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Sauer CS, Phetsanthad A, Riusech OL, Li L. Developing mass spectrometry for the quantitative analysis of neuropeptides. Expert Rev Proteomics 2021; 18:607-621. [PMID: 34375152 PMCID: PMC8522511 DOI: 10.1080/14789450.2021.1967146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function. AREAS COVERED We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements. EXPERT OPINION Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.
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Affiliation(s)
- Christopher S. Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Olga L. Riusech
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075, USA
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2
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Neves LX, Granato DC, Busso-Lopes AF, Carnielli CM, Patroni FMDS, De Rossi T, Oliveira AK, Ribeiro ACP, Brandão TB, Rodrigues AN, Lacerda PA, Uno M, Cervigne NK, Santos-Silva AR, Kowalski LP, Lopes MA, Paes Leme AF. Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis. Mol Cell Proteomics 2020; 20:100004. [PMID: 33578082 PMCID: PMC7950089 DOI: 10.1074/mcp.ra120.002227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/26/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Protease activity has been associated with pathological processes that can lead to cancer development and progression. However, understanding the pathological unbalance in proteolysis is challenging because changes can occur simultaneously at protease, their inhibitor, and substrate levels. Here, we present a pipeline that combines peptidomics, proteomics, and peptidase predictions for studying proteolytic events in the saliva of 79 patients and their association with oral squamous cell carcinoma (OSCC) prognosis. Our findings revealed differences in the saliva peptidome of patients with (pN+) or without (pN0) lymph-node metastasis and delivered a panel of ten endogenous peptides correlated with poor prognostic factors plus five molecules able to classify pN0 and pN+ patients (area under the receiver operating characteristic curve > 0.85). In addition, endopeptidases and exopeptidases putatively implicated in the processing of differential peptides were investigated using cancer tissue gene expression data from public repositories, reinforcing their association with poorer survival rates and prognosis in oral cancer. The dynamics of the OSCC-related proteolysis were further explored via the proteomic profiling of saliva. This revealed that peptidase/endopeptidase inhibitors exhibited reduced levels in the saliva of pN+ patients, as confirmed by selected reaction monitoring-mass spectrometry, while minor changes were detected in the level of saliva proteases. Taken together, our results indicated that proteolytic activity is accentuated in the saliva of patients with OSCC and lymph-node metastasis and, at least in part, is modulated by reduced levels of salivary peptidase inhibitors. Therefore, this integrated pipeline provided better comprehension and discovery of molecular features with implications in the oral cancer metastasis prognosis.
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Affiliation(s)
- Leandro Xavier Neves
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Daniela C Granato
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ariane Fidelis Busso-Lopes
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Carolina M Carnielli
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Fábio M de Sá Patroni
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Tatiane De Rossi
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ana Karina Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | | | | | - André Nimtz Rodrigues
- Department of Head and Neck Surgery, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Pammela Araujo Lacerda
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Miyuki Uno
- Center for Translational Research in Oncology, São Paulo Cancer Institute, São Paulo, Brazil
| | - Nilva K Cervigne
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Luiz Paulo Kowalski
- Head and Neck Surgery, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Marcio Ajudarte Lopes
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Adriana F Paes Leme
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil.
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Santambrogio L, Berendam SJ, Engelhard VH. The Antigen Processing and Presentation Machinery in Lymphatic Endothelial Cells. Front Immunol 2019; 10:1033. [PMID: 31134089 PMCID: PMC6513971 DOI: 10.3389/fimmu.2019.01033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/23/2019] [Indexed: 12/24/2022] Open
Abstract
Until a few years ago, lymphatic vessels and lymphatic endothelial cells (LEC) were viewed as part of a passive conduit for lymph and immune cells to reach lymph nodes (LN). However, recent work has shown that LEC are active immunological players whose interaction with dendritic cells and T cells is of important immunomodulatory relevance. While the immunological interaction between LEC and other immune cells has taken a center stage, molecular analysis of LEC antigen processing and presentation machinery is still lagging. Herein we review the current knowledge of LEC MHC I and MHC II antigen processing and presentation pathways, Including the role of LEC in antigen phagocytosis, classical, and non-classical MHC II presentation, proteasome processing and MHC I presentation, and cross-presentation. The ultimate goal is to provide an overview of the LEC antigen processing and presentation machinery that constitutes the molecular basis for their role in MHC I and MHC II-restricted immune responses.
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Affiliation(s)
- Laura Santambrogio
- Department of Pathology, Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, United States
| | - Stella J Berendam
- Department of Microbiology, Immunology and Cancer Biology, Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Victor H Engelhard
- Department of Microbiology, Immunology and Cancer Biology, Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA, United States
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Escamez S, Stael S, Vainonen JP, Willems P, Jin H, Kimura S, Van Breusegem F, Gevaert K, Wrzaczek M, Tuominen H. Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2199-2210. [PMID: 30753577 PMCID: PMC6460963 DOI: 10.1093/jxb/erz021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/29/2019] [Indexed: 05/04/2023]
Abstract
During plant vascular development, xylem tracheary elements (TEs) form water-conducting, empty pipes by genetically regulated cell death. Cell death is prevented from spreading to non-TEs by unidentified intercellular mechanisms, downstream of METACASPASE9 (MC9)-mediated regulation of autophagy in TEs. Here, we identified differentially abundant extracellular peptides in vascular-differentiating wild-type and MC9-down-regulated Arabidopsis cell suspensions. A peptide named Kratos rescued the abnormally high ectopic non-TE death resulting from either MC9 knockout or TE-specific overexpression of the ATG5 autophagy protein during experimentally induced vascular differentiation in Arabidopsis cotyledons. Kratos also reduced cell death following mechanical damage and extracellular ROS production in Arabidopsis leaves. Stress-induced but not vascular non-TE cell death was enhanced by another identified peptide, named Bia. Bia is therefore reminiscent of several known plant cell death-inducing peptides acting as damage-associated molecular patterns. In contrast, Kratos plays a novel extracellular cell survival role in the context of development and during stress response.
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Affiliation(s)
- Sacha Escamez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Correspondence:
| | - Simon Stael
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Patrick Willems
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Huiting Jin
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sachie Kimura
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Frank Van Breusegem
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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Contribution of the plasma and lymph Degradome and Peptidome to the MHC Ligandome. Immunogenetics 2018; 71:203-216. [PMID: 30343358 DOI: 10.1007/s00251-018-1093-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
Every biological fluid, blood, interstitial fluid and lymph, urine, saliva, lacrimal fluid, nipple aspirate, and spinal fluid, contains a peptidome-degradome derived from the cellular secretome along with byproducts of the metabolic/catabolic activities of each parenchymal organ. Clement et al. (J Proteomics 78:172-187, 2013), Clement et al. (J Biol Chem 291:5576-5595, 2016), Clement et al. (PLoS One 5:e9863, 2010), Clement et al. (Trends Immunol 32:6-11, 2011), Clement et al. (Front Immunol 4:424, 2013), Geho et al. (Curr Opin Chem Biol 10, 50-55, 2006), Interewicz et al. (Lymphology 37:65‑72, 2004), Leak et al. (Proteomics 4:753‑765, 2004), Popova et al. (PLoS One 9:e110873, 2014), Zhou et al. (Electrophoresis 25:1289‑1298, 2004), D'Alessandro et al. (Shock 42:509‑517, 2014), Dzieciatkowska et al. (Shock 42:485‑498, 2014), Dzieciatkowska et al. (Shock 35:331‑338, 2011), Jordan et al. (J Surg Res 143:130‑135, 2007), Peltz et al. (Surgery 146:347‑357, 2009), Zurawel et al. (Clin Proteomics 8:1, 2011), Ling et al. (Clin Proteomics 6:175‑193, 2010), Sturm et al. (Nat Commun 4:1616, 2013). Over the last decade, qualitative and quantitative analysis of the biological fluids peptidome and degradome have provided a dynamic measurement of tissue homeostasis as well as the tissue response to pathological damage. Proteomic profiling has mapped several of the proteases and resulting degradation by-products derived from cell cycle progression, organ/tissue remodeling and cellular growth, physiological apoptosis, hemostasis, and angiogenesis. Currently, a growing interest lies in the degradome observed during pathological conditions such as cancer, autoimmune diseases, and immune responses to pathogens as a way to exploit biological fluids as liquid biopsies for biomarker discovery Dzieciatkowska et al. (Shock 42:485-498, 2014), Dzieciatkowska et al. (Shock 35:331-338, 2011), Ling et al. (Clin Proteomics 6:175-193, 2010), Ugalde et al. (Methods Mol Biol 622:3-29, 2010), Quesada et al. (Nucleic Acids Res 37:D239‑243, 2009), Cal et al. (Front Biosci 12, 4661-4669, 2007), Shen et al. (PLoS One 5:e13133, 2010a), Antwi et al. (Mol Immunol 46:2931-2937, 2009a), Antwi et al. (J Proteome Res 8:4722‑4731, 2009b), Bedin et al. (J Cell Physiol 231, 915‑925, 2016), Bery et al. (Clin Proteomics 11:13, 2014), Bhalla et al. (Sci Rep 7:1511, 2017), Fan et al. (Diagn Pathol 7:45, 2012a), Fang et al. (Shock 34:291‑298, 2010), Fiedler et al. (Clin Cancer Res 15:3812‑3819, 2009), Fredolini et al. (AAPS J 12:504‑518, 2010), Greening et al. (Enzymes 42:27‑64, 2017), He et al. (PLoS One 8:e63724, 2013), Huang et al. (Int J Gynecol Cancer 28:355‑362, 2018), Hashiguchi et al. (Med Hypotheses 73:760‑763, 2009), Liotta and Petricoin (J Clin Invest 116:26‑30, 2006), Petricoin et al. (Nat Rev Cancer 6:961‑967, 2006), Shen et al. (J Proteome Res 9:2339‑2346, 2010a), Shen et al. (J Proteome Res 5:3154‑3160, 2006), Smith (Clin Proteomics 11:23, 2014), Wang et al. (Oncotarget 8:59376‑59386, 2017), Yang et al. (Clin Exp Med 12:79‑87, 2012a), Yang et al. (J Clin Lab Anal 26:148‑154, 2012b), Yang et al. (Anat Rec (Hoboken) 293:2027‑2033, 2010), Zapico-Muniz et al. (Pancreas 39:1293‑1298, 2010), Villanueva et al. (Mol Cell Proteomics 5:1840‑1852, 2006), Robbins et al. (J Clin Oncol 23:4835‑4837, 2005), Klupczynska et al. (Int J Mol Sci 17:410, 2016). In this review, we focus on the current knowledge of the degradome/peptidome observed in two main biological fluids (plasma and lymph) during physiological and pathological conditions and its importance for immune surveillance.
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Kessel C, McArdle A, Verweyen E, Weinhage T, Wittkowski H, Pennington SR, Foell D. Proteomics in Chronic Arthritis-Will We Finally Have Useful Biomarkers? Curr Rheumatol Rep 2018; 20:53. [PMID: 30008153 DOI: 10.1007/s11926-018-0762-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW Current technical advances enable the assessment of the complex changes in body fluid proteomes and thus allow for the discovery of biomarker signatures rather than just following differences of a single marker. In this review, we aim to summarize current approaches to discover and evaluate multi-biomarker panels for improved monitoring of chronic arthritis disease activity. RECENT FINDINGS Mass spectrometry and affinity proteomic methodologies have been used to identify biomarker panels in synovial fluid, serum, plasma, or urine of pediatric and adult chronic arthritis patients. Notably, despite the numerous efforts to develop new and better biomarker panels, very few have undergone extensive analytical and clinical validation and been adopted into routine use for patient benefit. There remains a significant gap between discovery of chronic arthritis biomarker signatures and their validation for clinical use.
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Affiliation(s)
- Christoph Kessel
- Department of Paediatric Rheumatology and Immunology, University of Muenster, Domagkstraße 3, 48149, Muenster, Germany
| | - Angela McArdle
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Emely Verweyen
- Department of Paediatric Rheumatology and Immunology, University of Muenster, Domagkstraße 3, 48149, Muenster, Germany
| | - Toni Weinhage
- Department of Paediatric Rheumatology and Immunology, University of Muenster, Domagkstraße 3, 48149, Muenster, Germany
| | - Helmut Wittkowski
- Department of Paediatric Rheumatology and Immunology, University of Muenster, Domagkstraße 3, 48149, Muenster, Germany
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Dirk Foell
- Department of Paediatric Rheumatology and Immunology, University of Muenster, Domagkstraße 3, 48149, Muenster, Germany.
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Abstract
This review will highlight our current understanding of the formation, circulation, and immunological role of lymphatic fluid. The formation of the extracellular fluid depends on the net balance between the hydrostatic and osmotic pressure gradients effective in the capillary beds. Lymph originates from the extracellular fluid and its composition combines the ultrafiltrated plasma proteins with the proteome generated by the metabolic activities of each parenchymal tissue. Several analyses have indicated how the lymph composition reflects the organs' physiological and pathological states. The collected lymphatic fluid moves from the capillaries into progressively larger collectors toward the draining lymph node aided by the lymphangion contractility and unidirectional valves, which prevent backflow. The proteomic composition of the lymphatic fluid is reflected in the MHC II peptidome presented by nodal antigen-presenting cells. Taken together, the past few years have generated new interest in the formation, transport, and immunological role of the lymphatic fluid.
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Methodology for Urine Peptidome Analysis Based on Nano-HPLC Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Methods Mol Biol 2018; 1719:311-318. [PMID: 29476520 DOI: 10.1007/978-1-4939-7537-2_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Urine is a sample of choice for noninvasive biomarkers search because it is easily available in large amounts and its molecular composition provides information on processes in the organism. The high potential of urine peptidomics has been demonstrated for clinical purpose. Several mass spectrometry based approaches have been successfully applied for urine peptidome analysis and potential biomarkers search. Summarizing literature data and our own experience we developed a protocol for comprehensive urine peptidome analysis. The technology includes several stages and consists of urine sample preparation by size exclusion chromatography and identification of featured peptides by nano-HPLC coupled to Fourier transform ion cyclotron resonance mass spectrometry, semiquantitative and statistical data analysis.
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9
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Kononikhin A, Starodubtseva N, Bugrova A, Shirokova V, Chagovets V, Indeykina M, Popov I, Kostyukevich Y, Vavina O, Muminova K, Khodzhaeva Z, Kan N, Frankevich V, Nikolaev E, Sukhikh G. An untargeted approach for the analysis of the urine peptidome of women with preeclampsia. J Proteomics 2016; 149:38-43. [DOI: 10.1016/j.jprot.2016.04.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/31/2016] [Accepted: 04/15/2016] [Indexed: 12/18/2022]
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Yeung RSM, Albani S, Feldman BM, Mellins E, Prakken B, Wedderburn LR. Enhancing translational research in paediatric rheumatology through standardization. Nat Rev Rheumatol 2016; 12:684-690. [PMID: 27652504 DOI: 10.1038/nrrheum.2016.156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The past decade has seen many successes in translational rheumatology, from dramatic improvements in outcomes brought about by novel biologic therapies, to the discovery of new monogenic inflammatory disorders. Advances in molecular medicine, combined with progress towards precision care, provide an excellent opportunity to accelerate the translation of biological understanding to the bedside. However, although the field of rheumatology is a leader in the standardization of data collection and measures of disease activity, it lags behind in standardization of biological sample collection and assay performance. Uniform approaches are necessary for robust collaborative research, particularly in rare diseases. Standardization is also critical to increase reproducibility between centres, a prerequisite for clinical implementation of translational research. This Perspectives article emphasizes the need for standardization and implementation of best practices, presented in the context of lessons learned from international biorepository networks.
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Affiliation(s)
- Rae S M Yeung
- Department of Paediatrics, Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Department of Immunology and the Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Salvatore Albani
- Duke-National University of Singapore Graduate Medical School, 8 College Road, 169857, Singapore
| | - Brian M Feldman
- Department of Paediatrics and Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; the Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Institute of Health Policy Management and Evaluation, The Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, Ontario M5T 3M7, Canada
| | - Elizabeth Mellins
- Department of Pediatrics and the Stanford Program in Immunology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA
| | - Berent Prakken
- Department of Immunology, University Medical Centre, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Lucy R Wedderburn
- Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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11
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Clement CC, Moncrieffe H, Lele A, Janow G, Becerra A, Bauli F, Saad FA, Perino G, Montagna C, Cobelli N, Hardin J, Stern LJ, Ilowite N, Porcelli SA, Santambrogio L. Autoimmune response to transthyretin in juvenile idiopathic arthritis. JCI Insight 2016; 1:85633. [PMID: 26973882 DOI: 10.1172/jci.insight.85633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) is the most common pediatric rheumatological condition. Although it has been proposed that JIA has an autoimmune component, the autoantigens are still unknown. Using biochemical and proteomic approaches, we identified the molecular chaperone transthyretin (TTR) as an antigenic target for B and T cell immune responses. TTR was eluted from IgG complexes and affinity purified from 3 JIA patients, and a statistically significant increase in TTR autoantibodies was observed in a group of 43 JIA patients. Three cryptic, HLA-DR1-restricted TTR peptides, which induced CD4+ T cell expansion and IFN-γ and TNF-α production in 3 out of 17 analyzed patients, were also identified. Misfolding, aggregation and oxidation of TTR, as observed in the synovial fluid of all JIA patients, enhanced its immunogenicity in HLA-DR1 transgenic mice. Our data point to TTR as an autoantigen potentially involved in the pathogenesis of JIA and to oxidation and aggregation as a mechanism facilitating TTR autoimmunity.
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Affiliation(s)
- Cristina C Clement
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Halima Moncrieffe
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Aditi Lele
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ginger Janow
- Department of Pediatric Rheumatology, Montefiore Medical Center, New York, New York, USA
| | - Aniuska Becerra
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Francesco Bauli
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Fawzy A Saad
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Giorgio Perino
- Department of Pathology, Hospital for Special Surgery, New York, New York, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, New York, New York, USA
| | - Neil Cobelli
- Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA
| | - John Hardin
- Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Norman Ilowite
- Department of Pediatric Rheumatology, Montefiore Medical Center, New York, New York, USA
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
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12
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Clement CC, Becerra A, Yin L, Zolla V, Huang L, Merlin S, Follenzi A, Shaffer SA, Stern LJ, Santambrogio L. The Dendritic Cell Major Histocompatibility Complex II (MHC II) Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity. J Biol Chem 2016; 291:5576-5595. [PMID: 26740625 DOI: 10.1074/jbc.m115.655738] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/26/2022] Open
Abstract
The repertoire of peptides displayed in vivo by MHC II molecules derives from a wide spectrum of proteins produced by different cell types. Although intracellular endosomal processing in dendritic cells and B cells has been characterized for a few antigens, the overall range of processing pathways responsible for generating the MHC II peptidome are currently unclear. To determine the contribution of non-endosomal processing pathways, we eluted and sequenced over 3000 HLA-DR1-bound peptides presented in vivo by dendritic cells. The processing enzymes were identified by reference to a database of experimentally determined cleavage sites and experimentally validated for four epitopes derived from complement 3, collagen II, thymosin β4, and gelsolin. We determined that self-antigens processed by tissue-specific proteases, including complement, matrix metalloproteases, caspases, and granzymes, and carried by lymph, contribute significantly to the MHC II self-peptidome presented by conventional dendritic cells in vivo. Additionally, the presented peptides exhibited a wide spectrum of binding affinity and HLA-DM susceptibility. The results indicate that the HLA-DR1-restricted self-peptidome presented under physiological conditions derives from a variety of processing pathways. Non-endosomal processing enzymes add to the number of epitopes cleaved by cathepsins, altogether generating a wider peptide repertoire. Taken together with HLA-DM-dependent and-independent loading pathways, this ensures that a broad self-peptidome is presented by dendritic cells. This work brings attention to the role of "self-recognition" as a dynamic interaction between dendritic cells and the metabolic/catabolic activities ongoing in every parenchymal organ as part of tissue growth, remodeling, and physiological apoptosis.
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Affiliation(s)
| | | | | | | | | | - Simone Merlin
- the School of Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Antonia Follenzi
- From the Departments of Pathology and; the School of Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Scott A Shaffer
- Biochemistry and Molecular Pharmacology and; the Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Lawrence J Stern
- the Departments of Pathology and; Biochemistry and Molecular Pharmacology and
| | - Laura Santambrogio
- From the Departments of Pathology and; Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461,.
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte AJ, Sheng G, Sylvester KG, Cohen HJ, Ling XB. Serological targeted analysis of an ITIH4 peptide isoform: a preterm birth biomarker and its associated SNP implications. J Genet Genomics 2015; 42:507-10. [PMID: 26408095 PMCID: PMC11186666 DOI: 10.1016/j.jgg.2015.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 11/18/2022]
Affiliation(s)
- Zhou Tan
- Institute of Developmental and Regenerative Biology, Hangzhou Normal University, Hangzhou 310029, China; Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Zhongkai Hu
- Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Emily Y Cai
- Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Cantas Alev
- Lab for Early Embryogenesis, RIKEN Center for Developmental Biology, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Ting Yang
- Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Zhen Li
- Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Joyce Sung
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Yasser Yehia El-Sayed
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Atul J Butte
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Guojun Sheng
- Lab for Early Embryogenesis, RIKEN Center for Developmental Biology, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Karl G Sylvester
- Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Harvey J Cohen
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Xuefeng B Ling
- Department of Surgery, Stanford University, Stanford, CA 94305, USA.
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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Abstract
The search for biomarkers in paediatric rheumatic diseases, particularly juvenile idiopathic arthritis (JIA), childhood lupus nephritis (LN), and juvenile idiopathic inflammatory myopathies (JIIMs) is attracting increased interest. In JIA, a number of biomarkers have shown potential for predicting clinical phenotype, disease activity and severity, clinical remission and relapse, response to treatment, and disease course over time. In systemic JIA, measurement of biomarkers that reflect the degree of activation and expansion of T cells and macrophages might be helpful for detecting subclinical macrophage activation syndrome. Urine biomarkers for childhood LN hold promise for facilitating early diagnosis and improving disease monitoring and assessment of response to therapy. Myositis-specific autoantibodies define distinct serological subgroups of JIIMs, albeit with similar clinical features, responses to therapy, and prognoses. Use of biomarkers may potentially help to avoid invasive procedures, such as renal biopsy in systemic lupus erythematosus and muscle biopsy in juvenile dermatomyositis. Incorporation of effective and reliable biomarkers into routine practice might facilitate adoption of a stratified approach to investigation and management, foster the implementation of research into the design of personalized and targeted therapies, and ultimately lead to more rational and effective clinical care.
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Abstract
Use of biomarkers in clinical practice has proved extremely valuable and is a rapidly expanding field. However, despite the huge potential of biomarkers, for juvenile idiopathic arthritis (JIA) there are currently no validated paediatric biomarkers available to help with setting up a more tailored approach on which drug choice could be based, to achieve remission early in the course of disease. Early remission reduces burden of disease, limits side effects from toxic and unnecessary medication, and, most importantly, enhances quality of life. Several studies have suggested promising biomarkers: these may be a protein, cellular component, mRNA, or genetic component, for example a single nucleotide polymorphism (SNP). Here we describe recent developments in the use of biomarkers for JIA and their potential to assist in management of disease by predicting disease phenotype, severity, progression, and response to treatment, and determining when patients have reached stable remission and can safely discontinue treatment.
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Sylvester KG, Ling XB, Liu GY, Kastenberg ZJ, Ji J, Hu Z, Peng S, Lau K, Abdullah F, Brandt ML, Ehrenkranz RA, Harris MC, Lee TC, Simpson J, Bowers C, Moss RL. A novel urine peptide biomarker-based algorithm for the prognosis of necrotising enterocolitis in human infants. Gut 2014; 63:1284-92. [PMID: 24048736 PMCID: PMC4161026 DOI: 10.1136/gutjnl-2013-305130] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Necrotising enterocolitis (NEC) is a major source of neonatal morbidity and mortality. The management of infants with NEC is currently complicated by our inability to accurately identify those at risk for progression of disease prior to the development of irreversible intestinal necrosis. We hypothesised that integrated analysis of clinical parameters in combination with urine peptide biomarkers would lead to improved prognostic accuracy in the NEC population. DESIGN Infants under suspicion of having NEC (n=550) were prospectively enrolled from a consortium consisting of eight university-based paediatric teaching hospitals. Twenty-seven clinical parameters were used to construct a multivariate predictor of NEC progression. Liquid chromatography/mass spectrometry was used to profile the urine peptidomes from a subset of this population (n=65) to discover novel biomarkers of NEC progression. An ensemble model for the prediction of disease progression was then created using clinical and biomarker data. RESULTS The use of clinical parameters alone resulted in a receiver-operator characteristic curve with an area under the curve of 0.817 and left 40.1% of all patients in an 'indeterminate' risk group. Three validated urine peptide biomarkers (fibrinogen peptides: FGA1826, FGA1883 and FGA2659) produced a receiver-operator characteristic area under the curve of 0.856. The integration of clinical parameters with urine biomarkers in an ensemble model resulted in the correct prediction of NEC outcomes in all cases tested. CONCLUSIONS Ensemble modelling combining clinical parameters with biomarker analysis dramatically improves our ability to identify the population at risk for developing progressive NEC.
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Affiliation(s)
- Karl G Sylvester
- Division of Pediatric Surgery, Lucile Packard Children’s Hospital, Stanford, USA
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - Xuefeng B Ling
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - G Y Liu
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Jun Ji
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - Zhongkai Hu
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - Sihua Peng
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - Ken Lau
- Department of Surgery, Stanford University School of Medicine, Stanford, USA
| | - Fizan Abdullah
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mary L Brandt
- Department of Surgery, Texas Children’s Hospital, Baylor College of Medicine, Houston, USA
| | | | | | - Timothy C Lee
- Department of Surgery, Texas Children’s Hospital, Baylor College of Medicine, Houston, USA
| | - Joyce Simpson
- Department of Pediatrics, Yale University School of Medicine, New Haven, USA
| | - Corinna Bowers
- Division of Pediatric Surgery, Nationwide Children’s Hospital, Columbus, USA
- Department of Surgery, Ohio State College of Medicine, Columbus, USA
| | - R Lawrence Moss
- Division of Pediatric Surgery, Nationwide Children’s Hospital, Columbus, USA
- Department of Surgery, Ohio State College of Medicine, Columbus, USA
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Smith CR, Batruch I, Bauça JM, Kosanam H, Ridley J, Bernardini MQ, Leung F, Diamandis EP, Kulasingam V. Deciphering the peptidome of urine from ovarian cancer patients and healthy controls. Clin Proteomics 2014; 11:23. [PMID: 24982608 PMCID: PMC4065538 DOI: 10.1186/1559-0275-11-23] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Background Ovarian cancer (OvCa) is the most lethal gynecological malignancy. The emergence of high-throughput technologies, such as mass spectrometry, has allowed for a paradigm shift in the way we search for novel biomarkers. Urine-based peptidomic profiling is a novel approach that may result in the discovery of noninvasive biomarkers for diagnosing patients with OvCa. In this study, the peptidome of urine from 6 ovarian cancer patients and 6 healthy controls was deciphered. Results Urine samples underwent ultrafiltration and the filtrate was subjected to solid phase extraction, followed by fractionation using strong cation exchange chromatography. These fractions were analyzed using an Orbitrap mass spectrometer. Over 4600 unique endogenous urine peptides arising from 713 proteins were catalogued, representing the largest urine peptidome reported to date. Each specimen was processed in triplicate and reproducibility at the protein (69-76%) and peptide (58-63%) levels were noted. More importantly, over 3100 unique peptides were detected solely in OvCa specimens. One such promising biomarker was leucine-rich alpha-2-glycoprotein (LRG1), where multiple peptides were found in all urines from OvCa patients, but only one peptide was found in one healthy control urine sample. Conclusions Mining the urine peptidome may yield highly promising novel OvCa biomarkers.
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Affiliation(s)
- Christopher R Smith
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ihor Batruch
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Josep Miquel Bauça
- Servei d'Anàlisis Clíniques, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Hari Kosanam
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julia Ridley
- Department of Psychosocial Oncology and Palliative Care, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada ; Division of Palliative Care, Department of Community and Palliative Medicine, University of Toronto, Toronto, ON, Canada
| | - Marcus Q Bernardini
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Felix Leung
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Eleftherios P Diamandis
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Vathany Kulasingam
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
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Cretu D, Diamandis EP, Chandran V. Delineating the synovial fluid proteome: recent advancements and ongoing challenges in biomarker research. Crit Rev Clin Lab Sci 2014; 50:51-63. [PMID: 23758541 DOI: 10.3109/10408363.2013.802408] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There is an urgent need for identifying novel serum biomarkers that can be used to improve diagnosis, predict disease progression or response to therapy, or serve as therapeutic targets for rheumatic diseases. Synovial fluid (SF) is secreted by and remains in direct contact with the synovial membrane, and can reflect the biochemical state of the joint under different physiological and pathological conditions. Therefore, SF is regarded as an excellent source for identifying biomarkers of rheumatologic diseases. The use of high-throughput and/or quantitative proteomics and sophisticated computational software applied to analyze the protein content of SF has been well-adopted as an approach to finding novel arthritis biomarkers. This review will focus on some of the potential pitfalls of biomarker studies using SF, summarize the status of the field of SF proteomics in general, as well as discuss some of the most promising biomarker study approaches using proteomics. A brief status of the biomarker discovery efforts in rheumatoid arthritis, osteoarthritis and juvenile idiopathic arthritis is also provided.
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Affiliation(s)
- Daniela Cretu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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21
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Xu MY, Jia XF, Qu Y, Zheng RD, Yuan ZH, Weng HL, Dooley S, Wang XP, Zhang LJ, Lu LG. Serum dihydroxyacetone kinase peptide m/z 520.3 as predictor of disease severity in patients with compensated chronic hepatitis B. J Transl Med 2013; 11:234. [PMID: 24289155 PMCID: PMC3851457 DOI: 10.1186/1479-5876-11-234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/13/2013] [Indexed: 01/06/2023] Open
Abstract
Background & aim Due to known limitations of liver biopsy, reliable non-invasive serum biomarkers for chronic liver diseases are needed. We performed serum peptidomics for such investigation in compensated chronic hepatitis B (CHB) patients. Methods Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) was used to identify differentially expressed peptides in sera from 40 CHB patients (20 with S0G0-S1G1 and 20 with S3G3-S4G4). Ion pair quantification from differentially expressed peptides in a validation set of sera from 86 CHB patients was done with multiple reaction monitoring (MRM). Results 21 differentially represented peptide peaks were found through LC-MS/MS. Ion pairs generated from eleven of these peptides (m/z < 800) were quantified by MRM. Summed peak area ratios of 6 ion pairs from peptide m/z 520.3 (176.1, 353.7, 459.8, 503.3, 351.3, 593.1), which was identified as dihydroxyacetone kinase (DAK) fragment, decreased from mild to advanced stages of fibrosis or inflammation. Area Under Receiver Operating Characteristic Curves (AUROCs) of five ion models discriminating fibrosis degrees were 0.871 ~ 0.915 (S2-4 versus S0-1) and 0.804 ~ 0.924 (S3-4 versus S0-2). AUROCs discriminating inflammation grades were 0.840 ~ 0.902 (G2-4 versus G0-1) and 0.787 ~ 0.888 (G3-4 versus G0-2). The diagnostic power of these models provides improved sensitivity and specificity for predicting disease progression as compared to aspartate aminotransferase to platelet ratio index (APRI), FIB-4, Forn’s index and serum DAK protein. Conclusions The peptide fragment (m/z 520.3) of DAK is a promising biomarker to guide timing of antiviral treatment and to avoid liver biopsy in compensated CHB patients.
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Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte AJ, Ling XB. Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia. PLoS One 2013; 8:e65571. [PMID: 23840341 PMCID: PMC3686758 DOI: 10.1371/journal.pone.0065571] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/27/2013] [Indexed: 01/20/2023] Open
Abstract
We sought to identify serological markers capable of diagnosing preeclampsia (PE). We performed serum peptide analysis (liquid chromatography mass spectrometry) of 62 unique samples from 31 PE patients and 31 healthy pregnant controls, with two-thirds used as a training set and the other third as a testing set. Differential serum peptide profiling identified 52 significant serum peptides, and a 19-peptide panel collectively discriminating PE in training sets (n = 21 PE, n = 21 control; specificity = 85.7% and sensitivity = 100%) and testing sets (n = 10 PE, n = 10 control; specificity = 80% and sensitivity = 100%). The panel peptides were derived from 6 different protein precursors: 13 from fibrinogen alpha (FGA), 1 from alpha-1-antitrypsin (A1AT), 1 from apolipoprotein L1 (APO-L1), 1 from inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), 2 from kininogen-1 (KNG1), and 1 from thymosin beta-4 (TMSB4). We concluded that serum peptides can accurately discriminate active PE. Measurement of a 19-peptide panel could be performed quickly and in a quantitative mass spectrometric platform available in clinical laboratories. This serum peptide panel quantification could provide clinical utility in predicting PE or differential diagnosis of PE from confounding chronic hypertension.
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Affiliation(s)
- Qiaojun Wen
- Department of Surgery, Stanford University, Stanford, California, United States of America
| | - Linda Y. Liu
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
| | - Ting Yang
- Department of Surgery, Stanford University, Stanford, California, United States of America
| | - Cantas Alev
- Lab for Early Embryogenesis, RIKEN Center for Developmental Biology, Chuo-Ku, Kobe, Hyogo, Japan
| | - Shuaibin Wu
- Department of Surgery, Stanford University, Stanford, California, United States of America
| | - David K. Stevenson
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
| | - Guojun Sheng
- Lab for Early Embryogenesis, RIKEN Center for Developmental Biology, Chuo-Ku, Kobe, Hyogo, Japan
| | - Atul J. Butte
- Department of Pediatrics, Stanford University, Stanford, California, United States of America
- * E-mail: (XBL); (AJB)
| | - Xuefeng B. Ling
- Department of Surgery, Stanford University, Stanford, California, United States of America
- * E-mail: (XBL); (AJB)
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Correlation analyses of clinical and molecular findings identify candidate biological pathways in systemic juvenile idiopathic arthritis. BMC Med 2012; 10:125. [PMID: 23092393 PMCID: PMC3523070 DOI: 10.1186/1741-7015-10-125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/23/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Clinicians have long appreciated the distinct phenotype of systemic juvenile idiopathic arthritis (SJIA) compared to polyarticular juvenile idiopathic arthritis (POLY). We hypothesized that gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with each disease would reveal distinct biological pathways when analyzed for significant associations with elevations in two markers of JIA activity, erythrocyte sedimentation rate (ESR) and number of affected joints (joint count, JC). METHODS PBMC RNA from SJIA and POLY patients was profiled by kinetic PCR to analyze expression of 181 genes, selected for relevance to immune response pathways. Pearson correlation and Student's t-test analyses were performed to identify transcripts significantly associated with clinical parameters (ESR and JC) in SJIA or POLY samples. These transcripts were used to find related biological pathways. RESULTS Combining Pearson and t-test analyses, we found 91 ESR-related and 92 JC-related genes in SJIA. For POLY, 20 ESR-related and 0 JC-related genes were found. Using Ingenuity Systems Pathways Analysis, we identified SJIA ESR-related and JC-related pathways. The two sets of pathways are strongly correlated. In contrast, there is a weaker correlation between SJIA and POLY ESR-related pathways. Notably, distinct biological processes were found to correlate with JC in samples from the earlier systemic plus arthritic phase (SAF) of SJIA compared to samples from the later arthritis-predominant phase (AF). Within the SJIA SAF group, IL-10 expression was related to JC, whereas lack of IL-4 appeared to characterize the chronic arthritis (AF) subgroup. CONCLUSIONS The strong correlation between pathways implicated in elevations of both ESR and JC in SJIA argues that the systemic and arthritic components of the disease are related mechanistically. Inflammatory pathways in SJIA are distinct from those in POLY course JIA, consistent with differences in clinically appreciated target organs. The limited number of ESR-related SJIA genes that also are associated with elevations of ESR in POLY implies that the SJIA associations are specific for SJIA, at least to some degree. The distinct pathways associated with arthritis in early and late SJIA raise the possibility that different immunobiology underlies arthritis over the course of SJIA.
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Ling XB, Lau K, Kanegaye JT, Pan Z, Peng S, Ji J, Liu G, Sato Y, Yu TTS, Whitin JC, Schilling J, Burns JC, Cohen HJ. A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses. BMC Med 2011; 9:130. [PMID: 22145762 PMCID: PMC3251532 DOI: 10.1186/1741-7015-9-130] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 12/06/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Kawasaki disease is an acute vasculitis of infants and young children that is recognized through a constellation of clinical signs that can mimic other benign conditions of childhood. The etiology remains unknown and there is no specific laboratory-based test to identify patients with Kawasaki disease. Treatment to prevent the complication of coronary artery aneurysms is most effective if administered early in the course of the illness. We sought to develop a diagnostic algorithm to help clinicians distinguish Kawasaki disease patients from febrile controls to allow timely initiation of treatment. METHODS Urine peptidome profiling and whole blood cell type-specific gene expression analyses were integrated with clinical multivariate analysis to improve differentiation of Kawasaki disease subjects from febrile controls. RESULTS Comparative analyses of multidimensional protein identification using 23 pooled Kawasaki disease and 23 pooled febrile control urine peptide samples revealed 139 candidate markers, of which 13 were confirmed (area under the receiver operating characteristic curve (ROC AUC 0.919)) in an independent cohort of 30 Kawasaki disease and 30 febrile control urine peptidomes. Cell type-specific analysis of microarrays (csSAM) on 26 Kawasaki disease and 13 febrile control whole blood samples revealed a 32-lymphocyte-specific-gene panel (ROC AUC 0.969). The integration of the urine/blood based biomarker panels and a multivariate analysis of 7 clinical parameters (ROC AUC 0.803) effectively stratified 441 Kawasaki disease and 342 febrile control subjects to diagnose Kawasaki disease. CONCLUSIONS A hybrid approach using a multi-step diagnostic algorithm integrating both clinical and molecular findings was successful in differentiating children with acute Kawasaki disease from febrile controls.
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Affiliation(s)
- Xuefeng B Ling
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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Ban E, Park SH, Kang MJ, Lee HJ, Song EJ, Yoo YS. Growing trend of CE at the omics level: The frontier of systems biology - An update. Electrophoresis 2011; 33:2-13. [DOI: 10.1002/elps.201100344] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 02/03/2023]
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26
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Pathogenesis of systemic juvenile idiopathic arthritis: some answers, more questions. Nat Rev Rheumatol 2011; 7:416-26. [PMID: 21647204 DOI: 10.1038/nrrheum.2011.68] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Systemic juvenile idiopathic arthritis (sJIA) has long been recognized as unique among childhood arthritides, because of its distinctive clinical and epidemiological features, including an association with macrophage activation syndrome. Here, we summarize research into sJIA pathogenesis. The triggers of disease are unknown, although infections are suspects. Once initiated, sJIA seems to be driven by innate proinflammatory cytokines. Endogenous Toll-like receptor ligands, including S100 proteins, probably synergize with cytokines to perpetuate inflammation. These and other findings support the hypothesis that sJIA is an autoinflammatory condition. Indeed, IL-1 is implicated as a pivotal cytokine, but the source of excess IL-1 activity remains obscure and the role of IL-1 in chronic arthritis is less clear. Another hypothesis is that a form of hemophagocytic lymphohistiocytosis underlies sJIA, with varying degrees of its expression across the spectrum of disease. Alternatively, sJIA with MAS might be a genetically distinct subtype. Yet another hypothesis proposes that inadequate downregulation of immune activation is central to sJIA, supporting evidence for which includes 'alternative activation' of monocyte and macrophages and possible deficiencies in IL-10 and T regulatory cells. Some altered immune phenotypes persist during clinically inactive disease, which suggests that this stage might represent compensated inflammation. Despite much progress being made, many questions remain, providing fertile ground for future research.
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Guzman NA, Phillips TM. Immunoaffinity capillary electrophoresis: A new versatile tool for determining protein biomarkers in inflammatory processes. Electrophoresis 2011; 32:1565-78. [DOI: 10.1002/elps.201000700] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/17/2011] [Accepted: 03/20/2011] [Indexed: 01/22/2023]
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Mustafa SA, Hoheisel JD, Alhamdani MSS. Secretome profiling with antibody microarrays. MOLECULAR BIOSYSTEMS 2011; 7:1795-801. [DOI: 10.1039/c1mb05071k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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