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Dongiovanni P, Meroni M, Aiello G, D’Amato A, Cenzato N, Casati S, Damiani G, Fenoglio C, Galimberti D, Grossi E, Prati D, Lamorte G, Bianco C, Valenti L, Soggiu A, Zapperi S, La Porta CAM, Del Fabbro M, Tartaglia GM. Salivary proteomic profile of young healthy subjects. Front Mol Biosci 2023; 10:1327233. [PMID: 38099196 PMCID: PMC10720708 DOI: 10.3389/fmolb.2023.1327233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Background: The incidence of noncommunicable diseases (NCDs) has been rapidly ramped up worldwide. Hence, there is an urgent need to non-invasively detect NCDs possibly by exploiting saliva as a 'liquid biopsy' to identify biomarkers of the health status. Since, the absence of standardized procedures of collection/analysis and the lack of normal ranges makes the use of saliva still tricky, our purpose was to outline a salivary proteomic profile which features healthy individuals. Methods: We collected saliva samples from 19 young blood donors as reference population and the proteomic profile was investigated through mass-spectrometry. Results: We identified 1,004 proteins of whose 243 proteins were shared by all subjects. By applying a data clustering approach, we found a set of six most representative proteins across all subjects including Coronin-1A, F-actin-capping protein subunit alpha, Immunoglobulin J chain, Prosaposin, 78 kDa glucose-regulated protein and Heat shock 70 kDa protein 1A and 1B. Conclusion: All of these proteins are involved in immune system activation, cellular stress responses, proliferation, and invasion thus suggesting their use as biomarkers in patients with NCDs.
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Affiliation(s)
- P. Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - M. Meroni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gilda Aiello
- Department of Human Science and Quality of Life Promotion, Telematic University San Raffaele, Rome, Italy
| | - A. D’Amato
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - N. Cenzato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Casati
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - G. Damiani
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - C. Fenoglio
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - D. Galimberti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Neurodegenerative Diseases Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - E. Grossi
- Villa Santa Maria Foundation, Tavernerio, Italy
| | - D. Prati
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. Lamorte
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - C. Bianco
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - L. Valenti
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - A. Soggiu
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Zapperi
- Department of Physics, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - C. A. M. La Porta
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - M. Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. M. Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
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2
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Korhonen L, Paul ER, Wåhlén K, Haring L, Vasar E, Vaheri A, Lindholm D. Multivariate analyses of immune markers reveal increases in plasma EN-RAGE in first-episode psychosis patients. Transl Psychiatry 2023; 13:326. [PMID: 37863883 PMCID: PMC10589203 DOI: 10.1038/s41398-023-02627-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
Immune cells and cytokines are largely recognized as significant factors in the pathophysiology of neuropsychiatric disorders. The possible role of other blood cells such as leukocytes in events of acute psychosis is in contrast only emerging. To study blood-born markers in acute psychosis we here evaluated plasma proteins in drug-naive first-episode psychosis (FEP) patients and healthy controls using a multiplex proximity extension assay technique. We analyzed a panel of 92 immune markers and plasma samples from 60 FEP patients and 50 controls and evaluated the changes obtained using multivariate statistical methods followed by protein pathway analyses. Data showed that 11 proteins are significantly different between FEP patients and healthy controls We observed increases in pro-inflammatory proteins such as interleukin-6, oncostatin-M, and transforming growth factor-alpha in FEP patients compared with controls. Likewise, the extracellular newly identified RAGE-binding protein (EN-RAGE) that regulates the expression of various cytokines was also elevated in the plasma of FEP patients. The results indicate that neutrophil-derived EN-RAGE could play an important role during the early phase of acute psychosis by stimulating cytokines and the immune response targeting thereby likely also the brain vasculature.
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Affiliation(s)
- Laura Korhonen
- Center for Social and Affective Neuroscience, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Biochemical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
- Department of Child and Adolescent Psychiatry, Linköping University, Linköping, Sweden Region Östergötland, Linköping, Sweden
| | - Elisabeth R Paul
- Center for Social and Affective Neuroscience, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karin Wåhlén
- Pain and Rehabilitation Center, Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Liina Haring
- Institute of Clinical Medicine University of Tartu; Psychiatry Clinic of Tartu University Hospital, Tartu, Estonia
| | - Eero Vasar
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Tartu, 50411, Estonia
| | - Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - Dan Lindholm
- Department of Biochemical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden.
- Department of Biochemistry and Developmental Biology, Medicum, University of Helsinki, PO Box 63, FI-00014, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2U, Tukholmankatu 8, FI-00290, Helsinki, Finland.
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3
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Shamir A, Yitzhaky A, Segev A, Haroutunian V, Katsel P, Hertzberg L. Up-Regulation of S100 Gene Family in Brain Samples of a Subgroup of Individuals with Schizophrenia: Meta-analysis. Neuromolecular Med 2023; 25:388-401. [PMID: 37005977 DOI: 10.1007/s12017-023-08743-4] [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: 12/01/2022] [Accepted: 03/12/2023] [Indexed: 04/04/2023]
Abstract
The S100 proteins family is known to affect neuroinflammation and astrocyte activation, which have been suggested to be contributors to the pathogenesis of schizophrenia. We conducted a systematic meta-analysis of S100 genes differential expression in postmortem samples of patients with schizophrenia vs. healthy controls, following the commonly used Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Twelve microarray datasets met the inclusion criteria (overall 511 samples, 253 schizophrenia and 258 controls were analyzed). Nine out of 21 genes were significantly up-regulated or with tendency for up-regulation. A per-sample fold change analysis indicated that the S100 genes' up-regulation was concentrated in a subgroup of the patients. None of the genes have been found to be down-regulated. ANXA3, which encodes Annexin 3 protein and was associated with neuroinflammation, was up-regulated and positively correlated with the S100 genes' expression pattern. In addition, astrocytes and endothelial cell markers were significantly correlated with S100A8 expression. S100 correlation with ANXA3 and endothelial cell markers suggests that the up-regulation we detected reflects increased inflammation. However, it might also reflect astrocytes abundance or activation. The fact that S100 proteins were shown to be up-regulated in blood samples and other body fluids of patients with schizophrenia suggests a potential role as biomarkers, which might help disease subtyping, and the development of etiological treatments for immune dysregulation in schizophrenia.
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Affiliation(s)
- Anat Shamir
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Aviv Segev
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Shalvata Mental Health Center, 13 Aliat Hanoar St, 45100, Hod Hasharon, Israel
| | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
| | - Pavel Katsel
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Libi Hertzberg
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel.
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
- Shalvata Mental Health Center, 13 Aliat Hanoar St, 45100, Hod Hasharon, Israel.
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4
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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5
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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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Consolidation of metabolomic, proteomic, and GWAS data in connective model of schizophrenia. Sci Rep 2023; 13:2139. [PMID: 36747015 PMCID: PMC9901842 DOI: 10.1038/s41598-023-29117-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Despite of multiple systematic studies of schizophrenia based on proteomics, metabolomics, and genome-wide significant loci, reconstruction of underlying mechanism is still a challenging task. Combination of the advanced data for quantitative proteomics, metabolomics, and genome-wide association study (GWAS) can enhance the current fundamental knowledge about molecular pathogenesis of schizophrenia. In this study, we utilized quantitative proteomic and metabolomic assay, and high throughput genotyping for the GWAS study. We identified 20 differently expressed proteins that were validated on an independent cohort of patients with schizophrenia, including ALS, A1AG1, PEDF, VTDB, CERU, APOB, APOH, FASN, GPX3, etc. and almost half of them are new for schizophrenia. The metabolomic survey revealed 18 group-specific compounds, most of which were the part of transformation of tyrosine and steroids with the prevalence to androgens (androsterone sulfate, thyroliberin, thyroxine, dihydrotestosterone, androstenedione, cholesterol sulfate, metanephrine, dopaquinone, etc.). The GWAS assay mostly failed to reveal significantly associated loci therefore 52 loci with the smoothened p < 10-5 were fractionally integrated into proteome-metabolome data. We integrated three omics layers and powered them by the quantitative analysis to propose a map of molecular events associated with schizophrenia psychopathology. The resulting interplay between different molecular layers emphasizes a strict implication of lipids transport, oxidative stress, imbalance in steroidogenesis and associated impartments of thyroid hormones as key interconnected nodes essential for understanding of how the regulation of distinct metabolic axis is achieved and what happens in the conditioned proteome and metabolome to produce a schizophrenia-specific pattern.
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7
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Brodbelt JS. Deciphering combinatorial post-translational modifications by top-down mass spectrometry. Curr Opin Chem Biol 2022; 70:102180. [PMID: 35779351 PMCID: PMC9489649 DOI: 10.1016/j.cbpa.2022.102180] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) create vast structural and functional diversity of proteins, ultimately modulating protein function and degradation, influencing cellular signaling, and regulating transcription. The combinatorial patterns of PTMs increase the heterogeneity of proteins and further mediates their interactions. Advances in mass spectrometry-based proteomics have resulted in identification of thousands of proteins and allowed characterization of numerous types and sites of PTMs. Examination of intact proteins, termed the top-down approach, offers the potential to map protein sequences and localize multiple PTMs on each protein, providing the most comprehensive cataloging of proteoforms. This review describes some of the dividends of using mass spectrometry to analyze intact proteins and showcases innovative strategies that have enhanced the promise of top-down proteomics for exploring the impact of combinatorial PTMs in unsurpassed detail.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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8
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Basingab F, Alsaiary A, Almontashri S, Alrofaidi A, Alharbi M, Azhari S, Algothmi K, Alhazmi S. Alterations in Immune-Related Defensin Alpha 4 ( DEFA4) Gene Expression in Health and Disease. Int J Inflam 2022; 2022:9099136. [PMID: 35668817 PMCID: PMC9167129 DOI: 10.1155/2022/9099136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022] Open
Abstract
Defensin Alpha 4 (DEFA4) is the fourth member of the Alpha Defensins family known as a part of antimicrobial peptides in the innate immune system. DEFA4 has a strong preference to kill Gram-negative bacteria more than Gram-positive bacteria. In addition, DEFA4 exhibits antiviral activity against human immunodeficiency virus type 1 (HIV-1) in vitro. Moreover, DEFA4 can act as an inhibitor of corticosterone production (Corticostatin). On the other hand, alternations in DEFA4 gene expression have been reported in different disorders such as diseases related to inflammation and immunity dysfunction, brain-related disorders, and various cancers. The up-regulation of DEFA4 appears to be involved in the malignant transformation or aggressive form of cancer. Interestingly, the modified version of DEFA4 fragment (1-11) was potent and efficient against antibiotic-resistant bacteria. This review provides a general background abSaudi Arabia out DEFA4 and sheds light on changes in DEFA4 gene expression in different diseases. The paper also discusses other aspects related to DEFA4 as an antimicrobial and antiviral agent. The research was conducted based on available articles obtained from databases starting from 1988 to the present.
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Affiliation(s)
- Fatemah Basingab
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abeer Alsaiary
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Biology Department, College of Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shahad Almontashri
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Alrofaidi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Safiah Alhazmi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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9
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Rodrigues JE, Martinho A, Santos V, Santa C, Madeira N, Martins MJ, Pato CN, Macedo A, Manadas B. Systematic Review and Meta-Analysis on MS-Based Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Bipolar Disorder. Int J Mol Sci 2022; 23:ijms23105460. [PMID: 35628270 PMCID: PMC9141521 DOI: 10.3390/ijms23105460] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BD) is a clinically heterogeneous condition, presenting a complex underlying etiopathogenesis that is not sufficiently characterized. Without molecular biomarkers being used in the clinical environment, several large screen proteomics studies have been conducted to provide valuable molecular information. Mass spectrometry (MS)-based techniques can be a powerful tool for the identification of disease biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids to assess BD biomarkers and identify relevant networks of biological pathways. Following PRISMA guidelines, we searched for studies using MS proteomics to identify proteomic differences between BD patients and healthy controls (PROSPERO database: CRD42021264955). Fourteen articles fulfilled the inclusion criteria, allowing the identification of 266 differentially expressed proteins. Gene ontology analysis identified complement and coagulation cascades, lipid and cholesterol metabolism, and focal adhesion as the main enriched biological pathways. A meta-analysis was performed for apolipoproteins (A-I, C-III, and E); however, no significant differences were found. Although the proven ability of MS proteomics to characterize BD, there are several confounding factors contributing to the heterogeneity of the findings. In the future, we encourage the scientific community to use broader samples and validation cohorts, integrating omics with bioinformatics tools towards providing a comprehensive understanding of proteome alterations, seeking biomarkers of BD, and contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis.
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Affiliation(s)
- Joao E. Rodrigues
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
| | - Ana Martinho
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
| | - Vítor Santos
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
| | - Catia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
| | - Nuno Madeira
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria J. Martins
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
- Medical Services, University of Coimbra Medical Services, 3004-517 Coimbra, Portugal
| | - Carlos N. Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA;
| | - Antonio Macedo
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-548 Coimbra, Portugal
- Correspondence: authors: (A.M.); (B.M.)
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal;
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
- Correspondence: authors: (A.M.); (B.M.)
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10
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Rodrigues JE, Martinho A, Santa C, Madeira N, Coroa M, Santos V, Martins MJ, Pato CN, Macedo A, Manadas B. Systematic Review and Meta-Analysis of Mass Spectrometry Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Schizophrenia. Int J Mol Sci 2022; 23:ijms23094917. [PMID: 35563307 PMCID: PMC9105255 DOI: 10.3390/ijms23094917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Mass spectrometry (MS)-based techniques can be a powerful tool to identify neuropsychiatric disorder biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids of schizophrenia (SCZ) patients to identify disease biomarkers and relevant networks of biological pathways. Following PRISMA guidelines, a search was performed for studies that used MS proteomics approaches to identify proteomic differences between SCZ patients and healthy control groups (PROSPERO database: CRD42021274183). Nineteen articles fulfilled the inclusion criteria, allowing the identification of 217 differentially expressed proteins. Gene ontology analysis identified lipid metabolism, complement and coagulation cascades, and immune response as the main enriched biological pathways. Meta-analysis results suggest the upregulation of FCN3 and downregulation of APO1, APOA2, APOC1, and APOC3 in SCZ patients. Despite the proven ability of MS proteomics to characterize SCZ, several confounding factors contribute to the heterogeneity of the findings. In the future, we encourage the scientific community to perform studies with more extensive sampling and validation cohorts, integrating omics with bioinformatics tools to provide additional comprehension of differentially expressed proteins. The produced information could harbor potential proteomic biomarkers of SCZ, contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis.
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Affiliation(s)
- João E. Rodrigues
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
| | - Ana Martinho
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
| | - Catia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
| | - Nuno Madeira
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Manuel Coroa
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
| | - Vítor Santos
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
| | - Maria J. Martins
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
- Medical Services, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Carlos N. Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA;
| | - Antonio Macedo
- Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal;
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-548 Coimbra, Portugal
- Correspondence: (A.M.); (B.M.)
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.E.R.); (A.M.); (C.S.); (M.J.M.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.); (V.S.)
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
- Correspondence: (A.M.); (B.M.)
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11
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A serum proteomic study of two case-control cohorts identifies novel biomarkers for bipolar disorder. Transl Psychiatry 2022; 12:55. [PMID: 35136035 PMCID: PMC8826439 DOI: 10.1038/s41398-022-01819-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/12/2021] [Accepted: 01/17/2022] [Indexed: 01/08/2023] Open
Abstract
We set out to identify novel protein associations with potential as clinically viable biomarkers for bipolar disorder. To this end, we used proximity extension assay to analyze 201 unique proteins in blood serum from two independent cohorts comprising patients with bipolar disorder and healthy controls (total n = 493). We identified 32 proteins significantly associated with bipolar disorder in both case-control cohorts after adjusting for relevant covariates. Twenty-two findings are novel to bipolar disorder, but 10 proteins have previously been associated with bipolar disorder: chitinase-3-like protein 1, C-C motif chemokine 3 (CCL3), CCL4, CCL20, CCL25, interleukin 10, growth/differentiation factor-15, matrilysin (MMP-7), pro-adrenomedullin, and TNF-R1. Next, we estimated the variance in serum protein concentrations explained by psychiatric drugs and found that some case-control associations may have been driven by psychiatric drugs. The highest variance explained was observed between lithium use and MMP-7, and in post-hoc analyses and found that the serum concentration of MMP-7 was positively associated with serum lithium concentration, duration of lithium therapy, and inversely associated with estimated glomerular filtration rate in an interaction with lithium. This is noteworthy given that MMP-7 has been suggested as a mediator of renal tubulointerstitial fibrosis, which is characteristic of lithium-induced nephropathy. Finally, we used machine learning to evaluate the classification performance of the studied biomarkers but the average performance in unseen data was fair to moderate (area under the receiver operating curve = 0.72). Taken together, our serum biomarker findings provide novel insight to the etiopathology of bipolar disorder, and we present a suggestive biomarker for lithium-induced nephropathy.
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12
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Guan F, Ni T, Zhu W, Williams LK, Cui LB, Li M, Tubbs J, Sham PC, Gui H. Integrative omics of schizophrenia: from genetic determinants to clinical classification and risk prediction. Mol Psychiatry 2022; 27:113-126. [PMID: 34193973 PMCID: PMC11018294 DOI: 10.1038/s41380-021-01201-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Schizophrenia (SCZ) is a debilitating neuropsychiatric disorder with high heritability and complex inheritance. In the past decade, successful identification of numerous susceptibility loci has provided useful insights into the molecular etiology of SCZ. However, applications of these findings to clinical classification and diagnosis, risk prediction, or intervention for SCZ have been limited, and elucidating the underlying genomic and molecular mechanisms of SCZ is still challenging. More recently, multiple Omics technologies - genomics, transcriptomics, epigenomics, proteomics, metabolomics, connectomics, and gut microbiomics - have all been applied to examine different aspects of SCZ pathogenesis. Integration of multi-Omics data has thus emerged as an approach to provide a more comprehensive view of biological complexity, which is vital to enable translation into assessments and interventions of clinical benefit to individuals with SCZ. In this review, we provide a broad survey of the single-omics studies of SCZ, summarize the advantages and challenges of different Omics technologies, and then focus on studies in which multiple omics data are integrated to unravel the complex pathophysiology of SCZ. We believe that integration of multi-Omics technologies would provide a roadmap to create a more comprehensive picture of interactions involved in the complex pathogenesis of SCZ, constitute a rich resource for elucidating the potential molecular mechanisms of the illness, and eventually improve clinical assessments and interventions of SCZ to address clinical translational questions from bench to bedside.
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Affiliation(s)
- Fanglin Guan
- Department of Forensic Psychiatry, School of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Tong Ni
- Department of Forensic Psychiatry, School of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Weili Zhu
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, China
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Long-Biao Cui
- Department of Clinical Psychology, School of Medical Psychology, Air Force Medical University, Xi'an, Shaanxi, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Justin Tubbs
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Pak-Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA.
- Behavioral Health Services, Henry Ford Health System, Detroit, MI, USA.
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13
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Boroumand M, Olianas A, Cabras T, Manconi B, Fanni D, Faa G, Desiderio C, Messana I, Castagnola M. Saliva, a bodily fluid with recognized and potential diagnostic applications. J Sep Sci 2021; 44:3677-3690. [PMID: 34350708 PMCID: PMC9290823 DOI: 10.1002/jssc.202100384] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022]
Abstract
Human whole saliva is a bodily fluid that can be obtained easily by noninvasive techniques. Specimens can be collected by the patient also at home in order to monitor health status and variations of several analytes of clinical interest. The contributions to whole saliva include secretions from salivary glands and, among others, from the gingival crevicular fluid that derives from the epithelial mucosa. Therefore, saliva is currently a relevant diagnostic fluid for many substances, including steroids, nonpeptide hormones, therapeutic drugs, and drugs of abuse. This review at first briefly describes the different contributions to whole saliva. A section illustrates the procedures for the collection, handling, and storage of salivary specimens. Another section describes the present use of whole saliva for diagnostic purposes and its specific utilization for the diagnosis of several local and systemic diseases. The final sections illustrate the future opportunities offered by various not conventional techniques with a focus on the most recent –omic investigations. It describes the various issues that have to be taken into account to avoid false positives and negatives, such as the strength of the experimental plan, the adequacy of the number of samples under study, and the proper choice of controls.
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Affiliation(s)
- Mozhgan Boroumand
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Roma, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Barbara Manconi
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Daniela Fanni
- Dipartimento di Scienze Mediche e Sanità Pubblica, Sezione di Patologia, Università di Cagliari, AOU of Cagliari, Cagliari, Italy.,Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, USA
| | - Gavino Faa
- Dipartimento di Scienze Mediche e Sanità Pubblica, Sezione di Patologia, Università di Cagliari, AOU of Cagliari, Cagliari, Italy.,Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, USA
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale Delle Ricerche, Roma, Italy
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale Delle Ricerche, Roma, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Roma, Italy
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14
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Rosa LK, Costa FS, Hauagge CM, Mobile RZ, de Lima AAS, Amaral CDB, Machado RC, Nogueira ARA, Brancher JA, de Araujo MR. Oral health, organic and inorganic saliva composition of men with Schizophrenia: Case-control study. J Trace Elem Med Biol 2021; 66:126743. [PMID: 33740480 DOI: 10.1016/j.jtemb.2021.126743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Schizophrenia (SCZ) presents complex challenges related to diagnosis and clinical monitoring. The study of conditions associated with SCZ can be facilitated by using potential markers and patterns that provide information to support the diagnosis and oral health. METHODS The salivary composition of patients diagnosed with SCZ (n = 50) was evaluated and compared to the control (n = 50). Saliva samples from male patients were collected and clinical parameters were evaluated. The concentration of total proteins and amylase were determined and salivary macro- and microelements were quantified by ICP OES and ICP-MS. Exploratory data analysis based on artificial intelligence tools was used in the investigation. RESULTS There was a significant increase in the salivary concentrations of Al, Fe, Li, Mg, Na, and V, higher prevalence of caries (p < 0.001), periodontal disease (p < 0.001), and reduced salivary flow rate (p = 0.019) in SCZ patients. Also, samples were grouped into six clusters. As, Co, Cr, Cu, Mn, Mo, Ni, Se, and Sr were correlated with each other, while Fe, K, Li, Ti, and V showed the highest concentrations in the samples distributed in the clusters with the highest association between SZC patients and controls. CONCLUSIONS The results obtained indicate changes in salivary flow, organic composition, and levels of macro- and microelements in SCZ patients. Salivary concentrations of Fe, Mg, and Na may be related to oral conditions, higher prevalence of caries, and periodontal disease. The exploratory analysis showed different patterns in the salivary composition of SCZ patients impacted by associations between oral health conditions and the use of medications. Future studies are encouraged to confirm the results investigated in this study.
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Affiliation(s)
- Letícia Kreutz Rosa
- Federal University of Paraná, Department of Stomatology, Curitiba, PR, 80210-170, Brazil
| | | | - Cecília Moraes Hauagge
- Federal University of Paraná, Department of Stomatology, Curitiba, PR, 80210-170, Brazil
| | - Rafael Zancan Mobile
- Federal University of Paraná, Department of Stomatology, Curitiba, PR, 80210-170, Brazil
| | | | - Clarice D B Amaral
- Federal University of Paraná, Department of Chemistry, Curitiba, PR, 81531-980, Brazil
| | - Raquel C Machado
- Federal University of São Carlos, Department of Chemistry, São Carlos, SP, 13565-905, Brazil
| | | | - João Armando Brancher
- Pontifícia Universidade Católica do Paraná, Escola de Ciências da Vida, Curitiba, PR, 80215-901, Brazil
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15
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Zgombić Popović V, Grgurević L, Trkulja V, Novak R, Negovetić-Vranić D. THE ROLE OF NEW TECHNOLOGIES IN DEFINING SALIVARY PROTEIN COMPOSITION FOLLOWING PLACEMENT OF FIXED ORTHODONTIC APPLIANCES - BREAKTHROUGH IN THE DEVELOPMENT OF NOVEL DIAGNOSTIC AND THERAPEUTIC PROCEDURES. Acta Clin Croat 2020; 59:480-488. [PMID: 34177058 PMCID: PMC8212653 DOI: 10.20471/acc.2020.59.03.12] [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] [Indexed: 12/02/2022] Open
Abstract
Human saliva is rich in proteins of variable functions (e.g., enzymes, immunoglobulins, cytokines) and origin (blood plasma, salivary glands, or oral microflora). Circadian dynamics, volume and composition (electrolytes, pH, protein, etc.) of secreted saliva vary with local and systemic physiological and pathophysiological conditions. Therefore, the composition of saliva, protein in particular, has been intensively investigated to identify the potential markers and/or mechanisms of systemic and local diseases. Proteomic techniques used for the analysis of biological fluids have enabled great advances in salivary protein stabilization (as the main precondition for their analysis) and detection of those found in saliva in very low concentrations, including small proteins and peptides. This review brings the main characteristics of current proteomic techniques such as liquid chromatography-mass spectrometry, two-dimensional electrophoresis-mass spectrometry, and surface-enhanced laser desorption ionization/time of flight/mass spectrometry. These techniques enable simultaneous identification of hundreds and thousands of protein molecules, as well as identifying those of a potential biological value in particular states. This literature review is focused on the state-of-the-art and possibilities offered by proteomic techniques in analyzing the effects of orthodontic appliances on salivary protein composition and searching for potential markers of therapeutic success/failure or for the molecules by which therapeutic effects are achieved.
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Affiliation(s)
| | - Lovorka Grgurević
- 1Orthonova Dental Polyclinic, Zagreb, Croatia; 2Drago Perović Department of Anatomy, School of Medicine, University of Zagreb, Zagreb, Croatia; 3Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia; 4Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia; 5Department of Pediatric and Preventive Dentistry, School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | - Vladimir Trkulja
- 1Orthonova Dental Polyclinic, Zagreb, Croatia; 2Drago Perović Department of Anatomy, School of Medicine, University of Zagreb, Zagreb, Croatia; 3Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia; 4Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia; 5Department of Pediatric and Preventive Dentistry, School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | - Ruđer Novak
- 1Orthonova Dental Polyclinic, Zagreb, Croatia; 2Drago Perović Department of Anatomy, School of Medicine, University of Zagreb, Zagreb, Croatia; 3Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia; 4Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia; 5Department of Pediatric and Preventive Dentistry, School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | - Dubravka Negovetić-Vranić
- 1Orthonova Dental Polyclinic, Zagreb, Croatia; 2Drago Perović Department of Anatomy, School of Medicine, University of Zagreb, Zagreb, Croatia; 3Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia; 4Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia; 5Department of Pediatric and Preventive Dentistry, School of Dental Medicine, University of Zagreb, Zagreb, Croatia
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16
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Abstract
Top-down mass spectrometry (MS) analyzes intact proteins at the proteoform level, which allows researchers to better understand the functions of protein modifications. Recently, top-down proteomics has increased in popularity due to advancements in high-resolution mass spectrometers, increased efficiency in liquid chromatography (LC) separation, and advances in data analysis software. Some unique protein proteoforms, which have been distinguished using top-down MS, have even been shown to exhibit marked variation in biological function compared to similar proteoforms. However, the qualitative identification of a particular proteoform may not be enough to determine the biological relevance of that proteoform. Quantitative top-down MS methods have been notably applied to the study of the differing biological functions of protein proteoforms and have allowed researchers to explore proteomes at the proteoform, rather than the peptide, level. Here, we review the top-down MS methods that have been used to quantitatively identify intact proteins, discuss current applications of quantitative top-down MS analysis, and present new areas where quantitative top-down MS analysis may be implemented.
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Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK 73019-5251, USA.
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17
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Deatherage Kaiser BL, Jacobs JM, Schepmoes AA, Brewer HM, Webb-Robertson BJM, Valtier S, Bebarta VS, Adkins JN. Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure. J Med Toxicol 2019; 16:49-60. [PMID: 31677050 DOI: 10.1007/s13181-019-00731-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 08/04/2019] [Accepted: 08/14/2019] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Non-medical use and abuse of prescription opioids is a growing problem in both the civilian and military communities, with minimal technologies for detecting hydrocodone use. This study explored the proteomic changes that occur in the oral fluid and blood plasma following controlled hydrocodone administration in 20 subjects. METHODS The global proteomic profile was determined for samples taken at four time points per subject: pre-exposure and 4, 6, or 168 hours post-exposure. The oral fluid samples analyzed herein provided greater differentiation between baseline and response time points than was observed with blood plasma, at least partially due to significant person-to-person relative variability in the plasma proteome. RESULTS A total of 399 proteins were identified from oral fluid samples, and the abundance of 118 of those proteins was determined to be significantly different upon metabolism of hydrocodone (4 and 6 hour time points) as compared to baseline levels in the oral fluid (pre-dose and 168 hours). CONCLUSIONS We present an assessment of the oral fluid and plasma proteome following hydrocodone administration, which demonstrates the potential of oral fluid as a noninvasive sample that may reveal features of hydrocodone in opioid use, and with additional study, may be useful for other opioids and in settings of misuse.
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Affiliation(s)
- Brooke L Deatherage Kaiser
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Sandra Valtier
- Science and Technology, 59th Medical Wing, JBSA-Lackland AFB, San Antonio, TX, USA
| | | | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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18
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Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc 2019; 14:119-152. [PMID: 30518910 DOI: 10.1038/s41596-018-0085-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP) strategies, which measure digested peptide mixtures, TDP provides highly specific molecular information that avoids the bioinformatic challenge of protein inference. However, the technique has been difficult to implement widely because of inherent limitations of existing sample preparation methods and instrumentation. Recent improvements in proteoform pre-fractionation and the availability of high-resolution benchtop mass spectrometers have made it possible to use high-throughput TDP for the analysis of complex clinical samples. Here, we provide a comprehensive protocol for analysis of a common sample type in translational research: human peripheral blood mononuclear cells (PBMCs). The pipeline comprises multiple workflows that can be treated as modular by the reader and used for various applications. First, sample collection and cell preservation are described for two clinical biorepository storage schemes. Cell lysis and proteoform pre-fractionation by gel-eluted liquid fractionation entrapment electrophoresis are then described. Importantly, instrument setup and liquid chromatography-tandem MS are described for TDP analyses, which rely on high-resolution Fourier-transform MS. Finally, data processing and analysis are described using two different, application-dependent software tools: ProSight Lite for targeted analyses of one or a few proteoforms and TDPortal for high-throughput TDP in discovery mode. For a single sample, the minimum completion time of the entire experiment is 72 h.
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Affiliation(s)
- Timothy K Toby
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - John Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
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19
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Manconi B, Liori B, Cabras T, Vincenzoni F, Iavarone F, Lorefice L, Cocco E, Castagnola M, Messana I, Olianas A. Top-down proteomic profiling of human saliva in multiple sclerosis patients. J Proteomics 2018; 187:212-222. [PMID: 30086402 DOI: 10.1016/j.jprot.2018.07.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
Multiple sclerosis is a chronic disease of the central nervous system characterized by inflammation, demyelination and neurodegeneration which is of undetermined origin. To date a single diagnostic test of multiple sclerosis does not exists and novel biomarkers are demanded for a more accurate and early diagnosis. In this study, we performed the quantitative analysis of 119 salivary peptides/proteins from 49 multiple sclerosis patients and 54 healthy controls by a mass spectrometry-based top-down proteomic approach. Statistical analysis evidenced different levels on 23 proteins: 8 proteins showed lower levels in multiple sclerosis patients with respect to controls and they were mono- and di-oxidized cystatin SN, mono- and di-oxidized cystatin S1, mono-oxidized cystatin SA and mono-phosphorylated statherin. 15 proteins showed higher levels in multiple sclerosis patients with respect to controls and they were antileukoproteinase, two proteoforms of Prolactin-Inducible Protein, P-C peptide (Fr.1-14, Fr. 26-44, and Fr. 36-44), SV1 fragment of statherin, cystatin SN Des1-4, cystatin SN P11 → L variant, and cystatin A T96 → M variant. The differences observed between the salivary proteomic profile of patients suffering from multiple sclerosis and healthy subjects is consistent with the inflammatory condition and altered immune response typical of the pathology. Data are available via ProteomeXchange with identifier PXD009440. SIGNIFICANCE To date a single diagnostic test of multiple sclerosis does not exist, and diagnosis is based on multiple tests which mainly include the analysis of cerebrospinal fluid. However, the need for lumbar puncture makes the analysis of cerebrospinal fluid impractical for monitoring disease activity and response to treatment. The possible use of saliva as a diagnostic fluid for oral and systemic diseases has been largely investigated, but only marginally in multiple sclerosis compared to other body fluids. Our study demonstrates that the salivary proteome of multiple sclerosis patients differs considerably compared to that of sex and age matched healthy individuals and suggests that some differences might be associated with the different disease-modifying therapy used to treat multiple sclerosis patients.
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Affiliation(s)
- Barbara Manconi
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari, Monserrato Campus, 09042 Monserrato, Cagliari, Italy.
| | - Barbara Liori
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari, Monserrato Campus, 09042 Monserrato, Cagliari, Italy
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari, Monserrato Campus, 09042 Monserrato, Cagliari, Italy
| | - Federica Vincenzoni
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy
| | - Federica Iavarone
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy
| | - Lorena Lorefice
- Department of Medical Sciences and Public Health, Multiple Sclerosis Center, Binaghi Hospital, ATS Sardegna, University of Cagliari, via Is Guadazzonis 2, 09126 Cagliari, Italy
| | - Eleonora Cocco
- Department of Medical Sciences and Public Health, Multiple Sclerosis Center, Binaghi Hospital, ATS Sardegna, University of Cagliari, via Is Guadazzonis 2, 09126 Cagliari, Italy
| | - Massimo Castagnola
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy; Institute of Chemistry of the Molecular Recognition CNR, L.go F. Vito 1, 00168 Rome, Italy
| | - Irene Messana
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy; Institute of Chemistry of the Molecular Recognition CNR, L.go F. Vito 1, 00168 Rome, Italy
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari, Monserrato Campus, 09042 Monserrato, Cagliari, Italy
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20
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Moriyama Y, Kotani T, Ushida T, Imai K, Nakano T, Tsuda H, Kikkawa F. Altered proteomic profile in umbilical arterial serum from mothers with schizophrenia. Schizophr Res 2018; 197:615-617. [PMID: 29510929 DOI: 10.1016/j.schres.2018.02.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/17/2018] [Accepted: 02/17/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Yoshinori Moriyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tomomi Kotani
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
| | - Takafumi Ushida
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Kenji Imai
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tomoko Nakano
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hiroyuki Tsuda
- Department of Obstetrics and Gynecology, Japanese Red Cross Nagoya Daiichi Hospital, 3-35 Michishita-cho, Nakamura-ku, Nagoya 453-8511, Japan
| | - Fumitaka Kikkawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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21
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Castagnola M, Scarano E, Passali GC, Messana I, Cabras T, Iavarone F, Di Cintio G, Fiorita A, De Corso E, Paludetti G. Salivary biomarkers and proteomics: future diagnostic and clinical utilities. ACTA OTORHINOLARYNGOLOGICA ITALICA 2018; 37:94-101. [PMID: 28516971 PMCID: PMC5463528 DOI: 10.14639/0392-100x-1598] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/12/2016] [Indexed: 12/16/2022]
Abstract
Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and -omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora. The most common aim of proteomic analysis is to discriminate between physiological and pathological conditions. A proteomic protocol to analyze the whole saliva proteome is not currently available. It is possible distinguish two type of proteomic platforms: top-down proteomics investigates intact naturally-occurring structure of a protein under examination; bottom-up proteomics analyses peptide fragments after pre-digestion (typically with trypsin). Because of this heterogeneity, many different biomarkers may be proposed for the same pathology. The salivary proteome has been characterised in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease Sjögren's syndrome and other autoimmune disorders such as SAPHO, schizophrenia and bipolar disorder, and genetic diseases like Down's Syndrome and Wilson disease. The results of research reported herein suggest that in the near future human saliva will be a relevant diagnostic fluid for clinical diagnosis and prognosis.
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Affiliation(s)
- M Castagnola
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Rome, Istituto di Chimica del Riconoscimento Molecolare C.N.R. Rome, Italy
| | - E Scarano
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - G C Passali
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - I Messana
- Life and Enviromental Sciences Department, University of Cagliari, and Istituto di Chimica del Riconoscimento Molecolare C.N.R. Rome, Italy
| | - T Cabras
- Life and Enviromental Sciences Department, University of Cagliari, Italy
| | - F Iavarone
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Rome, Italy
| | - G Di Cintio
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - A Fiorita
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - E De Corso
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
| | - G Paludetti
- Department of Head and Neck Surgery, "A. Gemelli" Hospital Foundation, Catholic University, Rome, Italy
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22
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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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23
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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24
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Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, Thomas PM, Friedewald JJ, Salomon DR, Abecassis MM, Kelleher NL. Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection. Proteomics 2017; 16:2048-58. [PMID: 27120713 DOI: 10.1002/pmic.201600008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/18/2016] [Accepted: 04/19/2016] [Indexed: 11/07/2022]
Abstract
Recent studies utilizing transcriptomics, metabolomics, and bottom up proteomics have identified molecular signatures of kidney allograft pathology. Although these results make significant progress toward non-invasive differential diagnostics of dysfunction of a transplanted kidney, they provide little information on the intact, often modified, protein molecules present during progression of this pathology. Because intact proteins underpin diverse biological processes, measuring the relative abundance of their modified forms promises to advance mechanistic understanding, and might provide a new class of biomarker candidates. Here, we used top down proteomics to inventory the modified forms of whole proteins in peripheral blood mononuclear cells (PBMCs) taken at the time of kidney biopsy for 40 kidney allograft recipients either with healthy transplants or those suffering acute rejection. Supported by gas-phase fragmentation of whole protein ions during tandem mass spectrometry, we identified 344 proteins mapping to 2905 distinct molecular forms (proteoforms). Using an initial implementation of a label-free approach to quantitative top down proteomics, we obtained evidence suggesting relative abundance changes in 111 proteoforms between the two patient groups. Collectively, our work is the first to catalog intact protein molecules in PBMCs and suggests differentially abundant proteoforms for further analysis.
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Affiliation(s)
- John P Savaryn
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Timothy K Toby
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Adam D Catherman
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - John J Friedewald
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, CA, USA
| | - Michael M Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Department of Chemistry, Northwestern University, Evanston, IL, USA
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25
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Huang TL, Lo LH, Shiea J, Su H. Rapid and simple analysis of disease-associated biomarkers of Taiwanese patients with schizophrenia using matrix-assisted laser desorption ionization mass spectrometry. Clin Chim Acta 2017; 473:75-81. [PMID: 28807542 DOI: 10.1016/j.cca.2017.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS) is an extremely sensitive analytical tool for characterizing biological compounds in bio samples. In this study, we applied MALDI-TOF MS to assess potential protein biomarkers in the peripheral blood mononuclear cells (PBMCs) of patients with schizophrenia in the acute phase, recovery phase and healthy controls in Taiwan. METHODS We recruited 40 participants, including 20 pairs of patients diagnosed with schizophrenia in the acute phase, after four-week treatment with drug in the recovery phase, and 20 healthy controls. The schizophrenic patients were diagnosed using Structured Clinical Interview for DSM-IV Axis I Disorders (SCID), and severity was assessed by a positive and negative symptom scale at baseline and at endpoint following four-week treatment with drug. The patients' PBMCs biomarkers were rapidly measured using a technique that combines MALDI-TOF MS and principle component analysis. A receiver operating characteristic curve was created for the evaluated biomarker. RESULTS Significant differences in α-defensins 1-3 were found between the patients in acute phase with schizophrenia and the healthy controls, but not between the schizophrenic patients in recovery phase and healthy controls or between the schizophrenic patients in acute phase and in recovery phase. CONCLUSIONS α-Defensins can be biomarkers of Taiwanese patients with schizophrenia, thus supporting the hypothesis that the inflammatory response and immunity system is correlated with the pathophysiology of schizophrenia. Moreover, the result also implies that α-defensins may be related in schizophrenia-associated disease not in efficacy of drug-treatment.
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Affiliation(s)
- Tiao-Lai Huang
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan; Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.
| | - Li-Hua Lo
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan
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26
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Schmitt A, Martins-de-Souza D, Akbarian S, Cassoli JS, Ehrenreich H, Fischer A, Fonteh A, Gattaz WF, Gawlik M, Gerlach M, Grünblatt E, Halene T, Hasan A, Hashimoto K, Kim YK, Kirchner SK, Kornhuber J, Kraus TFJ, Malchow B, Nascimento JM, Rossner M, Schwarz M, Steiner J, Talib L, Thibaut F, Riederer P, Falkai P. Consensus paper of the WFSBP Task Force on Biological Markers: Criteria for biomarkers and endophenotypes of schizophrenia, part III: Molecular mechanisms. World J Biol Psychiatry 2017; 18:330-356. [PMID: 27782767 DOI: 10.1080/15622975.2016.1224929] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Despite progress in identifying molecular pathophysiological processes in schizophrenia, valid biomarkers are lacking for both the disease and treatment response. METHODS This comprehensive review summarises recent efforts to identify molecular mechanisms on the level of protein and gene expression and epigenetics, including DNA methylation, histone modifications and micro RNA expression. Furthermore, it summarises recent findings of alterations in lipid mediators and highlights inflammatory processes. The potential that this research will identify biomarkers of schizophrenia is discussed. RESULTS Recent studies have not identified clear biomarkers for schizophrenia. Although several molecular pathways have emerged as potential candidates for future research, a complete understanding of these metabolic pathways is required to reveal better treatment modalities for this disabling condition. CONCLUSIONS Large longitudinal cohort studies are essential that pair a thorough phenotypic and clinical evaluation for example with gene expression and proteome analysis in blood at multiple time points. This approach might identify biomarkers that allow patients to be stratified according to treatment response and ideally also allow treatment response to be predicted. Improved knowledge of molecular pathways and epigenetic mechanisms, including their potential association with environmental influences, will facilitate the discovery of biomarkers that could ultimately be effective tools in clinical practice.
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Affiliation(s)
- Andrea Schmitt
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany.,b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Daniel Martins-de-Souza
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil.,c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Schahram Akbarian
- d Division of Psychiatric Epigenomics, Departments of Psychiatry and Neuroscience , Mount Sinai School of Medicine , New York , USA
| | - Juliana S Cassoli
- c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Hannelore Ehrenreich
- e Clinical Neuroscience , Max Planck Institute of Experimental Medicine, DFG Centre for Nanoscale Microscopy & Molecular Physiology of the Brain , Göttingen , Germany
| | - Andre Fischer
- f Research Group for Epigenetics in Neurodegenerative Diseases , German Centre for Neurodegenerative Diseases (DZNE), Göttingen , Germany.,g Department of Psychiatry and Psychotherapy , University Medical Centre Göttingen , Germany
| | - Alfred Fonteh
- h Neurosciences , Huntington Medical Research Institutes , Pasadena , CA , USA
| | - Wagner F Gattaz
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Michael Gawlik
- i Department of Psychiatry and Psychotherapy , University of Würzburg , Germany
| | - Manfred Gerlach
- j Centre for Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy , University of Würzburg , Germany
| | - Edna Grünblatt
- i Department of Psychiatry and Psychotherapy , University of Würzburg , Germany.,k Department of Child and Adolescent Psychiatry and Psychotherapy , Psychiatric Hospital, University of Zürich , Switzerland.,l Neuroscience Centre Zurich , University of Zurich and the ETH Zurich , Switzerland.,m Zurich Centre for Integrative Human Physiology , University of Zurich , Switzerland
| | - Tobias Halene
- d Division of Psychiatric Epigenomics, Departments of Psychiatry and Neuroscience , Mount Sinai School of Medicine , New York , USA
| | - Alkomiet Hasan
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
| | - Kenij Hashimoto
- n Division of Clinical Neuroscience , Chiba University Centre for Forensic Mental Health , Chiba , Japan
| | - Yong-Ku Kim
- o Department of Psychiatry , Korea University, College of Medicine , Republic of Korea
| | | | - Johannes Kornhuber
- p Department of Psychiatry and Psychotherapy , Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | | | - Berend Malchow
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
| | - Juliana M Nascimento
- c Laboratory of Neuroproteomics, Department of Biochemistry , Institute of Biology University of Campinas (UNICAMP), Campinas , SP , Brazil
| | - Moritz Rossner
- r Department of Psychiatry, Molecular and Behavioural Neurobiology , LMU Munich , Germany.,s Research Group Gene Expression , Max Planck Institute of Experimental Medicine , Göttingen , Germany
| | - Markus Schwarz
- t Institute for Laboratory Medicine, LMU Munich , Germany
| | - Johann Steiner
- u Department of Psychiatry , University of Magdeburg , Magdeburg , Germany
| | - Leda Talib
- b Laboratory of Neuroscience (LIM27) , Institute of Psychiatry, University of Sao Paulo , Sao Paulo , Brazil
| | - Florence Thibaut
- v Department of Psychiatry , University Hospital Cochin (site Tarnier), University of Paris-Descartes, INSERM U 894 Centre Psychiatry and Neurosciences , Paris , France
| | - Peter Riederer
- w Center of Psychic Health; Department of Psychiatry, Psychosomatics and Psychotherapy , University Hospital of Würzburg , Germany
| | - Peter Falkai
- a Department of Psychiatry and Psychotherapy , LMU Munich , Germany
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27
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de Jesus JR, Galazzi RM, de Lima TB, Banzato CEM, de Almeida Lima E Silva LF, de Rosalmeida Dantas C, Gozzo FC, Arruda MAZ. Simplifying the human serum proteome for discriminating patients with bipolar disorder of other psychiatry conditions. Clin Biochem 2017; 50:1118-1125. [PMID: 28662995 DOI: 10.1016/j.clinbiochem.2017.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 06/25/2017] [Indexed: 12/14/2022]
Abstract
PURPOSE An exploratory analysis using proteomic strategies in blood serum of patients with bipolar disorder (BD), and with other psychiatric conditions such as Schizophrenia (SCZ), can provide a better understanding of this disorder, as well as their discrimination based on their proteomic profile. METHODS The proteomic profile of blood serum samples obtained from patients with BD using lithium or other drugs (N=14), healthy controls, including non-family (HCNF; N=3) and family (HCF; N=9), patients with schizophrenia (SCZ; N=23), and patients using lithium for other psychiatric conditions (OD; N=4) were compared. Four methods for simplifying the serum samples proteome were evaluated for both removing the most abundant proteins and for enriching those of lower-abundance: protein depletion with acetonitrile (ACN), dithiothreitol (DTT), sequential depletion using DTT and ACN, and protein equalization using commercial ProteoMiner® kit (PM). For proteomic evaluation, 2-D DIGE and nanoLC-MS/MS analysis were employed. RESULTS PM method was the best strategy for removing proteins of high abundance. Through 2-D DIGE gel image comparison, 37 protein spots were found differentially abundant (p<0.05, Student's t-test), which exhibited ≥2.0-fold change of the average value of normalized spot intensities in the serum of SCZ, BD and OD patients compared to subject controls (HCF and HCNF). From these spots detected, 13 different proteins were identified: ApoA1, ApoE, ApoC3, ApoA4, Samp, SerpinA1, TTR, IgK, Alb, VTN, TR, C4A and C4B. CONCLUSIONS Proteomic analysis allowed the discrimination of patients with BD from patients with other mental disorders, such as SCZ. The findings in this exploratory study may also contribute for better understanding the pathophysiology of these disorders and finding potential serum biomarkers for these conditions.
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Affiliation(s)
- Jemmyson Romário de Jesus
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | - Rodrigo Moretto Galazzi
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | - Tatiani Brenelli de Lima
- Dalton Mass Spectrometry Group, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | | | | | | | - Fábio Cézar Gozzo
- Dalton Mass Spectrometry Group, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | - Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil.
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28
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Pacifico R, Davis RL. Transcriptome sequencing implicates dorsal striatum-specific gene network, immune response and energy metabolism pathways in bipolar disorder. Mol Psychiatry 2017; 22:441-449. [PMID: 27350034 DOI: 10.1038/mp.2016.94] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 12/12/2022]
Abstract
Bipolar disorder (BD) is a highly heritable and heterogeneous mental illness whose manifestations often include impulsive and risk-taking behavior. This particular phenotype suggests that abnormal striatal function could be involved in BD etiology, yet most transcriptomic studies of this disorder have concentrated on cortical brain regions. We believe we report the first transcriptome sequencing of the postmortem human dorsal striatum comparing bipolar (18) and control (17) subjects. Fourteen genes were detected as differentially expressed at a 5% false discovery rate, including a few immune response genes such as NLRC5, S100A12, LILRA4 and FCGBP, as well as an assortment of non-protein coding genes. Functional pathway analysis found an enrichment of upregulated genes across many immune/inflammation pathways and an enrichment of downregulated genes among oxidative phosphorylation pathways. Co-expression network analysis revealed 20 modules of highly interconnected genes; two of the modules were significantly enriched for BD susceptibility single-nucleotide polymorphisms deriving from a large genome-wide association study data set. Remarkably, the module with the highest genetic association signal for BD, which contained many genes from signaling pathways, was also enriched in markers characteristic of gene expression in dorsal striatum medium spiny neurons-unlike most other modules, which showed no such regional and neuronal specificity. These findings draw a link between BD etiology at the gene level and a specific brain region, and highlight striatal signaling pathways as potential targets for the development of novel treatments to manage BD.
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Affiliation(s)
- R Pacifico
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, USA
| | - R L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, USA
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Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017; 38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]
Abstract
This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.
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Affiliation(s)
- Monica Di Venere
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
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Top-down HPLC-ESI-MS proteomic analysis of saliva of edentulous subjects evidenced high levels of cystatin A, cystatin B and SPRR3. Arch Oral Biol 2017; 77:68-74. [PMID: 28178587 DOI: 10.1016/j.archoralbio.2017.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 01/23/2017] [Accepted: 01/29/2017] [Indexed: 01/20/2023]
Abstract
OBJECTIVE This study aims to analyze the salivary peptidome/proteome of edentulous subject with respect to dentate control subjects. DESIGN Unstimulated whole saliva, collected from 11 edentulous subjects (age 60-76 years) and 11 dentate age-matched control subjects, was immediately treated with 0.2% aqueous trifluoroacetic acid and the acidic soluble fraction analyzed by High Performace Liquid Chromatography-Mass Spectrometry. The relative abundance of the salivary peptides/proteins was determined by measuring the area of the High Performace Liquid Chromatography-Mass Spectrometry eXtracted Ion Current peaks which is linearly proportional to peptide/protein concentration under identical experimental conditions. Levels of salivary peptides/proteins in the two groups were compared by the nonparametric Mann-Whitney test to evidence statistically significant differences. RESULTS Levels of cystatin A, S-glutathionylated, S-cystenylated, S-S dimer derivatives of cystatin B and S-glutathionylated derivative of SPRR3, were found significantly higher in edentulous subjects with respect to dentate controls. The major peptides and proteins typically deriving from salivary glands did not show any statistically significant differences. CONCLUSIONS Cystatin A, S-glutathionylated, S-cystenylated, S-S dimer derivatives of cystatin B and S-glutathionylated derivative of SPRR3, which are mainly of intracellular origin and represent the major constituents of the cornified cell envelope are a clue of inflammation of mucosal epithelia.
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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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Sun X, Huang X, Tan X, Si Y, Wang X, Chen F, Zheng S. Salivary peptidome profiling for diagnosis of severe early childhood caries. J Transl Med 2016; 14:240. [PMID: 27527350 PMCID: PMC4986381 DOI: 10.1186/s12967-016-0996-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Severe early childhood caries (s-ECC), which has quite high prevalence among children, is a widespread problem with significant impacts among both developing and developed countries. At present, it is widely known that no early detective techniques and diagnostic tests could have high sensitivity and specificity when using for clinical screening of s-ECC. In this study, we had applied magnetic bead (MB)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to screen distinctive candidate biomarkers of this disease, so as to establish protein profiles and diagnostic models of s-ECC. METHODS Firstly, we used the technique mentioned above to detect specifically expressed peptides in saliva samples from ten children with s-ECC, separately at the time point of before, 1 and 4 weeks after dental treatment. Then a diagnostic model for s-ECC was established with the K nearest-neighbour method, which was validated in another six children in the next stage of study. After that, linear ion trap-orbitrap-mass spectrometry (LTQ-Orbitrap-MS) was performed to identify which of the proteins in saliva might be the origination of these peptides. RESULTS We found that seven peptide peaks were significantly different when comparing the three time points, among them two were higher, while other five were lower in the pre-treatment s-ECC group compared with post-treatment. The sensitivity and specificity of the diagnostic model we built were both 83.3 %. Two of these peptides were identified to be segments of histatin-1, which was one important secretory protein in saliva. CONCLUSIONS Hereby we confirmed that MB-based MALDI-TOF MS is an effective method for screening distinctive peptides from the saliva of junior patients with s-ECC, and histatin-1 may probably be one important candidate biomarker of this common dental disease. These findings might have bright prospect in future in establishing new diagnostic methods for s-ECC.
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Affiliation(s)
- Xiangyu Sun
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Xin Huang
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Xu Tan
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.,Stomatological Hospital of Guizhou Medical University, Guiyang, 550004, People's Republic of China
| | - Yan Si
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Xiaozhe Wang
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.
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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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de Jesus JR, Pessôa GDS, Sussulini A, Martínez JLC, Arruda MAZ. Proteomics strategies for bipolar disorder evaluation: From sample preparation to validation. J Proteomics 2016; 145:187-196. [PMID: 27113133 DOI: 10.1016/j.jprot.2016.04.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 02/06/2023]
Abstract
Bipolar disorder (BD) is a complex and costly psychiatric disorder, which affects one hundred million people worldwide. Due to its heterogeneity, correct BD diagnosis is still a challenge. In order to overcome this issue, different bioanalytical strategies have been proposed in the literature recently. Among these strategies, proteomic approaches have arisen as some of the most promising in the area. Thus, recent applications suggest protein profiles to further refine the proteome of BD as well as the discovery of novel protein biomarkers to facilitate diagnostics. In this review, the state-of-art of proteomic research in BD is summarized. Furthermore, important aspects of proteomics for understanding of BD, such as sample type and size, sampling, sample preparation, gel-based and gel-free proteomics, proteomic quantitative and protein validation are overviewed.
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Affiliation(s)
- Jemmyson Romário de Jesus
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil; UCIBIO-REQUIMTE, Chemistry Department, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Gustavo de Souza Pessôa
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alessandra Sussulini
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil
| | - José Luis Capelo Martínez
- UCIBIO-REQUIMTE, Chemistry Department, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Caparica, Portugal; ProteoMass Scientific Society, MadanPark, Rua dos Inventores s/n, Monte de Caparica, Caparica, Portugal
| | - Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil.
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Davalieva K, Maleva Kostovska I, Dwork AJ. Proteomics Research in Schizophrenia. Front Cell Neurosci 2016; 10:18. [PMID: 26909022 PMCID: PMC4754401 DOI: 10.3389/fncel.2016.00018] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/18/2016] [Indexed: 11/29/2022] Open
Abstract
Despite intense scientific efforts, the neuropathology and pathophysiology of schizophrenia are poorly understood. Proteomic studies, by testing large numbers of proteins for associations with disease, may contribute to the understanding of the molecular mechanisms of schizophrenia. They may also indicate the types and locations of cells most likely to harbor pathological alterations. Investigations using proteomic approaches have already provided much information on quantitative and qualitative protein patterns in postmortem brain tissue, peripheral tissues and body fluids. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, SELDI-TOF, shotgun proteomics with label-based (ICAT), and label-free (MSE) quantification have been applied to the study of schizophrenia for the past 15 years. This review summarizes the results, mostly from brain but also from other tissues and bodily fluids, of proteomics studies in schizophrenia. Emphasis is given to proteomics platforms, varying sources of material, proposed candidate biomarkers emerging from comparative proteomics studies, and the specificity of the putative markers in terms of other mental illnesses. We also compare proteins altered in schizophrenia with reports of protein or mRNA sequences that are relatively enriched in specific cell types. While proteomic studies of schizophrenia find abnormalities in the expression of many proteins that are not cell type-specific, there appears to be a disproportionate representation of proteins whose synthesis and localization are highly enriched in one or more brain cell type compared with other types of brain cells. Two of the three proteins most commonly altered in schizophrenia are aldolase C and glial fibrillary acidic protein, astrocytic proteins with entirely different functions, but the studies are approximately evenly divided with regard to the direction of the differences and the concordance or discordance between the two proteins. Alterations of common myelin-associated proteins were also frequently observed, and in four studies that identified alterations in at least two, all differences were downwards in schizophrenia, consistent with earlier studies examining RNA or targeting myelin-associated proteins.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov," Macedonian Academy of Sciences and Arts Skopje, Republic of Macedonia
| | - Ivana Maleva Kostovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov," Macedonian Academy of Sciences and Arts Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Molecular Imaging and Neuropathology, New York State Psychiatric InstituteNew York, NY, USA; Departments of Psychiatry and Pathology and Cell Biology, College of Physicians and Surgeons of Columbia UniversityNew York, NY, USA; Macedonian Academy of Sciences and ArtsSkopje, Republic of Macedonia
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O'Shea KS, McInnis MG. Neurodevelopmental origins of bipolar disorder: iPSC models. Mol Cell Neurosci 2015; 73:63-83. [PMID: 26608002 DOI: 10.1016/j.mcn.2015.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/14/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BP) is a chronic neuropsychiatric condition characterized by pathological fluctuations in mood from mania to depression. Adoption, twin and family studies have consistently identified a significant hereditary component to BP, yet there is no clear genetic event or consistent neuropathology. BP has been suggested to have a developmental origin, although this hypothesis has been difficult to test since there are no viable neurons or glial cells to analyze, and research has relied largely on postmortem brain, behavioral and imaging studies, or has examined proxy tissues including saliva, olfactory epithelium and blood cells. Neurodevelopmental factors, particularly pathways related to nervous system development, cell migration, extracellular matrix, H3K4 methylation, and calcium signaling have been identified in large gene expression and GWAS studies as altered in BP. Recent advances in stem cell biology, particularly the ability to reprogram adult somatic tissues to a pluripotent state, now make it possible to interrogate these pathways in viable cell models. A number of induced pluripotent stem cell (iPSC) lines from BP patient and healthy control (C) individuals have been derived in several laboratories, and their ability to form cortical neurons examined. Early studies suggest differences in activity, calcium signaling, blocks to neuronal differentiation, and changes in neuronal, and possibly glial, lineage specification. Initial observations suggest that differentiation of BP patient-derived neurons to dorsal telencephalic derivatives may be impaired, possibly due to alterations in WNT, Hedgehog or Nodal pathway signaling. These investigations strongly support a developmental contribution to BP and identify novel pathways, mechanisms and opportunities for improved treatments.
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Affiliation(s)
- K Sue O'Shea
- Department of Cell and Developmental Biology, University of Michigan, 3051 BSRB, 109 Zina Pitcher PL, Ann Arbor, MI 48109-2200, United States; Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States.
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States
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Turck CW, Filiou MD. What Have Mass Spectrometry-Based Proteomics and Metabolomics (Not) Taught Us about Psychiatric Disorders? MOLECULAR NEUROPSYCHIATRY 2015; 1:69-75. [PMID: 27602358 PMCID: PMC4996030 DOI: 10.1159/000381902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/25/2015] [Indexed: 12/16/2022]
Abstract
Understanding the molecular causes and finding appropriate therapies for psychiatric disorders are challenging tasks for research; -omics technologies are used to elucidate the molecular mechanisms underlying brain dysfunction in a hypothesis-free manner. In this review, we will focus on mass spectrometry-based proteomics and metabolomics and address how these approaches have contributed to our understanding of psychiatric disorders. Specifically, we will discuss what we have learned from mass spectrometry-based proteomics and metabolomics studies in rodent models and human cohorts, outline current limitations and discuss the potential of these methods for future applications in psychiatry.
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Nascimento JM, Martins-de-Souza D. The proteome of schizophrenia. NPJ SCHIZOPHRENIA 2015; 1:14003. [PMID: 27336025 PMCID: PMC4849438 DOI: 10.1038/npjschz.2014.3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/24/2022]
Abstract
On observing schizophrenia from a clinical point of view up to its molecular basis, one may conclude that this is likely to be one of the most complex human disorders to be characterized in all aspects. Such complexity is the reflex of an intricate combination of genetic and environmental components that influence brain functions since pre-natal neurodevelopment, passing by brain maturation, up to the onset of disease and disease establishment. The perfect function of tissues, organs, systems, and finally the organism depends heavily on the proper functioning of cells. Several lines of evidence, including genetics, genomics, transcriptomics, neuropathology, and pharmacology, have supported the idea that dysfunctional cells are causative to schizophrenia. Together with the above-mentioned techniques, proteomics have been contributing to understanding the biochemical basis of schizophrenia at the cellular and tissue level through the identification of differentially expressed proteins and consequently their biochemical pathways, mostly in the brain tissue but also in other cells. In addition, mass spectrometry-based proteomics have identified and precisely quantified proteins that may serve as biomarker candidates to prognosis, diagnosis, and medication monitoring in peripheral tissue. Here, we review all data produced by proteomic investigation in the last 5 years using tissue and/or cells from schizophrenic patients, focusing on postmortem brain tissue and peripheral blood serum and plasma. This information has provided integrated pictures of the biochemical systems involved in the pathobiology, and has suggested potential biomarkers, and warrant potential targets to alternative treatment therapies to schizophrenia.
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Affiliation(s)
- Juliana M Nascimento
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
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Costalonga M, Herzberg MC. The oral microbiome and the immunobiology of periodontal disease and caries. Immunol Lett 2014; 162:22-38. [PMID: 25447398 DOI: 10.1016/j.imlet.2014.08.017] [Citation(s) in RCA: 377] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/31/2014] [Accepted: 08/08/2014] [Indexed: 12/22/2022]
Abstract
The composition of the oral microbiome differs from one intraoral site to another, reflecting in part the host response and immune capacity at each site. By focusing on two major oral infections, periodontal disease and caries, new principles of disease emerge. Periodontal disease affects the soft tissues and bone that support the teeth. Caries is a unique infection of the dental hard tissues. The initiation of both diseases is marked by an increase in the complexity of the microbiome. In periodontitis, pathobionts and keystone pathogens such as Porphyromonas gingivalis appear in greater proportion than in health. As a keystone pathogen, P. gingivalis impairs host immune responses and appears necessary but not sufficient to cause periodontitis. Historically, dental caries had been causally linked to Streptococcus mutans. Contemporary microbiome studies now indicate that singular pathogens are not obvious in either caries or periodontitis. Both diseases appear to result from a perturbation among relatively minor constituents in local microbial communities resulting in dysbiosis. Emergent consortia of the minor members of the respective microbiomes act synergistically to stress the ability of the host to respond and protect. In periodontal disease, host protection first occurs at the level of innate gingival epithelial immunity. Secretory IgA antibody and other salivary antimicrobial systems also act against periodontopathic and cariogenic consortia. When the gingival immune response is impaired, periodontal tissue pathology results when matrix metalloproteinases are released from neutrophils and T cells mediate alveolar bone loss. In caries, several species are acidogenic and aciduric and appear to work synergistically to promote demineralization of the enamel and dentin. Whereas technically possible, particularly for caries, vaccines are unlikely to be commercialized in the near future because of the low morbidity of caries and periodontitis.
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Affiliation(s)
- Massimo Costalonga
- Division of Periodontology, Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, United States.
| | - Mark C Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, United States; Mucosal and Vaccine Research Center, Minneapolis VA Medical Center, Minneapolis, MN 55417, United States
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Kelleher NL, Thomas PM, Ntai I, Compton PD, LeDuc RD. Deep and quantitative top-down proteomics in clinical and translational research. Expert Rev Proteomics 2014; 11:649-51. [PMID: 25347991 DOI: 10.1586/14789450.2014.976559] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It has long been understood that it is proteins, expressed and post-translationally modified, that are the primary regulators of both the fate and the function of cells. The ability to measure differences in the expression of the constellation of unique protein forms (proteoforms) with complete molecular specificity has the potential to sharply improve the return on investment for mass spectrometry-based proteomics in translational research and clinical diagnostics.
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Affiliation(s)
- Neil L Kelleher
- Northwestern University, 2145 N. Sheridan Rd, Evanston, IL, 60208, USA
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