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Endo M, Yoshida T, Ishii K, Iwamoto T, Totsuka M, Hattori M. Site-specific glycosylation and single amino acid substitution dramatically reduced the immunogenicity of β-lactoglobulin. Biosci Biotechnol Biochem 2023; 87:426-433. [PMID: 36577145 DOI: 10.1093/bbb/zbac210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]
Abstract
To reduce the immunogenicity of β-lactoglobulin (BLG), we prepared recombinant BLG which has both site-specific glycosylation and single amino acid substitution (D28N/P126A), and expressed it in the methylotrophic yeast Pichia pastoris by fusion of the cDNA to the sequence coding for the α-factor signal peptide from Saccharomyces cerevisiae. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicated that the D28N/P126A was conjugated with a ∼4 kDa high-mannose chain. D28N/P126A retained ∼61% of the retinol-binding activity of BLG. Structural analyses by circular dichroism (CD) spectra, intrinsic fluorescence, and Enzyme-linked immunosorbent assay (ELISA) with monoclonal antibodies indicated that the surface structure of BLG was slightly changed by using protein engineering techniques, but D28N/P126A was covered by high-mannose chains and substituted amino acid without substantial disruption of native conformation. Antibody responses to the D28N/P126A considerably reduced in C57BL/6 mice. We conclude that inducing both site-specific glycosylation and single amino acid substitution simultaneously is an effective method to reduce the immunogenicity of BLG.
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Affiliation(s)
- Michio Endo
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tadashi Yoshida
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Keisatoi Ishii
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taku Iwamoto
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Mamoru Totsuka
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Makoto Hattori
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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2
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Gou X, Feng X, Shi H, Guo T, Xie R, Liu Y, Wang Q, Li H, Yang B, Chen L, Lu Y. PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants. Plant Biotechnol J 2022; 20:1417-1431. [PMID: 35398963 PMCID: PMC9241370 DOI: 10.1111/pbi.13823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/03/2022] [Indexed: 05/31/2023]
Abstract
Single amino acid substitution (SAAS) produces the most common variant of protein function change under physiological conditions. As the number of SAAS events in plants has increased exponentially, an effective prediction tool is required to help identify and distinguish functional SAASs from the whole genome as either potentially causal traits or as variants. Here, we constructed a plant SAAS database that stores 12 865 SAASs in 6172 proteins and developed a tool called Plant Protein Variation Effect Detector (PPVED) that predicts the effect of SAASs on protein function in plants. PPVED achieved an 87% predictive accuracy when applied to plant SAASs, an accuracy that was much higher than those from six human database software: SIFT, PROVEAN, PANTHER-PSEP, PhD-SNP, PolyPhen-2, and MutPred2. The predictive effect of six SAASs from three proteins in Arabidopsis and maize was validated with wet lab experiments, of which five substitution sites were accurately predicted. PPVED could facilitate the identification and characterization of genetic variants that explain observed phenotype variations in plants, contributing to solutions for challenges in functional genomics and systems biology. PPVED can be accessed under a CC-BY (4.0) license via http://www.ppved.org.cn.
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Affiliation(s)
- Xiangjian Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry SciencesWenjiangSichuanChina
| | - Tingting Guo
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Rongqian Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Triticeae Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
| | - Hongxiang Li
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Banglie Yang
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Lixue Chen
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
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3
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Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, Baets GD, Bromberg Y, Cao C, Capriotti E, Casadio R, Durme JV, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Pal LR, Radivojac P, Rousseau F, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SC, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat 2019; 40:1530-1545. [PMID: 31301157 PMCID: PMC7325732 DOI: 10.1002/humu.23868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/22/2019] [Accepted: 07/09/2019] [Indexed: 12/28/2022]
Abstract
Accurate prediction of the impact of genomic variation on phenotype is a major goal of computational biology and an important contributor to personalized medicine. Computational predictions can lead to a better understanding of the mechanisms underlying genetic diseases, including cancer, but their adoption requires thorough and unbiased assessment. Cystathionine-beta-synthase (CBS) is an enzyme that catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine, and in which variations are associated with human hyperhomocysteinemia and homocystinuria. We have created a computational challenge under the CAGI framework to evaluate how well different methods can predict the phenotypic effect(s) of CBS single amino acid substitutions using a blinded experimental data set. CAGI participants were asked to predict yeast growth based on the identity of the mutations. The performance of the methods was evaluated using several metrics. The CBS challenge highlighted the difficulty of predicting the phenotype of an ex vivo system in a model organism when classification models were trained on human disease data. We also discuss the variations in difficulty of prediction for known benign and deleterious variants, as well as identify methodological and experimental constraints with lessons to be learned for future challenges.
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Affiliation(s)
- Laura Kasak
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Constantina Bakolitsa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Changhua Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jasper Rine
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Dago F. Dimster-Denk
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Gaurav Pandey
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Greet De Baets
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Chen Cao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD, USA
| | - Emidio Capriotti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Joost Van Durme
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Vrije Universiteit Brussel, Brussels, Belgium
| | - Manuel Giollo
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Rachel Karchin
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - David Masica
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Ayodeji Olatubosun
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
| | - Predrag Radivojac
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | | | - Mauno Vihinen
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Jouni Väliaho
- Institute of Medical Technology, University of Tampere, Tampere, Finland
| | - Susanna Repo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John Moult
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA USA
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Petrosino M, Pasquo A, Novak L, Toto A, Gianni S, Mantuano E, Veneziano L, Minicozzi V, Pastore A, Puglisi R, Capriotti E, Chiaraluce R, Consalvi V. Characterization of human frataxin missense variants in cancer tissues. Hum Mutat 2019; 40:1400-1413. [PMID: 31074541 PMCID: PMC6744310 DOI: 10.1002/humu.23789] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
Abstract
Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumor-initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study, we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function, and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions; however, some of the variants show a decreased stability and a decreased functional activity in comparison with that of the wild-type protein.
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Affiliation(s)
- Maria Petrosino
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Current address: IRCCS Istituto Neurologico Carlo Besta, Milano, Italia
- European Brain Research Institute-Fondazione Rita Levi Montalcini, Roma, Italia
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory,FSN-TECFIS-DIM, Frascati, Italy
| | - Leonore Novak
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Elide Mantuano
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | | | - Velia Minicozzi
- INFN and Department of Physics, University of Rome Tor Vergata, Rome, Italy
| | - Annalisa Pastore
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Rita Puglisi
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Roberta Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Valerio Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
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5
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Hasegawa H, Hsu A, Tinberg CE, Siegler KE, Nazarian AA, Tsai MM. Single amino acid substitution in LC-CDR1 induces Russell body phenotype that attenuates cellular protein synthesis through eIF2α phosphorylation and thereby downregulates IgG secretion despite operational secretory pathway traffic. MAbs 2017; 9:854-873. [PMID: 28379093 DOI: 10.1080/19420862.2017.1314875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Amino acid sequence differences in the variable region of immunoglobulin (Ig) cause wide variations in secretion outputs. To address how a primary sequence difference comes to modulate Ig secretion, we investigated the biosynthetic process of 2 human IgG2κ monoclonal antibodies (mAbs) that differ only by one amino acid in the light chain complementarity-determining region 1 while showing ∼20-fold variance in secretion titer. Although poorly secreted, the lower-secreting mAb of the 2 was by no means defective in terms of its folding stability, antigen binding, and in vitro biologic activity. However, upon overexpression in HEK293 cells, the low-secreting mAb revealed a high propensity to aggregate into enlarged globular structures called Russell bodies (RBs) in the endoplasmic reticulum. While Golgi morphology was affected by the formation of RBs, secretory pathway membrane traffic remained operational in those cells. Importantly, cellular protein synthesis was severely suppressed in RB-positive cells through the phosphorylation of eIF2α. PERK-dependent signaling was implicated in this event, given the upregulation and nuclear accumulation of downstream effectors such as ATF4 and CHOP. These findings illustrated that the underlining process of poor Ig secretion in RB-positive cells was due to downregulation of Ig synthesis instead of a disruption or blockade of secretory pathway trafficking. Therefore, RB formation signifies an end of active Ig production at the protein translation level. Consequently, depending on how soon and how severely an antibody-expressing cell develops the RB phenotype, the productive window of Ig secretion can vary widely among the cells expressing different mAbs.
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Affiliation(s)
- Haruki Hasegawa
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Ann Hsu
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Christine E Tinberg
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Karen E Siegler
- c Department of Cardiometabolic Disorders , Amgen Inc. , South San Francisco , CA , USA
| | - Aaron A Nazarian
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Mei-Mei Tsai
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
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Ramanathan N, Ahmed M, Raffan E, Stewart CL, O'Rahilly S, Semple RK, Raef H, Rochford JJ. Identification and Characterisation of a Novel Pathogenic Mutation in the Human Lipodystrophy Gene AGPAT2 : C48R: A Novel Mutation in AGPAT2. JIMD Rep 2012; 9:73-80. [PMID: 23430550 PMCID: PMC3565662 DOI: 10.1007/8904_2012_181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/12/2022] Open
Abstract
Loss-of-function mutations in AGPAT2, encoding 1-acylglycerol-3-phosphate-O-acyltransferase 2 (AGPAT2), produce congenital generalised lipodystrophy (CGL). We screened the AGPAT2 gene in two siblings who presented with pseudoacromegaly, diabetes and severe dyslipidaemia and identified a novel mutation in AGPAT2 causing a single amino acid substitution, p.Cys48Arg. We subsequently investigated the molecular pathogenic mechanism linking both this mutation and the previously reported p.Leu228Pro mutation to clinical disease. Wild-type and mutant AGPAT2 were expressed in control and AGPAT2-deficient preadipocyte cell lines. mRNA and protein expression was determined, and the ability of each AGPAT2 species to rescue adipocyte differentiation in AGPAT2-deficient cells was assessed. Protein levels of both p.Cys48Arg and p.Leu228Pro AGPAT2 were significantly reduced compared with that of wild-type AGPAT2 despite equivalent mRNA levels. Stable expression of wild-type AGPAT2 partially rescued adipogenesis in AGPAT2 deficient preadipocytes, whereas stable expression of p.Cys48Arg or p.Leu228Pro AGPAT2 did not. In conclusion, unusually severe dyslipidaemia and pseudoacromegaloid overgrowth in patients with diabetes should alert physicians to the possibility of lipodystrophy. Both the previously unreported pathogenic p.Cys48Arg mutation in AGPAT2, and the known p.Leu228Pro mutation result in decreased AGPAT2 protein expression in developing adipocytes. It is most likely that the CGL seen in homozygous carriers of these mutations is largely accounted for by loss of protein expression.
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Affiliation(s)
- N Ramanathan
- Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Hills Road, Cambridge, CB2 0QQ, UK
- Institute of Medical Biology, Immunos, 8A Biomedical Grove, 138648, Singapore, Republic of Singapore
| | - M Ahmed
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, 3354, Riyadh, 11211, Saudi Arabia
| | - E Raffan
- Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Hills Road, Cambridge, CB2 0QQ, UK
| | - C L Stewart
- Institute of Medical Biology, Immunos, 8A Biomedical Grove, 138648, Singapore, Republic of Singapore
| | - S O'Rahilly
- Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Hills Road, Cambridge, CB2 0QQ, UK
| | - R K Semple
- Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Hills Road, Cambridge, CB2 0QQ, UK
| | - H Raef
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, 3354, Riyadh, 11211, Saudi Arabia
| | - J J Rochford
- Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Hills Road, Cambridge, CB2 0QQ, UK.
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