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Computational and Experimental Approaches to Predict Host-Parasite Protein-Protein Interactions. Methods Mol Biol 2018; 1819:153-173. [PMID: 30421403 DOI: 10.1007/978-1-4939-8618-7_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In host-parasite systems, protein-protein interactions are key to allow the pathogen to enter the host and persist within the host. The study of host-parasite molecular communication improves the understanding the mechanisms of infection, evasion of the host immune system and tropism across different tissues. Current trends in parasitology focus on unraveling host-parasite protein-protein interactions to aid the development of new strategies to combat pathogenic parasites with better treatments and prevention mechanisms. Due to the complexity of capturing experimentally these interactions, computational approaches integrating data from different sources (mainly "omics" data) become key to complement or support experimental approaches. Here, we focus on the application of experimental and computational methods in the prediction of host-parasite interactions and highlight the potential of each of these methods in specific contexts.
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Su KY, Watanabe A, Yeh CH, Kelsoe G, Kuraoka M. Efficient Culture of Human Naive and Memory B Cells for Use as APCs. THE JOURNAL OF IMMUNOLOGY 2016; 197:4163-4176. [PMID: 27815447 DOI: 10.4049/jimmunol.1502193] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 08/30/2016] [Indexed: 12/27/2022]
Abstract
The ability to culture and expand B cells in vitro has become a useful tool for studying human immunity. A limitation of current methods for human B cell culture is the capacity to support mature B cell proliferation. We developed a culture method to support the efficient activation and proliferation of naive and memory human B cells. This culture supports extensive B cell proliferation, with ∼103-fold increases following 8 d in culture and 106-fold increases when cultures are split and cultured for 8 more days. In culture, a significant fraction of naive B cells undergo isotype switching and differentiate into plasmacytes. Culture-derived (CD) B cells are readily cryopreserved and, when recovered, retain their ability to proliferate and differentiate. Significantly, proliferating CD B cells express high levels of MHC class II, CD80, and CD86. CD B cells act as APCs and present alloantigens and microbial Ags to T cells. We are able to activate and expand Ag-specific memory B cells; these cultured cells are highly effective in presenting Ag to T cells. We characterized the TCR repertoire of rare Ag-specific CD4+ T cells that proliferated in response to tetanus toxoid (TT) presented by autologous CD B cells. TCR Vβ usage by TT-activated CD4+ T cells differs from resting and unspecifically activated CD4+ T cells. Moreover, we found that TT-specific TCR Vβ usage by CD4+ T cells was substantially different between donors. This culture method provides a platform for studying the BCR and TCR repertoires within a single individual.
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Affiliation(s)
- Kuei-Ying Su
- Department of Immunology, Duke University, Durham, NC 27710.,Tzu Chi Medical Center, Hualien 970, Taiwan; and
| | - Akiko Watanabe
- Department of Immunology, Duke University, Durham, NC 27710
| | - Chen-Hao Yeh
- Department of Immunology, Duke University, Durham, NC 27710
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710; .,Human Vaccine Institute, Duke University, Durham, NC 27710
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de Assis RR, Ludolf F, Nakajima R, Jasinskas A, Oliveira GC, Felgner PL, Gaze ST, Loukas A, LoVerde PT, Bethony JM, Correa-Oliveira R, Calzavara-Silva CE. A next-generation proteome array for Schistosoma mansoni. Int J Parasitol 2016; 46:411-5. [PMID: 27131510 DOI: 10.1016/j.ijpara.2016.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/09/2016] [Accepted: 04/09/2016] [Indexed: 02/06/2023]
Abstract
A proteome microarray consisting of 992 Schistosoma mansoni proteins was produced and screened with sera to determine antibody signatures indicative of the clinical stages of schistosomiasis and the identification of subunit vaccine candidates. Herein, we describe the methods used to derive the gene list for this array (representing approximately 10% of the predicted S. mansoni proteome). We also probed a pilot version of the microarray with sera from individuals either acutely or chronically infected with S. mansoni from endemic areas in Brazil and sera from individuals resident outside the endemic area (USA) to determine if the array is functional and informative.
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Affiliation(s)
- Rafael Ramiro de Assis
- Laboratório de Imunologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil; Protein Microarray Laboratory, Division of Infectious Disease, School of Medicine, University of California, Irvine, CA, USA
| | - Fernanda Ludolf
- Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rie Nakajima
- Protein Microarray Laboratory, Division of Infectious Disease, School of Medicine, University of California, Irvine, CA, USA
| | - Al Jasinskas
- Protein Microarray Laboratory, Division of Infectious Disease, School of Medicine, University of California, Irvine, CA, USA
| | | | - Philip L Felgner
- Protein Microarray Laboratory, Division of Infectious Disease, School of Medicine, University of California, Irvine, CA, USA
| | - Soraya T Gaze
- Laboratório de Imunologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Alex Loukas
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Philip T LoVerde
- Departments of Biochemistry and Pathology, School of Medicine, University of Texas Health Science Center, 7703 Floyd Curl Dr., San Antonio, TX 78229, USA
| | - Jeffrey M Bethony
- Laboratório de Imunologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil; Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Science, The George Washington University, Washington, DC, USA.
| | - Rodrigo Correa-Oliveira
- Laboratório de Imunologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Carlos E Calzavara-Silva
- Laboratório de Imunologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil; Protein Microarray Laboratory, Division of Infectious Disease, School of Medicine, University of California, Irvine, CA, USA
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Major histocompatibility complex linked databases and prediction tools for designing vaccines. Hum Immunol 2015; 77:295-306. [PMID: 26585361 DOI: 10.1016/j.humimm.2015.11.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/29/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022]
Abstract
Presently, the major histocompatibility complex (MHC) is receiving considerable interest owing to its remarkable role in antigen presentation and vaccine design. The specific databases and prediction approaches related to MHC sequences, structures and binding/nonbinding peptides have been aggressively developed in the past two decades with their own benchmarks and standards. Before using these databases and prediction tools, it is important to analyze why and how the tools are constructed along with their strengths and limitations. The current review presents insights into web-based immunological bioinformatics resources that include searchable databases of MHC sequences, epitopes and prediction tools that are linked to MHC based vaccine design, including population coverage analysis. In T cell epitope forecasts, MHC class I binding predictions are very accurate for most of the identified MHC alleles. However, these predictions could be further improved by integrating proteasome cleavage (in conjugation with transporter associated with antigen processing (TAP) binding) prediction, as well as T cell receptor binding prediction. On the other hand, MHC class II restricted epitope predictions display relatively low accuracy compared to MHC class I. To date, pan-specific tools have been developed, which not only deliver significantly improved predictions in terms of accuracy, but also in terms of the coverage of MHC alleles and supertypes. In addition, structural modeling and simulation systems for peptide-MHC complexes enable the molecular-level investigation of immune processes. Finally, epitope prediction tools, and their assessments and guidelines, have been presented to immunologist for the design of novel vaccine and diagnostics.
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