We show that ATF6 activators increase AAT neutrophil elastase (NE) inhibitory activity, while reducing polymer accumulation for the majority of AATD variants, including the prominent Z variant. GP-based profiling of the residue-by-residue response to ATF6 activators captures an unexpected role of the "gate" area in managing AAT-specific activity. Our work establishes a new spatial covariant (SCV) understanding of the convertible state of the protein fold in response to genetic perturbation and active environmental management by proteostasis enhancement for precision medicine.
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Affiliation(s)
- Shuhong Sun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Pei Zhao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabe M Kline
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Xin Jiang
- Protego Biopharma, 10945 Vista Sorrento Parkway, San Diego, CA, USA
| | | | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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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.
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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
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