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Bethea M, Silvers S, Franklin L, Robinson RAS, Brady LJ, Vue N, Beasley HK, Kirabo A, Wanjalla CN, Shuler HD, Hinton A, McReynolds MR. A guide to establishing, implementing, and optimizing diversity, equity, inclusion, and accessibility (DEIA) committees. Am J Physiol Heart Circ Physiol 2024; 326:H786-H796. [PMID: 38276949 DOI: 10.1152/ajpheart.00583.2023] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Diversity, equity, inclusion, and accessibility (DEIA) efforts are increasingly recognized as critical for the success of academic institutions. These efforts are facilitated mainly through the formation of dedicated DEIA committees. DEIA committees enhance professional development and create a more inclusive environment, which benefits all members of the institution. Although leadership and faculty membership have recognized the importance and necessity of DEIA, the roles of DEIA committees may be more ambiguous. Although leadership and faculty may seek to support DEIA at their institutions, they may not always fully understand the necessity of these committees or how to successfully create a committee, foster and promote its success, and sustain its impact. Thus, here, we offer a background rationale and guide for strategically setting up DEIA committees for success and impact within an academic institution with applicability to scientific societies.
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Affiliation(s)
- Maigen Bethea
- Department of Pediatrics, Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Sophielle Silvers
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Latisha Franklin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Lillian J Brady
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama, Birmingham, Alabama, United States
| | - Neng Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Annet Kirabo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Haysetta D Shuler
- Department of Biological Sciences, Winston-Salem State University, Winston-Salem, North Carolina, United States
- Shuler Consulting, Winston-Salem, North Carolina, United States
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States
- The Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States
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Chung NA, May JC, Robinson RAS, McLean JA. Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules. J Am Soc Mass Spectrom 2024; 35:234-243. [PMID: 38082535 DOI: 10.1021/jasms.3c00338] [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: 02/08/2024]
Abstract
Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography-mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary for comparing across different IM techniques and laboratories, there has been little investigation into experimental factors beyond the mobility separation region that could potentially influence CCS measurements. The first-principles derived CCS of 15 chemical standards were evaluated across 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency of the CCS on the solvent composition was observed, with the larger analytes from this study (m/z > 400) exhibiting a characteristic increase in CCS at the intermediate (40-60%) solvent compositions. Parallels to the behavior of solvent viscosity and protonation site tautomers (protomers) were noted, although the origin of these solvent-dependent CCS trends is as yet unclear. Taken together, these findings document a solvent dependency on CCS, which, while minor (<0.5%), identifies an important need for reporting the solvent system when utilizing CCS in comparative ion mobility studies.
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Affiliation(s)
- Nadjali A Chung
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jody C May
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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Seymour CW, Urbanek KL, Nakayama A, Kennedy JN, Powell R, Robinson RAS, Kapp KL, Billiar TR, Vodovotz Y, Gelhaus SL, Cooper VS, Tang L, Mayr F, Reitz KM, Horvat C, Meyer NJ, Dickson RP, Angus D, Palmer OP. A Prospective Cohort Protocol for the Remnant Investigation in Sepsis Study. Crit Care Explor 2023; 5:e0974. [PMID: 38304708 PMCID: PMC10833627 DOI: 10.1097/cce.0000000000000974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Sepsis is a common and deadly syndrome, accounting for more than 11 million deaths annually. To mature a deeper understanding of the host and pathogen mechanisms contributing to poor outcomes in sepsis, and thereby possibly inform new therapeutic targets, sophisticated, and expensive biorepositories are typically required. We propose that remnant biospecimens are an alternative for mechanistic sepsis research, although the viability and scientific value of such remnants are unknown. METHODS AND RESULTS The Remnant Biospecimen Investigation in Sepsis study is a prospective cohort study of 225 adults (age ≥ 18 yr) presenting to the emergency department with community sepsis, defined as sepsis-3 criteria within 6 hours of arrival. The primary objective was to determine the scientific value of a remnant biospecimen repository in sepsis linked to clinical phenotyping in the electronic health record. We will study candidate multiomic readouts of sepsis biology, governed by a conceptual model, and determine the precision, accuracy, integrity, and comparability of proteins, small molecules, lipids, and pathogen sequencing in remnant biospecimens compared with paired biospecimens obtained according to research protocols. Paired biospecimens will include plasma from sodium-heparin, EDTA, sodium fluoride, and citrate tubes. CONCLUSIONS The study has received approval from the University of Pittsburgh Human Research Protection Office (Study 21120013). Recruitment began on October 25, 2022, with planned release of primary results anticipated in 2024. Results will be made available to the public, the funders, critical care societies, laboratory medicine scientists, and other researchers.
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Affiliation(s)
- Christopher W Seymour
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kelly Lynn Urbanek
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Anna Nakayama
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jason N Kennedy
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rachel Powell
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, TN
| | | | | | - Stacy L Gelhaus
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Lu Tang
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - Flo Mayr
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Katherine M Reitz
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Surgery, UPMC, Pittsburgh, PA
| | - Christopher Horvat
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Medicine Division, Center for Translational Lung Biology University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
- Division of Pulmonary & Critical Care Medicine, Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI
| | - Derek Angus
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Octavia Peck Palmer
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Critical Care Medicine, The CRISMA Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Kapp KL, Ji Choi M, Bai K, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. PATHWAYS ASSOCIATED WITH POSITIVE SEPSIS SURVIVAL OUTCOMES IN AFRICAN AMERICAN/BLACK AND NON-HISPANIC WHITE PATIENTS WITH URINARY TRACT INFECTION. Shock 2023; 60:362-372. [PMID: 37493584 PMCID: PMC10527228 DOI: 10.1097/shk.0000000000002176] [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] [Indexed: 07/27/2023]
Abstract
ABSTRACT Urinary tract infections (UTIs) are a common cause of sepsis worldwide. Annually, more than 60,000 US deaths can be attributed to sepsis secondary to UTIs, and African American/Black adults have higher incidence and case-fatality rates than non-Hispanic White adults. Molecular-level factors that may help partially explain differences in sepsis survival outcomes between African American/Black and Non-Hispanic White adults are not clear. In this study, patient samples (N = 166) from the Protocolized Care for Early Septic Shock cohort were analyzed using discovery-based plasma proteomics. Patients had sepsis secondary to UTIs and were stratified according to self-identified racial background and sepsis survival outcomes. Proteomics results suggest patient heterogeneity across mechanisms driving survival from sepsis secondary to UTIs. Differentially expressed proteins (n = 122, false discovery rate-adjusted P < 0.05) in Non-Hispanic White sepsis survivors were primarily in immune system pathways, while differentially expressed proteins (n = 47, false discovery rate-adjusted P < 0.05) in African American/Black patients were mostly in metabolic pathways. However, in all patients, regardless of racial background, there were 16 differentially expressed proteins in sepsis survivors involved in translation initiation and shutdown pathways. These pathways are potential targets for prognostic intervention. Overall, this study provides information about molecular factors that may help explain disparities in sepsis survival outcomes among African American/Black and Non-Hispanic White patients with primary UTIs.
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Affiliation(s)
- Kathryn L. Kapp
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kun Bai
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A. Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C. Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M. Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
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Abstract
The identification of thousands of proteins and their relative levels of expression has furthered understanding of biological processes and disease and stimulated new systems biology hypotheses. Quantitative proteomics workflows that rely on analytical assays such as mass spectrometry have facilitated high-throughput measurements of proteins partially due to multiplexing. Multiplexing allows proteome differences across multiple samples to be measured simultaneously, resulting in more accurate quantitation, increased statistical robustness, reduced analysis times, and lower experimental costs. The number of samples that can be multiplexed has evolved from as few as two to more than 50, with studies involving more than 10 samples being denoted as enhanced multiplexing or hyperplexing. In this review, we give an update on emerging multiplexing proteomics techniques and highlight advantages and limitations for enhanced multiplexing strategies.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
- Department of Neurology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Memory and Alzheimer's Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Brain Institute, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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6
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Mays A, Byars-Winston A, Hinton A, Marshall AG, Kirabo A, August A, Marlin BJ, Riggs B, Tolbert B, Wanjalla C, Womack C, Evans CS, Barnes C, Starbird C, Williams C, Reynolds C, Taabazuing C, Cameron CE, Murray DD, Applewhite D, Morton DJ, Lee D, Williams DW, Lynch D, Brady D, Lynch E, Rutaganira FUN, Silva GM, Shuler H, Saboor IA, Davis J, Dzirasa K, Hammonds-Odie L, Reyes L, Sweetwyne MT, McReynolds MR, Johnson MDL, Smith NA, Pittman N, Ajijola OA, Smith Q, Robinson RAS, Lewis SC, Murray SA, Black S, Neal SE, Andrisse S, Townsend S, Damo SM, Griffith TN, Lambert WM, Clemons WM. Juneteenth in STEMM and the barriers to equitable science. Cell 2023; 186:2510-2517. [PMID: 37295396 DOI: 10.1016/j.cell.2023.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 05/02/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
We are 52 Black scientists. Here, we establish the context of Juneteenth in STEMM and discuss the barriers Black scientists face, the struggles they endure, and the lack of recognition they receive. We review racism's history in science and provide institutional-level solutions to reduce the burdens on Black scientists.
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Affiliation(s)
- Alfred Mays
- Burroughs Wellcome Fund, Durham, NC 27709, USA
| | - Angela Byars-Winston
- Department of Medicine, Institute for Diversity Science, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Annet Kirabo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Avery August
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | - Bianca J Marlin
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Psychology, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Blake Riggs
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Blanton Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Celestine Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chad Womack
- National STEM Programs and Tech Initiatives at the education philanthropic charity, UNCF, Washington, DC 20001, USA
| | - Chantell S Evans
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Chrystal Starbird
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clintoria Williams
- Department of Neuroscience, Cell Biology & Physiology, College of Science and Mathematics, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, USA
| | - Corey Reynolds
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Mouse Phenotyping Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cornelius Taabazuing
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Debra D Murray
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Derrick J Morton
- Department of Biological Sciences, University of Southern California Los Angeles, Los Angeles, CA 90089, USA
| | - Dexter Lee
- Department of Physiology and Biophysics, Howard University College of Medicine, Washington, DC 20059, USA
| | - Dionna W Williams
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Donald Lynch
- Department of Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH, USA
| | - Donita Brady
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Erin Lynch
- University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Florentine U N Rutaganira
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Haysetta Shuler
- Winston-Salem State University Department of Biological Sciences, Winston-Salem, NC 27110, USA
| | - Ishmail Abdus Saboor
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience, Pharmacology, Meharry Medical College, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kafui Dzirasa
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Latanya Hammonds-Odie
- Department of Biological Sciences before School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Loretta Reyes
- Division of Pediatric Nephrology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael D L Johnson
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA; Valley Fever Center for Excellence, University of Arizona, Tucson, AZ, USA
| | - Nathan A Smith
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nikea Pittman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olujimi A Ajijola
- UCLA Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Quinton Smith
- School of Engineering, University of California, Irvine, CA 92697-3975, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Samantha C Lewis
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sandra A Murray
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 52013, USA.
| | - Sherilynn Black
- Office of the Provost and Division of Medical Education, Duke University, Durham, NC 27708, USA.
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stanley Andrisse
- Department of Physiology and Biophysics, Howard University College of Medicine, Washington, DC 20059, USA; Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Steven Townsend
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Steven M Damo
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA.
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - W Marcus Lambert
- Department of Epidemiology and Biostatistics, SUNY Downstate Health Sciences University, New York, NY 11203, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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7
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Patterson KL, Arul AB, Choi MJ, Oliver NC, Whitaker MD, Bodrick AC, Libby JB, Hansen S, Dumitrescu L, Gifford KA, Jefferson AL, Hohman TJ, Robinson RAS. Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses. J Am Soc Mass Spectrom 2023. [PMID: 37163770 DOI: 10.1021/jasms.3c00050] [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] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative accuracy, and provide opportunities for more decisive troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of N = 335 patient samples using tandem mass tag (TMTpro) 16-plex batches. Over the course of a 10-month data acquisition period for this cohort we collected 271 pooled QC LC-MS/MS result files obtained from MS/MS analysis of a patient-derived pooled plasma sample, representative of the entire cohort population. This sample was tagged with TMTzero or TMTpro reagents and used to inform the daily performance of the LC-MS/MS instruments and to allow within and across sample batch normalization. Analytical variability of a number of instrumental and data analysis metrics including protein and peptide identifications, peptide spectral matches (PSMs), number of obtained MS/MS spectra, average peptide abundance, percent of peptides with a Δ m/z between ±0.003 Da, percent of MS/MS spectra obtained at the maximum injection time, and the retention time of selected tracking peptides were evaluated to help inform the design of a robust LC-MS/MS QC workflow for use in future cohort studies. This study also led to general tips for using selected metrics to inform real-time troubleshooting of LC-MS/MS performance issues with daily QC checks.
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Affiliation(s)
- Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nekesa C Oliver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D Whitaker
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Angel C Bodrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - Julia B Libby
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Shania Hansen
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Logan Dumitrescu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Katherine A Gifford
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Angela L Jefferson
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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8
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Lingler JH, Ren D, Tamres LK, Knox ML, Mbawuike U, Williams IC, Robinson RAS, Cameron JL, Terry MH, Garrett M. Mechanisms by which Cultural-Centric Narrative Influences Interest in ADRD Research Among African American Adults. Gerontologist 2022:6955299. [PMID: 36544399 DOI: 10.1093/geront/gnac179] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Insufficient ethnoracial diversity is a pervasive challenge in Alzheimer's disease (AD) research. The Recruitment Innovations for Diversity Enhancement (RIDE) is grounded in the premise that culturally informed narratives of research participation can inspire individuals from a given culture-sharing group to consider research enrollment. This study examines factors associated with interest in AD research among Black or African American adults following exposure to RIDE narrative campaign materials. RESEARCH DESIGN AND METHODS A community-based sample of 500 Black or African American adults viewed RIDE narrative materials online and completed a survey of perceptions about research, AD risk, and likelihood of enrolling in AD research. Logistic regression examined predictors and mediators of self-reported likelihood of participating in AD research. RESULTS Most (72%) participants reported interest in being contacted for AD research opportunities. After controlling for key variables, prior experience with clinical research and trust in medical researchers emerged as independent predictors of likelihood of enrolling in AD research. Perceived burden of AD research partially mediated the effects of prior research experience and trust on likelihood of enrollment. Perceived benefits of AD research also played a mediating role, accounting for over one third of the effect of trust on likelihood of enrollment. DISCUSSION AND IMPLICATIONS This study advances the field's understanding of how narrative may function to enhance diversity in AD research. Findings suggest that participant narratives should address experiences regarding the burdens and potential benefits of AD research participation as these factors may influence decisions leading to subsequent research enrollment.
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Affiliation(s)
- Jennifer H Lingler
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,University of Pittsburgh Alzheimer's Disease Research Center, Pittsburgh, Pennsylvania, USA
| | - Dianxu Ren
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa K Tamres
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Melissa L Knox
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judy L Cameron
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Melita H Terry
- University of Pittsburgh Alzheimer's Disease Research Center, Pittsburgh, Pennsylvania, USA
| | - Marita Garrett
- Civically, Inc., Pittsburgh, Pennsylvania, USA.,Graduate School of Public & International Affairs, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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9
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Kapp KL, Arul AB, Zhang KC, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. Proteomic changes associated with racial background and sepsis survival outcomes. Mol Omics 2022; 18:923-937. [PMID: 36097965 DOI: 10.1039/d2mo00171c] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intra-abdominal infection is a common cause of sepsis, and intra-abdominal sepsis leads to ∼156 000 U.S. deaths annually. African American/Black adults have higher incidence and mortality rates from sepsis compared to Non-Hispanic White adults. A limited number of studies have traced survival outcomes to molecular changes; however, these studies primarily only included Non-Hispanic White adults. Our goal is to better understand molecular changes that may contribute to differences in sepsis survival in African American/Black and Non-Hispanic White adults with primary intra-abdominal infection. We employed discovery-based plasma proteomics of patient samples from the Protocolized Care for Early Septic Shock (ProCESS) cohort (N = 107). We identified 49 proteins involved in the acute phase response and complement system whose expression levels are associated with both survival outcome and racial background. Additionally, 82 proteins differentially-expressed in survivors were specific to African American/Black or Non-Hispanic White patients, suggesting molecular-level heterogeneity in sepsis patients in key inflammatory pathways. A smaller, robust set of 19 proteins were in common in African American/Black and Non-Hispanic White survivors and may represent potential universal molecular changes in sepsis. Overall, this study identifies molecular factors that may contribute to differences in survival outcomes in African American/Black patients that are not fully explained by socioeconomic or other non-biological factors.
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Affiliation(s)
- Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA
| | - Kevin C Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.,Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
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10
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King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [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: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
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Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
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11
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Khan MJ, Chung NA, Hansen S, Dumitrescu L, Hohman TJ, Kamboh MI, Lopez OL, Robinson RAS. Targeted Lipidomics To Measure Phospholipids and Sphingomyelins in Plasma: A Pilot Study To Understand the Impact of Race/Ethnicity in Alzheimer's Disease. Anal Chem 2022; 94:4165-4174. [PMID: 35235294 PMCID: PMC9126486 DOI: 10.1021/acs.analchem.1c03821] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The number of people suffering from Alzheimer's disease (AD) is increasing rapidly every year. One aspect of AD that is often overlooked is the disproportionate incidence of AD among African American/Black populations. With the recent development of novel assays for lipidomics analysis in recent times, there has been a drastic increase in the number of studies focusing on changes of lipids in AD. However, very few of these studies have focused on or even included samples from African American/Black individuals samples. In this study, we aimed to determine if the lipidome in AD is universal across non-Hispanic White and African American/Black individuals. To accomplish this, a targeted mass spectrometry lipidomics analysis was performed on plasma samples (N = 113) obtained from cognitively normal (CN, N = 54) and AD (N = 59) individuals from African American/Black (N = 56) and non-Hispanic White (N = 57) backgrounds. Five lipids (PS 18:0_18:0, PS 18:0_20:0, PC 16:0_22:6, PC 18:0_22:6, and PS 18:1_22:6) were altered between AD and CN sample groups (p value < 0.05). Upon racial stratification, there were notable differences in lipids that were unique to African American/Black or non-Hispanic White individuals. PS 20:0_20:1 was reduced in AD in samples from non-Hispanic White but not African American/Black adults. We also tested whether race/ethnicity significantly modified the association between lipids and AD status by including a race × diagnosis interaction term in a linear regression model. PS 20:0_20:1 showed a significant interaction (p = 0.004). The discovery of lipid changes in AD in this study suggests that identifying relevant lipid biomarkers for diagnosis will require diversity in sample cohorts.
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Affiliation(s)
- Mostafa J Khan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nadjali A Chung
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Shania Hansen
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States.,Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - M Ilyas Kamboh
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States.,Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Oscar L Lopez
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States.,Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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12
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Desaire H, Stepler KE, Robinson RAS. Exposing the Brain Proteomic Signatures of Alzheimer's Disease in Diverse Racial Groups: Leveraging Multiple Data Sets and Machine Learning. J Proteome Res 2022; 21:1095-1104. [PMID: 35276041 PMCID: PMC9097891 DOI: 10.1021/acs.jproteome.1c00966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/20/2023]
Abstract
Recent studies have highlighted that the proteome can be used to identify potential biomarker candidates for Alzheimer's disease (AD) in diverse cohorts. Furthermore, the racial and ethnic background of participants is an important factor to consider to ensure the effectiveness of potential biomarkers for representative populations. A promising approach to survey potential biomarker candidates for diagnosing AD in diverse cohorts is the application of machine learning to proteomics data sets. Herein, we leveraged six existing bottom-up proteomics data sets, which included non-Hispanic White, African American/Black, and Hispanic participants, to study protein changes in AD and cognitively unimpaired participants. Machine learning models were applied to these data sets and resulted in the identification of amyloid-β precursor protein (APP) and heat shock protein β-1 (HSPB1) as two proteins that have high ability to distinguish AD; however, each protein's performance varied based upon the racial and ethnic background of the participants. HSPB1 particularly was helpful for generating high areas under the curve (AUCs) for African American/Black participants. Overall, HSPB1 improved the performance of the machine learning models when combined with APP and/or participant age and is a potential candidate that should be further explored in AD biomarker discovery efforts.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Kaitlyn E Stepler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, United States.,Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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13
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Canto AM, Godoi AB, Matos AHB, Geraldis JC, Rogerio F, Alvim MKM, Yasuda CL, Ghizoni E, Tedeschi H, Veiga DFT, Henning B, Souza W, Rocha CS, Vieira AS, Dias EV, Carvalho BS, Gilioli R, Arul AB, Robinson RAS, Cendes F, Lopes-Cendes I. Benchmarking the proteomic profile of animal models of mesial temporal epilepsy. Ann Clin Transl Neurol 2022; 9:454-467. [PMID: 35238489 PMCID: PMC8994989 DOI: 10.1002/acn3.51533] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We compared the proteomic signatures of the hippocampal lesion induced in three different animal models of mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE+HS): the systemic pilocarpine model (PILO), the intracerebroventricular kainic acid model (KA), and the perforant pathway stimulation model (PPS). METHODS We used shotgun proteomics to analyze the proteomes and find enriched biological pathways of the dorsal and ventral dentate gyrus (DG) isolated from the hippocampi of the three animal models. We also compared the proteomes obtained in the animal models to that from the DG of patients with pharmacoresistant MTLE+HS. RESULTS We found that each animal model presents specific profiles of proteomic changes. The PILO model showed responses predominantly related to neuronal excitatory imbalance. The KA model revealed alterations mainly in synaptic activity. The PPS model displayed abnormalities in metabolism and oxidative stress. We also identified common biological pathways enriched in all three models, such as inflammation and immune response, which were also observed in tissue from patients. However, none of the models could recapitulate the profile of molecular changes observed in tissue from patients. SIGNIFICANCE Our results indicate that each model has its own set of biological responses leading to epilepsy. Thus, it seems that only using a combination of the three models may one replicate more closely the mechanisms underlying MTLE+HS as seen in patients.
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Affiliation(s)
- Amanda M Canto
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Alexandre B Godoi
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Alexandre H B Matos
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Jaqueline C Geraldis
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Fabio Rogerio
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marina K M Alvim
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Clarissa L Yasuda
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Enrico Ghizoni
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Helder Tedeschi
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Diogo F T Veiga
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Barbara Henning
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Welliton Souza
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Cristiane S Rocha
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - André S Vieira
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Elayne V Dias
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rovilson Gilioli
- Laboratory of Animal Quality Control, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Fernando Cendes
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
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14
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Pumford AD, Arul AB, Ford KI, Robinson RAS. Automation of On-Resin Enrichment of S-Nitrosylated Proteins for Oxidized Cysteine-Selective cPILOT. Vanderbilt Undergrad Res J 2021; 11:43-51. [PMID: 35615079 PMCID: PMC9129232 DOI: 10.15695/vurj.v11i1.5096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
S-Nitrosylation (SNO) is a cysteine post-translational modification that increases with normal aging and is present in Alzheimer's disease and other aging-related illnesses. Detection of SNO-modified proteins can be challenging; however, we previously developed a robust quantitative proteomics approach termed "Oxidized Cysteine-Selective combined precursor isobaric labeling and isobaric tagging (OxcyscPILOT)" that allows for detection of endogenous SNO-modified proteins. OxcyscPILOT involves enrichment of SNO-modified proteins using a thiol-based resin. This enrichment is performed manually, and wash steps with the resin require numerous stages and buffer reagents. The goal of this study is to transfer the manual protocol to an automated liquid handler system in order to reduce wash steps, increase sample throughput, and minimize experimental error. In order to accomplish this, we evaluated the Biomek i7 liquid handler automated workstation and a Positive Pressure ALP (PPA) apparatus to conduct automated on-resin enrichment. Our findings provide starting pressure conditions for the use of PPA in an automated OxcyscPILOT proteomics workflow that could be transferred to other robotic liquid handling systems.
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15
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Arul AB, Robinson RAS. Automated Sample Multiplexing by using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT). J Vis Exp 2020. [PMID: 33393514 DOI: 10.3791/61342] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We have introduced a high throughput quantitative proteomics workflow, combined precursor isotopic labeling and isobaric tagging (cPILOT) capable of multiplexing up to 22 or 24 samples with tandem mass tags or isobaric N,N-dimethyl leucine isobaric tags, respectively, in a single experiment. This enhanced sample multiplexing considerably reduces mass spectrometry acquisition times and increases the utility of the expensive commercial isobaric reagents. However, the manual process of sample handling and pipetting steps in the strategy can be labor intensive, time consuming, and introduce sample loss and quantitative error. These limitations can be overcome through the incorporation of automation. Here we transferred the manual cPILOT protocol to an automated liquid handling device that can prepare large sample numbers (i.e., 96 samples) in parallel. Overall, automation increases feasibility and reproducibility of cPILOT and allows for broad usage by other researchers with comparable automation devices.
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Affiliation(s)
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University; Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center; Vanderbilt Brain Institute, Vanderbilt University Medical Center; Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center;
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16
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Stepler KE, Mahoney ER, Kofler J, Hohman TJ, Lopez OL, Robinson RAS. Inclusion of African American/Black adults in a pilot brain proteomics study of Alzheimer's disease. Neurobiol Dis 2020; 146:105129. [PMID: 33049317 PMCID: PMC7990397 DOI: 10.1016/j.nbd.2020.105129] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) disproportionately affects certain racial and ethnic subgroups, such as African American/Black and Hispanic adults. Genetic, comorbid, and socioeconomic risk factors contribute to this disparity; however, the molecular contributions have been largely unexplored. Herein, we conducted a pilot proteomics study of postmortem brains from African American/Black and non-Hispanic White adults neuropathologically diagnosed with AD compared to closely-matched cognitively normal individuals. Examination of hippocampus, inferior parietal lobule, and globus pallidus regions using quantitative proteomics resulted in 568 differentially-expressed proteins in AD. These proteins were consistent with the literature and included glial fibrillary acidic protein, peroxiredoxin-1, and annexin A5. In addition, 351 novel proteins in AD were identified, which could partially be due to cohort diversity. From linear regression analyses, we identified 185 proteins with significant race x diagnosis interactions across various brain regions. These differences generally were reflective of differential expression of proteins in AD that occurred in only a single racial/ethnic group. Overall, this pilot study suggests that disease understanding can be furthered by including diversity in racial/ethnic groups; however, this must be done on a larger scale.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Emily R Mahoney
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States of America
| | - Timothy J Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, United States of America; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, United States of America
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America; Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States of America.
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17
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Khan MJ, Codreanu SG, Goyal S, Wages PA, Gorti SKK, Pearson MJ, Uribe I, Sherrod SD, McLean JA, Porter NA, Robinson RAS. Evaluating a targeted multiple reaction monitoring approach to global untargeted lipidomic analyses of human plasma. Rapid Commun Mass Spectrom 2020; 34:e8911. [PMID: 32738001 PMCID: PMC9126483 DOI: 10.1002/rcm.8911] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 05/04/2023]
Abstract
RATIONALE The Lipidyzer platform was recently updated on a SCIEX QTRAP 6500+ mass spectrometer and offers a targeted lipidomics assay including 1150 different lipids. We evaluated this targeted approach using human plasma samples and compared the results against a global untargeted lipidomics method using a high-resolution Q Exactive HF Orbitrap mass spectrometer. METHODS Lipids from human plasma samples (N = 5) were extracted using a modified Bligh-Dyer approach. A global untargeted analysis was performed using a Thermo Orbitrap Q Exactive HF mass spectrometer, followed by data analysis using Progenesis QI software. Multiple reaction monitoring (MRM)-based targeted analysis was performed using a QTRAP 6500+ mass spectrometer, followed by data analysis using SCIEX OS software. The samples were injected on three separate days to assess reproducibility for both approaches. RESULTS Overall, 465 lipids were identified from 11 lipid classes in both approaches, of which 159 were similar between the methods, 168 lipids were unique to the MRM approach, and 138 lipids were unique to the untargeted approach. Phosphatidylcholine and phosphatidylethanolamine species were the most commonly identified using the untargeted approach, while triacylglycerol species were the most commonly identified using the targeted MRM approach. The targeted MRM approach had more consistent relative abundances across the three days than the untargeted approach. Overall, the coefficient of variation for inter-day comparisons across all lipid classes was ∼ 23% for the untargeted approach and ∼ 9% for the targeted MRM approach. CONCLUSIONS The targeted MRM approach identified similar numbers of lipids to a conventional untargeted approach, but had better representation of 11 lipid classes commonly identified by both approaches. Based on the separation methods employed, the conventional untargeted approach could better detect phosphatidylcholine and sphingomyelin lipid classes. The targeted MRM approach had lower inter-day variability than the untargeted approach when tested using a small group of plasma samples. These studies highlight the advantages in using targeted MRM approaches for human plasma lipidomics analysis.
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Affiliation(s)
- Mostafa J Khan
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sandeep Goyal
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Phillip A Wages
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | | | | | - Isabel Uribe
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Stacy D Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ned A Porter
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
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18
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Urbina‐Blanco CA, Jilani SZ, Speight IR, Bojdys MJ, Friščić T, Stoddart JF, Nelson TL, Mack J, Robinson RAS, Waddell EA, Lutkenhaus JL, Godfrey M, Abboud MI, Aderinto SO, Aderohunmu D, Bibič L, Borges J, Dong VM, Ferrins L, Fung FM, John T, Lim FPL, Masters SL, Mambwe D, Thordarson P, Titirici M, Tormet‐González GD, Unterlass MM, Wadle A, Yam VW, Yang Y. A Diverse View of Science to Catalyse Change. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Safia Z. Jilani
- Department of Chemistry Georgetown University Washington DC 20057 USA
| | - Isaiah R. Speight
- Department of Chemistry Vanderbilt University Nashville TN 37235 USA
| | - Michael J. Bojdys
- Department of Chemistry, King's College, London (UK) and Department of Chemistry Humboldt-Universität zu Berlin Berlin 12489 Germany
| | - Tomislav Friščić
- Department of Chemistry McGill University Montréal QC H3A 0B8 Canada
| | - J. Fraser Stoddart
- Department of Chemistry Northwestern University Evanston IL 60208 USA
- Institute for Molecular Design and Synthesis Tianjin University Tianjin 300072 People's Republic of China
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - Toby L. Nelson
- Department of Chemistry Oklahoma State University Stillwater OK 74078 USA
| | - James Mack
- Department of Chemistry University of Cincinnati Cincinnati OH 45221 USA
| | | | - Emanuel A. Waddell
- Department of Chemistry University of Alabama in Huntsville Huntsville AL 35899 USA
| | - Jodie L. Lutkenhaus
- Artie McFerrin Department of Chemical Engineering Texas A&M University College Station TX 77843 USA
| | - Murrell Godfrey
- Department of Chemistry The University of Mississippi University MS 38677 USA
| | - Martine I. Abboud
- Department of Chemistry University of Oxford Chemistry Research Laboratory Oxford OX1 3TA UK
| | | | - Damilola Aderohunmu
- Department of Chemistry Covenant University, CST, Canaanland Ota Ogun State Nigeria
| | - Lučka Bibič
- School of Pharmacy University of East Anglia Norwich NR4 7TJ UK
| | - João Borges
- Department of Chemistry CICECO—Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago Aveiro 3810-193 Portugal
| | - Vy M. Dong
- Department of Chemistry University of California Irvine CA 92697 USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology Northeastern University Boston MA 02115 USA
| | - Fun Man Fung
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Torsten John
- Leibniz Institute of Surface Engineering (IOM) Leipzig 04318 Germany
| | - Felicia P. L. Lim
- School of Pharmacy Monash University Malaysia Selangor Darul Ehsan 47500 Malaysia
| | - Sarah L. Masters
- School of Physical and Chemical Sciences University of Canterbury Christchurch 8140 New Zealand
| | - Dickson Mambwe
- Department of Chemistry University of Cape Town Rondebosch Capetown 7701 South Africa
| | - Pall Thordarson
- School of Chemistry The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology The University of New South Wales Sydney NSW 2052 Australia
| | - Maria‐Magdalena Titirici
- Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ UK
| | | | - Miriam M. Unterlass
- Institute of Materials Chemistry Technische Universität Wien Vienna 1060 Austria
| | - Austin Wadle
- Department of Civil & Environmental Engineering Duke University Pratt School of Engineering Durham NC 27708 USA
| | - Vivian W.‐W. Yam
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Hong Kong People's Republic of China
| | - Ying‐Wei Yang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC) College of Chemistry Jilin University Changchun 130012 People's Republic of China
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19
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Urbina‐Blanco CA, Jilani SZ, Speight IR, Bojdys MJ, Friščić T, Stoddart JF, Nelson TL, Mack J, Robinson RAS, Waddell EA, Lutkenhaus JL, Godfrey M, Abboud MI, Aderinto SO, Aderohunmu D, Bibič L, Borges J, Dong VM, Ferrins L, Fung FM, John T, Lim FPL, Masters SL, Mambwe D, Thordarson P, Titirici M, Tormet‐González GD, Unterlass MM, Wadle A, Yam VW, Yang Y. A Diverse View of Science to Catalyse Change. Angew Chem Int Ed Engl 2020; 59:18306-18310. [PMID: 33448562 PMCID: PMC7590070 DOI: 10.1002/anie.202009834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/03/2022]
Abstract
Valuing diversity leads to scientific excellence, the progress of science and most importantly, it is simply the right thing to do. We can value diversity not only in words, but also in actions.
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Affiliation(s)
| | - Safia Z. Jilani
- Department of ChemistryGeorgetown UniversityWashingtonDC20057USA
| | | | - Michael J. Bojdys
- Department of Chemistry, King's College, London (UK) and Department of ChemistryHumboldt-Universität zu BerlinBerlin12489Germany
| | | | - J. Fraser Stoddart
- Department of ChemistryNorthwestern UniversityEvanstonIL60208USA
- Institute for Molecular Design and SynthesisTianjin UniversityTianjin300072People's Republic of China
- School of ChemistryUniversity of New South WalesSydneyNSW2052Australia
| | - Toby L. Nelson
- Department of ChemistryOklahoma State UniversityStillwaterOK74078USA
| | - James Mack
- Department of ChemistryUniversity of CincinnatiCincinnatiOH45221USA
| | | | - Emanuel A. Waddell
- Department of ChemistryUniversity of Alabama in HuntsvilleHuntsvilleAL35899USA
| | - Jodie L. Lutkenhaus
- Artie McFerrin Department of Chemical EngineeringTexas A&M UniversityCollege StationTX77843USA
| | - Murrell Godfrey
- Department of ChemistryThe University of MississippiUniversityMS38677USA
| | - Martine I. Abboud
- Department of ChemistryUniversity of Oxford Chemistry Research LaboratoryOxfordOX1 3TAUK
| | | | - Damilola Aderohunmu
- Department of ChemistryCovenant University, CST, CanaanlandOtaOgun StateNigeria
| | - Lučka Bibič
- School of PharmacyUniversity of East AngliaNorwichNR4 7TJUK
| | - João Borges
- Department of ChemistryCICECO—Aveiro Institute of MaterialsUniversity of AveiroCampus Universitário de SantiagoAveiro3810-193Portugal
| | - Vy M. Dong
- Department of ChemistryUniversity of CaliforniaIrvineCA92697USA
| | - Lori Ferrins
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMA02115USA
| | - Fun Man Fung
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
| | - Torsten John
- Leibniz Institute of Surface Engineering (IOM)Leipzig04318Germany
| | - Felicia P. L. Lim
- School of PharmacyMonash University MalaysiaSelangor Darul Ehsan47500Malaysia
| | - Sarah L. Masters
- School of Physical and Chemical SciencesUniversity of CanterburyChristchurch8140New Zealand
| | - Dickson Mambwe
- Department of ChemistryUniversity of Cape TownRondeboschCapetown7701South Africa
| | - Pall Thordarson
- School of ChemistryThe Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and TechnologyThe University of New South WalesSydneyNSW2052Australia
| | | | | | - Miriam M. Unterlass
- Institute of Materials ChemistryTechnische Universität WienVienna1060Austria
| | - Austin Wadle
- Department of Civil & Environmental EngineeringDuke University Pratt School of EngineeringDurhamNC27708USA
| | - Vivian W.‐W. Yam
- Institute of Molecular Functional Materials and Department of ChemistryThe University of Hong KongHong KongPeople's Republic of China
| | - Ying‐Wei Yang
- State Key Laboratory of Inorganic Synthesis and Preparative ChemistryInternational Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC)College of ChemistryJilin UniversityChangchun130012People's Republic of China
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20
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Robinson RAS, Williams IC, Cameron JL, Ward K, Knox M, Terry M, Tamres L, Mbawuike U, Garrett M, Lingler JH. Framework for creating storytelling materials to promote African American/Black adult enrollment in research on Alzheimer's disease and related disorders. Alzheimers Dement (N Y) 2020; 6:e12076. [PMID: 32995472 PMCID: PMC7507510 DOI: 10.1002/trc2.12076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/11/2022]
Abstract
INTRODUCTION African American/Black adults are severely underrepresented in basic, clinical, and behavioral research studies in Alzheimer's disease and related disorders (ADRD). Innovative, evidence-based, and culturally salient strategies can maximize the recruitment of African American/Black adults into ADRD research. METHODS We conducted and analyzed semi-structured interviews to capture the research participation stories of African American/Black participants and study partners from the University of Pittsburgh's Alzheimer's Disease Research Center. The themes and messaging principles generated through this process informed the development of video- and text-based materials that were evaluated for community member acceptance using focus groups. RESULTS Focus group individuals (N = 36) generally favorably rated the video and text materials, characterizing them as "interesting," "realistic," and "convincing." DISCUSSION Capturing the narratives of African American/Black research participants is a critical component to developing culturally relevant materials for broader dissemination and is essential to advancing beyond information-only recruitment approaches, which tend to rely disproportionately on negative messages.
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Affiliation(s)
- Renã A. S. Robinson
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Department of NeurologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Memory & Alzheimer's CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Brain InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
| | | | - Judy L. Cameron
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Keisha Ward
- Department of Geriatric MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Melissa Knox
- School of NursingUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Melita Terry
- City of WilkinsburgPartnership for Positive ProgressPittsburghPennsylvaniaUSA
| | - Lisa Tamres
- School of NursingUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Uchenna Mbawuike
- School of NursingUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marita Garrett
- City of WilkinsburgPartnership for Positive ProgressPittsburghPennsylvaniaUSA
| | - Jennifer H. Lingler
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
- School of NursingUniversity of PittsburghPittsburghPennsylvaniaUSA
- University of Pittsburgh Alzheimer's Disease Research CenterPittsburghPennsylvaniaUSA
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21
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Urbina-Blanco CA, Jilani SZ, Speight IR, Bojdys MJ, Friščić T, Stoddart JF, Nelson TL, Mack J, Robinson RAS, Waddell EA, Lutkenhaus JL, Godfrey M, Abboud MI, Aderinto SO, Aderohunmu D, Bibič L, Borges J, Dong VM, Ferrins L, Fung FM, John T, Lim FPL, Masters SL, Mambwe D, Thordarson P, Titirici MM, Tormet-González GD, Unterlass MM, Wadle A, Yam VWW, Yang YW. A Diverse View of Science to Catalyse Change. J Am Chem Soc 2020; 142:14393-14396. [PMID: 32803980 DOI: 10.1021/jacs.0c07877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Safia Z Jilani
- Department of Chemistry, Georgetown University, Washington, DC, United States
| | - Isaiah R Speight
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Michael J Bojdys
- Department of Chemistry, King's College London, London, United Kingdon.,Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tomislav Friščić
- Department of Chemistry, McGill University, Montréal, Quebec, Canada
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States.,Institute for Molecular Design and Synthesis, Tianjin University, Tianjin, People's Republic of China.,School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Toby L Nelson
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, United States
| | - James Mack
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Emanuel A Waddell
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama, United States
| | - Jodie L Lutkenhaus
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States
| | - Murrell Godfrey
- Department of Chemistry, The University of Mississippi, University, Mississippi, United States
| | - Martine I Abboud
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, Oxford, United Kingdom
| | - Stephen O Aderinto
- Department of Chemistry, The University of Sheffield, Sheffield, United Kingdom
| | - Damilola Aderohunmu
- Department of Chemistry, Covenant University, CST, Canaanland, Ogun State, Nigeria
| | - Lučka Bibič
- School of Pharmacy, University of East Anglia, Norwich, United Kingdom
| | - João Borges
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Vy M Dong
- Department of Chemistry, University of California, Irvine, California, United States
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States
| | - Fun Man Fung
- Department of Chemistry, National University of Singapore, Singapore
| | - Torsten John
- Leibniz Institute of Surface Engineering (IOM), Leipzig, Germany
| | - Felicia P L Lim
- School of Pharmacy, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Sarah L Masters
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Dickson Mambwe
- Department of Chemistry, University of Cape Town, Rondebosch, Capetown, South Africa
| | - Pall Thordarson
- School of Chemistry, The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales, Australia
| | - Maria-Magdalena Titirici
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | | | - Miriam M Unterlass
- Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria
| | - Austin Wadle
- Department of Civil & Environmental Engineering, Duke University Pratt School of Engineering, Durham, North Carolina, United States
| | - Vivian W-W Yam
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Ying-Wei Yang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, Changchun, People's Republic of China
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22
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Amin B, Robinson RAS. Dataset of quantitative proteomic analysis to understand aging processes in rabbit liver. Data Brief 2020; 31:105701. [PMID: 32490075 PMCID: PMC7262418 DOI: 10.1016/j.dib.2020.105701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 11/27/2022] Open
Abstract
Here, we present a proteomics dataset of liver proteins to understand aging in rabbits, which complements the publication “Quantitative proteomics to study aging in rabbit liver” [1]. This dataset was generated to understand the molecular basis and metabolic changes of aging processes in liver, which is the main organ involved in metabolism, detoxification, transport, and signaling. Proteins from young, middle, and old age rabbits were extracted and digested. Generated peptides were labeled with light or heavy dimethyl groups at their N-termini, while lysine amines were labeled with TMT10-plex using a cPILOT workflow [2]. Labeled peptides were fractionated by basic pH reverse phase chromatography and analyzed with online reverse phase LC coupled with tandem mass spectrometry (MS/MS and MS3). The RAW files were generated using a Fusion Lumos Orbitrap mass spectrometer (Thermo Scientific) and processed with Proteome Discoverer (PD) version 2.2 to generate a list of identified and quantified proteins. Data was searched against the Rabbit UniProtKB redundant database. A total of 3,867 proteins were identified corresponding to 2,586 protein groups and 22,229 peptides. Dynamic levels of age-related proteins associated with fat metabolism, mitochondrial dysfunction, and protein degradation were detected. The mass spectrometry proteomics data (RAW files) and processed Proteome Discoverer 2.2 files (MSF files) have been deposited to the Proteomics Identification Database (PRIDE) ProteomeXchange Consortium and can be accessed with the dataset identifier PDX013220 (http://www.ebi.ac.uk/pride/archive/projects/PXD013220).
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Affiliation(s)
- Bushra Amin
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235.,Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232.,Vanderbilt Memory & Alzheimer's Center, Nashville, TN 37212.,Vanderbilt Institute of Chemical Biology, Nashville, TN 37232.,Vanderbilt Brain Institute, Nashville, TN 37232
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23
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Abstract
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In vivo fast photochemical oxidation of proteins
(IV-FPOP) is a hydroxyl radical protein footprinting method used to
study protein structure and protein–protein interactions. Oxidatively
modified proteins by IV-FPOP are analyzed by mass spectrometry (MS),
and the extent of oxidation is quantified by label-free MS. Peptide
oxidation changes yield useful information about protein structure,
due to changes in solvent accessibility. However, the sample size
necessary for animal studies requires increased sample preparation
and instrument time. Here, we report the combined application of IV-FPOP
and the enhanced multiplexing strategy combined precursor isotopic
labeling and isobaric tagging (cPILOT) for higher-throughput analysis
of oxidative modifications in C. elegans. Key differences
in the performance of label-free MS and cPILOT were identified. The
addition of oxygen (+16) was the most abundant modification identified
among all known possible FPOP modifications. This study presents IV-FPOP
coupled with enhanced multiplexing strategies such as cPILOT to increase
throughput of studies seeking to examine oxidative protein modifications.
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Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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King CD, Robinson RAS. Evaluating Combined Precursor Isotopic Labeling and Isobaric Tagging Performance on Orbitraps To Study the Peripheral Proteome of Alzheimer's Disease. Anal Chem 2020; 92:2911-2916. [PMID: 31940168 PMCID: PMC7932850 DOI: 10.1021/acs.analchem.9b01974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Indexed: 12/17/2022]
Abstract
Combined precursor isotopic labeling and isobaric tagging (cPILOT) is an enhanced multiplexing strategy currently capable of analyzing up to 24 samples simultaneously. This capability is especially helpful when studying multiple tissues and biological replicates in models of disease, such as Alzheimer's disease (AD). Here, cPILOT was used to study proteomes from heart, liver, and brain tissues in a late-stage amyloid precursor protein/presenilin-1 (APP/PS-1) human transgenic double-knock-in mouse model of AD. The original global cPILOT assay developed on an Orbitrap Velos instrument was transitioned to an Orbitrap Fusion Lumos instrument. The advantages of faster scan rates, lower limits of detection, and synchronous precursor selection on the Fusion Lumos afford greater numbers of isobarically tagged peptides to be quantified in comparison to the Orbitrap Velos. Parameters such as LC gradient, m/z isolation window, dynamic exclusion, targeted mass analyses, and synchronous precursor scan were optimized leading to >600 000 PSMs, corresponding to 6074 proteins. Overall, these studies inform of system-wide changes in brain, heart, and liver proteins from a mouse model of AD.
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Affiliation(s)
- Christina D King
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Renã A S Robinson
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
- Department of Neurology , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
- Vanderbilt Memory & Alzheimer's Center , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
- Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States
- Vanderbilt Brain Institute , Vanderbilt University , Nashville , Tennessee 37232 , United States
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25
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Urbina-Blanco CA, Mack J, Yang YW, Wadle A, Titirici MM, Masters SL, Man Fung F, Borges J, Aderinto SO, Lutkenhaus JL, Robinson RAS, Nelson TL, Stoddart JF, Friščić T, Bojdys MJ, Speight IR, Jilani SZ. A diverse view of science to catalyse change. CROAT CHEM ACTA 2020. [DOI: 10.5562/diversity2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Valuing diversity leads to scientific excellence, the progress of science and, most importantly, it is simply the right thing to do. We must value diversity not only in words, but also in actions.
This article is co-published in the following journals: Nature Chemistry (<a target="_blank" rel="nofollow" href="https://doi.org/10.1038/s41557-020-0529-x">https://doi.org/10.1038/s41557-020-0529-x</a>), Chemical Science (<a target="_blank" rel="nofollow" href="https://doi.org/10.1039/D0SC90150D">https://doi.org/10.1039/D0SC90150D</a>), Journal of the American Chemical Society (<a target="_blank" rel="nofollow" href="https://doi.org/10.1021/jacs.0c07877">https://doi.org/10.1021/jacs.0c07877</a>), Angewandte Chemie International Edition (<a target="_blank" rel="nofollow" href="https://doi.org/%2010.1002/anie.202009834">https://doi.org/ 10.1002/anie.202009834</a>), Canadian Journal of Chemistry (<a target="_blank" rel="nofollow" href="https://doi.org/10.1139/cjc-2020-0323">https://doi.org/10.1139/cjc-2020-0323</a>), and Croatica Chemica Acta (<a target="_blank" rel="nofollow" href="https://doi.org/10.5562/diversity2020">https://doi.org/10.5562/diversity2020</a>).
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Affiliation(s)
| | - James Mack
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Ying-Wei Yang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Austin Wadle
- Department of Civil & Environmental Engineering, Duke University Pratt School of Engineering, Durham, NC, USA
| | - Maria-Magdalena Titirici
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
| | - Sarah L. Masters
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Fun Man Fung
- Department of Chemistry, National University of Singapore, Singapore
| | - João Borges
- Department of Chemistry, CICECO – Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | | | - Jodie L. Lutkenhaus
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Toby L. Nelson
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | | | - Tomislav Friščić
- Department of Chemistry, McGill University, Montréal, Quebec, Canada
| | | | | | - Safia Z. Jilani
- Department of Chemistry, Georgetown University, Washington, D.C., United States
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Urbina-Blanco CA, Jilani SZ, Speight IR, Bojdys MJ, Friščić T, Stoddart JF, Nelson TL, Mack J, Robinson RAS, Waddell EA, Lutkenhaus JL, Godfrey M, Abboud MI, Aderinto SO, Aderohunmu D, Bibič L, Borges J, Dong VM, Ferrins L, Fung FM, John T, Lim FPL, Masters SL, Mambwe D, Thordarson P, Titirici MM, Tormet-González GD, Unterlass MM, Wadle A, Yam VWW, Yang YW. A diverse view of science to catalyse change. Chem Sci 2020. [DOI: 10.1039/d0sc90150d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Valuing diversity leads to scientific excellence, the progress of science and, most importantly, it is simply the right thing to do. We must value diversity not only in words, but also in actions.
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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Stepler KE, Robinson RAS. The Potential of ‘Omics to Link Lipid Metabolism and Genetic and Comorbidity Risk Factors of Alzheimer’s Disease in African Americans. Advances in Experimental Medicine and Biology 2019; 1118:1-28. [DOI: 10.1007/978-3-030-05542-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Alzheimer's disease (AD) is a debilitating dementia with complex pathophysiological alterations including modifications to endogenous cysteine. S-nitrosylation (SNO) is a well-studied posttranslational modification (PTM) in the context of AD while S-glutathionylation (PSSG) remains less studied. Excess reactive oxygen and reactive nitrogen species (ROS/RNS) directly or indirectly generate SNO and PSSG. SNO is dysregulated in AD and plays a pervasive role in processes such as protein function, cell signaling, metabolism, and apoptosis. Despite some studies into the role of SNO in AD, multiple identified SNO proteins lack deep investigation and SNO modifications outside of brain tissues are limited, leaving the full role of SNO in AD to be elucidated. PSSG homeostasis is perturbed in AD and may affect a myriad of cellular processes. Here we overview the role of nitric oxide (NO) in AD, discuss proteomic methodologies to investigate SNO and PSSG, and review SNO and PSSG in AD. A more thorough understanding of SNO, PSSG, and other cysteinyl PTMs in AD will be helpful for the development of novel therapeutics against neurodegenerative diseases.
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Affiliation(s)
- Ryan R Dyer
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Katarena I Ford
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, United States; Vanderbilt Memory & Alzheimer's Center, Nashville, TN, United States; Vanderbilt Institute of Chemical Biology, Nashville, TN, United States; Vanderbilt Brain Institute, Nashville, TN, United States.
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Frost DC, Rust CJ, Robinson RAS, Li L. Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing by a Combined Precursor Isotopic Labeling and Isobaric Tagging Approach. Anal Chem 2018; 90:10664-10669. [PMID: 30095893 DOI: 10.1021/acs.analchem.8b01301] [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] [Indexed: 01/26/2023]
Abstract
Multiplex isobaric tags have become valuable tools for high-throughput quantitative analysis of complex biological samples in discovery-based proteomics studies. Hybrid labeling strategies that pair stable isotope mass difference labeling with multiplex isobaric tag-based quantification further facilitate these studies by greatly increasing multiplexing capability. In this work, we present a cost-effective chemical labeling approach that couples duplex stable isotope dimethyl labeling with our custom 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags in a combined precursor isotopic labeling and isobaric tagging (cPILOT) strategy that is compatible with a wide variety of biological samples and permits 24-plex quantification in a single LC-MS/MS experiment. We demonstrate the utility of the DiLeu cPILOT approach by labeling yeast digests and performing proof-of-principle quantification experiments on the Orbitrap Fusion Lumos.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States
| | - Clayton J Rust
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Renã A S Robinson
- Department of Chemistry , Vanderbilt University , 5423 Stevenson Center , Nashville , Tennessee 37235 , United States
| | - Lingjun Li
- School of Pharmacy , University of Wisconsin-Madison , 777 Highland Avenue , Madison , Wisconsin 53705 , United States.,Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
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31
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Robinson AR, Yousefzadeh MJ, Rozgaja TA, Wang J, Li X, Tilstra JS, Feldman CH, Gregg SQ, Johnson CH, Skoda EM, Frantz MC, Bell-Temin H, Pope-Varsalona H, Gurkar AU, Nasto LA, Robinson RAS, Fuhrmann-Stroissnigg H, Czerwinska J, McGowan SJ, Cantu-Medellin N, Harris JB, Maniar S, Ross MA, Trussoni CE, LaRusso NF, Cifuentes-Pagano E, Pagano PJ, Tudek B, Vo NV, Rigatti LH, Opresko PL, Stolz DB, Watkins SC, Burd CE, Croix CMS, Siuzdak G, Yates NA, Robbins PD, Wang Y, Wipf P, Kelley EE, Niedernhofer LJ. Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging. Redox Biol 2018; 17:259-273. [PMID: 29747066 PMCID: PMC6006678 DOI: 10.1016/j.redox.2018.04.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 11/20/2022] Open
Abstract
Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/∆ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/∆ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/∆ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/∆ mice never exceeded that observed in old WT mice. Surprisingly, levels of reactive oxygen species (ROS) were increased in tissues of Ercc1-/∆ mice to an extent identical to naturally-aged WT mice. Increased enzymatic production of ROS and decreased antioxidants contributed to the elevation in oxidative stress in both Ercc1-/∆ and aged WT mice. Chronic treatment of Ercc1-/∆ mice with the mitochondrial-targeted radical scavenger XJB-5-131 attenuated oxidative DNA damage, senescence and age-related pathology. Our findings indicate that nuclear genotoxic stress arises, at least in part, due to mitochondrial-derived ROS, and this spontaneous DNA damage is sufficient to drive increased levels of ROS, cellular senescence, and the consequent age-related physiological decline.
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Affiliation(s)
- Andria R Robinson
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA; University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tania A Rozgaja
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jin Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Xuesen Li
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeremy S Tilstra
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Chelsea H Feldman
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Siobhán Q Gregg
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Erin M Skoda
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Céline Frantz
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harris Bell-Temin
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hannah Pope-Varsalona
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aditi U Gurkar
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Luigi A Nasto
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Paediatric Orthopaedics, G. Gaslini Children's Hospital, Genoa, Italy
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Heike Fuhrmann-Stroissnigg
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Sara J McGowan
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Jamie B Harris
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Salony Maniar
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Mark A Ross
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christy E Trussoni
- Division of Gastroenterology and Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas F LaRusso
- Division of Gastroenterology and Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eugenia Cifuentes-Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Patrick J Pagano
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nam V Vo
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lora H Rigatti
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Patricia L Opresko
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Donna B Stolz
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christin E Burd
- Department of Molecular Genetics, Cancer Biology and Genetics, The Ohio State University, Columbus OH 43210 USA
| | - Claudette M St Croix
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gary Siuzdak
- The Scripps Research Institute California, La Jolla, CA 92037, USA
| | - Nathan A Yates
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Biomedical Mass Spectrometry Center, Schools of the Health Sciences University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Paul D Robbins
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Eric E Kelley
- Department of Physiology & Pharmacology, West Virginia University, Morgantown, WV 26506, USA.
| | - Laura J Niedernhofer
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute, Jupiter, FL 33458, USA.
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Chiu CF, Dar HH, Kapralov AA, Robinson RAS, Kagan VE, Star A. Nanoemitters and innate immunity: the role of surfactants and bio-coronas in myeloperoxidase-catalyzed oxidation of pristine single-walled carbon nanotubes. Nanoscale 2017; 9:5948-5956. [PMID: 28440832 PMCID: PMC6584033 DOI: 10.1039/c6nr07706d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are experimentally utilized in in vivo imaging and photothermal cancer therapy owing to their unique physicochemical and electronic properties. For these applications, pristine carbon nanotubes are often modified by polymer surfactant coatings to improve their biocompatibility, adding more complexity to their recognition and biodegradation by immuno-competent cells. Here, we investigate the oxidative degradation of SWCNTs catalyzed by neutrophil myeloperoxidase (MPO) using bandgap near-infrared (NIR) photoluminescence and Raman spectroscopy. Our results show diameter-dependence at the initial stages of the oxidative degradation of sodium cholate-, DNA-, and albumin-coated SWCNTs, but not phosphatidylserine-coated SWCNTs. Moreover, sodium deoxycholate- and phospholipid-polyethylene glycol coated SWCNTs were not oxidized under the same reaction conditions, indicating that a surfactant can greatly impact the biodegradability of a nanomaterial. Our data also revealed that possible binding between MPO and surfactant coated-SWCNTs was unfavorable, suggesting that oxidation is likely caused by a hypochlorite generated through halogenation cycles of free MPO, and not MPO bound to the surface of SWCNTs. The identification of SWCNT diameters and coatings that retain NIR fluorescence during the interactions with the components of an innate immune system is important for their applications in in vivo imaging.
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Affiliation(s)
- Cheuk Fai Chiu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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King CD, Dudenhoeffer JD, Gu L, Evans AR, Robinson RAS. Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT). J Vis Exp 2017. [PMID: 28518113 DOI: 10.3791/55406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is an increasing demand to analyze many biological samples for disease understanding and biomarker discovery. Quantitative proteomics strategies that allow simultaneous measurement of multiple samples have become widespread and greatly reduce experimental costs and times. Our laboratory developed a technique called combined precursor isotopic labeling and isobaric tagging (cPILOT), which enhances sample multiplexing of traditional isotopic labeling or isobaric tagging approaches. Global cPILOT can be applied to samples originating from cells, tissues, bodily fluids, or whole organisms and gives information on relative protein abundances across different sample conditions. cPILOT works by 1) using low pH buffer conditions to selectively dimethylate peptide N-termini and 2) using high pH buffer conditions to label primary amines of lysine residues with commercially-available isobaric reagents (see Table of Materials/Reagents). The degree of sample multiplexing available is dependent on the number of precursor labels used and the isobaric tagging reagent. Here, we present a 12-plex analysis using light and heavy dimethylation combined with six-plex isobaric reagents to analyze 12 samples from mouse tissues in a single analysis. Enhanced multiplexing is helpful for reducing experimental time and cost and more importantly, allowing comparison across many sample conditions (biological replicates, disease stage, drug treatments, genotypes, or longitudinal time-points) with less experimental bias and error. In this work, the global cPILOT approach is used to analyze brain, heart, and liver tissues across biological replicates from an Alzheimer's disease mouse model and wild-type controls. Global cPILOT can be applied to study other biological processes and adapted to increase sample multiplexing to greater than 20 samples.
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Affiliation(s)
| | | | | | - Adam R Evans
- Large Molecule Analytical Development, Pharmaceutical Development & Manufacturing Science, Janssen Research and Development
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Robinson RAS, Amin B, Guest PC. Multiplexing Biomarker Methods, Proteomics and Considerations for Alzheimer’s Disease. Advances in Experimental Medicine and Biology 2017; 974:21-48. [DOI: 10.1007/978-3-319-52479-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Affiliation(s)
- Renã A S Robinson
- Renã A. S. Robinson, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Melanie Föcking
- Melanie Föcking, Department of Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Daniel Martins-de-Souza
- Daniel Martins-de-Souza, Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Henderson M, Rice B, Sebastian A, Sullivan PG, King C, Robinson RAS, Reed TT. Neuroproteomic study of nitrated proteins in moderate traumatic brain injured rats treated with gamma glutamyl cysteine ethyl ester administration post injury: Insight into the role of glutathione elevation in nitrosative stress. Proteomics Clin Appl 2016; 10:1218-1224. [PMID: 27739215 DOI: 10.1002/prca.201600004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 05/02/2016] [Revised: 08/30/2016] [Accepted: 10/10/2016] [Indexed: 01/18/2023]
Abstract
PURPOSE The aims of this study are to establish a time point to determine the most beneficial time to administer GCEE post incident to reduce oxidative damage and second, by using redox proteomics, to determine if GCEE can readily suppress 3-NT modification in TBI animals. EXPERIMENTAL DESIGN By using a moderate traumatic brain injury model with Wistar rats, it is hypothesized that the role of 3-nitrotyrosine (3-NT) formation as an intermediate will predict the involvement of protein nitration/nitrosation and oxidative damage in the brain. RESULTS In this experiment, the levels of protein carbonyls, 4-hydroxynonenal, and 3-nitrotyrosine were significantly elevated in TBI injured, saline treated rats compared with those who sustained an injury and were treated with 150 mg/kg of the glutathione mimetic, GCEE. CONCLUSION AND CLINICAL RELEVANCE Determining the existence of elevated 3-NT levels provides insight into the relationship between the protein nitration/nitrosation and the oxidative damage, which can determine the pathogenesis and progression of specific neurological diseases.
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Affiliation(s)
- Moses Henderson
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, USA
| | - Brittany Rice
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, USA
| | - Andrea Sebastian
- Spinal Cord & Brian Injury Research Center, University of Kentucky, Lexington, KY, USA
| | - Patrick G Sullivan
- Spinal Cord & Brian Injury Research Center, University of Kentucky, Lexington, KY, USA
| | - Christina King
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tanea T Reed
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, USA
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Gu L, Robinson RAS. High-throughput endogenous measurement of S-nitrosylation in Alzheimer's disease using oxidized cysteine-selective cPILOT. Analyst 2016; 141:3904-15. [PMID: 27152368 DOI: 10.1039/c6an00417b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible cysteine modifications play important physiological roles such as modulating enzymatic catalysis, maintaining redox homeostasis and conducting cellular signaling. These roles can be critical in the context of disease. Oxidative modifications such as S-nitrosylation (SNO) are signatures of neurodestruction in conditions of oxidative stress however are also indicators of neuroprotection and normal signaling in cellular environments with low concentrations of reactive oxygen and nitrogen species. SNO is a dynamic and low abundance modification and requires sensitive and selective analytical methods for its detection in biological tissues. Here we present an enhanced multiplexing strategy to study SNO in complex mixtures arising from tissues. This method, termed oxidized cysteine-selective cPILOT (OxcyscPILOT), allows simultaneous analysis of SNO-modified peptides in 12 samples. OxcyscPILOT has three primary steps: (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing SNO on a solid phase resin, and (3) isotopic labeling and isobaric tagging of enriched peptides on the solid phase resin. This approach offers the advantage of allowing total protein abundance levels to be measured simultaneously with endogenous SNO levels and measurement of SNO levels across four biological replicates in a single analysis. Furthermore, the relative amount of SNO on a specific cysteine site can also be determined. A well-known model of Alzheimer's disease, the APP/PS-1 transgenic mouse model, was selected for demonstration of the method as several SNO-modified proteins have previously been reported in brain and synaptosomes from AD subjects. OxcyscPILOT analysis resulted in identification of 138 SNO-modified cysteines in brain homogenates that correspond to 135 proteins. Many of these SNO-modified proteins were only present in wild-type or AD mice, whereas 93 proteins had SNO signals in both WT and AD. Pathway analysis links SNO-modified proteins to various biological pathways especially metabolism and signal transduction, consistent with previous reports in the literature. The OxcyscPILOT strategy provides enhanced multiplexing capability to current redox proteomics methods to study oxidative modifications of cysteine.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Gu L, Robinson RAS. A simple isotopic labeling method to study cysteine oxidation in Alzheimer's disease: oxidized cysteine-selective dimethylation (OxcysDML). Anal Bioanal Chem 2016; 408:2993-3004. [PMID: 26800981 DOI: 10.1007/s00216-016-9307-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 10/13/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 02/01/2023]
Abstract
Cysteine is widely involved in redox signaling pathways through a number of reversible and irreversible modifications. Reversible modifications (e.g., S-glutathionylation, S-nitrosylation, disulfide bonds, and sulfenic acid) are used to protect proteins from oxidative attack and maintain cellular homeostasis, while irreversible oxidations (e.g., sulfinic acid and sulfonic acid) serve as hallmarks of oxidative stress. Proteomic analysis of cysteine-enriched peptides coupled with reduction of oxidized thiols can be used to measure the oxidation states of cysteine, which is helpful for elucidating the role that oxidative stress plays in biology and disease. As an extension of our previously reported cysDML method, we have developed oxidized cysteine-selective dimethylation (OxcysDML), to investigate the site-specific total oxidation of cysteine residues in biologically relevant samples. OxcysDML employs (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing reversibly oxidized cysteine by a solid phase resin, and (3) isotopic labeling of peptide amino groups to quantify cysteine modifications arising from different biological conditions. On-resin enrichment and labeling minimizes sample handing time and improves efficiency in comparison with other redox proteomic methods. OxcysDML is also inexpensive and flexible, as it can accommodate the exploration of various cysteine modifications. Here, we applied the method to liver tissues from a late-stage Alzheimer's disease (AD) mouse model and wild-type (WT) controls. Because we have previously characterized this proteome using the cysDML approach, we are able here to probe deeper into the redox status of cysteine in AD. OxcysDML identified 1129 cysteine sites (from 527 proteins), among which 828 cysteine sites underwent oxidative modifications. Nineteen oxidized cysteine sites had significant alteration levels in AD and represent proteins involved in metabolic processes. Overall, we have demonstrated OxcysDML as a simple, rapid, robust, and inexpensive redox proteomic approach that is useful for gaining deeper insight into the proteome of AD.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA.
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Cao Z, Evans AR, Robinson RAS. MS(3)-based quantitative proteomics using pulsed-Q dissociation. Rapid Commun Mass Spectrom 2015; 29:1025-1030. [PMID: 26044269 DOI: 10.1002/rcm.7192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 01/31/2015] [Accepted: 03/08/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Isobaric tagging reagents, such as tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ), are high-throughput methods that allow the analysis of multiple samples simultaneously, which reduces instrument time and error. Accuracy and precision of isobaric tags are limited, however, in tandem mass spectrometry (MS/MS) acquisition due to co-isolation and co-fragmentation of neighboring peptide peaks in precursor scans. Here we present a MS(3) method using pulsed-Q dissociation (PQD) in ion trap and Orbitrap instrumentation as a means to improve ratio distortion and maintain high numbers of identified and quantified proteins. METHODS Mouse brain protein digests were labeled with TMT-128, 129, 130, 131 reagents, mixed in the following molar ratios 1:1:2:5, respectively, and analyzed using HCD-MS(3) and PQD-MS(3) methods. The most intense fragment ion (termed as HCD-MS(3)-top ion or PQD-MS(3)-top ion) or y1 ion (i.e., lysine-TMT tag ion; termed as HCD-MS(3)-y1 or PQD-MS(3)-y1) in collision-induced dissociation (CID) MS/MS was selected for MS(3). RESULTS Calculated protein ratios obtained in HCD-MS(3)-top ion and PQD-MS(3)-top ion, HCD-MS(3)-y1, and PQD-MS(3)-y1 are accurate and PQD-MS(3) methods resulted in higher numbers of identified and quantified peptide spectral counts and proteins. CONCLUSIONS PQD-MS(3) methods increase the amount of MS/MS spectra collected and number of quantified proteins and are accessible to those researchers with not only an orbitrap but also an ion trap mass spectrometer.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Adam R Evans
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Evans AR, Gu L, Guerrero R, Robinson RAS. Global cPILOT analysis of the APP/PS-1 mouse liver proteome. Proteomics Clin Appl 2015; 9:872-84. [PMID: 25620666 DOI: 10.1002/prca.201400149] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 10/01/2014] [Revised: 11/20/2014] [Accepted: 01/21/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE A quantitative proteomics strategy called combined precursor isotopic labeling and isobaric tagging (cPILOT) was designed to discover alterations in the amyloid precursor protein/presenilin-1 (APP/PS-1) mouse liver proteome. The multiplexing strategy allows simultaneous quantitation of 12 samples in a single experiment. EXPERIMENTAL DESIGN For cPILOT samples, six APP/PS-1 and six heterozygous mouse livers were modified using precursor dimethylation (pH 2.5) followed by isobaric tagging (pH 8.0). Samples were pooled, fractioned with strong cation exchange, and analyzed using RPLC-MS(3) for protein identification and relative quantitation. In order to increase proteome coverage, a two-tiered data collection strategy was employed. Six duplex precursor dimethylation experiments were also performed to verify cPILOT protein quantitation. RESULTS The combination of cPILOT with precursor dimethylation data resulted in 2437 total liver proteins identified and 77 differentially expressed proteins in APP/PS-1 liver. Differentially expressed proteins are involved in metabolic processes such as B-oxidation, pyruvate metabolism, and glucose regulation. CONCLUSIONS AND CLINICAL RELEVANCE cPILOT expands protein quantitation using isobaric tags and can be applied to any clinical laboratory interested in enhanced multiplexing strategies. Differentially expressed proteins in APP/PS-1 mouse liver suggest the potential use of ketone bodies to alleviate metabolic dysregulation in Alzheimer's disease brain. Our work also suggests alterations in the alanine cycle potentially leading to hyperammonia production, may contribute to Alzheimer's disease pathogenesis.
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Affiliation(s)
- Adam R Evans
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rodolfo Guerrero
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. J Am Soc Mass Spectrom 2015; 26:615-630. [PMID: 25588721 DOI: 10.1007/s13361-014-1059-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/22/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Cysteine-selective proteomics approaches simplify complex protein mixtures and improve the chance of detecting low abundant proteins. It is possible that cysteinyl-peptide/protein enrichment methods could be coupled to isotopic labeling and isobaric tagging methods for quantitative proteomics analyses in as few as two or up to 10 samples, respectively. Here we present two novel cysteine-selective proteomics approaches: cysteine-selective dimethyl labeling (cysDML) and cysteine-selective combined precursor isotopic labeling and isobaric tagging (cPILOT). CysDML is a duplex precursor quantification technique that couples cysteinyl-peptide enrichment with on-resin stable-isotope dimethyl labeling. Cysteine-selective cPILOT is a novel 12-plex workflow based on cysteinyl-peptide enrichment, on-resin stable-isotope dimethyl labeling, and iodoTMT tagging on cysteine residues. To demonstrate the broad applicability of the approaches, we applied cysDML and cPILOT methods to liver tissues from an Alzheimer's disease (AD) mouse model and wild-type (WT) controls. From the cysDML experiments, an average of 850 proteins were identified and 594 were quantified, whereas from the cPILOT experiment, 330 and 151 proteins were identified and quantified, respectively. Overall, 2259 unique total proteins were detected from both cysDML and cPILOT experiments. There is tremendous overlap in the proteins identified and quantified between both experiments, and many proteins have AD/WT fold-change values that are within ~20% error. A total of 65 statistically significant proteins are differentially expressed in the liver proteome of AD mice relative to WT. The performance of cysDML and cPILOT are demonstrated and advantages and limitations of using multiple duplex experiments versus a single 12-plex experiment are highlighted.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Cao Z, Robinson RAS. The role of proteomics in understanding biological mechanisms of sepsis. Proteomics Clin Appl 2014; 8:35-52. [PMID: 24339042 DOI: 10.1002/prca.201300101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 09/30/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 11/10/2022]
Abstract
Sepsis is a systemic inflammatory state caused by infection. Complications of this infection with multiple organ failure lead to more lethal conditions, such as severe sepsis and septic shock. Sepsis is one of the leading causes of US deaths. Novel biomarkers with high sensitivity and specificity may be helpful for early diagnosis of sepsis and for improvement of patient outcomes through the development of new therapies. Mass spectrometry-based proteomics offers powerful tools to identify such biomarkers and furthermore to give insight to fundamental mechanisms of this clinical condition. In this review, we summarize findings from proteomics studies of sepsis and how their applications have provided more understanding into the pathogenesis of septic infection. Literatures related to "proteomics", "sepsis", "systemic inflammatory response syndrome", "severe sepsis", "septic infection", and "multiple organ dysfunction syndrome" were searched using PubMed. Findings about neonatal and adult sepsis are discussed separately. Within the adult sepsis studies, results are grouped based on the models (e.g., human or animal). Across investigations in clinical populations and in rodent and mammalian animal models, biological pathways, such as inflammatory and acute phase response, coagulation, complement, mitochondrial energy metabolism, chaperones, and oxidative stress, are altered at the protein level. These proteomics studies have discovered many novel biomarker candidates of septic infection. Validation the clinical use of these biomarker candidates may significantly impact the diagnosis and prognosis of sepsis. In addition, the molecular mechanisms revealed by these studies may also guide the development of more effective treatments.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Butterfield DA, Gu L, Di Domenico F, Robinson RAS. Mass spectrometry and redox proteomics: applications in disease. Mass Spectrom Rev 2014; 33:277-301. [PMID: 24930952 DOI: 10.1002/mas.21374] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 06/03/2023]
Abstract
Proteomics techniques are continuously being developed to further understanding of biology and disease. Many of the pathways that are relevant to disease mechanisms rely on the identification of post-translational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation. Much attention has also been focused on oxidative PTMs which include protein carbonyls, protein nitration, and the incorporation of fatty acids and advanced glycation products to amino acid side chains, amongst others. The introduction of these PTMs in the cell can occur due to the attack of reactive oxygen and nitrogen species (ROS and RNS, respectively) on proteins. ROS and RNS can be present as a result of normal metabolic processes as well as external factors such as UV radiation, disease, and environmental toxins. The imbalance of ROS and RNS with antioxidant cellular defenses leads to a state of oxidative stress, which has been implicated in many diseases. Redox proteomics techniques have been used to characterize oxidative PTMs that result as a part of normal cell signaling processes as well as oxidative stress conditions. This review highlights many of the redox proteomics techniques which are currently available for several oxidative PTMs and brings to the reader's attention the application of redox proteomics for understanding disease pathogenesis in neurodegenerative disorders and others such as cancer, kidney, and heart diseases.
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Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40506
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Cao Z, Robinson RAS. Proteome characterization of splenocytes from an A
βpp/ps-
1 Alzheimer's disease model. Proteomics 2014; 14:291-7. [DOI: 10.1002/pmic.201300130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 10/22/2013] [Accepted: 11/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Zhiyun Cao
- Department of Chemistry; University of Pittsburgh; Pittsburgh PA USA
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Cao Z, Yende S, Kellum JA, Angus DC, Robinson RAS. Proteomics reveals age-related differences in the host immune response to sepsis. J Proteome Res 2013; 13:422-32. [PMID: 24266763 DOI: 10.1021/pr400814s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sepsis is commonly caused by community-acquired pneumonia (CAP) and may develop into severe sepsis, characterized by multiple organ failure. The risk of severe sepsis among CAP patients and subsequent mortality increases sharply after the age of 65. The molecular mechanisms associated with this age-related risk are not fully understood. To better understand factors involved with increased incidence and mortality of severe sepsis in the elderly, we used a nested case-control study of patients enrolled in a multicenter observational cohort of 2320 participants with CAP. We identified a total of 39 CAP patients 50-65 and 70-85 years old who did or did not develop severe sepsis. Plasma samples were obtained on presentation to the emergency department and prior to therapeutic interventions. A semiquantitative plasma proteomics workflow was applied which incorporated tandem immunoaffinity depletion, iTRAQ labeling, strong cation exchange fractionation, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 772 proteins were identified, of which 58 proteins exhibit statistically significant differences in expression levels among patients with severe sepsis as a function of age. Differentially expressed proteins are involved in pathways such as acute phase response, coagulation signaling, atherosclerosis signaling, lipid metabolism, and production of nitric oxide and reactive oxygen species. This study provides insight into factors that may explain age-related differences in incidence of severe sepsis in the elderly.
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Affiliation(s)
- Zhiyun Cao
- Department of Chemistry and ‡The Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Laboratory and Department of Critical Care Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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Evans AR, Robinson RAS. Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS(3) acquisition. Proteomics 2013; 13:3267-72. [PMID: 24124127 DOI: 10.1002/pmic.201300198] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/28/2013] [Indexed: 12/17/2022]
Abstract
Recently, we reported a novel proteomics quantitation scheme termed "combined precursor isotopic labeling and isobaric tagging (cPILOT)" that allows for the identification and quantitation of nitrated peptides in as many as 12-16 samples in a single experiment. cPILOT offers enhanced multiplexing and posttranslational modification specificity, however excludes global quantitation for all peptides present in a mixture and underestimates reporter ion ratios similar to other isobaric tagging methods due to precursor co-isolation. Here, we present a novel chemical workflow for cPILOT that can be used for global tagging of all peptides in a mixture. Specifically, through low pH precursor dimethylation of tryptic or LysC peptides followed by high pH tandem mass tags, the same reporter ion can be used twice in a single experiment. Also, to improve triple-stage mass spectrometry (MS(3) ) data acquisition, a selective MS(3) method that focuses on product selection of the y1 fragment of lysine-terminated peptides is incorporated into the workflow. This novel cPILOT workflow has potential for global peptide quantitation that could lead to enhanced sample multiplexing and increase the number of quantifiable spectra obtained from MS(3) acquisition methods.
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Affiliation(s)
- Adam R Evans
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Abstract
Oxidative modifications can have significant effects on protein structure in solution. Here, the structures and stabilities of oxidized ubiquitin ions electrosprayed from an aqueous solution (pH 2) are studied by ion mobility spectrometry-mass spectrometry (IMS-MS). IMS-MS has proven to be a valuable technique to assess gas phase and in many cases, solution structures. Herein, in vitro oxidation is performed by Fenton chemistry with Fe(II)/hydrogen peroxide. Most molecules in solution remain unmodified, whereas ∼20% of the population belongs to an M+16 Da oxidized species. Ions of low charge states (+7 and +8) show substantial variance in collision cross section distributions between unmodified and oxidized species. Novel and previously reported gaussian conformers are used to model cross section distributions for +7 and +8 oxidized ubiquitin ions, respectively, in order to correlate variances in observed gas-phase distributions to changes in populations of solution states. Based on gaussian modeling, oxidized ions of charge state +7 have an A-state conformation which is more populated for oxidized relative to unmodified ions. Oxidized ubiquitin ions of charge state +8 have a distribution of conformers arising from native-state ubiquitin and higher intensities of A- and U-state conformers relative to unmodified ions. This work provides evidence that incorporation of a single oxygen atom to ubiquitin leads to destabilization of the native state in an acidic solution (pH ∼2) and to unfolding of gas-phase compact structures.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Liqing Gu
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Renã A. S. Robinson
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
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Sultana R, Robinson RAS, Lange MB, Fiorini A, Galvan V, Fombonne J, Baker A, Gorostiza O, Zhang J, Cai J, Pierce WM, Bredesen DE, Butterfield DA. Do proteomics analyses provide insights into reduced oxidative stress in the brain of an Alzheimer disease transgenic mouse model with an M631L amyloid precursor protein substitution and thereby the importance of amyloid-beta-resident methionine 35 in Alzheimer disease pathogenesis? Antioxid Redox Signal 2012; 17:1507-14. [PMID: 22500616 PMCID: PMC3448937 DOI: 10.1089/ars.2011.4470] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The single methionine (Met/M) residue of amyloid-beta (Aβ) peptide, at position 35 of the 42-mer, has important relevance for Aβ-induced oxidative stress and neurotoxicity. Recent in vivo brain studies in a transgenic (Tg) Alzheimer disease (AD) mouse model with Swedish and Indiana familial AD mutations in human amyloid precursor protein (APP) (referred to as the J20 Tg mouse) demonstrated increased levels of oxidative stress. However, the substitution of the Met631 residue of APP to leucine (Leu/L) (M631L in human APP numbering, referred to as M631L Tg and corresponding to residue 35 of Aβ1-42) resulted in no significant in vivo oxidative stress levels, thereby supporting the hypothesis that Met-35 of Aβ contributes to oxidative insult in the AD brain. It is conceivable that oxidative stress mediated by Met-35 of Aβ is important in regulating numerous downstream effects, leading to differential levels of relevant biochemical pathways in AD. Therefore, in the current study using proteomics, we tested the hypothesis that several brain proteins involved in pathways such as energy and metabolism, antioxidant activity, proteasome degradation, and pH regulation are altered in J20Tg versus M631L Tg AD mice.
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Affiliation(s)
- Rukhsana Sultana
- Department of Chemistry, Center of Membrane Sciences, University of Kentucky, Lexington, KY 40506, USA
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