Chromatin states encoding fate commitment and plasticity of tolerant CD8 T cells

描述(申请人提供)：大多数与自身抗原反应的CD8 T细胞在胸腺发育过程中被删除，逃避消除的细胞必须在外周保持耐受，以防止自身免疫损伤。然而，许多候选癌症抗原是自身抗原，对这些蛋白的耐受会阻碍抗肿瘤T细胞反应。我们最近证实，这种自身/肿瘤抗原特异的CD8T细胞具有与功能无反应相关的耐受特异性基因程序，反映在它们对抗原的反应中无法增殖，缺乏关键的转录因子和效应功能所需的分子(S)，并表达与免疫细胞功能降低相关的基因。然而，耐受性并不是一种不可逆转的、固定的分化状态：耐受性基因程序可以在体内淋巴细胞减少诱导的内稳态增殖(HP)期间被暂时覆盖，从而挽救抗原的反应性和功能。一旦幽门螺杆菌的增殖驱动结束，T细胞退出细胞周期，耐受基因的特征就会重新出现。 无论细胞是否再次遇到耐受的自身抗原。这些发现表明，持续的抗原暴露并不是维持耐受性所必需的，并表明自我耐受性T细胞对最初与周围自身抗原相遇(S)时建立的耐受性程序进行了“记忆”。我们的具体假设是，自我耐受代表了一种独特的分化状态，这种状态是由“耐受性特异性”程序通过“耐受性特异性”染色质标记和调节元件在表观遗传上印记的。基因表达的表观遗传调控机制刚刚开始被理解，部分是通过DNA元素百科全书(ENCODE)项目最近的工作，揭示了染色质可及性、基因表达、DNA甲基化和调控因子占据模式之间的新关系，并确定了新的转录因子顺式调控基序。拟议的研究将确定与不同的CD8 T细胞分化和功能状态相关的染色质状态，以确定自我耐受和功能T细胞的承诺、命运和可塑性的表观遗传学基础。阐明染色质状态如何编码和维持耐受状态，不仅可以确定癌症免疫治疗的干预性临床机会，还可以为减轻自身免疫和移植排斥反应的危险提供策略建议。其具体目标是：1)通过使用ENCODE技术和对染色质状态的全面、高分辨率的全基因组分析来确定在耐受T细胞中唯一编码的表观遗传程序，从而确定与建立和维持自身耐受相关的细胞内在调节机制(S)；以及2)确定消除耐受印记和表观遗传记忆的潜在机制和策略，以实现与长期挽救和分化自身/肿瘤特异性CD8T细胞为功能性抗原反应性T细胞相关的永久重新编程。

DESCRIPTION (provided by applicant): Most CD8 T cells reactive with self-antigens are deleted during thymic development, and the cells that evade elimination must be rendered tolerant in the periphery to prevent autoimmune injury. However, many candidate cancer antigens are self-antigens, and tolerance to these proteins can impede anti-tumor T cell responses. We recently demonstrated that such self/tumor-antigen specific CD8 T cells harbor a tolerance- specific gene program associated with functional unresponsiveness reflected by their inability to proliferate in response to antigen, lack key transcription factors and molecules needed for effector function(s), and express genes associated with reduced immune cell function. However, tolerance is not an irreversible, fixed differentiation state: the tolerance gen program can be temporarily overridden during periods of lymphopenia- induced homeostatic proliferation (HP) in vivo, resulting in rescue of antigen responsiveness and function. Once the proliferative drive of HP ends and T cells exit the cell cycle, the tolerance gene signature is re- imposed regardless of whether the cells re-encounter the tolerizing self-antigen. These findings demonstrate that continuous antigen exposure is not required to maintain tolerance, and suggest that self-tolerant T cells "remember" the tolerance program established during the initial encounter(s) with self-antigen in the periphery. Our specific hypothesis is that self-tolerance represents a unique differentiation state that is maintained by a "tolerance-specific" program epigenetically imprinted through "tolerance-specific" chromatin marks and regulatory elements. Epigenetic regulatory mechanisms of gene expression are just beginning to be understood, in part through recent work by The Encyclopedia of DNA elements (ENCODE) project, revealing new relationships between chromatin accessibility, gene expression, DNA-methylation and regulatory factor occupancy patterns, and identifying novel cis-regulatory motifs of transcription factor. The proposed studies will determine the chromatin states associated with distinct CD8 T cell differentiation and functional states to define the epigenetic underpinnings of commitment fate and plasticity of self-tolerant and functional T cells. Elucidating how chromatin states encode and maintain the tolerant state may not only identify interventional clinical opportunities for cancer immunotherapy, but also suggest strategies for mitigating the dangers of autoimmunity and transplant rejection. The Specific Aims are to: 1) Define the cell-intrinsic regulatory mechanism(s) associated with the establishment and maintenance of self-tolerance by using ENCODE technologies with comprehensive, high- resolution genome-wide analysis of chromatin states to identify the epigenetic program uniquely encoded in tolerant T cells; and 2) Determine the underlying mechanism(s) and strategies by which tolerance imprinting and epigenetic memory can be erased to achieve permanent re-programming associated with long-term rescue and differentiation of self/tumor-specific CD8 T cells into functional antigen-responsive T cells.