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Macedo-da-Silva J, Mule SN, Rosa-Fernandes L, Palmisano G. A computational pipeline elucidating functions of conserved hypothetical Trypanosoma cruzi proteins based on public proteomic data. Adv Protein Chem Struct Biol 2024; 138:401-428. [PMID: 38220431 DOI: 10.1016/bs.apcsb.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The proteome is complex, dynamic, and functionally diverse. Functional proteomics aims to characterize the functions of proteins in biological systems. However, there is a delay in annotating the function of proteins, even in model organisms. This gap is even greater in other organisms, including Trypanosoma cruzi, the causative agent of the parasitic, systemic, and sometimes fatal disease called Chagas disease. About 99.8% of Trypanosoma cruzi proteome is not manually annotated (unreviewed), among which>25% are conserved hypothetical proteins (CHPs), calling attention to the knowledge gap on the protein content of this organism. CHPs are conserved proteins among different species of various evolutionary lineages; however, they lack functional validation. This study describes a bioinformatics pipeline applied to public proteomic data to infer possible biological functions of conserved hypothetical Trypanosoma cruzi proteins. Here, the adopted strategy consisted of collecting differentially expressed proteins between the epimastigote and metacyclic trypomastigotes stages of Trypanosoma cruzi; followed by the functional characterization of these CHPs applying a manifold learning technique for dimension reduction and 3D structure homology analysis (Spalog). We found a panel of 25 and 26 upregulated proteins in the epimastigote and metacyclic trypomastigote stages, respectively; among these, 18 CHPs (8 in the epimastigote stage and 10 in the metacyclic stage) were characterized. The data generated corroborate the literature and complement the functional analyses of differentially regulated proteins at each stage, as they attribute potential functions to CHPs, which are frequently identified in Trypanosoma cruzi proteomics studies. However, it is important to point out that experimental validation is required to deepen our understanding of the CHPs.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil; Centre for Motor Neuron Disease Research, Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, Sydney, NSW, Australia
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
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Santiago VF, Rosa-Fernandes L, Macedo-da-Silva J, Angeli CB, Mule SN, Marinho CRF, Torrecilhas AC, Marie SNK, Palmisano G. Isolation of Extracellular Vesicles Using Titanium Dioxide Microspheres. Adv Exp Med Biol 2024; 1443:1-22. [PMID: 38409413 DOI: 10.1007/978-3-031-50624-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Extracellular vesicles (EVs) are bilayer membrane particles released from several cell types to the extracellular environment. EVs have a crucial role in cell-cell communication, involving different biological processes in health and diseases. Due to the potential of biomarkers for several diseases as diagnostic and therapeutic tools, it is relevant to understand the biology of the EVs and their content. One of the current challenges involving EVs is regarding the purification method, which is a critical step for EV's functional and characterization studies. Ultracentrifugation is the most used method for EV isolation, where the nanoparticles are separated in sequential centrifugation to isolate the EVs based on their size. However, for viscous biofluids such as plasma, there is a co-isolation of the most abundant proteins, which can impair the EV's protein identification due to the low abundance of these proteins and signal suppression by the most abundant plasma proteins. Emerging techniques have gained attention in recent years. Titanium dioxide (TiO2) is one of the most promising techniques due to its property for selective isolation based on the interaction with phospholipids in the EV membrane. Using a small amount of TiO2 beads and a low volume of plasma, it is possible to isolate EVs with reduced plasma protein co-isolation. This study describes a comprehensive workflow for the isolation and characterization of plasma extracellular vesicles (EVs) using mass spectrometry-based proteomics techniques. The aim of this chapter is describe the EV isolation using TiO2 beads enrichment and high-throughput mass spectrometry techniques to efficiently identify the protein composition of EVs in a fast and straightforward manner.
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Affiliation(s)
- Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Torrecilhas
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Departamento de Ciências Farmacêuticas; Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários. Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Suely N K Marie
- Laboratory of Molecular and Cellular Biology (LIM15), Department of Neurology, Fac-uldade de Medicina FMUSP, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia.
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Macedo-da-Silva J, Rosa-Fernandes L, Santiago VF, Blanes CA, Marie SKN, Palmisano G. Mass Spectrometry-Based Characterization of Protein Aggregates in Tissues and Biofluids. Adv Exp Med Biol 2024; 1443:257-267. [PMID: 38409426 DOI: 10.1007/978-3-031-50624-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Protein aggregation is a common mechanism in multiple neurodegenerative and heart diseases and the accumulation of proteins in aggregates is toxic to cells, causing injury and death. The degree of protein aggregation directly correlates with the severity of the disease. Misfolded proteins present thermodynamic barriers that culminate in the loss of structure and function and the exposure of hydrophobic residues. The exposure of hydrophobic residues is the driving force behind protein aggregation, as it reduces surface free energy and increases the propensity for the formation of large insoluble aggregates. Exploring the protein content of aggregates is fundamental to understanding their formation mechanism and pathophysiological effects. We demonstrate here a method for isolating aggregated protein content in human plasma and mouse brain samples. The samples were characterized by mass spectrometry analysis, transmission electron microscopy, and western blotting. We report the identification of proteins associated with neurodegenerative diseases in the isolated pellets. The western blotting analyses of the isolated pellet showed the positivity for CD89 and CD63, consolidated markers of exosomes, confirming the presence of exosomes within the pellet but not in the supernatant in human plasma. Notably, the concomitant isolation of exosomes together with the protein aggregates was feasible starting from 200 μL of human plasma. Moreover, the presented methodology separated albumin from the aggregated pellet, allowing identification of larger diversity of proteins through mass spectrometry analysis.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, Sydney, Australia
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, Sydney, Australia
| | - Verônica Feijoli Santiago
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, England, UK
| | - Claudia Angeli Blanes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Macquarie University, Sydney, Australia.
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Lazari LC, Santiago VF, de Oliveira GS, Mule SN, Angeli CB, Rosa-Fernandes L, Palmisano G. Glycosort: A Computational Solution to Post-process Quantitative Large-Scale Intact Glycopeptide Analyses. Adv Exp Med Biol 2024; 1443:23-32. [PMID: 38409414 DOI: 10.1007/978-3-031-50624-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Protein glycosylation is a post-translational modification involving the addition of carbohydrates to proteins and plays a crucial role in protein folding and various biological processes such as cell recognition, differentiation, and immune response. The vast array of natural sugars available allows the generation of plenty of unique glycan structures in proteins, adding complexity to the regulation and biological functions of glycans. The diversity is further increased by enzymatic site preferences and stereochemical conjugation, leading to an immense amount of different glycan structures. Understanding glycosylation heterogeneity is vital for unraveling the impact of glycans on different biological functions. Evaluating site occupancies and structural heterogeneity aids in comprehending glycan-related alterations in biological processes. Several software tools are available for large-scale glycoproteomics studies; however, integrating identification and quantitative data to assess heterogeneity complexity often requires extensive manual data processing. To address this challenge, we present a python script that automates the integration of Byonic and MaxQuant outputs for glycoproteomic data analysis. The script enables the calculation of site occupancy percentages by glycans and facilitates the comparison of glycan structures and site occupancies between two groups. This automated tool offers researchers a means to organize and interpret their high-throughput quantitative glycoproteomic data effectively.
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Affiliation(s)
- Lucas C Lazari
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gilberto S de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Faculty of Science and Engineering, Sydney, Australia.
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5
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Andreone L, dos Santos A, Wailemann R, Terra L, Gomes V, Macedo da Silva J, Rosa-Fernandes L, Sogayar M, Palmisano G, Labriola L, Perone M. Cotransplantation of marginal mass allogeneic islets with 3D culture-derived adult human skin cells improves glycemia in diabetic mice. Braz J Med Biol Res 2023; 56:e12611. [PMID: 37792778 PMCID: PMC10515501 DOI: 10.1590/1414-431x2023e12611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/09/2023] [Indexed: 10/06/2023] Open
Abstract
Islet transplantation represents a therapeutic option for type 1 diabetes (T1D). Long-term viability of transplanted islets requires improvement. Mesenchymal stromal cells (MSCs) have been proposed as adjuvants for islet transplantation facilitating grafting and functionality. Stem cell aggregation provides physiological interactions between cells and enhances the in situ concentration of modulators of inflammation and immunity. We established a hanging-drop culture of adult human skin fibroblast-like cells as spheroids, and skin spheroid-derived cells (SphCs) were characterized. We assessed the potential of SphCs in improving islet functionality by cotransplantation with a marginal mass of allogeneic islets in an experimental diabetic mouse model and characterized the secretome of SphCs by mass spectrometry-based proteomics. SphCs were characterized as multipotent progenitors and their coculture with anti-CD3 stimulated mouse splenocytes decreased CD4+ T cell proliferation with skewed cytokine secretion through an increase in the Th2/Th1 ratio profile. SphCs-conditioned media attenuated apoptosis of islets induced by cytokine challenge in vitro and importantly, intratesticular SphCs administration did not show tumorigenicity in immune-deficient mice. Moreover, SphCs improved glycemic control when cotransplanted with a marginal mass of allogeneic islets in a diabetic mouse model without pharmacological immunosuppression. SphCs' protein secretome differed from its paired skin fibroblast-like counterpart in containing 70% of up- and downregulated proteins and biological processes that overall positively influenced islets such as cytoprotection, cellular stress, metabolism, and survival. In summary, SphCs improved the performance of transplanted allogeneic islets in an experimental T1D model, without pharmacological immunosuppression. Future research is warranted to identify SphCs-secreted factors responsible for islets' endurance.
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Affiliation(s)
- L. Andreone
- Immuno-Endocrinology, Diabetes & Metabolism Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET - Universidad Austral, Pilar, Argentina
- Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Argentina
| | - A.F. dos Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R.A.M. Wailemann
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - L.F. Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - V.M. Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - J. Macedo da Silva
- Departamento de Parasitologia, Instituto de Biosciências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - L. Rosa-Fernandes
- Departamento de Parasitologia, Instituto de Biosciências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M.C. Sogayar
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
- Centro de Terapia Celular e Molecular, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G. Palmisano
- Departamento de Parasitologia, Instituto de Biosciências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - L. Labriola
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M.J. Perone
- Immuno-Endocrinology, Diabetes & Metabolism Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET - Universidad Austral, Pilar, Argentina
- Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Argentina
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6
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Davidson JM, Wu SSL, Rayner SL, Cheng F, Duncan K, Russo C, Newbery M, Ding K, Scherer NM, Balez R, García-Redondo A, Rábano A, Rosa-Fernandes L, Ooi L, Williams KL, Morsch M, Blair IP, Di Ieva A, Yang S, Chung RS, Lee A. The E3 Ubiquitin Ligase SCF Cyclin F Promotes Sequestosome-1/p62 Insolubility and Foci Formation and is Dysregulated in ALS and FTD Pathogenesis. Mol Neurobiol 2023; 60:5034-5054. [PMID: 37243816 PMCID: PMC10415446 DOI: 10.1007/s12035-023-03355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
Amyotrophic lateral sclerosis (ALS)- and frontotemporal dementia (FTD)-linked mutations in CCNF have been shown to cause dysregulation to protein homeostasis. CCNF encodes for cyclin F, which is part of the cyclin F-E3 ligase complex SCFcyclinF known to ubiquitylate substrates for proteasomal degradation. In this study, we identified a function of cyclin F to regulate substrate solubility and show how cyclin F mechanistically underlies ALS and FTD disease pathogenesis. We demonstrated that ALS and FTD-associated protein sequestosome-1/p62 (p62) was a canonical substrate of cyclin F which was ubiquitylated by the SCFcyclinF complex. We found that SCFcyclin F ubiquitylated p62 at lysine(K)281, and that K281 regulated the propensity of p62 to aggregate. Further, cyclin F expression promoted the aggregation of p62 into the insoluble fraction, which corresponded to an increased number of p62 foci. Notably, ALS and FTD-linked mutant cyclin F p.S621G aberrantly ubiquitylated p62, dysregulated p62 solubility in neuronal-like cells, patient-derived fibroblasts and induced pluripotent stem cells and dysregulated p62 foci formation. Consistently, motor neurons from patient spinal cord tissue exhibited increased p62 ubiquitylation. We suggest that the p.S621G mutation impairs the functions of cyclin F to promote p62 foci formation and shift p62 into the insoluble fraction, which may be associated to aberrant mutant cyclin F-mediated ubiquitylation of p62. Given that p62 dysregulation is common across the ALS and FTD spectrum, our study provides insights into p62 regulation and demonstrates that ALS and FTD-linked cyclin F mutant p.S621G can drive p62 pathogenesis associated with ALS and FTD.
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Affiliation(s)
- Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia.
| | - Sharlynn S L Wu
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Flora Cheng
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Kimberley Duncan
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Carlo Russo
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Michelle Newbery
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Kunjie Ding
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Natalie M Scherer
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Rachelle Balez
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Alberto García-Redondo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, Madrid, Spain
| | - Alberto Rábano
- Neuropathology Department and CIEN Tissue Bank, Alzheimer's Centre Reina Sofia-CIEN Foundation, 28031, Madrid, Spain
| | - Livia Rosa-Fernandes
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Antonio Di Ieva
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
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7
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Santiago VF, Dombrowski JG, Kawahara R, Rosa-Fernandes L, Mule SN, Murillo O, Santana TV, Coutinho JVP, Macedo-da-Silva J, Lazari LC, Peixoto EPM, Ramirez MI, Larsen MR, Marinho CRF, Palmisano G. Complement System Activation Is a Plasma Biomarker Signature during Malaria in Pregnancy. Genes (Basel) 2023; 14:1624. [PMID: 37628675 PMCID: PMC10454407 DOI: 10.3390/genes14081624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Malaria in pregnancy (MiP) is a public health problem in malaria-endemic areas, contributing to detrimental outcomes for both mother and fetus. Primigravida and second-time mothers are most affected by severe anemia complications and babies with low birth weight compared to multigravida women. Infected erythrocytes (IE) reach the placenta, activating the immune response by placental monocyte infiltration and inflammation. However, specific markers of MiP result in poor outcomes, such as low birth weight, and intrauterine growth restriction for babies and maternal anemia in women infected with Plasmodium falciparum are limited. In this study, we identified the plasma proteome signature of a mouse model infected with Plasmodium berghei ANKA and pregnant women infected with Plasmodium falciparum infection using quantitative mass spectrometry-based proteomics. A total of 279 and 249 proteins were quantified in murine and human plasma samples, of which 28% and 30% were regulated proteins, respectively. Most of the regulated proteins in both organisms are involved in complement system activation during malaria in pregnancy. CBA anaphylatoxin assay confirmed the complement system activation by the increase in C3a and C4a anaphylatoxins in the infected plasma compared to non-infected plasma. Moreover, correlation analysis showed the association between complement system activation and reduced head circumference in newborns from Pf-infected mothers. The data obtained in this study highlight the correlation between the complement system and immune and newborn outcomes resulting from malaria in pregnancy.
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Affiliation(s)
- Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Jamille Gregorio Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Rebeca Kawahara
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Analytical Glycoimmunology Group, Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Oscar Murillo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Pulmonary Immunology, Center for Biomedical Research, University of Texas Health Center Science at Tyler, Tyler, TX 75708, USA
| | - Thais Viggiani Santana
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Joao Victor Paccini Coutinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Lucas Cardoso Lazari
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Erika Paula Machado Peixoto
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Marcel Ivan Ramirez
- Cell Biology Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | | | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Analytical Glycoimmunology Group, Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
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8
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Suddull HJ, Rosa-Fernandes L, Lee A. How can proteomics help solve the lack of biomarkers to aid in the early diagnosis of motor neuron disease (MND)? Expert Rev Proteomics 2023; 20:121-123. [PMID: 37480213 DOI: 10.1080/14789450.2023.2240513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Affiliation(s)
- Hannah Jane Suddull
- Macquarie University Centre for Motor Neuron Disease Research, Sydney, Australia
| | - Livia Rosa-Fernandes
- Macquarie University Centre for Motor Neuron Disease Research, Sydney, Australia
| | - Albert Lee
- Macquarie University Centre for Motor Neuron Disease Research, Sydney, Australia
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da Silva Santos Y, Gamon THM, de Azevedo MSP, Telezynski BL, de Souza EE, de Oliveira DBL, Dombrowski JG, Rosa-Fernandes L, Palmisano G, de Moura Carvalho LJ, Luvizotto MCR, Wrenger C, Covas DT, Curi R, Marinho CRF, Durigon EL, Epiphanio S. Virulence Profiles of Wild-Type, P.1 and Delta SARS-CoV-2 Variants in K18-hACE2 Transgenic Mice. Viruses 2023; 15:v15040999. [PMID: 37112979 PMCID: PMC10146242 DOI: 10.3390/v15040999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Since December 2019, the world has been experiencing the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we now face the emergence of several variants. We aimed to assess the differences between the wild-type (Wt) (Wuhan) strain and the P.1 (Gamma) and Delta variants using infected K18-hACE2 mice. The clinical manifestations, behavior, virus load, pulmonary capacity, and histopathological alterations were analyzed. The P.1-infected mice showed weight loss and more severe clinical manifestations of COVID-19 than the Wt and Delta-infected mice. The respiratory capacity was reduced in the P.1-infected mice compared to the other groups. Pulmonary histological findings demonstrated that a more aggressive disease was generated by the P.1 and Delta variants compared to the Wt strain of the virus. The quantification of the SARS-CoV-2 viral copies varied greatly among the infected mice although it was higher in P.1-infected mice on the day of death. Our data revealed that K18-hACE2 mice infected with the P.1 variant develop a more severe infectious disease than those infected with the other variants, despite the significant heterogeneity among the mice.
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Affiliation(s)
- Yasmin da Silva Santos
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Malaria Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Thais Helena Martins Gamon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Marcela Santiago Pacheco de Azevedo
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Bruna Larotonda Telezynski
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Danielle Bruna Leal de Oliveira
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
| | - Jamille Gregório Dombrowski
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
| | | | | | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05508-040, Brazil
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Rui Curi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo 08060-070, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo 05503-900, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Scientific Plataform Pasteur/USP, University of São Paulo, São Paulo 05508-020, Brazil
| | - Sabrina Epiphanio
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
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Macedo-da-Silva J, Rosa-Fernandes L, Gomes VDM, Santiago VF, Santos DM, Molnar CMS, Barboza BR, de Souza EE, Marques RF, Boscardin SB, Durigon EL, Marinho CRF, Wrenger C, Marie SKN, Palmisano G. Protein Arginylation Is Regulated during SARS-CoV-2 Infection. Viruses 2023; 15:v15020290. [PMID: 36851505 PMCID: PMC9964439 DOI: 10.3390/v15020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In 2019, the world witnessed the onset of an unprecedented pandemic. By February 2022, the infection by SARS-CoV-2 has already been responsible for the death of more than 5 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER stress and activation of the unfolded protein response (UPR) pathway. Degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-degron pathway. RESULTS The role of protein arginylation during SARS-CoV-2 infection was elucidated. Protein arginylation was studied in Vero CCL-81, macrophage-like THP1, and Calu-3 cells infected at different times. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure levels of arginyl-tRNA-protein transferase (ATE1) and its substrates. Dysregulation of the N-degron pathway was specifically identified during coronavirus infections compared to other respiratory viruses. We demonstrated that during SARS-CoV-2 infection, there is an increase in ATE1 expression in Calu-3 and Vero CCL-81 cells. On the other hand, infected macrophages showed no enzyme regulation. ATE1 and protein arginylation was variant-dependent, as shown using P1 and P2 viral variants and HEK 293T cells transfection with the spike protein and receptor-binding domains (RBD). In addition, we report that ATE1 inhibitors, tannic acid and merbromine (MER) reduce viral load. This finding was confirmed in ATE1-silenced cells. CONCLUSIONS We demonstrate that ATE1 is increased during SARS-CoV-2 infection and its inhibition has potential therapeutic value.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Vinicius de Morais Gomes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Deivid Martins Santos
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | | | - Bruno Rafael Barboza
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Rodolfo Ferreira Marques
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Silvia Beatriz Boscardin
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
- Correspondence: or ; Tel.: +55-11-99920-8662
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11
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Rosa-Fernandes L, Bedrat A, dos Santos MLB, Pinto A, Lucena E, Silva TP, Melo RC, Palmisano G, Cardoso CA, Barbosa RH. Global RNAseq of ocular cells reveals gene dysregulation in both asymptomatic and with Congenital Zika Syndrome infants exposed prenatally to Zika virus. Exp Cell Res 2022; 414:113086. [DOI: 10.1016/j.yexcr.2022.113086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022]
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Lazari LC, Zerbinati RM, Rosa-Fernandes L, Santiago VF, Rosa KF, Angeli CB, Schwab G, Palmieri M, Sarmento DJS, Marinho CRF, Almeida JD, To K, Giannecchini S, Wrenger C, Sabino EC, Martinho H, Lindoso JAL, Durigon EL, Braz-Silva PH, Palmisano G. MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19. J Oral Microbiol 2022; 14:2043651. [PMID: 35251522 PMCID: PMC8890567 DOI: 10.1080/20002297.2022.2043651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Lucas C. Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Klaise F. Rosa
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Claudia B. Angeli
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Claudio R. F. Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University, São José dos Campos, Brazil
| | - Kelvin To
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li KaShing Faculty of Medicine of the University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Herculano Martinho
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emílio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
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13
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Coutinho JVP, Macedo-da-Silva J, Mule SN, Kronenberger T, Rosa-Fernandes L, Wrenger C, Palmisano G. Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study. Adv Protein Chem Struct Biol 2022; 131:277-309. [PMID: 35871894 PMCID: PMC9181370 DOI: 10.1016/bs.apcsb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
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Affiliation(s)
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Germany,Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tuebingen, Germany,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), Tuebingen, Germany
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,Faculty of Science and engineering, Macquarie University, Sydney, NSW, Australia,Corresponding author:
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14
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Lazari LC, Rosa-Fernandes L, Palmisano G. Machine Learning Approaches to Analyze MALDI-TOF Mass Spectrometry Protein Profiles. Methods Mol Biol 2022; 2511:375-394. [PMID: 35838976 DOI: 10.1007/978-1-0716-2395-4_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Machine learning is being employed for the development of diagnostic methods for several diseases, but prognostic techniques are still poorly explored. The development of such approaches is essential to assist healthcare workers to ensure the most appropriate treatment for patients. In this chapter, we demonstrate a detailed protocol for the application of machine learning to MALDI-TOF MS spectra of COVID-19-infected plasma samples for risk classification and biomarker identification.
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Affiliation(s)
- Lucas C Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Sao Paulo, Brazil.
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15
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Rosa-Fernandes L, Oba-Shinjo SM, Macedo-da-Silva J, Marie SKN, Palmisano G. Aberrant Protein Glycosylation in Brain Cancers, with Emphasis on Glioblastoma. Advances in Experimental Medicine and Biology 2022; 1382:39-70. [DOI: 10.1007/978-3-031-05460-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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16
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Lazari LC, Rosa-Fernandes L, Palmisano G. Identification of Circulating Biomarkers of COVID-19 Using MALDI-TOF Mass Spectrometry. Methods Mol Biol 2022; 2511:175-182. [PMID: 35838960 DOI: 10.1007/978-1-0716-2395-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Matrix-assisted laser desorption/ionization source coupled with time-of-flight mass analyzer mass spectrometry (MALDI-TOF MS) is being widely used to obtain proteomic profiles for clinical purposes, as a fast, low-cost, robust, and efficient technique. Here we describe a method for biofluid analysis using MALDI-TOF MS for rapid acquisition of proteomic signatures of COVID-19 infected patients. By using solid-phase extraction, the method allows the analysis of biofluids in less than 15 min.
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Affiliation(s)
- Lucas C Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.
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17
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Trombetta-Lima M, Rosa-Fernandes L, Angeli CB, Moretti IF, Franco YM, Mousessian AS, Wakamatsu A, Lerario AM, Oba-Shinjo SM, Pasqualucci CA, Marie SKN, Palmisano G. Extracellular Matrix Proteome Remodeling in Human Glioblastoma and Medulloblastoma. J Proteome Res 2021; 20:4693-4707. [PMID: 34533964 DOI: 10.1021/acs.jproteome.1c00251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Medulloblastomas (MBs) and glioblastomas (GBMs) are high-incidence central nervous system tumors. Different origin sites and changes in the tissue microenvironment have been associated with the onset and progression. Here, we describe differences between the extracellular matrix (ECM) signatures of these tumors. We compared the proteomic profiles of MB and GBM decellularized tumor samples between each other and their normal decellularized brain site counterparts. Our analysis revealed that 19, 28, and 11 ECM proteins were differentially expressed in MBs, GBMs, and in both MBs and GBMs, respectively. Next, we validated key findings by using a protein tissue array with 53 MB and 55 GBM cases and evaluated the clinical relevance of the identified differentially expressed proteins through their analysis on publicly available datasets, 763 MB samples from the GSE50161 and GSE85217 studies, and 115 GBM samples from RNAseq-TCGA. We report a shift toward a denser fibrillary ECM as well as a clear alteration in the glycoprotein signature, which influences the tumor pathophysiology. MS data have been submitted to the PRIDE repository, project accession: PXD023350.
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Affiliation(s)
- Marina Trombetta-Lima
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil.,Faculty of Science and Engineering, Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen 9713 AV, The Netherlands
| | - Livia Rosa-Fernandes
- Parasitology Department, Instituto de Ciências Biomédicas (ICBUSP), Universidade de Sao Paulo, Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Claudia B Angeli
- Parasitology Department, Instituto de Ciências Biomédicas (ICBUSP), Universidade de Sao Paulo, Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Isabele F Moretti
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Yollanda M Franco
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Adaliana S Mousessian
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Alda Wakamatsu
- Hepatic Pathology Laboratory (LIM 14), Pathology Department, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Sao Paulo 01246-903, Brazil
| | - Antonio M Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sueli M Oba-Shinjo
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Carlos A Pasqualucci
- Brazilian Aging Brain Study Group, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Sao Paulo 01246-903, Brazil
| | - Suely K N Marie
- Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo 01246-903, Brazil
| | - Giuseppe Palmisano
- Parasitology Department, Instituto de Ciências Biomédicas (ICBUSP), Universidade de Sao Paulo, Sao Paulo, Sao Paulo 05508-000, Brazil
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18
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Mule SN, Rosa-Fernandes L, Coutinho JVP, Gomes VDM, Macedo-da-Silva J, Santiago VF, Quina D, de Oliveira GS, Thaysen-Andersen M, Larsen MR, Labriola L, Palmisano G. Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay. J Proteomics 2021; 248:104355. [PMID: 34450331 DOI: 10.1016/j.jprot.2021.104355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/08/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
A new method to probe the conformational changes of glycoproteins on a systems-wide scale, termed limited deglycosylation assay (LDA), is described. The method measures the differential rate of deglycosylation of N-glycans on natively folded proteins by the common peptide:N-glycosidase F (PNGase F) enzyme which in turn informs on their spatial presentation and solvent exposure on the protein surface hence ultimately the glycoprotein conformation. LDA involves 1) protein-level N-deglycosylation under native conditions, 2) trypsin digestion, 3) glycopeptide enrichment, 4) peptide-level N-deglycosylation and 5) quantitative MS-based analysis of formerly N-glycosylated peptides (FNGPs). LDA was initially developed and the experimental conditions optimized using bovine RNase B and fetuin. The method was then applied to glycoprotein extracts from LLC-MK2 epithelial cells upon treatment with dithiothreitol to induce endoplasmic reticulum stress and promote protein misfolding. Data from the LDA and 3D structure analysis showed that glycoproteins predominantly undergo structural changes in loops/turns upon ER stress as exemplified with detailed analysis of ephrin-A5, GALNT10, PVR and BCAM. These results show that LDA accurately reports on systems-wide conformational changes of glycoproteins induced under controlled treatment regimes. Thus, LDA opens avenues to study glycoprotein structural changes in a range of other physiological and pathophysiological conditions relevant to acute and chronic diseases. SIGNIFICANCE: We describe a novel method termed limited deglycosylation assay (LDA), to probe conformational changes of glycoproteins on a systems-wide scale. This method improves the current toolbox of structural proteomics by combining site and conformational-specific PNGase F enzymatic activity with large scale quantitative proteomics. X-ray crystallography, nuclear magnetic resonance spectroscopy and cryoEM techniques are the major techniques applied to elucidate macromolecule structures. However, the size and heterogeneity of the oligosaccharide chains poses several challenges to the applications of these techniques to glycoproteins. The LDA method presented here, can be applied to a range of pathophysiological conditions and expanded to investigate PTMs-mediated structural changes in complex proteomes.
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Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - João V P Coutinho
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Vinícius De Morais Gomes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Verônica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel Quina
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Gilberto Santos de Oliveira
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK, Denmark
| | - Letícia Labriola
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil.
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19
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Coutinho JVP, Rosa-Fernandes L, Mule SN, de Oliveira GS, Manchola NC, Santiago VF, Colli W, Wrenger C, Alves MJM, Palmisano G. The thermal proteome stability profile of Trypanosoma cruzi in epimastigote and trypomastigote life stages. J Proteomics 2021; 248:104339. [PMID: 34352427 DOI: 10.1016/j.jprot.2021.104339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/24/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022]
Abstract
Trypanosoma cruzi is a flagellate protozoa being the etiological agent of Chagas disease, a neglected tropical disease, which still poses a public health problem worldwide. The intricate molecular changes during T. cruzi-host interaction have been explored using different largescale omics techniques. However, protein stability is largely unknown. Thermal proteome profiling (TPP) methodology has the potential to characterize proteome-wide stability highlighting key proteins during T. cruzi infection and life stage transition from the invertebrate to the mammalian host. In the present work, T. cruzi epimastigotes and trypomastigotes cell lysates were subjected to TPP workflow and analyzed by quantitative large-scale mass spectrometry-based proteomics to fit a melting profile for each protein. A total of 2884 proteins were identified and associated to 1741 melting curves being 1370 in trypomastigotes (TmAVG 53.53 °C) and 1279 in epimastigotes (TmAVG 50.89 °C). A total of 453 proteins were identified with statistically different melting profiles between the two life stages. Proteins associated to pathogenesis and intracellular transport had regulated melting temperatures. Membrane and glycosylated proteins had a higher average Tm in trypomastigotes compared to epimastigotes. This study represents the first large-scale comparison of parasite protein stability between life stages. SIGNIFICANCE: Trypanosoma cruzi, a unicellular flagellate parasite, is the etiological agent of Chagas disease, endemic in South America and affecting more that 7 million people worldwide. There is an intense research to identify novel chemotherapeutic and diagnostic targets of Chagas disease. Proteomic approaches have helped in elucidating the quantitative proteome and PTMs changes of T. cruzi during life cycle transition and upon different biotic and abiotic stimuli. However, a comprehensive knowledge of the protein-protein interaction and protein conformation is still missing. In order to fill this gap, this manuscript elucidates the T. cruzi Y strain proteome-wide thermal stability map in the epimastigote and trypomastigote life stages. Comparison between life stages showed a higher average melting temperature stability for trypomastigotes than epimastigotes indicating a host temperature adaptation. Both presented a selective thermal stability shift for cellular compartments, molecular functions and biological processes based on the T. cruzi life stage. Membrane and glycosylated proteins presented a higher thermal stability in trypomastigotes when compared to the epimastigotes.
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Affiliation(s)
- Joao V P Coutinho
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Simon Ngao Mule
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Gilberto Santos de Oliveira
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | | | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Walter Colli
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | | | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil.
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20
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Lazari LC, Ghilardi FDR, Rosa-Fernandes L, Assis DM, Nicolau JC, Santiago VF, Dalçóquio TF, Angeli CB, Bertolin AJ, Marinho CR, Wrenger C, Durigon EL, Siciliano RF, Palmisano G. Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19. Life Sci Alliance 2021; 4:e202000946. [PMID: 34168074 PMCID: PMC8321665 DOI: 10.26508/lsa.202000946] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infection poses a global health crisis. In parallel with the ongoing world effort to identify therapeutic solutions, there is a critical need for improvement in the prognosis of COVID-19. Here, we report plasma proteome fingerprinting that predict high (hospitalized) and low-risk (outpatients) cases of COVID-19 identified by a platform that combines machine learning with matrix-assisted laser desorption ionization mass spectrometry analysis. Sample preparation, MS, and data analysis parameters were optimized to achieve an overall accuracy of 92%, sensitivity of 93%, and specificity of 92% in dataset without feature selection. We identified two distinct regions in the MALDI-TOF profile belonging to the same proteoforms. A combination of SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins, both already described as biomarkers for viral infections in the acute phase. Unbiased discrimination of high- and low-risk COVID-19 patients using a technology that is currently in clinical use may have a prompt application in the noninvasive prognosis of COVID-19. Further validation will consolidate its clinical utility.
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Affiliation(s)
- Lucas Cardoso Lazari
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - José Carlos Nicolau
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Claudio Rf Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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21
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Mule SN, Gomes VDM, Wailemann RAM, Macedo-da-Silva J, Rosa-Fernandes L, Larsen MR, Labriola L, Palmisano G. HSPB1 influences mitochondrial respiration in ER-stressed beta cells. Biochim Biophys Acta Proteins Proteom 2021; 1869:140680. [PMID: 34051341 DOI: 10.1016/j.bbapap.2021.140680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023]
Abstract
Beta-cell death and dysfunction are involved in the development of type 1 and 2 diabetes. ER-stress impairs beta-cells function resulting in pro-apoptotic stimuli that promote cell death. Hence, the identification of protective mechanisms in response to ER-stress could lead to novel therapeutic targets and insight in the pathology of these diseases. Here, we report the identification of proteins involved in dysregulated pathways upon thapsigargin treatment of MIN6 cells. Utilizing quantitative proteomics we identified upregulation of proteins involved in protein folding, unfolded protein response, redox homeostasis, proteasome processes associated with endoplasmic reticulum and downregulation of TCA cycle, cellular respiration, lipid metabolism and ribosome assembly processes associated to mitochondria and eukaryotic initiation translation factor components. Subsequently, pro-inflammatory cytokine treatment was performed to mimic pathological changes observed in beta-cells during diabetes. Cytokines induced ER stress and impaired mitochondrial function in beta-cells corroborating the results obtained with the proteomic approach. HSPB1 levels are increased by prolactin on pancreatic beta-cells and this protein is a key factor for cytoprotection although its role has not been fully elucidated. Here we show that while up-regulation of HSPB1 was able to restore the mitochondrial dysfunction induced by beta-cells' exposure to inflammatory cytokines, silencing of this chaperone abrogated the beneficial effects promoted by PRL. Taken together, our results outline the importance of HSPB1 to mitigate beta-cell dysfunction. Further studies are needed to elucidate its role in diabetes.
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Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Vinícius De Morais Gomes
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Rosangela A M Wailemann
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Janaina Macedo-da-Silva
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | - Letícia Labriola
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.
| | - Giuseppe Palmisano
- GlycoProteomics laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil.
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22
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Macedo-da-Silva J, Santiago VF, Rosa-Fernandes L, Marinho CRF, Palmisano G. Protein glycosylation in extracellular vesicles: Structural characterization and biological functions. Mol Immunol 2021; 135:226-246. [PMID: 33933815 DOI: 10.1016/j.molimm.2021.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed particles involved in intercellular communication, delivery of biomolecules from donor to recipient cells, cellular disposal and homeostasis, potential biomarkers and drug carriers. The content of EVs includes DNA, lipids, metabolites, proteins, and microRNA, which have been studied in various diseases, such as cancer, diabetes, pregnancy, neurodegenerative, and cardiovascular disorders. EVs are enriched in glycoconjugates and exhibit specific glycosignatures. Protein glycosylation is a co- and post-translational modification (PTM) that plays an important role in the expression and function of exosomal proteins. N- and O-linked protein glycosylation has been mapped in exosomal proteins. The purpose of this review is to highlight the importance of glycosylation in EVs proteins. Initially, we describe the main PTMs in EVs with a focus on glycosylation. Then, we explore glycan-binding proteins describing the main findings of studies that investigated the glycosylation of EVs in cancer, pregnancy, infectious diseases, diabetes, mental disorders, and animal fluids. We have highlighted studies that have developed innovative methods for studying the content of EVs. In addition, we present works related to lipid glycosylation. We explored the content of studies deposited in public databases, such as Exocarta and Vesiclepedia. Finally, we discuss analytical methods for structural characterization of glycoconjugates and present an overview of the critical points of the study of glycosylation EVs, as well as perspectives in this field.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Verônica F Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil.
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23
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Mule SN, Costa-Martins AG, Rosa-Fernandes L, de Oliveira GS, Rodrigues CMF, Quina D, Rosein GE, Teixeira MMG, Palmisano G. PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile. Commun Biol 2021; 4:324. [PMID: 33707618 PMCID: PMC7952728 DOI: 10.1038/s42003-021-01762-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/24/2021] [Indexed: 01/31/2023] Open
Abstract
The etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationships between organisms based on differential mass spectrometry-based quantitative features. In particular, large scale quantitative bottom-up proteomics features (MS1, iBAQ and LFQ) were analyzed using maximum parsimony, showing a correlation between T. cruzi DTUs and closely related trypanosomes' protein expression and sequence-based clustering. Character mapping enabled the identification of synapomorphies, herein the proteins and their respective expression profiles that differentiate T. cruzi DTUs and trypanosome species. The distance matrices based on phylogenetics and PhyloQuant clustering showed statistically significant correlation highlighting the complementarity between the two strategies. Moreover, PhyloQuant allows the identification of differentially regulated and strain/DTU/species-specific proteins, and has potential application in the identification of specific biomarkers and candidate therapeutic targets.
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Affiliation(s)
- Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Carla Monadeli F Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Quina
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Graziella E Rosein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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24
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dos Santos-Donado PR, Donado-Pestana CM, Kawahara R, Rosa-Fernandes L, Palmisano G, Finardi-Filho F. Comparative analysis of the protein profile from biofortified cultivars of quality protein maize and conventional maize by gel-based and gel-free proteomic approaches. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Rosa-Fernandes L, Barbosa RH, dos Santos MLB, Angeli CB, Silva TP, Melo RCN, de Oliveira GS, Lemos B, Van Eyk JE, Larsen MR, Cardoso CA, Palmisano G. Cellular Imprinting Proteomics Assay: A Novel Method for Detection of Neural and Ocular Disorders Applied to Congenital Zika Virus Syndrome. J Proteome Res 2020; 19:4496-4515. [PMID: 32686424 PMCID: PMC7640952 DOI: 10.1021/acs.jproteome.0c00320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Indexed: 12/24/2022]
Abstract
Congenital Zika syndrome was first described due to increased incidence of congenital abnormalities associated with Zika virus (ZIKV) infection. Since the eye develops as part of the embryo central nervous system (CNS) structure, it becomes a specialized compartment able to display symptoms of neurodegenerative diseases and has been proposed as a noninvasive approach to the early diagnosis of neurological diseases. Ocular lesions result from defects that occurred during embryogenesis and can become apparent in newborns exposed to ZIKV. Furthermore, the absence of microcephaly cannot exclude the occurrence of ocular lesions and other CNS manifestations. Considering the need for surveillance of newborns and infants with possible congenital exposure, we developed a method termed cellular imprinting proteomic assay (CImPA) to evaluate the ocular surface proteome specific to infants exposed to ZIKV during gestation compared to nonexposure. CImPA combines surface cells and fluid capture using membrane disks and a large-scale quantitative proteomics approach, which allowed the first-time report of molecular alterations such as neutrophil degranulation, cell death signaling, ocular and neurological pathways, which are associated with ZIKV infection with and without the development of congenital Zika syndrome, CZS. Particularly, infants exposed to ZIKV during gestation and without early clinical symptoms could be detected using the CImPA method. Lastly, this methodology has broad applicability as it could be translated in the study of several neurological diseases to identify novel diagnostic biomarkers. Data are available via ProteomeXchange with identifier PXD014038.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense, Denmark
| | - Raquel Hora Barbosa
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
- Molecular
and Integrative Physiological Sciences Program, Department of Environmental
Health, Harvard School of Public Health, Boston, Massachusetts, United States
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
- Genetics
Program, National Cancer Institute, Rio de Janeiro, Brazil
| | - Maria Luiza B. dos Santos
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
| | - Claudia B. Angeli
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Thiago P. Silva
- Laboratory
of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Rossana C. N. Melo
- Laboratory
of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Gilberto Santos de Oliveira
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Bernardo Lemos
- Molecular
and Integrative Physiological Sciences Program, Department of Environmental
Health, Harvard School of Public Health, Boston, Massachusetts, United States
| | - Jennifer E Van Eyk
- Advanced
Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker
Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Martin R. Larsen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense, Denmark
| | - Claudete Araújo Cardoso
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
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26
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Macedo-da-Silva J, Marinho CRF, Palmisano G, Rosa-Fernandes L. Lights and Shadows of TORCH Infection Proteomics. Genes (Basel) 2020; 11:E894. [PMID: 32764347 PMCID: PMC7464470 DOI: 10.3390/genes11080894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/25/2022] Open
Abstract
Congenital abnormalities cause serious fetal consequences. The term TORCH is used to designate the most common perinatal infections, where: (T) refers to toxoplasmosis, (O) means "others" and includes syphilis, varicella-zoster, parvovirus B19, zika virus (ZIKV), and malaria among others, (R) refers to rubella, (C) relates to cytomegalovirus infection, and (H) to herpes simplex virus infections. Among the main abnormalities identified in neonates exposed to congenital infections are central nervous system (CNS) damage, microcephaly, hearing loss, and ophthalmological impairment, all requiring regular follow-up to monitor its progression. Protein changes such as mutations, post-translational modifications, abundance, structure, and function may indicate a pathological condition before the onset of the first symptoms, allowing early diagnosis and understanding of a particular disease or infection. The term "proteomics" is defined as the science that studies the proteome, which consists of the total protein content of a cell, tissue or organism in a given space and time, including post-translational modifications (PTMs) and interactions between proteins. Currently, quantitative bottom-up proteomic strategies allow rapid and high throughput characterization of complex biological mixtures. Investigating proteome modulation during host-pathogen interaction helps in elucidating the mechanisms of infection and in predicting disease progression. This "molecular battle" between host and pathogen is a key to identify drug targets and diagnostic markers. Here, we conducted a survey on proteomic techniques applied to congenital diseases classified in the terminology "TORCH", including toxoplasmosis, ZIKV, malaria, syphilis, human immunodeficiency virus (HIV), herpes simplex virus (HSV) and human cytomegalovirus (HCVM). We have highlighted proteins and/or protein complexes actively involved in the infection. Most of the proteomic studies reported have been performed in cell line models, and the evaluation of tissues (brain, muscle, and placenta) and biofluids (plasma, serum and urine) in animal models is still underexplored. Moreover, there are a plethora of studies focusing on the pathogen or the host without considering the triad mother-fetus-pathogen as a dynamic and interconnected system.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Livia Rosa-Fernandes
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
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27
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Fonseca LD, Eler JP, Pereira MA, Rosa AF, Alexandre PA, Moncau CT, Salvato F, Rosa-Fernandes L, Palmisano G, Ferraz JBS, Fukumasu H. Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle. Sci Rep 2019; 9:5364. [PMID: 30926873 PMCID: PMC6441086 DOI: 10.1038/s41598-019-41813-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.
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Affiliation(s)
- Leydiana D Fonseca
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Joanir P Eler
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Mikaele A Pereira
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Alessandra F Rosa
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Pâmela A Alexandre
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Cristina T Moncau
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Fernanda Salvato
- Institute of Biology, State University of Campinas, Campinas, 13083-862, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - José B S Ferraz
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil.
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Rosa-Fernandes L, Cugola FR, Russo FB, Kawahara R, de Melo Freire CC, Leite PEC, Bassi Stern AC, Angeli CB, de Oliveira DBL, Melo SR, Zanotto PMDA, Durigon EL, Larsen MR, Beltrão-Braga PCB, Palmisano G. Zika Virus Impairs Neurogenesis and Synaptogenesis Pathways in Human Neural Stem Cells and Neurons. Front Cell Neurosci 2019; 13:64. [PMID: 30949028 PMCID: PMC6436085 DOI: 10.3389/fncel.2019.00064] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/11/2019] [Indexed: 11/21/2022] Open
Abstract
Growing evidences have associated Zika virus (ZIKV) infection with congenital malformations, including microcephaly. Nonetheless, signaling mechanisms that promote the disease outcome are far from being understood, affecting the development of suitable therapeutics. In this study, we applied shotgun mass spectrometry (MS)-based proteomics combined with cell biology approaches to characterize altered molecular pathways on human neuroprogenitor cells (NPC) and neurons derived from induced pluripotent stem cells infected by ZIKV-BR strain, obtained from the 2015 Brazilian outbreak. Furthermore, ZIKV-BR infected NPCs showed unique alteration of pathways involved in neurological diseases, cell death, survival and embryonic development compared to ZIKV-AF, showing a human adaptation of the Brazilian viral strain. Besides, infected neurons differentiated from NPC presented an impairment of neurogenesis and synaptogenesis processes. Taken together, these data explain that CNS developmental arrest observed in Congenital Zika Syndrome is beyond neuronal cell death.
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Affiliation(s)
- Livia Rosa-Fernandes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Fernanda Rodrigues Cugola
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Fabiele Baldino Russo
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Rebeca Kawahara
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Paulo Emílio Corrêa Leite
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Carolina Bassi Stern
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Claudia Blanes Angeli
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Stella Rezende Melo
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Cristina Baleeiro Beltrão-Braga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
- School of Arts Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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29
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Kawahara R, Rosa-Fernandes L, Dos Santos AF, Bandeira CL, Dombrowski JG, Souza RM, Da Fonseca MP, Festuccia WT, Labriola L, Larsen MR, Marinho CRF, Palmisano G. Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria. Mol Cell Proteomics 2019; 18:182-199. [PMID: 30242111 PMCID: PMC6356084 DOI: 10.1074/mcp.ra118.000907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/15/2018] [Indexed: 12/27/2022] Open
Abstract
Malaria in pregnancy is a public health concern in malaria-endemic areas. Accumulation of maternal immune cells in the placenta and increased levels of inflammatory cytokines caused by sequestration of Plasmodium falciparum-infected erythrocytes have been associated to poor neonatal outcomes, including low birth weight because of fetal growth restriction. Little is known about the molecular changes occurring in a P. falciparum-infected placenta that has developed placental malaria during pregnancy but had the parasites cleared by pharmacological treatment (past infection). We conducted an integrated proteome, phosphoproteome and glycoproteome analysis in past P. falciparum-infected placentas aiming to find molecular changes associated with placental malaria. A total of 2946 proteins, 1733 N-linked glycosites and 4100 phosphosites were identified and quantified in this study, disclosing overrepresented processes related to oxidative stress, protein folding and regulation of apoptosis in past-infected placentas Moreover, AKT and ERK signaling pathways activation, together with clinical data, were further correlated to an increased apoptosis in past-infected placentas. This study showed apoptosis-related mechanisms associated with placental malaria that can be further explored as therapeutic target against adverse pregnancy outcomes.
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Affiliation(s)
- Rebeca Kawahara
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Biochemistry and Molecular biology, University of Southern Denmark, Odense, Denmark
| | | | - Carla Letícia Bandeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Rodrigo M Souza
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - William T Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Leticia Labriola
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular biology, University of Southern Denmark, Odense, Denmark
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil;.
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil;.
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30
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Carregari VC, Rosa-Fernandes L, Baldasso P, Bydlowski SP, Marangoni S, Larsen MR, Palmisano G. Author Correction: Snake Venom Extracellular vesicles (SVEVs) reveal wide molecular and functional proteome diversity. Sci Rep 2018; 8:15908. [PMID: 30349050 PMCID: PMC6198013 DOI: 10.1038/s41598-018-33284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Victor Corassolla Carregari
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil.,GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paulo Baldasso
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Sergio Paulo Bydlowski
- Laboratory of Genetics and Molecular Hematology (LIM31), University of São Paulo Medical School (FMUSP), São Paulo, Brazil
| | - Sergio Marangoni
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.
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31
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Kawahara R, Ortega F, Rosa-Fernandes L, Guimarães V, Quina D, Nahas W, Schwämmle V, Srougi M, Leite KRM, Thaysen-Andersen M, Larsen MR, Palmisano G. Distinct urinary glycoprotein signatures in prostate cancer patients. Oncotarget 2018; 9:33077-33097. [PMID: 30237853 PMCID: PMC6145689 DOI: 10.18632/oncotarget.26005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Novel biomarkers are needed to complement prostate specific antigen (PSA) in prostate cancer (PCa) diagnostic screening programs. Glycoproteins represent a hitherto largely untapped resource with a great potential as specific and sensitive tumor biomarkers due to their abundance in bodily fluids and their dynamic and cancer-associated glycosylation. However, quantitative glycoproteomics strategies to detect potential glycoprotein cancer markers from complex biospecimen are only just emerging. Here, we describe a glycoproteomics strategy for deep quantitative mapping of N- and O-glycoproteins in urine with a view to investigate the diagnostic value of the glycoproteome to discriminate PCa from benign prostatic hyperplasia (BPH), two conditions that remain difficult to clinically stratify. Total protein extracts were obtained, concentrated and digested from urine of six PCa patients (Gleason score 7) and six BPH patients. The resulting peptide mixtures were TMT-labeled and mixed prior to a multi-faceted sample processing including hydrophilic interaction liquid chromatography (HILIC) and titanium dioxide SPE based enrichment, endo-/exoglycosidase treatment and HILIC-HPLC pre-fractionation. The isolated N- and O-glycopeptides were detected and quantified using high resolution mass spectrometry. We accurately quantified 729 N-glycoproteins spanning 1,310 unique N-glycosylation sites and observed 954 and 965 unique intact N- and O-glycopeptides, respectively, across the two disease conditions. Importantly, a panel of 56 intact N-glycopeptides perfectly discriminated PCa and BPH (ROC: AUC = 1). This study has generated a panel of intact glycopeptides that has a potential for PCa detection.
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Affiliation(s)
- Rebeca Kawahara
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Fabio Ortega
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Vanessa Guimarães
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Daniel Quina
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Willian Nahas
- Instituto do Câncer do Estado de São Paulo, ICESP, São Paulo, Brazil
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | - Katia R M Leite
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, LIM55, São Paulo, Brazil
| | | | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, USP, São Paulo, Brazil
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32
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Carregari VC, Rosa-Fernandes L, Baldasso P, Bydlowski SP, Marangoni S, Larsen MR, Palmisano G. Snake Venom Extracellular vesicles (SVEVs) reveal wide molecular and functional proteome diversity. Sci Rep 2018; 8:12067. [PMID: 30104604 PMCID: PMC6089973 DOI: 10.1038/s41598-018-30578-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Proteins constitute almost 95% of snake venom's dry weight and are produced and released by venom glands in a solubilized form during a snake bite. These proteins are responsible for inducing several pharmacological effects aiming to immobilize and initiate the pre-digestion of the prey. This study shows that proteins can be secreted and confined in snake venom extracellular vesicles (SVEVs) presenting a size distribution between 50 nm and 500 nm. SVEVs isolated from lyophilized venoms collected from four different species of snakes (Agkistrodon contortrix contortrix, Crotalus atrox, Crotalus viridis and Crotalus cerberus oreganus) were analyzed by mass spectrometry-based proteomic, which allowed the identification of proteins belonging to eight main functional protein classes such as SVMPs, serine proteinases, PLA2, LAAO, 5'nucleotidase, C-type lectin, CRISP and Disintegrin. Biochemical assays indicated that SVEVs are functionally active, showing high metalloproteinase and fibrinogenolytic activity besides being cytotoxic against HUVEC cells. Overall, this study comprehensively depicts the protein composition of SVEVs for the first time. In addition, the molecular function of some of the described proteins suggests a central role for SVEVs in the cytotoxicity of the snake venom and sheds new light in the envenomation process.
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Affiliation(s)
- Victor Corassolla Carregari
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil.,GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paulo Baldasso
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Sergio Paulo Bydlowski
- Laboratory of Genetics and Molecular Hematology (LIM31), University of São Paulo Medical School (FMUSP), São Paulo, Brazil
| | - Sergio Marangoni
- Department of Biochemistry, Institute of Biology (IB), Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.
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33
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Freire CCDM, Palmisano G, Braconi CT, Cugola FR, Russo FB, Beltrão-Braga PC, Iamarino A, Lima Neto DFD, Sall AA, Rosa-Fernandes L, Larsen MR, Zanotto PMDA. NS1 codon usage adaptation to humans in pandemic Zika virus. Mem Inst Oswaldo Cruz 2018; 113:e170385. [PMID: 29768530 PMCID: PMC5942634 DOI: 10.1590/0074-02760170385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/20/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Zika virus (ZIKV) was recognised as a zoonotic pathogen in Africa and southeastern Asia. Human infections were infrequently reported until 2007, when the first known epidemic occurred in Micronesia. After 2013, the Asian lineage of ZIKV spread along the Pacific Islands and Americas, causing severe outbreaks with millions of human infections. The recent human infections of ZIKV were also associated with severe complications, such as an increase in cases of Guillain-Barre syndrome and the emergence of congenital Zika syndrome. OBJECTIVES To better understand the recent and rapid expansion of ZIKV, as well as the presentation of novel complications, we compared the genetic differences between the African sylvatic lineage and the Asian epidemic lineage that caused the recent massive outbreaks. FINDINGS The epidemic lineages have significant codon adaptation in NS1 gene to translate these proteins in human and Aedes aegypti mosquito cells compared to the African zoonotic lineage. Accordingly, a Brazilian epidemic isolate (ZBR) produced more NS1 protein than the MR766 African lineage (ZAF) did, as indicated by proteomic data from infections of neuron progenitor cells-derived neurospheres. Although ZBR replicated more efficiently in these cells, the differences observed in the stoichiometry of ZIKV proteins were not exclusively explained by the differences in viral replication between the lineages. MAIN CONCLUSIONS Our findings suggest that natural, silent translational selection in the second half of 20th century could have improved the fitness of Asian ZIKV lineage in human and mosquito cells.
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Affiliation(s)
| | - Giuseppe Palmisano
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Parasitologia, São Paulo, SP, Brasil
| | - Carla T Braconi
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brasil
| | - Fernanda R Cugola
- Universidade de São Paulo, Laboratório de Células-Tronco, Departamento de Cirurgia, São Paulo, SP, Brasil
| | - Fabiele B Russo
- Universidade de São Paulo, Laboratório de Células-Tronco, Departamento de Cirurgia, São Paulo, SP, Brasil
| | - Patricia Cb Beltrão-Braga
- Universidade de São Paulo, Laboratório de Células-Tronco, Departamento de Cirurgia, São Paulo, SP, Brasil.,Universidade de São Paulo, Escola de Artes, Ciências e Humanidades, Departamento de Obstetrícia, São Paulo, SP, Brasil
| | - Atila Iamarino
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brasil
| | - Daniel Ferreira de Lima Neto
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brasil
| | | | - Livia Rosa-Fernandes
- University of Southern Denmark, Department of Biochemistry and Molecular Biology, Odense, Denmark
| | - Martin R Larsen
- University of Southern Denmark, Department of Biochemistry and Molecular Biology, Odense, Denmark
| | - Paolo Marinho de Andrade Zanotto
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brasil
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34
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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35
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Kawahara R, Ortega F, Rosa-Fernandes L, Guimaraes V, Leite K, Nahas W, Srougi M, Larsen M, Palmisano G. MP87-03 URINARY MMP-9 AS CANDIDATE FOR A NON-INVASIVE PROSTATE CANCER BIOMARKER REVEALED BY QUANTITATIVE PROTEOMICS ANALYSIS. J Urol 2017. [DOI: 10.1016/j.juro.2017.02.2707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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