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Salgado JCS, Alnoch RC, Polizeli MDLTDM, Ward RJ. Microenzymes: Is There Anybody Out There? Protein J 2024; 43:393-404. [PMID: 38507106 DOI: 10.1007/s10930-024-10193-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20-60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions.
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Affiliation(s)
- Jose Carlos Santos Salgado
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil.
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil.
| | - Robson Carlos Alnoch
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
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2
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Pournajaf S, Afsordeh N, Pourgholami MH. In vivo C6 glioma models: an update and a guide toward a more effective preclinical evaluation of potential anti-glioblastoma drugs. Rev Neurosci 2024; 35:183-195. [PMID: 37651618 DOI: 10.1515/revneuro-2023-0067] [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: 06/24/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023]
Abstract
Glioblastoma multiform (GBM) is the most common primary brain tumor with a poor prognosis and few therapeutic choices. In vivo, tumor models are useful for enhancing knowledge of underlying GBM pathology and developing more effective therapies/agents at the preclinical level, as they recapitulate human brain tumors. The C6 glioma cell line has been one of the most widely used cell lines in neuro-oncology research as they produce tumors that share the most similarities with human GBM regarding genetic, invasion, and expansion profiles and characteristics. This review provides an overview of the distinctive features and the different animal models produced by the C6 cell line. We also highlight specific applications of various C6 in vivo models according to the purpose of the study and offer some technical notes for more convenient/repeatable modeling. This work also includes novel findings discovered in our laboratory, which would further enhance the feasibility of the model in preclinical GBM investigations.
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Affiliation(s)
- Safura Pournajaf
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Nastaran Afsordeh
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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3
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Song YX, Li X, Nie SD, Hu ZX, Zhou D, Sun DY, Zhou GY, Wang Y, Liu JJ, Song T, Wang S. Extracellular vesicles released by glioma cells are decorated by Annexin A2 allowing for cellular uptake via heparan sulfate. Cancer Gene Ther 2023; 30:1156-1166. [PMID: 37231059 DOI: 10.1038/s41417-023-00627-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/20/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Extracellular vesicles (EVs) play a crucial role in regulating cell behavior by delivering their cargo to target cells. However, the mechanisms underlying EV-cell interactions are not well understood. Previous studies have shown that heparan sulfate (HS) on target cell surfaces can act as receptors for exosomes uptake, but the ligand for HS on EVs has not been identified. In this study, we isolated EVs from glioma cell lines and glioma patients and identified Annexin A2 (AnxA2) on EVs as a key HS-binding ligand and mediator of EV-cell interactions. Our findings suggest that HS plays a dual role in EV-cell interactions, where HS on EVs captures AnxA2, and on target cells, it acts as a receptor for AnxA2. Removal of HS from the EV surface inhibits EV-target cell interaction by releasing AnxA2. Furthermore, we found that AnxA2-mediated binding of EVs to vascular endothelial cells promotes angiogenesis, and that antibody against AnxA2 inhibited the ability of glioma-derived EVs to stimulate angiogenesis by reducing the uptake of EVs. Our study also suggests that the AnxA2-HS interaction may accelerate the glioma-derived EVs-mediated angiogenesis and that combining AnxA2 on glioma cells with HS on endothelial cells may effectively improve the prognosis evaluation of glioma patients.
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Affiliation(s)
- Yu-Xi Song
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Xin Li
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China.
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China.
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China.
| | - Sheng-Dan Nie
- Institute of Clinical Medicine, Hunan provincial people's hospital, the first affiliated hospital of Hunan Normal University, Changsha, China
| | - Zhong-Xu Hu
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Di Zhou
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Ding-Ya Sun
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Gao-Ya Zhou
- Department of Neurology, Brain hospital of Hunan Province, Changsha, China
| | - Ying Wang
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jia-Jia Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Tao Song
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China.
| | - Shan Wang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China.
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4
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Mohaupt P, Roucou X, Delaby C, Vialaret J, Lehmann S, Hirtz C. The alternative proteome in neurobiology. Front Cell Neurosci 2022; 16:1019680. [PMID: 36467612 PMCID: PMC9712206 DOI: 10.3389/fncel.2022.1019680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/02/2022] [Indexed: 10/13/2023] Open
Abstract
Translation involves the biosynthesis of a protein sequence following the decoding of the genetic information embedded in a messenger RNA (mRNA). Typically, the eukaryotic mRNA was considered to be inherently monocistronic, but this paradigm is not in agreement with the translational landscape of cells, tissues, and organs. Recent ribosome sequencing (Ribo-seq) and proteomics studies show that, in addition to currently annotated reference proteins (RefProt), other proteins termed alternative proteins (AltProts), and microproteins are encoded in regions of mRNAs thought to be untranslated or in transcripts annotated as non-coding. This experimental evidence expands the repertoire of functional proteins within a cell and potentially provides important information on biological processes. This review explores the hitherto overlooked alternative proteome in neurobiology and considers the role of AltProts in pathological and healthy neuromolecular processes.
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Affiliation(s)
- Pablo Mohaupt
- LBPC-PPC, Université de Montpellier, IRMB CHU de Montpellier, INM INSERM, Montpellier, France
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Constance Delaby
- LBPC-PPC, Université de Montpellier, IRMB CHU de Montpellier, INM INSERM, Montpellier, France
| | - Jérôme Vialaret
- LBPC-PPC, Université de Montpellier, IRMB CHU de Montpellier, INM INSERM, Montpellier, France
| | - Sylvain Lehmann
- LBPC-PPC, Université de Montpellier, IRMB CHU de Montpellier, INM INSERM, Montpellier, France
| | - Christophe Hirtz
- LBPC-PPC, Université de Montpellier, IRMB CHU de Montpellier, INM INSERM, Montpellier, France
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5
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Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
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6
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Zhang Z, Li Y, Yuan W, Wang Z, Wan C. Proteomic-driven identification of short open reading frame-encoded peptides. Proteomics 2022; 22:e2100312. [PMID: 35384297 DOI: 10.1002/pmic.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zheng Zhang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Yujie Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Wenqian Yuan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Zhiwei Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
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Cardon T, Fournier I, Salzet M. Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs. Front Cell Dev Biol 2022; 9:703583. [PMID: 35004666 PMCID: PMC8733697 DOI: 10.3389/fcell.2021.703583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.
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Affiliation(s)
- Tristan Cardon
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
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8
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Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations. Metabolites 2021; 12:metabo12010002. [PMID: 35050124 PMCID: PMC8778087 DOI: 10.3390/metabo12010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the rest of the strip (R)—with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.
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Chuang HC, Chen MH, Chen YM, Yang HY, Ciou YR, Hsueh CH, Tsai CY, Tan TH. BPI overexpression suppresses Treg differentiation and induces exosome-mediated inflammation in systemic lupus erythematosus. Am J Cancer Res 2021; 11:9953-9966. [PMID: 34815797 PMCID: PMC8581436 DOI: 10.7150/thno.63743] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
Background: Serum-derived exosomes are correlated with disease severity of human systemic lupus erythematosus (SLE). The proteins in the T-cell-derived exosomes from SLE patients could contribute to inflammation. Methods: We characterized proteins of T cell-derived exosomes from SLE patients and healthy controls by proteomics. To study the potential pathogenic role of the identified exosomal protein, we generated and characterized T-cell-specific transgenic mice that overexpressed the identified protein in T cells using immunohistochemistry, immunoblotting, and single-cell RNA sequencing. Results: We identified an overexpressed protein, bactericidal/permeability-increasing protein (BPI), in SLE T cells and T-cell-derived exosomes. T-cell-specific BPI transgenic (Lck-BPI Tg) mice showed multi-tissue inflammation with early induction of serum IL-1β levels, as well as serum triglyceride and creatinine levels. Interestingly, exosomes of Lck-BPI Tg T cells stimulated IL-1β expression of wild-type recipient macrophages. Remarkably, adoptive transfer of BPI-containing exosomes increased serum IL-1β and autoantibody levels in recipient mice. The transferred exosomes infiltrated into multiple tissues of recipient mice, resulting in hepatitis, nephritis, and arthritis. ScRNA-seq showed that Lck-BPI Tg T cells displayed a decrease of Treg population, which was concomitant with ZFP36L2 upregulation and Helios downregulation. Furthermore, in vitro Treg differentiation was reduced by BPI transgene and enhanced by BPI knockout. Conclusions: BPI is a negative regulator of Treg differentiation. BPI overexpression in T-cell-derived exosomes or peripheral blood T cells may be a biomarker and pathogenic factor for human SLE nephritis, hepatitis, and arthritis.
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Role of Exosomal MicroRNAs and Their Crosstalk with Oxidative Stress in the Pathogenesis of Osteoporosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6301433. [PMID: 34336108 PMCID: PMC8315851 DOI: 10.1155/2021/6301433] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022]
Abstract
Osteoporosis (OP) is an aging-related disease involving permanent bone tissue atrophy. Most patients with OP show high levels of oxidative stress (OS), which destroys the microstructure of bone tissue and promotes disease progression. Exosomes (exos) help in the delivery of microRNAs (miRNAs) and allow intercellular communication. In OP, exosomal miRNAs modulate several physiological processes, including the OS response. In the present review, we aim to describe how exosomal miRNAs and OS contribute to OP. We first summarize the relationship of OS with OP and then detail the features of exos along with the functions of exo-related miRNAs. Further, we explore the interplay between exosomal miRNAs and OS in OP and summarize the functional role of exos in OP. Finally, we identify the advantages of exo-based miRNA delivery in treatment strategies for OP. Our review seeks to improve the current understanding of the mechanism underlying OP pathogenesis and lay the foundation for the development of novel theranostic approaches for OP.
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11
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Pistono C, Bister N, Stanová I, Malm T. Glia-Derived Extracellular Vesicles: Role in Central Nervous System Communication in Health and Disease. Front Cell Dev Biol 2021; 8:623771. [PMID: 33569385 PMCID: PMC7868382 DOI: 10.3389/fcell.2020.623771] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Glial cells are crucial for the maintenance of correct neuronal functionality in a physiological state and intervene to restore the equilibrium when environmental or pathological conditions challenge central nervous system homeostasis. The communication between glial cells and neurons is essential and extracellular vesicles (EVs) take part in this function by transporting a plethora of molecules with the capacity to influence the function of the recipient cells. EVs, including exosomes and microvesicles, are a heterogeneous group of biogenetically distinct double membrane-enclosed vesicles. Once released from the cell, these two types of vesicles are difficult to discern, thus we will call them with the general term of EVs. This review is focused on the EVs secreted by astrocytes, oligodendrocytes and microglia, aiming to shed light on their influence on neurons and on the overall homeostasis of the central nervous system functions. We collect evidence on neuroprotective and homeostatic effects of glial EVs, including neuronal plasticity. On the other hand, current knowledge of the detrimental effects of the EVs in pathological conditions is addressed. Finally, we propose directions for future studies and we evaluate the potential of EVs as a therapeutic treatment for neurological disorders.
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Affiliation(s)
- Cristiana Pistono
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nea Bister
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Iveta Stanová
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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12
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Brunet MA, Lucier JF, Levesque M, Leblanc S, Jacques JF, Al-Saedi HRH, Guilloy N, Grenier F, Avino M, Fournier I, Salzet M, Ouangraoua A, Scott M, Boisvert FM, Roucou X. OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Res 2021; 49:D380-D388. [PMID: 33179748 PMCID: PMC7779043 DOI: 10.1093/nar/gkaa1036] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one's bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-François Lucier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Maxime Levesque
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-Francois Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Hassan R H Al-Saedi
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Frederic Grenier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Mariano Avino
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Michel Salzet
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Aïda Ouangraoua
- Informatics Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
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Fabre B, Combier JP, Plaza S. Recent advances in mass spectrometry-based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions. Curr Opin Chem Biol 2021; 60:122-130. [PMID: 33401134 DOI: 10.1016/j.cbpa.2020.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Short open reading frame (sORF)-encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.
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Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France.
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
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Cardon T, Fournier I, Salzet M. SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data. Microorganisms 2020; 8:E2036. [PMID: 33352703 PMCID: PMC7766365 DOI: 10.3390/microorganisms8122036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this "ghost proteome" was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts, we were interested in finding out their interaction with the viral protein coming from the SARS-CoV-2 virus, responsible for the 2020 COVID-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by affinity purification in co-immunoprecipitation (co-IP) in the perspective of drug repurposing. The initial work revealed the interaction between 332 human cellular reference proteins (RefProts) with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study), plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the ghost proteome for discovering new therapeutic targets, and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies.
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Affiliation(s)
- Tristan Cardon
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
- Institut Universitaire de France, 75000 Paris, France
| | - Michel Salzet
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
- Institut Universitaire de France, 75000 Paris, France
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Cardon T, Fournier I, Salzet M. Shedding Light on the Ghost Proteome. Trends Biochem Sci 2020; 46:239-250. [PMID: 33246829 DOI: 10.1016/j.tibs.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023]
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.
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Affiliation(s)
- Tristan Cardon
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
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Pistono C, Bister N, Stanová I, Malm T. Glia-Derived Extracellular Vesicles: Role in Central Nervous System Communication in Health and Disease. Front Cell Dev Biol 2020. [PMID: 33569385 DOI: 10.3389/cell.2020.623771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Glial cells are crucial for the maintenance of correct neuronal functionality in a physiological state and intervene to restore the equilibrium when environmental or pathological conditions challenge central nervous system homeostasis. The communication between glial cells and neurons is essential and extracellular vesicles (EVs) take part in this function by transporting a plethora of molecules with the capacity to influence the function of the recipient cells. EVs, including exosomes and microvesicles, are a heterogeneous group of biogenetically distinct double membrane-enclosed vesicles. Once released from the cell, these two types of vesicles are difficult to discern, thus we will call them with the general term of EVs. This review is focused on the EVs secreted by astrocytes, oligodendrocytes and microglia, aiming to shed light on their influence on neurons and on the overall homeostasis of the central nervous system functions. We collect evidence on neuroprotective and homeostatic effects of glial EVs, including neuronal plasticity. On the other hand, current knowledge of the detrimental effects of the EVs in pathological conditions is addressed. Finally, we propose directions for future studies and we evaluate the potential of EVs as a therapeutic treatment for neurological disorders.
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Affiliation(s)
- Cristiana Pistono
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nea Bister
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Iveta Stanová
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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