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首页> 外文期刊>Immunology: An Official Journal of the British Society for Immunology >Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments.
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Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments.

机译：实验精细映射与HIV-1表位的计算机模拟预测结果的比较表明，仍需要进行制图实验。

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摘要

Methods for identifying physiologically relevant CD8 T-cell epitopes are critically important not only for the development of T-cell-based vaccines but also for understanding host-pathogen interactions. As experimentally mapping an optimal CD8 T-cell epitope is a tedious procedure, many bioinformatic tools have been developed that predict which peptides bind to a given MHC molecule. We assessed the ability of the CD8 T-cell epitope prediction tools syfpeithi, ctlpred and iedb to foretell nine experimentally mapped optimal HIV-specific epitopes. Randomly - for any of the subjects' HLA type and with any matching score - the optimal epitope was predicted in seven of nine epitopes using syfpeithi, in three of nine epitopes using ctlpred and in all nine of nine epitopes using iedb. The optimal epitope within the three highest ranks was given in four of nine epitopes applying syfpeithi, in two of nine epitopes applying ctlpred and in seven of nine epitopes applying iedb when screening for all of the subjects' HLA types. Knowing the HLA restriction of the peptide of interest improved the ranking of the optimal epitope within the predicted results. Epitopes restricted by common HLA alleles were more likely to be predicted than those restricted by uncommon HLA alleles. Epitopes with aberrant lengths compared with the usual HLA-class I nonamers were most likely not predicted. Application of epitope prediction tools together with literature searches for already described optimal epitopes narrows down the possibilities of optimal epitopes within a screening peptide of interest. However, in our opinion, the actual fine-mapping of a CD8 T-cell epitope cannot yet be replaced.
机译：鉴定生理相关的CD8 T细胞表位的方法不仅对于开发基于T细胞的疫苗，而且对于理解宿主与病原体的相互作用都至关重要。由于实验性地绘制最佳CD8 T细胞表位是一项繁琐的过程，因此已经开发出许多生物信息学工具，这些工具可以预测哪些肽与给定的MHC分子结合。我们评估了CD8 T细胞表位预测工具syfpeithi，ctlpred和iedb预测9种实验性映射的最佳HIV特异性表位的能力。随机-对于任何受试者的HLA类型和任何匹配分数-使用syfpeithi预测了9个表位中的7个，使用ctlpred的9个表位中的3个以及使用iedb预测了9个表位的所有9个中的最佳表位。在筛选所有受试者的HLA类型时，应用syfpeithi的9个表位中的4个，应用ctlpred的9个表位中的2个以及应用iedb的9个表位中的7个给出了三个最高等级中的最佳表位。知道目标肽的HLA限制可改善最佳表位在预测结果中的排名。与受罕见HLA等位基因限制的抗原决定簇相比，受普通HLA等位基因限制的抗原决定簇更有可能被预测。与通常的HLA-I类九聚体相比长度异常的表位最有可能无法预测。表位预测工具的应用以及对已经描述的最佳表位的文献搜索，缩小了目标筛选肽中最佳表位的可能性。然而，在我们看来，CD8 T细胞表位的实际精细映射尚无法替代。

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