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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: 5] [Impact Index Per Article: 5.0] [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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Guest PC. Proteomic Mapping of the Human Myelin Proteome. Methods Mol Biol 2022; 2343:191-202. [PMID: 34473323 DOI: 10.1007/978-1-0716-1558-4_12] [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] [Indexed: 06/13/2023]
Abstract
Alzheimer's disease (AD) is a degenerative cognitive condition that affects individuals with an increasing prevalence in older age groups. There are currently five drugs on the market for AD but no new effective ones have been discovered for decades. There has been increasing interest in the use of natural remedies such as special diets and plant extracts but these require further study. Based on the known effects on white matter and neuronal conductance in Alzheimer's disease, we present a protocol for proteomic analysis of myelin-enriched brain fractions as a way of identifying potential biomarkers of efficacy. This fingerprint could be used in screening assays for novel compounds for treatment of AD.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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Dos Santos RV, Grillo G, Fonseca H, Stanisic D, Tasic L. Hesperetin as an inhibitor of the snake venom serine protease from Bothrops jararaca. Toxicon 2021; 198:64-72. [PMID: 33940046 DOI: 10.1016/j.toxicon.2021.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
The majority (90%) of the snakebite envenomation in Brazil accounts for Bothrops from the Viperidae family. Some snake venom serine proteases provoke blood coagulation in ophidian accident victims because of their fibrinolytic activity, one of those proteases from Bothrops jararaca (B. jararaca) has been chosen for this study. Our objectives were to isolate and characterize the target serine protease; isolate, purify, and characterize the orange bagasse flavone (hesperetin, Hst), and investigate the interactions between the targets, enzyme, and hesperetin. The purified serine protease was named BjSP24 because of its molecular mass and proteolytic activity. BjSP24 was folded and characterized using circular dichroism and showed low alpha-helix contents (7.7%). BjSP24 exhibited sequence similarity to other known snake venom serine proteases as measured in the enzyme tryptic peptides' LC-MS/MS run. Hesperetin was obtained within the expected yield and with the predominance of 2S isomer (82%). It acted as a mixed inhibitor for the serine protease (SVSP) from Bothrops jararaca snake venom observed in three different in vitro experiments, fluorescence, kinetics, and SSTD-NMR. It is still to determine if hesperetin might aid-in reverting the on site blood clotting problems just after snakebite accidents.
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Affiliation(s)
- Roney Vander Dos Santos
- Biological Chemistry Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Giovanna Grillo
- Biological Chemistry Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Henrique Fonseca
- Biological Chemistry Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Danijela Stanisic
- Biological Chemistry Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ljubica Tasic
- Biological Chemistry Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Martins-de-Souza D, Guest PC, Reis-de-Oliveira G, Schmitt A, Falkai P, Turck CW. An overview of the human brain myelin proteome and differences associated with schizophrenia. World J Biol Psychiatry 2021; 22:271-287. [PMID: 32602824 DOI: 10.1080/15622975.2020.1789217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Disturbances in the myelin sheath drive disruptions in neural transmission and brain connectivity as seen in schizophrenia. Here, the myelin proteome was characterised in schizophrenia patients and healthy controls to visualise differences in proteomic profiles. METHODS A liquid chromatography tandem mass spectrometry-based shotgun proteomic analysis was performed of a myelin-enriched fraction of postmortem brain samples from schizophrenia patients (n = 12) and mentally healthy controls (n = 8). In silico pathway analyses were performed on the resulting data. RESULTS The present characterisation of the human myelinome led to the identification of 480 non-redundant proteins, of which 102 proteins are newly annotated to be associated with the myelinome. Levels of 172 of these proteins were altered between schizophrenia patients and controls. These proteins were mainly associated with glial cell differentiation, metabolism/energy, synaptic vesicle function and neurodegeneration. The hub proteins with the highest degree of connectivity in the network included multiple kinases and synaptic vesicle transport proteins. CONCLUSIONS Together these findings suggest disruptive effects on synaptic activity and therefore neural transmission and connectivity, consistent with the dysconnectivity hypothesis of schizophrenia. Further studies on these proteins may lead to the identification of potential drug targets related to the synaptic dysconnectivity in schizophrenia and other psychiatric and neurodegenerative disorders.
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Affiliation(s)
- Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil.,Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil.,D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Christoph W Turck
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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Reis-de-Oliveira G, Zuccoli GS, Fioramonte M, Schimitt A, Falkai P, Almeida V, Martins-de-Souza D. Digging deeper in the proteome of different regions from schizophrenia brains. J Proteomics 2020; 223:103814. [PMID: 32389842 DOI: 10.1016/j.jprot.2020.103814] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a psychiatric disorder that affects 21 million people worldwide. Despite several studies having been shown that some brain regions may play a critical role in the pathophysiology of schizophrenia, the molecular basis to explain this diversity is still lacking. The cerebellum (CER), caudate nucleus (CAU), and posterior cingulate cortex (PCC) are areas associated with negative and cognitive symptoms in schizophrenia. In this study, we performed shotgun proteomics of the aforementioned brain regions, collected postmortem from patients with schizophrenia and compared with the mentally healthy group. In addition, we performed a proteomic analysis of nuclear and mitochondrial fractions of these same regions. Our results presented 106, 727 and 135 differentially regulated proteins in the CAU, PCC, and CER, respectively. Pathway enrichment analysis revealed dysfunctions associated with synaptic processes in the CAU, transport in the CER, and in energy metabolism in the PCC. In all brain areas, we found that proteins related to oligodendrocytes and the metabolic processes were dysregulated in schizophrenia. SIGNIFICANCE: Schizophrenia is a complex and heterogeneous psychiatric disorder. Despite much research having been done to increase the knowledge about the role of each region in the pathophysiology of this disorder, the molecular mechanisms underlying it are still lacking. We performed shotgun proteomics in the postmortem cerebellum (CER), caudate nucleus (CAU) and posterior cingulate cortex (PCC) from patients with schizophrenia and compared with healthy controls. Our findings suggest that each aforementioned region presents dysregulations in specific molecular pathways, such as energy metabolism in the PCC, transport in the CER, and synaptic process in the CAU. Additionally, these areas presented dysfunctions in oligodendrocytes and metabolic processes. Our results may highlight future directions for the development of novel clinical approaches for specific therapeutic targets.
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Affiliation(s)
- G Reis-de-Oliveira
- Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - G S Zuccoli
- Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - M Fioramonte
- Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - A Schimitt
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University (LMU), Munich, Germany; Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, University of São Paulo, São Paulo, Brazil
| | - P Falkai
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University (LMU), Munich, Germany
| | - V Almeida
- Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - D Martins-de-Souza
- Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil; D'Or Institute for Research and Education (IDOR), São Paulo, Brazil; Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil.
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Guest PC. Brain Proteomic Analysis on the Effects of the Antidepressant Fluoxetine. Methods Mol Biol 2020; 2138:419-430. [PMID: 32219768 DOI: 10.1007/978-1-0716-0471-7_31] [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] [Indexed: 06/10/2023]
Abstract
Psychiatric disorders such as major depression are linked to early mortality, and patients affected by these conditions are at an increased risk of developing other diseases that are characteristic of the old and very old. Antidepressants are prescribed in the treatment of depression, although the mechanism of how they exert their therapeutic effects is only partly understood. To shed further light on their mode of action, this chapter presents a protocol using two-dimensional differential in-gel electrophoresis (2D-DIGE) combined with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for identifying a proteomic signature in guinea pig brains after treatment with the antidepressant, fluoxetine. As this signature pointed toward changes in synaptic structure, we also present a protocol for Western blot analysis targeting selected proteins identified by the combined 2D-DIGE-MALDI-TOF mass spectrometry procedure. Such validation experiments are critical for the translation of putative biomarkers into preclinical and clinical studies.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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