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Veras PST, Ramos PIP, de Menezes JPB. In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. Front Cell Infect Microbiol 2018; 8:326. [PMID: 30283744 PMCID: PMC6157484 DOI: 10.3389/fcimb.2018.00326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
Leishmaniasis is a vector-borne, neglected tropical disease with a worldwide distribution that can present in a variety of clinical forms, depending on the parasite species and host genetic background. The pathogenesis of this disease remains far from being elucidated because the involvement of a complex immune response orchestrated by host cells significantly affects the clinical outcome. Among these cells, macrophages are the main host cells, produce cytokines and chemokines, thereby triggering events that contribute to the mediation of the host immune response and, subsequently, to the establishment of infection or, alternatively, disease control. There has been relatively limited commercial interest in developing new pharmaceutical compounds to treat leishmaniasis. Moreover, advances in the understanding of the underlying biology of Leishmania spp. have not translated into the development of effective new chemotherapeutic compounds. As a result, biomarkers as surrogate disease endpoints present several potential advantages to be used in the identification of targets capable of facilitating therapeutic interventions considered to ameliorate disease outcome. More recently, large-scale genomic and proteomic analyses have allowed the identification and characterization of the pathways involved in the infection process in both parasites and the host, and these analyses have been shown to be more effective than studying individual molecules to elucidate disease pathogenesis. RNA-seq and proteomics are large-scale approaches that characterize genes or proteins in a given cell line, tissue, or organism to provide a global and more integrated view of the myriad biological processes that occur within a cell than focusing on an individual gene or protein. Bioinformatics provides us with the means to computationally analyze and integrate the large volumes of data generated by high-throughput sequencing approaches. The integration of genomic expression and proteomic data offers a rich multi-dimensional analysis, despite the inherent technical and statistical challenges. We propose that these types of global analyses facilitate the identification, among a large number of genes and proteins, those that hold potential as biomarkers. The present review focuses on large-scale studies that have identified and evaluated relevant biomarkers in macrophages in response to Leishmania infection.
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Affiliation(s)
- Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil.,National Institute of Tropical Disease, Brasilia, Brazil
| | - Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil
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Islam MT, Mohamedali A, Ahn SB, Nawar I, Baker MS, Ranganathan S. A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes. Methods Mol Biol 2017; 1549:163-176. [PMID: 27975291 DOI: 10.1007/978-1-4939-6740-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data. We present here a simple and intuitive workflow for the research community to investigate and mine this data, not only to extract relevant data but also to segregate usable, quality data to develop hypotheses for investigation and validation. We apply an MS evidence workflow for verifying peptides of proteins from one's own data as well as publicly available databases. We then integrate a suite of freely available bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology and biochemical pathways. We also provide an example of the functional annotation of missing proteins in human chromosome 7 data from the NeXtProt database, where no evidence is available at the proteomic, antibody, or structural levels. We give examples of protocols, tools and detailed flowcharts that can be extended or tailored to interpret and annotate the proteome of any novel organism.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Abidali Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ishmam Nawar
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.
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Neves GWP, Curty NDA, Kubitschek-Barreira PH, Fontaine T, Souza GHMF, Cunha ML, Goldman GH, Beauvais A, Latgé JP, Lopes-Bezerra LM. Modifications to the composition of the hyphal outer layer of Aspergillus fumigatus modulates HUVEC proteins related to inflammatory and stress responses. J Proteomics 2016; 151:83-96. [PMID: 27321585 DOI: 10.1016/j.jprot.2016.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/20/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022]
Abstract
Aspergillus fumigatus, the main etiologic agent causing invasive aspergillosis, can induce an inflammatory response and a prothrombotic phenotype upon contact with human umbilical vein endothelial cells (HUVECs). However, the fungal molecules involved in this endothelial response remain unknown. A. fumigatus hyphae produce an extracellular matrix composed of galactomannan, galactosaminogalactan and α-(1,3)-glucan. In this study, we investigated the consequences of UGM1 gene deletion in A. fumigatus, which produces a mutant with increased galactosaminogalactan production. The ∆ugm1 mutant exhibited an HUVEC-hyperadhesive phenotype and induced increased endothelial TNF-α secretion and tissue factor mRNA overexpression in this "semi-professional" immune host cell. Using a shotgun proteomics approach, we show that the A. fumigatus ∆ugm1 strain can modulate the levels of proteins in important endothelial pathways related to the inflammatory response mediated by TNF-α and to stress response pathways. Furthermore, a purified galactosaminogalactan fraction was also able to induce TNF-α secretion and the coincident HUVEC pathways regulated by the ∆ugm1 mutant, which overexpresses this component, as demonstrated by fluorescence microscopy. This work contributes new data regarding endothelial mechanisms in response to A. fumigatus infection. SIGNIFICANCE Invasive aspergillosis is the main opportunistic fungal infection described in neutropenic hematologic patients. One important clinical aspect of this invasive fungal infection is vascular thrombosis, which could be related, at least in part, to the activation of endothelial cells, as shown in previous reports from our group. It is known that direct contact between the A. fumigatus hyphal cell wall and the HUVEC cell surface is necessary to induce an endothelial prothrombotic phenotype and secretion of pro-inflammatory cytokines, though the cell surface components of this angioinvasive fungus that trigger this endothelial response are unknown. The present work employs a discovery-driven proteomics approach to reveal the role of one important cell wall polysaccharide of A. fumigatus, galactosaminogalactan, in the HUVEC interaction and the consequent mechanisms of endothelial activation. This is the first report of the overall panel of proteins related to the HUVEC response to a specific and purified cell wall component of the angioinvasive fungus A. fumigatus.
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Affiliation(s)
- Gabriela Westerlund Peixoto Neves
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Campus Maracanã, Pavilhão Haroldo Lisboa da Cunha sl 501D, CEP: 20550-013, Rio de Janeiro, RJ, Brazil
| | - Nathália de Andrade Curty
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Campus Maracanã, Pavilhão Haroldo Lisboa da Cunha sl 501D, CEP: 20550-013, Rio de Janeiro, RJ, Brazil
| | - Paula Helena Kubitschek-Barreira
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Campus Maracanã, Pavilhão Haroldo Lisboa da Cunha sl 501D, CEP: 20550-013, Rio de Janeiro, RJ, Brazil
| | - Thierry Fontaine
- Unité des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | | | - Marcel Lyra Cunha
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Campus Maracanã, Pavilhão Haroldo Lisboa da Cunha sl 501D, CEP: 20550-013, Rio de Janeiro, RJ, Brazil
| | - Gustavo H Goldman
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Av. do Cafe S/N, Monte Alegre, CEP:14040-903, Ribeirao Preto, SP, Brazil
| | - Anne Beauvais
- Unité des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Jean-Paul Latgé
- Unité des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Leila M Lopes-Bezerra
- Laboratory of Cellular Mycology and Proteomics, Universidade do Estado do Rio de Janeiro, Campus Maracanã, Pavilhão Haroldo Lisboa da Cunha sl 501D, CEP: 20550-013, Rio de Janeiro, RJ, Brazil.
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Benito-Martin A, Peinado H. FunRich proteomics software analysis, let the fun begin! Proteomics 2015; 15:2555-6. [DOI: 10.1002/pmic.201500260] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/02/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Alberto Benito-Martin
- Children's Cancer and Blood Foundation Laboratories; Department of Pediatrics; Weill Cornell Medical College; New York NY USA
| | - Héctor Peinado
- Children's Cancer and Blood Foundation Laboratories; Department of Pediatrics; Weill Cornell Medical College; New York NY USA
- Microenvironment and Metastasis Laboratory; Department of Molecular Oncology, Spanish National Cancer Research Centre (CNIO); Madrid Spain
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