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Tordai H, Torres O, Csepi M, Padányi R, Lukács GL, Hegedűs T. Analysis of AlphaMissense data in different protein groups and structural context. Sci Data 2024; 11:495. [PMID: 38744964 PMCID: PMC11094042 DOI: 10.1038/s41597-024-03327-8] [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] [Received: 12/04/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Single amino acid substitutions can profoundly affect protein folding, dynamics, and function. The ability to discern between benign and pathogenic substitutions is pivotal for therapeutic interventions and research directions. Given the limitations in experimental examination of these variants, AlphaMissense has emerged as a promising predictor of the pathogenicity of missense variants. Since heterogenous performance on different types of proteins can be expected, we assessed the efficacy of AlphaMissense across several protein groups (e.g. soluble, transmembrane, and mitochondrial proteins) and regions (e.g. intramembrane, membrane interacting, and high confidence AlphaFold segments) using ClinVar data for validation. Our comprehensive evaluation showed that AlphaMissense delivers outstanding performance, with MCC scores predominantly between 0.6 and 0.74. We observed low performance on disordered datasets and ClinVar data related to the CFTR ABC protein. However, a superior performance was shown when benchmarked against the high quality CFTR2 database. Our results with CFTR emphasizes AlphaMissense's potential in pinpointing functional hot spots, with its performance likely surpassing benchmarks calculated from ClinVar and ProteinGym datasets.
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Affiliation(s)
- Hedvig Tordai
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Odalys Torres
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Máté Csepi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Rita Padányi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gergely L Lukács
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Tamás Hegedűs
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- HUN-REN-SU Biophysical Virology Research Group, Budapest, Hungary.
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2
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedüs T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. Nat Commun 2023; 14:6868. [PMID: 37891162 PMCID: PMC10611759 DOI: 10.1038/s41467-023-42586-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR posttranslational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their posttranslational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding.
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Affiliation(s)
- Naoto Soya
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Haijin Xu
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Ariel Roldan
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Zhengrong Yang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Haoxin Ye
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Fan Jiang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Aiswarya Premchandar
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Susan P C Cole
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Kingston, ON, Canada
| | - John Kappes
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Tamás Hegedüs
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085, Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Gergely L Lukacs
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada.
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3
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedus T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563107. [PMID: 37905074 PMCID: PMC10614980 DOI: 10.1101/2023.10.19.563107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR post-translational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their post-translational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding. One-Sentence Summary Allosteric interdomain communication and its modulation are critical determinants of ABCC-transporters post-translational conformational biogenesis, misfolding, and pharmacological rescue.
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4
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Tordai H, Suhajda E, Sillitoe I, Nair S, Varadi M, Hegedus T. Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology. Int J Mol Sci 2022; 23:8877. [PMID: 36012140 PMCID: PMC9408558 DOI: 10.3390/ijms23168877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 02/06/2023] Open
Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Affiliation(s)
- Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, 1111 Budapest, Hungary
- Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sreenath Nair
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Mihaly Varadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, 1052 Budapest, Hungary
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Sengupta S, Sahasrabuddhe D, Wangikar PP. Transporter engineering for the development of cyanobacteria as cell factories: A text analytics guided survey. Biotechnol Adv 2021; 54:107816. [PMID: 34411662 DOI: 10.1016/j.biotechadv.2021.107816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are attractive candidates for photoautotrophic production of platform chemicals due to their inherent ability to utilize carbon dioxide as the sole carbon source. Metabolic pathways can be engineered more readily in cyanobacteria compared to higher photosynthetic organisms. Although significant progress has been made in pathway engineering, intracellular accumulation of the product is a potential bottleneck in large-scale production. Likewise, substrate uptake is known to limit growth and product formation. These limitations can potentially be addressed by targeted and controlled expression of transporter proteins in the metabolically engineered strains. This review focuses on the transporters that have been explored in cyanobacteria. To highlight the progress on characterization and application of cyanobacterial transporters, we applied text analytics to extract relevant information from over 1000 publications. We have categorized the transporters based on their source, their function and the solute they transport. Further, the review provides insights into the potential of transporters in the metabolic engineering of cyanobacteria for improved product titer.
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Affiliation(s)
- Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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6
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Medically Important Alterations in Transport Function and Trafficking of ABCG2. Int J Mol Sci 2021; 22:ijms22062786. [PMID: 33801813 PMCID: PMC8001156 DOI: 10.3390/ijms22062786] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
Several polymorphisms and mutations in the human ABCG2 multidrug transporter result in reduced plasma membrane expression and/or diminished transport function. Since ABCG2 plays a pivotal role in uric acid clearance, its malfunction may lead to hyperuricemia and gout. On the other hand, ABCG2 residing in various barrier tissues is involved in the innate defense mechanisms of the body; thus, genetic alterations in ABCG2 may modify the absorption, distribution, excretion of potentially toxic endo- and exogenous substances. In turn, this can lead either to altered therapy responses or to drug-related toxic reactions. This paper reviews the various types of mutations and polymorphisms in ABCG2, as well as the ways how altered cellular processing, trafficking, and transport activity of the protein can contribute to phenotypic manifestations. In addition, the various methods used for the identification of the impairments in ABCG2 variants and the different approaches to correct these defects are overviewed.
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Kroll T, Prescher M, Smits SHJ, Schmitt L. Structure and Function of Hepatobiliary ATP Binding Cassette Transporters. Chem Rev 2020; 121:5240-5288. [PMID: 33201677 DOI: 10.1021/acs.chemrev.0c00659] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The liver is beyond any doubt the most important metabolic organ of the human body. This function requires an intensive crosstalk within liver cellular structures, but also with other organs. Membrane transport proteins are therefore of upmost importance as they represent the sensors and mediators that shuttle signals from outside to the inside of liver cells and/or vice versa. In this review, we summarize the known literature of liver transport proteins with a clear emphasis on functional and structural information on ATP binding cassette (ABC) transporters, which are expressed in the human liver. These primary active membrane transporters form one of the largest families of membrane proteins. In the liver, they play an essential role in for example bile formation or xenobiotic export. Our review provides a state of the art and comprehensive summary of the current knowledge of hepatobiliary ABC transporters. Clearly, our knowledge has improved with a breath-taking speed over the last few years and will expand further. Thus, this review will provide the status quo and will lay the foundation for new and exciting avenues in liver membrane transporter research.
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Affiliation(s)
- Tim Kroll
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Martin Prescher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Nasr R, Lorendeau D, Khonkarn R, Dury L, Pérès B, Boumendjel A, Cortay JC, Falson P, Chaptal V, Baubichon-Cortay H. Molecular analysis of the massive GSH transport mechanism mediated by the human Multidrug Resistant Protein 1/ABCC1. Sci Rep 2020; 10:7616. [PMID: 32377003 PMCID: PMC7203140 DOI: 10.1038/s41598-020-64400-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
The transporter Multidrug Resistance Protein 1 (MRP1, ABCC1) is implicated in multidrug resistant (MDR) phenotype of cancer cells. Glutathione (GSH) plays a key role in MRP1 transport activities. In addition, a ligand-stimulated GSH transport which triggers the death of cells overexpressing MRP1, by collateral sensitivity (CS), has been described. This CS could be a way to overcome the poor prognosis for patients suffering from a chemoresistant cancer. The molecular mechanism of such massive GSH transport and its connection to the other transport activities of MRP1 are unknown. In this context, we generated MRP1/MRP2 chimeras covering different regions, MRP2 being a close homolog that does not trigger CS. The one encompassing helices 16 and 17 led to the loss of CS and MDR phenotype without altering basal GSH transport. Within this region, the sole restoration of the original G1228 (D1236 in MRP2) close to the extracellular loop between the two helices fully rescued the CS (massive GSH efflux and cell death) but not the MDR phenotype. The flexibility of that loop and the binding of a CS agent like verapamil could favor a particular conformation for the massive transport of GSH, not related to other transport activities of MRP1.
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Affiliation(s)
- Rachad Nasr
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
| | - Doriane Lorendeau
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
| | - Ruttiros Khonkarn
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Lauriane Dury
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
| | - Basile Pérès
- Department of Molecular Pharmacochemistry (DPM), UMR 5063, Grenoble Alpes University, 38041, Grenoble, France
| | - Ahcène Boumendjel
- Department of Molecular Pharmacochemistry (DPM), UMR 5063, Grenoble Alpes University, 38041, Grenoble, France
| | - Jean-Claude Cortay
- INSERM U1052, CNRS-University of Lyon UMR-5286, Cancer Research Center of Lyon (CRCL), 69008, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France
| | - Hélène Baubichon-Cortay
- Drug Resistance and Membrane Proteins group, IBCP, UMR 5086, CNRS-University of Lyon, 69367, Lyon, France.
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Lu X, Liu L, Shan W, Kong L, Chen N, Lou Y, Zeng S. The Role of the Sodium-taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) in Related Liver Disease. Curr Drug Metab 2019; 20:377-389. [PMID: 31258056 DOI: 10.2174/1389200220666190426152830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/10/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Sodium Taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) play significant roles as membrane transporters because of their presence in the enterohepatic circulation of bile salts. They have emerged as promising drug targets in related liver disease. METHODS We reviewed the literature published over the last 20 years with a focus on NTCP and BSEP. RESULTS This review summarizes the current perception about structure, function, genetic variation, and regulation of NTCP and BSEP, highlights the effects of their defects in some hepatic disorders, and discusses the application prospect of new transcriptional activators in liver diseases. CONCLUSION NTCP and BSEP are important proteins for transportation and homeostasis maintenance of bile acids. Further research is needed to develop new models for determining the structure-function relationship of bile acid transporters and screening for substrates and inhibitors, as well as to gain more information about the regulatory genetic mechanisms involved in the processes of liver injury.
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Affiliation(s)
- Xiaoyang Lu
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Lin Liu
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Wenya Shan
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Limin Kong
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Na Chen
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Yan Lou
- The First Affiliated Hospital, Zhejiang University, Zhejiang, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, China
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10
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Fernández-Murga ML, Petrov PD, Conde I, Castell JV, Goméz-Lechón MJ, Jover R. Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems. Food Chem Toxicol 2018; 120:196-212. [PMID: 29990576 DOI: 10.1016/j.fct.2018.07.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/12/2022]
Abstract
Despite growing research, drug-induced liver injury (DILI) remains a serious issue of increasing importance to the medical community that challenges health systems, pharmaceutical industries and drug regulatory agencies. Drug-induced cholestasis (DIC) represents a frequent manifestation of DILI in humans, which is characterised by an impaired canalicular bile flow resulting in a detrimental accumulation of bile constituents in blood and tissues. From a clinical point of view, cholestatic DILI generates a wide spectrum of presentations and can be a diagnostic challenge. The drug classes mostly associated with DIC are anti-infectious, anti-diabetic, anti-inflammatory, psychotropic and cardiovascular agents, steroids, and other miscellaneous drugs. The molecular mechanisms of DIC have been investigated since the 1980s but they remain debatable. It is recognised that altered expression and/or function of hepatobiliary membrane transporters underlies some forms of cholestasis, and this and other concomitant mechanisms are very likely in DIC. Deciphering these processes may pave the ways for diagnosis, prognosis and prevention, for which currently major gaps and caveats exist. In this review, we summarise recent advances in the field of DIC, including clinical aspects, the potential mechanisms postulated so far and the in vitro systems that can be useful to investigate and identify new cholestatic drugs.
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Affiliation(s)
- M Leonor Fernández-Murga
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Petar D Petrov
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Isabel Conde
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Jose V Castell
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Spain
| | - M José Goméz-Lechón
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain.
| | - Ramiro Jover
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Spain.
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11
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Bergam P, Reisecker JM, Rakvács Z, Kucsma N, Raposo G, Szakacs G, van Niel G. ABCB6 Resides in Melanosomes and Regulates Early Steps of Melanogenesis Required for PMEL Amyloid Matrix Formation. J Mol Biol 2018; 430:3802-3818. [PMID: 29940187 DOI: 10.1016/j.jmb.2018.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 01/08/2023]
Abstract
Genetically inheritable pigmentation defects provide a unique opportunity to reveal the function of proteins contributing to melanogenesis. Dyschromatosis universalis hereditaria (DUH) is a rare pigmentary genodermatosis associated with mutations in the ABCB6 gene. Here we use optical and electron microscopy imaging combined with biochemical tools to investigate the localization and function of ABCB6 in pigment cells. We show that ABCB6 localizes to the membrane of early melanosomes and lysosomes of the human melanocytic cell line MNT-1. Depletion of ABCB6 by siRNA impaired PMEL amyloidogenesis in early melanosomes and induced aberrant accumulation of multilamellar aggregates in pigmented melanosomes. PMEL fibril formation and normal maturation of pigmented melanosomes could be restored by the overexpression of wild-type ABCB6 but not by variants containing an inactivating catalytic mutation (K629M) or the G579E DUH mutation. In line with the impairment of PMEL matrix formation in the absence of ABCB6, morphological analysis of the retinal pigment epithelium of ABCB6 knockout mice revealed a significant decrease of melanosome numbers. Our study extends the localization of ABCB6 to melanosomes, suggesting a potential link between the function of ABCB6 and the etiology of DUH to amyloid formation in pigment cells.
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Affiliation(s)
- Ptissam Bergam
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France
| | | | - Zsófia Rakvács
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary
| | - Nóra Kucsma
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary
| | - Graça Raposo
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France
| | - Gergely Szakacs
- Institute of Cancer Research, Medical University Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary.
| | - Guillaume van Niel
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France; Center for Psychiatry and Neuroscience, Hopital Saint-Anne, Université Descartes, INSERM U894, Paris, France.
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12
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Molinski SV, Shahani VM, Subramanian AS, MacKinnon SS, Woollard G, Laforet M, Laselva O, Morayniss LD, Bear CE, Windemuth A. Comprehensive mapping of cystic fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site. Proteins 2018; 86:833-843. [DOI: 10.1002/prot.25496] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | | | | | - Onofrio Laselva
- Programme in Molecular Structure and Function; Research Institute, Hospital for Sick Children; Toronto Ontario M5G 0A4 Canada
| | | | - Christine E. Bear
- Programme in Molecular Structure and Function; Research Institute, Hospital for Sick Children; Toronto Ontario M5G 0A4 Canada
- Department of Physiology; University of Toronto; Toronto Ontario M5S 1A8 Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario M5S 1A8 Canada
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Tordai H, Jakab K, Gyimesi G, András K, Brózik A, Sarkadi B, Hegedus T. ABCMdb reloaded: updates on mutations in ATP binding cassette proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074791. [PMID: 28365738 PMCID: PMC5467578 DOI: 10.1093/database/bax023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/23/2017] [Indexed: 12/26/2022]
Abstract
ABC (ATP-Binding Cassette) proteins with altered function are responsible for numerous human diseases. To aid the selection of positions and amino acids for ABC structure/function studies we have generated a database, ABCMdb (Gyimesi et al., ABCMdb: a database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application. Hum Mutat 2012; 33:1547–1556.), with interactive tools. The database has been populated with mentions of mutations extracted from full text papers, alignments and structural models. In the new version of the database we aimed to collect the effect of mutations from databases including ClinVar. Because of the low number of available data, even in the case of the widely studied disease-causing ABC proteins, we also included the possible effects of mutations based on SNAP2 and PROVEAN predictions. To aid the interpretation of variations in non-coding regions, the database was supplemented with related DNA level information. Our results emphasize the importance of in silico predictions because of the sparse information available on variants and suggest that mutations at analogous positions in homologous ABC proteins have a strong predictive power for the effects of mutations. Our improved ABCMdb advances the design of both experimental studies and meta-analyses in order to understand drug interactions of ABC proteins and the effects of mutations on functional expression. Database URL:http://abcm2.hegelab.org
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Affiliation(s)
- Hedvig Tordai
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | - Kristóf Jakab
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland and
| | - Kinga András
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | - Anna Brózik
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Balázs Sarkadi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Tamás Hegedus
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
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Chaperones rescue the energetic landscape of mutant CFTR at single molecule and in cell. Nat Commun 2017; 8:398. [PMID: 28855508 PMCID: PMC5577305 DOI: 10.1038/s41467-017-00444-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/29/2017] [Indexed: 12/14/2022] Open
Abstract
Molecular chaperones are pivotal in folding and degradation of the cellular proteome but their impact on the conformational dynamics of near-native membrane proteins with disease relevance remains unknown. Here we report the effect of chaperone activity on the functional conformation of the temperature-sensitive mutant cystic fibrosis channel (∆F508-CFTR) at the plasma membrane and after reconstitution into phospholipid bilayer. Thermally induced unfolding at 37 °C and concomitant functional inactivation of ∆F508-CFTR are partially suppressed by constitutive activity of Hsc70 and Hsp90 chaperone/co-chaperone at the plasma membrane and post-endoplasmic reticulum compartments in vivo, and at single-molecule level in vitro, indicated by kinetic and thermodynamic remodeling of the mutant gating energetics toward its wild-type counterpart. Thus, molecular chaperones can contribute to functional maintenance of ∆F508-CFTR by reshaping the conformational energetics of its final fold, a mechanism with implication in the regulation of metastable ABC transporters and other plasma membrane proteins activity in health and diseases. The F508 deletion (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) is the most common CF causing mutation. Here the authors show that cytosolic chaperones shift the F508del channel conformation to the native fold by kinetic and thermodynamic remodelling of the gating energetics towards that of wild-type CTFR.
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Hegde RN, Subramanian A, Pothukuchi P, Parashuraman S, Luini A. Rare ER protein misfolding-mistrafficking disorders: Therapeutic developments. Tissue Cell 2017; 49:175-185. [PMID: 28222887 DOI: 10.1016/j.tice.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022]
Abstract
The presence of a functional protein at the appropriate location in the cell is the result of the processes of transcription, translation, folding and trafficking to the correct destination. There are numerous diseases that are caused by protein misfolding, mainly due to mutations in the respective gene. The consequences of this misfolding may be that proteins effectively lose their function, either by being removed by the cellular quality control machinery or by accumulating at the incorrect intracellular or extracellular location. A number of mutations that lead to protein misfolding and affect trafficking to the final destination, e.g. Cystic fibrosis, Wilson's disease, and Progressive Familial Intrahepatic 1 cholestasis, result in proteins that retain partial function if their folding and trafficking is restored either by molecular or pharmacological means. In this review, we discuss several mutant proteins within this class of misfolding diseases and provide an update on the status of molecular and therapeutic developments and potential therapeutic strategies being developed to counter these diseases.
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Affiliation(s)
| | - Advait Subramanian
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | | | | | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Naples, Italy; Istituto di Ricovero e Cura a Carattere Scientifico SDN, Naples, Italy
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Ran Y, Thibodeau PH. Stabilization of Nucleotide Binding Domain Dimers Rescues ABCC6 Mutants Associated with Pseudoxanthoma Elasticum. J Biol Chem 2016; 292:1559-1572. [PMID: 27994049 DOI: 10.1074/jbc.m116.759811] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/08/2016] [Indexed: 12/31/2022] Open
Abstract
ABC transporters are polytopic membrane proteins that utilize ATP binding and hydrolysis to facilitate transport across biological membranes. Forty-eight human ABC transporters have been identified in the genome, and the majority of these are linked to heritable disease. Mutations in the ABCC6 (ATP binding cassette transporter C6) ABC transporter are associated with pseudoxanthoma elasticum, a disease of altered elastic properties in multiple tissues. Although ∼200 mutations have been identified in pseudoxanthoma elasticum patients, the underlying structural defects associated with the majority of these are poorly understood. To evaluate the structural consequences of these missense mutations, a combination of biophysical and cell biological approaches were applied to evaluate the local and global folding and assembly of the ABCC6 protein. Structural and bioinformatic analyses suggested that a cluster of mutations, representing roughly 20% of the patient population with identified missense mutations, are located in the interface between the transmembrane domain and the C-terminal nucleotide binding domain. Biochemical and cell biological analyses demonstrate these mutations influence multiple steps in the biosynthetic pathway, minimally altering local domain structure but adversely impacting ABCC6 assembly and trafficking. The differential impacts on local and global protein structure are consistent with hierarchical folding and assembly of ABCC6. Stabilization of specific domain-domain interactions via targeted amino acid substitution in the catalytic site of the C-terminal nucleotide binding domain restored proper protein trafficking and cell surface localization of multiple biosynthetic mutants. This rescue provides a specific mechanism by which chemical chaperones could be developed for the correction of ABCC6 biosynthetic defects.
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Affiliation(s)
- Yanchao Ran
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Patrick H Thibodeau
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania 15219.
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A single active catalytic site is sufficient to promote transport in P-glycoprotein. Sci Rep 2016; 6:24810. [PMID: 27117502 PMCID: PMC4846820 DOI: 10.1038/srep24810] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/05/2016] [Indexed: 11/23/2022] Open
Abstract
P-glycoprotein (Pgp) is an ABC transporter responsible for the ATP-dependent efflux of chemotherapeutic compounds from multidrug resistant cancer cells. Better understanding of the molecular mechanism of Pgp-mediated transport could promote rational drug design to circumvent multidrug resistance. By measuring drug binding affinity and reactivity to a conformation-sensitive antibody we show here that nucleotide binding drives Pgp from a high to a low substrate-affinity state and this switch coincides with the flip from the inward- to the outward-facing conformation. Furthermore, the outward-facing conformation survives ATP hydrolysis: the post-hydrolytic complex is stabilized by vanadate, and the slow recovery from this state requires two functional catalytic sites. The catalytically inactive double Walker A mutant is stabilized in a high substrate affinity inward-open conformation, but mutants with one intact catalytic center preserve their ability to hydrolyze ATP and to promote drug transport, suggesting that the two catalytic sites are randomly recruited for ATP hydrolysis.
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Telbisz Á, Homolya L. Recent advances in the exploration of the bile salt export pump (BSEP/ABCB11) function. Expert Opin Ther Targets 2015; 20:501-14. [PMID: 26573700 DOI: 10.1517/14728222.2016.1102889] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The bile salt export pump (BSEP/ABCB11), residing in the apical membrane of hepatocyte, mediates the secretion of bile salts into the bile. A range of human diseases is associated with the malfunction of BSEP, including fatal hereditary liver disorders and mild cholestatic conditions. Manifestation of these diseases primarily depends on the mutation type; however, other factors such as hormonal changes and drug interactions can also trigger or influence the related diseases. AREAS COVERED Here, we summarize the recent knowledge on BSEP by covering its transport properties, cellular localization, regulation and major mutations/polymorphisms, as well as the hereditary and acquired diseases associated with BSEP dysfunction. We discuss the different model expression systems employed to understand the function of the BSEP variants, their drug interactions and the contemporary therapeutic interventions. EXPERT OPINION The limitations of the available model expression systems for BSEP result in controversial conclusions, and obstruct our deeper insight into BSEP deficiencies and BSEP-related drug interactions. The knowledge originating from different methodologies, such as clinical studies, molecular genetics, as well as in vitro and in silico modeling, should be integrated and harmonized. Increasing availability of robust molecular biological tools and our better understanding of the mechanism of BSEP deficiencies should make the personalized, mutation-based therapeutic interventions more attainable.
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Affiliation(s)
- Ágnes Telbisz
- a Institute of Enzymology, Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest 1117 , Hungary
| | - László Homolya
- a Institute of Enzymology, Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest 1117 , Hungary
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Varma S, Revencu N, Stephenne X, Scheers I, Smets F, Beleza-Meireles A, Reding R, Roskams T, Sokal EM. Retargeting of bile salt export pump and favorable outcome in children with progressive familial intrahepatic cholestasis type 2. Hepatology 2015; 62:198-206. [PMID: 25847299 DOI: 10.1002/hep.27834] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/30/2015] [Indexed: 12/24/2022]
Abstract
UNLABELLED We investigated predictors of clinical evolution in progressive familial intrahepatic cholestasis type 2 patients and how they relate to bile salt export pump (BSEP) expression and its (re)targeting. Our retrospective study included 22 children with progressive familial intrahepatic cholestasis type 2. Clinical, biochemical, and histological characteristics were reviewed on admittance and following treatment with either ursodeoxycholic acid alone (10 mg/kg thrice daily, n = 19) or partial biliary diversion (n = 3). Immunostaining of BSEP was performed in 20 patients. Response to treatment was defined as normalization of pruritus, disappearance of jaundice, and alanine aminotransferase (ALT) levels <1.5 times the upper limit of normal. Ten of 22 patients were responders, and paired biopsies were available in six. De novo or retargeted canalicular expression of BSEP occurred in four of these six, two of whom exhibited baseline intracellular expression. Twelve of 22 were nonresponders and exhibited earlier onset of jaundice (<9 months), neonatal cholestasis, and higher ALT levels. An ALT >165 IU/L produced 72% sensitivity and 55% specificity in predicting nonresponse. Seven patients were still responding at last follow-up (median = 20 months, range 5-67 months). Three responders relapsed after 56, 72, and 82 months, respectively. Of nine surviving responders, median relapse-free survival time was 72 months (95% confidence interval 48-96 months) and 5-year relapse-free survival was 75% (95% confidence interval 33-100%). Intracellular BSEP at baseline was seen in six, of whom five were responders. Genetic analysis was performed in 17 of 22, confirming diagnosis in 13 (76%) and in four (24%) in whom only heterozygous mutation was identified. CONCLUSION De novo or retargeted canalicular expression of BSEP occurs in treatment responders; children with late-onset presentation, lower ALT, and intracellular BSEP expression are likely to respond, at least transiently, to nontransplant treatment.
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Affiliation(s)
- Sharat Varma
- Service de Gastroentérologie et Hépatologie Pédiatrique
| | | | | | | | | | | | - Raymond Reding
- Unités de Chirurgie Pédiatrique, Université Catholique de Louvain, Cliniques Universitaires St. Luc, Brussels, Belgium
| | - Tania Roskams
- Katholiek Universiteit Leuven, University Hospital Gasthuisberg, Leuven, Belgium
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Vohra S, Biggin PC. Mutationmapper: a tool to aid the mapping of protein mutation data. PLoS One 2013; 8:e71711. [PMID: 23951226 PMCID: PMC3739722 DOI: 10.1371/journal.pone.0071711] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/01/2013] [Indexed: 12/25/2022] Open
Abstract
There has been a rapid increase in the amount of mutational data due to, amongst other things, an increase in single nucleotide polymorphism (SNP) data and the use of site-directed mutagenesis as a tool to help dissect out functional properties of proteins. Many manually curated databases have been developed to index point mutations but they are not sustainable with the ever-increasing volume of scientific literature. There have been considerable efforts in the automatic extraction of mutation specific information from raw text involving use of various text-mining approaches. However, one of the key problems is to link these mutations with its associated protein and to present this data in such a way that researchers can immediately contextualize it within a structurally related family of proteins. To aid this process, we have developed an application called MutationMapper. Point mutations are extracted from abstracts and are validated against protein sequences in Uniprot as far as possible. Our methodology differs in a fundamental way from the usual text-mining approach. Rather than start with abstracts, we start with protein sequences, which facilitates greatly the process of validating a potential point mutation identified in an abstract. The results are displayed as mutations mapped on to the protein sequence or a multiple sequence alignment. The latter enables one to readily pick up mutations performed at equivalent positions in related proteins. We demonstrate the use of MutationMapper against several examples including a single sequence and multiple sequence alignments. The application is available as a web-service at http://mutationmapper.bioch.ox.ac.uk.
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Affiliation(s)
- Shabana Vohra
- Structural Bioinformatics and Computational Biochemistry, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, Department of Biochemistry, Oxford, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, Department of Biochemistry, Oxford, United Kingdom
- * E-mail:
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Wei CH, Harris BR, Kao HY, Lu Z. tmVar: a text mining approach for extracting sequence variants in biomedical literature. Bioinformatics 2013; 29:1433-9. [PMID: 23564842 DOI: 10.1093/bioinformatics/btt156] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Text-mining mutation information from the literature becomes a critical part of the bioinformatics approach for the analysis and interpretation of sequence variations in complex diseases in the post-genomic era. It has also been used for assisting the creation of disease-related mutation databases. Most of existing approaches are rule-based and focus on limited types of sequence variations, such as protein point mutations. Thus, extending their extraction scope requires significant manual efforts in examining new instances and developing corresponding rules. As such, new automatic approaches are greatly needed for extracting different kinds of mutations with high accuracy. RESULTS Here, we report tmVar, a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants described at protein, DNA and RNA levels according to a standard nomenclature developed by the Human Genome Variation Society. By doing so, we cover several important types of mutations that were not considered in past studies. Using a novel CRF label model and feature set, our method achieves higher performance than a state-of-the-art method on both our corpus (91.4 versus 78.1% in F-measure) and their own gold standard (93.9 versus 89.4% in F-measure). These results suggest that tmVar is a high-performance method for mutation extraction from biomedical literature. AVAILABILITY tmVar software and its corpus of 500 manually curated abstracts are available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/pub/tmVar
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Affiliation(s)
- Chih-Hsuan Wei
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), 8600 Rockville Pike, Bethesda, MD 20894, USA
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Gromiha MM, Ou YY. Bioinformatics approaches for functional annotation of membrane proteins. Brief Bioinform 2013; 15:155-68. [DOI: 10.1093/bib/bbt015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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