(PQ3) Disruption of immune surveillance by aneuploidy and aberrant MHCII expression

此新的R 01申请是为了响应资助机会RFA-CA-15-008“研究 NCI挑衅性问题的答案”。待检验的假设是对PQ 3的响应。我们假设 免疫监视对癌症患者个体和群体的益处可能 取决于非整倍体的水平和主要组织相容性复合体（MHC）的表达 II类（MHCII）肿瘤。我们进一步预测，一个由肿瘤定义的个体群体， 非整倍体和低MHCII表达的患者有更高的进展风险和不良结局， 通过调节肿瘤内免疫浸润物的大小和组成来降低对免疫治疗的无反应性。 在这个新的范例中，我们还建议研究非整倍体的可能致病机制- 诱导蛋白毒性应激。这项研究将结合基因组分析和免疫学 询问UCSD Moores癌症中心的患者，并最终将通过TCGA寻求验证 数据以及来自免疫治疗试验的数据。我们提出四个目标。 (1)验证非整倍体/MHC II作为疾病进展和临床结局的预测因子。TCGA数据将 询问非整倍性和MHCII表达水平与总生存率之间的相关性。 免疫治疗（ICPi）试验的反应。(2)为了测量自然免疫反应的标志物， 根据非整倍体/MHC II状态分组的癌症患者。我们将研究 肿瘤浸润性T细胞通过分析与TERT反应的TCR，一种由癌细胞表达的抗原， 分化阶段，作为自体抗癌反应的代表。通过比较肿瘤浸润 我们期望确定（a）肿瘤的非整倍体/MHCII特征是否预测T细胞 （B）较低的免疫T细胞浸润显示高TCR异质性。(3)以确定是否 非整倍体/MHCII状态干扰对ICPi治疗的反应。我们将确定是否高非整倍体/低 MHCII表达损害ICPi治疗后的免疫再激活，并使用来自应答者和 无应答患者。(4)为了确定蛋白毒性应激是否是 非整倍性干扰免疫应答。由于非整倍体诱导蛋白毒性应激， UPR提供了癌细胞生物学和免疫监视之间的机制联系。体外和体内 使用具有药理学诱导的非整倍性的细胞的实验将用于确定 该UPR细胞非自主效应可以解释局部免疫的破坏，即，数量和 肿瘤浸润骨髓细胞的特征。 我们相信，在癌症基因组和免疫监视之间的界面上进行分析， 揭示了免疫介导的癌症控制的一般规则。这可能有助于对患者及其临床 轨迹，并更准确地预测对免疫疗法的临床反应。 !

This new R01 application is submitted in response to Funding Opportunity RFA-CA-15-008 “Research Answers to NCI's Provocative Questions”. The hypothesis to be tested is in response to PQ3. We hypothesize that the benefit afforded by immune surveillance to the individual and populations of cancer patients may depend on the levels of aneuploidy and expression of the Major Histocompatibility Complex (MHC) complex Class II (MHCII) in the tumor. We further predict that a population of individuals defined by tumors with high aneuploidy and low MHCII expression is at higher risk of progression and poor outcome, and unresponsiveness to immunotherapy by regulating the size and composition of intra-tumor immune infiltrates. Within this new paradigm, we also propose to investigate the possible causative mechanism of aneuploidy- induced proteotoxic stress. The study will be a combination of genomic analyses and immunological interrogation in UCSD Moores Cancer Center patients, and will ultimately seek validation in through TCGA data as well as data from immunotherapy trials. We propose four Aims. (1) To validate aneuploidy/MHC II as predictors of progression and clinical outcome. TCGA data will be interrogated to relate an association between aneuploidy and levels of MHCII expression to overall survival. and response in immunotherapy (ICPi) trials. (2) To measure markers of natural immune response in cancer patients grouped according to aneuploidy/MHC II status. We will study the size and clonality of tumor-infiltrating T cells by profiling TCR reactive with TERT, an antigen expressed by cancer cells at every stage of differentiation, as a proxy of the autochthonous anti-cancer response. By comparing tumor-infiltrating T cells to circulating T cells, we expect to determine if (a) tumor the aneuploidy/MHCII signature predicts T cell infiltration, and (b) lower immune T cell infiltration displays high TCR heterogeneity. (3) To determine whether aneuploidy/MHCII status interferes with response to ICPi therapy. We will determine if high aneuploidy/low MHCII expression impairs immune reactivation after ICPi therapy, and use immunoscore from responder and nonresponder patients. (4) To determine whether proteotoxic stress is the mechanism by which aneuploidy interferes with immune response. Because aneuploidy induces proteotoxic stress, the ensuing UPR provides a mechanistic link between cancer cell biology and immune surveillance. In vitro and in vivo experiments using cells with pharmacologically-induced aneuploidy will be used to determine the extent to which UPR cell nonautonomous effects may account for a disruption of local immunity, i.e., number and characteristics of tumor infiltrating myeloid cells. We believe that an analysis at the interface between cancer genomic and immune surveillance may reveal general rules for immune-mediated control of cancer. This may help stratify patients and their clinical trajectory, and predict clinical responses to immunotherapy more accurately. !