Characterization of HIV-Specific CD4+ T Cell Responses against Peptides Selected with Broad Population and Pathogen Coverage

CD4+ T cells orchestrate immunity against viral infections, but their importance in HIV infection remains controversial. Nevertheless, comprehensive studies have associated increase in breadth and functional characteristics of HIV-specific CD4+ T cells with decreased viral load. A major challenge for the identification of HIV-specific CD4+ T cells targeting broadly reactive epitopes in populations with diverse ethnic background stems from the vast genomic variation of HIV and the diversity of the host cellular immune system. Here, we describe a novel epitope selection strategy, PopCover, that aims to resolve this challenge, and identify a set of potential HLA class II-restricted HIV epitopes that in concert will provide optimal viral and host coverage. Using this selection strategy, we identified 64 putative epitopes (peptides) located in the Gag, Nef, Env, Pol and Tat protein regions of HIV. In total, 73% of the predicted peptides were found to induce HIV-specific CD4+ T cell responses. The Gag and Nef peptides induced most responses. The vast majority of the peptides (93%) had predicted restriction to the patient’s HLA alleles. Interestingly, the viral load in viremic patients was inversely correlated to the number of targeted Gag peptides. In addition, the predicted Gag peptides were found to induce broader polyfunctional CD4+ T cell responses compared to the commonly used Gag-p55 peptide pool. These results demonstrate the power of the PopCover method for the identification of broadly recognized HLA class II-restricted epitopes. All together, selection strategies, such as PopCover, might with success be used for the evaluation of antigen-specific CD4+ T cell responses and design of future vaccines.

CD4+ T细胞（CD4+ T cells）是介导抗病毒免疫的核心调控细胞，但其在HIV感染中的功能地位仍存争议。尽管如此，多项系统性研究已证实，HIV特异性CD4+ T细胞的表位广度与功能特性的提升，与患者体内病毒载量降低显著相关。针对不同种族背景人群中鉴定靶向广谱表位的HIV特异性CD4+ T细胞所面临的核心挑战，源于HIV庞大的基因组变异与宿主细胞免疫系统的多样性。本研究报道了一种全新的表位筛选策略PopCover，旨在破解上述难题，并筛选出一组潜在的人类白细胞抗原（HLA）II类限制性HIV表位，该表位集合可协同实现最优的病毒与宿主覆盖范围。利用该筛选策略，我们在HIV的Gag、Nef、Env、Pol及Tat蛋白区域中，共鉴定出64个推定表位（肽段）。经实验验证，总计73%的预测肽段可诱导HIV特异性CD4+ T细胞应答。其中，Gag与Nef肽段诱导的应答最为显著。绝大多数肽段（93%）被预测可匹配患者的HLA等位基因并发挥限制性作用。有趣的是，病毒血症患者的病毒载量与靶向Gag肽段的数量呈负相关关系。此外，相较于当前通用的Gag-p55肽段库，预测的Gag肽段可诱导更为广泛的多功能CD4+ T细胞应答。上述结果证实了PopCover方法在鉴定广谱识别的HLA II类限制性表位方面的应用价值。综上，诸如PopCover这类表位筛选策略，有望成功应用于抗原特异性CD4+ T细胞应答的评估，以及未来疫苗的设计开发。