Human immune signatures of Dengue virus and Mycobacterium Tuberculosis exposure in infection, disease and vaccination

我们的应用程序的基本前提是提供公正的，非假设驱动的分析， 与两种重要的人类疾病相关的免疫特征（IMS），即登革病毒（DENV） 和结核分枝杆菌（Mtb）。在本周期，我们成功地完成了既定目标 在最初的提议中提出，并且已经表征了与DENV和Mtb相关的记忆T细胞IMS， 背景：1）天然免疫和/或感染控制，2）活动性和严重疾病，以及3） 获得许可的或实验性疫苗的管理。我们小组已经研究了DENV和Mtb几年了。 由于以下原因：1）它们都是当前的全球健康问题，2）记忆T细胞是 从根本上与这些疾病的保护性免疫有关，3）抗原特异性T细胞应答 在体外检测到足够的数量，使它们可用于“组学”研究，而不需要 体外扩增，4）与自然感染/免疫和严重疾病相关的人体标本 很容易大量获得。重债穷国倡议的研究格式非常适合于完成 拟议的使命。每一个项目和核心过去和现在都严重依赖于 程序.在重债穷国倡议方面，我们能够实现协同作用，受益于规模经济， 将具有不同专业知识的调查人员聚集在一起。 因此，我们开发了一个临界质量，在建议的扩展中得到广泛利用， 关于：1）经验丰富的研究者团队，2）与该领域领导者的临床合作， 3)广泛收集受多种不同HLA I类和II类分子限制的表位， 允许以前所未有的精度分析记忆T细胞，4）与特定T细胞相关的IMS 代表免疫关键参与者的子集，以及5）建立的“组学”测定和分析管道， 生成与DENV和Mtb相关的IMS。 在这个提议的扩展中，我们计划建立在DENV和Mtb中T细胞IMS的定义上。 在当前的5年供资期内，通过扩大以下方面的重要性和维度， 在多个方向上观察，但相关和协同。如上所述，工作 在当前周期中进行的鉴定IMS与自然感染中的特定T细胞亚群相关， 疫苗接种和急性/严重疾病。同样清楚的是，这些T细胞亚群本身 异质的在这里，我们将利用单细胞测序来“向下钻取”并建立特定细胞的IMS。 导致这种异质性的细胞类型。第二个维度将通过考虑额外的 细胞亚群对于DENV，这将通过测定整个未分级PBMC的IMS来实现。 由DENV记忆T细胞识别的表位刺激。对于结核病，我们将把重点扩大到 非常规的CD 4-CD 8-双阴性T细胞，我们发现它们对细菌感染有反应。 裂解物而不是常规的肽表位。

The fundamental premise of our application is to provide unbiased, non-hypothesis driven analyses of immune signatures (IMS) associated with two important human diseases, namely dengue virus (DENV) and Mycobacterium tuberculosis (Mtb). In the current cycle, we successfully accomplished the goals set forth in the original proposal and have characterized memory T cell IMS associated with DENV and Mtb in the context of: 1) natural immunity and/or control of infection, 2) active and severe disease, and 3) administration of licensed or experimental vaccines. Our group has studied DENV and Mtb for several years for the following reasons: 1) they are both current global health problems, 2) memory T cells are fundamentally associated with protective immunity for these diseases, 3) antigen-specific T cell responses are detected in sufficient numbers ex vivo, making them accessible for “omics” studies without the need for in vitro expansion, and 4) human specimens associated with natural infection/immunity and severe disease are easily accessible in large numbers. The HIPC study format was ideally suited to accomplish the proposed mission. Each project and core was and remains critically dependent on other elements of the program. In the context of HIPC, we were able to realize synergies, benefit from economies of scale, and bring groups of investigators with different expertise together. As a result, we developed a critical mass that is extensively leveraged in the proposed extension, based on: 1) an established team of experienced investigators, 2) clinical collaborations with leaders in the field, 3) an extensive collection of epitopes restricted by a variety of different HLA class I and II molecules to allow an analysis of memory T cells with unprecedented precision, 4) IMS associated with specific T cell subsets representing key players in immunity, and 5) established “omics” assays and analysis pipelines to generate IMS related to DENV and Mtb. In this proposed extension, we plan to build on the definition of the T cell IMS in DENV and Mtb accomplished in the current 5-year funding period by expanding the significance and the dimensionality of the observations in multiple, yet related and synergistic, directions. As mentioned above, the work performed in the current cycle identified IMS associated with specific T cell subsets in natural infection, vaccination, and acute/severe disease. It is also clear that these T cell subsets are themselves heterogeneous. Here, we will utilize single-cell sequencing to “drill down” and establish IMS of the specific cell types responsible for this heterogeneity. The second dimension will “drill up” by considering additional cell subsets. For DENV, this will be accomplished by determining the IMS of whole unfractionated PBMC stimulated by epitopes recognized by DENV memory T cells. For Mtb, we will extend our focus to unconventional CD4-CD8-double-negative T cells which we have found to be responsive to bacterial lysates but not conventional peptide epitopes.