4DN Interrogation of T Cell Exhaustion in Cancer

4DN 探究癌症中 T 细胞耗竭

• 批准号: 10264091
• 负责人: Ansuman Satpathy
• 金额: $ 52.36万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10264091
• 关键词: 3-Dimensional; Antigens; Architecture; CRISPR/Cas technology; Cancer Patient; Cell Proliferation; Cell model; Cells; Chromatin; Chromosome Structures; Chronic; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Consensus; Coupled; Custom; Data; Data Set; Development; Engineering; Enhancers; Epigenetic Process; Exhibits; Future; Gene Expression; Genetic Transcription; Genome; Goals; Human; Immune; Immune System Diseases; Immunology; Immunotherapy; Laboratories; Malignant Neoplasms; Maps; Measurement; Measures; Memory; Methods; Modeling; Molecular; Molecular Conformation; Pathway interactions; Patients; Phenotype; Process; Protocols documentation; Regulator Genes; Regulatory Element; Research; Signal Transduction; Skin Cancer; Software Tools; T cell regulation; T cell response; T-Cell Development; T-Cell Receptor; T-Lymphocyte; Technology; Testing; Tumor Antigens; anti-tumor immune response; cancer care; cancer cell; cancer immunotherapy; cancer type; chimeric antigen receptor T cells; clinical care; cohesin; design; epigenome; epigenomics; exhaust; exhaustion; functional genomics; genome editing; genome sciences; genome sequencing; genome-wide; genomic tools; high throughput technology; improved; in vivo; inhibitory surface receptor; insight; neoplastic cell; next generation; novel; programs; promoter; response; single-cell RNA sequencing; transcriptome sequencing; treatment response; tumor

PROJECT ABSTRACT/SUMMARY Immunotherapies that enhance the ability of T cells to recognize and kill tumor cells have been transformational in the treatment of human cancer, but immunotherapy is not effective in all patients or cancers, and therefore studies interrogating the molecular basis for durable T cell responses to cancer are needed. A critical barrier for the sustained activation of tumor-infiltrating T cells is the development of T cell ‘exhaustion,’ which leads to the stable expression of inhibitory surface receptors, poor response to tumor antigens, and low cell proliferation and persistence of T cells in vivo. However, to date, it has been difficult to study the gene regulatory mechanisms that control the development of T cell exhaustion in humans, due to a lack of sensitive genomic tools to study primary immune cells from patients. We recently developed a suite of high-throughput epigenomic technologies that enable the measurement of three-dimensional (3D) genome conformation and single-cell chromatin accessibility in primary T cells from human tumors. In the proposed research, we aim to utilize these methods to identify changes in 4D nucleome (4DN) organization and accessibility that underlie the development of human T cell exhaustion. In Aim 1, we will define 3D genome interactions that occur in human T cell exhaustion in patients with advanced skin cancer. Exhaustion-associated genome conformation will be compared across several cancer types to identify a consensus exhaustion profile, and these findings will be integrated with chromatin accessibility and gene expression data to identify transcriptional effects of 3D changes. In Aim 2, we will determine the dynamics and reversibility of regulatory 3D interactions in exhaustion using a novel chimeric antigen-receptor (CAR)-T cell model. In Aim 3, we will perturb these interactions using CRISPR/Cas9 genome editing in primary T cells, coupled with single-cell epigenomic read-outs, to engineer improved, durable, next- generation immunotherapies. If successful, these findings will have a direct impact on the future design of immunotherapy strategies, which will have a significant impact on the clinical care of cancer patients. Finally, we will facilitate the dissemination of these findings by freely distributing protocols and data and releasing custom software tools, and we will use these studies as a collaborative launch point in the 4DN network. We anticipate that these results will lead to novel insights into the molecular regulation of T cell exhaustion and serve as an effective research program for Dr. Satpathy to establish his independent laboratory at the interface of immunology and genome science.

项目摘要/总结 增强T细胞识别和杀死肿瘤细胞能力的免疫疗法已经发生转变 在治疗人类癌症中，但免疫疗法并非对所有患者或癌症都有效，因此 需要研究探究 T 细胞对癌症持久反应的分子基础。 肿瘤浸润 T 细胞的持续激活导致 T 细胞“衰竭”，从而导致 抑制性表面受体的稳定表达，对肿瘤抗原的反应较差，细胞增殖和增殖能力低下 然而，迄今为止，研究基因调控机制还很困难。 由于缺乏敏感的基因组工具来研究，控制人类 T 细胞耗竭的发展 我们最近开发了一套高通量表观基因组技术。 能够测量三维 (3D) 基因组构象和单细胞染色质 在拟议的研究中，我们的目标是利用这些方法来检测来自人类肿瘤的原代 T 细胞。 识别 4D 核组 (4DN) 组织和可及性的变化，这些变化是人类发展的基础 在目标 1 中，我们将定义人类 T 细胞耗竭中发生的 3D 基因组相互作用。 将比较患有晚期皮肤癌的患者的基因组构象。 几种癌症类型以确定共识的耗竭概况，这些发现将与 在目标 2 中，我们利用染色质可及性和基因表达数据来识别 3D 变化的转录效应。 将使用一种新型嵌合体确定耗尽状态下监管 3D 相互作用的动态性和可逆性 在目标 3 中，我们将使用 CRISPR/Cas9 基因组扰乱这些相互作用。 在原代 T 细胞中进行编辑，结合单细胞表观基因组读数，以设计改进的、持久的、下一代的 如果成功，这些发现将直接影响下一代免疫疗法的设计。 免疫治疗策略，这将对癌症患者的临床护理产生重大影响。 将通过自由分发协议和数据并发布自定义内容来促进这些发现的传播 软件工具，我们将使用这些研究作为 4DN 网络中的协作启动点。 这些结果将为 T 细胞耗竭的分子调节带来新的见解，并可作为 Satpathy 博士的有效研究计划是在交界处建立他的独立实验室 免疫学和基因组科学。