1
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Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. Mol Psychiatry 2014; 19:294-301. [PMID: 23439483 DOI: 10.1038/mp.2013.16] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/14/2012] [Accepted: 01/02/2013] [Indexed: 12/18/2022]
Abstract
Many putative genetic factors that confer risk to neurodevelopmental disorders such as autism spectrum disorders (ASDs) and X-linked intellectual disability (XLID), and to neuropsychiatric disorders including attention deficit hyperactivity disorder (ADHD) and schizophrenia (SZ) have been identified in individuals from diverse human populations. Although there is significant aetiological heterogeneity within and between these conditions, recent data show that genetic factors contribute to their comorbidity. Many studies have identified candidate gene associations for these mental health disorders, albeit this is often done in a piecemeal fashion with little regard to the inherent molecular complexity. Here, we sought to abstract relationships from our knowledge of systems level biology to help understand the unique and common genetic drivers of these conditions. We undertook a global and systematic approach to build and integrate available data in gene networks associated with ASDs, XLID, ADHD and SZ. Complex network concepts and computational methods were used to investigate whether candidate genes associated with these conditions were related through mechanisms of gene regulation, functional protein-protein interactions, transcription factor (TF) and microRNA (miRNA) binding sites. Although our analyses show that genetic variations associated with the four disorders can occur in the same molecular pathways and functional domains, including synaptic transmission, there are patterns of variation that define significant differences between disorders. Of particular interest is DNA variations located in intergenic regions that comprise regulatory sites for TFs or miRNA. Our approach provides a hypothetical framework, which will help discovery and analysis of candidate genes associated with neurodevelopmental and neuropsychiatric disorders.
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2
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Bhattacharjee M, Sharma R, Goel R, Balakrishnan L, Renuse S, Advani J, Gupta ST, Verma R, Pinto SM, Sekhar NR, Nair B, Prasad TSK, Harsha HC, Jois R, Shankar S, Pandey A. A multilectin affinity approach for comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy. Clin Proteomics 2013; 10:11. [PMID: 24010407 PMCID: PMC3846907 DOI: 10.1186/1559-0275-10-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/11/2013] [Indexed: 11/10/2022] Open
Abstract
Background Arthritis refers to inflammation of joints and includes common disorders such as rheumatoid arthritis (RA) and spondyloarthropathies (SpAs). These diseases differ mainly in terms of their clinical manifestations and the underlying pathogenesis. Glycoproteins in synovial fluid might reflect the disease activity status in the joints affected by arthritis; yet they have not been systematically studied previously. Although markers have been described for assisting in the diagnosis of RA, there are currently no known biomarkers for SpA. Materials and methods We sought to determine the relative abundance of glycoproteins in RA and SpA by lectin affinity chromatography coupled to iTRAQ labeling and LC-MS/MS analysis. We also used ELISA to validate the overexpression of VCAM-1, one of the candidate proteins identified in this study, in synovial fluid from RA patients. Results and discussion We identified proteins that were previously reported to be overexpressed in RA including metalloproteinase inhibitor 1 (TIMP1), myeloperoxidase (MPO) and several S100 proteins. In addition, we discovered several novel candidates that were overexpressed in SpA including Apolipoproteins C-II and C-III and the SUN domain-containing protein 3 (SUN3). Novel molecules found overexpressed in RA included extracellular matrix protein 1 (ECM1) and lumican (LUM). We validated one of the candidate biomarkers, vascular cell adhesion molecule 1 (VCAM1), in 20 RA and SpA samples using ELISA and confirmed its overexpression in RA (p-value <0.01). Our quantitative glycoproteomic approach to study arthritic disorders should open up new avenues for additional proteomics-based discovery studies in rheumatological disorders.
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Affiliation(s)
- Mitali Bhattacharjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Rakesh Sharma
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal University, Madhav Nagar, Manipal 576104, India
| | - Nirujogi Raja Sekhar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India.,Manipal University, Madhav Nagar, Manipal 576104, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Ramesh Jois
- Department of Rheumatology, Fortis Hospital, Bangalore 560076, India
| | - Subramanian Shankar
- Department of Internal Medicine, Armed Forces Medical College, Pune 411040, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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3
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Kalra H, Simpson RJ, Ji H, Aikawa E, Altevogt P, Askenase P, Bond VC, Borràs FE, Breakefield X, Budnik V, Buzas E, Camussi G, Clayton A, Cocucci E, Falcon-Perez JM, Gabrielsson S, Gho YS, Gupta D, Harsha HC, Hendrix A, Hill AF, Inal JM, Jenster G, Krämer-Albers EM, Lim SK, Llorente A, Lötvall J, Marcilla A, Mincheva-Nilsson L, Nazarenko I, Nieuwland R, Nolte-'t Hoen ENM, Pandey A, Patel T, Piper MG, Pluchino S, Prasad TSK, Rajendran L, Raposo G, Record M, Reid GE, Sánchez-Madrid F, Schiffelers RM, Siljander P, Stensballe A, Stoorvogel W, Taylor D, Thery C, Valadi H, van Balkom BWM, Vázquez J, Vidal M, Wauben MHM, Yáñez-Mó M, Zoeller M, Mathivanan S. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol 2012; 10:e1001450. [PMID: 23271954 PMCID: PMC3525526 DOI: 10.1371/journal.pbio.1001450] [Citation(s) in RCA: 961] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.
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Affiliation(s)
- Hina Kalra
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Richard J. Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Hong Ji
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Elena Aikawa
- Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Altevogt
- Tumor Immunology Programme, German Cancer Research Center, Heidelberg, Germany
| | - Philip Askenase
- Department of Medicine, Yale Medical School, New Haven, Connecticut, United States of America
| | - Vincent C. Bond
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Francesc E. Borràs
- IVECAT, LIRAD-BST, Institut d'Investigació Germans Trias i Pujol, Dept de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Xandra Breakefield
- Department of Neurology, Massachusetts General Hospital, and Neuroscience Program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Edit Buzas
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Giovanni Camussi
- Department of Internal Medicine, Centre for Molecular Biotechnology and Centre for Research in Experimental Medicine, Torino, Italy
| | - Aled Clayton
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Velindre Cancer Centre, Whitchurch, Cardiff, United Kingdom
| | - Emanuele Cocucci
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Immune Disease Institute and Program in Cellular and Molecular Medicine at Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Juan M. Falcon-Perez
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Susanne Gabrielsson
- Translational Immunology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Yong Song Gho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dwijendra Gupta
- Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad, India
| | | | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Andrew F. Hill
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Jameel M. Inal
- Cellular and Molecular Immunology Research Centre, Faculty of Life Sciences, London Metropolitan University, London, United Kingdom
| | - Guido Jenster
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Sai Kiang Lim
- A*STAR Institute of Medical Biology and Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alicia Llorente
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
| | - Jan Lötvall
- Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Antonio Marcilla
- Área de Parasitología, Departamento de Biología Celular y Parasitología, Universitat de València, Burjassot (Valencia), Spain
| | | | - Irina Nazarenko
- Department of Environmental Health Sciences, University Medical Center Freiburg, Freiburg, Germany
| | - Rienk Nieuwland
- Department of Clinical Chemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Esther N. M. Nolte-'t Hoen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tushar Patel
- Mayo Clinic, Jacksonville, Florida, United States of America
| | - Melissa G. Piper
- Department of Internal Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Davis Heart & Lung Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Stefano Pluchino
- Center for Brain Repair and Wellcome Trust-MRC Stem Cell Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Lawrence Rajendran
- Systems and Cell Biology of Neurodegeneration, Division of Psychiatry Research, University of Zurich, Zurich, Switzerland
| | | | | | - Gavin E. Reid
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | | | - Raymond M. Schiffelers
- Laboratory of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pia Siljander
- Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Finland
| | | | - Willem Stoorvogel
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Douglas Taylor
- Department of Obstetrics, Gynecology and Women's Health and James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Clotilde Thery
- Institut Curie Centre de Recherche, Paris, France
- INSERM U932, Paris, France
| | - Hadi Valadi
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bas W. M. van Balkom
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Michel Vidal
- UMR 5235 CNRS-University Montpellier II, Montpellier, France
| | - Marca H. M. Wauben
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Life Sciences, Utrecht University, Utrecht, The Netherlands
| | - María Yáñez-Mó
- Unidad de Investigación, Hospital Santa Cristina, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
| | - Margot Zoeller
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- * E-mail:
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4
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Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 2012; 12:1134-41. [PMID: 22577014 DOI: 10.1002/pmic.201200042] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Software advancements in the last several years have had a significant impact on proteomics from method development to data analysis. Herein, we detail a method, which uses our in-house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins. The method consists of four main steps from generation of a testable hypothesis, method development, peptide refinement, to peptide validation. The ultimate goal is to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance. It is important to emphasize that this method allows the user to perform this refinement procedure in the sample matrix and organism of interest with the instrumentation available. Finally, the method is demonstrated in a case study to determine the best peptide to monitor the abundance of surfactant protein B in lung aspirates.
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Affiliation(s)
- Michael S Bereman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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5
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Mathivanan S, Ji H, Tauro BJ, Chen YS, Simpson RJ. Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry. J Proteomics 2012; 76 Spec No.:141-9. [PMID: 22796352 DOI: 10.1016/j.jprot.2012.06.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/05/2012] [Accepted: 06/21/2012] [Indexed: 01/15/2023]
Abstract
Secreted proteins encoded by mutated genes (mutant proteins) are a particularly rich source of biomarkers being not only components of the cancer secretome but also actually implicated in tumorigenesis. One of the challenges of proteomics-driven biomarker discovery research is that the bulk of secreted mutant proteins cannot be identified directly and quantified by mass spectrometry due to the lack of mutated peptide information in extant proteomics databases. Here we identify, using an integrated genomics and proteomics strategy (referred to iMASp - identification of Mutated And Secreted proteins), 112 putative mutated tryptic peptides (corresponding to 57 proteins) in the collective secretomes derived from a panel of 18 human colorectal cancer (CRC) cell lines. Central to this iMASp was the creation of Human Protein Mutant Database (HPMD), against which experimentally-derived secretome peptide spectra were searched. Eight of the identified mutated tryptic peptides were confirmed by RT-PCR and cDNA sequencing of RNA extracted from those CRC cells from which the mutation was identified by mass spectrometry. The iMASp technology promises to improve the link between proteomics and genomic mutation data thereby providing an effective tool for targeting tryptic peptides with mutated amino acids as potential cancer biomarker candidates. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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6
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Lopitz-Otsoa F, Rodriguez-Suarez E, Aillet F, Casado-Vela J, Lang V, Matthiesen R, Elortza F, Rodriguez MS. Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs). J Proteomics 2012; 75:2998-3014. [DOI: 10.1016/j.jprot.2011.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 10/14/2022]
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7
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Kollipara S, Agarwal N, Varshney B, Paliwal J. Technological Advancements in Mass Spectrometry and Its Impact on Proteomics. ANAL LETT 2011. [DOI: 10.1080/00032719.2010.520386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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8
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Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC–MS for biomarker discovery. Talanta 2011; 83:1209-24. [DOI: 10.1016/j.talanta.2010.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 01/30/2023]
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9
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Blakeley P, Siepen JA, Lawless C, Hubbard SJ. Investigating protein isoforms via proteomics: a feasibility study. Proteomics 2010; 10:1127-40. [PMID: 20077415 DOI: 10.1002/pmic.200900445] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Alternative splicing (AS) and processing of pre-messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl-annotated genes for which proteomic data exists that informs on AS exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken via proteomics for the first time, we find support for over 600 AS genes. However, although peptide identifications support only a small fraction of alternative protein isoforms that are annotated in Ensembl, many more variants are amenable to proteomic identification. There remains a sizeable gap between these existing identifications (10-52% of AS genes) and those that are theoretically feasible (90-99%). We also compare annotations between Swiss-Prot and Ensembl, recommending use of both to maximize coverage of AS. We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies.
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Affiliation(s)
- Paul Blakeley
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, UK
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10
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Current World Literature. Curr Opin Oncol 2010; 22:70-5. [DOI: 10.1097/cco.0b013e328334b4d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Simpson RJ, Lim JW, Moritz RL, Mathivanan S. Exosomes: proteomic insights and diagnostic potential. Expert Rev Proteomics 2009; 6:267-83. [PMID: 19489699 DOI: 10.1586/epr.09.17] [Citation(s) in RCA: 815] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exosomes are 40-100-nm diameter membrane vesicles of endocytic origin that are released by most cell types upon fusion of multivesicular bodies with the plasma membrane, presumably as a vehicle for cell-free intercellular communication. While early studies focused on their secretion from diverse cell types in vitro, exosomes have now been identified in body fluids such as urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, breast milk, saliva and blood. Exosomes have pleiotropic biological functions, including immune response, antigen presentation, intracellular communication and the transfer of RNA and proteins. While they have also been implicated in the transport and propagation of infectious cargo, such as prions, and retroviruses, including HIV, suggesting a role in pathological situations, recent studies suggest that the presence of such infectious cargo may be artefacts of exosome-purification strategies. Improvements in mass spectrometry-based proteomic tools, both hardware and software, coupled with improved purification schemes for exosomes, has allowed more in-depth proteome analyses, contributing immensely to our understanding of the molecular composition of exosomes. Proteomic cataloguing of exosomes from diverse cell types has revealed a common set of membrane and cytosolic proteins, suggesting the evolutionary importance of these membrane particles. Additionally, exosomes express an array of proteins that reflect the originating host cell. Recent findings that exosomes contain inactive forms of both mRNA and microRNA that can be transferred to another cell and be functional in that new environment, have initiated many microRNA profiling studies of exosomes circulating in blood. These studies highlight the potential of exosomal microRNA profiles for use as diagnostic biomarkers of disease through a noninvasive blood test. The exacerbated release of exosomes in tumor cells, as evidenced by their increased levels in blood during the late stage of a disease and their overexpression of certain tumor cell biomarkers, suggests an important role of exosomes in diagnosis and biomarker studies. The aim of this article is to provide a brief overview of exosomes, including methods used to isolate and characterize exosomes. New advances in proteomic methods, and both mass spectrometry hardware and informatics tools will be covered briefly.
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Affiliation(s)
- Richard J Simpson
- Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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Xi H, Park J, Ding G, Lee YH, Li Y. SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. Nucleic Acids Res 2009; 37:D913-20. [PMID: 19036792 PMCID: PMC2686442 DOI: 10.1093/nar/gkn848] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/29/2008] [Accepted: 10/16/2008] [Indexed: 01/19/2023] Open
Abstract
Some mutations resulting in protein sequence change might be tightly related to certain human diseases by affecting its roles, such as sickle cell anemia. Until now several databases, such as PMD, OMIM and HGMD, have been developed, providing useful information about human disease-related mutation. Tandem mass spectrometry (MS) has been used for characterizing proteins in various conditions; however, there is no system in place for finding disease-related mutated proteins within the MS results. Here, a Systematical Platform for Identifying Mutated Proteins (SysPIMP; http://pimp.starflr.info/) was developed to efficiently identify human disease-related mutated proteins within MS results. SysPIMP comprises of three layers: (i) a standardized data warehouse, (ii) a pipeline layer for maintaining human disease databases and X!Tandem and BLAST and (iii) a web-based interface. From OMIM AV part, PMD and SwissProt databases, 35,497 non-redundant human disease-related mutated sequences were collected with disease information described by OMIM terms. With the interfaces to browse sequences archived in SysPIMP, X!Tandem, an open source database-search engine used to identify proteins within MS data, was integrated into SysPIMP to help support the detection of potential human disease-related mutants in MS results. In addition, together with non-redundant disease-related mutated sequences, original non-mutated sequences are also provided in SysPIMP for comparative research. Based on this system, SysPIMP will be the platform for efficiently and intensively studying human diseases caused by mutation.
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Affiliation(s)
- Hong Xi
- Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Jongsun Park
- Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Guohui Ding
- Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Yong-Hwan Lee
- Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Yixue Li
- Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Center for Fungal Genetic Resource, Seoul National University, Seoul 151-921, Korea, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Center for Bioinformation Technology, Shanghai, China
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13
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Ferrer-Alcón M, Arteta D, Guerrero MJ, Fernandez-Orth D, Simón L, Martinez A. The use of gene array technology and proteomics in the search of new targets of diseases for therapeutics. Toxicol Lett 2008; 186:45-51. [PMID: 19022361 DOI: 10.1016/j.toxlet.2008.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
The advent of functional genomics has been greatly broadening our view and accelerating our way in numerous medical research fields. The complete genomic data acquired from the human genome project and the desperate clinical need of comprehensive analytical tools to study complex diseases, has allowed rapid evolution of genomic and proteomic technologies, speeding the rate and number of discoveries in new biomarkers. By jointly using genomics, proteomics and bioinformatics there is a great potential to make considerable contribution to biomarker identification and to revolutionize both the development of new therapies and drug development process.
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Affiliation(s)
- Marcel Ferrer-Alcón
- Progenika Biopharma, S.A., Zamudio Technology Park, 48160 Derio, Vizcaya, Spain.
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Debouck C. Integrating genomics across drug discovery and development. Toxicol Lett 2008; 186:9-12. [PMID: 18930125 DOI: 10.1016/j.toxlet.2008.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 09/17/2008] [Indexed: 12/22/2022]
Abstract
The sequencing of the human genome was an exceptional achievement, but it was not an end in itself as it set the foundation for building new knowledge in biology and medicine. The laborious, multifaceted science of drug discovery and development also draws tremendous benefits from mining the human genome and exploiting the large palette of genomic technologies. This article discusses how diverse genomic tools have been used to date and how they will continue to be utilized in the future to impact drug discovery and development. Integrating genomics across drug discovery and development will undoubtedly help to shorten timelines, increase success rates at all stages and ultimately bring the right drugs to the right patients at the right times.
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