Immune responses against HIV-induced cell-derived neoepitopes and HIV control

描述（由申请人提供）：目前旨在鉴定保护性细胞毒性T细胞（CTL）应答和设计抗HIV疫苗的策略是基于以下假设：HIV感染期间引发的免疫应答仅针对HIV表位。这些策略的局限性是HIV特异性保护性免疫应答的不确定性以及许多HIV特异性CTL对HIV施加压力导致病毒突变和随后的免疫逃逸的事实。因此，引发HIV特异性CTL应答可能不足以阻断HIV的传播。该提议将具体地测试以下假设：非常规HIV诱导的宿主衍生的新表位在HIV感染的细胞中（但不在健康细胞中）独特地加工和呈递，引发有助于自发HIV免疫控制的CTL应答。这些HIV诱导的宿主衍生抗病毒表位（HDAE）和相应的CTL应答（不受免疫压力影响）的鉴定将在具有弱HIV特异性CTL应答的HIV自发控制者的独特队列中进行。细胞和HIV蛋白通过胞质溶胶中的蛋白酶体和其他肽酶降解成表位或表位前体，然后在内质网中修剪，然后装载到MHC-I上并展示在细胞表面以供CTL识别。基于新的表位加工测定，我们显示了一些HIV表位的优先加工，这一特性依赖于我们用来改变不相关表位产生的基序。我们还确定了一个新的因素参与表位加工效率，即高度可变的最佳HIV表位的细胞内稳定性，也由特定的基序驱动。在HIV感染的细胞中，我们最近发现的抗原加工机制的表达和活性的改变，额外的HIV编码的蛋白酶的存在以及特异性细胞靶标的大量降解沿着，可能改变细胞蛋白的降解模式并产生HDAE。然而，通过细胞肽的全面筛选来鉴定HDAE特异性CTL应答是不可能的。通过与微软研究院的合作，我们将建立一个定制的预测程序，并扫描人类基因组，寻找感染艾滋病毒的原代细胞中产生的抗原肽。通过创新的基于质谱的分析，我们将鉴定在HIV感染的CD 4 T细胞的胞质溶胶中唯一发现的抗原前体。它们的身份将通过计算分析和靶蛋白的体外降解来确认。我们将筛选HIV感染者对HDAE的CTL应答，分离HDAE特异性CTL并评估其抗病毒能力。我们还将评估单核细胞来源的树突状细胞交叉呈递HIV感染的CD 4 T细胞内源性加工的HDAE以刺激CTL的能力，CTL的抗病毒能力将被评估。该提案依赖于跨学科的合作，涉及计算科学，为原代细胞设计的新型生物化学和免疫学测定。确定HDAE将有助于设计新的免疫原，引发CTL反应，将防止艾滋病毒传播。 刺激针对HIV的有效免疫应答的表位的产生和呈递是合理疫苗设计的关键。我们推测，HIV诱导的非常规细胞蛋白质降解导致细胞衍生的新表位的产生，有助于免疫控制。该项目旨在通过创新的生物化学和计算方法鉴定这些HIV诱导的细胞衍生的新表位，并评估细胞毒性T细胞对这些新表位的抗病毒能力。

DESCRIPTION (provided by applicant): Current strategies aiming at identifying protective cytotoxic T cell (CTL) responses and designing vaccines against HIV are based on the assumption that immune responses elicited during HIV infection are only directed against HIV epitopes. The limitations of these strategies are the elusiveness of HIV-specific protective immune responses and the fact that many HIV-specific CTL exert pressure on HIV leading to viral mutations and subsequent immune escape. Thus eliciting HIV-specific CTL responses may not be sufficient to block the transmission of HIV. This proposal will specifically test the hypothesis that unconventional HIV-induced host- derived neoepitopes uniquely processed and presented in HIV-infected cells (but not in healthy cells) elicit CTL responses contributing to spontaneous HIV immune control. The identification of these HIV-induced Host- Derived Antiviral Epitopes (HDAE) and corresponding CTL responses -not subjected to immune pressure- will be performed in a unique cohort of HIV spontaneous controllers with weak HIV-specific CTL responses. Cellular and HIV proteins are degraded into epitopes or epitope precursors by the proteasome and other peptidases in the cytosol and then trimmed in the endoplasmic reticulum before being loaded onto MHC-I and displayed at the cell surface for recognition by CTL. Building on novel epitope processing assays, we showed preferential processing of some HIV epitopes, a property that relies on motifs we used to alter the production of irrelevant epitopes. We also identified a novel factor involved in epitope processing efficiency, namely the highly variable intracellular stability of optimal HIV epitopes, also driven by specific motifs. In HIV-infected cells, the altered expression and activities of the antigen processing machinery that we recently identified, the presence of an additional HIV-encoded protease along with massive degradation of specific cellular targets are likely to alter the degradation pattern of cellular proteins and produce HDAE. Yet it is impossible to identify HDAE-specific CTL responses by a comprehensive screen of cellular peptides. Through a collaboration with Microsoft Research, we will build a customized prediction program and scan the human genome for antigenic peptides produced in HIV-infected primary cells. With an innovative mass spectrometry- based analysis, we will identify antigenic precursors uniquely found in the cytosol of HIV-infected CD4 T cells from HIV controllers. Their identity will be confirmed through computational analysis and in vitro degradation of target proteins. We will screen HIV-infected persons for CTL responses against HDAE, isolate HDAE-specific CTL and assess their antiviral capacity. We will also assess the capacity of monocyte-derived dendritic cells to cross-present HDAE endogenously processed by HIV-infected CD4 T cells, to stimulate CTL whose antiviral capacity will be assessed. This proposal relies on a cross-disciplinary collaboration involving computational science, novel biochemical and immunological assays designed for primary cells. Identifying HDAE will contribute to the design of novel immunogens eliciting CTL responses that will prevent HIV transmission. The production and presentation of epitopes stimulating efficient immune responses against HIV is key to rational vaccine design. We hypothesize that HIV-induced unconventional degradation of cellular proteins leads to the production of cell-derived novel epitopes contributing to immune control. This project seeks to identify these HIV- induced cell-derived neoepitopes through innovative biochemical and computational approaches and to assess the antiviral capacity of cytotoxic T cells against these neoepitopes.