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

此新的R01申请是为了响应资助机会RFA-CA-15-008研究 NCI的挑衅性问题的答案“。要检验的假设是对PQ3的回应。我们假设 免疫监测为癌症患者的个人和群体提供的好处可能 取决于主要组织相容性复合体(MHC)复合体的非整倍体和表达水平 肿瘤中的II类(MHCII)。我们进一步预测，由高发病率肿瘤定义的个体群体 非整倍体和低MHCII表达具有更高的进展风险和不良预后 通过调节肿瘤内免疫浸润物的大小和成分对免疫治疗无反应。 在这一新的范式中，我们还建议研究非整倍体的可能原因机制-- 诱导的蛋白毒性应激。这项研究将是基因组分析和免疫学的结合 UCSD摩尔癌症中心患者的审问，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。我们提出了四个目标。 (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数据将是 询问非整倍体和MHCII表达水平与总存活率之间的关系。 和免疫治疗(ICPI)试验中的反应。(2)检测人群自然免疫反应标志物 癌症患者按非整倍体/MHC II状态分组。我们将研究大小和克隆性 TERT与肿瘤细胞表达的TERT的TCR反应 分化阶段，作为本源抗癌反应的代用品。通过比较肿瘤浸润性 T细胞到循环T细胞，我们希望确定(A)肿瘤非整倍体/MHCII特征是否预示T细胞 (2)免疫功能低下的T细胞浸润表现出高度的TCR异质性。(3)确定是否 非整倍体/MHCII状态干扰对ICPI治疗的反应。我们将确定高非整倍体/低 MHCII表达损害ICPI治疗后的免疫再激活，并使用应答者和 无反应的病人。(4)确定蛋白毒性应激是否是 非整倍体干扰免疫反应。因为非整倍体诱导蛋白毒性应激，所以随之而来的 UPR在癌细胞生物学和免疫监测之间提供了一种机械联系。体外和体内 使用药物诱导的非整倍体细胞的实验将被用来确定 哪些UPR细胞的非自主效应可以解释局部免疫的破坏，即数量和 肿瘤浸润性髓系细胞的特点。 我们认为，对癌症基因组和免疫监测之间的界面进行分析可能会 揭示免疫介导的癌症控制的一般规则。这可能有助于对患者和他们的临床进行分层 轨迹，并更准确地预测免疫治疗的临床反应。 好了！

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. !