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Enemark JH. Mechanistic complexities of sulfite oxidase: An enzyme with multiple domains, subunits, and cofactors. J Inorg Biochem 2023; 247:112312. [PMID: 37441922 DOI: 10.1016/j.jinorgbio.2023.112312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/13/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023]
Abstract
Sulfite oxidase (SO) deficiency, an inherited disease that causes severe neonatal neurological problems and early death, arises from defects in the biosynthesis of the molybdenum cofactor (Moco) (general sulfite oxidase deficiency) or from inborn errors in the SUOX gene for SO (isolated sulfite oxidase deficiency, ISOD). The X-ray structure of the highly homologous homonuclear dimeric chicken sulfite oxidase (cSO) provides a template for locating ISOD mutation sites in human sulfite oxidase (hSO). Catalysis occurs within an individual subunit of hSO, but mutations that disrupt the hSO dimer are pathological. The catalytic cycle of SO involves five metal oxidation states (MoVI, MoV, MoIV, FeIII, FeII), two intramolecular electron transfer (IET) steps, and couples a two-electron oxygen atom transfer reaction at the Mo center with two one-electron transfers from the integral b-type heme to exogenous cytochrome c, the physiological oxidant. Several ISOD examples are analyzed using steady-state, stopped-flow, and laser flash photolysis kinetics and physical measurements of recombinant variants of hSO and native cSO. In the structure of cSO, Mo…Fe = 32 Å, much too long for efficient IET through the protein. Interdomain motion that brings the Mo and heme centers closer together to facilitate IET is supported indirectly by decreasing the length of the interdomain tether, by changes in the charges of surface residues of the Mo and heme domains, as well as by preliminary molecular dynamics calculations. However, direct dynamic measurements of interdomain motion are in their infancy.
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Affiliation(s)
- John H Enemark
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 East University Blvd, Tucson, AZ 85721-0041, United States of America.
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Zhang R, Hao Y, Xu Y, Qin J, Wang Y, Kumar Dey S, Li C, Wang H, Banerjee S. Whole exome sequencing identified a homozygous novel mutation in SUOX gene causes extremely rare autosomal recessive isolated sulfite oxidase deficiency. Clin Chim Acta 2022; 532:115-122. [PMID: 35679912 DOI: 10.1016/j.cca.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Isolated sulfite oxidase deficiency (ISOD) is a rare type of life-threatening neurometabolic disorders characterized by neonatal intractable seizures and severe developmental delay with an autosomal recessive mode of inheritance. Germline mutation in SUOX gene causes ISOD. Till date, only 32 mutations of SUOX gene have been identified and reported to be associated with ISOD. METHODS Here, we investigated a 5-days old Chinese female child, presented with intermittent tremor or seizures of limbs, neonatal encephalopathy, subarachnoid cyst and haemorrhage, dysplasia of corpus callosum, neonatal convulsion, hyperlactatemia, severe metabolic acidosis, hyperglycemia, and hyperkalemia. RESULTS Whole exome sequencing identified a novel homozygous transition (c.1227G > A) in exon 6 of the SUOX gene in the proband. This novel homozygous variant leads to the formation of a truncated sulfite oxidase (p.Trp409*) of 408 amino acids. This variant causes partial loss of the dimerization domain of sulfite oxidase. Hence, it is a loss-of-function variant. Proband's father and mother is carrying this novel variant in a heterozygous state. This variant was not found in 200 ethnically matched normal healthy control individuals. CONCLUSIONS Our study not only expanded the mutational spectrum of SUOX gene associated with ISOD, but also strongly suggested the significance of whole exome sequencing for identifying candidate genes and novel disease-causing variants.
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Affiliation(s)
- Rui Zhang
- Division of Maternal-Fetal Medicine, Jinan University-affiliated Shenzhen Bao'an Women's and Children's Hospital, Shenzhen 518102, China
| | - Yajing Hao
- Department of Radiology, Jinan University-affiliated Shenzhen Bao'an Women's and Children's Hospital, Jinan University, Shenzhen 518102, China
| | - Ying Xu
- Department of Ultrasound, Jinan University-affiliated Shenzhen Bao'an Women's and Children's Hospital, Shenzhen 518102, China
| | - Jiale Qin
- Department of Radiology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanfang Wang
- Department of Ultrasound, Jinan University-affiliated Shenzhen Bao'an Women's and Children's Hospital, Shenzhen 518102, China
| | - Subrata Kumar Dey
- Department of Biotechnology, Centre for Genetic Studies, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology (Formerly West Bengal University of Technology), Salt Lake City, Kolkata, India
| | - Chen Li
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huilin Wang
- Division of Maternal-Fetal Medicine, Jinan University-affiliated Shenzhen Bao'an Women's and Children's Hospital, Shenzhen 518102, China.
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China.
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Kaczmarek AT, Bender D, Gehling T, Kohl JB, Daimagüler HS, Santamaria-Araujo JA, Liebau MC, Koy A, Cirak S, Schwarz G. A defect in molybdenum cofactor binding causes an attenuated form of sulfite oxidase deficiency. J Inherit Metab Dis 2022; 45:169-182. [PMID: 34741542 DOI: 10.1002/jimd.12454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Isolated sulfite oxidase deficiency (ISOD) is a rare recessive and infantile lethal metabolic disorder, which is caused by functional loss of sulfite oxidase (SO) due to mutations of the SUOX gene. SO is a mitochondrially localized molybdenum cofactor (Moco)- and heme-dependent enzyme, which catalyzes the vital oxidation of toxic sulfite to sulfate. Accumulation of sulfite and sulfite-related metabolites such as S-sulfocysteine (SSC) are drivers of severe neurodegeneration leading to early childhood death in the majority of ISOD patients. Full functionality of SO is dependent on correct insertion of the heme cofactor and Moco, which is controlled by a highly orchestrated maturation process. This maturation involves the translation in the cytosol, import into the intermembrane space (IMS) of mitochondria, cleavage of the mitochondrial targeting sequence, and insertion of both cofactors. Moco insertion has proven as the crucial step in this maturation process, which enables the correct folding of the homodimer and traps SO in the IMS. Here, we report on a novel ISOD patient presented at 17 months of age carrying the homozygous mutation NM_001032386.2 (SUOX):c.1097G > A, which results in the expression of SO variant R366H. Our studies show that histidine substitution of Arg366, which is involved in coordination of the Moco-phosphate, causes a severe reduction in Moco insertion efficacy in vitro and in vivo. Expression of R366H in HEK SUOX-/- cells mimics the phenotype of patient's fibroblasts, representing a loss of SO expression and specific activity. Our studies disclose a general paradigm for a kinetic defect in Moco insertion into SO caused by residues involved in Moco coordination resulting in the case of R366H in an attenuated form of ISOD.
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Affiliation(s)
- Alexander Tobias Kaczmarek
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Daniel Bender
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Department of Pediatric Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Titus Gehling
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Joshua Benedict Kohl
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Hülya-Sevcan Daimagüler
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | | | - Max Christoph Liebau
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Anne Koy
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Sebahattin Cirak
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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Kaczmarek AT, Bahlmann N, Thaqi B, May P, Schwarz G. Machine learning-based identification and characterization of 15 novel pathogenic SUOX missense mutations. Mol Genet Metab 2021; 134:188-194. [PMID: 34420858 DOI: 10.1016/j.ymgme.2021.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022]
Abstract
Isolated sulfite oxidase deficiency (ISOD) is a rare hereditary metabolic disease caused by absence of functional sulfite oxidase (SO) due to mutations of the SUOX gene. SO oxidizes toxic sulfite and sulfite accumulation is associated with neurological disorders, progressive brain atrophy and early death. Similarities of these neurological symptoms to abundant diseases like neonatal encephalopathy underlines the raising need to increase the awareness for ISOD. Here we report an interdisciplinary approach utilizing exome/genome data derived from gnomAD database as well as published variants to predict the pathogenic outcome of 303 naturally occurring SO missense variants and combining these with activity determination. We identified 15 novel ISOD-causing SO variants and generated a databank of pathogenic SO missense variants to support future diagnosis of ISOD patients. We found six inactive variants (W101G, H118Y, E197K, R217W, S427W, D512Y, Q518R) and seven (D110H, P119S, G121E, G130R, Y140C, R269H, Q396P, R459Q) with severe reduction in activity. Based on the Hardy-Weinberg-equilibrium and the combination of our results with published SO missense and protein truncating variants, we calculated the first comprehensive incidence rate for ISOD of 1 in 1,377,341 births and provide a pathogenicity score to 303 naturally occurring SO missense variants.
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Affiliation(s)
- Alexander Tobias Kaczmarek
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Nike Bahlmann
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Germany
| | - Besarta Thaqi
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany.
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Du P, Hassan RN, Luo H, Xie J, Zhu Y, Hu Q, Yan J, Jiang W. Identification of a novel SUOX pathogenic variants as the cause of isolated sulfite oxidase deficiency in a Chinese pedigree. Mol Genet Genomic Med 2021; 9:e1590. [PMID: 33405344 PMCID: PMC8077164 DOI: 10.1002/mgg3.1590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 11/07/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Isolated sulfite oxidase deficiency (ISOD) is a life-threatening rare autosomal recessive disorder caused by pathogenic variants in SUOX (OMIM 606887) gene. The aim of our study was to establish a comprehensive genetic diagnosis strategy for the pathogenicity analysis of the SUOX gene within a limited time and to lay the foundation for precise genetic counseling, prenatal diagnosis, and preimplantation genetic diagnosis. METHODS Two offspring from one set of parents were studied. Next-generation sequencing (NGS) was used to screen for disease-causing gene variants in a family with ISOD. Then, Sanger sequencing was performed to verify the presence of candidate variants. Sulfite, homocysteine and uric acid levels were detected in the patients. According to the ACMG/AMP guidelines, the pathogenicity level of novel variants was annotated. RESULTS The nonsense pathogenic variant (c.1200C > G (p.Y400*)) and a duplication (c.1549_1574dup (p.I525 Mfs*102)) were found in the SUOX gene in the proband. The nonsense mutation (c.1200C > G (p.Y400*), pathogenic, isolated sulfite oxidase deficiency, autosomal recessive) has been reported as pathogenic and the duplication (c.1549_1574dup (p.I525 Mfs*102), pathogenic, isolated sulfite oxidase deficiency, autosomal recessive) was novel, which was classified as pathogenic according to the ACMG/AMP Standards and Guidelines. CONCLUSION We established the pathogenicity assessment in ISOD patients based on ACMG/AMP Standards and Guidelines and this is the first ISOD patient reported in mainland China. We also discovered that ISOD is caused by SUOX gene duplication mutation, which enriches the spectrum of SUOX pathogenic variants.
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Affiliation(s)
- Peng Du
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Reem N Hassan
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hualei Luo
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jie Xie
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yue Zhu
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qiuyue Hu
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jin Yan
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weiying Jiang
- Department of Medical Genetics, ZhongShan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Bender D, Kaczmarek AT, Santamaria-Araujo JA, Stueve B, Waltz S, Bartsch D, Kurian L, Cirak S, Schwarz G. Impaired mitochondrial maturation of sulfite oxidase in a patient with severe sulfite oxidase deficiency. Hum Mol Genet 2019; 28:2885-2899. [DOI: 10.1093/hmg/ddz109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/09/2019] [Accepted: 05/07/2019] [Indexed: 01/24/2023] Open
Abstract
AbstractSulfite oxidase (SO) is encoded by the nuclear SUOX gene and catalyzes the final step in cysteine catabolism thereby oxidizing sulfite to sulfate. Oxidation of sulfite is dependent on two cofactors within SO, a heme and the molybdenum cofactor (Moco), the latter forming the catalytic site of sulfite oxidation. SO localizes to the intermembrane space of mitochondria where both—pre-SO processing and cofactor insertion—are essential steps during SO maturation. Isolated SO deficiency (iSOD) is a rare inborn error of metabolism caused by mutations in the SUOX gene that lead to non-functional SO. ISOD is characterized by rapidly progressive neurodegeneration and death in early infancy. We diagnosed an iSOD patient with homozygous mutation of SUOX at c.1084G>A replacing Gly362 to serine. To understand the mechanism of disease, we expressed patient-derived G362S SO in Escherichia coli and surprisingly found full catalytic activity, while in patient fibroblasts no SO activity was detected, suggesting differences between bacterial and human expression. Moco reconstitution of apo-G362S SO was found to be approximately 90-fold reduced in comparison to apo-WT SO in vitro. In line, levels of SO-bound Moco in cells overexpressing G362S SO were significantly reduced compared to cells expressing WT SO providing evidence for compromised maturation of G362S SO in cellulo. Addition of molybdate to culture medium partially rescued impaired Moco binding of G362S SO and restored SO activity in patient fibroblasts. Thus, this study demonstrates the importance of the orchestrated maturation of SO and provides a first case of Moco-responsive iSOD.
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Affiliation(s)
- Daniel Bender
- Department of Chemistry, Institute for Biochemistry, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
| | - Alexander Tobias Kaczmarek
- Department of Chemistry, Institute for Biochemistry, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
| | | | - Burkard Stueve
- Abteilung für Kinderneurologie, Epileptologie und Sozialpädiatrie, Kliniken Köln, Kinderkrankenhaus, 51058 Cologne, Germany
| | - Stephan Waltz
- Abteilung für Kinderneurologie, Epileptologie und Sozialpädiatrie, Kliniken Köln, Kinderkrankenhaus, 51058 Cologne, Germany
| | - Deniz Bartsch
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
| | - Sebahattin Cirak
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
- Klinik für Kinderheilkunde und Jugendmedizin, Uniklinikum Köln, 50937 Cologne, Germany
| | - Guenter Schwarz
- Department of Chemistry, Institute for Biochemistry, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne Germany
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Velayutham M, Hemann CF, Cardounel AJ, Zweier JL. Sulfite Oxidase Activity of Cytochrome c: Role of Hydrogen Peroxide. Biochem Biophys Rep 2016; 5:96-104. [PMID: 26709389 PMCID: PMC4689149 DOI: 10.1016/j.bbrep.2015.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In humans, sulfite is generated endogenously by the metabolism of sulfur containing amino acids such as methionine and cysteine. Sulfite is also formed from exposure to sulfur dioxide, one of the major environmental pollutants. Sulfite is used as an antioxidant and preservative in dried fruits, vegetables, and beverages such as wine. Sulfite is also used as a stabilizer in many drugs. Sulfite toxicity has been associated with allergic reactions characterized by sulfite sensitivity, asthma, and anaphylactic shock. Sulfite is also toxic to neurons and cardiovascular cells. Recent studies suggest that the cytotoxicity of sulfite is mediated by free radicals; however, molecular mechanisms involved in sulfite toxicity are not fully understood. Cytochrome c (cyt c) is known to participate in mitochondrial respiration and has antioxidant and peroxidase activities. Studies were performed to understand the related mechanism of oxidation of sulfite and radical generation by ferric cytochrome c (Fe3+cyt c) in the absence and presence of H2O2. Electron paramagnetic resonance (EPR) spin trapping studies using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) were performed with sulfite, Fe3+cyt c, and H2O2. An EPR spectrum corresponding to the sulfite radical adducts of DMPO (DMPO-SO3-) was obtained. The amount of DMPO-SO3- formed from the oxidation of sulfite by the Fe3+cyt c increased with sulfite concentration. In addition, the amount of DMPO-SO3- formed by the peroxidase activity of Fe3+cyt c also increased with sulfite and H2O2 concentration. From these results, we propose a mechanism in which the Fe3+cyt c and its peroxidase activity oxidizes sulfite to sulfite radical. Our results suggest that Fe3+cyt c could have a novel role in the deleterious effects of sulfite in biological systems due to increased production of sulfite radical. It also shows that the increased production of sulfite radical may be responsible for neurotoxicity and some of the injuries which occur to humans born with molybdenum cofactor and sulfite oxidase deficiencies. Cytochrome c oxidizes sulfite to sulfite radical. In the presence of H2O2, sulfite radical generation from cyt c increases. The formation of sulfite radical is sulfite concentration dependent. This mechanism of sulfite radical formation may be important in sulfite toxicity.
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Affiliation(s)
- Murugesan Velayutham
- Center for Biomedical EPR Spectroscopy and Imaging, Davis Heart and Lung Research Institute, and Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, Ohio 43210 ; Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15219
| | - Craig F Hemann
- Center for Biomedical EPR Spectroscopy and Imaging, Davis Heart and Lung Research Institute, and Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, Ohio 43210
| | - Arturo J Cardounel
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15219
| | - Jay L Zweier
- Center for Biomedical EPR Spectroscopy and Imaging, Davis Heart and Lung Research Institute, and Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, Ohio 43210
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