1
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Feng T, Jie M, Deng K, Yang J, Jiang H. Targeted plasma proteomic analysis uncovers a high-performance biomarker panel for early diagnosis of gastric cancer. Clin Chim Acta 2024; 558:119675. [PMID: 38631604 DOI: 10.1016/j.cca.2024.119675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Gastric cancer (GC) is characterized by high morbidity, high mortality and low early diagnosis rate. Early diagnosis plays a crucial role in radically treating GC. The aim of this study was to identify plasma biomarkers for GC and early GC diagnosis. METHODS We quantified 369 protein levels with plasma samples from discovery cohort (n = 88) and validation cohort (n = 50) via high-throughput proximity extension assay (PEA) utilizing the Olink-Explore-384-Cardiometabolic panel. The multi-protein signatures were derived from LASSO and Ridge regression models. RESULTS In the discovery cohort, 13 proteins (GDF15, ITIH3, BOC, DPP7, EGFR, AMY2A, CCDC80, CD163, GPNMB, LTBP2, CTSZ, CCL18 and NECTIN2) were identified to distinguish GC (Stage I-IV) and early GC (HGIN-I) groups from control group with AUC of 0.994 and AUC of 0.998, severally. The validation cohort yielded AUC of 0.930 and AUC of 0.818 for GC and early GC, respectively. CONCLUSIONS This study identified a multi-protein signature with the potential to benefit clinical GC diagnosis, especially for Asian and early GC patients, which may contribute to the development of a less-invasive, convenient, and efficient early screening tool, promoting early diagnosis and treatment of GC and ultimately improving patient survival.
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Affiliation(s)
- Tong Feng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Minwen Jie
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Kai Deng
- Department of Gastroenterology & Hepatology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jinlin Yang
- Department of Gastroenterology & Hepatology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Hao Jiang
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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2
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Wenk D, Zuo C, Kislinger T, Sepiashvili L. Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers. Clin Proteomics 2024; 21:6. [PMID: 38287260 PMCID: PMC10826105 DOI: 10.1186/s12014-024-09452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological matrices with numerous advantages that make it attractive for clinical applications in oncology. The use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodologies has allowed laboratories to overcome challenges associated with immunoassays that are more widely used for tumor marker measurements. Yet, clinical implementation of targeted proteomics methodologies has so far been limited to a few cancer markers. This is due to numerous challenges associated with paucity of robust validation studies of new biomarkers and the labor-intensive and operationally complex nature of LC-MS/MS workflows. The purpose of this review is to provide an overview of targeted proteomics applications in cancer, workflows used in targeted proteomics, and requirements for clinical validation and implementation of targeted proteomics assays. We will also discuss advantages and challenges of targeted MS-based proteomics assays for clinical cancer biomarker analysis and highlight some recent developments that will positively contribute to the implementation of this technique into clinical laboratories.
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Affiliation(s)
- Deborah Wenk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charlotte Zuo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Research Tower, Room 9-807, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Lusia Sepiashvili
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Ave, Rm 3606, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Sickkids Research Institute, Toronto, ON, Canada.
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3
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Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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4
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Nguyen CDL, Jimenez-Moreno AC, Merker M, Bowers CJ, Nikolenko N, Hentschel A, Müntefering T, Isham A, Ruck T, Vorgerd M, Dobelmann V, Gourdon G, Schara-Schmidt U, Gangfuss A, Schröder C, Sickmann A, Gross C, Gorman G, Stenzel W, Kollipara L, Hathazi D, Spendiff S, Gagnon C, Preusse C, Duchesne E, Lochmüller H, Roos A. Periostin as a blood biomarker of muscle cell fibrosis, cardiomyopathy and disease severity in myotonic dystrophy type 1. J Neurol 2023; 270:3138-3158. [PMID: 36892629 DOI: 10.1007/s00415-023-11633-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND AND PURPOSE Myotonic dystrophy type 1 (DM1) is the most common form of adult-onset muscular dystrophy and is caused by an repeat expansion [r(CUG)exp] located in the 3' untranslated region of the DMPK gene. Symptoms include skeletal and cardiac muscle dysfunction and fibrosis. In DM1, there is a lack of established biomarkers in routine clinical practice. Thus, we aimed to identify a blood biomarker with relevance for DM1-pathophysiology and clinical presentation. METHODS We collected fibroblasts from 11, skeletal muscles from 27, and blood samples from 158 DM1 patients. Moreover, serum, cardiac, and skeletal muscle samples from DMSXL mice were included. We employed proteomics, immunostaining, qPCR and ELISA. Periostin level were correlated with CMRI-data available for some patients. RESULTS Our studies identified Periostin, a modulator of fibrosis, as a novel biomarker candidate for DM1: proteomic profiling of human fibroblasts and murine skeletal muscles showed significant dysregulation of Periostin. Immunostaining on skeletal and cardiac muscles from DM1 patients and DMSXL mice showed an extracellular increase of Periostin, indicating fibrosis. qPCR studies indicated increased POSTN expression in fibroblasts and muscle. Quantification of Periostin in blood samples from DMSXL mice and two large validation cohorts of DM1 patients showed decreased levels in animals and diseased individuals correlating with repeat expansion and disease severity and presence of cardiac symptoms identified by MRI. Analyses of longitudinal blood samples revealed no correlation with disease progression. CONCLUSIONS Periostin might serve as a novel stratification biomarker for DM1 correlating with disease severity, presence of cardiac malfunction and fibrosis.
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Affiliation(s)
- Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | | | - Monika Merker
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | | | | | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Thomas Müntefering
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Angus Isham
- Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Tobias Ruck
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Matthias Vorgerd
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, 44789, Bochum, Germany
| | - Vera Dobelmann
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Genevieve Gourdon
- Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Laboratory CTGDM, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Ulrike Schara-Schmidt
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Andrea Gangfuss
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Charlotte Schröder
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Claudia Gross
- Institute of Clinical Genetics and Tumor Genetics Bonn, Maximilianstraße 28D, 53111, Bonn, Germany
| | - Grainne Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Denisa Hathazi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sally Spendiff
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Cynthia Gagnon
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,School of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada
| | - Corinna Preusse
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elise Duchesne
- Department of Health Sciences, Université du Québec à Chicoutimi, Québec, Canada
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico, Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Andreas Roos
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, 44789, Bochum, Germany. .,Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany. .,Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.
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5
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Van Haver D, Dendooven A, Impens F. Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples. Methods Mol Biol 2023; 2718:213-233. [PMID: 37665462 DOI: 10.1007/978-1-0716-3457-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Amyloidosis is a group of rare pathologies characterized by abnormal folding and deposition of susceptible proteins in tissues and organs. Diagnosis of amyloidosis often relies on immunohistochemistry of formalin-fixed paraffin-embedded (FFPE) patient samples; however, dependency on antibodies for protein staining is one of the major pitfalls of this approach, especially for the detection of rare amyloidosis types. In recent years, mass spectrometry-based proteomics has emerged as a promising alternative for adequate detection and amyloid typing, despite the fact that preparing FFPE samples for proteomics remains a challenging task. Major hurdles are removal of formalin-induced protein cross-links and water-insoluble paraffin prior to mass spectrometry analysis. With the recent development of the suspension trapping protocol, enabling the use of high concentrations of SDS, these obstacles can be overcome. In this chapter, we describe the implementation of suspension trapping for FFPE sample processing and its application to analyze human amyloidosis samples, comparing a standard procedure with probe sonication with a more advanced workflow based on ultrasonication.
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Affiliation(s)
- Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- Laboratory for Experimental Medicine and Pediatrics, Antwerp University, Edegem, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, Ghent, Belgium.
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6
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Henry M, Meleady P. Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems. Methods Mol Biol 2023; 2699:255-269. [PMID: 37647003 DOI: 10.1007/978-1-0716-3362-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Liquid chromatography/mass spectrometry (LC/MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization, and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin-based depletion column followed by either protein In-Gel enzymatic digestion or protein In-Solution enzymatic digestion using a simple kit-based approach (i.e., using the PreOmics iST sample preparation kit), followed by analysis using one-dimensional reverse-phase chromatography (RPC) or high pH reversed-phase peptide fractionation.
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Affiliation(s)
- Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.
- School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.
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7
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Müller T, Cremonini MA, Kliewer G, Krijgsveld J. Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics. Methods Mol Biol 2023; 2718:181-211. [PMID: 37665461 DOI: 10.1007/978-1-0716-3457-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a rapidly maturing discipline, thus gaining momentum for routine molecular profiling of clinical specimens to improve disease classification, diagnostics, and therapy development. Yet, hurdles need to be overcome to enhance reproducibility in preanalytical sample processing, especially in large, quantity-limited sample cohorts. Therefore, automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3) was developed as a streamlined workflow that integrates all tasks from tissue lysis and protein extraction, protein cleanup, and proteolysis. It enables the concurrent processing of 96 clinical samples of any type (fresh-frozen or FFPE tissue, liquid biopsies, or cells) on an automated liquid handling platform, which can be directly interfaced to LC-MS for proteome analysis of clinical specimens with high sensitivity, high reproducibility, and short turn-around times.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | | | - Georg Kliewer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Heidelberg, Germany.
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8
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Dressler FF, Schoenfeld J, Revyakina O, Vogele D, Kiefer S, Kirfel J, Gemoll T, Perner S. Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens. Clin Proteomics 2022; 19:10. [PMID: 35501693 DOI: 10.1186/s12014-022-09346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins. Methods Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS). Results Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09346-0.
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9
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Babu M, Singh N, Datta A. In Vitro Oxygen Glucose Deprivation Model of Ischemic Stroke: A Proteomics-Driven Systems Biological Perspective. Mol Neurobiol 2022; 59:2363-2377. [PMID: 35080759 DOI: 10.1007/s12035-022-02745-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/11/2022] [Indexed: 01/17/2023]
Abstract
Oxygen glucose deprivation (OGD) of brain cells is the commonest in vitro model of ischemic stroke that is used extensively for basic and preclinical stroke research. Protein mass spectrometry is one of the most promising and rapidly evolving technologies in biomedical research. A systems-level understanding of cell-type-specific responses to oxygen and glucose deprivation without systemic influence is a prerequisite to delineate the response of the neurovascular unit following ischemic stroke. In this systematic review, we summarize the proteomics studies done on different OGD models. These studies have followed an expression or interaction proteomics approach. They have been primarily used to understand the cellular pathophysiology of ischemia-reperfusion injury or to assess the efficacy of interventions as potential treatment options. We compile the limitations of OGD model and downstream proteomics experiment. We further show that despite having limitations, several proteins shortlisted as altered in in vitro OGD-proteomics studies showed comparable regulation in ischemic stroke patients. This showcases the translational potential of this approach for therapeutic target and biomarker discovery. We next discuss the approaches that can be adopted for cell-type-specific validation of OGD-proteomics results in the future. Finally, we briefly present the research questions that can be addressed by OGD-proteomics studies using emerging techniques of protein mass spectrometry. We have also created a web resource compiling information from OGD-proteomics studies to facilitate data sharing for community usage. This review intends to encourage preclinical stroke community to adopt a hypothesis-free proteomics approach to understand cell-type-specific responses following ischemic stroke.
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Affiliation(s)
- Manju Babu
- Laboratory of Translational Neuroscience, Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, Karnataka, India
| | - Nikhil Singh
- Laboratory of Translational Neuroscience, Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, Karnataka, India
| | - Arnab Datta
- Laboratory of Translational Neuroscience, Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, Karnataka, India.
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10
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Dey KK, Sun H, Wang Z, Niu M, Wang H, Jiao Y, Sun X, Li Y, Peng J. Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry. Methods Mol Biol 2022; 2420:21-37. [PMID: 34905163 PMCID: PMC8890903 DOI: 10.1007/978-1-0716-1936-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mass spectrometry (MS) has become a mainstream platform for comprehensive profiling of proteome, especially with the improvement of multiplexed tandem mass tag labeling coupled with two-dimensional liquid chromatography and tandem mass spectrometry (TMT-LC/LC-MS/MS). Recently, we have established a robust method for direct profiling of undepleted cerebrospinal fluid (CSF) proteome with the 16-plex TMTpro method, in which we optimized parameters in experimental steps of sample preparation, TMT labeling, LC/LC fractionation, tandem mass spectrometry, and computational data processing. The extensive LC fractionation not only enhances proteome coverage of the CSF but also alleviates ratio distortion of TMT quantification. The crucial quality control steps and improvements specific for the TMT16 analysis are highlighted. More than 3000 proteins can be quantified in a single experiment from 16 different CSF samples. This multiplexed method offers a powerful tool for profiling a variety of complex biofluids samples such as CSF, serum/plasma, and other clinical specimens.
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11
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Nakajima D, Ohara O, Kawashima Y. Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation. Methods Mol Biol 2022; 2420:39-52. [PMID: 34905164 DOI: 10.1007/978-1-0716-1936-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dried blood spots (DBS) are widely used for screening molecular profiles, including enzymatic activity. However, hydrophilic proteins present in large amounts in blood inhibit detection of other proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without preenrichment. Sodium carbonate precipitation (SCP) can concentrate hydrophobic proteins from DBS and effectively remove soluble hydrophilic proteins. Furthermore, SCP combination with data-independent acquisition (DIA) for quantitative LC-MS/MS enhanced the proteome analysis sensitivity and quantification limits. In this protocol, we have described in detail a simple preenrichment method using SCP and a deep proteome analysis method for LC-MS/MS data using DIA.
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12
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Casado P, Hijazi M, Gerdes H, Cutillas PR. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine. Methods Mol Biol 2021; 2420:87-106. [PMID: 34905168 DOI: 10.1007/978-1-0716-1936-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The identification of biomarkers for companion diagnostics is revolutionizing the development of treatments tailored to individual patients in different disease areas including cancer. Precision medicine is most frequently based on the detection of genomic markers that correlate with the efficacy of selected targeted therapies. However, since nongenetic mechanisms also contribute to disease biology, there is a considerable interest of using proteomic techniques as additional source of biomarkers to personalize therapies. In this chapter, we describe label-free mass spectrometry methods for proteomic and phosphoproteomic analysis compatible with routine analysis of clinical samples. We also outline bioinformatic pipelines based on statistical learning that use these proteomics datasets as input to quantify kinase activities and predict drug responses in cancer cells.
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Affiliation(s)
- Pedro Casado
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Maruan Hijazi
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Henry Gerdes
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Pedro R Cutillas
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK.
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13
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
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14
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Rossi F, L'Imperio V, Marti HP, Svarstad E, Smith A, Bolognesi MM, Magni F, Pagni F, Pieruzzi F. Proteomics for the study of new biomarkers in Fabry disease: State of the art. Mol Genet Metab 2021; 132:86-93. [PMID: 33077353 DOI: 10.1016/j.ymgme.2020.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/25/2022]
Abstract
Nephropathy represents a major complication of Fabry Disease and its accurate characterization is of paramount importance in predicting the disease progression and assessing the therapeutic responses. The diagnostic process still relies on performing renal biopsy, nevertheless many efforts have been made to discover early reliable biomarkers allowing us to avoid invasive procedures. In this field, proteomics offers a sensitive and fast method leading to an accurate detection of specific pathological proteins and the discovery of diagnostic and prognostic biomarkers that reflect disease progression and facilitate the evaluation of therapeutic responses. Here, we report a review of selected literature focusing on the investigation of several proteomic techniques highlighting their advantages, limitations and future perspectives in their application in the routine study of Fabry Nephropathy.
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Affiliation(s)
- Federica Rossi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Hans-Peter Marti
- Department of Medicine, Haukeland University Hospital, Jonas Lies Vei 65, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Maddalena Maria Bolognesi
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Federico Pieruzzi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
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15
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Porsdam Mann S, Treit PV, Geyer PE, Omenn GS, Mann M. Ethical principles, opportunities and constraints in clinical proteomics. Mol Cell Proteomics 2021:mcp.RA120.002435. [PMID: 33397710 DOI: 10.1074/mcp.ra120.002435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 11/06/2022] Open
Abstract
Recent advances in MS-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with the impact on the health, privacy, and well-being of individuals. Here we conducted and report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the results of our accompanying paper extracting individual-sensitive results from patient samples, and the literature addressing similar issues in genomics. The spectrum of potential issues ranges from patient re-identification to incidental findings of clinical significance. The latter can be divided into actionable and unactionable findings. Some of these have the potential to be employed in discriminatory or privacy-infringing ways. However, incidental findings may also have great positive potential. A plasma proteome profile, for instance, could inform on the general health or disease status of an individual regardless of the narrow diagnostic question that prompted it. We suggest that early discussion of ethical issues in clinical proteomics is important to ensure that eventual regulations reflect the considered judgment of the community as well as to anticipate opportunities and problems that may arise as the technology matures further.
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Affiliation(s)
| | | | - Philipp Emanuel Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Germany
| | - Gilbert S Omenn
- Center for Computational Med. & Bioinformatic, University of Michigan, United States
| | - Matthias Mann
- Dept. Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Germany
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16
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Vainer ED, Kania-Almog J, Zatara G, Levin Y, Vainer GW. Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors. Mol Cell Proteomics 2020; 19:1619-1631. [PMID: 32641473 PMCID: PMC8015011 DOI: 10.1074/mcp.ra120.002152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Indexed: 11/14/2022] Open
Abstract
Using a simple, environment friendly proteome extraction (TOP), we were able to optimize the analysis of clinical samples. Using our TOP method we analyzed a clinical cohort of microsatellite stable (MSS) and unstable (MSI-H) colorectal carcinoma (CRC). We identified a tumor cell specific, STAT1-centered, immune signature expressed by the MSI-H tumor cells. We then showed that long, but not short, exposure to Interferon-γ induces a similar signature in vitro We identified 10 different temporal protein expression patterns, classifying the Interferon-γ protein temporal regulation in CRC. Our data sheds light on the changes that tumor cells undergo under long-term immunological pressure in vivo, the importance of STAT proteins in specific biological scenarios. The data generated could help find novel clinical biomarkers and therapeutic approaches.
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Affiliation(s)
- Elez D Vainer
- Department of Gastroenterology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Juliane Kania-Almog
- Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ghadeer Zatara
- Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad W Vainer
- Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
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17
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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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18
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Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteomics 2020; 17:17. [PMID: 32489335 PMCID: PMC7247207 DOI: 10.1186/s12014-020-09283-w] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
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Affiliation(s)
- Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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19
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Abstract
Introduction: After the genomic era, the analysis of the proteome has gained increasing importance. Peptides and/or proteins present in tissue or body fluids can depict health and are prone to change during disease, not only in configuration but also in abundance. Early on, high throughput proteome analysis was implemented in the diagnostic of therapy-linked or induced complications arising after allogeneic hematopoietic stem cell transplantation (HSCT). Several proteomic approaches are currently used in the prediction or diagnosis of acute and/or chronic graft-versus-host disease (GvHD).Areas covered: This review will report on two high throughput proteomics technologies used in the clinical setting to date, namely enzyme-linked-immunosorbent assays (ELISA) for key proteins involved in the pathogenesis of acute GvHD and on capillary electrophoresis coupled on-line to mass spectrometry (CE-MS). Here, we summarize the current data and discuss the strength as well as the limitations of each method and compare the usefulness and practicability in the post-HSCT setting for prediction and diagnosis of acute GvHD.Expert commentary: Both technologies are applied in the clinic and have been tested on several hundred patients after HSCT. The data from both technologies may complement each other in diagnosis of GvHD.
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Affiliation(s)
- Eva M Weissinger
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Debora Basílio-Queirós
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Lisa M Bieling
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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20
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Abstract
The data-dependent acquisition in mass spectrometry-based proteomics combined with quantitative analysis using isobaric labeling (iTRAQ and TMT) inevitably introduces missing values in proteomic experiments where a number of LC-runs are combined, especially in the growing field of shotgun clinical proteomics, where the protein profiles from the proteomics analysis of several hundred patient samples are compared and correlated to clinical traits such as a specific disease or disease treatment in order to link specific outcomes to one or more proteins. In the context of clinical research it is evident that missing values in such datasets reduce the power of the downstream statistical analysis therefore may hampers the linking of the expression of disease traits to the expression of specific proteins that may be useful for prognostic, diagnostic, or predictive purposes. In our study, we tested three data imputation approaches initially developed for microarray data for the imputation of missing values in datasets that are generated by several runs of shotgun proteomic experiments and where the data were relative protein abundances based on isobaric tags (iTRAQ and TMT). Our conclusion is that imputation methods based on k Nearest Neighbors successfully impute missing values in datasets with up to 50% missing values.
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Affiliation(s)
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark.
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21
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Bernal I, van Ham M, Jänsch L. Immune Monitoring of Human Mucosal-Associated Invariant T Cells by Quantitative Proteomics. Methods Mol Biol 2019; 2098:209-218. [PMID: 31792825 DOI: 10.1007/978-1-0716-0207-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Molecular phenotypes of mucosal-associated invariant T (MAIT) cells are correlating with individual susceptibilities and outcomes in human diseases. Quantitative proteome strategies can examine such variations in the functional and druggable inventory of MAIT cells comprehensively, but protocols for the support of translational and clinical studies are still rare. Here, we describe a protocol in which MR1-restricted MAIT cells were isolated from blood donations by FACS and are then characterized by quantitative proteomics (iTRAQ-LC-MS/MS) to complement information about their unique effector phenotype and to investigate donor-/patient- or disease-specific variations in protein networks with high precision.
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Affiliation(s)
- Isabel Bernal
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,ESF Graduate School ABINEP, Magdeburg, Germany
| | - Marco van Ham
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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22
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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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23
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Tang J, Fu J, Wang Y, Luo Y, Yang Q, Li B, Tu G, Hong J, Cui X, Chen Y, Yao L, Xue W, Zhu F. Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains. Mol Cell Proteomics 2019; 18:1683-1699. [PMID: 31097671 PMCID: PMC6682996 DOI: 10.1074/mcp.ra118.001169] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
The label-free proteome quantification (LFQ) is multistep workflow collectively defined by quantification tools and subsequent data manipulation methods that has been extensively applied in current biomedical, agricultural, and environmental studies. Despite recent advances, in-depth and high-quality quantification remains extremely challenging and requires the optimization of LFQs by comparatively evaluating their performance. However, the evaluation results using different criteria (precision, accuracy, and robustness) vary greatly, and the huge number of potential LFQs becomes one of the bottlenecks in comprehensively optimizing proteome quantification. In this study, a novel strategy, enabling the discovery of the LFQs of simultaneously enhanced performance from thousands of workflows (integrating 18 quantification tools with 3,128 manipulation chains), was therefore proposed. First, the feasibility of achieving simultaneous improvement in the precision, accuracy, and robustness of LFQ was systematically assessed by collectively optimizing its multistep manipulation chains. Second, based on a variety of benchmark datasets acquired by various quantification measurements of different modes of acquisition, this novel strategy successfully identified a number of manipulation chains that simultaneously improved the performance across multiple criteria. Finally, to further enhance proteome quantification and discover the LFQs of optimal performance, an online tool (https://idrblab.org/anpela/) enabling collective performance assessment (from multiple perspectives) of the entire LFQ workflow was developed. This study confirmed the feasibility of achieving simultaneous improvement in precision, accuracy, and robustness. The novel strategy proposed and validated in this study together with the online tool might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.
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Affiliation(s)
- Jing Tang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China; ¶Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Fu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Bo Li
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jiajun Hong
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuejiao Cui
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yuzong Chen
- ‖Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Lixia Yao
- **Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905, United States
| | - Weiwei Xue
- §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- ‡College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; §School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
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Gugatschka M, Darnhofer B, Grossmann T, Schittmayer M, Hortobagyi D, Kirsch A, Karpf E, Brcic L, Birner-Gruenberger R, Karbiener M. Proteomic Analysis of Vocal Fold Fibroblasts Exposed to Cigarette Smoke Extract: Exploring the Pathophysiology of Reinke's Edema. Mol Cell Proteomics 2019; 18:1511-1525. [PMID: 31123107 PMCID: PMC6683006 DOI: 10.1074/mcp.ra119.001272] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/17/2019] [Indexed: 11/06/2022] Open
Abstract
Reinke's edema is a smoking-associated, benign, mostly bilateral lesion of the vocal folds leading to difficulties in breathing and voice problems. Pronounced histological changes such as damaged microvessels or immune cell infiltration have been described in the vocal fold connective tissue, the lamina propria Thus, vocal fold fibroblasts, the main cell type of the lamina propria, have been postulated to play a critical role in disease mediation. Yet information about the pathophysiology is still scarce and treatment is only surgical, i.e. symptomatic. To explore the pathophysiology of Reinke's edema, we exposed near-primary human vocal fold fibroblasts to medium conditioned with cigarette smoke extract for 24 h as well as 4 days followed by quantitative mass spectrometry.Proteomic analyses after 24 h revealed that cigarette smoke increased proteins previously described to be involved in oxidative stress responses in other contexts. Correspondingly, gene sets linked to metabolism of xenobiotics and reactive oxygen species were significantly enriched among cigarette smoke-induced proteins. Among the proteins most downregulated by cigarette smoke, we identified fibrillar collagens COL1A1 and COL1A2; this reduction was validated by complementary methods. Further, we found a significant increase of UDP-glucose 6-dehydrogenase, generating a building block for biosynthesis of hyaluronan, another crucial component of the vocal fold lamina propria In line with this result, hyaluronan levels were significantly increased because of cigarette smoke exposure. Long term treatment of 4 days did not lead to significant changes.The current findings corroborate previous studies but also reveal new insights in possible disease mechanisms of Reinke's edema. We postulate that changes in the composition of the vocal folds' extracellular matrix -reduction of collagen fibrils, increase of hyaluronan- may lead to the clinical findings. This might ease the identification of better, disease-specific treatment options.
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Affiliation(s)
- Markus Gugatschka
- ‡Division of Phoniatrics, Medical University of Graz, Graz, Austria.
| | - Barbara Darnhofer
- ¶Omics Center Graz, BioTechMed-Graz, Graz, Austria; ‖Austrian Center of Industrial Biotechnology, Graz, Austria
| | - Tanja Grossmann
- ‡Division of Phoniatrics, Medical University of Graz, Graz, Austria
| | - Matthias Schittmayer
- §Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria; ¶Omics Center Graz, BioTechMed-Graz, Graz, Austria; ‖Austrian Center of Industrial Biotechnology, Graz, Austria
| | - David Hortobagyi
- ‡Division of Phoniatrics, Medical University of Graz, Graz, Austria
| | - Andrijana Kirsch
- ‡Division of Phoniatrics, Medical University of Graz, Graz, Austria
| | - Eva Karpf
- **Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Luka Brcic
- **Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ruth Birner-Gruenberger
- §Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria; ¶Omics Center Graz, BioTechMed-Graz, Graz, Austria; ‖Austrian Center of Industrial Biotechnology, Graz, Austria; **Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Michael Karbiener
- ‡Division of Phoniatrics, Medical University of Graz, Graz, Austria; §§Takeda, Vienna, Austria
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Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L. Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance. Mol Cell Proteomics 2019; 18:1242-1254. [PMID: 30948622 PMCID: PMC6553938 DOI: 10.1074/mcp.ra118.001288] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/26/2019] [Indexed: 12/14/2022] Open
Abstract
Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%.The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA.In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.
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Affiliation(s)
| | - Jan Muntel
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | | | - Tejas Gandhi
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | - Charlotte Macron
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Jérôme Carayol
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Oliver Rinner
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | - Arne Astrup
- ¶Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Wim H M Saris
- ‖NUTRIM, School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Jörg Hager
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Armand Valsesia
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Lukas Reiter
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland;
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26
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Berggrund M, Enroth S, Lundberg M, Assarsson E, Stålberg K, Lindquist D, Hallmans G, Grankvist K, Olovsson M, Gyllensten U. Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay. Mol Cell Proteomics 2019; 18:735-743. [PMID: 30692274 PMCID: PMC6442356 DOI: 10.1074/mcp.ra118.001208] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/24/2019] [Indexed: 12/16/2022] Open
Abstract
Human papillomavirus (HPV) is recommended as the primary test in cervical cancer screening, with co-testing by cytology for HPV-positive women to identify cervical lesions. Cytology has low sensitivity and there is a need to identify biomarkers that could identify dysplasia that are likely to progress to cancer. We searched for plasma proteins that could identify women with cervical cancer using the multiplex proximity extension assay (PEA). The abundance of 100 proteins were measured in plasma collected at the time of diagnosis of patients with invasive cervical cancer and in population controls using the Olink Multiplex panels CVD II, INF I, and ONC II. Eighty proteins showed increased levels in cases compared with controls. We identified a signature of 11 proteins (PTX3, ITGB1BP2, AXIN1, STAMPB, SRC, SIRT2, 4E-BP1, PAPPA, HB-EGF, NEMO and IL27) that distinguished cases and controls with a sensitivity of 0.96 at a specificity of 1.0. This signature was evaluated in a prospective replication cohort with samples collected before, at or after diagnosis and achieved a sensitivity of 0.78 and a specificity 0.56 separating samples collected at the time of diagnosis of invasive cancer from samples collected prior to diagnosis. No difference in abundance was seen between samples collected prior to diagnosis or after treatment as compared with population controls, indicating that this protein signature is mainly informative close to time of diagnosis. Further studies are needed to determine the optimal window in time prior to diagnosis for these biomarker candidates.
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Affiliation(s)
- Malin Berggrund
- From the ‡Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory (SciLifeLab) Uppsala, Box 815, Uppsala University, SE-75108 Uppsala, Sweden
| | - Stefan Enroth
- From the ‡Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory (SciLifeLab) Uppsala, Box 815, Uppsala University, SE-75108 Uppsala, Sweden
| | - Martin Lundberg
- §OLINK Proteomics, Uppsala Science Park, SE-751 83, Uppsala, Sweden
| | - Erika Assarsson
- §OLINK Proteomics, Uppsala Science Park, SE-751 83, Uppsala, Sweden
| | - Karin Stålberg
- Department of Women's and Children's Health, 751 85, Uppsala University, Uppsala, Sweden
| | - David Lindquist
- Department of Radiation Sciences, Umeå University, SE-90187 Umeå, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, SE-90187 Umeå, Sweden
| | - Kjell Grankvist
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, SE-90185 Umeå, Sweden
| | - Matts Olovsson
- Department of Women's and Children's Health, 751 85, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- From the ‡Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory (SciLifeLab) Uppsala, Box 815, Uppsala University, SE-75108 Uppsala, Sweden;.
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27
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Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
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28
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Barrachina F, Jodar M, Delgado-Dueñas D, Soler-Ventura A, Estanyol JM, Mallofré C, Ballescà JL, Oliva R. Stable-protein Pair Analysis as A Novel Strategy to Identify Proteomic Signatures: Application To Seminal Plasma From Infertile Patients. Mol Cell Proteomics 2019; 18:S77-S90. [PMID: 30518674 PMCID: PMC6427235 DOI: 10.1074/mcp.ra118.001248] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Our aim was to define seminal plasma proteome signatures of infertile patients categorized according to their seminal parameters using TMT-LC-MS/MS. To that extent, quantitative proteomic data was analyzed following two complementary strategies: (1) the conventional approach based on standard statistical analyses of relative protein quantification values; and (2) a novel strategy focused on establishing stable-protein pairs. By conventional analyses, the abundance of some seminal plasma proteins was found to be positively correlated with sperm concentration. However, this correlation was not found for all the peptides within a specific protein, bringing to light the high heterogeneity existing in the seminal plasma proteome because of both the proteolytic fragments and/or the post-translational modifications. This issue was overcome by conducting the novel stable-protein pairs analysis proposed herein. A total of 182 correlations comprising 24 different proteins were identified in the normozoospermic-control population, whereas this proportion was drastically reduced in infertile patients with altered seminal parameters (18 in patients with reduced sperm motility, 0 in patients with low sperm concentration and 3 in patients with no sperm in the ejaculate). These results suggest the existence of multiple etiologies causing the same alteration in seminal parameters. Additionally, the repetition of the stable-protein pair analysis in the control group by adding the data from a single patient at a time enabled to identify alterations in the stable-protein pairs profile of individual patients with altered seminal parameters. These results suggest potential underlying pathogenic mechanisms in individual infertile patients, and might open up a window to its application in the personalized diagnostic of male infertility.
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Affiliation(s)
- Ferran Barrachina
- From the ‡Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain and Biochemistry and Molecular Genetics Service, Hospital Clínic, Barcelona, Spain
| | - Meritxell Jodar
- From the ‡Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain and Biochemistry and Molecular Genetics Service, Hospital Clínic, Barcelona, Spain
| | - David Delgado-Dueñas
- From the ‡Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain and Biochemistry and Molecular Genetics Service, Hospital Clínic, Barcelona, Spain
| | - Ada Soler-Ventura
- From the ‡Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain and Biochemistry and Molecular Genetics Service, Hospital Clínic, Barcelona, Spain
| | - Josep Maria Estanyol
- Proteomics Unit, Scientific Technical Services, University of Barcelona, Barcelona, Spain
| | - Carme Mallofré
- Department of Pathology, University of Barcelona, Hospital Clínic, Barcelona, Spain
| | - Josep Lluís Ballescà
- Clinic Institute of Gynaecology, Obstetrics and Neonatology, Hospital Clínic, Barcelona, Spain
| | - Rafael Oliva
- From the ‡Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain and Biochemistry and Molecular Genetics Service, Hospital Clínic, Barcelona, Spain;.
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29
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Shen ZQ, Shi B, Wang TR, Jiao J, Shang XJ, Wu QJ, Zhou YM, Cao TF, Du Q, Wang XX, Li D. Characterization of the Sperm Proteome and Reproductive Outcomes with in Vitro, Fertilization after a Reduction in Male Ejaculatory Abstinence Period. Mol Cell Proteomics 2019; 18:S109-S117. [PMID: 30126978 PMCID: PMC6427236 DOI: 10.1074/mcp.ra117.000541] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
Semen samples from men after a short ejaculatory abstinence show improved sperm quality and result in increased pregnancy rates, but the underlying mechanisms remain unclear. Herein, we report that ejaculates from short (1-3 h) compared with long (3-7 days) periods of abstinence showed increases in motile sperm count, sperm vitality, normal sperm morphology, acrosome reaction capacity, total antioxidant capacity, sperm mitochondrial membrane potential, high DNA stainability, and a decrease in the sperm DNA fragmentation index (p, < 0.05). Sperm proteomic analysis showed 322 differentially expressed proteins (minimal fold change of ±1.5 or greater and p, < 0.05), with 224 upregulated and 98 downregulated. These differentially expressed proteins are profoundly involved in specific cellular processes, such as motility and capacitation, oxidative stress, and metabolism. Interestingly, protein trimethyllysine modification was increased, and butyryllysine, propionyllysine, and malonyllysine modifications were decreased in ejaculates from a short versus, long abstinence (p, < 0.05). Finally, the rates of implantation, clinical pregnancy, and live births from in vitro, fertilization treatments were significantly increased in semen samples after a short abstinence. Our study provides preliminary mechanistic insights into improved sperm quality and pregnancy outcomes associated with spermatozoa retrieved after a short ejaculatory abstinence.
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Affiliation(s)
- Zi-Qi Shen
- From the ‡Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Bei Shi
- Department of Physiology, College of Basic Medical Science, China Medical University, Shenyang 110122, China
| | - Tian-Ren Wang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jiao Jiao
- From the ‡Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xue-Jun Shang
- Department of Andrology, Jinling Hospital Affiliated to Nanjing University School of Medicine, Nanjing 210002, China
| | - Qi-Jun Wu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yi-Ming Zhou
- ‡Department of Medicine, Brigham and Women's Hospital, Harvard Institutes of Medicine, Harvard Medical School, Boston, MA 02115
| | - Tie-Feng Cao
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06520, USA
| | - Qiang Du
- From the ‡Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xiu-Xia Wang
- From the ‡Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China;.
| | - Da Li
- From the ‡Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China;.
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30
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Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Balateu-Paños D, Colom-Cadena M, Gomez-Giro G, Muñoz L, Querol-Vilaseca M, Pegueroles J, Rami L, Lladó A, Molinuevo JL, Tainta M, Clarimón J, Spires-Jones T, Blesa R, Fortea J, Martínez-Lage P, Sánchez-Valle R, Sabidó E, Bayés À, Belbin O. Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid. Mol Cell Proteomics 2019; 18:546-560. [PMID: 30606734 PMCID: PMC6398205 DOI: 10.1074/mcp.ra118.001290] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
A biomarker of synapse loss, an early event in Alzheimer's disease (AD) pathophysiology that precedes neuronal death and symptom onset, would be a much-needed prognostic biomarker. With direct access to the brain interstitial fluid, the cerebrospinal fluid (CSF) is a potential source of synapse-derived proteins. In this study, we aimed to identify and validate novel CSF biomarkers of synapse loss in AD. Discovery: Combining shotgun proteomics of the CSF with an exhaustive search of the literature and public databases, we identified 251 synaptic proteins, from which we selected 22 for further study. Verification: Twelve proteins were discarded because of poor detection by Selected Reaction Monitoring (SRM). We confirmed the specific expression of 9 of the remaining proteins (Calsynytenin-1, GluR2, GluR4, Neurexin-2A, Neurexin-3A, Neuroligin-2, Syntaxin-1B, Thy-1, Vamp-2) at the human synapse using Array Tomography microscopy and biochemical fractionation methods. Exploration: Using SRM, we monitored these 9 synaptic proteins (20 peptides) in a cohort of CSF from cognitively normal controls and subjects in the pre-clinical and clinical AD stages (n = 80). Compared with controls, peptides from 8 proteins were elevated 1.3 to 1.6-fold (p < 0.04) in prodromal AD patients. Validation: Elevated levels of a GluR4 peptide at the prodromal stage were replicated (1.3-fold, p = 0.04) in an independent cohort (n = 60). Moreover, 7 proteins were reduced at preclinical stage 1 (0.6 to 0.8-fold, p < 0.04), a finding that was replicated (0.7 to 0.8-fold, p < 0.05) for 6 proteins in a third cohort (n = 38). In a cross-cohort meta-analysis, 6 synaptic proteins (Calsyntenin-1, GluR4, Neurexin-2A, Neurexin-3A, Syntaxin-1B and Thy-1) were reduced 0.8-fold (p < 0.05) in preclinical AD, changes that precede clinical symptoms and CSF markers of neurodegeneration. Therefore, these proteins could have clinical value for assessing disease progression, especially in preclinical stages of AD.
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Affiliation(s)
- Alberto Lleó
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Raúl Núñez-Llaves
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Daniel Alcolea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Cristina Chiva
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | | | - Martí Colom-Cadena
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Gemma Gomez-Giro
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Laia Muñoz
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Marta Querol-Vilaseca
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Jordi Pegueroles
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Lorena Rami
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Albert Lladó
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - José L Molinuevo
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Mikel Tainta
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
- ¶¶Servicio de Neurologia, Organización Sanitaria Integrada Goierri-Alto Urola, Osakidetza, Zumárraga, España
| | - Jordi Clarimón
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Tara Spires-Jones
- ‖‖Centre for Discovery Brain Sciences and UK Dementia Research Institute, University of Edinburgh EH8 9JZ, UK
| | - Rafael Blesa
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Juan Fortea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Pablo Martínez-Lage
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
| | - Raquel Sánchez-Valle
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Eduard Sabidó
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | - Àlex Bayés
- ***Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025, Barcelona, Spain
- ‡‡‡Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Olivia Belbin
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
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Liu Y, Li Z, Xu Z, Jin X, Gong Y, Xia X, Yao Y, Xu Z, Zhou Y, Xu H, Li S, Peng Y, Wu X, Dai L. Proteomic Maps of Human Gastrointestinal Stromal Tumor Subgroups. Mol Cell Proteomics 2019; 18:923-935. [PMID: 30804049 DOI: 10.1074/mcp.ra119.001361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/18/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal stromal tumor (GIST) is a common sarcoma of gastrointestinal tract (GIT) with high metastatic and recurrence rates, but the proteomic features are still less understood. Here we performed systematic quantitative proteome profiling of GIST from 13 patients classified into very low/low, intermediate and high risk subgroups. An extended cohort of GIST (n = 131) was used for immunohistochemical validation of proteins of interest. In total, 9177 proteins were quantified, covering 55.9% of the GIT transcriptome from The Human Protein Altas. Out of the 9177 quantified proteins, 4930 proteins were observed in all 13 cases with 517 upregulated and 187 downregulated proteins in tumorous tissues independent of risk stage. Pathway analysis showed that the downregulated proteins were mostly enriched in metabolic pathway, whereas the upregulated proteins mainly belonged to spliceosome pathway. In addition, 131 proteins showed differentially expressed patterns among GIST subgroups with statistical significance. The 13 GIST cases were classified into 3 subgroups perfectly based on the expression of these proteins. The intensive comparison of molecular phenotypes and possible functions of quantified oncoproteins, tumor suppressors, phosphatases and kinases between GIST subgroups was carried out. Immunohistochemical analysis of the phosphatase PTPN1 (n = 117) revealed that the GIST patients with high PTPN1 expression had low chances of developing metastasis. Collectively, this work provides valuable information for understanding the inherent biology and evolution of GIST.
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Affiliation(s)
- Yu Liu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhigui Li
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhiqiang Xu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiuxiu Jin
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yanqiu Gong
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xuyang Xia
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yuqin Yao
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhaofen Xu
- §Department of Pathology, The Second People's Hospital of Neijiang City, Sichuan province, Neijiang 641000, China
| | - Yong Zhou
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heng Xu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Shuangqing Li
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Peng
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoting Wu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China;.
| | - Lunzhi Dai
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China;.
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Cavassan NRV, Camargo CC, de Pontes LG, Barraviera B, Ferreira RS, Miot HA, Abbade LPF, Dos Santos LD. Correlation between chronic venous ulcer exudate proteins and clinical profile: A cross-sectional study. J Proteomics 2019; 192:280-290. [PMID: 30261322 DOI: 10.1016/j.jprot.2018.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/13/2023]
Abstract
Chronic venous ulcers affect the quality of life of patients around the world. The aims of this study were to identify the proteins expressed in chronic venous ulcer exudates, to categorize them according to their roles and to correlate them with the clinical and epidemiological aspects of the disease. The study population consisted of 37 ulcers from 28 patients, and the inflammatory exudates of these thirty-seven ulcers were subjected to tryptic digestion and mass spectrometry analysis. Twenty-three patients were female (62.2%), and five (37.8%) were male. The patients had a mean age of 70 (±10.1) years. Of the patients, 73% adhered to compression and rest, 81.1% reported a history of primary varices, 54.1% reported a history of systemic arterial hypertension, 54.1% reported a history of devitalized tissue in the wound bed and 64.9% reported ulcers with more than ten years of evolution. Seventy-six proteins were identified, and they were grouped according to their primary role in the healing process. Eight correlations between clinical and epidemiological data and protein expression were noteworthy: diabetes mellitus vs. Ig gamma-2 and apolipoprotein-A1 and albumin; congestive heart failure vs. Ig lambda-2; colonization vs. actin; compressive therapy vs. Ig kappa; systemic arterial hypertension vs. alpha-2-macroglobulin and apolipoprotein-A1; area of ulcer vs. apolipoprotein-A1; race vs. heavy chain Ig and Ig γ-1 chain; age and race vs. Ig γ-1 chain. These associations may help to elucidate the prognosis and chronicity of chronic venous ulcers based on secreted proteins.
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Affiliation(s)
- Nayara Rodrigues Vieira Cavassan
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Caio Cavassan Camargo
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Letícia Gomes de Pontes
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Benedito Barraviera
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil; Center for the Study of Venoms and Venomous Animals (CEVAP), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Rui Seabra Ferreira
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil; Center for the Study of Venoms and Venomous Animals (CEVAP), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Hélio Amante Miot
- Department of Dermatology and Radiology, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Luciana Patrícia Fernandes Abbade
- Department of Dermatology and Radiology, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Lucilene Delazari Dos Santos
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil; Center for the Study of Venoms and Venomous Animals (CEVAP), Sao Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil.
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Bache N, Geyer PE, Bekker-Jensen DB, Hoerning O, Falkenby L, Treit PV, Doll S, Paron I, Müller JB, Meier F, Olsen JV, Vorm O, Mann M. A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics. Mol Cell Proteomics 2018; 17:2284-2296. [PMID: 30104208 PMCID: PMC6210218 DOI: 10.1074/mcp.tir118.000853] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/13/2018] [Indexed: 12/03/2022] Open
Abstract
Because of low throughput and limited robustness, nano-scale liquid chromatography has been a bottleneck for advancing proteomics in biomedical research. Here, we developed and evaluated two new LC concepts—“pre-formed gradients” and “offset gradients for peptide re-focusing”—that are both implemented in the Evosep One instrument. We evaluated robustness with more than 2000 HeLa runs, demonstrated absence of cross-contamination with crude plasma samples, high proteome coverage by fractionated HeLa and routinely measuring more than 5000 proteins/sample in just 21 minutes. To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop. An auxiliary gradient creates an offset, ensuring the re-focusing of the peptides before the separation on the analytical column by a single high-pressure pump. This simplified design enables robust operation over thousands of sample injections. Furthermore, the steps between injections are performed in parallel, reducing overhead time to a few minutes and allowing analysis of more than 200 samples per day. From fractionated HeLa cell lysates, deep proteomes covering more than 130,000 sequence unique peptides and close to 10,000 proteins were rapidly acquired. Using this data as a library, we demonstrate quantitation of 5200 proteins in only 21 min. Thus, the new system - termed Evosep One - analyzes samples in an extremely robust and high throughput manner, without sacrificing in depth proteomics coverage.
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Affiliation(s)
| | - Philipp E Geyer
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Peter V Treit
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia Doll
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Igor Paron
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Müller
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Meier
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Vorm
- From the ‡Evosep Biosystems, Odense, Denmark
| | - Matthias Mann
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; .,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Prieto DA, Chan KC, Johann DJ Jr, Ye X, Whitely G, Blonder J. Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context of Drug Target/Biomarker Discovery. Methods Mol Biol 2017; 1647:71-90. [PMID: 28808996 DOI: 10.1007/978-1-4939-7201-2_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The discovery of novel drug targets and biomarkers via mass spectrometry (MS)-based proteomic analysis of clinical specimens has proven to be challenging. The wide dynamic range of protein concentration in clinical specimens and the high background/noise originating from highly abundant proteins in tissue homogenates and serum/plasma encompass two major analytical obstacles. Immunoaffinity depletion of highly abundant blood-derived proteins from serum/plasma is a well-established approach adopted by numerous researchers; however, the utilization of this technique for immunodepletion of tissue homogenates obtained from fresh frozen clinical specimens is lacking. We first developed immunoaffinity depletion of highly abundant blood-derived proteins from tissue homogenates, using renal cell carcinoma as a model disease, and followed this study by applying it to different tissue types. Tissue homogenate immunoaffinity depletion of highly abundant proteins may be equally important as is the recognized need for depletion of serum/plasma, enabling more sensitive MS-based discovery of novel drug targets, and/or clinical biomarkers from complex clinical samples. Provided is a detailed protocol designed to guide the researcher through the preparation and immunoaffinity depletion of fresh frozen tissue homogenates for two-dimensional liquid chromatography, tandem mass spectrometry (2D-LC-MS/MS)-based molecular profiling of tissue specimens in the context of drug target and/or biomarker discovery.
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Vialaret J, Schmit PO, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Identification of multiple proteoforms biomarkers on clinical samples by routine Top-Down approaches. Data Brief 2018; 18:1013-21. [PMID: 29900270 DOI: 10.1016/j.dib.2018.03.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/09/2018] [Accepted: 03/19/2018] [Indexed: 01/25/2023] Open
Abstract
Top-Down approaches have an extremely high biological relevance, especially when it comes to biomarker discovery, but the necessary pre-fractionation constraints are not easily compatible with the robustness requirements and the size of clinical sample cohorts. We have demonstrated that intact protein profiling studies could be run on UHR-Q-ToF with limited pre-fractionation (Schmit et al., 2017) [1]. The dataset presented herein is an extension of this research. Proteoforms known to play a role in the pathophysiology process of Alzheimer's disease were identified as candidate biomarkers. In this article, mass spectrometry performance of these candidates are demonstrated.
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Abstract
Blood proteome analysis for biomarker discovery represents one of the most challenging tasks to be achieved through clinical proteomics due to the sample complexity, such as the extreme heterogeneity of proteins in very dynamic concentrations, and to the observation of proper sampling and storage conditions. Quantitative and qualitative proteomics profiling of plasma and serum could be useful both for the early detection of diseases and for the evaluation of pathological status. Two main sources of variability can affect the precision and accuracy of the quantitative experiments designed for biomarker discovery and validation. These sources are divided into two categories, pre-analytical and analytical, and are often ignored; however, they can contribute to consistent errors and misunderstanding in biomarker research. In this chapter, we review critical pre-analytical and analytical variables that can influence quantitative proteomics. According to guidelines accepted by proteomics community, we propose some recommendations and strategies for a proper proteomics analysis addressed to biomarker studies.
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Affiliation(s)
- Viviana Greco
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Luisa Pieroni
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Andrea Urbani
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy. .,Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Rome, Italy.
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Park EC, Lee SY, Yun SH, Choi CW, Lee H, Song HS, Jun S, Kim GH, Lee CS, Kim SI. Clinical proteomic analysis of scrub typhus infection. Clin Proteomics 2018; 15:6. [PMID: 29449793 PMCID: PMC5812041 DOI: 10.1186/s12014-018-9181-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
Background
Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection. Methods Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects. One-dimensional sodium dodecyl sulphate–polyacrylamide gel electrophoresis followed by liquid chromatography-tandem mass spectrometry was performed to identify differentially abundant proteins using quantitative proteomic approaches. Bioinformatic analysis was then performed using Ingenuity Pathway Analysis. Results Proteomic analysis identified 236 serum proteins, of which 32 were differentially expressed in normal subjects, naive scrub typhus patients and patients treated with antibiotics. Comparative bioinformatic analysis of the identified proteins revealed up-regulation of proteins involved in immune responses, especially complement system, following infection with O. tsutsugamushi, and normal expression was largely rescued by antibiotic treatment. Conclusions This is the first proteomic study of clinical serum samples from scrub typhus patients. Proteomic analysis identified changes in protein expression upon infection with O. tsutsugamushi and following antibiotic treatment. Our results provide valuable information for further investigation of scrub typhus therapy and diagnosis. Electronic supplementary material The online version of this article (10.1186/s12014-018-9181-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edmond Changkyun Park
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,2Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Sang-Yeop Lee
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,2Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114 Republic of Korea
| | - Sung Ho Yun
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea
| | - Chi-Won Choi
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,4Division of Life Science, Tunneling Nanotube Research Center, Korea University, Seoul, 02841 Republic of Korea
| | - Hayoung Lee
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Hyun Seok Song
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,2Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Sangmi Jun
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,2Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Gun-Hwa Kim
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea.,4Division of Life Science, Tunneling Nanotube Research Center, Korea University, Seoul, 02841 Republic of Korea
| | - Chang-Seop Lee
- 5Department of Internal Medicine, Chonbuk National University Medical School, Jeonju, 54986 Republic of Korea.,6Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, 54907 Republic of Korea
| | - Seung Il Kim
- 1Drug & Disease Target Team, Korea Basic Science Institute (KBSI), Cheongju, 28119 Republic of Korea.,2Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114 Republic of Korea.,3Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
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Abstract
Within the context of this section, biomarkers are defined as a panel of proteins and peptides that are predictive of the risk for developing a pathological condition. It is important to note here that the use of the descriptor 'panel' is purposeful in that single "biomarkers" are rarely sufficient to permit accurate prediction of a pathological condition. More specifically, the primary application of a biomarker panel is that it serves as a molecular indicator of the severity of a disease or its early response to treatment. In this way, biomarkers enable the application of precision medicine, an approach that tailors specific interventions to those individuals that would most benefit. For a recent comprehensive review of the proteomic-based biomarker development process with a focus on bladder cancer, the reader is directed to Frantzi et al. [Clin Transl Med 3:7, 2014], or a special issue with multiple reviews [Stuhler and Poschmann, Biochim Biophys Acta Proteins Proteomics 1844:859-1058, Elsevier, B V, 2014].
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Datta A, Chai YL, Tan JM, Lee JH, Francis PT, Chen CP, Sze SK, Lai MKP. An iTRAQ-based proteomic analysis reveals dysregulation of neocortical synaptopodin in Lewy body dementias. Mol Brain 2017; 10:36. [PMID: 28800743 PMCID: PMC5553757 DOI: 10.1186/s13041-017-0316-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/21/2017] [Indexed: 02/08/2023] Open
Abstract
Lewy body dementias are the second most common cause of neurodegenerative dementia in the elderly after Alzheimer's disease (AD). The two clinical subgroups of Lewy body dementias, namely, dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD), are differentiated by the chronology of cognitive symptoms relative to parkinsonism. At present, there remains a debate on whether DLB and PDD are separate disease entities, or fall within the same spectrum of Lewy body dementias. In this study, we compared the detergent-soluble proteome via an 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) analysis of pooled lysates from the prefrontal cortex (BA9) of DLB (n = 19) and PDD (n = 21) patients matched a priori for amyloid (total Aβ42) burden, semi-quantitative scores for Lewy bodies and neurofibrillary tangles together with age-matched control (n = 21) subjects. A total of 1914 proteins were confidently identified by iTRAQ (false discovery rate = 0%). None of the proteins showed a significant yet opposite regulation in between DLB and PDD when compared to aged controls in the proteomic data set as well as following immunoblot analysis of the pooled and individual lysates involving all 61 subjects. The postsynaptic protein, synaptopodin (SYNPO) was significantly down-regulated in both DLB and PDD subgroups, suggesting a defective synaptic transmission in the demented patients. In conclusion, the largely similar proteome of DLB and PDD matched for amyloid burden suggests that variations in concomitant AD-related pathology, abnormal post-translational modifications or protein-protein interactions, defective intracellular trafficking or misfolding of proteins could play a part in driving the clinically observed differences between these two subgroups of Lewy body dementias. This further indicates that amyloid-targeting therapeutic strategies may show different efficacies in DLB versus PDD.
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Affiliation(s)
- Arnab Datta
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, Building 10 Room 6N318, Bethesda, MD 20814, USA.
| | - Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jing Min Tan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jasinda H Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Paul T Francis
- Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK.
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Morales-Betanzos CA, Lee H, Gonzalez-Ericsson PI, Balko JM, Johnson DB, Zimmerman LJ, Liebler DC. WITHDRAWN: Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanoma. Mol Cell Proteomics 2017:mcp.M117.067942. [PMID: 28416578 DOI: 10.1074/mcp.m117.067942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 11/06/2022] Open
Abstract
This article has been withdrawn by the authors. We discovered an error after this manuscript was published as a Paper in Press. Specifically, we learned that the structures of glycans presented for the PD-L1 peptide were drawn and labeled incorrectly. We wish to withdraw this article and submit a corrected version for review.
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Affiliation(s)
| | - Hyoungjoo Lee
- Vanderbilt University School of Medicine, United States
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Naru J, Aggarwal R, Mohanty AK, Singh U, Bansal D, Kakkar N, Agnihotri N. Identification of differentially expressed proteins in retinoblastoma tumors using mass spectrometry-based comparative proteomic approach. J Proteomics 2017; 159:77-91. [PMID: 28232133 DOI: 10.1016/j.jprot.2017.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 01/24/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
In India, retinoblastoma is among the top five childhood cancers. Children mostly present with extraocular extension and high risk features that results in unsatisfactory treatment and low survival rate. In addition, lack of potential therapeutic and prognostic targets is another challenge in the management of retinoblastoma. We studied comparative proteome of retinoblastoma patients (HPV positive and negative (n=4 each) and controls (n=4), in order to identify potential retinoblastoma-specific protein targets. 2D-DIGE coupled MALDI-TOF/TOF mass spectrometry identified 39 unique proteins. Highly deregulated proteins were GFAP,RBP3,APOA1,CRYAA,CRABP1,SAG and TF. Gene ontology (Panther 7.0) revealed majority of proteins to be associated with metabolic processes (26%) and catalytic activity (38%). 8 proteins were significantly upregulated in HPV positive vis-a-vis HPV negative cases. Patient group exhibited 12 upregulated and 18 downregulated proteins compared to controls. Pathway and network analysis (IPA software) revealed CTNNB1 as most significantly regulated signalling pathway in HPV positive than HPV negative retinoblastoma. The trends in transcriptional change of 9 genes were consistent with those at proteomic level. The Western blot analysis confirmed the expression pattern of RBP3,GFAP and CRABP1. We suggest GFAP,RBP3,CRABP1,CRYAAA,APOA1 and SAG as prospective targets that could further be explored as potential candidates in therapy and may further assist in studying the disease mechanism. SIGNIFICANCE In this study we evaluated tumor tissue specimens from retinoblastoma patients and identified 39 differentially regulated proteins compared to healthy retina. From these, we propose RBP3, CRABP1, GFAP, CRYAA, APOA1 and SAG as promising proteomic signatures that could further be explored as efficient prognostic and therapeutic targets in retinoblastoma. The present study is not only a contribution to the ongoing endeavour for the discovery of proteomic signatures in retinoblastoma, but, may also act as a starting point for future studies aimed at uncovering novel targets for further therapeutic interventions and improving patient outcomes.
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Abstract
Liquid chromatography-mass spectrometry (LC-MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin based depletion column followed by either protein In-gel enzymatic digestion or protein in-solution enzymatic digestion and then analysis by one-dimensional reverse-phase chromatography or two-dimensional strong cation exchange (SCX)-reverse-phase chromatography (RPC).
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Affiliation(s)
- Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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43
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Lam MPY, Lau E, Ng DCM, Wang D, Ping P. Cardiovascular proteomics in the era of big data: experimental and computational advances. Clin Proteomics 2016; 13:23. [PMID: 27980500 PMCID: PMC5137214 DOI: 10.1186/s12014-016-9124-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/24/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond merely inventorying protein species, and address sophisticated questions on cardiac physiology. The advent of massive mass spectrometry datasets has in turn led to increasing intersection between proteomics and big data science. Here we review new frontiers in technological developments and their applications to cardiovascular medicine. The impact of big data science on cardiovascular proteomics investigations and translation to medicine is highlighted.
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Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Edward Lau
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Dominic C M Ng
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Ding Wang
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Peipei Ping
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Medicine, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Bioinformatics, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
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Abstract
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.
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Affiliation(s)
- Somaditya Mukherjee
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
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Abstract
Proteomics has emerged as a promising field in the post-genomic era. Notwithstanding the great advances provided by gene expression analysis in cancer, the lack of a correlation between gene expression and protein levels has highlighted the need for a proteomic focus on cancer. Although the increasing knowledge regarding cancer biology, a reliable marker to improve diagnosis, prognosis and treatment for cancer patients is not a reality at present. In this review, we address the main considerations regarding proteomics-based studies and their clinical applications on cancer research, highlighting some considerations related to strengths and limitations of proteomics-based studies and its application to clinical practice.
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Affiliation(s)
- Carolina Panis
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil; Laboratório de Mediadores Inflamatórios, Universidade Estadual do Oeste do Paraná, UNIOESTE, Campus Francisco Beltrão, Paraná, Brazil.
| | - Luciana Pizzatti
- Laboratório de Biologia Molecular e Proteômica do Sangue - LABMOPS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Eliana Abdelhay
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil
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46
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Naru J, Aggarwal R, Singh U, Mohanty AK, Bansal D, Mangat N, Kakkar N, Agnihotri N. Proteomic analysis of differentially expressed proteins in vitreous humor of patients with retinoblastoma using iTRAQ-coupled ESI-MS/MS approach. Tumour Biol 2016; 37:13915-13926. [PMID: 27488116 DOI: 10.1007/s13277-016-5162-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022] Open
Abstract
There is close proximity of vitreous humor with the tumor bulk in eyes with retinoblastoma. This renders vitreous humor a promising source to evaluate disease-specific protein targets in retinoblastoma. We studied the differential proteome of vitreous fluid in retinoblastoma tumors (n = 4) as compared to controls (n = 4). The vitreous humor was depleted off the high abundant fraction using MARS-6 affinity column. Subsequently, the tryptic peptides were derivatised with iTRAQ labels. The labelled peptides were pooled and subjected to fractionation using bRPLC. This was followed by protein identification and quantification using electrospray ionisation mass spectrometry (ESI-MS/MS) approach. The identified proteins were subjected to bioinformatics analysis utilizing PANTHER 7.0 and IPA software. Four hundred and thirty-one non-redundant (362 upregulated and 69 downregulated) proteins (≥2 unique peptides, ± 1.5 folds, p < 0.05) were identified. The majority of the proteins were cytoplasmic (40 %), majorly involved in catalytic (32.7 %) and binding activities (26.3 %). Highly deregulated proteins included MMP2, TNC, CD44, SUZ12 and CRABP1. The protein expression of GFAP, CRABP1, MMP2 and TNC was validated by western blotting. Pathway and network analyses revealed p38MAPK and Akt signalling to be the most significantly regulated pathways in retinoblastoma. This is the first report of differential vitreous proteome of retinoblastoma and highlights novel protein targets, such as MMP2, TNC and CRABP1. Further investigations into unravelling the biological role of the proteins and their prospects of being utilised as potential candidates in therapeutics are warranted.
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Affiliation(s)
- Jasmine Naru
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Room No. 19, Research block A, 4th floor, Chandigarh, 160012, India.,Department of Biochemistry, Panjab University, Chandigarh, 160025, India
| | - Ritu Aggarwal
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Room No. 19, Research block A, 4th floor, Chandigarh, 160012, India.
| | - Usha Singh
- Department of Ophthalmology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ashok Kumar Mohanty
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, India
| | - Deepak Bansal
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Navdeep Mangat
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Nandita Kakkar
- Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Navneet Agnihotri
- Department of Biochemistry, Panjab University, Chandigarh, 160025, India
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García Á. Platelet clinical proteomics: Facts, challenges, and future perspectives. Proteomics Clin Appl 2016; 10:767-73. [PMID: 26948058 DOI: 10.1002/prca.201500125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/17/2016] [Accepted: 02/29/2016] [Indexed: 11/08/2022]
Abstract
In recent years, proteomics has been applied to platelet clinical research. Platelets are small enucleated cells that play a fundamental role in hemostasis. In a pathological context, unwanted platelet activation is related to various diseases, primarily thrombosis, but also cancer metastasis, inflammation, immunity, and neurodegenerative diseases. The absence of a nucleus is one of the reasons why proteomics can be considered an ideal analytical tool for platelet research. Indeed, platelet proteomics has allowed the identification of many novel signaling proteins and receptors, several of which are being pursued as potential therapeutic targets. Encouraged by this success, several research groups have recently initiated clinical proteomics studies covering diseases where platelets are involved in some way, such as coronary artery disease, storage pool diseases, uremia, cystic fibrosis, and Alzheimer disease. The goal was to identify platelet biomarkers and drug targets that can help to improve the treatment/diagnosis of the disease and provide further mechanistic evidences of the role platelets play in the pathology. The present article will comment on the recent progress of clinical proteomics in the context of platelet research, challenges, and perspectives for the future ahead.
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Affiliation(s)
- Ángel García
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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49
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Lavatelli F, di Fonzo A, Palladini G, Merlini G. Systemic amyloidoses and proteomics: The state of the art. EuPA Open Proteom 2016; 11:4-10. [PMID: 29900105 PMCID: PMC5988550 DOI: 10.1016/j.euprot.2016.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/01/2016] [Accepted: 02/16/2016] [Indexed: 12/11/2022]
Abstract
Proteomics is an established approach for diagnostic amyloid typing. Mass spectrometry-based methods to analyze amyloid precursors have been developed. Proteomic studies are ongoing to identify novel biomarkers and clarify disease mechanisms.
Systemic amyloidoses are caused by misfolding-prone proteins that polymerize in tissues, causing organ dysfunction. Since proteins are etiological agents of these diseases, proteomics was soon recognized as a privileged instrument for their investigation. Mass spectrometry-based proteomics has acquired a fundamental role in management of systemic amyloidoses, being now considered a gold standard approach for amyloid typing. In parallel, approaches for analyzing circulating amyloid precursors have been developed. Moreover, differential and functional proteomics hold promise for identifying novel biomarkers and clarifying disease mechanisms. This review discusses recent proteomics achievements in systemic amyloidoses, providing a perspective on its present and future applications.
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Affiliation(s)
- Francesca Lavatelli
- Amyloidosis Research and Treatment Center and Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Andrea di Fonzo
- Amyloidosis Research and Treatment Center and Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center and Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center and Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy.,Clinical Chemistry Laboratory, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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50
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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