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Open AccessArticle

Epitope Prediction Assays Combined with Validation Assays Strongly Narrows down Putative Cytotoxic T Lymphocyte Epitopes

1
Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, HPC EB88, 9700 RB Groningen, The Netherlands
2
Department of Gynecological Oncology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, HPC EB88, 9700 RB Groningen, The Netherlands
*
Author to whom correspondence should be addressed.
Academic Editor: Mary Lenora (Nora) Disis
Vaccines 2015, 3(2), 203-220; https://doi.org/10.3390/vaccines3020203
Received: 20 January 2015 / Accepted: 16 March 2015 / Published: 24 March 2015
(This article belongs to the Special Issue Cancer Vaccines)
Tumor vaccine design requires prediction and validation of immunogenic MHC class I epitopes expressed by target cells as well as MHC class II epitopes expressed by antigen-presenting cells essential for the induction of optimal immune responses. Epitope prediction methods are based on different algorithms and are instrumental for a first screening of possible epitopes. However, their results do not reflect a one-to-one correlation with experimental data. We combined several in silico prediction methods to unravel the most promising C57BL/6 mouse-restricted Hepatitis C virus (HCV) MHC class I epitopes and validated these epitopes in vitro and in vivo. Cytotoxic T lymphocyte (CTL) epitopes within the HCV non-structural proteins were identified, and proteasomal cleavage sites and helper T cell (Th) epitopes at close proximity to these CTL epitopes were analyzed using multiple prediction algorithms. This combined in silico analysis enhances the precision of identification of functional HCV-specific CTL epitopes. This approach will be applicable to the design of human vaccines not only for HCV, but also for other antigens in which T-cell responses play a crucial role. View Full-Text
Keywords: HCV; CTL epitopes; Th epitopes; therapeutic vaccine HCV; CTL epitopes; Th epitopes; therapeutic vaccine
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Ip, P.P.; Nijman, H.W.; Daemen, T. Epitope Prediction Assays Combined with Validation Assays Strongly Narrows down Putative Cytotoxic T Lymphocyte Epitopes. Vaccines 2015, 3, 203-220.

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