1
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West EE, Merle NS, Kamiński MM, Palacios G, Kumar D, Wang L, Bibby JA, Overdahl K, Jarmusch AK, Freeley S, Lee DY, Thompson JW, Yu ZX, Taylor N, Sitbon M, Green DR, Bohrer A, Mayer-Barber KD, Afzali B, Kazemian M, Scholl-Buergi S, Karall D, Huemer M, Kemper C. Loss of CD4 + T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection. Immunity 2023; 56:2036-2053.e12. [PMID: 37572656 PMCID: PMC10576612 DOI: 10.1016/j.immuni.2023.07.014] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Arginase 1 (Arg1), the enzyme catalyzing the conversion of arginine to ornithine, is a hallmark of IL-10-producing immunoregulatory M2 macrophages. However, its expression in T cells is disputed. Here, we demonstrate that induction of Arg1 expression is a key feature of lung CD4+ T cells during mouse in vivo influenza infection. Conditional ablation of Arg1 in CD4+ T cells accelerated both virus-specific T helper 1 (Th1) effector responses and its resolution, resulting in efficient viral clearance and reduced lung pathology. Using unbiased transcriptomics and metabolomics, we found that Arg1-deficiency was distinct from Arg2-deficiency and caused altered glutamine metabolism. Rebalancing this perturbed glutamine flux normalized the cellular Th1 response. CD4+ T cells from rare ARG1-deficient patients or CRISPR-Cas9-mediated ARG1-deletion in healthy donor cells phenocopied the murine cellular phenotype. Collectively, CD4+ T cell-intrinsic Arg1 functions as an unexpected rheostat regulating the kinetics of the mammalian Th1 lifecycle with implications for Th1-associated tissue pathologies.
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Affiliation(s)
- Erin E West
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Nicolas S Merle
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Marcin M Kamiński
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gustavo Palacios
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Luopin Wang
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Jack A Bibby
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kirsten Overdahl
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, NC, USA
| | - Alan K Jarmusch
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, NC, USA
| | - Simon Freeley
- School of Immunology and Microbial Sciences, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | | | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Zu-Xi Yu
- Pathology Core, NHLBI, NIH, Bethesda, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Rare Tumor Initiative, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA; Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier, CNRS, Montpellier, France
| | - Marc Sitbon
- Pediatric Oncology Branch, Rare Tumor Initiative, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA; Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier, CNRS, Montpellier, France
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrea Bohrer
- Inflammation and Innate Immunity Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Sabine Scholl-Buergi
- Clinic for Pediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniela Karall
- Clinic for Pediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Huemer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Pediatric Endocrinology and Diabetology, University Children's Hospital Basel, Basel, Switzerland; Department of Pediatrics, Landeskrankenhaus (LKH) Bregenz, Bregenz, Austria
| | - Claudia Kemper
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.
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2
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Chao AS, Matak P, Pegram K, Powers J, Hutson C, Jo R, Dubois L, Thompson JW, Smith PB, Jain V, Liu C, Younge NE, Rikard B, Reyes EY, Shinohara ML, Gregory SG, Goldberg RN, Benner EJ. 20-αHydroxycholesterol, an oxysterol in human breast milk, reverses mouse neonatal white matter injury through Gli-dependent oligodendrogenesis. Cell Stem Cell 2023; 30:1054-1071.e8. [PMID: 37541211 PMCID: PMC10625465 DOI: 10.1016/j.stem.2023.07.010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/21/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023]
Abstract
White matter injuries (WMIs) are the leading cause of neurologic impairment in infants born premature. There are no treatment options available. The most common forms of WMIs in infants occur prior to the onset of normal myelination, making its pathophysiology distinctive, thus requiring a tailored approach to treatment. Neonates present a unique opportunity to repair WMIs due to a transient abundance of neural stem/progenitor cells (NSPCs) present in the germinal matrix with oligodendrogenic potential. We identified an endogenous oxysterol, 20-αHydroxycholesterol (20HC), in human maternal breast milk that induces oligodendrogenesis through a sonic hedgehog (shh), Gli-dependent mechanism. Following WMI in neonatal mice, injection of 20HC induced subventricular zone-derived oligodendrogenesis and improved myelination in the periventricular white matter, resulting in improved motor outcomes. Targeting the oligodendrogenic potential of postnatal NSPCs in neonates with WMIs may be further developed into a novel approach to mitigate this devastating complication of preterm birth.
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Affiliation(s)
- Agnes S Chao
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Pavle Matak
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Kelly Pegram
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - James Powers
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Collin Hutson
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Rebecca Jo
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Laura Dubois
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - P Brian Smith
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Vaibhav Jain
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Chunlei Liu
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Noelle E Younge
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Blaire Rikard
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Estefany Y Reyes
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Simon G Gregory
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ronald N Goldberg
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Eric J Benner
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA.
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3
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Bitto A, Grillo AS, Ito TK, Stanaway IB, Nguyen BMG, Ying K, Tung H, Smith K, Tran N, Velikanje G, Urfer SR, Snyder JM, Barton J, Sharma A, Kayser EB, Wang L, Smith DL, Thompson JW, DuBois L, DePaolo W, Kaeberlein M. Acarbose suppresses symptoms of mitochondrial disease in a mouse model of Leigh syndrome. Nat Metab 2023; 5:955-967. [PMID: 37365290 DOI: 10.1038/s42255-023-00815-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/04/2023] [Indexed: 06/28/2023]
Abstract
Mitochondrial diseases represent a spectrum of disorders caused by impaired mitochondrial function, ranging in severity from mortality during infancy to progressive adult-onset disease. Mitochondrial dysfunction is also recognized as a molecular hallmark of the biological ageing process. Rapamycin, a drug that increases lifespan and health during normative ageing, also increases survival and reduces neurological symptoms in a mouse model of the severe mitochondrial disease Leigh syndrome. The Ndufs4 knockout (Ndufs4-/-) mouse lacks the complex I subunit NDUFS4 and shows rapid onset and progression of neurodegeneration mimicking patients with Leigh syndrome. Here we show that another drug that extends lifespan and delays normative ageing in mice, acarbose, also suppresses symptoms of disease and improves survival of Ndufs4-/- mice. Unlike rapamycin, acarbose rescues disease phenotypes independently of inhibition of the mechanistic target of rapamycin. Furthermore, rapamycin and acarbose have additive effects in delaying neurological symptoms and increasing maximum lifespan in Ndufs4-/- mice. We find that acarbose remodels the intestinal microbiome and alters the production of short-chain fatty acids. Supplementation with tributyrin, a source of butyric acid, recapitulates some effects of acarbose on lifespan and disease progression, while depletion of the endogenous microbiome in Ndufs4-/- mice appears to fully recapitulate the effects of acarbose on healthspan and lifespan in these animals. To our knowledge, this study provides the first evidence that alteration of the gut microbiome plays a significant role in severe mitochondrial disease and provides further support for the model that biological ageing and severe mitochondrial disorders share underlying common mechanisms.
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Affiliation(s)
- Alessandro Bitto
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Anthony S Grillo
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Takashi K Ito
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Ian B Stanaway
- Division of Nephrology, School of Medicine, University of Washington, Seattle, WA, USA
- Harborview Medical Center, Kidney Research Institute, Seattle, WA, USA
| | - Bao M G Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kejun Ying
- T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | | | - Ngoc Tran
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Gunnar Velikanje
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Silvan R Urfer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica M Snyder
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Jacob Barton
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Ayush Sharma
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Daniel L Smith
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Laura DuBois
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - William DePaolo
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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4
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Giamberardino CD, Schell WA, Tenor JL, Toffaletti DL, Palmucci JR, Marius C, Boua JVK, Soltow Q, Mansbach R, Moseley MA, Thompson JW, Dubois LG, Hope W, Perfect JR, Shaw KJ. Efficacy of APX2039 in a Rabbit Model of Cryptococcal Meningitis. mBio 2022; 13:e0234722. [PMID: 36222509 PMCID: PMC9765414 DOI: 10.1128/mbio.02347-22] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Cryptococcal Meningitis (CM) is uniformly fatal if not treated, and treatment options are limited. We previously reported on the activity of APX2096, the prodrug of the novel Gwt1 inhibitor APX2039, in a mouse model of CM. Here, we investigated the efficacy of APX2039 in mouse and rabbit models of CM. In the mouse model, the controls had a mean lung fungal burden of 5.95 log10 CFU/g, whereas those in the fluconazole-, amphotericin B-, and APX2039-treated mice were 3.56, 4.59, and 1.50 log10 CFU/g, respectively. In the brain, the control mean fungal burden was 7.97 log10 CFU/g, while the burdens were 4.64, 7.16, and 1.44 log10 CFU/g for treatment with fluconazole, amphotericin B, and APX2039, respectively. In the rabbit model of CM, the oral administration of APX2039 at 50 mg/kg of body weight twice a day (BID) resulted in a rapid decrease in the cerebrospinal fluid (CSF) fungal burden, and the burden was below the limit of detection by day 10 postinfection. The effective fungicidal activity (EFA) was -0.66 log10 CFU/mL/day, decreasing from an average of 4.75 log10 CFU/mL to 0 CFU/mL, over 8 days of therapy, comparing favorably with good clinical outcomes in humans associated with reductions of the CSF fungal burden of -0.4 log10 CFU/mL/day, and, remarkably, 2-fold the EFA of amphotericin B deoxycholate in this model (-0.33 log10 CFU/mL/day). A total drug exposure of the area under the concentration-time curve from 0 to 24 h (AUC0-24) of 25 to 50 mg · h/L of APX2039 resulted in near-maximal antifungal activity. These data support the further preclinical and clinical evaluation of APX2039 as a new oral fungicidal monotherapy for the treatment of CM. IMPORTANCE Cryptococcal meningitis (CM) is a fungal disease with significant global morbidity and mortality. The gepix Gwt1 inhibitors are a new class of antifungal drugs. Here, we demonstrated the efficacy of APX2039, the second member of the gepix class, in rabbit and mouse models of cryptococcal meningitis. We also analyzed the drug levels in the blood and cerebrospinal fluid in the highly predictive rabbit model and built a mathematical model to describe the behavior of the drug with respect to the elimination of the fungal pathogen. We demonstrated that the oral administration of APX2039 resulted in a rapid decrease in the CSF fungal burden, with an effective fungicidal activity of -0.66 log10 CFU/mL/day, comparing favorably with good clinical outcomes in humans associated with reductions of -0.4 log10 CFU/mL/day. The drug APX2039 had good penetration of the central nervous system and is an excellent candidate for future clinical testing in humans for the treatment of CM.
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Affiliation(s)
- Charles D. Giamberardino
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
| | - Wiley A. Schell
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
| | - Jennifer L. Tenor
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
| | - Dena L. Toffaletti
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
| | - Julia R. Palmucci
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
| | - Choiselle Marius
- Duke University School of Medicine, Department of Surgery, Durham, North Carolina, USA
| | - Jane-Valeriane K. Boua
- Duke University School of Medicine, Department of Neurosurgery, Durham, North Carolina, USA
| | | | | | - M. Arthur Moseley
- Duke University School of Medicine, Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Durham, North Carolina, USA
| | - J. Will Thompson
- Duke University School of Medicine, Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Durham, North Carolina, USA
| | - Laura G. Dubois
- Duke University School of Medicine, Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Durham, North Carolina, USA
| | - William Hope
- Antimicrobial Pharmacodynamics and Therapeutics, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - John R. Perfect
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, North Carolina, USA
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5
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Berger M, Cooter M, Roesler AS, Chunga S, Park J, Modliszewski JL, VanDusen KW, Thompson JW, Moseley A, Devinney MJ, Smani S, Hall A, Cai V, Browndyke JN, Lutz MW, Corcoran DL. Erratum to: APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. J Alzheimers Dis 2022; 90:1339-1340. [PMID: 36373324 PMCID: PMC9756142 DOI: 10.3233/jad-229018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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6
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Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem 2022; 94:9508-9513. [PMID: 35729701 PMCID: PMC10654755 DOI: 10.1021/acs.analchem.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The family of deubiquitinases (DUBs) comprises ∼100 enzymes that cleave ubiquitin from substrate proteins and thereby regulate key aspects of human physiology. DUBs have recently emerged as disease-relevant and chemically tractable, although currently there are no approved DUB-targeting drugs and most preclinical small molecules are low-potency and/or multitargeted. We paired a novel capillary electrophoresis microchip containing an integrated, "on-chip" C18 bed (SPE-ZipChip) with a TMT version of our recently described PRM-LIVE acquisition scheme on a timsTOF Pro mass spectrometer to facilitate rapid activity-based protein profiling of DUB inhibitors. We demonstrate the ability of the SPE-ZipChip to improve proteome coverage of complex samples as well as the quantitation integrity of CE-PRM-LIVE for TMT labeled samples. These technologies provide a platform to accurately quantify competitive binding of covalent and reversible inhibitors in a multiplexed assay that spans 49 endogenous DUBs in less than 15 min.
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Affiliation(s)
- He Zhu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Scott Mellors
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Wai Cheung Chan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Will Thompson
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Ariana S Bratt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | | | - Gary Kruppa
- Bruker S.R.O., District Brno-City 61900 Czech Republic
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
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7
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Trub AG, Wagner GR, Anderson KA, Crown SB, Zhang GF, Thompson JW, Ilkayeva OR, Stevens RD, Grimsrud PA, Kulkarni RA, Backos DS, Meier JL, Hirschey MD. Statin therapy inhibits fatty acid synthase via dynamic protein modifications. Nat Commun 2022; 13:2542. [PMID: 35538051 PMCID: PMC9090928 DOI: 10.1038/s41467-022-30060-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Statins are a class of drug widely prescribed for the prevention of cardiovascular disease, with pleiotropic cellular effects. Statins inhibit HMG-CoA reductase (HMGCR), which converts the metabolite HMG-CoA into mevalonate. Recent discoveries have shown HMG-CoA is a reactive metabolite that can non-enzymatically modify proteins and impact their activity. Therefore, we predicted that inhibition of HMGCR by statins might increase HMG-CoA levels and protein modifications. Upon statin treatment, we observe a strong increase in HMG-CoA levels and modification of only a single protein. Mass spectrometry identifies this protein as fatty acid synthase (FAS), which is modified on active site residues and, importantly, on non-lysine side-chains. The dynamic modifications occur only on a sub-pool of FAS that is located near HMGCR and alters cellular signaling around the ER and Golgi. These results uncover communication between cholesterol and lipid biosynthesis by the substrate of one pathway inhibiting another in a rapid and reversible manner.
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Affiliation(s)
- Alec G Trub
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Department of Pharmacology & Cancer Biology, Durham, NC, USA
| | - Gregory R Wagner
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Durham, NC, USA
| | - Kristin A Anderson
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Department of Pharmacology & Cancer Biology, Durham, NC, USA
| | - Scott B Crown
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
| | - Guo-Fang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Durham, NC, USA
| | - J Will Thompson
- Department of Pharmacology & Cancer Biology, Durham, NC, USA
- Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC, 27710, USA
| | - Olga R Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Durham, NC, USA
| | - Robert D Stevens
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
| | - Paul A Grimsrud
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Durham, NC, USA
| | - Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Matthew D Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Durham, NC, USA.
- Department of Pharmacology & Cancer Biology, Durham, NC, USA.
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Durham, NC, USA.
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8
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West EE, Freeley S, Kaminski MM, Merle NS, Veenbergen S, Lee DY, St. John-Williams L, Thompson JW, Green DR, Scholl-Buergi S, Karall D, Huemer M, Kemper C. Setting the pace: CD4 T cell-intrinsic Arginase 1 orchestrates Th1 induction and contraction. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.165.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
CD4 T cell-intrinsic engagement of the complement receptor CD46 controls nutrient influx and the metabolic reprogramming events that are essential for both the initiation and contraction of human Th1 responses, characterized by IFN-g and IL-10 production respectively. Here, we demonstrate that CD46 also orchestrates T cell arginine metabolism by upregulating the arginine transporter CAT-1 and, unexpectedly, Arginase 1 (Arg1). Arg1 has been well characterized in macrophages where it is associated with the IL-10 secreting M2 type, but its expression or function in T cells has not been described. Surprisingly, in CD4 T cell, Arg1 seems to restrain IL-10 production and contraction: T cells isolated from four patients with rare Arg1 deficiency mount strong Th1 responses but display significantly increased IL-10 switching and early contraction when compared to healthy control cells. Similarly, Arg1fl/fl CD4-cre+ mice infected with influenza virus are characterized by an enhanced Th1 response that contracts more rapidly, resulting in viral control and significantly reduced lung pathology. Unexpectedly, both Arg1-deficient mouse and human T cells produce normal levels of nitric oxide (NO) and polyamines. Metabolic profiling rather revealed that T cells lacking Arg1 have enhanced glycolysis, reduced TCA-cycle intermediates, and engage an “alternative” glutamine pathway often utilized by cancer cells. Normalization of these metabolic perturbations, through the targeting of specific metabolic enzymes, restored typical Th1 induction/contraction. Overall, these data unveil an unexpected intrinsic role for Arginase 1 as a pacemaker of the Th1 lifecycle, which could be harnessed for the amelioration Th1-driven pathologies.
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Affiliation(s)
- Erin E West
- 1Complement and Inflammation Research Section, NHLBI, NIH
| | | | | | | | | | | | | | | | | | | | | | | | - Claudia Kemper
- 1Complement and Inflammation Research Section, NHLBI, NIH
- 9University of Lubeck, Germany
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9
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Asokan A, Ibrahim MS, Thompson JW, Haddad FS. Debridement, antibiotics, and implant retention in non-oncological femoral megaprosthesis infections: minimum 5 year follow-up. J Exp Orthop 2022; 9:32. [PMID: 35403987 PMCID: PMC9001793 DOI: 10.1186/s40634-022-00469-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 05/31/2023] Open
Abstract
Purpose Megaprostheses are increasingly utilised outside of the oncological setting, and remain at significant risk of periprosthetic joint infection (PJI). Debridement, antibiotic, and implant retention (DAIR) is an established treatment for PJI, however its use in non-oncological patients with femoral megaprostheses has not been widely reported. There are significant differences in patient physiology, treatment goals, and associated risks between these patient cohorts. Methods We identified 14 patients who underwent DAIR for a PJI of their femoral megaprostheses, between 2000 and 2014, whom had their index procedure secondary to non-oncological indications. Patients were managed as part of a multidisciplinary team, with our standardised surgical technique including exchange of all mobile parts, and subsequent antibiotic therapy for a minimum of 3 months. Patients were followed up for a minimum of 5 years. Results Patients included six proximal femoral replacements, five distal femoral replacements, and three total femoral replacements. No patients were lost to follow-up. There were six males and eight females, with a mean age of 67.2 years, and mean ASA of 2.3. Nine patients (64.3%) successfully cleared their infection following DAIR at a minimum of 5 year follow-up. Five patients (35.7%) required further revision surgery, with four patients cleared of infection. No patients who underwent DAIR alone suffered complications as a result of the procedure. Conclusions The use of DAIR in these complex patients can lead to successful outcomes, but the risk of further revision remains high. The success rate (64.3%) remains on par with other studies evaluating DAIR in megaprostheses and in primary arthroplasty. This study indicates judicious use of DAIR can be an appropriate part of the treatment algorithm. Level of evidence II
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Affiliation(s)
- A Asokan
- Department of Trauma and Orthopaedic Surgery, University College Hospital, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK.
| | - M S Ibrahim
- Department of Trauma and Orthopaedic Surgery, University College Hospital, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - J W Thompson
- Department of Trauma and Orthopaedic Surgery, University College Hospital, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - F S Haddad
- Department of Trauma and Orthopaedic Surgery, University College Hospital, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
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10
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Huang D, Wang Y, Thompson JW, Yin T, Alexander PB, Qin D, Mudgal P, Wu H, Liang Y, Tan L, Pan C, Yuan L, Wan Y, Li QJ, Wang XF. Cancer-cell-derived GABA promotes β-catenin-mediated tumour growth and immunosuppression. Nat Cell Biol 2022; 24:230-241. [PMID: 35145222 PMCID: PMC8852304 DOI: 10.1038/s41556-021-00820-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022]
Abstract
Many cancers have an unusual dependence on glutamine. However, most previous studies have focused on the contribution of glutamine to metabolic building blocks and the energy supply. Here, we report that cancer cells with aberrant expression of glutamate decarboxylase 1 (GAD1) rewire glutamine metabolism for the synthesis of γ-aminobutyric acid (GABA)-a prominent neurotransmitter-in non-nervous tissues. An analysis of clinical samples reveals that increased GABA levels predict poor prognosis. Mechanistically, we identify a cancer-intrinsic pathway through which GABA activates the GABAB receptor to inhibit GSK-3β activity, leading to enhanced β-catenin signalling. This GABA-mediated β-catenin activation both stimulates tumour cell proliferation and suppresses CD8+ T cell intratumoural infiltration, such that targeting GAD1 or GABABR in mouse models overcomes resistance to anti-PD-1 immune checkpoint blockade therapy. Our findings uncover a signalling role for tumour-derived GABA beyond its classic function as a neurotransmitter that can be targeted pharmacologically to reverse immunosuppression.
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Affiliation(s)
- De Huang
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Chongqing, China
- Southwest Hospital, Chongqing, China
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tao Yin
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Peter B Alexander
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Diyuan Qin
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | | | | | - Yaosi Liang
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Christopher Pan
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Lifeng Yuan
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ying Wan
- Southwest Hospital, Chongqing, China
| | - Qi-Jing Li
- Department of Immunology, Duke University Medical Center, Durham, NC, USA.
| | - Xiao-Fan Wang
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
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11
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Abdi K, Abramsky R, Andescavage N, Bambi J, Basu S, Bearer C, Benner EJ, Biselele T, Bliznyuk N, Breckpot J, Carey G, Chao A, Christiansen LI, Comani S, Croce P, De Vos M, Dereymaeker A, Dubois L, Eisch AJ, Epstein A, Geva N, Geva Y, Gewillig M, Gillis S, Goldberg RN, Gram M, Gregory S, Guez-Barber D, Hayakawa M, Henriksen NL, Hermans T, Hershkovitz R, Holgersen K, Holmqvist B, Jain V, Jansen K, Kandula V, Kapse K, Kawaguchi M, Khair A, Khazaei M, Kidokoro H, Kiffer FC, Kisilewicz K, Kumai S, Lacaille H, Ley D, Limperopoulos C, Lindholm SEH, Lukusa P, Lundberg R, MacFarlane P, Matak P, Mavinga L, Mayer C, Mbayabo G, Mitsumatsu T, Mubungu G, Murnick J, Nakata T, Narita H, Nataraj P, Natsume J, Naulaers G, Nikam R, Ortenlöf N, Ottolini K, Pan X, Pankratova S, Pegram K, Penn AA, Pradhan S, Raeisi K, Rickman N, Rikard B, Rotem R, Sangild PT, Sato Y, Sawamura F, Shany E, Shelef I, Shiraki A, Smets L, Sura L, Suzui R, Suzuki T, Tady BP, Taga G, Tamburro G, Thewissen L, Thompson JW, Thymann T, Tokat C, Vacher CM, Valdes C, Vallius S, Vatolin S, Watanabe H, Weintraub AY, Weiss M, Yamamoto H, Yaniv SS, Younge N, Yun S, Zappasodi F. Proceedings of the 13th International Newborn Brain Conference: Fetal and/or neonatal brain development, both normal and abnormal. J Neonatal Perinatal Med 2022; 15:411-426. [PMID: 35431185 DOI: 10.3233/npm-229002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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12
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VanDusen KW, Li YJ, Cai V, Hall A, Hiles S, Thompson JW, Moseley MA, Cooter M, Acker L, Levy JH, Ghadimi K, Quiñones QJ, Devinney MJ, Chung S, Terrando N, Moretti EW, Browndyke JN, Mathew JP, Berger M. Cerebrospinal Fluid Proteome Changes in Older Non-Cardiac Surgical Patients with Postoperative Cognitive Dysfunction. J Alzheimers Dis 2021; 80:1281-1297. [PMID: 33682719 PMCID: PMC8052629 DOI: 10.3233/jad-201544] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Postoperative cognitive dysfunction (POCD), a syndrome of cognitive deficits occurring 1–12 months after surgery primarily in older patients, is associated with poor postoperative outcomes. POCD is hypothesized to result from neuroinflammation; however, the pathways involved remain unclear. Unbiased proteomic analyses have been used to identify neuroinflammatory pathways in multiple neurologic diseases and syndromes but have not yet been applied to POCD. Objective: To utilize unbiased mass spectrometry-based proteomics to identify potential neuroinflammatory pathways underlying POCD. Methods: Unbiased LC-MS/MS proteomics was performed on immunodepleted cerebrospinal fluid (CSF) samples obtained before, 24 hours after, and 6 weeks after major non-cardiac surgery in older adults who did (n = 8) or did not develop POCD (n = 6). Linear mixed models were used to select peptides and proteins with intensity differences for pathway analysis. Results: Mass spectrometry quantified 8,258 peptides from 1,222 proteins in > 50%of patient samples at all three time points. Twelve peptides from 11 proteins showed differences in expression over time between patients with versus without POCD (q < 0.05), including proteins previously implicated in neurodegenerative disease pathophysiology. Additionally, 283 peptides from 182 proteins were identified with trend-level differences (q < 0.25) in expression over time between these groups. Among these, pathway analysis revealed that 50 were from 17 proteins mapping to complement and coagulation pathways (q = 2.44*10–13). Conclusion: These data demonstrate the feasibility of performing unbiased mass spectrometry on perioperative CSF samples to identify pathways associated with POCD. Additionally, they provide hypothesis-generating evidence for CSF complement and coagulation pathway changes in patients with POCD.
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Affiliation(s)
- Keith W VanDusen
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA.,Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Victor Cai
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Ashley Hall
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Sarah Hiles
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - J Will Thompson
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - M Arthur Moseley
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Mary Cooter
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Leah Acker
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Jerrold H Levy
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Kamrouz Ghadimi
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Quintin J Quiñones
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Michael J Devinney
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Stacey Chung
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Niccolò Terrando
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Eugene W Moretti
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Jeffrey N Browndyke
- Department of Psychiatry & Behavioral Sciences, Division of Geriatric Behavioral Health, Duke University Medical Center, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke University Medical Center, Durham, NC, USA
| | - Joseph P Mathew
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Miles Berger
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
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13
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Wignadasan W, Thompson JW, Ibrahim M, Kayani B, Magan A, Haddad FS. Day-case unicompartmental knee arthroplasty: a literature review and development of a novel hospital pathway. Ann R Coll Surg Engl 2021; 104:165-173. [PMID: 34323112 DOI: 10.1308/rcsann.2021.0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/22/2022] Open
Abstract
INTRODUCTION We have seen unparalleled changes in our healthcare systems globally as a result of the COVID-19 pandemic. As we strive to regenerate our full capacity elective services in order to contest the increasing demand for lower limb arthroplasty, this pandemic has allowed us a rare opportunity to revise and develop novel elective arthroplasty pathways intended to improve patient care and advance healthcare efficiency. We present an extensive evidence-based review of the approaches used to achieve day-case unicompartmental arthroplasty (UKA) as well as the development of a day-case UKA care pathway in a UK NHS institution based on the evidence provided in the literature. METHODS An extensive search of the literature was performed for articles that reported on readmission or complication rates ≥30 days postoperatively following day-case UKA. FINDINGS Fifteen manuscripts reporting the results of day-case UKA, defined as discharged on the same calendar day of surgery, were included in our review. Mean reported complication rates for day-case and inpatient UKA within the follow-up periods were 4.05% and 6.52%, respectively. Mean readmission rates were 2.71% and 4.36% for day-case and inpatient UKA, respectively. The mean rate of successful same-day discharge was 92.45%. CONCLUSION We introduce our institutional Elective Day Surgery Arthroplasty Pathway (EDSAP) founded upon the evidence presented in the literature. Stringent patient selection complimented by a well-defined day-case arthroplasty pathway is fundamental for successful commencement of day-case UKA in the NHS.
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Affiliation(s)
| | - J W Thompson
- University College London Hospitals, UK.,The Princess Grace Hospital, UK
| | - M Ibrahim
- University College London Hospitals, UK.,The Princess Grace Hospital, UK
| | - B Kayani
- University College London Hospitals, UK.,The Princess Grace Hospital, UK
| | - A Magan
- University College London Hospitals, UK
| | - F S Haddad
- University College London Hospitals, UK.,The Princess Grace Hospital, UK
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14
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Adams KJ, Wilson JG, Millington DS, Moseley MA, Colton CA, Thompson JW, Gottschalk WK. Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring In Vivo Arginine Isotope Incorporation in Alzheimer's Disease Mouse Models. J Am Soc Mass Spectrom 2021; 32:1448-1458. [PMID: 34028275 DOI: 10.1021/jasms.1c00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Immune-based metabolic reprogramming of arginine utilization in the brain contributes to the neuronal pathology associated with Alzheimer's disease (AD). To enable our long-term goals of differentiation of AD mouse model genotypes, ages, and sexes based on activity of this pathway, we describe here the novel dosing (using uniformly labeled (13C615N4) arginine) and analysis methods using capillary electrophoresis high-resolution accurate-mass mass spectrometry for isotope tracing of metabolic products of arginine. We developed a pseudoprimed infusion-dosing regimen, using repeated injections, to achieve a steady state of uniformly labeled arginine in 135-195 min post bolus dose. Incorporation of stable isotope labeled carbon and nitrogen from uniformly labeled arginine into a host of downstream metabolites was measured in vivo in mice using serially sampled dried blood spots from the tail. In addition to the dried blood spot time course samples, total isotope incorporation into arginine-related metabolites was measured in the whole brain and plasma after 285 min. Preliminary demonstration of the technique identified differences isotope incorporation in arginine metabolites between male and female mice in a mouse-model of sporadic Alzheimer's disease (APOE4/huNOS2). The technique described herein will permit arginine pathway activity differentiation between mouse genotypes, ages, sexes, or drug treatments in order to elucidate the contribution of this pathway to Alzheimer's disease.
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Affiliation(s)
- Kendra J Adams
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27710, United States
| | - Joan G Wilson
- Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - David S Millington
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27710, United States
| | - Carol A Colton
- Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27710, United States
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - W Kirby Gottschalk
- Department of Neurology, Duke University, Durham, North Carolina 27710, United States
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15
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Langley RJ, Migaud ME, Flores L, Thompson JW, Kean EA, Mostellar MM, Mowry M, Luckett P, Purcell LD, Lovato J, Gandotra S, Benton R, Files DC, Harrod KS, Gillespie MN, Morris PE. A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure. Sci Rep 2021; 11:10515. [PMID: 34006901 PMCID: PMC8131588 DOI: 10.1038/s41598-021-89716-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/05/2021] [Indexed: 12/25/2022] Open
Abstract
Acute respiratory failure (ARF) requiring mechanical ventilation, a complicating factor in sepsis and other disorders, is associated with high morbidity and mortality. Despite its severity and prevalence, treatment options are limited. In light of accumulating evidence that mitochondrial abnormalities are common in ARF, here we applied broad spectrum quantitative and semiquantitative metabolomic analyses of serum from ARF patients to detect bioenergetic dysfunction and determine its association with survival. Plasma samples from surviving and non-surviving patients (N = 15/group) were taken at day 1 and day 3 after admission to the medical intensive care unit and, in survivors, at hospital discharge. Significant differences between survivors and non-survivors (ANOVA, 5% FDR) include bioenergetically relevant intermediates of redox cofactors nicotinamide adenine dinucleotide (NAD) and NAD phosphate (NADP), increased acyl-carnitines, bile acids, and decreased acyl-glycerophosphocholines. Many metabolites associated with poor outcomes are substrates of NAD(P)-dependent enzymatic processes, while alterations in NAD cofactors rely on bioavailability of dietary B-vitamins thiamine, riboflavin and pyridoxine. Changes in the efficiency of the nicotinamide-derived cofactors' biosynthetic pathways also associate with alterations in glutathione-dependent drug metabolism characterized by substantial differences observed in the acetaminophen metabolome. Based on these findings, a four-feature model developed with semi-quantitative and quantitative metabolomic results predicted patient outcomes with high accuracy (AUROC = 0.91). Collectively, this metabolomic endotype points to a close association between mitochondrial and bioenergetic dysfunction and mortality in human ARF, thus pointing to new pharmacologic targets to reduce mortality in this condition.
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Affiliation(s)
| | - Marie E Migaud
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Lori Flores
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - J Will Thompson
- Duke University Center for Genomic and Computational Biology, Durham, NC, USA
| | - Elizabeth A Kean
- University of South Alabama College of Medicine, Mobile, AL, USA
| | | | - Matthew Mowry
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Patrick Luckett
- Washington University in Saint Louis, Saint Louis, MO, USA
- University of South Alabama School of Computing, Mobile, AL, USA
| | - Lina D Purcell
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - James Lovato
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Sheetal Gandotra
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
- University of Alabama-Birmingham College of Medicine, Birmingham, AL, USA
| | - Ryan Benton
- University of South Alabama School of Computing, Mobile, AL, USA
| | - D Clark Files
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Kevin S Harrod
- University of Alabama-Birmingham College of Medicine, Birmingham, AL, USA
| | - Mark N Gillespie
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Peter E Morris
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kentucky Health Care, 206E Mathews Building, Lexington, KY, 40506-0047, USA.
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16
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Dutta P, Kodigepalli KM, LaHaye S, Thompson JW, Rains S, Nagel C, Thatcher K, Hinton RB, Lincoln J. KPT-330 Prevents Aortic Valve Calcification via a Novel C/EBPβ Signaling Pathway. Circ Res 2021; 128:1300-1316. [PMID: 33601919 PMCID: PMC8085092 DOI: 10.1161/circresaha.120.318503] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Punashi Dutta
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Karthik M. Kodigepalli
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Stephanie LaHaye
- The Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH, USA
| | - J. Will Thompson
- Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Sarah Rains
- Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Duke Proteomics and Metabolomics Shared Resource, Durham, NC, USA
| | - Casey Nagel
- Ocean Ridge Biosciences, Deerfield Beach, Florida, USA
| | - Kaitlyn Thatcher
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Robert B. Hinton
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Joy Lincoln
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
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17
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Bryan J, Mandan A, Kamat G, Gottschalk WK, Badea A, Adams KJ, Thompson JW, Colton CA, Mukherjee S, Lutz MW. Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. Alzheimers Dement 2021; 17:561-573. [PMID: 33480182 PMCID: PMC8044005 DOI: 10.1002/alz.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age or sex. Evaluation of AD biological pathways in the context of interactions with these covariates is critical to the understanding of AD as well as the development of model systems used to study the disease. METHODS Gene set enrichment methods are powerful tools used to interpret gene-level statistics at the level of biological pathways. We introduce a method for quantifying gene set enrichment using likelihood ratio-derived test statistics (gsLRT), which accounts for sample covariates like age and sex. We then use our method to test for age and sex interactions with protein expression levels in AD and to compare the pathway results between human and mouse species. RESULTS Our method, based on nested logistic regressions is competitive with the existing standard for gene set testing in the context of linear models and complex experimental design. The gene sets we identify as having a significant association with AD-both with and without additional covariate interactions-are validated by previous studies. Differences between gsLRT results on mouse and human datasets are observed. DISCUSSION Characterizing biological pathways involved in AD builds on the important work involving single gene drivers. Our gene set enrichment method finds pathways that are significantly related to AD while accounting for covariates that may be relevant to disease development. The method highlights commonalities and differences between human AD and mouse models, which may inform the development of higher fidelity models for the study of AD.
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Affiliation(s)
- Jordan Bryan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Arpita Mandan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Gauri Kamat
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | | | - Alexandra Badea
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Kendra J. Adams
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | | | - Carol A. Colton
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Department of Neurology, Duke University, Durham, NC 27708, USA
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18
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Naggie S, Lusk S, Thompson JW, Mock M, Moylan C, Lucas JE, Dubois L, St John-Williams L, Moseley MA, Patel K. Metabolomic Signature as a Predictor of Liver Disease Events in Patients With HIV/HCV Coinfection. J Infect Dis 2021; 222:2012-2020. [PMID: 32502252 DOI: 10.1093/infdis/jiaa316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Advanced liver disease due to hepatitis C virus (HCV) is a leading cause of human immunodeficiency virus (HIV)-related morbidity and mortality. There remains a need to develop noninvasive predictors of clinical outcomes in persons with HIV/HCV coinfection. METHODS We conducted a nested case-control study in 126 patients with HIV/HCV and utilized multiple quantitative metabolomic assays to identify a prognostic profile that predicts end-stage liver disease (ESLD) events including ascites, hepatic encephalopathy, hepatocellular carcinoma, esophageal variceal bleed, and spontaneous bacterial peritonitis. Each analyte class was included in predictive modeling, and area under the receiver operator characteristic curves (AUC) and accuracy were determined. RESULTS The baseline model including demographic and clinical data had an AUC of 0.79. Three models (baseline plus amino acids, lipid metabolites, or all combined metabolites) had very good accuracy (AUC, 0.84-0.89) in differentiating patients at risk of developing an ESLD complication up to 2 years in advance. The all combined metabolites model had sensitivity 0.70, specificity 0.85, positive likelihood ratio 4.78, and negative likelihood ratio 0.35. CONCLUSIONS We report that quantification of a novel set of metabolites may allow earlier identification of patients with HIV/HCV who have the greatest risk of developing ESLD clinical events.
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Affiliation(s)
- Susanna Naggie
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA.,Duke University School of Medicine, Durham, North Carolina, USA
| | - Sam Lusk
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - J Will Thompson
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Meredith Mock
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Cynthia Moylan
- Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Laura Dubois
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Lisa St John-Williams
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - M Arthur Moseley
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Keyur Patel
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA.,University of Toronto, Toronto, Ontario, Canada
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19
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MahmoudianDehkordi S, Ahmed AT, Bhattacharyya S, Han X, Baillie RA, Arnold M, Skime MK, John-Williams LS, Moseley MA, Thompson JW, Louie G, Riva-Posse P, Craighead WE, McDonald W, Krishnan R, Rush AJ, Frye MA, Dunlop BW, Weinshilboum RM, Kaddurah-Daouk R. Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression. Transl Psychiatry 2021; 11:153. [PMID: 33654056 PMCID: PMC7925685 DOI: 10.1038/s41398-020-01097-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are the first-line treatment for major depressive disorder (MDD), yet their mechanisms of action are not fully understood and their therapeutic benefit varies among individuals. We used a targeted metabolomics approach utilizing a panel of 180 metabolites to gain insights into mechanisms of action and response to citalopram/escitalopram. Plasma samples from 136 participants with MDD enrolled into the Mayo Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) were profiled at baseline and after 8 weeks of treatment. After treatment, we saw increased levels of short-chain acylcarnitines and decreased levels of medium-chain and long-chain acylcarnitines, suggesting an SSRI effect on β-oxidation and mitochondrial function. Amines-including arginine, proline, and methionine sulfoxide-were upregulated while serotonin and sarcosine were downregulated, suggesting an SSRI effect on urea cycle, one-carbon metabolism, and serotonin uptake. Eighteen lipids within the phosphatidylcholine (PC aa and ae) classes were upregulated. Changes in several lipid and amine levels correlated with changes in 17-item Hamilton Rating Scale for Depression scores (HRSD17). Differences in metabolic profiles at baseline and post-treatment were noted between participants who remitted (HRSD17 ≤ 7) and those who gained no meaningful benefits (<30% reduction in HRSD17). Remitters exhibited (a) higher baseline levels of C3, C5, alpha-aminoadipic acid, sarcosine, and serotonin; and (b) higher week-8 levels of PC aa C34:1, PC aa C34:2, PC aa C36:2, and PC aa C36:4. These findings suggest that mitochondrial energetics-including acylcarnitine metabolism, transport, and its link to β-oxidation-and lipid membrane remodeling may play roles in SSRI treatment response.
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Affiliation(s)
- Siamak MahmoudianDehkordi
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC USA
| | - Ahmed T. Ahmed
- grid.66875.3a0000 0004 0459 167XDepartment of Neurology, Mayo Clinic, Rochester, MN USA
| | - Sudeepa Bhattacharyya
- grid.252381.f0000 0001 2169 5989Department of Biological Sciences and Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR USA
| | - Xianlin Han
- grid.267309.90000 0001 0629 5880University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | | | - Matthias Arnold
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC USA ,grid.4567.00000 0004 0483 2525Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michelle K. Skime
- grid.66875.3a0000 0004 0459 167XDepartment of Psychiatry and Psychology, Mayo Clinic, Rochester, MN USA
| | - Lisa St. John-Williams
- grid.26009.3d0000 0004 1936 7961Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710 USA
| | - M. Arthur Moseley
- grid.26009.3d0000 0004 1936 7961Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710 USA
| | - J. Will Thompson
- grid.26009.3d0000 0004 1936 7961Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710 USA
| | - Gregory Louie
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC USA
| | - Patricio Riva-Posse
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA USA
| | - W. Edward Craighead
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA USA
| | - William McDonald
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA USA
| | - Ranga Krishnan
- grid.262743.60000000107058297Department of Psychiatry, Rush Medical College, Chicago, IL USA
| | - A. John Rush
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Professor Emeritus, Department of Pediatrics, Duke University School of Medicine, Durham, NC USA ,grid.416992.10000 0001 2179 3554Department of Psychiatry, Texas Tech University, Health Sciences Center, Permian Basin, TX USA
| | - Mark A. Frye
- grid.66875.3a0000 0004 0459 167XDepartment of Psychiatry and Psychology, Mayo Clinic, Rochester, MN USA
| | - Boadie W. Dunlop
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA USA
| | - Richard M. Weinshilboum
- grid.66875.3a0000 0004 0459 167XDepartment of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA. .,Department of Medicine, Duke University, Durham, NC, USA. .,Duke Institute of Brain Sciences, Duke University, Durham, NC, USA.
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20
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Berger M, Cooter M, Roesler AS, Chung S, Park J, Modliszewski JL, VanDusen KW, Thompson JW, Moseley A, Devinney MJ, Smani S, Hall A, Cai V, Browndyke JN, Lutz MW, Corcoran DL. APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. J Alzheimers Dis 2020; 79:511-530. [PMID: 33337362 PMCID: PMC7902966 DOI: 10.3233/jad-200747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background: APOE4 has been hypothesized to increase Alzheimer’s disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear. Objective: Characterize cerebrospinal fluid (CSF) proteomic changes related to APOE4 copy number. Methods: We analyzed targeted proteomic data from ADNI CSF samples using a linear regression model adjusting for age, sex, and APOE4 copy number, and additional linear models also adjusting for AD clinical status or for CSF Aβ, tau, or p-tau levels. False discovery rate was used to correct for multiple comparisons correction. Results: Increasing APOE4 copy number was associated with a significant decrease in a CRP peptide level across all five models (q < 0.05 for each), and with significant increases in ALDOA, CH3L1 (YKL-40), and FABPH peptide levels (q < 0.05 for each) except when controlling for AD clinical status or neurodegeneration biomarkers (i.e., CSF tau or p-tau). In all models except the one controlling for CSF Aβ levels, though not statistically significant, there was a consistent inverse direction of association between APOE4 copy number and the levels of all 24 peptides from all 8 different complement proteins measured. The odds of this happening by chance for 24 unrelated peptides would be less than 1 in 16 million. Conclusion: Increasing APOE4 copy number was associated with decreased CSF CRP levels across all models, and increased CSF ALDOA, CH3L1, and FABH levels when controlling for CSF Aβ levels. Increased APOE4 copy number may also be associated with decreased CSF complement pathway protein levels, a hypothesis for investigation in future studies.
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Affiliation(s)
- Miles Berger
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA
| | - Mary Cooter
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Alexander S Roesler
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Stacey Chung
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - John Park
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | | | - Keith W VanDusen
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - J Will Thompson
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Arthur Moseley
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Michael J Devinney
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Shayan Smani
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Ashley Hall
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Victor Cai
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Jeffrey N Browndyke
- Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA.,Department of Psychiatry & Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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21
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Hannigan MM, Hoffman AM, Thompson JW, Zheng T, Nicchitta CV. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. Mol Cell Proteomics 2020; 19:1826-1849. [PMID: 32788342 DOI: 10.1074/mcp.ra120.002228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins operate in concert with membrane-associated ribosomes to facilitate ER-localized translation. Little is known, however, regarding the spatial organization of ER-localized translation. This question is of growing significance as it is now known that ER-bound ribosomes contribute to secretory, integral membrane, and cytosolic protein synthesis alike. To explore this question, we utilized quantitative proximity proteomics to identify neighboring protein networks for the candidate ribosome interactors SEC61β (subunit of the protein translocase), RPN1 (oligosaccharyltransferase subunit), SEC62 (translocation integral membrane protein), and LRRC59 (ribosome binding integral membrane protein). Biotin labeling time course studies of the four BioID reporters revealed distinct labeling patterns that intensified but only modestly diversified as a function of labeling time, suggesting that the ER membrane is organized into discrete protein interaction domains. Whereas SEC61β and RPN1 reporters identified translocon-associated networks, SEC62 and LRRC59 reporters revealed divergent protein interactomes. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, with the latter likely representing proximity to an ER luminal chaperone reflux pathway. In contrast, the LRRC59 interactome is highly enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins, uncovering a functional link between LRRC59 and mRNA translation regulation. Importantly, analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Moreover, [35S]-methionine incorporation assays revealed that siRNA silencing of LRRC59 expression reduced steady state translation levels on the ER by ca. 50%, and also impacted steady state translation levels in the cytosol compartment. Collectively, these data reveal a functional domain organization for the ER and identify a key role for LRRC59 in the organization and regulation of local translation.
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Affiliation(s)
- Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Duke Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.
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22
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Friede KA, Infeld MM, Tan RS, Knickerbocker HJ, Myers RA, Dubois LG, Thompson JW, Kaddurah‐Daouk R, Ginsburg GS, Ortel TL, Voora D. Influence of Sex on Platelet Reactivity in Response to Aspirin. J Am Heart Assoc 2020; 9:e014726. [PMID: 32654613 PMCID: PMC7660714 DOI: 10.1161/jaha.119.014726] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 05/06/2020] [Indexed: 01/29/2023]
Abstract
Background There are sex differences in the efficacy and safety of aspirin for the prevention of myocardial infarction and stroke. Whether this is explained by underlying differences in platelet reactivity and aspirin response remains poorly understood. Methods and Results Healthy volunteers (n=378 208 women) and patients with coronary artery disease or coronary artery disease risk factors (n=217 112 women) took aspirin for 4 weeks. Light transmittance aggregometry using platelet-rich plasma was used to measure platelet reactivity in response to epinephrine, collagen, and ADP at baseline, 3 hours after the first aspirin dose, and after 4 weeks of daily aspirin therapy. A subset of patients underwent pharmacokinetic and pharmacodynamic assessment with levels of salicylate and cyclooxygenase-1-derived prostaglandin metabolites and light transmittance aggregometry in response to arachidonic acid and after ex vivo exposure to aspirin. At baseline, women had increased platelet aggregation in response to ADP and collagen. Innate platelet response to aspirin, assessed with ex vivo aspirin exposure of baseline platelets, did not differ by sex. Three hours after the first oral aspirin dose, platelet aggregation was inhibited in women to a greater degree in response to epinephrine and to a lesser degree with collagen. After 4 weeks of daily therapy, despite higher salicylate concentrations and greater cyclooxygenase-1 inhibition, women exhibited an attenuation of platelet inhibition in response to epinephrine and ADP. Conclusions We observed agonist-dependent sex differences in platelet responses to aspirin. Despite higher cyclooxygenase-1 inhibition, daily aspirin exposure resulted in a paradoxical attenuation of platelet inhibition in response to epinephrine and ADP over time in women but not in men.
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Affiliation(s)
- Kevin A. Friede
- Division of CardiologyDuke UniversityDurhamNC
- Center for Applied Genomics & Precision MedicineDuke UniversityDurhamNC
| | - Margaret M. Infeld
- Division of CardiologyLarner College of Medicine at the University of VermontBurlingtonVT
| | - Ru San Tan
- Department of CardiologyNational Heart CentreSingapore
| | | | - Rachel A. Myers
- Center for Applied Genomics & Precision MedicineDuke UniversityDurhamNC
| | - Laura G. Dubois
- Center for Genomic and Computational BiologyDuke UniversityDurhamNC
| | - J. Will Thompson
- Center for Genomic and Computational BiologyDuke UniversityDurhamNC
| | | | - Geoffrey S. Ginsburg
- Division of CardiologyDuke UniversityDurhamNC
- Center for Applied Genomics & Precision MedicineDuke UniversityDurhamNC
| | | | - Deepak Voora
- Division of CardiologyDuke UniversityDurhamNC
- Center for Applied Genomics & Precision MedicineDuke UniversityDurhamNC
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23
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Harreld JH, Kaufman RA, Kang G, Maron G, Mitchell W, Thompson JW, Srinivasan A. Utility of Pre-Hematopoietic Cell Transplantation Sinus CT Screening in Children and Adolescents. AJNR Am J Neuroradiol 2020; 41:911-916. [PMID: 32273266 DOI: 10.3174/ajnr.a6509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/03/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND PURPOSE The clinical benefit of pre-hematopoietic cell transplantation sinus CT screening remains uncertain, while the risks of CT radiation and anesthesia are increasingly evident. We sought to re-assess the impact of screening sinus CT on pretransplantation patient management and prediction of posttransplantation invasive fungal rhinosinusitis. MATERIALS AND METHODS Pretransplantation noncontrast screening sinus CTs for 100 consecutive patients (mean age, 11.9 ± 5.5 years) were graded for mucosal thickening (Lund-Mackay score) and for signs of noninvasive or invasive fungal rhinosinusitis (sinus calcification, hyperattenuation, bone destruction, extrasinus inflammation, and nasal mucosal ulceration). Posttransplantation sinus CTs performed for sinus-related symptoms were similarly graded. Associations of Lund-Mackay scores, clinical assessments, changes in pretransplantation clinical management (additional antibiotic or fungal therapy, sinonasal surgery, delayed transplantation), and subsequent development of sinus-related symptoms or invasive fungal rhinosinusitis were tested (exact Wilcoxon rank sums, Fisher exact test, significance P < .05). RESULTS Mean pretransplantation screening Lund-Mackay scores (n = 100) were greater in patients with clinical symptoms (8.07 ± 6.00 versus 2.48 ± 3.51, P < .001) but were not associated with pretransplantation management changes and did not predict posttransplantation sinus symptoms (n = 21, P = .47) or invasive fungal rhinosinusitis symptoms (n = 2, P = .59). CONCLUSIONS Pre-hematopoietic cell transplantation sinus CT does not meaningfully contribute to pretransplantation patient management or prediction of posttransplantation sinus disease, including invasive fungal rhinosinusitis, in children. The risks associated with CT radiation and possible anesthesia are not warranted in this setting.
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Affiliation(s)
- J H Harreld
- From the Departments of Diagnostic Imaging (J.H.H., R.A.K.),
| | - R A Kaufman
- From the Departments of Diagnostic Imaging (J.H.H., R.A.K.)
| | | | | | - W Mitchell
- Bone Marrow Transplantation and Cellular Therapy (W.M., A.S.), and
| | - J W Thompson
- Surgery (J.W.T.), St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Otolaryngology (J.W.T.), University of Tennessee Health Sciences Center, Memphis, Tennessee
| | - A Srinivasan
- Bone Marrow Transplantation and Cellular Therapy (W.M., A.S.), and
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24
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Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, Ky K, Kapahi P, Sharma V, MacCoss MJ, Moseley MA, Colton CA, MacLean BX, Schilling B, Thompson JW. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. J Proteome Res 2020; 19:1447-1458. [PMID: 31984744 DOI: 10.1021/acs.jproteome.9b00640] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [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: 01/14/2023]
Abstract
Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method development and data processing with a 10 year history supporting six major instrument vendors. Designed initially for proteomics analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring, high-resolution mass spectrometry, and calibrated quantification. This fundamental expansion of Skyline from a peptide-sequence-centric tool to a molecule-centric tool makes it agnostic to the source of the molecule while retaining Skyline features critical for workflows in both peptide and more general biomolecular research. The data visualization and interrogation features already available in Skyline, such as peak picking, chromatographic alignment, and transition selection, have been adapted to support small molecule data, including metabolomics. Herein, we explain the conceptual workflow for small molecule analysis using Skyline, demonstrate Skyline performance benchmarked against a comparable instrument vendor software tool, and present additional real-world applications. Further, we include step-by-step instructions on using Skyline for small molecule quantitative method development and data analysis on data acquired with a variety of mass spectrometers from multiple instrument vendors.
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Affiliation(s)
- Kendra J Adams
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States.,Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - Brian Pratt
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Neelanjan Bose
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Laura G Dubois
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Kevin M Perrott
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Karina Ky
- University of California San Francisco, San Francisco, California 94143, United States
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Carol A Colton
- Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States.,Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
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25
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Zhao N, Ren Y, Yamazaki Y, Qiao W, Li F, Felton LM, Mahmoudiandehkordi S, Kueider-Paisley A, Sonoustoun B, Arnold M, Shue F, Zheng J, Attrebi ON, Martens YA, Li Z, Bastea L, Meneses AD, Chen K, Thompson JW, St John-Williams L, Tachibana M, Aikawa T, Oue H, Job L, Yamazaki A, Liu CC, Storz P, Asmann YW, Ertekin-Taner N, Kanekiyo T, Kaddurah-Daouk R, Bu G. Alzheimer's Risk Factors Age, APOE Genotype, and Sex Drive Distinct Molecular Pathways. Neuron 2020; 106:727-742.e6. [PMID: 32199103 DOI: 10.1016/j.neuron.2020.02.034] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/26/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Evidence suggests interplay among the three major risk factors for Alzheimer's disease (AD): age, APOE genotype, and sex. Here, we present comprehensive datasets and analyses of brain transcriptomes and blood metabolomes from human apoE2-, apoE3-, and apoE4-targeted replacement mice across young, middle, and old ages with both sexes. We found that age had the greatest impact on brain transcriptomes highlighted by an immune module led by Trem2 and Tyrobp, whereas APOE4 was associated with upregulation of multiple Serpina3 genes. Importantly, these networks and gene expression changes were mostly conserved in human brains. Finally, we observed a significant interaction between age, APOE genotype, and sex on unfolded protein response pathway. In the periphery, APOE2 drove distinct blood metabolome profile highlighted by the upregulation of lipid metabolites. Our work identifies unique and interactive molecular pathways underlying AD risk factors providing valuable resources for discovery and validation research in model systems and humans.
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Affiliation(s)
- Na Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wenhui Qiao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Fuyao Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Lindsey M Felton
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Siamak Mahmoudiandehkordi
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27708, USA
| | - Alexandra Kueider-Paisley
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27708, USA
| | | | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27708, USA; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria 85764, Germany
| | - Francis Shue
- Neuroscience Graduate Program, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jiaying Zheng
- Neuroscience Graduate Program, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Olivia N Attrebi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Zonghua Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Ligia Bastea
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Axel D Meneses
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Kai Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27701, USA
| | - Lisa St John-Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Masaya Tachibana
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Tomonori Aikawa
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Hiroshi Oue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Lucy Job
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Akari Yamazaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27708, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neuroscience Graduate Program, Mayo Clinic, Jacksonville, FL 32224, USA.
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Ahmed AT, MahmoudianDehkordi S, Bhattacharyya S, Arnold M, Liu D, Neavin D, Moseley MA, Thompson JW, Williams LSJ, Louie G, Skime MK, Wang L, Riva-Posse P, McDonald W, Bobo WV, Craighead WE, Krishnan R, Weinshilboum RM, Dunlop BW, Millington DS, Rush AJ, Frye MA, Kaddurah-Daouk R. Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypes. J Affect Disord 2020; 264:90-97. [PMID: 32056779 PMCID: PMC7024064 DOI: 10.1016/j.jad.2019.11.122] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/17/2019] [Accepted: 11/29/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Acylcarnitines have important functions in mitochondrial energetics and β-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profiles can help biochemically distinguish the three phenotypic subtypes of major depressive disorder (MDD): core depression (CD+), anxious depression (ANX+), and neurovegetative symptoms of melancholia (NVSM+). METHODS Depressed outpatients (n = 240) from the Mayo Clinic Pharmacogenomics Research Network were treated with citalopram or escitalopram for eight weeks. Plasma samples collected at baseline and after eight weeks of treatment with citalopram or escitalopram were profiled for short-, medium- and long-chain acylcarnitine levels using AbsoluteIDQ®p180-Kit and LC-MS. Linear mixed effects models were used to examine whether acylcarnitine levels discriminated the clinical phenotypes at baseline or eight weeks post-treatment, and whether temporal changes in acylcarnitine profiles differed between groups. RESULTS Compared to ANX+, CD+ and NVSM+ had significantly lower concentrations of short- and long-chain acylcarnitines at both baseline and week 8. In NVSM+, the medium- and long-chain acylcarnitines were also significantly lower in NVSM+ compared to ANX+. Short-chain acylcarnitine levels increased significantly from baseline to week 8 in CD+ and ANX+, whereas medium- and long-chain acylcarnitines significantly decreased in CD+ and NVSM+. CONCLUSIONS In depressed patients treated with SSRIs, β-oxidation and mitochondrial energetics as evaluated by levels and changes in acylcarnitines may provide the biochemical basis of the clinical heterogeneity of MDD, especially when combined with clinical characteristics.
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Affiliation(s)
- Ahmed T. Ahmed
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Siamak MahmoudianDehkordi
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States; Department of Medicine, Duke University, Durham, NC, United States; Duke Institute of Brain Sciences, Duke University, Durham, NC, United States.
| | - Sudeepa Bhattacharyya
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Duan Liu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States.
| | - Drew Neavin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States.
| | - M. Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - J. Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - Lisa St John Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, United States.
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States.
| | - Michelle K. Skime
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States.
| | - Patricio Riva-Posse
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.
| | - William McDonald
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - William V. Bobo
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - W. Edward Craighead
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - Ranga Krishnan
- Department of Psychiatry, Rush Medical College, Chicago, IL, United States.
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - David S. Millington
- Professor Emeritus, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - A. John Rush
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC.,Department of Psychiatry, Texas Tech University, Health Sciences Center, Permian Basin, TX, USA,Professor Emeritus, Duke-National University of Singapore, Singapore
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | | | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States; Department of Medicine, Duke University, Durham, NC, United States; Duke Institute of Brain Sciences, Duke University, Durham, NC, United States.
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Shuford CM, Johnson JS, Thompson JW, Holland PL, Hoofnagle AN, Grant RP. More sensitivity is always better: Measuring sub-clinical levels of serum thyroglobulin on a µLC–MS/MS system. Clinical Mass Spectrometry 2020; 15:29-35. [DOI: 10.1016/j.clinms.2020.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 10/25/2022]
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28
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Thompson JW, Adams KJ, Adamski J, Asad Y, Borts D, Bowden JA, Byram G, Dang V, Dunn WB, Fernandez F, Fiehn O, Gaul DA, Hühmer AFR, Kalli A, Koal T, Koeniger S, Mandal R, Meier F, Naser FJ, O’Neil D, Pal A, Patti GJ, Pham-Tuan H, Prehn C, Raynaud FI, Shen T, Southam AD, St. John-Williams L, Sulek K, Vasilopoulou CG, Viant M, Winder CL, Wishart D, Zhang L, Zheng J, Moseley MA. International Ring Trial of a High Resolution Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis. Anal Chem 2019; 91:14407-14416. [PMID: 31638379 PMCID: PMC7310668 DOI: 10.1021/acs.analchem.9b02908] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A challenge facing metabolomics in the analysis of large human cohorts is the cross-laboratory comparability of quantitative metabolomics measurements. In this study, 14 laboratories analyzed various blood specimens using a common experimental protocol provided with the Biocrates AbsoluteIDQ p400HR kit, to quantify up to 408 metabolites. The specimens included human plasma and serum from male and female donors, mouse and rat plasma, as well as NIST SRM 1950 reference plasma. The metabolite classes covered range from polar (e.g., amino acids and biogenic amines) to nonpolar (e.g., diacyl- and triacyl-glycerols), and they span 11 common metabolite classes. The manuscript describes a strict system suitability testing (SST) criteria used to evaluate each laboratory's readiness to perform the assay, and provides the SST Skyline documents for public dissemination. The study found approximately 250 metabolites were routinely quantified in the sample types tested, using Orbitrap instruments. Interlaboratory variance for the NIST SRM-1950 has a median of 10% for amino acids, 24% for biogenic amines, 38% for acylcarnitines, 25% for glycerolipids, 23% for glycerophospholipids, 16% for cholesteryl esters, 15% for sphingolipids, and 9% for hexoses. Comparing to consensus values for NIST SRM-1950, nearly 80% of comparable analytes demonstrated bias of <50% from the reference value. The findings of this study result in recommendations of best practices for system suitability, quality control, and calibration. We demonstrate that with appropriate controls, high-resolution metabolomics can provide accurate results with good precision across laboratories, and the p400HR therefore is a reliable approach for generating consistent and comparable metabolomics data.
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Affiliation(s)
- J. Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
- Department of Pharmacology and Cancer Biology, Duke School of Medicine, Durham, NC
| | - Kendra J. Adams
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yasmin Asad
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - David Borts
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011
- Thermo Fisher Scientific, San Jose, CA
| | - John A. Bowden
- National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, 1333 Center Road, University of Florida, Gainesville, Florida 32610, United States
| | - Gregory Byram
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | - Viet Dang
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011
| | | | - Facundo Fernandez
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | - Oliver Fiehn
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | | | | | | | | | - Rupasri Mandal
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Florian Meier
- Max Planck Institute of Biochemistry, Munich, Germany
| | - Fuad J. Naser
- Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA
| | - Donna O’Neil
- University of Birmingham and Phenome Centre Birmingham, UK
| | - Akos Pal
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - Gary J. Patti
- Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA
| | | | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florence I. Raynaud
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - Tong Shen
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | | | - Lisa St. John-Williams
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | | | - Mark Viant
- University of Birmingham and Phenome Centre Birmingham, UK
| | | | - David Wishart
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Lun Zhang
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Jiamin Zheng
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - M. Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
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Harrison A, Hardison RL, Wallace RM, Fitch J, Heimlich DR, Bryan MO, Dubois L, John-Williams LS, Sebra RP, White P, Moseley MA, Thompson JW, Justice SS, Mason KM. Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae. NPJ Biofilms Microbiomes 2019; 5:33. [PMID: 31700653 PMCID: PMC6831627 DOI: 10.1038/s41522-019-0105-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/03/2019] [Indexed: 01/14/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHI) is a human-restricted pathogen with an essential requirement for heme-iron acquisition. We previously demonstrated that microevolution of NTHI promotes stationary phase survival in response to transient heme-iron restriction. In this study, we examine the metabolic contributions to biofilm formation using this evolved NTHI strain, RM33. Quantitative analyses identified 29 proteins, 55 transcripts, and 31 metabolites that significantly changed within in vitro biofilms formed by RM33. The synthesis of all enzymes within the tryptophan and glycogen pathways was significantly increased in biofilms formed by RM33 compared with the parental strain. In addition, increases were observed in metabolite transport, adhesin production, and DNA metabolism. Furthermore, we observed pyruvate as a pivotal point in the metabolic pathways associated with changes in cAMP phosphodiesterase activity during biofilm formation. Taken together, changes in central metabolism combined with increased stores of nutrients may serve to counterbalance nutrient sequestration.
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Affiliation(s)
- Alistair Harrison
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
| | - Rachael L. Hardison
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
| | - Rachel M. Wallace
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
| | - James Fitch
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Steve and Cindy Rasmussen Institute for Genomic Medicine, 575 Children’s Crossroad, Columbus, OH 43215 USA
| | - Derek R. Heimlich
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
| | - Meghan O’ Bryan
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
| | - Laura Dubois
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, 701 West Main Street, Durham, NC 27701 USA
| | - Lisa St. John-Williams
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, 701 West Main Street, Durham, NC 27701 USA
| | - Robert P. Sebra
- Icahn School of Medicine at Mount Sinai, Icahn Institute and Department of Genetics & Genomic Sciences, 1 Gustave L. Levy Place, New York, NY 10029 USA
| | - Peter White
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Steve and Cindy Rasmussen Institute for Genomic Medicine, 575 Children’s Crossroad, Columbus, OH 43215 USA
| | - M. Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, 701 West Main Street, Durham, NC 27701 USA
| | - J. Will Thompson
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, 701 West Main Street, Durham, NC 27701 USA
| | - Sheryl S. Justice
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
- Infectious Diseases Institute, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH 43205 USA
| | - Kevin M. Mason
- The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Center for Microbial Pathogenesis, 700 Children’s Drive, Columbus, OH 43205 USA
- Infectious Diseases Institute, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH 43205 USA
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30
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St John-Williams L, Mahmoudiandehkordi S, Arnold M, Massaro T, Blach C, Kastenmüller G, Louie G, Kueider-Paisley A, Han X, Baillie R, Motsinger-Reif AA, Rotroff D, Nho K, Saykin AJ, Risacher SL, Koal T, Moseley MA, Tenenbaum JD, Thompson JW, Kaddurah-Daouk R. Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts. Sci Data 2019; 6:212. [PMID: 31624257 PMCID: PMC6797798 DOI: 10.1038/s41597-019-0181-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/10/2019] [Indexed: 12/28/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. The mechanism of disease development and progression is not well understood, but increasing evidence suggests multifactorial etiology, with a number of genetic, environmental, and aging-related factors. There is a growing body of evidence that metabolic defects may contribute to this complex disease. To interrogate the relationship between system level metabolites and disease susceptibility and progression, the AD Metabolomics Consortium (ADMC) in partnership with AD Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for patients in the ADNI1 cohort. We used the Biocrates Bile Acids platform to evaluate the association of metabolic levels with disease risk and progression. We detail the quantitative metabolomics data generated on the baseline samples from ADNI1 and ADNIGO/2 (370 cognitively normal, 887 mild cognitive impairment, and 305 AD). Similar to our previous reports on ADNI1, we present the tools for data quality control and initial analysis. This data descriptor represents the third in a series of comprehensive metabolomics datasets from the ADMC on the ADNI.
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Affiliation(s)
- Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, Duke University, Durham, NC, USA
| | | | - Matthias Arnold
- Department of Psychiatry & Behavioral Sciences, Duke University, Durham, NC, USA
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tyler Massaro
- Duke Clinical Research Institute, Duke University, Durham, NC, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Gregory Louie
- Department of Psychiatry & Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | | | - Alison A Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daniel Rotroff
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, Duke University, Durham, NC, USA
| | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, Duke University, Durham, NC, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry & Behavioral Sciences, Duke University, Durham, NC, USA.
- Duke Institute for Brain Sciences, Duke University, Durham, NC, USA.
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31
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Antonia AL, Gibbs KD, Trahair ED, Pittman KJ, Martin AT, Schott BH, Smith JS, Rajagopal S, Thompson JW, Reinhardt RL, Ko DC. Pathogen Evasion of Chemokine Response Through Suppression of CXCL10. Front Cell Infect Microbiol 2019; 9:280. [PMID: 31440475 PMCID: PMC6693555 DOI: 10.3389/fcimb.2019.00280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 01/10/2023] Open
Abstract
Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on an immune response with well-regulated cytokine signaling. Here we describe a pathogen-mediated mechanism of evading CXCL10, a chemokine with diverse antimicrobial functions, including T cell recruitment. Infection with L. major in a human monocyte cell line induced robust CXCL10 transcription without increasing extracellular CXCL10 protein concentrations. We found that this transcriptionally independent suppression of CXCL10 is mediated by the virulence factor and protease, glycoprotein-63 (gp63). Specifically, GP63 cleaves CXCL10 after amino acid A81 at the base of a C-terminal alpha-helix. Cytokine cleavage by GP63 demonstrated specificity, as GP63 cleaved CXCL10 and its homologs, which all bind the CXCR3 receptor, but not distantly related chemokines, such as CXCL8 and CCL22. Further characterization demonstrated that CXCL10 cleavage activity by GP63 was produced by both extracellular promastigotes and intracellular amastigotes. Crucially, CXCL10 cleavage impaired T cell chemotaxis in vitro, indicating that cleaved CXCL10 cannot signal through CXCR3. Ultimately, we propose CXCL10 suppression is a convergent mechanism of immune evasion, as Salmonella enterica and Chlamydia trachomatis also suppress CXCL10. This commonality suggests that counteracting CXCL10 suppression may provide a generalizable therapeutic strategy against intracellular pathogens. Importance Leishmaniasis, an infectious disease that annually affects over one million people, is caused by intracellular parasites that have evolved to evade the host's attempts to eliminate the parasite. Cutaneous leishmaniasis results in disfiguring skin lesions if the host immune system does not appropriately respond to infection. A family of molecules called chemokines coordinate recruitment of the immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that Leishmania (L.) spp. employ to suppress host chemokines: a Leishmania-encoded protease cleaves chemokines known to recruit T cells that fight off infection. We observe that other common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, reduce levels of the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival.
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Affiliation(s)
- Alejandro L. Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Kyle D. Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Esme D. Trahair
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Kelly J. Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Amelia T. Martin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Benjamin H. Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Jeffrey S. Smith
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC, United States
| | - Sudarshan Rajagopal
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC, United States
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States
| | - J. Will Thompson
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, School of Medicine, Duke University, Durham, NC, United States
| | - Richard Lee Reinhardt
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States
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32
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Schaller TH, Foster MW, Thompson JW, Spasojevic I, Normantaite D, Moseley MA, Sanchez-Perez L, Sampson JH. Pharmacokinetic Analysis of a Novel Human EGFRvIII:CD3 Bispecific Antibody in Plasma and Whole Blood Using a High-Resolution Targeted Mass Spectrometry Approach. J Proteome Res 2019; 18:3032-3041. [PMID: 31267741 DOI: 10.1021/acs.jproteome.9b00145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 01/15/2023]
Abstract
Bispecific single chain antibody fragments (bi-scFv) represent an emerging class of biotherapeutics. We recently developed a fully human bi-scFv (EGFRvIII:CD3 bi-scFv) with the goal of redirecting CD3-expressing T cells to recognize and destroy malignant, EGFRvIII-expressing glioma. In mice, we showed that EGFRvIII:CD3 bi-scFv effectively treats orthotopic patient-derived malignant glioma and syngeneic glioblastoma. Here, we developed a targeted assay for pharmacokinetic (PK) analysis of EGFRvIII:CD3 bi-scFv, a necessary step in the drug development process. Using microflow liquid chromatography coupled to a high resolution parallel reaction monitoring mass spectrometry, and data analysis in Skyline, we developed a bottom-up proteomic assay for quantification of EGFRvIII:CD3 bi-scFv in both plasma and whole blood. Importantly, a protein calibrator, along with stable isotope-labeled EGFRvIII:CD3 bi-scFv protein, were used for absolute quantification. A PK analysis in a CD3 humanized mouse revealed that EGFRvIII:CD3 bi-scFv in plasma and whole blood has an initial half-life of ∼8 min and a terminal half-life of ∼2.5 h. Our results establish a sensitive, high-throughput assay for direct quantification of EGFRvIII:CD3 bi-scFv without the need for immunoaffinity enrichment. Moreover, these pharmacokinetic parameters will guide drug optimization and dosing regimens in future IND-enabling and phase I studies of EGFRvIII:CD3 bi-scFv.
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Affiliation(s)
- Teilo H Schaller
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States.,Department of Pathology , Duke University Medical Center , Durham , North Carolina , United States
| | - Matthew W Foster
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - Ivan Spasojevic
- Duke Cancer Institute PK/PD Core Laboratory , Durham , North Carolina , United States.,Department of Medicine , Duke University School of Medicine , Durham , North Carolina , United States
| | - Deimante Normantaite
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - Luis Sanchez-Perez
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States
| | - John H Sampson
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States.,Department of Pathology , Duke University Medical Center , Durham , North Carolina , United States
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Davidson PL, Thompson JW, Foster MW, Moseley MA, Byrne M, Wray GA. A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins. Evol Dev 2019; 21:188-204. [PMID: 31102332 PMCID: PMC7232848 DOI: 10.1111/ede.12289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 09/29/2018] [Revised: 12/20/2018] [Accepted: 02/27/2019] [Indexed: 01/20/2023]
Abstract
A dramatic life history switch that has evolved numerous times in marine invertebrates is the transition from planktotrophic (feeding) to lecithotrophic (nonfeeding) larval development-an evolutionary tradeoff with many important developmental and ecological consequences. To attain a more comprehensive understanding of the molecular basis for this switch, we performed untargeted lipidomic and proteomic liquid chromatography-tandem mass spectrometry on eggs and larvae from three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and the distantly related planktotroph Lytechinus variegatus. We identify numerous molecular-level changes possibly associated with the evolution of lecithotrophy in H. erythrogramma. We find the massive lipid stores of H. erythrogramma eggs are largely composed of low-density, diacylglycerol ether lipids that, contrary to expectations, appear to support postmetamorphic development and survivorship. Rapid premetamorphic development in this species may instead be powered by upregulated carbohydrate metabolism or triacylglycerol metabolism. We also find proteins involved in oxidative stress regulation are upregulated in H. erythrogramma eggs, and apoB-like lipid transfer proteins may be important for echinoid oogenic nutrient provisioning. These results demonstrate how mass spectrometry can enrich our understanding of life history evolution and organismal diversity by identifying specific molecules associated with distinct life history strategies and prompt new hypotheses about how and why these adaptations evolve.
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Affiliation(s)
| | - J. Will Thompson
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Matthew W. Foster
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - M. Arthur Moseley
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Maria Byrne
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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Brooks ER, Lin DC, Langman CB, Thompson JW, St John-Williams L, Furth SL, Warady B, Haymond S. Metabolomic Patterns in Adolescents With Mild to Moderate CKD. Kidney Int Rep 2019; 4:720-723. [PMID: 31080927 PMCID: PMC6506724 DOI: 10.1016/j.ekir.2019.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/26/2018] [Accepted: 01/14/2019] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ellen R Brooks
- Division of Kidney Diseases, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - David C Lin
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pathology, Northwestern University Feinberg School of Medicine Chicago, Illinois, USA
| | - Craig B Langman
- Division of Kidney Diseases, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Susan L Furth
- Division of Nephrology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Bradley Warady
- Division of Pediatric Nephrology, The Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Shannon Haymond
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pathology, Northwestern University Feinberg School of Medicine Chicago, Illinois, USA
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West EE, Freeley S, Kaminski MM, Veenbergen S, Lee DY, St. John-Williams L, Thompson JW, Green DR, Scholl-Buergi S, Karall D, Huemer M, Kemper C. You are what you eat: CD46 regulated amino acid usage dictates T cell function. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.56.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Engagement of the complement receptor CD46 on T cells drives Th1 responses and upregulates nutrient and amino acid channels, such as GLUT1 and LAT1. We found that CD46 stimulation upregulates both the arginine transporter SLC7A1 (CAT-1) on human CD4 T cells and, unexpectedly, Arginase 1 expression in these cells, indicating that CD46 may regulate arginine metabolism in T cells. While Arginase 1 has been well characterized in macrophages where it is associated with the IL-10 secreting M2 type, its function in T cells has not been described. During contraction human Th1 cells switch from IFN-γ to IL-10 production and to a self-regulatory phenotype, thus we assessed the role of Arginase 1 in Th1 induction and/or contraction. Surprisingly, CD4 T cells isolated from four patients with rare Arginase 1 deficiency initially mount Th1 responses but display significantly increased IL-10 switching with earlier cellular collapse when compared to healthy control cells. Importantly, although T cells from patients with Arginase 1 deficiency have increased arginine levels, as expected, they produce normal levels of polyamines and NO. Metabolic profiling of the patients’ cells demonstrates that they shunt into a compensatory ‘glutamine usage pathway’ for their critical ornithine and polyamine generation. Analysis of changes in glutamine metabolites and their corresponding downstream pathways, along with in vivo influenza infections of Arg1fl/fl CD4-cre+ mice validate and further define the in vivo role of this novel T cell modulating pathway. Overall, these data demonstrate an unexpected intrinsic role for Arginase 1 and unveil an important compensatory mechanism used to maintain protective Th1 function in the absence of normal arginine catabolism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Claudia Kemper
- 1National Institutes of Health/NHLBI
- 2Kings College London, United Kingdom
- 8University of Lubeck, Germany
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Fisher-Wellman KH, Draper JA, Davidson MT, Williams AS, Narowski TM, Slentz DH, Ilkayeva OR, Stevens RD, Wagner GR, Najjar R, Hirschey MD, Thompson JW, Olson DP, Kelly DP, Koves TR, Grimsrud PA, Muoio DM. Respiratory Phenomics across Multiple Models of Protein Hyperacylation in Cardiac Mitochondria Reveals a Marginal Impact on Bioenergetics. Cell Rep 2019; 26:1557-1572.e8. [PMID: 30726738 PMCID: PMC6478502 DOI: 10.1016/j.celrep.2019.01.057] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/02/2018] [Accepted: 01/15/2019] [Indexed: 11/25/2022] Open
Abstract
Acyl CoA metabolites derived from the catabolism of carbon fuels can react with lysine residues of mitochondrial proteins, giving rise to a large family of post-translational modifications (PTMs). Mass spectrometry-based detection of thousands of acyl-PTMs scattered throughout the proteome has established a strong link between mitochondrial hyperacylation and cardiometabolic diseases; however, the functional consequences of these modifications remain uncertain. Here, we use a comprehensive respiratory diagnostics platform to evaluate three disparate models of mitochondrial hyperacylation in the mouse heart caused by genetic deletion of malonyl CoA decarboxylase (MCD), SIRT5 demalonylase and desuccinylase, or SIRT3 deacetylase. In each case, elevated acylation is accompanied by marginal respiratory phenotypes. Of the >60 mitochondrial energy fluxes evaluated, the only outcome consistently observed across models is a ∼15% decrease in ATP synthase activity. In sum, the findings suggest that the vast majority of mitochondrial acyl PTMs occur as stochastic events that minimally affect mitochondrial bioenergetics.
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Affiliation(s)
- Kelsey H Fisher-Wellman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - James A Draper
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Michael T Davidson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Ashley S Williams
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Tara M Narowski
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorothy H Slentz
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Robert D Stevens
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Gregory R Wagner
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Rami Najjar
- Cell Signaling Technologies, Danvers, MA 01923, USA
| | - Mathew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - David P Olson
- Department of Pediatrics, Division of Pediatric Endocrinology, Michigan Medicine, Ann Arbor, MI 48109, USA
| | - Daniel P Kelly
- Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Timothy R Koves
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA.
| | - Deborah M Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA.
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MahmoudianDehkordi S, Arnold M, Nho K, Ahmad S, Jia W, Xie G, Louie G, Kueider-Paisley A, Moseley MA, Thompson JW, St John Williams L, Tenenbaum JD, Blach C, Baillie R, Han X, Bhattacharyya S, Toledo JB, Schafferer S, Klein S, Koal T, Risacher SL, Kling MA, Motsinger-Reif A, Rotroff DM, Jack J, Hankemeier T, Bennett DA, De Jager PL, Trojanowski JQ, Shaw LM, Weiner MW, Doraiswamy PM, van Duijn CM, Saykin AJ, Kastenmüller G, Kaddurah-Daouk R. Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome. Alzheimers Dement 2019; 15:76-92. [PMID: 30337151 PMCID: PMC6487485 DOI: 10.1016/j.jalz.2018.07.217] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [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: 03/20/2018] [Revised: 07/01/2018] [Accepted: 07/31/2018] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Increasing evidence suggests a role for the gut microbiome in central nervous system disorders and a specific role for the gut-brain axis in neurodegeneration. Bile acids (BAs), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer's disease (AD). METHODS Serum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1464 subjects including 370 cognitively normal older adults, 284 with early mild cognitive impairment, 505 with late mild cognitive impairment, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for confounders and multiple testing. RESULTS In AD compared to cognitively normal older adults, we observed significantly lower serum concentrations of a primary BA (cholic acid [CA]) and increased levels of the bacterially produced, secondary BA, deoxycholic acid, and its glycine and taurine conjugated forms. An increased ratio of deoxycholic acid:CA, which reflects 7α-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response-related genes implicated in AD showed associations with BA profiles. DISCUSSION We report for the first time an association between altered BA profile, genetic variants implicated in AD, and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut-liver-brain axis in the pathogenesis of AD.
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Affiliation(s)
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, HI, USA; Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Guoxiang Xie
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | | | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - Lisa St John Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Durham, NC, USA
| | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | | | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jon B Toledo
- Department of Neurology, Houston Methodist Hospital, Houston, TX, USA
| | | | | | | | - Shannon L Risacher
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mitchel Allan Kling
- Behavioral Health Service, Crescenz VA Medical Center and Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - John Jack
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, The Netherlands
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Columbia University College of Physicians and Surgeons Department of Neurology, Center for Translational & Computational Neuroimmunology, New York, NY, USA
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael W Weiner
- Center for Imaging of Neurodegenerative Diseases, Department of Radiology, San Francisco VA Medical Center/University of California San Francisco, San Francisco, CA, USA
| | - P Murali Doraiswamy
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA.
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Hardison RL, Heimlich DR, Harrison A, Beatty WL, Rains S, Moseley MA, Thompson JW, Justice SS, Mason KM. Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development. mSphere 2018; 3:3/5/e00286-18. [PMID: 30209128 PMCID: PMC6135960 DOI: 10.1128/msphere.00286-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nutrient limitation restricts bacterial growth in privileged sites such as the middle ear. Transient heme-iron restriction of nontypeable Haemophilus influenzae (NTHI), the major causative agent of chronic and recurrent otitis media (OM), promotes new and diverse phenotypes that can influence planktonic, biofilm, and intracellular lifestyles of NTHI. However, the bacterial responses to nutrient restriction that impact intracellular fate and survival of NTHI are unknown. In this work, we provide evidence for the role of transient heme-iron restriction in promoting the formation of intracellular bacterial communities (IBCs) of NTHI both in vitro and in vivo in a preclinical model of OM. We show that transient heme-iron restriction of NTHI results in significantly increased invasion and intracellular populations that escape or evade the endolysosomal pathway for increased intracellular survival. In contrast, NTHI continuously exposed to heme-iron traffics through the endolysosomal pathway for degradation. The use of pharmacological inhibitors revealed that prior heme-iron status does not appear to influence NTHI internalization through endocytic pathways. However, inhibition of macropinocytosis altered the intracellular fate of transiently restricted NTHI for degradation in the endolysosomal pathway. Furthermore, prevention of macropinocytosis significantly reduced the number of IBCs in cultured middle ear epithelial cells, providing evidence for the feasibility of this approach to reduce OM persistence. These results reveal that microenvironmental cues can influence the intracellular fate of NTHI, leading to new mechanisms for survival during disease progression.IMPORTANCE Otitis media is the most common bacterial infection in childhood. Current therapies are limited in the prevention of chronic or recurrent otitis media which leads to increased antibiotic exposure and represents a significant socioeconomic burden. In this study, we delineate the effect of nutritional limitation on the intracellular trafficking pathways used by nontypeable Haemophilus influenzae (NTHI). Moreover, transient limitation of heme-iron led to the development of intracellular bacterial communities that are known to contribute to persistence and recurrence in other diseases. New approaches for therapeutic interventions that reduce the production of intracellular bacterial communities and promote trafficking through the endolysosomal pathway were revealed through the use of pharmacological inhibition of macropinocytosis. This work demonstrates the importance of an intracellular niche for NTHI and provides new approaches for intervention for acute, chronic, and recurring episodes of otitis media.
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Affiliation(s)
- Rachael L Hardison
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
- The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Derek R Heimlich
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Alistair Harrison
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Wandy L Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sarah Rains
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Sheryl S Justice
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kevin M Mason
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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Mabe NW, Fox DB, Lupo R, Decker AE, Phelps SN, Thompson JW, Alvarez JV. Epigenetic silencing of tumor suppressor Par-4 promotes chemoresistance in recurrent breast cancer. J Clin Invest 2018; 128:4413-4428. [PMID: 30148456 DOI: 10.1172/jci99481] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/13/2018] [Indexed: 12/12/2022] Open
Abstract
Tumor relapse is the leading cause of death in breast cancer, largely due to the fact that recurrent tumors are frequently resistant to chemotherapy. We previously reported that downregulation of the proapoptotic protein Par-4 promotes tumor recurrence in genetically engineered mouse models of breast cancer recurrence. In the present study, we examined the mechanism and functional significance of Par-4 downregulation in recurrent tumors. We found that epithelial-to-mesenchymal transition (EMT) promotes epigenetic silencing of Par-4 in recurrent tumors. Par-4 silencing proceeded through binding of the EMT transcription factor Twist to the Par-4 promoter, where Twist induced a unique bivalent chromatin domain. This bivalent configuration conferred plasticity at the Par-4 promoter, and Par-4 silencing could be reversed with pharmacologic inhibitors of Ezh2 and HDAC1/2. Using an epigenome editing approach to reexpress Par-4 by specifically reversing the histone modifications found in recurrent tumors, we found that Par-4 reexpression sensitized recurrent tumors to chemotherapy in vitro and in vivo. Upon reexpression, Par-4 bound to the protein phosphatase PP1, caused widespread changes in phosphorylation of cytoskeletal proteins, and cooperated with microtubule-targeting drugs to induce mitotic defects. These results identify Twist-induced epigenetic silencing of Par-4 as a targetable axis that promotes chemoresistance in recurrent breast cancer.
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Affiliation(s)
| | | | - Ryan Lupo
- Department of Pharmacology and Cancer Biology, and
| | - Amy E Decker
- Department of Pharmacology and Cancer Biology, and
| | | | - J Will Thompson
- Department of Pharmacology and Cancer Biology, and.,Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
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Yuan L, Zhai L, Qian L, Huang D, Ding Y, Xiang H, Liu X, Thompson JW, Liu J, He YH, Chen XQ, Hu J, Kong QP, Tan M, Wang XF. Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death. Cell Res 2018; 28:625-643. [PMID: 29808012 DOI: 10.1038/s41422-018-0043-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/19/2018] [Accepted: 04/25/2018] [Indexed: 12/31/2022] Open
Abstract
Cellular senescence is a fundamental cell fate playing a significant role throughout the natural aging process. However, the molecular determinants distinguishing senescence from other cell-cycle arrest states such as quiescence and post-mitotic state, and the specified mechanisms underlying cell-fate decisions towards senescence versus cell death in response to cellular stress stimuli remain less understood. Employing multi-omics approaches, we revealed that switching off the specific mitochondrial processing machinery involving the peptidase IMMP2L serves as the foundation of the senescence program, which was also observed during the mammalian aging process. Mechanistically, we demonstrate that IMMP2L processes and thus activates at least two substrates, mitochondrial metabolic enzyme glycerol-3-phosphate dehydrogenase (GPD2) and cell death regulator apoptosis-inducing factor (AIF). For cells destined to senesce, concerted shutdown of the IMMP2L-GPD2 and IMMP2L-AIF signaling axes collaboratively drives the senescent process by reprogramming mitochondria-associated redox status, phospholipid metabolism and signaling network, and simultaneously blocking cell death under oxidative stress conditions.
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Affiliation(s)
- Lifeng Yuan
- Graduate Program in Molecular Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Linhui Zhai
- Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lili Qian
- Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - De Huang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yi Ding
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Handan Xiang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jing Hu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Minjia Tan
- Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Fan Wang
- Graduate Program in Molecular Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA. .,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA.
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Juvvadi PR, Moseley MA, Hughes CJ, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Geromanos SJ, Wildgoose J, Richardson K, Langridge JI, Vissers JPC, Steinbach WJ. Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs. J Proteome Res 2017; 17:780-793. [PMID: 29251506 DOI: 10.1021/acs.jproteome.7b00499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 12/14/2022]
Abstract
Calcineurin is a critical cell-signaling protein that orchestrates growth, stress response, virulence, and antifungal drug resistance in several fungal pathogens. Blocking calcineurin signaling increases the efficacy of several currently available antifungals and suppresses drug resistance. We demonstrate the application of a novel scanning quadrupole DIA method for the analysis of changes in the proteins coimmunoprecipitated with calcineurin during therapeutic antifungal drug treatments of the deadly human fungal pathogen Aspergillus fumigatus. Our experimental design afforded an assessment of the precision of the method as demonstrated by peptide- and protein-centric analysis from eight replicates of the study pool QC samples. Two distinct classes of clinically relevant antifungal drugs that are guideline recommended for the treatment of invasive "aspergillosis" caused by Aspergillus fumigatus, the azoles (voriconazole) and the echinocandins (caspofungin and micafungin), which specifically target the fungal plasma membrane and the fungal cell wall, respectively, were chosen to distinguish variations occurring in the proteins coimmunoprecipitated with calcineurin. Novel potential interactors were identified in response to the different drug treatments that are indicative of the possible role for calcineurin in regulating these effectors. Notably, treatment with voriconazole showed increased immunoprecipitation of key proteins involved in membrane ergosterol biosynthesis with calcineurin. In contrast, echinocandin (caspofungin or micafungin) treatments caused increased immunoprecipitation of proteins involved in cell-wall biosynthesis and septation. Furthermore, abundant coimmunoprecipitation of ribosomal proteins with calcineurin occurred exclusively in echinocandins treatment, indicating reprogramming of cellular growth mechanisms during different antifungal drug treatments. While variations in the observed calcineurin immunoprecipitated proteins may also be due to changes in their expression levels under different drug treatments, this study suggests an important role for calcineurin-dependent cellular mechanisms in response to antifungal treatment of A. fumigatus that warrants future studies.
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Affiliation(s)
- Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Sarah Lennon
- Waters Corporation , Wilmslow SK9 4AX, United Kingdom
| | - Simon R Perkins
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | | | | | | | | | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center , Durham, North Carolina 27710, United States
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42
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Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Steinbach WJ, Geromanos SJ, Wildgoose J, Langridge JI, Richardson K, Vissers JPC. Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res 2017; 17:770-779. [PMID: 28901143 DOI: 10.1021/acs.jproteome.7b00464] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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: 11/30/2022]
Abstract
A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA method is discussed, and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semiquantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterized human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publicly available data that used similar chromatographic conditions but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with >90% overlap of the detected proteins.
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Affiliation(s)
- M Arthur Moseley
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | - Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Sarah Lennon
- Waters Corporation , Wilmslow SK9 4AX, United Kingdom
| | - Simon R Perkins
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center , Durham, North Carolina 27710, United States
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43
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St John-Williams L, Blach C, Toledo JB, Rotroff DM, Kim S, Klavins K, Baillie R, Han X, Mahmoudiandehkordi S, Jack J, Massaro TJ, Lucas JE, Louie G, Motsinger-Reif AA, Risacher SL, Saykin AJ, Kastenmüller G, Arnold M, Koal T, Moseley MA, Mangravite LM, Peters MA, Tenenbaum JD, Thompson JW, Kaddurah-Daouk R. Targeted metabolomics and medication classification data from participants in the ADNI1 cohort. Sci Data 2017; 4:170140. [PMID: 29039849 PMCID: PMC5644370 DOI: 10.1038/sdata.2017.140] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/08/2017] [Indexed: 02/01/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute to disease pathogenesis. The Alzheimer Disease Metabolomics Consortium (ADMC) in partnership with Alzheimer Disease Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for AD. Using targeted and non- targeted metabolomics and lipidomics platforms we are mapping metabolic pathway and network failures across the trajectory of disease. In this report we present quantitative metabolomics data generated on serum from 199 control, 356 mild cognitive impairment and 175 AD subjects enrolled in ADNI1 using AbsoluteIDQ-p180 platform, along with the pipeline for data preprocessing and medication classification for confound correction. The dataset presented here is the first of eight metabolomics datasets being generated for broad biochemical investigation of the AD metabolome. We expect that these collective metabolomics datasets will provide valuable resources for researchers to identify novel molecular mechanisms contributing to AD pathogenesis and disease phenotypes.
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Affiliation(s)
- Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Jon B Toledo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Neurology, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
| | - Sungeun Kim
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Electrical and Computer Engineering, State University of New York, Oswego, NY 13126, USA
| | | | | | - Xianlin Han
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA
| | - Siamak Mahmoudiandehkordi
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
| | - John Jack
- Department of Electrical and Computer Engineering, State University of New York, Oswego, NY 13126, USA
| | - Tyler J Massaro
- Department of Psychiatry and Behavioral Sciences, and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
| | - Joseph E Lucas
- Duke Social Sciences Research Institute, Duke University, Durham, NC 27708, USA
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany.,German Center for Diabetes Research, Neuherberg D-85764, Germany
| | - Matthias Arnold
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Therese Koal
- BIOCRATES Life Sciences AG, Innsbruck 6020, Austria
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | | | | | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, and the Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
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44
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Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando AM, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyötyläinen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Köfeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson R, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qiu Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, St John-Williams L, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trötzmüller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res 2017; 58:2275-2288. [PMID: 28986437 DOI: 10.1194/jlr.m079012] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.
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Affiliation(s)
- John A Bowden
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Alan Heckert
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Candice Z Ulmer
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Christina M Jones
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Jeremy P Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Linda Ahonen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Yazen Alnouti
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - Aaron M Armando
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Joost Brandsma
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Tomas Cajka
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michelle A Cinel
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Romain A Colas
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Serge Cremers
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Edward A Dennis
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Alexander Fauland
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michael S Gardner
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Katherine H Gotlinger
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Aveline Huipeng Neo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | | | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Hongfeng Jiang
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Houli Jiang
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jiang Jiang
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Maureen Kachman
- Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI
| | | | | | | | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Johan Kolmert
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Grielof Koster
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Michael Leadley
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Karen Lin
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Krishna Rao Maddipati
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
| | - Danielle McDougall
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Renu Nandakumar
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rainey Patterson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Jason S Pierce
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Martin Post
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Anthony D Postle
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Rebecca Pugh
- Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Oswald Quehenberger
- Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Parsram Ramrup
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jon Rees
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Barbara Rembiesa
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Denis Reynaud
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Mary R Roth
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Charles N Serhan
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stephen E Somerville
- Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | | | - Hiroaki Takeda
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Rhishikesh Thakare
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | | | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jacquelyn M Weir
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ruth Welti
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Libin Yao
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xueqing Heather Zhao
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Senlin Zhou
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
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45
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Foster MW, Yang Z, Gooden DM, Thompson JW, Ball CH, Turner ME, Hou Y, Pi J, Moseley MA, Que LG. Correction to “Proteomic Characterization of the Cellular Response to Nitrosative Stress Mediated by S-Nitrosoglutathione Reductase Inhibition”. J Proteome Res 2017. [DOI: 10.1021/acs.jproteome.7b00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kimbung S, Chang CY, Bendahl PO, Dubois L, Thompson JW, McDonnell DP, Borgquist S. Impact of 27-hydroxylase (CYP27A1) and 27-hydroxycholesterol in breast cancer. Endocr Relat Cancer 2017; 24:339-349. [PMID: 28442559 DOI: 10.1530/erc-16-0533] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/08/2022]
Abstract
The impact of systemic 27-hydroxycholesterol (27HC) and intratumoral CYP27A1 expression on pathobiology and clinical response to statins in breast cancer needs clarification. 27HC is an oxysterol produced from cholesterol by the monooxygenase CYP27A1, which regulates intracellular cholesterol homeostasis. 27HC also acts as an endogenous selective estrogen receptor (ER) modulator capable of increasing breast cancer growth and metastasis. 27HC levels can be modulated by statins or direct inhibition of CYP27A1, thereby attenuating its pro-tumorigenic activities. Herein, the effect of statins on serum 27HC and tumor-specific CYP27A1 expression was evaluated in 42 breast cancer patients treated with atorvastatin within a phase II clinical trial. Further, the associations between CYP27A1 expression with other primary tumor pathological features and clinical outcomes were studied in two additional independent cohorts. Statin treatment effectively decreased serum 27HC and deregulated CYP27A1 expression in tumors. However, these changes were not associated with anti-proliferative responses to statin treatment. CYP27A1 was heterogeneously expressed among primary tumors, with high expression significantly associated with high tumor grade, ER negativity and basal-like subtype. High CYP27A1 expression was independently prognostic for longer recurrence-free and overall survival. Importantly, the beneficial effect of high CYP27A1 in ER-positive breast cancer seemed limited to women aged ≤50 years. These results establish a link between CYP27A1 and breast cancer pathobiology and prognosis and propose that the efficacy of statins in reducing serum lipids does not directly translate to anti-proliferative effects in tumors. Changes in other undetermined serum or tumor factors suggestively mediate the anti-proliferative effects of statins in breast cancer.
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Affiliation(s)
- Siker Kimbung
- Division of Oncology and PathologyDepartment of Clinical Sciences, Lund, Lund University, Sweden
| | - Ching-Yi Chang
- Department of Pharmacology and Cancer BiologyDuke University School of Medicine, Durham, NC, USA
| | - Pär-Ola Bendahl
- Division of Oncology and PathologyDepartment of Clinical Sciences, Lund, Lund University, Sweden
| | - Laura Dubois
- Duke Proteomics and Metabolomics ResourceDuke University School of Medicine, Durham, NC, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer BiologyDuke University School of Medicine, Durham, NC, USA
- Duke Proteomics and Metabolomics ResourceDuke University School of Medicine, Durham, NC, USA
| | - Donald P McDonnell
- Department of Pharmacology and Cancer BiologyDuke University School of Medicine, Durham, NC, USA
| | - Signe Borgquist
- Division of Oncology and PathologyDepartment of Clinical Sciences, Lund, Lund University, Sweden
- Clinical Trial UnitClinical Studies Sweden, Forum South, Skåne University Hospital, Lund, Sweden
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Nho K, Dehkordi SM, Motsinger‐Reif A, Baillie RA, Bhattacharyya S, Tenenbaum JD, Thompson JW, St. John Williams L, Moseley MA, Koal T, Saykin AJ, Doraiswamy M, Kaddurah‐Daouk RF. [F2–01–03]: GUT DERIVED BILE ACID METABOLITES CORRELATE WITH STRUCTURAL AND FUNCTIONAL NEUROIMAGING MEASURES IN ALZHEIMER's DISEASE. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.07.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kwangsik Nho
- Indiana Alzheimer Disease CenterIndianapolisINUSA
- Indiana University School of MedicineIndianapolisINUSA
- NC State UniversityRaleighNCUSA
- North Carolina State UniversityRaleighNCUSA
- Rosa & Co. LLCSan CarlosCAUSA
| | | | | | | | | | | | | | | | | | - Therese Koal
- Indiana Alzheimer Disease CenterIndianapolisINUSA
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Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metab 2017; 25:838-855.e15. [PMID: 28380376 PMCID: PMC5444661 DOI: 10.1016/j.cmet.2017.03.003] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 09/26/2016] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
Abstract
Sirtuins are NAD+-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine. The metabolites leading to these post-translational modifications are intermediates in leucine oxidation, and we show a primary role for SIRT4 in controlling this pathway in mice. Furthermore, we find that dysregulated leucine metabolism in SIRT4KO mice leads to elevated basal and stimulated insulin secretion, which progressively develops into glucose intolerance and insulin resistance. These findings identify a robust enzymatic activity for SIRT4, uncover a mechanism controlling branched-chain amino acid flux, and position SIRT4 as a crucial player maintaining insulin secretion and glucose homeostasis during aging.
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Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Kelsey Fisher-Wellman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Darren Stuart
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Brett S Peterson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Jonathan D Douros
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Gregory R Wagner
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Michelle F Green
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - R Michael Sivley
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Robert D Stevens
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John A Capra
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jonathan E Campbell
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Deborah M Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA.
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Alfaqih MA, Nelson ER, Liu W, Safi R, Jasper JS, Macias E, Geradts J, Thompson JW, Dubois LG, Freeman MR, Chang CY, Chi JT, McDonnell DP, Freedland SJ. CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer. Cancer Res 2017; 77:1662-1673. [PMID: 28130224 PMCID: PMC5687884 DOI: 10.1158/0008-5472.can-16-2738] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [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: 10/10/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 11/16/2022]
Abstract
In this study, we used a bioinformatic approach to identify genes whose expression is dysregulated in human prostate cancers. One of the most dramatically downregulated genes identified encodes CYP27A1, an enzyme involved in regulating cellular cholesterol homeostasis. Importantly, lower CYP27A1 transcript levels were associated with shorter disease-free survival and higher tumor grade. Loss of CYP27A1 in prostate cancer was confirmed at the protein level by immunostaining for CYP27A1 in annotated tissue microarrays. Restoration of CYP27A1 expression in cells where its gene was silenced attenuated their growth in vitro and in tumor xenografts. Studies performed in vitro revealed that treatment of prostate cancer cells with 27-hydroxycholesterol (27HC), an enzymatic product of CYP27A1, reduced cellular cholesterol content in prostate cancer cell lines by inhibiting the activation of sterol regulatory-element binding protein 2 and downregulating low-density lipoprotein receptor expression. Our findings suggest that CYP27A1 is a critical cellular cholesterol sensor in prostate cells and that dysregulation of the CYP27A1/27HC axis contributes significantly to prostate cancer pathogenesis. Cancer Res; 77(7); 1662-73. ©2017 AACR.
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Affiliation(s)
- Mahmoud A Alfaqih
- Department of Surgery, Duke University, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Erik R Nelson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign; and University of Illinois Cancer Center, Chicago, Illinois
| | - Wen Liu
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Rachid Safi
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Jeffery S Jasper
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Everardo Macias
- Department of Surgery, Duke University, Durham, North Carolina
- Department of Surgery and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Joseph Geradts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
- Department of Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Laura G Dubois
- Department of Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina
| | - Michael R Freeman
- Department of Surgery and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ching-Yi Chang
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina.
| | - Stephen J Freedland
- Department of Surgery and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
- Surgery Section, Durham VA Medical Center, Durham, North Carolina
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50
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Toledo JB, Arnold M, Kastenmüller G, Chang R, Baillie RA, Han X, Thambisetty M, Tenenbaum JD, Suhre K, Thompson JW, John-Williams LS, MahmoudianDehkordi S, Rotroff DM, Jack JR, Motsinger-Reif A, Risacher SL, Blach C, Lucas JE, Massaro T, Louie G, Zhu H, Dallmann G, Klavins K, Koal T, Kim S, Nho K, Shen L, Casanova R, Varma S, Legido-Quigley C, Moseley MA, Zhu K, Henrion MYR, van der Lee SJ, Harms AC, Demirkan A, Hankemeier T, van Duijn CM, Trojanowski JQ, Shaw LM, Saykin AJ, Weiner MW, Doraiswamy PM, Kaddurah-Daouk R. Metabolic network failures in Alzheimer's disease: A biochemical road map. Alzheimers Dement 2017; 13:965-984. [PMID: 28341160 DOI: 10.1016/j.jalz.2017.01.020] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. METHODS Fasting serum samples from the Alzheimer's Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. RESULTS Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ1-42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. DISCUSSION Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery.
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Affiliation(s)
- Jon B Toledo
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Neurology, Houston Methodist Hospital, Houston, TX, USA.
| | - Matthias Arnold
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Rui Chang
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Xianlin Han
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Physiology and Biophysics, Weill Cornell Medical College, Qatar, Doha, Qatar
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lisa St John-Williams
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Siamak MahmoudianDehkordi
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - John R Jack
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Joseph E Lucas
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
| | - Tyler Massaro
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
| | - Gregory Louie
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Hongjie Zhu
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | | | | | | | - Sungeun Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ramon Casanova
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Sudhir Varma
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | | | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Kuixi Zhu
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Y R Henrion
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Amy C Harms
- Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Ayse Demirkan
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
| | - Thomas Hankemeier
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands; Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands; Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; The Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael W Weiner
- Department of Radiology, Center for Imaging of Neurodegenerative Diseases, San Francisco VA Medical Center/University of California San Francisco, San Francisco, CA, USA
| | - P Murali Doraiswamy
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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