Identification of novel CD4 and CD8 T cell epitopes for targeting in HIV-1 vaccine design

关键词：蛋白质组学、免疫学、病毒学。开发疫苗来对抗人类免疫缺陷病毒1型(HIV-1)的感染是具有挑战性的，因为这种病毒拥有多种免疫逃避策略，使其能够在所有发生系统性感染的人身上持续存在。因此，需要新的、合理设计的疫苗策略来引起比感染期间自然诱导的反应更有效的反应。预防HIV-1疫苗开发的两种互补方法包括诱导广谱中和抗体(BNab)反应以阻断感染的建立，以及诱导CD8T细胞反应以在感染后早期根除病毒并防止长期持续感染。CD8 T细胞疫苗对慢性感染HIV-1的患者也有潜在的治疗作用。对与HIV-1感染者病毒血症的良好控制相关的CD8 T细胞反应特征的分析表明，靶向于感染细胞上快速呈现的Gag衍生表位(在主要组织相容性复合体(MHC)下调之前)；以及靶向保守的病毒序列中的表位，其中逃逸导致病毒适应的高成本，以及诱导对广泛表位的共显性反应以最大限度地减少病毒突变逃逸，是有益的(McMichael et al，2010)。同样，临床前模型中显示的唯一能够使约50%的接种动物在病毒攻击后根除感染的T细胞诱导疫苗被发现诱导了大量的CD8 T细胞反应，这些T细胞反应异常地受到非经典I类分子MHC-E和MHC II类分子限制的靶表位，这些表位在感染细胞上不受下调(Hansen等人，2013,2016)。最近质谱学(MS)技术的进步现在使得基于MS的方法能够应用于询问细胞系或原代细胞中MHC结合的免疫表位(Croft et al，2015)。使用这项技术评估HIV感染的原代CD4T细胞上MHC I类呈现的多肽，我们最近不仅发现了来自传统病毒开放阅读框架和隐蔽表位的多肽(Ternette等人，2016)，而且发现了来自HIV-1 5‘前导序列的新多肽，以前人们认为它没有翻译(未发表的数据)。该项目的第一个目标将是扩展这项工作，目标一是识别HIV感染细胞上呈现的翻译后修饰的HIV-1多肽；3.鉴定感染艾滋病毒细胞后迅速出现的病毒多肽；比较HIV感染细胞和未感染细胞上的自体多肽，以深入了解T细胞或自然杀伤(NK)细胞可识别的自体配体；以及使用体外HIV潜伏期模型来评估潜伏感染细胞上呈现的HIV和自体多肽的谱系。后续研究将讨论在HIV感染期间是否会对由女士识别的新表位引发T细胞反应，识别新表位的T细胞株/克隆也将被产生，并在生产性和潜伏性HIV感染的体外模型中评估其抗病毒效果，以深入了解针对这些表位在HIV CD8 T细胞疫苗设计中的作用。

Keywords: Proteomics, Immunology, Virology.Development of vaccines to combat infection with human immunodeficiency virus type 1 (HIV-1) is challenging, as the virus possesses multiple immune evasion strategies that enable it to persist in all individuals who develop systemic infection. Novel, rationally-designed vaccine strategies are thus required to elicit responses that are more efficacious than those naturally induced during infection. Two complementary approaches for prophylactic HIV-1 vaccine development entail induction of broadly-neutralising antibody (bnAb) responses to block the establishment of infection, and induction of CD8 T cell responses to eradicate virus early after infection and prevent long-term persistent infection. CD8 T cell-based vaccines also have potential therapeutic utility in individuals chronically infected with HIV-1.Analysis of features of CD8 T cell responses associated with good control of viremia in HIV-1-infected individuals suggests that targeting of Gag-derived epitopes that are rapidly presented on infected cells (prior to major histocompatibility complex (MHC) downregulation); and targeting of epitopes in conserved viral sequences where escape incurs high costs to virus fitness, together with induction of co-dominant responses to a breadth of epitopes to minimise viral mutational escape, are beneficial (reviewed by McMichael et al, 2010). Similarly the only T cell-inducing vaccine shown in preclinical models to enable ~50% of vaccinated animals to eradicate infection following virus challenge was found to have induced a tremendous breadth of CD8 T cell responses that, unusually, targeted epitopes restricted by the non-classical class I molecule MHC-E and by MHC class II, which are not down-regulated on infected cells (Hansen et al, 2013, 2016).Recent advances in mass spectrometry (MS) technology now enable application of MS-based approaches for interrogation of the MHC-bound immunopeptidome of cell lines or primary cells (Croft et al, 2015). Using this technique to assess the repertoire of peptides presented with MHC class I on HIV-infected primary CD4 T cells, we recently identified not only peptides derived from the conventional viral open reading frames and cryptic epitopes (Ternette et al, 2016), but also novel peptides derived from the HIV-1 5' leader sequence, which was previously not thought to be translated (unpublished data). The first aim of this project will be to extend this work, aiming i. to identify post-translationally-modified HIV-1 peptides presented on HIV-infected cells; ii. to identify viral peptides presented very rapidly following infection of cells with HIV; iii. to compare the repertoire of self peptides presented on HIV-infected and uninfected cells to gain insight into self ligands available for recognition by T or natural killer (NK) cells; and iv. to use an in vitro HIV latency model to assess the repertoire of HIV and self peptides presented on latently infected cells. Follow-on studies will address whether T cell responses are elicited during HIV infection to novel epitopes identified by MS. T cell lines/clones that recognise novel epitopes will also be generated and their antiviral efficacy evaluated in in vitro models of productive and latent HIV infection to give insight into the utility of targeting these epitopes in HIV CD8 T cell vaccine design.