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Bhuvaneshwar K, Gusev Y. Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review. Brief Bioinform 2024; 25:bbae098. [PMID: 38493340 PMCID: PMC10944574 DOI: 10.1093/bib/bbae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 03/18/2024] Open
Abstract
Translational bioinformatics and data science play a crucial role in biomarker discovery as it enables translational research and helps to bridge the gap between the bench research and the bedside clinical applications. Thanks to newer and faster molecular profiling technologies and reducing costs, there are many opportunities for researchers to explore the molecular and physiological mechanisms of diseases. Biomarker discovery enables researchers to better characterize patients, enables early detection and intervention/prevention and predicts treatment responses. Due to increasing prevalence and rising treatment costs, mental health (MH) disorders have become an important venue for biomarker discovery with the goal of improved patient diagnostics, treatment and care. Exploration of underlying biological mechanisms is the key to the understanding of pathogenesis and pathophysiology of MH disorders. In an effort to better understand the underlying mechanisms of MH disorders, we reviewed the major accomplishments in the MH space from a bioinformatics and data science perspective, summarized existing knowledge derived from molecular and cellular data and described challenges and areas of opportunities in this space.
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Affiliation(s)
- Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
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2
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LaCasse Z, Chivte P, Kress K, Seethi VDR, Bland J, Alhoori H, Kadkol SS, Gaillard ER. Enhancing saliva diagnostics: The impact of amylase depletion on MALDI-ToF MS profiles as applied to COVID-19. J Mass Spectrom Adv Clin Lab 2024; 31:59-71. [PMID: 38323116 PMCID: PMC10846328 DOI: 10.1016/j.jmsacl.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Introduction Human saliva contains a wealth of proteins that can be monitored for disease diagnosis and progression. Saliva, which is easy to collect, has been extensively studied for the diagnosis of numerous systemic and infectious diseases. However, the presence of amylase, the most abundant protein in saliva, can obscure the detection of low-abundance proteins by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-ToF MS), thus reducing its diagnostic utility. Objectives In this study, we used a device to deplete salivary amylase from water-gargle samples by affinity adsorption. Following depletion, saliva proteome profiling was performed using MALDI-ToF MS on gargle samples from individuals confirmed to have COVID-19 based on nasopharyngeal (NP) swab reverse transcription quantitative polymerase chain reaction (RT-qPCR). Results The depletion of amylase led to increased signal intensities of various peaks and the detection of previously unobserved peaks in the MALDI-ToF MS spectra. The overall specificity and sensitivity after amylase depletion were 100% and 85.17%, respectively, for detecting COVID-19. Conclusion This simple, rapid, and inexpensive technique for depleting salivary amylase can reveal spectral diversity in saliva using MALDI-ToF MS, expose low-abundance proteins, and assist in establishing novel biomarkers for diseases.
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Affiliation(s)
- Zane LaCasse
- Departments of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Prajkta Chivte
- Departments of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Kari Kress
- Departments of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
- Thermo Fisher Scientific, Rockford, IL 61101, USA
| | | | - Joshua Bland
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hamed Alhoori
- Departments of Computer Science, Northern Illinois University, DeKalb, IL 60115, USA
| | - Shrihari S. Kadkol
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Elizabeth R. Gaillard
- Departments of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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3
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Wormwood KL, Charette L, Ryan JP, Darie CC, Woods AG. A Proteomics Investigation of Salivary Profiles as Potential Biomarkers for Autism Spectrum Disorder (ASD). Protein J 2023; 42:607-620. [PMID: 37566278 DOI: 10.1007/s10930-023-10146-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that affects approximately 1/68 children, with a more recent study suggesting numbers as high as 1/36. According to Diagnostic and Statistical Manual of Mental Disorders, the etiology of ASD is unknown and diagnosis of this disorder is behavioral. There is currently no biomarker signature for ASD, however, identifying a biomarker signature is crucial as it would aid in diagnosis, identifying treatment targets, monitoring treatments, and identifying the etiology of the disorder. Here we used nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) to investigate the saliva from individuals with ASD and matched controls in a 14 vs 14 study. We found numerous proteins to have statistically significant dysregulations, including lactotransferrin, transferrin, polymeric immunoglobulin receptor, Ig A L, Ig J chain, mucin 5 AC, and lipocalin 1 isoform X1. These findings are consistent with previous studies by our lab, and others, and point to dysregulations in the immune system, lipid metabolism and/or transport, and gastrointestinal disturbances, which are common and reoccurring topics in ASD research.
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Affiliation(s)
- Kelly L Wormwood
- Biochemistry & Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave, Box 5810, Potsdam, NY, 13699, USA
| | - Laci Charette
- Center for Neurobehavioral Health and Department of Psychology, SUNY Plattsburgh, Plattsburgh, NY, USA
| | - Jeanne P Ryan
- Center for Neurobehavioral Health and Department of Psychology, SUNY Plattsburgh, Plattsburgh, NY, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave, Box 5810, Potsdam, NY, 13699, USA.
| | - Alisa G Woods
- Biochemistry & Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave, Box 5810, Potsdam, NY, 13699, USA
- Center for Neurobehavioral Health and Department of Psychology, SUNY Plattsburgh, Plattsburgh, NY, USA
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Messana I, Manconi B, Cabras T, Boroumand M, Sanna MT, Iavarone F, Olianas A, Desiderio C, Rossetti DV, Vincenzoni F, Contini C, Guadalupi G, Fiorita A, Faa G, Castagnola M. The Post-Translational Modifications of Human Salivary Peptides and Proteins Evidenced by Top-Down Platforms. Int J Mol Sci 2023; 24:12776. [PMID: 37628956 PMCID: PMC10454625 DOI: 10.3390/ijms241612776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
In this review, we extensively describe the main post-translational modifications that give rise to the multiple proteoforms characterized to date in the human salivary proteome and their potential role. Most of the data reported were obtained by our group in over twenty-five years of research carried out on human saliva mainly by applying a top-down strategy. In the beginning, we describe the products generated by proteolytic cleavages, which can occur before and after secretion. In this section, the most relevant families of salivary proteins are also described. Next, we report the current information concerning the human salivary phospho-proteome and the limited news available on sulfo-proteomes. Three sections are dedicated to the description of glycation and enzymatic glycosylation. Citrullination and N- and C-terminal post-translational modifications (PTMs) and miscellaneous other modifications are described in the last two sections. Results highlighting the variation in the level of some proteoforms in local or systemic pathologies are also reviewed throughout the sections of the manuscript to underline the impact and relevance of this information for the development of new diagnostic biomarkers useful in clinical practice.
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Affiliation(s)
- Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy; (I.M.); (C.D.); (D.V.R.)
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | | | - Maria Teresa Sanna
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | - Federica Iavarone
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (F.I.); (F.V.)
- Fondazione Policlinico Universitario A. Gemelli Fondazione IRCCS, 00168 Rome, Italy;
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy; (I.M.); (C.D.); (D.V.R.)
| | - Diana Valeria Rossetti
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Consiglio Nazionale delle Ricerche, 00168 Rome, Italy; (I.M.); (C.D.); (D.V.R.)
| | - Federica Vincenzoni
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (F.I.); (F.V.)
- Fondazione Policlinico Universitario A. Gemelli Fondazione IRCCS, 00168 Rome, Italy;
| | - Cristina Contini
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | - Giulia Guadalupi
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (B.M.); (M.T.S.); (A.O.); (C.C.); (G.G.)
| | - Antonella Fiorita
- Fondazione Policlinico Universitario A. Gemelli Fondazione IRCCS, 00168 Rome, Italy;
- Dipartimento di Scienze dell’Invecchiamento, Neurologiche, Ortopediche e della Testa e del Collo, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gavino Faa
- Unit of Pathology, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy;
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Massimo Castagnola
- Proteomics Laboratory, European Center for Brain Research, (IRCCS) Santa Lucia Foundation, 00168 Rome, Italy;
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Top-Down Proteomics Detection of Potential Salivary Biomarkers for Autoimmune Liver Diseases Classification. Int J Mol Sci 2023; 24:ijms24020959. [PMID: 36674470 PMCID: PMC9866740 DOI: 10.3390/ijms24020959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
(1) Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases characterized by chronic hepatic inflammation and progressive liver fibrosis. The possible use of saliva as a diagnostic tool has been explored in several oral and systemic diseases. The use of proteomics for personalized medicine is a rapidly emerging field. (2) Salivary proteomic data of 36 healthy controls (HCs), 36 AIH and 36 PBC patients, obtained by liquid chromatography/mass spectrometry top-down pipeline, were analyzed by multiple Mann-Whitney test, Kendall correlation, Random Forest (RF) analysis and Linear Discriminant Analysis (LDA); (3) Mann-Whitney tests provided indications on the panel of differentially expressed salivary proteins and peptides, namely cystatin A, statherin, histatin 3, histatin 5 and histatin 6, which were elevated in AIH patients with respect to both HCs and PBC patients, while S100A12, S100A9 short, cystatin S1, S2, SN and C showed varied levels in PBC with respect to HCs and/or AIH patients. RF analysis evidenced a panel of salivary proteins/peptides able to classify with good accuracy PBC vs. HCs (83.3%), AIH vs. HCs (79.9%) and PBC vs. AIH (80.2%); (4) RF appears to be an attractive machine-learning tool suited for classification of AIH and PBC based on their different salivary proteomic profiles.
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6
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Silva-Costa LC, Smith BJ. Post-translational Modifications in Brain Diseases: A Future for Biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:129-141. [DOI: 10.1007/978-3-031-05460-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Potential of Salivary Biomarkers in Autism Research: A Systematic Review. Int J Mol Sci 2021; 22:ijms221910873. [PMID: 34639213 PMCID: PMC8509590 DOI: 10.3390/ijms221910873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
The diagnostic process for autism spectrum disorders (ASD) is based on a behavioral analysis of the suspected individual. Despite intensive research, no specific and valid biomarker has been identified for ASD, but saliva, with its advantages such as non-invasive collection, could serve as a suitable alternative to other body fluids. As a source of nucleic acid of both human and microbial origin, protein and non-protein molecules, saliva offers a complex view on the current state of the organism. Additionally, the use of salivary markers seems to be less complicated not only for ASD screening but also for revealing the etiopathogenesis of ASD, since enrolling neurotypical counterparts willing to participate in studies may be more feasible. The aim of the presented review is to provide an overview of the current research performed on saliva in relation to ASD, mutual complementing, and discrepancies that result in difficulties applying the observed markers in clinical practice. We emphasize the methodological limitations of saliva collection and processing as well as the lack of information regarding ASD diagnosis, which is critically discussed.
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Foreman RE, George AL, Reimann F, Gribble FM, Kay RG. Peptidomics: A Review of Clinical Applications and Methodologies. J Proteome Res 2021; 20:3782-3797. [PMID: 34270237 DOI: 10.1021/acs.jproteome.1c00295] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improvements in both liquid chromatography (LC) and mass spectrometry (MS) instrumentation have greatly enhanced proteomic and small molecule metabolomic analysis in recent years. Less focus has been on the improved capability to detect and quantify small bioactive peptides, even though the exact sequences of the peptide species produced can have important biological consequences. Endogenous bioactive peptide hormones, for example, are generated by the targeted and regulated cleavage of peptides from their prohormone sequence. This process may include organ specific variants, as proglucagon is converted to glucagon in the pancreas but glucagon-like peptide-1 (GLP-1) in the small intestine, with glucagon raising, whereas GLP-1, as an incretin, lowering blood glucose. Therefore, peptidomics workflows must preserve the structure of the processed peptide products to prevent the misidentification of ambiguous peptide species. The poor in vivo and in vitro stability of peptides in biological matrices is a major factor that needs to be considered when developing methods to study them. The bioinformatic analysis of peptidomics data sets requires the inclusion of specific post-translational modifications, which are critical for the function of many bioactive peptides. This review aims to discuss and contrast the various extraction, analytical, and bioinformatics approaches used for human peptidomics studies in a multitude of matrices.
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Affiliation(s)
- Rachel E Foreman
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Amy L George
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Frank Reimann
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Fiona M Gribble
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Richard G Kay
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
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Mesleh AG, Abdulla SA, El-Agnaf O. Paving the Way toward Personalized Medicine: Current Advances and Challenges in Multi-OMICS Approach in Autism Spectrum Disorder for Biomarkers Discovery and Patient Stratification. J Pers Med 2021; 11:jpm11010041. [PMID: 33450950 PMCID: PMC7828397 DOI: 10.3390/jpm11010041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder characterized by impairments in two main areas: social/communication skills and repetitive behavioral patterns. The prevalence of ASD has increased in the past two decades, however, it is not known whether the evident rise in ASD prevalence is due to changes in diagnostic criteria or an actual increase in ASD cases. Due to the complexity and heterogeneity of ASD, symptoms vary in severity and may be accompanied by comorbidities such as epilepsy, attention deficit hyperactivity disorder (ADHD), and gastrointestinal (GI) disorders. Identifying biomarkers of ASD is not only crucial to understanding the biological characteristics of the disorder, but also as a detection tool for its early screening. Hence, this review gives an insight into the main areas of ASD biomarker research that show promising findings. Finally, it covers success stories that highlight the importance of precision medicine and the current challenges in ASD biomarker discovery studies.
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Affiliation(s)
- Areej G. Mesleh
- Division of Genomics and Precision Medicine (GPM), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha 34110, Qatar;
| | - Sara A. Abdulla
- Neurological Disorder Center, Qatar Biomedical Research Institute (QBRI), HBKU, Doha 34110, Qatar
- Correspondence: (S.A.A.); (O.E.-A.)
| | - Omar El-Agnaf
- Division of Genomics and Precision Medicine (GPM), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha 34110, Qatar;
- Neurological Disorder Center, Qatar Biomedical Research Institute (QBRI), HBKU, Doha 34110, Qatar
- Correspondence: (S.A.A.); (O.E.-A.)
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10
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Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery. Int J Mol Sci 2020; 21:ijms21176274. [PMID: 32872562 PMCID: PMC7504551 DOI: 10.3390/ijms21176274] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022] Open
Abstract
Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by behavioral alterations and currently affect about 1% of children. Significant genetic factors and mechanisms underline the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders or variants. However, a range of metabolic abnormalities has been highlighted in many patients, by identifying biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient depending on the specific genomic and other omics findings. The progressive identification of new proteins and metabolites acting as biomarker candidates, combined with patient genetic and clinical data and environmental factors, including microbiota, would bring us towards advanced clinical decision support systems (CDSSs) assisted by machine learning models for advanced ASD-personalized medicine. Herein, we will discuss novel computational solutions to evaluate new proteome and metabolome ASD biomarker candidates, in terms of their recurrence in the reviewed literature and laboratory medicine feasibility. Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added value in the near future for the clinical management of ASD.
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Murtaza N, Uy J, Singh KK. Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders. Mol Autism 2020; 11:27. [PMID: 32317014 PMCID: PMC7171839 DOI: 10.1186/s13229-020-00334-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Proteomics is the large-scale study of the total protein content and their overall function within a cell through multiple facets of research. Advancements in proteomic methods have moved past the simple quantification of proteins to the identification of post-translational modifications (PTMs) and the ability to probe interactions between these proteins, spatially and temporally. Increased sensitivity and resolution of mass spectrometers and sample preparation protocols have drastically reduced the large amount of cells required and the experimental variability that had previously hindered its use in studying human neurological disorders. Proteomics offers a new perspective to study the altered molecular pathways and networks that are associated with autism spectrum disorders (ASD). The differences between the transcriptome and proteome, combined with the various types of post-translation modifications that regulate protein function and localization, highlight a novel level of research that has not been appropriately investigated. In this review, we will discuss strategies using proteomics to study ASD and other neurological disorders, with a focus on how these approaches can be combined with induced pluripotent stem cell (iPSC) studies. Proteomic analysis of iPSC-derived neurons have already been used to measure changes in the proteome caused by patient mutations, analyze changes in PTMs that resulted in altered biological pathways, and identify potential biomarkers. Further advancements in both proteomic techniques and human iPSC differentiation protocols will continue to push the field towards better understanding ASD disease pathophysiology. Proteomics using iPSC-derived neurons from individuals with ASD offers a window for observing the altered proteome, which is necessary in the future development of therapeutics against specific targets.
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Affiliation(s)
- Nadeem Murtaza
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Jarryll Uy
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada.
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Shen L, Liu X, Zhang H, Lin J, Feng C, Iqbal J. Biomarkers in autism spectrum disorders: Current progress. Clin Chim Acta 2020; 502:41-54. [DOI: 10.1016/j.cca.2019.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
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Katsani KR, Sakellari D. Saliva proteomics updates in biomedicine. ACTA ACUST UNITED AC 2019; 26:17. [PMID: 31890650 PMCID: PMC6909541 DOI: 10.1186/s40709-019-0109-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/25/2019] [Indexed: 12/25/2022]
Abstract
In the years of personalized (or precision) medicine the 'omics' methodologies in biomedical sciences-genomics, transcriptomics, proteomics and metabolomics-are helping researchers to detect quantifiable biological characteristics, or biomarkers, that will best define the human physiology and pathologies. Proteomics use high throughput and high efficiency approaches with the support of bioinformatic tools in order to identify and quantify the total protein content of cells, tissues or biological fluids. Saliva receives a lot of attention as a rich biological specimen that offers a number of practical and physiological advantages over blood and other biological fluids in monitoring human health. The aim of this review is to present the latest advances in saliva proteomics for biomedicine.
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Affiliation(s)
- Katerina R Katsani
- 1Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dimitra Sakellari
- 2Department of Preventive Dentistry, Periodontology and Implant Biology, School of Dentistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Pichitpunpong C, Thongkorn S, Kanlayaprasit S, Yuwattana W, Plaingam W, Sangsuthum S, Aizat WM, Baharum SN, Tencomnao T, Hu VW, Sarachana T. Phenotypic subgrouping and multi-omics analyses reveal reduced diazepam-binding inhibitor (DBI) protein levels in autism spectrum disorder with severe language impairment. PLoS One 2019; 14:e0214198. [PMID: 30921354 PMCID: PMC6438570 DOI: 10.1371/journal.pone.0214198] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 03/08/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The mechanisms underlying autism spectrum disorder (ASD) remain unclear, and clinical biomarkers are not yet available for ASD. Differences in dysregulated proteins in ASD have shown little reproducibility, which is partly due to ASD heterogeneity. Recent studies have demonstrated that subgrouping ASD cases based on clinical phenotypes is useful for identifying candidate genes that are dysregulated in ASD subgroups. However, this strategy has not been employed in proteome profiling analyses to identify ASD biomarker proteins for specific subgroups. METHODS We therefore conducted a cluster analysis of the Autism Diagnostic Interview-Revised (ADI-R) scores from 85 individuals with ASD to predict subgroups and subsequently identified dysregulated genes by reanalyzing the transcriptome profiles of individuals with ASD and unaffected individuals. Proteome profiling of lymphoblastoid cell lines from these individuals was performed via 2D-gel electrophoresis, and then mass spectrometry. Disrupted proteins were identified and compared to the dysregulated transcripts and reported dysregulated proteins from previous proteome studies. Biological functions were predicted using the Ingenuity Pathway Analysis (IPA) program. Selected proteins were also analyzed by Western blotting. RESULTS The cluster analysis of ADI-R data revealed four ASD subgroups, including ASD with severe language impairment, and transcriptome profiling identified dysregulated genes in each subgroup. Screening via proteome analysis revealed 82 altered proteins in the ASD subgroup with severe language impairment. Eighteen of these proteins were further identified by nano-LC-MS/MS. Among these proteins, fourteen were predicted by IPA to be associated with neurological functions and inflammation. Among these proteins, diazepam-binding inhibitor (DBI) protein was confirmed by Western blot analysis to be expressed at significantly decreased levels in the ASD subgroup with severe language impairment, and the DBI expression levels were correlated with the scores of several ADI-R items. CONCLUSIONS By subgrouping individuals with ASD based on clinical phenotypes, and then performing an integrated transcriptome-proteome analysis, we identified DBI as a novel candidate protein for ASD with severe language impairment. The mechanisms of this protein and its potential use as an ASD biomarker warrant further study.
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Affiliation(s)
- Chatravee Pichitpunpong
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Surangrat Thongkorn
- PhD Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Songphon Kanlayaprasit
- PhD Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wasana Yuwattana
- B.Sc. Program in Medical Technology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Waluga Plaingam
- College of Oriental Medicine, Rangsit University, Pathum Thani, Thailand
| | - Siriporn Sangsuthum
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Tewin Tencomnao
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie Wailin Hu
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Tewarit Sarachana
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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15
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A New Approach for the Diagnosis of Systemic and Oral Diseases Based on Salivary Biomolecules. DISEASE MARKERS 2019; 2019:8761860. [PMID: 30906485 PMCID: PMC6398069 DOI: 10.1155/2019/8761860] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022]
Abstract
Early diagnosis represents the target of contemporary medicine and has an important role in the prognosis and further treatment. Saliva is a biofluid that generated a high interest among researchers due to its multiple advantages over other body fluids. The multitude of components that can act as biomarkers influenced the existing technologies to develop protocols that could allow saliva to become the new noninvasive diagnostic method. Saliva as a diagnostic tool can bring substantial addition to the diagnostic armamentarium, providing important information about oral and general health. The diagnostic applications of saliva extended and had a rapid evolution due to the advancement in salivaomics. The present review summarizes the latest researches in saliva-related studies and explores the information and correlations that saliva can offer regarding the systemic and oral diseases, highlighting its great potential of diagnosis. It is expected that in the future specific guidelines and results regarding the salivary diagnostics are to be available, together with high-sensitivity and specificity tests for multiple systemic and oral diseases.
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16
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Woods AG, Wormwood KL, Iosifescu DV, Murrough J, Darie CC. Protein Biomarkers in Major Depressive Disorder: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:585-600. [DOI: 10.1007/978-3-030-15950-4_35] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Proteomic Investigations of Autism Spectrum Disorder: Past Findings, Current Challenges, and Future Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:235-252. [DOI: 10.1007/978-3-030-05542-4_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Shen L, Zhao Y, Zhang H, Feng C, Gao Y, Zhao D, Xia S, Hong Q, Iqbal J, Liu XK, Yao F. Advances in Biomarker Studies in Autism Spectrum Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:207-233. [PMID: 30747425 DOI: 10.1007/978-3-030-05542-4_11] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a neurological and developmental condition that begins early in childhood and lasts throughout life. The epidemiology of ASD is continuously increasing all over the world with huge social and economical burdens. As the etiology of autism is not completely understood, there is still no medication available for the treatment of this disorder. However, some behavioral interventions are available to improve the core and associated symptoms of autism, particularly when initiated at an early stage. Thus, there is an increasing demand for finding biomarkers for ASD. Although diagnostic biomarkers have not yet been established, research efforts have been carried out in neuroimaging and biological analyses including genomics and gene testing, proteomics, metabolomics, transcriptomics, and studies of the immune system, inflammation, and microRNAs. Here, we will review the current progress in these fields and focus on new methods, developments, research strategies, and studies of blood-based biomarkers.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China.
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Danqing Zhao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, People's Republic of China
| | - Sijian Xia
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Qi Hong
- Maternal and Child Health Hospital of Baoan, Shenzhen, People's Republic of China
| | - Javed Iqbal
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Xu Kun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
| | - Fang Yao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, People's Republic of China
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19
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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20
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Farah R, Haraty H, Salame Z, Fares Y, Ojcius DM, Said Sadier N. Salivary biomarkers for the diagnosis and monitoring of neurological diseases. Biomed J 2018; 41:63-87. [PMID: 29866603 PMCID: PMC6138769 DOI: 10.1016/j.bj.2018.03.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/13/2018] [Accepted: 03/29/2018] [Indexed: 12/17/2022] Open
Abstract
Current research efforts on neurological diseases are focused on identifying novel disease biomarkers to aid in diagnosis, provide accurate prognostic information and monitor disease progression. With advances in detection and quantification methods in genomics, proteomics and metabolomics, saliva has emerged as a good source of samples for detection of disease biomarkers. Obtaining a sample of saliva offers multiple advantages over the currently tested biological fluids as it is a non-invasive, painless and simple procedure that does not require expert training or harbour undesirable side effects for the patients. Here, we review the existing literature on salivary biomarkers and examine their validity in diagnosing and monitoring neurodegenerative and neuropsychiatric disorders such as autism and Alzheimer's, Parkinson's and Huntington's disease. Based on the available research, amyloid beta peptide, tau protein, lactoferrin, alpha-synuclein, DJ-1 protein, chromogranin A, huntingtin protein, DNA methylation disruptions, and micro-RNA profiles provide display a reliable degree of consistency and validity as disease biomarkers.
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Affiliation(s)
- Raymond Farah
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - Hayat Haraty
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - Ziad Salame
- Research Department, Faculty of Dental Medicine, Lebanese University, Beirut, Lebanon
| | - Youssef Fares
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - David M Ojcius
- Department of Biomedical Sciences, University of the Pacific, Arthur Dugoni School of Dentistry, San Francisco, CA, USA.
| | - Najwane Said Sadier
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
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21
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Chang HY, Chen CT, Ko CL, Chen YJ, Chen YJ, Hsu WL, Juo CG, Sung TY. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Anal Chem 2017; 89:13128-13136. [DOI: 10.1021/acs.analchem.7b02343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chu-Ling Ko
- Department
of Computer Science, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chiun-Gung Juo
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- PharmaEssentia Corp., Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
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22
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Szoko N, McShane AJ, Natowicz MR. Proteomic explorations of autism spectrum disorder. Autism Res 2017; 10:1460-1469. [DOI: 10.1002/aur.1803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/30/2017] [Accepted: 04/01/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Nicholas Szoko
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic; Cleveland OH
| | - Adam J. McShane
- Pathology & Laboratory Medicine Institute, Cleveland Clinic; Cleveland OH
| | - Marvin R. Natowicz
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic; Cleveland OH
- Pathology & Laboratory Medicine Institute, Cleveland Clinic; Cleveland OH
- Genomic Medicine, Neurology and Pediatrics Institutes, Cleveland Clinic; Cleveland OH
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23
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Hassaneen M, Maron JL. Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations. Front Public Health 2017; 5:83. [PMID: 28473973 PMCID: PMC5397421 DOI: 10.3389/fpubh.2017.00083] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
In the last decade, technological advances, combined with an improved appreciation of the ability of saliva to inform caregivers about both oral health and systemic disease, have led to the emergence of salivary diagnostic platforms. However, the majority of these assays have targeted diseases that more commonly affect the adult population, largely neglecting infants and children who arguably could benefit the most from non-invasive assessment tools for health monitoring. Gaining access into development, infection, and disease through comprehensive "omic" analyses of saliva could significantly improve care and enhance health access. In this review, we will highlight novel applications of salivary diagnostics in pediatrics across the "omic" spectrum, including at the genomic, transcriptomic, proteomic, microbiomic, and metabolomic level. The challenges to implementing salivary platforms into care, including the effects of age, diet, and developmental stage on salivary components, will be reviewed. Ultimately, large-scale, multicenter trials must be performed to establish normative biomarker values across the age spectrum to accurately discriminate between health and disease. Only then can salivary diagnostics truly translate into pediatric care.
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Affiliation(s)
- Mona Hassaneen
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, USA
| | - Jill L. Maron
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, USA
- Division of Newborn Medicine, Floating Hospital for Children at Tufts Medical Center, Boston, MA, USA
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24
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Kaczor-Urbanowicz KE, Martin Carreras-Presas C, Aro K, Tu M, Garcia-Godoy F, Wong DT. Saliva diagnostics - Current views and directions. Exp Biol Med (Maywood) 2016; 242:459-472. [PMID: 27903834 DOI: 10.1177/1535370216681550] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a "mirror of the body," can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term "Salivaomics" aimed to highlight the rapid development of knowledge about various "omics" constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome. In the last few years, researchers have developed new technologies and validated a wide range of salivary biomarkers that will soon make the use of saliva a clinical reality. However, a great need still exists for convenient and accurate point-of-care devices that can serve as a non-invasive diagnostic tool. In addition, there is an urgent need to decipher the scientific rationale and mechanisms that convey systemic diseases to saliva. Another promising technology called liquid biopsy enables detection of circulating tumor cells (CTCs) and fragments of tumor DNA in saliva, thus enabling non-invasive early detection of various cancers. The newly developed technology-electric field-induced release and measurement (EFIRM) provides near perfect detection of actionable mutations in lung cancer patients. These recent advances widened the salivary diagnostic approach from the oral cavity to the whole physiological system, and thus point towards a promising future of salivary diagnostics for personalized individual medicine applications including clinical decisions and post-treatment outcome predictions. Impact statement The purpose of this mini-review is to make an update about the present and future applications of saliva as a diagnostic biofluid in many fields of science such as dentistry, medicine and pharmacotherapy. Using saliva as a fluid for diagnostic purposes would be a huge breakthrough for both patients and healthcare providers since saliva collection is easy, non-invasive and inexpensive. We will go through the current main diagnostic applications of saliva, and provide a highlight on the emerging, newly developing technologies and tools for cancer screening, detection and monitoring.
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Affiliation(s)
| | | | - Katri Aro
- 1 School of Dentistry, Center for Oral/Head & Neck Oncology Research, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Tu
- 1 School of Dentistry, Center for Oral/Head & Neck Oncology Research, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Franklin Garcia-Godoy
- 3 College of Dentistry, University of Tennessee Health Science Center, Bioscience Research Center, Memphis, TN 38163, USA
| | - David Tw Wong
- 1 School of Dentistry, Center for Oral/Head & Neck Oncology Research, University of California at Los Angeles, Los Angeles, CA 90095, USA
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25
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Giusti L, Ciregia F, Mazzoni MR, Lucacchini A. Proteomics insight into psychiatric disorders: an update on biological fluid biomarkers. Expert Rev Proteomics 2016; 13:941-950. [DOI: 10.1080/14789450.2016.1230499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Federica Ciregia
- Department of Pharmacy, University of Pisa, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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26
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Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:499-519. [PMID: 27306313 PMCID: PMC5373801 DOI: 10.1146/annurev-anchem-071015-041550] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.
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Affiliation(s)
- Timothy K Toby
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
| | - Luca Fornelli
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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27
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Wormwood KL, Aslebagh R, Channaveerappa D, Dupree EJ, Borland MM, Ryan JP, Darie CC, Woods AG. Salivary proteomics and biomarkers in neurology and psychiatry. Proteomics Clin Appl 2015; 9:899-906. [PMID: 25631118 DOI: 10.1002/prca.201400153] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/04/2014] [Accepted: 01/27/2015] [Indexed: 12/30/2022]
Abstract
Biomarkers are greatly needed in the fields of neurology and psychiatry, to provide objective and earlier diagnoses of CNS conditions. Proteomics and other omics MS-based technologies are tools currently being utilized in much recent CNS research. Saliva is an interesting alternative biomaterial for the proteomic study of CNS disorders, with several advantages. Collection is noninvasive and saliva has many proteins. It is easier to collect than blood and can be collected by professionals without formal medical training. For psychiatric and neurological patients, supplying a saliva sample is less anxiety-provoking than providing a blood sample, and is less embarrassing than producing a urine specimen. The use of saliva as a biomaterial has been researched for the diagnosis of and greater understanding of several CNS conditions, including neurodegenerative diseases, autism, and depression. Salivary biomarkers could be used to rule out nonpsychiatric conditions that are often mistaken for psychiatric/neurological conditions, such as fibromyalgia, and potentially to assess cognitive ability in individuals with compromised brain function. As MS and omics technology advances, the sensitivity and utility of assessing CNS conditions using distal human biomaterials such as saliva is becoming increasingly possible.
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Affiliation(s)
- Kelly L Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Roshanak Aslebagh
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Emmalyn J Dupree
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Megan M Borland
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Jeanne P Ryan
- Department of Psychology, SUNY Plattsburgh, Plattsburgh, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.,Center for Neurobehavioral Health, SUNY Plattsburgh, Plattsburgh, NY, USA
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28
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Messana I, Cabras T, Iavarone F, Manconi B, Huang L, Martelli C, Olianas A, Sanna MT, Pisano E, Sanna M, Arba M, D'Alessandro A, Desiderio C, Vitali A, Pirolli D, Tirone C, Lio A, Vento G, Romagnoli C, Cordaro M, Manni A, Gallenzi P, Fiorita A, Scarano E, Calò L, Passali GC, Picciotti PM, Paludetti G, Fanos V, Faa G, Castagnola M. Chrono-proteomics of human saliva: variations of the salivary proteome during human development. J Proteome Res 2015; 14:1666-77. [PMID: 25761918 DOI: 10.1021/pr501270x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important contribution to the variability of any proteome is given by the time dimension that should be carefully considered to define physiological modifications. To this purpose, whole saliva proteome was investigated in a wide age range. Whole saliva was collected from 17 preterm newborns with a postconceptional age at birth of 178-217 days. In these subjects sample collection was performed serially starting immediately after birth and within about 1 year follow-up, gathering a total of 111 specimens. Furthermore, whole saliva was collected from 182 subjects aged between 0 and 17 years and from 23 adults aged between 27 and 57 years. The naturally occurring intact salivary proteome of the 316 samples was analyzed by low- and high-resolution HPLC-ESI-MS platforms. Proteins peculiar of the adults appeared in saliva with different time courses during human development. Acidic proline-rich proteins encoded by PRH2 locus and glycosylated basic proline-rich proteins encoded by PRB3 locus appeared following 180 days of postconceptional age, followed at 7 months (±2 weeks) by histatin 1, statherin, and P-B peptide. The other histatins and acidic proline-rich proteins encoded by PRH1 locus appeared in whole saliva of babies from 1 to 3 weeks after the normal term of delivery, S-type cystatins appeared at 1 year (±3 months), and basic proline-rich proteins appeared at 4 years (±1 year) of age. All of the proteinases involved in the maturation of salivary proteins were more active in preterm than in at-term newborns, on the basis of the truncated forms detected. The activity of the Fam20C kinase, involved in the phosphorylation of various proteins, started around 180 days of postconceptional age, slowly increased reaching values comparable to adults at about 2 years (±6 months) of age. Instead, MAPK14 involved in the phosphorylation of S100A9 was fully active since birth also in preterm newborns.
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Affiliation(s)
- Irene Messana
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Tiziana Cabras
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Federica Iavarone
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Barbara Manconi
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Liling Huang
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Claudia Martelli
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Alessandra Olianas
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Maria Teresa Sanna
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Elisabetta Pisano
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Monica Sanna
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Morena Arba
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Alfredo D'Alessandro
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Claudia Desiderio
- ∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
| | - Alberto Vitali
- ∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
| | - Davide Pirolli
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Chiara Tirone
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | - Alessandra Lio
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | - Giovanni Vento
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | | | - Massimo Cordaro
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Armando Manni
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Patrizia Gallenzi
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Antonella Fiorita
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Emanuele Scarano
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Lea Calò
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | | | | | - Gaetano Paludetti
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Vassilios Fanos
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Gavino Faa
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Massimo Castagnola
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy.,∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
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de Sousa-Pereira P, Cova M, Abrantes J, Ferreira R, Trindade F, Barros A, Gomes P, Colaço B, Amado F, Esteves PJ, Vitorino R. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach. Proteomics 2015; 15:1598-607. [PMID: 25641928 DOI: 10.1002/pmic.201400083] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 12/01/2014] [Accepted: 01/13/2015] [Indexed: 01/31/2023]
Abstract
Despite the importance of saliva in the regulation of oral cavity homeostasis, few studies have been conducted to quantitatively compare the saliva of different mammal species. Aiming to define a proteome signature of mammals' saliva, an in-depth SDS-PAGE-LC coupled to MS/MS (GeLC-MS/MS) approach was used to characterize the saliva from primates (human), carnivores (dog), glires (rat and rabbit), and ungulates (sheep, cattle, horse). Despite the high variability in the number of distinct proteins identified per species, most protein families were shared by the mammals studied with the exception of cattle and horse. Alpha-amylase is an example that seems to reflect the natural selection related to digestion efficacy and food recognition. Casein protein family was identified in all species but human, suggesting an alternative to statherin in the protection of hard tissues. Overall, data suggest that different proteins might assure a similar role in the regulation of oral cavity homeostasis, potentially explaining the specific mammals' salivary proteome signature. Moreover, some protein families were identified for the first time in the saliva of some species, the presence of proline-rich proteins in rabbit's saliva being a good example.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
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Ngounou Wetie AG, Wormwood KL, Russell S, Ryan JP, Darie CC, Woods AG. A Pilot Proteomic Analysis of Salivary Biomarkers in Autism Spectrum Disorder. Autism Res 2015; 8:338-50. [DOI: 10.1002/aur.1450] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/25/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; 8 Clarkson Avenue Potsdam New York 13699-5810
| | - Kelly L. Wormwood
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; 8 Clarkson Avenue Potsdam New York 13699-5810
| | - Stefanie Russell
- SUNY Plattsburgh Neuropsychology Clinic and Psychoeducation Services; 101 Broad Street Plattsburgh New York 12901
| | - Jeanne P. Ryan
- SUNY Plattsburgh Neuropsychology Clinic and Psychoeducation Services; 101 Broad Street Plattsburgh New York 12901
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; 8 Clarkson Avenue Potsdam New York 13699-5810
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; 8 Clarkson Avenue Potsdam New York 13699-5810
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Woods AG, Wormwood KL, Wetie AGN, Aslebagh R, Crimmins BS, Holsen TM, Darie CC. Autism spectrum disorder: an omics perspective. Proteomics Clin Appl 2014; 9:159-68. [PMID: 25311756 DOI: 10.1002/prca.201400116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/11/2014] [Accepted: 10/07/2014] [Indexed: 01/02/2023]
Abstract
Current directions in autism spectrum disorder (ASD) research may require moving beyond genetic analysis alone, based on the complexity of the disorder, heterogeneity and convergence of genetic alterations at the cellular/functional level. Mass spectrometry (MS) has been increasingly used to study CNS disorders, including ASDs. Proteomic research using MS is directed at understanding endogenous protein changes that occur in ASD. This review focuses on how MS has been used to study ASDs, with particular focus on proteomic analysis. Other neurodevelopmental disorders have been investigated using MS, including fragile X syndrome (FXS) and Smith-Lemli-Opitz Syndrome (SLOS), genetic syndromes highly associated with ASD comorbidity.
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Affiliation(s)
- Alisa G Woods
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA; SUNY Plattsburgh Neuropsychology Clinic and Psychoeducation Services, Plattsburgh, NY, USA
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32
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Top-down analytical platforms for the characterization of the human salivary proteome. Bioanalysis 2014; 6:563-81. [PMID: 24568357 DOI: 10.4155/bio.13.349] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive analysis and characterization of the human salivary proteome is an important step towards the possible use of saliva for diagnostic and prognostic purposes. The contribution of the different sources to whole saliva, and the evaluation of individual variability and physiological modifications have been investigated by top-down proteomic approaches, disclosing the faceted and complex profile of the human salivary proteome. All this information is essential to develop saliva protein biomarkers. In this Review the major results obtained in the field by top-down platforms, and the improvements required to allow a more complete picture, will be discussed.
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Dean OM, Turner A, Malhi GS, Ng C, Cotton SM, Dodd S, Sarris J, Samuni Y, Tanious M, Dowling N, Waterdrinker A, Smith D, Berk M. Design and rationale of a 16-week adjunctive randomized placebo-controlled trial of mitochondrial agents for the treatment of bipolar depression. ACTA ACUST UNITED AC 2014; 37:3-12. [PMID: 25295681 DOI: 10.1590/1516-4446-2013-1341] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 05/05/2014] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Bipolar disorder places a significant burden on individuals, caregivers and family, and the broader community. Current treatments are believed to be more effective against manic symptoms, leaving a shortfall in recovery during the depressive phase of the illness. The current study draws on recent evidence suggesting that, in addition to increased oxidative load, alterations in mitochondrial function occur in bipolar disorder. METHODS This 16-week study aims to explore the potential benefits of N-acetylcysteine (NAC) alone or in combination (CT) with selected nutraceuticals believed to enhance mitochondrial function. The study includes adults diagnosed with bipolar disorder currently experiencing an episode of depression. Participants are asked to take NAC, CT, or placebo in addition to any usual treatments. A post-discontinuation visit is conducted 4 weeks following the treatment phase. RESULTS The primary outcome of the study will be mean change on the Montgomery-Asberg Depression Rating Scale. Secondary outcomes include functioning, substance use, mania ratings, and quality of life. Blood samples will be collected at baseline and week 16 to explore biochemical alterations following treatment. CONCLUSION This study may provide a novel adjunctive treatment for bipolar depression. Analysis of biological samples may assist in understanding the therapeutic benefits and the underlying etiology of bipolar depression. TRIAL REGISTRATION Australian and New Zealand Clinical Trial Registry ACTRN12612000830897.
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Affiliation(s)
- Olivia M Dean
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Alyna Turner
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Gin S Malhi
- Discipline of Psychiatry, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Chee Ng
- Department of Psychiatry University of Melbourne, Melbourne, Australia
| | - Sue M Cotton
- Orygen Youth Health Research Centre, Melbourne, Australia
| | - Seetal Dodd
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | | | - Yuval Samuni
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Michelle Tanious
- Discipline of Psychiatry, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Nathan Dowling
- Department of Psychiatry University of Melbourne, Melbourne, Australia
| | - Astrid Waterdrinker
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Deidre Smith
- Department of Psychiatry University of Melbourne, Melbourne, Australia
| | - Michael Berk
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
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Abstract
The term 'casein kinase' has been widely used for decades to denote protein kinases sharing the ability to readily phosphorylate casein in vitro. These fall into three main classes: two of them, later renamed as protein kinases CK1 (casein kinase 1, also known as CKI) and CK2 (also known as CKII), are pleiotropic members of the kinome functionally unrelated to casein, whereas G-CK, or genuine casein kinase, responsible for the phosphorylation of casein in the Golgi apparatus of the lactating mammary gland, has only been identified recently with Fam20C [family with sequence similarity 20C; also known as DMP-4 (dentin matrix protein-4)], a member of the four-jointed family of atypical protein kinases, being responsible for the phosphorylation of many secreted proteins. In hindsight, therefore, the term 'casein kinase' is misleading in every instance; in the case of CK1 and CK2, it is because casein is not a physiological substrate, and in the case of G-CK/Fam20C/DMP-4, it is because casein is just one out of a plethora of its targets, and a rather marginal one at that. Strikingly, casein kinases altogether, albeit representing a minimal proportion of the whole kinome, appear to be responsible for the generation of up to 40-50% of non-redundant phosphosites currently retrieved in human phosphopeptides database. In the present review, a short historical explanation will be provided accounting for the usage of the same misnomer to denote three unrelated classes of protein kinases, together with an update of our current knowledge of these pleiotropic enzymes, sharing the same misnomer while playing very distinct biological roles.
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Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L. Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics 2014; 14:1211-22. [DOI: 10.1002/pmic.201300378] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/10/2014] [Accepted: 02/25/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Si Wu
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Joseph N. Brown
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Da Meng
- Computational Mathematics Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Xiaowen Liu
- Department of BioHealth Informatics; Indiana University-Purdue University Indianapolis; Indianapolis IN USA
| | - Haizhen Zhang
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Ronald J. Moore
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Pavel Pevzner
- Department of Computer Science and Engineering; University of California, San Diego; La Jolla CA USA
| | - Richard D. Smith
- Biological Sciences Division; Pacific Northwest National Laboratories; Richland WA USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
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Jia C, Yu Q, Wang J, Li L. Qualitative and quantitative top-down mass spectral analysis of crustacean hyperglycemic hormones in response to feeding. Proteomics 2014; 14:1185-94. [PMID: 24532205 DOI: 10.1002/pmic.201300331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/07/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022]
Abstract
An efficient pipeline for peptide discovery accelerates peptidomic analysis and facilitates a better understanding of the functional roles of neuropeptides. However, qualitative and quantitative analysis of large neuropeptides is challenging due to the bigger molecular sizes, multiple PTMs, and interference by homologous isoforms. Herein, we refined two methodologies in the pipeline for highly confident and efficient MS-based peptide discovery. For the qualitative analysis, the so-called "high resolution/accurate mass" measurement on Orbitrap mass spectrometers was integrated with computer-assisted homology search, which was successfully applied to decipher the substituted amino acid residues in large neuropeptides by referring to homologous sequences. For the quantitative analysis, a new isotopic labeling-assisted top-down MS strategy was developed, which enabled direct monitoring of the abundance changes of endogenous large neuropeptides. By using the refined peptide discovery pipeline, one novel crustacean hyperglycemic hormone (CHH) from the Dungeness crab sinus glands was confidently identified and de novo sequenced, and its relative abundance was quantified. Comparative analysis of CHHs in unfed and fed crabs revealed that the peptide abundance in the sinus glands was significantly increased after food intake, suggesting that the release of CHHs might be altered by feeding behavior.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, WI, USA
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Amado F, Lobo MJC, Domingues P, Duarte JA, Vitorino R. Salivary peptidomics. Expert Rev Proteomics 2014; 7:709-21. [DOI: 10.1586/epr.10.48] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Cuevas-Córdoba B, Santiago-García J. Saliva: a fluid of study for OMICS. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:87-97. [PMID: 24404837 DOI: 10.1089/omi.2013.0064] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Saliva is a fluid that can be collected easily and noninvasively. Its functions in the oral cavity are well known. Advances in molecular biology and technology, as well as research conducted by the various disciplines of omics (genomics, transcriptomics, proteomics, metabolomics, and metagenomics) have contributed to the identification and characterization of salivary components, including DNA, RNA, proteins, metabolites, and microorganisms. These biomolecules enter the saliva through extracellular and intracellular routes, providing information from several organs and systems and raising the possibility of their use as disease biomarkers. In recent years, these factors have expanded the potential use of saliva as a diagnostic fluid for oral and systemic diseases. This review integrates information regarding salivary biomolecules studied through omics and explores their utility as biomarkers for the diagnosis of several infectious and noninfectious diseases, and the opportunity they represent for the development of point of care devices for clinical application. We also discuss the advantages, disadvantages, and challenges to be overcome in order to establish saliva as a useful fluid for the accurate diagnosis and monitoring of a wide range of diseases.
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Vitorino R, Ferreira R, Caseiro A, Amado F. Salivary Peptidomics Targeting Clinical Applications. COMPREHENSIVE ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-62650-9.00009-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:427-454. [PMID: 25014346 DOI: 10.1146/annurev-anchem-071213-020216] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
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Biomarkers in major depressive disorder: the role of mass spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:545-60. [PMID: 24952202 DOI: 10.1007/978-3-319-06068-2_27] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Major depressive disorder (MDD) is common. Despite numerous available treatments, many individuals fail to improve clinically. MDD continues to be diagnosed exclusively via behavioral rather than biological methods. Biomarkers-which include measurements of genes, proteins, and patterns of brain activity-may provide an important objective tool for the diagnosis of MDD or in the rational selection of treatments. Proteomic analysis and validation of its results as biomarkers is less explored than other areas of biomarker research in MDD. Mass spectrometry (MS) is a comprehensive, unbiased means of proteomic analysis, which can be complemented by directed protein measurements, such as Western Blotting. Prior studies have focused on MS analysis of several human biomaterials in MDD, including human post-mortem brain, cerebrospinal fluid (CSF), blood components, and urine. Further studies utilizing MS and proteomic analysis in MDD may help solidify and establish biomarkers for use in diagnosis, identification of new treatment targets, and understanding of the disorder. The ultimate goal is the validation of a biomarker or a biomarker signature that facilitates a convenient and inexpensive predictive test for depression treatment response and helps clinicians in the rational selection of next-step treatments.
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Mass spectrometry for the study of autism and neurodevelopmental disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:525-44. [PMID: 24952201 DOI: 10.1007/978-3-319-06068-2_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mass spectrometry (MS) has been increasingly used to study central nervous system disorders, including autism spectrum disorders (ASDs). The first studies of ASD using MS focused on the identification of external toxins, but current research is more directed at understanding endogenous protein changes that occur in ASD (ASD proteomics). This chapter focuses on how MS has been used to study ASDs, with particular focus on proteomic analysis. Other neurodevelopmental disorders have been investigated using this technique, including genetic syndromes associated with autism such as fragile X syndrome and Smith-Lemli-Opitz syndrome.
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The potential of biomarkers in psychiatry: focus on proteomics. J Neural Transm (Vienna) 2013; 122 Suppl 1:S9-18. [DOI: 10.1007/s00702-013-1134-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/02/2013] [Indexed: 02/06/2023]
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Woods AG, Ngounou Wetie AG, Sokolowska I, Russell S, Ryan JP, Michel TM, Thome J, Darie CC. Mass spectrometry as a tool for studying autism spectrum disorder. J Mol Psychiatry 2013; 1:6. [PMID: 25408899 PMCID: PMC4223881 DOI: 10.1186/2049-9256-1-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/13/2012] [Indexed: 12/04/2022] Open
Abstract
Autism spectrum disorders (ASDs) are increasing in incidence but have an incompletely understood etiology. Tools for uncovering clues to the cause of ASDs and means for diagnoses are valuable to the field. Mass Spectrometry (MS) has been a useful method for evaluating differences between individuals with ASDs versus matched controls. Different biological substances can be evaluated using MS, including urine, blood, saliva, and hair. This technique has been used to evaluate relatively unsupported hypotheses based on introduction of exogenous factors, such as opiate and heavy metal excretion theories of ASDs. MS has also been used to support disturbances in serotonin-related molecules, which have been more consistently observed in ASDs. Serotonergic system markers, markers for oxidative stress, cholesterol system disturbances, peptide hypo-phosphorylation and methylation have been measured using MS in ASDs, although further analyses with larger numbers of subjects are needed (as well as consideration of behavioral data). Refinements in MS and data analysis are ongoing, allowing for the possibility that future studies examining body fluids and specimens from ASD subjects could continue to yield novel insights. This review summarizes MS investigations that have been conducted to study ASD to date and provides insight into future promising applications for this technique, with focus on proteomic studies.
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Affiliation(s)
- Alisa G Woods
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Stefanie Russell
- Department of Psychology, State University of New York at Plattsburgh, 101 Broad Street, Plattsburgh, NY 12901 USA
| | - Jeanne P Ryan
- Department of Psychology, State University of New York at Plattsburgh, 101 Broad Street, Plattsburgh, NY 12901 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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Castagnola M, Cabras T, Iavarone F, Vincenzoni F, Vitali A, Pisano E, Nemolato S, Scarano E, Fiorita A, Vento G, Tirone C, Romagnoli C, Cordaro M, Paludetti G, Faa G, Messana I. Top-down platform for deciphering the human salivary proteome. J Matern Fetal Neonatal Med 2013; 25:27-43. [PMID: 23025766 DOI: 10.3109/14767058.2012.714647] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Proteomic platforms can be classified in bottom-up strategies, which analyze the sample after proteolytic digestion, and top-down strategies, which analyze the intact naturally occurring proteome. Bottom-up platforms are high-throughput because they can investigate a large number of proteins, regardless of their dimension. Nonetheless, information on post-translational modifications (PTMs) can be lost, especially those regarding naturally occurring cleavages and alternative splicing. Top-down platforms cannot cover vast proteomes, however, they can disclose subtle structural variations occurring during protein maturation and allow label-free relative quantifications in an unlimited number of samples. A repertoire of 256 masses belonging to naturally occurring proteins and peptides consistently detected by RP-HPLC-ESI-MS analysis of the acidic soluble fraction of human whole saliva is presented in this study. Of them, 233 have been identified, while 23 are still pending for the definitive characterization. The present review reports average and mono-isotopic masses of the peptides and proteins detected, RP-HPLC elution times, PTMs, origin and quali-quantitative variations observed in several physiological and pathological conditions. The information reported can be a reference for users of top-down RP-HPLC-ESI-MS proteomic platforms applied to the study of the human salivary proteome as well as of other human bodily fluids.
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Affiliation(s)
- Massimo Castagnola
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica, Largo Francesco Vito 1, Rome, Italy.
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Amado FML, Ferreira RP, Vitorino R. One decade of salivary proteomics: current approaches and outstanding challenges. Clin Biochem 2012; 46:506-17. [PMID: 23103441 DOI: 10.1016/j.clinbiochem.2012.10.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/13/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.
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Affiliation(s)
- Francisco M L Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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Castagnola M, Cabras T, Iavarone F, Fanali C, Nemolato S, Peluso G, Bosello SL, Faa G, Ferraccioli G, Messana I. The human salivary proteome: a critical overview of the results obtained by different proteomic platforms. Expert Rev Proteomics 2012; 9:33-46. [PMID: 22292822 DOI: 10.1586/epr.11.77] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of new separation techniques and different mass spectrometry instrumental devices, as well as the great availability of specific reactants, offers ample choice to scientists for carrying out high-throughput proteomic studies and being competitive in the field today. However, the different options available often do not provide comparable results, which can be linked to factors such as the strategy adopted, the nature of the sample and the instrumental availability. In this critical review, the results obtained so far in the study of human saliva by different proteomic approaches will be compared and discussed.
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Affiliation(s)
- Massimo Castagnola
- Istituto di Biochimica e di Biochimica Clinica, Facoltà di Medicina, Università Cattolica, Largo F. Vito, 00168, Roma, Italy.
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Halgand F, Zabrouskov V, Bassilian S, Souda P, Loo JA, Faull KF, Wong DT, Whitelegge JP. Defining intact protein primary structures from saliva: a step toward the human proteome project. Anal Chem 2012; 84:4383-95. [PMID: 22509742 DOI: 10.1021/ac203337s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Top-down mass spectrometry has been used to investigate structural diversity within some abundant salivary protein families. In this study, we report the identification of two isoforms of protein II-2 which differed in mass by less than 1 Da, the determination of a sequence for protein IB8a that was best satisfied by including a mutation and a covalent modification in the C-terminal part, and the assignment of a sequence of a previously unreported protein of mass 10433 Da. The final characterization of Peptide P-J was achieved, and the discovery of a truncated form of this peptide was reported. The first sequence assignment was done at low resolution using a hybrid quadrupole time-of-flight instrument to quickly identify and characterize proteins, and data acquisition was switched to Fourier-transform ion cyclotron resonance (FTICR) for proteins that required additional sequence coverage and certainty of assignment. High-resolution and high mass accuracy mass spectrometry on a FTICR-mass spectrometry (MS) instrument combined with electron-capture dissociation (ECD) provided the most informative data sets, with the more frequent presence of "unique" ions that unambiguously define the primary structure. A mixture of predictable and unusual post-translational modifications in the protein sequence precluded the use of shotgun-annotated databases at this stage, requiring manual iterations of sequence refinement in many cases. This led us to propose guidelines for an iterative processing workflow of MS and MSMS data sets that allow researchers to completely assign the identity and the structure of a protein.
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Affiliation(s)
- F Halgand
- NPI-Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States.
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Morzel M, Jeannin A, Lucchi G, Truntzer C, Pecqueur D, Nicklaus S, Chambon C, Ducoroy P. Human infant saliva peptidome is modified with age and diet transition. J Proteomics 2012; 75:3665-73. [PMID: 22575268 DOI: 10.1016/j.jprot.2012.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/18/2012] [Indexed: 11/16/2022]
Abstract
In order to describe developmental changes in human salivary peptidome, whole saliva was obtained from 98 infants followed longitudinally at 3 and 6months of age. Data on teeth eruption and diet at the age of 6months were also recorded. Salivary peptide extracts were characterised by label-free MALDI-MS. Peptides differentially expressed between the two ages, and those significantly affected by teeth eruption or introduction of solid foods were identified by MALDI TOF-TOF and LC ESI MS-MS. Out of 81 peaks retained for statistical analysis, 26 were overexpressed at the age of 6months. Exposure to solid foods had a more pronounced effect on profiles (overexpression of nine peaks) than teeth eruption (overexpression of one peak). Differential peaks corresponded to fragments of acidic and basic PRPs, statherin and histatin. Comparison with existing knowledge on adult saliva peptidome revealed that proteolytic processing of salivary proteins is qualitatively quite comparable in infants and in adults. However, age and diet are modulators of salivary peptidome in human infants.
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Affiliation(s)
- Martine Morzel
- CNRS, UMR6265 Centre des Sciences du Goût et de l'Alimentation, F-21000 Dijon, France.
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de Jong EP, van Riper SK, Koopmeiners JS, Carlis JV, Griffin TJ. Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery. Clin Chim Acta 2011; 412:2284-8. [PMID: 21889499 PMCID: PMC3196990 DOI: 10.1016/j.cca.2011.08.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 01/15/2023]
Abstract
BACKGROUND Proteomic studies in saliva have demonstrated its potential as a diagnostic biofluid, however the salivary peptidome is less studied. Here we study the effects of several sample collection and handling factors on salivary peptide abundance levels. METHODS Salivary peptides were isolated using an ultrafiltration device and analyzed by tandem mass spectrometry. A panel of 41 peptides common after various treatments were quantified and normalized. We evaluated the effects of freezing rate of the samples, nutritional status of the donors (fed vs. fasted), and room-temperature sample degradation on peptide abundance levels. Repeatability of our sample processing method and our instrumental analysis method were investigated. RESULTS Increased sample freezing rate produced higher levels of peptides. Donor nutritional status had no influence on the levels of measured peptides. No significant difference was detected in donors' saliva following 5, 10 and 15 min of room-temperature degradation. Sample processing and instrumental variability were relatively small, with median CVs of 9.6 and 6.6. CONCLUSIONS Peptide abundance levels in saliva are rather forgiving towards variations in sample handling and donor nutritional status. Differences in freezing methods may affect peptide abundance, so consistency in freezing samples is preferred. Our results are valuable for standardizing sample collection and handling methods for peptidomic-based biomarker studies in saliva.
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Affiliation(s)
- Ebbing P. de Jong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota; 321 Church St. SE, 6-155 Jackson Hall; Minneapolis, MN 55455
| | - Susan K. van Riper
- Biomedical Informatics and Computational Biology, University of Minnesota; 321 Church St. SE, 6-155 Jackson Hall; Minneapolis, MN 55455
| | - Joseph S. Koopmeiners
- Department of Biostatistics, University of Minnesota; 321 Church St. SE, 6-155 Jackson Hall; Minneapolis, MN 55455
| | - John V. Carlis
- Biomedical Informatics and Computational Biology, University of Minnesota; 321 Church St. SE, 6-155 Jackson Hall; Minneapolis, MN 55455
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota; 321 Church St. SE, 6-155 Jackson Hall; Minneapolis, MN 55455
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