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López-Gómez J, Villarreal L, Andrés M, Ponte I, Xicoy B, Zamora L, Vilaseca M, Roque A. Quantification of Histone H1 Subtypes Using Targeted Proteomics. Biomolecules 2024; 14:1221. [PMID: 39456154 PMCID: PMC11506705 DOI: 10.3390/biom14101221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 09/20/2024] [Accepted: 09/24/2024] [Indexed: 10/28/2024] Open
Abstract
Histone H1 is involved in the regulation of chromatin structure. Human somatic cells express up to seven subtypes. The variability in the proportions of somatic H1s (H1 complement) is one piece of evidence supporting their functional specificity. Alterations in the protein levels of different H1 subtypes have been observed in cancer, suggesting their potential as biomarkers and that they might play a role in disease development. We have developed a mass spectrometry-based (MS) parallel reaction monitoring (PRM) assay suitable for the quantification of H1 subtypes. Our PRM method is based on the quantification of unique peptides for each subtype, providing high specificity. Evaluation of the PRM performance on three human cell lines, HeLa, K562, and T47D, showed high reproducibility and sensitivity. Quantification values agreed with the electrophoretic and Western blot data, indicating the accuracy of the method. We used PRM to quantify the H1 complement in peripheral blood samples of healthy individuals and chronic myeloid leukemia (CML) patients. In CML, the first line of therapy is a tyrosine kinase inhibitor, imatinib. Our preliminary data revealed differences in the H1 complement in CML patients between imatinib responders and non-responders. These results support further research to determine if the H1 content or subtype composition could help predict imatinib response.
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MESH Headings
- Humans
- Proteomics/methods
- Histones/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/blood
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- HeLa Cells
- Mass Spectrometry/methods
- K562 Cells
- Imatinib Mesylate/pharmacology
- Imatinib Mesylate/therapeutic use
- Cell Line, Tumor
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Affiliation(s)
- Jordi López-Gómez
- Biochemistry and Molecular Biology Department, Biosciences Faculty, Autonomous University of Barcelona, 08193 Bellaterra, Spain; (J.L.-G.); (M.A.); (I.P.)
| | - Laura Villarreal
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain; (L.V.); (M.V.)
- The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Marta Andrés
- Biochemistry and Molecular Biology Department, Biosciences Faculty, Autonomous University of Barcelona, 08193 Bellaterra, Spain; (J.L.-G.); (M.A.); (I.P.)
| | - Inma Ponte
- Biochemistry and Molecular Biology Department, Biosciences Faculty, Autonomous University of Barcelona, 08193 Bellaterra, Spain; (J.L.-G.); (M.A.); (I.P.)
| | - Blanca Xicoy
- Hematology Service, Catalan Institute of Oncology-Germans Trias i Pujol Hospital, Josep Carreras Leukaemia Research Institute, Autonomous University of Barcelona, 08025 Barcelona, Spain; (B.X.); (L.Z.)
| | - Lurdes Zamora
- Hematology Service, Catalan Institute of Oncology-Germans Trias i Pujol Hospital, Josep Carreras Leukaemia Research Institute, Autonomous University of Barcelona, 08025 Barcelona, Spain; (B.X.); (L.Z.)
- Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain; (L.V.); (M.V.)
- The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Alicia Roque
- Biochemistry and Molecular Biology Department, Biosciences Faculty, Autonomous University of Barcelona, 08193 Bellaterra, Spain; (J.L.-G.); (M.A.); (I.P.)
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2
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Han J, Liu CX, Liu J, Wang CR, Wang SC, Miao G. AGC kinases OXI1 and AGC2-2 regulate camalexin secretion and disease resistance by phosphorylating transporter PDR6. PLANT PHYSIOLOGY 2024; 195:1835-1850. [PMID: 38535832 DOI: 10.1093/plphys/kiae186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/28/2024] [Indexed: 06/30/2024]
Abstract
Plant transporters regulating the distribution of secondary metabolites play critical roles in defending against pathogens, insects, and interacting with beneficial microbes. The phosphorylation of these transporters can alter their activity, stability, and intracellular protein trafficking. However, the regulatory mechanism underlying this modification remains elusive. In this study, we discovered two orthologs of mammalian PKA, PKG, and PKC (AGC) kinases, oxidative signal-inducible 1 (OXI1) and its closest homologue, AGC subclass 2 member 2 (AGC2-2; 75% amino acid sequence identity with OXI1), associated with the extracellular secretion of camalexin and Arabidopsis (Arabidopsis thaliana) resistance to Pseudomonas syringae, and Botrytis cinerea. These kinases can undergo in vitro kinase reactions with three pleiotropic drug resistance (PDR) transporters: PDR6, PDR8, and PDR12. Moreover, our investigation confirmed PDR6 interaction with OXI1 and AGC2-2. By performing LC-MS/MS and parallel reaction monitoring, we identified the phosphorylation sites on PDR6 targeted by these kinases. Notably, chitin-induced PDR6 phosphorylation at specific residues, namely S31, S33, S827, and T832. Additional insights emerged by expressing dephosphorylated PDR6 variants in a pdr6 mutant background, revealing that the target residues S31, S33, and S827 promote PDR6 efflux activity, while T832 potentially contributes to PDR6 stability within the plasma membrane. The findings of this study elucidate partial mechanisms involved in the activity regulation of PDR-type transporters, providing valuable insights for their potential application in future plant breeding endeavors.
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Affiliation(s)
- Juan Han
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
- Institute of Digital Ecology and Health, Huainan Normal University, Huainan, Anhui Province 232038, China
| | - Chang-Xin Liu
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
| | - Jian Liu
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
| | - Cheng-Run Wang
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan, Anhui Province 232038, China
| | - Shun-Chang Wang
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan, Anhui Province 232038, China
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan, Anhui Province 232038, China
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan, Anhui Province 232038, China
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3
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Aleksic M, Meng X. Protein Haptenation and Its Role in Allergy. Chem Res Toxicol 2024; 37:850-872. [PMID: 38834188 PMCID: PMC11187640 DOI: 10.1021/acs.chemrestox.4c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
Humans are exposed to numerous electrophilic chemicals either as medicines, in the workplace, in nature, or through use of many common cosmetic and household products. Covalent modification of human proteins by such chemicals, or protein haptenation, is a common occurrence in cells and may result in generation of antigenic species, leading to development of hypersensitivity reactions. Ranging in severity of symptoms from local cutaneous reactions and rhinitis to potentially life-threatening anaphylaxis and severe hypersensitivity reactions such as Stephen-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN), all these reactions have the same Molecular Initiating Event (MIE), i.e. haptenation. However, not all individuals who are exposed to electrophilic chemicals develop symptoms of hypersensitivity. In the present review, we examine common chemistry behind the haptenation reactions leading to formation of neoantigens. We explore simple reactions involving single molecule additions to a nucleophilic side chain of proteins and complex reactions involving multiple electrophilic centers on a single molecule or involving more than one electrophilic molecule as well as the generation of reactive molecules from the interaction with cellular detoxification mechanisms. Besides generation of antigenic species and enabling activation of the immune system, we explore additional events which result directly from the presence of electrophilic chemicals in cells, including activation of key defense mechanisms and immediate consequences of those reactions, and explore their potential effects. We discuss the factors that work in concert with haptenation leading to the development of hypersensitivity reactions and those that may act to prevent it from developing. We also review the potential harnessing of the specificity of haptenation in the design of potent covalent therapeutic inhibitors.
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Affiliation(s)
- Maja Aleksic
- Safety
and Environmental Assurance Centre, Unilever,
Colworth Science Park, Sharnbrook, Bedford MK44
1LQ, U.K.
| | - Xiaoli Meng
- MRC
Centre for Drug Safety Science, Department of Molecular and Clinical
Pharmacology, The University of Liverpool, Liverpool L69 3GE, U.K.
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4
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Srikanth KD, Elahi H, Chander P, Washburn HR, Hassler S, Mwirigi JM, Kume M, Loucks J, Arjarapu R, Hodge R, Shiers SI, Sankaranarayanan I, Erdjument-Bromage H, Neubert TA, Campbell ZT, Paik R, Price TJ, Dalva MB. VLK drives extracellular phosphorylation of EphB2 to govern the EphB2-NMDAR interaction and injury-induced pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585314. [PMID: 38562765 PMCID: PMC10983893 DOI: 10.1101/2024.03.18.585314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phosphorylation of hundreds of protein extracellular domains is mediated by two kinase families, yet the significance of these kinases is underexplored. Here, we find that the presynaptic release of the tyrosine directed-ectokinase, Vertebrate Lonesome Kinase (VLK/Pkdcc), is necessary and sufficient for the direct extracellular interaction between EphB2 and GluN1 at synapses, for phosphorylation of the ectodomain of EphB2, and for injury-induced pain. Pkdcc is an essential gene in the nervous system, and VLK is found in synaptic vesicles, and is released from neurons in a SNARE-dependent fashion. VLK is expressed by nociceptive sensory neurons where presynaptic sensory neuron-specific knockout renders mice impervious to post-surgical pain, without changing proprioception. VLK defines an extracellular mechanism that regulates protein-protein interaction and non-opioid-dependent pain in response to injury.
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Affiliation(s)
- Kolluru D Srikanth
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Hajira Elahi
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Praveen Chander
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Halley R Washburn
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Shayne Hassler
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- College of Medicine, University of Houston; Houston, TX 77004, USA
| | - Juliet M Mwirigi
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Moeno Kume
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Jessica Loucks
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
| | - Rohita Arjarapu
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
| | - Rachel Hodge
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Stephanie I Shiers
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Zachary T Campbell
- Department of Anesthesiology, University of Wisconsin-Madison; Madison, WI 53792, USA
| | - Raehum Paik
- Department of Anesthesiology, University of Wisconsin-Madison; Madison, WI 53792, USA
- Department of Genetics, University of Texas Health Science Center at San Antonio; San Antonio, TX 78229, USA
| | - Theodore J Price
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Matthew B Dalva
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
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5
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Jiang L, Qin J, Dai Y, Zhao S, Zhan Q, Cui P, Ren L, Wang X, Zhang R, Gao C, Zhou Y, Cai S, Wang G, Xie W, Tang X, Shi M, Ma F, Liu J, Wang T, Wang C, Svrcek M, Bardier-Dupas A, Emile JF, de Mestier L, Bachet JB, Nicolle R, Cros J, Laurent-Puig P, Wei M, Song B, Jing W, Guo S, Zheng K, Jiang H, Wang H, Deng X, Chen H, Tian Q, Wang S, Shi S, Jin G, Yin T, Fang H, Chen S, Shen B. Prospective observational study on biomarkers of response in pancreatic ductal adenocarcinoma. Nat Med 2024; 30:749-761. [PMID: 38287168 DOI: 10.1038/s41591-023-02790-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
Adjuvant chemotherapy benefits patients with resected pancreatic ductal adenocarcinoma (PDAC), but the compromised physical state of post-operative patients can hinder compliance. Biomarkers that identify candidates for prompt adjuvant therapy are needed. In this prospective observational study, 1,171 patients with PDAC who underwent pancreatectomy were enrolled and extensively followed-up. Proteomic profiling of 191 patient samples unveiled clinically relevant functional protein modules. A proteomics-level prognostic risk model was established for PDAC, with its utility further validated using a publicly available external cohort. More importantly, through an interaction effect regression analysis leveraging both clinical and proteomic datasets, we discovered two biomarkers (NDUFB8 and CEMIP2), indicative of the overall sensitivity of patients with PDAC to adjuvant chemotherapy. The biomarkers were validated through immunohistochemistry on an internal cohort of 386 patients. Rigorous validation extended to two external multicentic cohorts-a French multicentric cohort (230 patients) and a cohort from two grade-A tertiary hospitals in China (466 patients)-enhancing the robustness and generalizability of our findings. Moreover, experimental validation through functional assays was conducted on PDAC cell lines and patient-derived organoids. In summary, our cohort-scale integration of clinical and proteomic data demonstrates the potential of proteomics-guided prognosis and biomarker-aided adjuvant chemotherapy for PDAC.
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Affiliation(s)
- Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiejie Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Cui
- Burning Rock Biotech, Guangzhou, China
| | - Lingjie Ren
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenxu Gao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanting Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | - Xiaomei Tang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfang Ma
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Magali Svrcek
- Department of Pathology, Saint-Antoine Hospital - Sorbonne Universités, Paris, France
| | - Armelle Bardier-Dupas
- Department of Pathology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Jean Francois Emile
- Department of Pathology, Ambroise Paré Hospital - Université Saint Quentin en Yvelines, Paris, France
| | - Louis de Mestier
- Department of Pancreatology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Jean-Baptiste Bachet
- Department of Gastroenterology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Remy Nicolle
- Université Paris Cité, FHU MOSAIC, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, Paris, France
| | - Jerome Cros
- Department of Pathology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Pierre Laurent-Puig
- Department of Biochemistry, Hôpital Européen Georges Pompidou, Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université Paris Cité, Equipe labellisée Ligue Nationale contre le cancer, CNRS, Paris, France
| | - Miaoyan Wei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bin Song
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Jing
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Kailian Zheng
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hui Jiang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pathology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Tian
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengyue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Tong Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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6
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Selenium Nanoparticles (SeNPs) Immunomodulation Is More Than Redox Improvement: Serum Proteomics and Transcriptomic Analyses. Antioxidants (Basel) 2022; 11:antiox11050964. [PMID: 35624828 PMCID: PMC9137598 DOI: 10.3390/antiox11050964] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Selenium nanoparticles (SeNPs) are a novel elemental form selenium and often reported to possess beneficial bioactivities such as anticancer, promoting bone growth and immunomodulation. Our previous study demonstrated that chitosan-stabilized SeNPs have strong activity in immunomodulation. However, the mechanism underlying the immunomodulation of SeNPs is still unknown. The aim of this study is to identify the molecular mechanisms involved in SeNP-induced immunomodulation. Using zebrafish, as a common immunological animal model with a highly conserved molecular mechanism with other vertebrates, we conducted serum proteomic and tissue transcriptome analyses on individuals fed with SeNP in healthy or disease conditions. We also compared differences between SeNPs and an exogenous antioxidant Trolox in immune activity and redox regulation. Our results suggest that the immunomodulation activity was highly related to antioxidant activity and lipid metabolism. Interestingly, the biological functions enhanced by SeNP were almost identical in the healthy and disease conditions. However, while the SeNP was suppressing ROS in healthy individuals, it promoted ROS formation during disease condition. This might be related to the defense mechanism against pathogens. SOD and NFkβ appeared to be the key molecular switch changing effect of SeNPs when individuals undergo infection, indicating the close relationship between immune and redox regulation.
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7
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Landim-Vieira M, Childers MC, Wacker AL, Garcia MR, He H, Singh R, Brundage EA, Johnston JR, Whitson BA, Chase PB, Janssen PML, Regnier M, Biesiadecki BJ, Pinto JR, Parvatiyar MS. Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and nonischemic human hearts. eLife 2022; 11:74919. [PMID: 35502901 PMCID: PMC9122498 DOI: 10.7554/elife.74919] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphorylation and acetylation of sarcomeric proteins are important for fine-tuning myocardial contractility. Here, we used bottom-up proteomics and label-free quantification to identify novel post-translational modifications (PTMs) on β-myosin heavy chain (β-MHC) in normal and failing human heart tissues. We report six acetylated lysines and two phosphorylated residues: K34-Ac, K58-Ac, S210-P, K213-Ac, T215-P, K429-Ac, K951-Ac, and K1195-Ac. K951-Ac was significantly reduced in both ischemic and nonischemic failing hearts compared to nondiseased hearts. Molecular dynamics (MD) simulations show that K951-Ac may impact stability of thick filament tail interactions and ultimately myosin head positioning. K58-Ac altered the solvent-exposed SH3 domain surface - known for protein-protein interactions - but did not appreciably change motor domain conformation or dynamics under conditions studied. Together, K213-Ac/T215-P altered loop 1's structure and dynamics - known to regulate ADP-release, ATPase activity, and sliding velocity. Our study suggests that β-MHC acetylation levels may be influenced more by the PTM location than the type of heart disease since less protected acetylation sites are reduced in both heart failure groups. Additionally, these PTMs have potential to modulate interactions between β-MHC and other regulatory sarcomeric proteins, ADP-release rate of myosin, flexibility of the S2 region, and cardiac myofilament contractility in normal and failing hearts.
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Affiliation(s)
- Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Matthew C Childers
- Department of Bioengineering, College of Medicine, University of WashingtonSeattleUnited States
| | - Amanda L Wacker
- Department of Nutrition and Integrative Physiology, The Florida State UniversityTallahasseeUnited States
| | - Michelle Rodriquez Garcia
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Huan He
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States,Translational Science Laboratory, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Rakesh Singh
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States,Translational Science Laboratory, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Elizabeth A Brundage
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Bryan A Whitson
- Department of Surgery, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - P Bryant Chase
- Department of Biological Science, The Florida State UniversityTallahasseeUnited States
| | - Paul ML Janssen
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Michael Regnier
- Department of Bioengineering, College of Medicine, University of WashingtonSeattleUnited States
| | - Brandon J Biesiadecki
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - J Renato Pinto
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Michelle S Parvatiyar
- Department of Nutrition and Integrative Physiology, The Florida State UniversityTallahasseeUnited States
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8
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Moya R, Odena MA, Gallego M, de Oliveira E, Carnés J. Absolute quantification of Bet v 1 in birch polymerized allergenic extracts via mass spectrometry-targeted analysis. Clin Exp Allergy 2021; 52:276-285. [PMID: 34854138 DOI: 10.1111/cea.14067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/15/2021] [Accepted: 11/27/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Quantifying major allergens is essential for evaluating the quality and efficacy of allergenic extracts. They are usually measured in non-polymerized extracts using immunoassays. However, the direct measurement of allergens in allergoids is currently not supported. This study set out to develop a method for quantifying Bet v 1 in polymerized birch extracts using mass spectrometry-based targeted analysis. METHODS Three isotopically labelled peptide sequences of Bet v 1 were synthetized and used as internal standards for the development of a mass spectrometry-based targeted analysis. The calibration curves of the three peptides to assess the linearity and limit of detection, as well as reverse calibration curves with a constant amount of sample, were constructed. The Bet v 1 content was determined and measured in 18 batches of depigmented (native extracts purified by a mild acid treatment) and depigmented-polymerized extracts. RESULTS Bet v 1 isoforms were identified in both type of extracts by mass spectrometry. According to mass spectrometry-targeted analysis depigmented and depigmented-polymerized extracts exhibited mean values of 70.5 and 73.5 µg Bet v 1/mg of lyophilized extract, respectively. A statistically significant correlation between the allergen content of both extracts was identified. Statistically significant differences were observed when the Bet v 1 content in non-polymerized extracts was measured via mass spectrometry (70.5 ± 11.6 µg/mg) or immunoassay (83.7 ± 19.8 µg/mg). CONCLUSIONS These results represent the first direct quantification of Bet v 1 in allergoids using mass spectrometry-based targeted analysis. The proposed method demonstrates robustness and reliability and constitutes a promising alternative for detailed characterization of polymerized allergenic extracts.
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Affiliation(s)
- Raquel Moya
- R&D Allergy & Immunology Unit. LETI Pharma, Madrid, Spain
| | - M Antonia Odena
- Proteomic Platform Core Facility. Parc Científic de Barcelona, Barcelona, Spain
| | - Mayte Gallego
- R&D Allergy & Immunology Unit. LETI Pharma, Madrid, Spain
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9
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Tang J, Fu J, Wang Y, Li B, Li Y, Yang Q, Cui X, Hong J, Li X, Chen Y, Xue W, Zhu F. ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Brief Bioinform 2021; 21:621-636. [PMID: 30649171 PMCID: PMC7299298 DOI: 10.1093/bib/bby127] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA's capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Li
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yinghong Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Xuejiao Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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10
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Heil LR, Remes PM, MacCoss MJ. Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring. J Proteome Res 2021; 20:4435-4442. [PMID: 34319745 DOI: 10.1021/acs.jproteome.1c00377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM's strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time-of-flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel and that high-resolution data are not necessary to obtain high-quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on an Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high-resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision and that the linear ion trap's superior sensitivity gives it better lower limits of quantitation for over 62% of peptides in the assay.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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11
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Pham TK, Buczek WA, Mead RJ, Shaw PJ, Collins MO. Proteomic Approaches to Study Cysteine Oxidation: Applications in Neurodegenerative Diseases. Front Mol Neurosci 2021; 14:678837. [PMID: 34177463 PMCID: PMC8219902 DOI: 10.3389/fnmol.2021.678837] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 11/15/2022] Open
Abstract
Oxidative stress appears to be a key feature of many neurodegenerative diseases either as a cause or consequence of disease. A range of molecules are subject to oxidation, but in particular, proteins are an important target and measure of oxidative stress. Proteins are subject to a range of oxidative modifications at reactive cysteine residues, and depending on the level of oxidative stress, these modifications may be reversible or irreversible. A range of experimental approaches has been developed to characterize cysteine oxidation of proteins. In particular, mass spectrometry-based proteomic methods have emerged as a powerful means to identify and quantify cysteine oxidation sites on a proteome scale; however, their application to study neurodegenerative diseases is limited to date. Here we provide a guide to these approaches and highlight the under-exploited utility of these methods to measure oxidative stress in neurodegenerative diseases for biomarker discovery, target engagement and to understand disease mechanisms.
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Affiliation(s)
- Trong Khoa Pham
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Weronika A. Buczek
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Richard J. Mead
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Mark O. Collins
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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12
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Miura K, Suzuki T, Sun H, Takada H, Ishizawa Y, Mizuta H, Dohmae N, Simizu S. Requirement for C-mannosylation to be secreted and activated a disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4). Biochim Biophys Acta Gen Subj 2020; 1865:129833. [PMID: 33358865 DOI: 10.1016/j.bbagen.2020.129833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND C-mannosylation is a unique type of glycosylation. A disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4) is a multidomain extracellular metalloproteinase that contains several potential C-mannosylation sites. Although some ADAMTS family proteins have been reported to be C-mannosylated proteins, whether C-mannosylation affects the activation and protease activity of these proteins is unclear. METHODS We established wild-type and mutant ADAMTS4-overexpressing HT1080 cell lines. Recombinant ADAMTS4 was purified from the conditioned medium of the wild-type ADAMTS4-overexpressing cells, and the C-mannosylation sites of ADAMTS4 were identified by LC-MS/MS. The processing, secretion, and intracellular localization of ADAMTS4 were examined by immunoblot and immunofluorescence analyses. ADAMTS4 enzymatic activity was evaluated by assessing the cleavage of recombinant aggrecan. RESULTS We identified that ADAMTS4 is C-mannosylated at Trp404 in the metalloprotease domain and at Trp523, Trp526, and Trp529 in the thrombospondin type 1 repeat (TSR). The replacement of Trp404 with Phe affected ADAMTS4 processing, without affecting secretion and intracellular localization. In contrast, the substitution of Trp523, Trp526, and Trp529 with Phe residues suppressed ADAMTS4 secretion, processing, intracellular trafficking, and enzymatic activity. CONCLUSIONS Our results demonstrated that the C-mannosylation of ADAMTS4 plays important roles in protein processing, intracellular trafficking, secretion, and enzymatic activity. GENERAL SIGNIFICANCE Because C-mannosylation appears to regulate many ADAMTS4 functions, C-mannosylation may also affect other members of the ADAMTS superfamily.
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Affiliation(s)
- Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Wako, 351-0198, Japan
| | - Hongkai Sun
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Haruka Takada
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Yudai Ishizawa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Hayato Mizuta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Wako, 351-0198, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan.
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13
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Osada Y, Suzuki T, Mizuta H, Mori K, Miura K, Dohmae N, Simizu S. The fibrinogen C-terminal domain is seldom C-mannosylated but its C-mannosylation is important for the secretion of microfibril-associated glycoprotein 4. Biochim Biophys Acta Gen Subj 2020; 1864:129637. [DOI: 10.1016/j.bbagen.2020.129637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022]
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14
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Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. MASS SPECTROMETRY REVIEWS 2020; 39:229-244. [PMID: 28691345 PMCID: PMC5799042 DOI: 10.1002/mas.21540] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/01/2017] [Indexed: 05/03/2023]
Abstract
Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
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Affiliation(s)
- Lindsay K Pino
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brian C Searle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brook Nunn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
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15
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Ji F, Zhu Z, Zhang M, Zhang H, Zhu L, Cai X, Liu W, Song J, Li M, Cai Z. 6-OH-BDE-47 exposure-induced Parkinson's disease pathology in Sprague Dawley rat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135184. [PMID: 32000351 DOI: 10.1016/j.scitotenv.2019.135184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
6-Hydroxy-BDE-47 (6-OH-BDE-47) is an important in vivo metabolite derived from 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), a ubiquitous environmental pollutant. The chemical has been widely detected in environmental and biological samples. However, as a potential neurotoxin, whether 6-OH-BDE-47 could promote the development of typical neurodegenerative diseases such as Parkinson's disease (PD) is still unknown. Here, we tested the potential PD-related neurotoxic effect of 6-OH-BDE-47 in rat. The chemical with levels of 0.1, 1 and 10 µg was stereotaxically injected into the right midbrain regions of rat where contain abundant dopaminergic neurons. The resulting deteriorated motor function and decreased levels of striatal dopamine and nigrostriatal tyrosine hydroxylase indicate the dopaminergic neuron loss after the injection. Proteomics study revealed that protein degradation pathways were affected. Western blot analysis confirmed that 6-OH-BDE-47 could inhibit ubiquitination and autophagy, resulting in the increased formation of α-synuclein (α-syn) aggregate, an important pathological hallmark of PD. Overall, our study demonstrated that the 6-OH-BDE-47 administration could induce motor defect by impairing dopaminergic system and promote α-syn aggregation by inhibiting ubiquitination and autophagy, suggesting that the occurrence of 6-OH-BDE-47 in brain could be a risk for developing PD.
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Affiliation(s)
- Fenfen Ji
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhou Zhu
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Mengtao Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huan Zhang
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xiaodong Cai
- Department of Functional Neurology & Neurosurgery, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Wenlan Liu
- The Central Laboratory and Shenzhen Key Laboratory of Neurosurgery, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Juxian Song
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China; Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Min Li
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China.
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16
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Mei L, Montoya MR, Quanrud GM, Tran M, Villa-Sharma A, Huang M, Genereux JC. Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. J Proteome Res 2020; 19:1565-1573. [PMID: 32138514 DOI: 10.1021/acs.jproteome.9b00825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantitative multiplexing capacity of isobaric tandem mass tags (TMT) has increased the throughput of affinity purification mass spectrometry (AP-MS) to characterize protein interaction networks of immunoprecipitated bait proteins. However, variable bait levels between replicates can convolute interactor identification. We compared the Student's t-test and Pearson's R correlation as methods to generate t-statistics and assessed the significance of interactors following TMT-AP-MS. Using a simple linear model of protein recovery in immunoprecipitates to simulate reporter ion ratio distributions, we found that correlation-derived t-statistics protect against bait variance while robustly controlling type I errors (false positives). We experimentally determined the performance of these two approaches for determining t-statistics under two experimental conditions: irreversible prey association to the Hsp40 mutant DNAJB8H31Q followed by stringent washing, and reversible association to 14-3-3ζ with gentle washing. Correlation-derived t-statistics performed at least as well as Student's t-statistics for each sample and with substantial improvement in performance for experiments with high bait-level variance. Deliberately varying bait levels over a large range fails to improve selectivity but does increase the robustness between runs. The use of correlation-derived t-statistics should improve identification of interactors using TMT-AP-MS. Data are available via ProteomeXchange with identifier PXD016613.
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Affiliation(s)
- Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Guy M Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Minh Tran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Athena Villa-Sharma
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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17
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Wang P, Yao S, Kosami K, Guo T, Li J, Zhang Y, Fukao Y, Kaneko‐Kawano T, Zhang H, She Y, Wang P, Xing W, Hanada K, Liu R, Kawano Y. Identification of endogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:415-428. [PMID: 31301098 PMCID: PMC6953209 DOI: 10.1111/pbi.13208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/30/2019] [Accepted: 07/10/2019] [Indexed: 05/10/2023]
Abstract
Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. We identified 236 SSPs including members of two known small signalling peptide families, namely rapid alkalinization factors and phytosulfokines, as well as many other protein families that are known to be involved in immunity, such as proteinase inhibitors and pathogenesis-related protein families. We also isolated 52 unannotated SSPs and among them, we found one gene which we named immune response peptide (IRP) that appeared to encode the precursor of a small signalling peptide regulating rice immunity. In rice suspension cells, the expression of IRP was induced by bacterial peptidoglycan and fungal chitin. Overexpression of IRP enhanced the expression of a defence gene, PAL1 and induced the activation of the MAPKs in rice suspension cells. Moreover, the IRP protein level increased in suspension cell medium after chitin treatment. Collectively, we established a simple and efficient pipeline to discover SSP candidates that probably play important roles in rice immunity and identified 52 unannotated SSPs that may be useful for further elucidation of rice immunity. Our method can be applied to identify SSPs that are involved not only in immunity but also in other plant functions.
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Affiliation(s)
- Pingyu Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaolun Yao
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ken‐ichi Kosami
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Ting Guo
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jing Li
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanyuan Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yoichiro Fukao
- Department of BioinformaticsRitsumeikan UniversityShigaJapan
| | | | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Yi‐Min She
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Present address:
Centre for Biologics EvaluationBiologics and Genetic Therapies Directorate, Health CanadaOttawaOntarioCanada
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Weiman Xing
- Biomolecular Structure and DesignShanghai Center for Plant Stress BiologyShanghaiChina
| | - Kousuke Hanada
- Department of Bioscience and BioinformaticsKyushu Institute of TechnologyFukuokaJapan
| | - Renyi Liu
- Center for Agroforestry Mega Data Science and FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yoji Kawano
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Kihara Institute for Biological ResearchYokohama City UniversityKanagawaJapan
- Institute of Plant Science and ResourcesOkayama UniversityOkayamaJapan
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18
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Gurjar SA, Wheeler JX, Wadhwa M, Thorpe R, Kimber I, Derrick JP, Dearman RJ, Metcalfe C. The impact of thioredoxin reduction of allosteric disulfide bonds on the therapeutic potential of monoclonal antibodies. J Biol Chem 2019; 294:19616-19634. [PMID: 31727737 PMCID: PMC6926469 DOI: 10.1074/jbc.ra119.010637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/04/2019] [Indexed: 12/21/2022] Open
Abstract
Therapeutic mAbs are used to manage a wide range of cancers and autoimmune disorders. However, mAb-based treatments are not always successful, highlighting the need for a better understanding of the factors influencing mAb efficacy. Increased levels of oxidative stress associated with several diseases are counteracted by the activities of various oxidoreductase enzymes, such as thioredoxin (Trx), which also reduces allosteric disulfide bonds in proteins, including mAbs. Here, using an array of in vitro assays, we explored the functional effects of Trx-mediated reduction on the mechanisms of action of six therapeutic mAbs. We found that Trx reduces the interchain disulfide bonds of the mAbs, after which they remain intact but have altered function. In general, this reduction increased antigen-binding capacity, resulting in, for example, enhanced tumor necrosis factor (TNF) neutralization by two anti-TNF mAbs. Conversely, Trx reduction decreased the antiproliferative activity of an anti-tyrosine kinase-type cell-surface receptor HER2 mAb. In all of the mAbs, Fc receptor binding was abrogated by Trx activity, with significant loss in both complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity (ADCC) activity of the mAbs tested. We also confirmed that without alkylation, Trx-reduced interchain disulfide bonds reoxidize, and ADCC activity is restored. In summary, Trx-mediated reduction has a substantial impact on the functional effects of an mAb, including variable effects on antigen binding and Fc function, with the potential to significantly impact mAb efficacy in vivo.
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Affiliation(s)
- Shalom A Gurjar
- Division of Biotherapeutics, The National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Jun X Wheeler
- Division of Technology Development and Infrastructure, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Meenu Wadhwa
- Division of Biotherapeutics, The National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Robin Thorpe
- Division of Biotherapeutics, The National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Ian Kimber
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Jeremy P Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Rebecca J Dearman
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Clive Metcalfe
- Division of Biotherapeutics, The National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
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19
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Rathore R, Sonwane BP, Jagadeeshaprasad MG, Kahar S, Santhakumari B, Unnikrishnan AG, Kulkarni MJ. Glycation of glucose sensitive lysine residues K36, K438 and K549 of albumin is associated with prediabetes. J Proteomics 2019; 208:103481. [PMID: 31394310 DOI: 10.1016/j.jprot.2019.103481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
Prediabetes is a risk factor for the development of diabetes. Early diagnosis of prediabetes may prevent the onset and progression of diabetes and its associated complications. Therefore, this study aimed at the identification of novel markers for efficient prediction of prediabetes. In this pursuit, we have evaluated the ability of glycated peptides of albumin in predicting prediabetes. Glycated peptides of in vitro glycated albumin were characterized by data dependent acquisition and parallel reaction monitoring using LC-HRMS. Amongst 14 glycated peptides characterized in vitro, four peptides, particularly, FK(CML)DLGEENFK, K(AML)VPQVSTPTLVEVSR, K(CML)VPQVSTPTLVEVSR, and K(AML)QTALVELVK, corresponding to 3 glucose sensitive lysine residues K36, K438, and K549, respectively showed significantly higher abundance in prediabetes than control. Additionally, the abundance of three of these peptides, namely K(AML)QTALVELVK, K(CML)VPQVSTPTLVEVSR and FK(CML)DLGEENFK was >1.8-fold in prediabetes, which was significantly higher than the differences observed for FBG, PPG, and HbA1c. Further, the four glycated peptides showed a significant correlation with FBG, PPG, HbA1c, triglycerides, VLDL, and HDL. This study supports that glycated peptides of glucose sensitive lysine residues K36, K438 and K549 of albumin could be potentially useful markers for prediction of prediabetes. SIGNIFICANCE: Undiagnosed prediabetes may lead to diabetes and associated complications. This study reports targeted quantification of four glycated peptides particulary FK(CML)DLGEENFK, K(AML)VPQVSTPTLVEVSR, K(CML)VPQVSTPTLVEVSR, and K(AML)QTALVELVK, corresponding to 3 glucose sensitive lysine residues K36, K438 and K549 respectively by parallel reaction monitoring in healthy and prediabetic subjects. These peptides showed significantly higher abundance in prediabetes than healthy subjects, and showed significant correlation with various clinical parameters including FBG, PPG, HbA1c, and altered lipid profile. Therefore, together these four peptides constitute a panel of markers that can be useful for prediction of prediabetes.
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Affiliation(s)
- Rajeshwari Rathore
- Proteomics Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Babasaheb P Sonwane
- Proteomics Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M G Jagadeeshaprasad
- Proteomics Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - B Santhakumari
- Proteomics Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Mahesh J Kulkarni
- Proteomics Facility, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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20
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Protein profiling and pseudo-parallel reaction monitoring to monitor a fusion-associated conformational change in hemagglutinin. Anal Bioanal Chem 2019; 411:4987-4998. [PMID: 31254054 DOI: 10.1007/s00216-019-01921-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/22/2022]
Abstract
Influenza infection requires viral escape from early endosomes into the cytosol, which is enabled by an acid-induced irreversible conformational transformation in the viral protein hemagglutinin. Despite the direct relationship between this conformational change and infectivity, label-free methods for characterizing this and other protein conformational changes in biological mixtures are limited. While the chemical reactivity of the protein backbone and side-chain residues is a proxy for protein conformation, coupling this reactivity to quantitative mass spectrometry is a challenge in complex environments. Herein, we evaluate whether electrophilic amidination coupled with pseudo-parallel reaction monitoring is an effective label-free approach to detect the fusion-associated conformational transformation in recombinant hemagglutinin (rHA). We identified rHA peptides that are differentially amidinated between the pre- and post-fusion states, and validated that this difference relies upon the fusion-associated conformational switch. We further demonstrate that we can distinguish the fusion profile in a matrix of digested cellular lysate. This fusion assay can be used to evaluate fusion competence for modified HA. Graphical abstract.
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21
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Stafford JM, Lee CH, Voigt P, Descostes N, Saldaña-Meyer R, Yu JR, Leroy G, Oksuz O, Chapman JR, Suarez F, Modrek AS, Bayin NS, Placantonakis DG, Karajannis MA, Snuderl M, Ueberheide B, Reinberg D. Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma. SCIENCE ADVANCES 2018; 4:eaau5935. [PMID: 30402543 PMCID: PMC6209383 DOI: 10.1126/sciadv.aau5935] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/27/2018] [Indexed: 05/17/2023]
Abstract
A methionine substitution at lysine-27 on histone H3 variants (H3K27M) characterizes ~80% of diffuse intrinsic pontine gliomas (DIPG) and inhibits polycomb repressive complex 2 (PRC2) in a dominant-negative fashion. Yet, the mechanisms for this inhibition and abnormal epigenomic landscape have not been resolved. Using quantitative proteomics, we discovered that robust PRC2 inhibition requires levels of H3K27M greatly exceeding those of PRC2, seen in DIPG. While PRC2 inhibition requires interaction with H3K27M, we found that this interaction on chromatin is transient, with PRC2 largely being released from H3K27M. Unexpectedly, inhibition persisted even after PRC2 dissociated from H3K27M-containing chromatin, suggesting a lasting impact on PRC2. Furthermore, allosterically activated PRC2 is particularly sensitive to H3K27M, leading to the failure to spread H3K27me from PRC2 recruitment sites and consequently abrogating PRC2's ability to establish H3K27me2-3 repressive chromatin domains. In turn, levels of polycomb antagonists such as H3K36me2 are elevated, suggesting a more global, downstream effect on the epigenome. Together, these findings reveal the conditions required for H3K27M-mediated PRC2 inhibition and reconcile seemingly paradoxical effects of H3K27M on PRC2 recruitment and activity.
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Affiliation(s)
- James M. Stafford
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Philipp Voigt
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gary Leroy
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Fernando Suarez
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pediatrics, NYUSoM, New York, NY, USA
| | - Aram S. Modrek
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
| | - N. Sumru Bayin
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
| | - Dimitris G. Placantonakis
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Neurosurgery, NYUSoM, New York, NY, USA
- Kimmel Center for Stem Cell Biology, NYUSoM, New York, NY, USA
- Neuroscience Institute, NYUSoM, New York, NY, USA
| | - Matthias A. Karajannis
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pediatrics, NYUSoM, New York, NY, USA
| | - Matija Snuderl
- Laura and Isaac Perlmutter Cancer Center, NYUSoM, New York, NY, USA
- Department of Pathology, Division of Neuropathology, NYUSoM, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Proteomics Laboratory, NYUSoM, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYUSoM, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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22
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Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B. Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline. Mol Cell Proteomics 2018; 17:1239-1244. [PMID: 29487113 DOI: 10.1074/mcp.ra117.000543] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/21/2018] [Indexed: 11/06/2022] Open
Abstract
To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers and readers immediate visual access to the data behind published conclusions, we present Panorama Public (https://panoramaweb.org/public.url), a repository of Skyline documents supporting published results. Panorama Public is built on Panorama, an open source data management system for mass spectrometry data processed with the Skyline targeted mass spectrometry environment. The Panorama web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via a web-browser. Skyline users can easily upload their documents to a Panorama server and allow other researchers to explore uploaded results in the Panorama web-interface through a variety of familiar summary graphs as well as annotated views of the chromatographic peaks processed with Skyline. This makes Panorama ideal for sharing targeted, quantitative results contained in Skyline documents with collaborators, reviewers, and the larger proteomics community. The Panorama Public repository employs the full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review.
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Affiliation(s)
- Vagisha Sharma
- From the ‡University of Washington, Seattle, Washington 98195
| | | | | | - Christina Ludwig
- ‖Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, Freising, Germany
| | - Jacob D Jaffe
- **The Broad Institute, Cambridge, Massachusetts 02142
| | | | - Brendan MacLean
- From the ‡University of Washington, Seattle, Washington 98195;
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23
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Ramirez MI, Amorim MG, Gadelha C, Milic I, Welsh JA, Freitas VM, Nawaz M, Akbar N, Couch Y, Makin L, Cooke F, Vettore AL, Batista PX, Freezor R, Pezuk JA, Rosa-Fernandes L, Carreira ACO, Devitt A, Jacobs L, Silva IT, Coakley G, Nunes DN, Carter D, Palmisano G, Dias-Neto E. Technical challenges of working with extracellular vesicles. NANOSCALE 2018; 10:881-906. [PMID: 29265147 DOI: 10.1039/c7nr08360b] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Extracellular Vesicles (EVs) are gaining interest as central players in liquid biopsies, with potential applications in diagnosis, prognosis and therapeutic guidance in most pathological conditions. These nanosized particles transmit signals determined by their protein, lipid, nucleic acid and sugar content, and the unique molecular pattern of EVs dictates the type of signal to be transmitted to recipient cells. However, their small sizes and the limited quantities that can usually be obtained from patient-derived samples pose a number of challenges to their isolation, study and characterization. These challenges and some possible options to overcome them are discussed in this review.
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Affiliation(s)
- Marcel I Ramirez
- Fundação Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brazil and Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ivana Milic
- School of Life and Health Sciences, Aston University, England, UK
| | | | | | - Muhammad Nawaz
- Universidade de São Paulo, São Paulo, SP, Brazil and University of Gothenburg, Sweden
| | - Naveed Akbar
- Division of Cardiovascular Medicine, University of Oxford, Oxford, England, UK
| | - Yvonne Couch
- Acute Stroke Programme, RDM-Investigative Medicine, University of Oxford, Oxford, England, UK
| | - Laura Makin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, England, UK
| | - Fiona Cooke
- University of St Andrews, St Andrews, Fife, Scotland, UK
| | - Andre L Vettore
- Federal University of São Paulo campus Diadema, Diadema, Brazil
| | | | | | - Julia A Pezuk
- Universidade Anhanguera de São Paulo, São Paulo, Brazil
| | - Lívia Rosa-Fernandes
- Universidade de São Paulo, São Paulo, SP, Brazil and University of Southern Denmark, Odense, Denmark
| | | | - Andrew Devitt
- School of Life and Health Sciences, Aston University, England, UK
| | | | | | - Gillian Coakley
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK
| | - Diana N Nunes
- CIPE, A.C.Camargo Cancer Center, São Paulo, SP, Brazil.
| | - Dave Carter
- Oxford Brookes University, Oxford, England, UK
| | - Giuseppe Palmisano
- Universidade de São Paulo, São Paulo, SP, Brazil and IRCCS, Fondazione Santa Lucia, Rome, Italy
| | - Emmanuel Dias-Neto
- CIPE, A.C.Camargo Cancer Center, São Paulo, SP, Brazil. and Universidade de São Paulo, São Paulo, SP, Brazil
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25
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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26
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Kilambi HV, Manda K, Rai A, Charakana C, Bagri J, Sharma R, Sreelakshmi Y. Green-fruited Solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4803-4819. [PMID: 29048567 PMCID: PMC5853803 DOI: 10.1093/jxb/erx288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/21/2017] [Indexed: 05/22/2023]
Abstract
Members of the tomato clade exhibit a wide diversity in fruit color, but the mechanisms governing inter-species diversity of coloration are largely unknown. The carotenoid profiles, carotenogenic gene expression and proteome profiles of green-fruited Solanum habrochaites (SH), orange-fruited S. galapagense, and red-fruited S. pimpinellifolium were compared with cultivated tomato [S. lycopersicum cv. Ailsa Craig (SL)] to decipher the molecular basis of coloration diversity. Green-fruited SH, though it showed normal expression of chromoplast-specific phytoene synthase1 and lycopene β-cyclase genes akin to orange/red-fruited species, failed to accumulate lycopene and β-carotene. The SH phytoene synthase1 cDNA encoded an enzymatically active protein, whereas the lycopene β-cyclase cDNA was barely active. Consistent with its green-fruited nature, SH's fruits retained chloroplast structure and PSII activity, and had impaired chlorophyll degradation with high pheophorbide a levels. Comparison of the fruit proteomes with SL revealed retention of the proteome complement related to photosynthesis in SH. Targeted peptide monitoring revealed a low abundance of key carotenogenic and sequestration proteins in SH compared with tomato. The green-fruitedness of SH appears to stem from blocks at several critical steps regulating fruit-specific carotenogenesis namely the absence of chloroplast to chromoplast transformation, block in carotenoid biosynthesis, and a dearth of carotenoid sequestering proteins.
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Affiliation(s)
- Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kalyani Manda
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Avanish Rai
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Chaitanya Charakana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Jayram Bagri
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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27
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Woo J, Han D, Wang JI, Park J, Kim H, Kim Y. Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation. J Proteome Res 2017; 16:3419-3432. [DOI: 10.1021/acs.jproteome.7b00445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Dohyun Han
- Proteomics
Core Facility, Biomedical Research Institute, Seoul National University Hospital, 101 Daehangro, Seoul 110-799, Korea
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28
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Zavialova MG, Shevchenko VE, Nikolaev EN, Zgoda VG. Is myelin basic protein a potential biomarker of brain cancer? EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:192-196. [PMID: 29028399 DOI: 10.1177/1469066717719810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Myelin basic protein is a potential biomarker for the central nervous system diseases in which the myelin sheath is destroyed. Using pseudo-selected reaction monitoring and the method of standard additions, we have measured the myelin basic protein level in the cerebrospinal fluid of patients with neurotrauma (n = 6), chronic neurodegenerative diseases (n = 2) and brain cancer (n = 5). Myelin basic protein was detected only in four out of five cerebrospinal fluid samples of patients with brain cancer. The cerebrospinal fluid myelin basic protein level ranged from 3.7 to 8.8 ng ml-1. We suggest that monitoring of myelin basic protein in cerebrospinal fluid can serve as a diagnostic test for the brain cancer.
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Affiliation(s)
- M G Zavialova
- 1 Institute of Biomedical Chemistry (IBMC), Moscow, Russia
| | - V E Shevchenko
- 2 Blokhin Russian Cancer Research Center, Moscow, Russia
| | - E N Nikolaev
- 1 Institute of Biomedical Chemistry (IBMC), Moscow, Russia
- 3 Skolkovo Institute of Science and Technology (Skoltech), Skolkovo, Russia
| | - V G Zgoda
- 1 Institute of Biomedical Chemistry (IBMC), Moscow, Russia
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29
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Duan J, Gaffrey MJ, Qian WJ. Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines. MOLECULAR BIOSYSTEMS 2017; 13:816-829. [PMID: 28357434 PMCID: PMC5493446 DOI: 10.1039/c6mb00861e] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein thiols play a crucial role in redox signaling, in the regulation of enzymatic activity and protein function, and in maintaining redox homeostasis in living systems. The unique chemical reactivity of the thiol group makes protein cysteines susceptible to reactions with reactive oxygen and nitrogen species that form various reversible and irreversible post-translational modifications (PTMs). The reversible PTMs in particular are major components of redox signaling and are involved in the regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in both healthy and disease states has been increasingly recognized. Herein, we review recent advances in quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including general considerations of sample processing, chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for specific biological applications. Although technical limitations remain, redox proteomics is paving the way to a better understanding of redox signaling and regulation in both healthy and disease states.
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Affiliation(s)
- Jicheng Duan
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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30
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A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition. Anal Chim Acta 2017; 964:7-23. [DOI: 10.1016/j.aca.2017.01.059] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/18/2023]
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Federspiel JD, Codreanu SG, Goyal S, Albertolle ME, Lowe E, Teague J, Wong H, Guengerich FP, Liebler DC. Specificity of Protein Covalent Modification by the Electrophilic Proteasome Inhibitor Carfilzomib in Human Cells. Mol Cell Proteomics 2016; 15:3233-3242. [PMID: 27503896 DOI: 10.1074/mcp.m116.059709] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 12/25/2022] Open
Abstract
Carfilzomib (CFZ) is a second-generation proteasome inhibitor that is Food and Drug Administration and European Commission approved for the treatment of relapsed or refractory multiple myeloma. CFZ is an epoxomicin derivative with an epoxyketone electrophilic warhead that irreversibly adducts the catalytic threonine residue of the β5 subunit of the proteasome. Although CFZ produces a highly potent, sustained inactivation of the proteasome, the electrophilic nature of the drug could potentially produce off-target protein adduction. To address this possibility, we synthesized an alkynyl analog of CFZ and investigated protein adduction by this analog in HepG2 cells. Using click chemistry coupled with streptavidin based IP and shotgun tandem mass spectrometry (MS/MS), we identified two off-target proteins, cytochrome P450 27A1 (CYP27A1) and glutathione S-transferase omega 1 (GSTO1), as targets of the alkynyl CFZ probe. We confirmed the adduction of CYP27A1 and GSTO1 by streptavidin capture and immunoblotting methodology and then site-specifically mapped the adducts with targeted MS/MS methods. Although CFZ adduction of CYP27A1 and GSTO1 in vitro decreased the activities of these enzymes, the small fraction of these proteins modified by CFZ in intact cells should limit the impact of these off-target modifications. The data support the high selectivity of CFZ for covalent modification of its therapeutic targets, despite the presence of a reactive electrophile. The approach we describe offers a generalizable method to evaluate the safety profile of covalent protein-modifying therapeutics.
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Affiliation(s)
- Joel D Federspiel
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Simona G Codreanu
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Sandeep Goyal
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Matthew E Albertolle
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Eric Lowe
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - Juli Teague
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - Hansen Wong
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - F Peter Guengerich
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Daniel C Liebler
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee;
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Izquierdo-Serra M, Bautista-Barrufet A, Trapero A, Garrido-Charles A, Díaz-Tahoces A, Camarero N, Pittolo S, Valbuena S, Pérez-Jiménez A, Gay M, García-Moll A, Rodríguez-Escrich C, Lerma J, de la Villa P, Fernández E, Pericàs MÀ, Llebaria A, Gorostiza P. Optical control of endogenous receptors and cellular excitability using targeted covalent photoswitches. Nat Commun 2016; 7:12221. [PMID: 27436051 PMCID: PMC4961765 DOI: 10.1038/ncomms12221] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 06/10/2016] [Indexed: 12/15/2022] Open
Abstract
Light-regulated drugs allow remotely photoswitching biological activity and enable plausible therapies based on small molecules. However, only freely diffusible photochromic ligands have been shown to work directly in endogenous receptors and methods for covalent attachment depend on genetic manipulation. Here we introduce a chemical strategy to covalently conjugate and photoswitch the activity of endogenous proteins and demonstrate its application to the kainate receptor channel GluK1. The approach is based on photoswitchable ligands containing a short-lived, highly reactive anchoring group that is targeted at the protein of interest by ligand affinity. These targeted covalent photoswitches (TCPs) constitute a new class of light-regulated drugs and act as prosthetic molecules that photocontrol the activity of GluK1-expressing neurons, and restore photoresponses in degenerated retina. The modularity of TCPs enables the application to different ligands and opens the way to new therapeutic opportunities. Biological activity can be photoswitched by light-regulated drugs, but so far only diffusible ligands have been shown to work on endogenous receptors. Here the authors develop targeted covalent photoswitches that couple to a protein target by ligand affinity, and demonstrate photocontrol of GluK1-expressing neurons.
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Affiliation(s)
| | - Antoni Bautista-Barrufet
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain
| | - Ana Trapero
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Institut de Química Avançada de Catalunya (IQAC-CSIC), Barcelona 08034, Spain
| | | | - Ariadna Díaz-Tahoces
- Instituto de Bioingeniería, Universidad Miguel Hernández (UMH), Elche 03202, Spain
| | - Nuria Camarero
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain
| | - Silvia Pittolo
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain
| | - Sergio Valbuena
- Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante 03550, Spain
| | | | - Marina Gay
- Institut de Recerca en Biomedicina (IRBB), Barcelona 08028, Spain
| | | | - Carles Rodríguez-Escrich
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain
| | - Juan Lerma
- Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante 03550, Spain
| | - Pedro de la Villa
- Universidad de Alcalá de Henares (UAH), Alcalá de Henares 28871, Spain
| | - Eduardo Fernández
- Instituto de Bioingeniería, Universidad Miguel Hernández (UMH), Elche 03202, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza 50018, Spain
| | - Miquel À Pericàs
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain.,Departament de Química Inorgànica i Orgànica, Universitat de Barcelona (UB), Barcelona 08007, Spain
| | - Amadeu Llebaria
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Barcelona 08034, Spain
| | - Pau Gorostiza
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza 50018, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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Federspiel JD, Codreanu SG, Palubinsky AM, Winland AJ, Betanzos CM, McLaughlin B, Liebler DC. Assembly Dynamics and Stoichiometry of the Apoptosis Signal-regulating Kinase (ASK) Signalosome in Response to Electrophile Stress. Mol Cell Proteomics 2016; 15:1947-61. [PMID: 27006476 DOI: 10.1074/mcp.m115.057364] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 01/29/2023] Open
Abstract
Apoptosis signal-regulating kinase 1 (ASK1) is a key sensor kinase in the mitogen-activated protein kinase pathway that transduces cellular responses to oxidants and electrophiles. ASK1 is regulated by a large, dynamic multiprotein signalosome complex, potentially including over 90 reported ASK1-interacting proteins. We employed both shotgun and targeted mass spectrometry assays to catalogue the ASK1 protein-protein interactions in HEK-293 cells treated with the prototypical lipid electrophile 4-hydroxy-2-nonenal (HNE). Using both epitope-tagged overexpression and endogenous expression cell systems, we verified most of the previously reported ASK1 protein-protein interactions and identified 14 proteins that exhibited dynamic shifts in association with ASK1 in response to HNE stress. We used precise stable isotope dilution assays to quantify protein stoichiometry in the ASK signalosome complex and identified ASK2 at a 1:1 stoichiometric ratio with ASK1 and 14-3-3 proteins (YWHAQ, YWHAB, YWHAH, and YWHAE) collectively at a 0.5:1 ratio with ASK1 as the main components. Several other proteins, including ASK3, PARK7, PRDX1, and USP9X were detected with stoichiometries of 0.1:1 or less. These data support an ASK signalosome comprising a multimeric core complex of ASK1, ASK2, and 14-3-3 proteins, which dynamically engages other binding partners needed to mediate diverse stress-response signaling events. This study further demonstrates the value of combining global and targeted MS approaches to interrogate multiprotein complex composition and dynamics.
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Affiliation(s)
- Joel D Federspiel
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine
| | - Simona G Codreanu
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine
| | - Amy M Palubinsky
- §Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University
| | - Ama J Winland
- ¶Department of Neurology, Vanderbilt University, Nashville, Tennessee, 37232
| | | | - BethAnn McLaughlin
- ¶Department of Neurology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Daniel C Liebler
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine;
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Analysis of Urinary Prostate-Specific Antigen Glycoforms in Samples of Prostate Cancer and Benign Prostate Hyperplasia. DISEASE MARKERS 2016; 2016:8915809. [PMID: 27065039 PMCID: PMC4811082 DOI: 10.1155/2016/8915809] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/22/2016] [Accepted: 02/03/2016] [Indexed: 11/17/2022]
Abstract
Glycans of prostate-specific antigen (PSA) in prostate cancer were found to be different from that in benign disease. It is difficult to analyze heterogeneous PSA glycoforms in each individual specimen because of low protein abundance and the limitation of detection sensitivity. We developed a method for prostate cancer diagnosis based on PSA glycoforms. Specific glycoforms were screened in each clinical sample based on liquid chromatography-tandem mass spectrometry with ion accumulation. To look for potential biomarkers, normalized abundance of each glycoform in benign prostate hyperplasia (BPH) and in prostate cancer was evaluated. The PSA glycoform, Hex5HexNAc4NeuAc1dHex1, and monosialylated, sialylated, and unfucosylated glycoforms differed significantly between the prostate cancer and BPH samples. The detection sensitivity (87.5%) and specificity (60%) for prostate cancer identification are higher than those of the serum PSA marker. As low as 100 amol PSA could be detected with the ion accumulation method which has not been reported before. The improved detection specificity can help reduce unnecessary examinations.
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35
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Kawahara R, Bollinger JG, Rivera C, Ribeiro ACP, Brandão TB, Paes Leme AF, MacCoss MJ. A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva. Proteomics 2015; 16:159-73. [PMID: 26552850 DOI: 10.1002/pmic.201500224] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/27/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022]
Abstract
Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source of biomarkers. In this study, we build an SRM assay that targets fourteen OSCC candidate biomarker proteins, which were evaluated in a set of clinically-derived saliva samples. Using Skyline software package, we demonstrated a statistically significant higher abundance of the C1R, LCN2, SLPI, FAM49B, TAGLN2, CFB, C3, C4B, LRG1, SERPINA1 candidate biomarkers in the saliva of OSCC patients. Furthermore, our study also demonstrated that CFB, C3, C4B, SERPINA1 and LRG1 are associated with the risk of developing OSCC. Overall, this study successfully used targeted proteomics to measure in saliva a panel of biomarker candidates for OSCC.
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Affiliation(s)
- Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - César Rivera
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ana Carolina P Ribeiro
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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36
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Barbariga M, Curnis F, Andolfo A, Zanardi A, Lazzaro M, Conti A, Magnani G, Volontè MA, Ferrari L, Comi G, Corti A, Alessio M. Ceruloplasmin functional changes in Parkinson's disease-cerebrospinal fluid. Mol Neurodegener 2015; 10:59. [PMID: 26537957 PMCID: PMC4634150 DOI: 10.1186/s13024-015-0055-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/29/2015] [Indexed: 01/23/2023] Open
Abstract
Background Ceruloplasmin, a ferroxidase present in cerebrospinal fluid (CSF), plays a role in iron homeostasis protecting tissues from oxidative damage. Its reduced enzymatic activity was reported in Parkinson’s disease (PD) contributing to the pathological iron accumulation. We previously showed that ceruloplasmin is modified by oxidation in vivo, and, in addition, in vitro by deamidation of specific NGR-motifs that foster the gain of integrin-binding function. Here we investigated whether the loss of ceruloplasmin ferroxidase activity in the CSF of PD patients was accompanied by NGR-motifs deamidation and gain of function. Results We have found that endogenous ceruloplasmin in the CSF of PD patients showed structural changes, deamidation of the 962NGR-motif which is usually hidden within the ceruloplasmin structure, and the gain of integrin-binding function. These effects occur owing to the presence of abnormal levels of hydrogen peroxide we detected in the CSF of PD patients. Interestingly, the pathological CSF's environment of PD patients promoted the same modifications in the exogenously added ceruloplasmin, which in turn resulted in loss of ferroxidase-activity and acquisition of integrin-binding properties. Conclusions We show that in pathological oxidative environment of PD-CSF the endogenous ceruloplasmin, in addition to loss-of-ferroxidase function, is modified as to gain integrin-binding function. These findings, beside the known role of ceruloplasmin in iron homeostasis, might have important pathogenic implications due to the potential triggering of signals mediated by the unusual integrin binding in cells of central nervous system. Furthermore, there are pharmacological implications because, based on data obtained in murine models, the administration of ceruloplasmin has been proposed as potential therapeutic treatment of PD, however, the observed CSF's pro-oxidant properties raise the possibility that in human the ceruloplasmin-based therapeutic approach might not be efficacious. Electronic supplementary material The online version of this article (doi:10.1186/s13024-015-0055-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Barbariga
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Present address: Translational Neurology group, Wallenberg Neuroscience Center, BMC A10, 221 84, Lund, Sweden.
| | - Flavio Curnis
- Tumor Biology and Vascular Targeting, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Annapaola Andolfo
- ProMiFa-Protein Microsequencing Facility, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Alan Zanardi
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Vita-Salute San Raffaele University, via Olgettina 60, 20132, Milan, Italy.
| | - Massimo Lazzaro
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Antonio Conti
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Giuseppe Magnani
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Maria Antonietta Volontè
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Laura Ferrari
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Giancarlo Comi
- INSPE-Institute of Experimental Neurology, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy. .,Vita-Salute San Raffaele University, via Olgettina 60, 20132, Milan, Italy.
| | - Angelo Corti
- Tumor Biology and Vascular Targeting, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Massimo Alessio
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
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Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW. Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. Anal Chem 2015; 87:10222-9. [PMID: 26398777 PMCID: PMC5677521 DOI: 10.1021/acs.analchem.5b02983] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in commercial mass spectrometers with higher resolving power and faster scanning capabilities have expanded their functionality beyond traditional data-dependent acquisition (DDA) to targeted proteomics with higher precision and multiplexing. Using an orthogonal quadrupole time-of flight (QqTOF) LC-MS system, we investigated the feasibility of implementing large-scale targeted quantitative assays using scheduled, high resolution multiple reaction monitoring (sMRM-HR), also referred to as parallel reaction monitoring (sPRM). We assessed the selectivity and reproducibility of PRM, also referred to as parallel reaction monitoring, by measuring standard peptide concentration curves and system suitability assays. By evaluating up to 500 peptides in a single assay, the robustness and accuracy of PRM assays were compared to traditional SRM workflows on triple quadrupole instruments. The high resolution and high mass accuracy of the full scan MS/MS spectra resulted in sufficient selectivity to monitor 6-10 MS/MS fragment ions per target precursor, providing flexibility in postacquisition assay refinement and optimization. The general applicability of the sPRM workflow was assessed in complex biological samples by first targeting 532 peptide precursor ions in a yeast lysate, and then 466 peptide precursors from a previously generated candidate list of differentially expressed proteins in whole cell lysates from E. coli. Lastly, we found that sPRM assays could be rapidly and efficiently developed in Skyline from DDA libraries when acquired on the same QqTOF platform, greatly facilitating their successful implementation. These results establish a robust sPRM workflow on a QqTOF platform to rapidly transition from discovery analysis to highly multiplexed, targeted peptide quantitation.
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Affiliation(s)
- Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Foege Building S113, 3720 15th Avenue NE, Seattle, Washington 98195, United States
| | - Jason M. Held
- Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Alexandria K. Sahu
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Matthew J. Rardin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Dylan J. Sorensen
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Theodore Peters
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, 2160 South First Avenue, Maywood, Illinois 60153, United States
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Foege Building S113, 3720 15th Avenue NE, Seattle, Washington 98195, United States
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
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Lesur A, Ancheva L, Kim YJ, Berchem G, van Oostrum J, Domon B. Screening protein isoforms predictive for cancer using immunoaffinity capture and fast LC-MS in PRM mode. Proteomics Clin Appl 2015; 9:695-705. [PMID: 25656350 DOI: 10.1002/prca.201400158] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 01/11/2023]
Abstract
PURPOSE We report an immunocapture strategy to extract proteins known to harbor driver mutations for a defined cancer type before the simultaneous assessment of their mutational status by MS. Such a method bypasses the sensitivity and selectivity issues encountered during the analysis of unfractionated complex biological samples. EXPERIMENTAL DESIGN Fast LC separations using short nanobore columns hyphenated with a high-resolution quadrupole-orbitrap mass spectrometer have been devised to take advantage of fast MS cycle times in conjunction with sharp chromatographic peak widths to accelerate the sample analysis throughput. Such an analytical platform is well suited to analyze simple protein mixtures obtained after immunoaffinity enrichment. RESULTS After establishing the technical performance of the platform, the method was applied to the quantitative profiling of cellular Ras and EGFR protein isoforms, as well as serum amyloid A isoforms in plasma. CONCLUSIONS AND CLINICAL RELEVANCE Immunoaffinity purification combined with fast LC-MS detection for the detection of driver mutations in tissue and tumor biomarkers in plasma samples can assist clinicians to select an optimal therapeutic intervention for patients.
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Affiliation(s)
- Antoine Lesur
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Lina Ancheva
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Yeoun Jin Kim
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Guy Berchem
- Laboratory of Experimental Hemato-Oncology, CRP-Santé, Strassen, Luxembourg.,Centre Hospitalier Luxembourg (CHL), Strassen, Luxembourg
| | - Jan van Oostrum
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
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Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM. Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell 2015; 159:1615-25. [PMID: 25525879 DOI: 10.1016/j.cell.2014.11.046] [Citation(s) in RCA: 313] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/12/2014] [Accepted: 11/21/2014] [Indexed: 12/20/2022]
Abstract
Sirtuins (SIRTs) are critical enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, mitochondrial SIRT4 and SIRT5 have little to no deacetylase activity, and a robust catalytic activity for SIRT4 has been elusive. Here, we establish SIRT4 as a cellular lipoamidase that regulates the pyruvate dehydrogenase complex (PDH). Importantly, SIRT4 catalytic efficiency for lipoyl- and biotinyl-lysine modifications is superior to its deacetylation activity. PDH, which converts pyruvate to acetyl-CoA, has been known to be primarily regulated by phosphorylation of its E1 component. We determine that SIRT4 enzymatically hydrolyzes the lipoamide cofactors from the E2 component dihydrolipoyllysine acetyltransferase (DLAT), diminishing PDH activity. We demonstrate SIRT4-mediated regulation of DLAT lipoyl levels and PDH activity in cells and in vivo, in mouse liver. Furthermore, metabolic flux switching via glutamine stimulation induces SIRT4 lipoamidase activity to inhibit PDH, highlighting SIRT4 as a guardian of cellular metabolism.
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Affiliation(s)
- Rommel A Mathias
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA; Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Adam Oberstein
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Hanna G Budayeva
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Rumela Chakrabarti
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Elizabeth A Rowland
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas Shenk
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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40
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Schmerberg CM, Liang Z, Li L. Data-independent MS/MS quantification of neuropeptides for determination of putative feeding-related neurohormones in microdialysate. ACS Chem Neurosci 2015; 6:174-80. [PMID: 25552291 PMCID: PMC4304520 DOI: 10.1021/cn500253u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
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Food consumption is an important
behavior that is regulated by
an intricate array of neuropeptides (NPs). Although many feeding-related
NPs have been identified in mammals, precise mechanisms are unclear
and difficult to study in mammals, as current methods are not highly
multiplexed and require extensive a priori knowledge about analytes.
New advances in data-independent acquisition (DIA) MS/MS and the open-source
quantification software Skyline have opened up the possibility to
identify hundreds of compounds and quantify them from a single DIA
MS/MS run. An untargeted DIA MSE quantification method
using Skyline software for multiplexed, discovery-driven quantification
was developed and found to produce linear calibration curves for peptides
at physiologically relevant concentrations using a protein digest
as internal standard. By using this method, preliminary relative quantification
of the crab Cancer borealis neuropeptidome (<2
kDa, 137 peptides from 18 families) was possible in microdialysates
from 8 replicate feeding experiments. Of these NPs, 55 were detected
with an average mass error below 10 ppm. The time-resolved profiles
of relative concentration changes for 6 are shown, and there is great
potential for the use of this method in future experiments to aid
in correlation of NP changes with behavior. This work presents an
unbiased approach to winnowing candidate NPs related to a behavior
of interest in a functionally relevant manner, and demonstrates the
success of such a UPLC-MSE quantification method using
the open source software Skyline.
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Affiliation(s)
- Claire M. Schmerberg
- Translational
Neuroscience, Psychiatry Department, Duke University Medical Center, Durham, North Carolina 27708, United States
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41
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Zav'ialova MG, Zgoda VG, Kharybin ON, Nikolaev EN. [In vitro protein phosphorylation as a template for SRM method development]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 60:668-76. [PMID: 25552507 DOI: 10.18097/pbmc20146006668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphorylation is one of the most common posttranslational modification (PTM) of proteins. Main challenge of phosphoprotein detection is their low abundance comparing to abundance of unmodified proteins. The method of selected reactions monitoring (SRM) allows to perform very sensitive and selective analysis of desired PTMs. Using myelin basic protein (MBP) as a model we have developed a method for phosphoprotein detection by SRM. The method is based on obtaining of phosphoproteins in a reconstituted kinase system and following usage these phosphorylated protein as a template for the development of the SRM method. The developed method was successfully applied for detection of phosphopeptides of myelin basic protein in the samples of human brain glioma.
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Affiliation(s)
| | - V G Zgoda
- Orekhovich Institute of Biomedical Chemistry (IBMC)
| | - O N Kharybin
- Orekhovich Institute of Biomedical Chemistry (IBMC)
| | - E N Nikolaev
- Orekhovich Institute of Biomedical Chemistry (IBMC); Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
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42
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Bereman MS. Tools for monitoring system suitability in LC MS/MS centric proteomic experiments. Proteomics 2014; 15:891-902. [DOI: 10.1002/pmic.201400373] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/12/2014] [Accepted: 10/13/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Michael S. Bereman
- Department of Biological Sciences, Center for Human Health and the Environment; North Carolina State University; Raleigh NC USA
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43
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Bauer M, Ahrné E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A. Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites. J Proteome Res 2014; 13:5973-88. [DOI: 10.1021/pr500860c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna P. Baron
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Luca L. Fava
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Santamaria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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44
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Ritorto MS, Ewan R, Perez-Oliva AB, Knebel A, Buhrlage SJ, Wightman M, Kelly SM, Wood NT, Virdee S, Gray NS, Morrice NA, Alessi DR, Trost M. Screening of DUB activity and specificity by MALDI-TOF mass spectrometry. Nat Commun 2014; 5:4763. [PMID: 25159004 PMCID: PMC4147353 DOI: 10.1038/ncomms5763] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 07/21/2014] [Indexed: 12/22/2022] Open
Abstract
Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analysing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAB/MPN/Mov34 metalloenzyme DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs. Deubiquitylases (DUBs) remove ubiquitin chains from proteins. Here the authors develop a mass spectrometry-based DUB activity screen using unmodified diubiquitin isomers to characterize substrate specificity for 42 human DUBs, and assess the potency and selectivity of 11 DUB inhibitors.
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Affiliation(s)
- Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Richard Ewan
- 1] MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK [2]
| | - Ana B Perez-Oliva
- 1] MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK [2]
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara J Buhrlage
- 1] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, SGM 628, Boston, Massachusetts 02115, USA
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sharon M Kelly
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nathanael S Gray
- 1] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, SGM 628, Boston, Massachusetts 02115, USA
| | - Nicholas A Morrice
- The Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
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45
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Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. Panorama: a targeted proteomics knowledge base. J Proteome Res 2014; 13:4205-10. [PMID: 25102069 PMCID: PMC4156235 DOI: 10.1021/pr5006636] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Panorama
is a web application for storing, sharing, analyzing,
and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software
tool for targeted proteomics experiments. Panorama allows laboratories
to store and organize curated results contained in Skyline documents
with fine-grained permissions, which facilitates distributed collaboration
and secure sharing of published and unpublished data via a web-browser
interface. It is fully integrated with the Skyline workflow and supports
publishing a document directly to a Panorama server from the Skyline
user interface. Panorama captures the complete Skyline document information
content in a relational database schema. Curated results published
to Panorama can be aggregated and exported as chromatogram libraries.
These libraries can be used in Skyline to pick optimal targets in
new experiments and to validate peak identification of target peptides.
Panorama is open-source and freely available. It is distributed as
part of LabKey Server,2 an open source
biomedical research data management system. Laboratories and organizations
can set up Panorama locally by downloading and installing the software
on their own servers. They can also request freely hosted projects
on https://panoramaweb.org, a Panorama server maintained
by the Department of Genome Sciences at the University of Washington.
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Affiliation(s)
- Vagisha Sharma
- University of Washington , Seattle, Washington 98195, United States
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46
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Fiedler KL, McGrath SC, Callahan JH, Ross MM. Characterization of grain-specific peptide markers for the detection of gluten by mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5835-5844. [PMID: 24866027 DOI: 10.1021/jf500997j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Global and targeted mass spectrometry-based proteomic approaches were developed to discover, evaluate, and apply gluten peptide markers to detect low parts per million (ppm) wheat contamination of oats. Prolamins were extracted from wheat, barley, rye, and oat flours and then reduced, alkylated, and digested with chymotrypsin. The resulting peptides were subjected to LC-MS/MS analysis and database matching. No peptide markers common to wheat, barley, and rye were identified that could be used for global gluten detection. However, many grain-specific peptide markers were identified, and a set of these markers was selected for gluten detection and grain differentiation. Wheat flour was spiked into gluten-free oat flour at concentrations of 1-100,000 ppm and analyzed to determine the lowest concentration at which the wheat "contaminant" could be confidently detected in the mixture. The same 2D ion trap instrument that was used for the global proteomics approach was used for the targeted proteomics approach, providing a seamless transition from target discovery to application. A powerful, targeted MS/MS method enabled detection of two wheat peptide markers at the 10 ppm wheat flour-in-oat flour concentration. Because gluten comprises approximately 10% of wheat flour protein, the reported wheat gluten-specific peptides can enable detection of approximately 1 ppm of wheat gluten in oats.
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Affiliation(s)
- Katherine L Fiedler
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, Maryland 20740, United States
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47
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Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2014; 10:551-66. [PMID: 24206228 DOI: 10.1586/14789450.2013.858022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.
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Affiliation(s)
- Kai Pong Law
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, Level 1, 14 Medical Drive, 117599, Singapore
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48
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Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ. Implementation of statistical process control for proteomic experiments via LC MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:581-7. [PMID: 24496601 PMCID: PMC4020592 DOI: 10.1007/s13361-013-0824-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/22/2013] [Accepted: 12/25/2013] [Indexed: 05/11/2023]
Abstract
Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface, which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution), and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.
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Affiliation(s)
- Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA,
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49
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Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13:907-17. [PMID: 24443746 PMCID: PMC3945918 DOI: 10.1074/mcp.m113.036095] [Citation(s) in RCA: 431] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/14/2014] [Indexed: 12/25/2022] Open
Abstract
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
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Affiliation(s)
- Steven A. Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Bruno Domon
- ‖Luxembourg Clinical Proteomics Center, Luxembourg
| | | | | | | | - Ruth Hüttenhain
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- ‖‖University of California San Francisco, California
| | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | - DR Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Ruedi Aebersold
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Emily Boja
- National Cancer Institute, NIH Bethesda, Maryland
| | | | | | | | | | - Daniel Chan
- Johns Hopkins University, Baltimore, Maryland
| | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Jerry S.H. Lee
- National Cancer Institute, NIH Bethesda, Maryland
- Johns Hopkins University, Baltimore, Maryland
| | | | - Robert Moritz
- **Institute for Systems Biology, Seattle, Washington
| | | | | | | | | | | | | | | | - Gordon Whiteley
- Liedos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research
| | - Arun Wiita
- ‖‖University of California San Francisco, California
| | - Susan Weintraub
- University of Texas Health Science Center, San Antonio, Texas
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50
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Abstract
Moving past the discovery phase of proteomics, the term targeted proteomics combines multiple approaches investigating a certain set of proteins in more detail. One such targeted proteomics approach is the combination of liquid chromatography and selected or multiple reaction monitoring mass spectrometry (SRM, MRM). SRM-MS requires prior knowledge of the fragmentation pattern of peptides, as the presence of the analyte in a sample is determined by measuring the m/z values of predefined precursor and fragment ions. Using scheduled SRM-MS, many analytes can robustly be monitored allowing for high-throughput sample analysis of the same set of proteins over many conditions. In this chapter, fundaments of SRM-MS are explained as well as an optimized SRM pipeline from assay generation to data analyzed.
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Affiliation(s)
- H Alexander Ebhardt
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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