Single cell epigenomics in cancer immunity and immunotherapy

项目总结/摘要 该提案概述了一个为期五年的职业发展计划博士安苏曼Satpathy，医学博士，博士与 目标是为他作为一名学术物理学家和科学家的独立研究生涯做好准备。Satpathy医生 完成了医学博士学位和博士他在圣路易斯的华盛顿大学从事免疫学研究， 在斯坦福大学医院和诊所的临床病理学。在他的住院医生期间，Satpathy博士进行了基础科学研究 霍华德·张博士是皮肤病学教授和皮肤病中心主任， 斯坦福大学基因组科学卓越奖。Chang博士是基因组学领域的专家， 癌症生物学，并曾担任导师，许多医生，科学家谁已经过渡到 在学术医学中的独立地位。斯坦福大学提供了一个优秀的环境博士。 Satpathy发展他的独立研究生涯。首先，Satpathy博士的咨询委员会由以下人员组成： Drs. Mackall，Montine，Greenleaf和Galli拥有与各个方面相关的多样化和广泛的科学专业知识 以及作为科学导师的成功记录。第二，Satpathy博士将获得 通过学校提供的教育资源，获得更多的科学和专业技能。 医学和博士后事务办公室。第三，Chang实验室内的研究基础设施， 邻近的核心设施将使Satpathy博士能够有效地执行本文所述的科学目标。 提议拟议研究的长期目标是研究免疫疗法的表观遗传基础 晚期基底细胞癌（BCC）患者的耐药性。临床免疫疗法，增强 T淋巴细胞破坏癌细胞的能力已在晚期皮肤中表现出显着的功效 癌症，但只有一部分患者对治疗有反应。Satpathy博士在Chang实验室的短暂时间里， 开发了新的测序技术，使原代免疫细胞的表观基因组研究， 新发现的患者。在目标1中，我们将同时进行表观基因组和T细胞受体 在单细胞中测序以鉴定肿瘤特异性CD 8+肿瘤中T细胞功能障碍的表观遗传特征- 浸润性T淋巴细胞（TIL）。这种整合方法将分离克隆性肿瘤中的调控网络， 特异性T细胞来自同一患者的背景非反应性T细胞。在目标2中，我们将使用此技术 鉴定与BCC患者免疫治疗抗性相关的CD 8 + TIL中的调节特征 接受抗PD-1免疫治疗在目标3中，我们将使用以下方法设计持久的T细胞免疫治疗反应： 原代T细胞中调控位点的基因组编辑。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 将导致对免疫疗法抗性的分子调节的新见解，并作为一种有效的 Satpathy博士的培训计划，以启动他作为学术医生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.