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

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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.