Single cell epigenomics in cancer immunity and immunotherapy

项目摘要/摘要 这份提案概述了安苏曼·萨特帕西博士的五年职业发展计划。 目标是为他的独立研究生涯做准备，成为一名学术内科医生兼科学家。萨特帕西医生 在圣路易斯的华盛顿大学完成了免疫学的医学博士和博士学位，并成为医学住院医师 斯坦福医院和诊所的临床病理学专业。在住院期间，萨特帕西博士进行了基础科学研究 皮肤病中心主任、皮肤科教授霍华德·张博士在实验室进行的研究 斯坦福大学基因组科学专业的杰出学生。张博士是基因组学领域的专家， 癌症生物学，以前曾担任过许多医生和科学家的导师，这些医生和科学家已经过渡到 在学术医学方面的独立立场。斯坦福大学为博士提供了一个出色的环境。 萨特帕西发展他的独立研究事业。首先，萨特帕西博士的咨询委员会由以下成员组成 麦考尔博士、蒙蒂娜博士、格林利夫博士和加利博士在各个方面都有广泛的科学专长。 作为科学导师的这项提议和非常成功的记录。第二，萨特帕西博士将获得 通过学校提供的教育资源获得额外的科学和专业技能 医学和博士后事务办公室。第三，常实验室的研究基础设施和 邻近的核心设施将使萨特帕西博士能够有效地实现本文件中描述的科学目标 求婚。拟议研究的长期目标是研究免疫疗法的表观遗传学基础。 晚期基底细胞癌患者的耐药情况。临床免疫疗法可增强 T淋巴细胞破坏癌细胞的能力在晚期皮肤中显示出显著的疗效 癌症，但只有一小部分患者对治疗有效。在萨特帕西博士在张实验室的短暂时间里，他 开发了新的测序技术，使初级免疫细胞的表观基因组研究能够从 有新发现的分辨率的患者。在目标1中，我们将同时进行表观基因组和T细胞受体 单细胞测序以确定肿瘤特异性CD8肿瘤中T细胞功能障碍的表观遗传学特征 浸润性T淋巴细胞(TIL)。这种综合的方法将分离克隆性肿瘤的调控网络- 同一患者背景非反应性T细胞中的特异性T细胞。在目标2中，我们将使用此技术来 识别与基底细胞癌患者免疫治疗耐药相关的CD8 TIL中的调节信号 接受抗PD-1免疫治疗。在目标3中，我们将使用以下技术设计持久的T细胞免疫治疗反应 初级T细胞中调节位点的基因组编辑。最后，我们将促进这些调查结果的传播。 通过自由分发协议和数据以及发布定制软件工具。我们预计这些结果 将导致对免疫治疗耐药性的分子调控的新见解，并作为一种有效的 萨蒂希博士的培训计划，以开启他作为一名学术内科科学家的独立职业生涯。

PROJECT SUMMARY/ABSTRACT This proposal outlines a five-year career development program for Dr. Ansuman Satpathy, M.D., Ph.D. with the goal of preparing him for an independent research career as an academic physician-scientist. Dr. Satpathy completed his M.D. and Ph.D. in Immunology at Washington University in St. Louis and his medical residency in Clinical Pathology at Stanford Hospital and Clinics. During his residency, Dr. Satpathy performed basic science research in the lab of Dr. Howard Chang, who is a Professor of Dermatology and Director of the Center for Excellence in Genome Science at Stanford University. Dr. Chang is an expert in the fields of genomics and cancer biology and has previously served as a mentor to many physician-scientists who have transitioned to independent positions in academic medicine. Stanford University provides an outstanding environment for Dr. Satpathy to develop his independent research career. First, Dr. Satpathy's Advisory Committee comprised of Drs. Mackall, Montine, Greenleaf, and Galli has diverse and extensive scientific expertise relevant to all aspects of this proposal and highly successful track records as scientific mentors. Second, Dr. Satpathy will acquire additional scientific and professional skills through educational resources available through the School of Medicine and Office of Postdoctoral Affairs. Third, the research infrastructure within the Chang lab and neighboring core facilities will enable Dr. Satpathy to efficiently perform the scientific aims described in this proposal. The long-term goal of the proposed research is to study the epigenetic basis for immunotherapy resistance in patients with advanced basal cell carcinoma (BCC). Clinical immunotherapies that enhance the ability of T lymphocytes to destroy cancer cells have demonstrated remarkable efficacy in advanced skin cancers, but only a subset of patients respond to therapy. During Dr. Satpathy’s brief time in the Chang lab, he developed novel sequencing technologies which enable epigenomic studies in primary immune cells from patients with newfound resolution. In Aim 1, we will perform simultaneous epigenome and T cell receptor sequencing in single cells to identify epigenetic signatures of T cell dysfunction in tumor-specific CD8+ tumor- infiltrating T lymphocytes (TILs). This integrative approach will separate regulatory networks in clonal tumor- specific T cells from background non-reactive T cells in the same patient. In Aim 2, we will use this technique to identify regulatory signatures in CD8+ TILs that are associated with immunotherapy resistance in BCC patients receiving anti-PD-1 immunotherapy. In Aim 3, we will engineer durable T cell immunotherapy responses using genome editing of regulatory sites in primary T cells. Finally, we will facilitate the dissemination of these findings by freely distributing protocols and data and releasing custom software tools. We anticipate that these results will lead to novel insights into the molecular regulation of immunotherapy resistance and serve as an effective training program for Dr. Satpathy to launch his independent career as an academic physician scientist.