Single Cell and Immunogenomics

单细胞和免疫基因组学

• 批准号: 10465100
• 负责人: Kenneth James Livak
• 金额: $ 28.26万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-14 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10465100
• 关键词: AML/MDS; Address; Affect; Algorithms; Allogenic; Antigen Targeting; Antigens; Applications Grants; Binding; Cell Line; Cell physiology; Cells; Characteristics; Clinical; Collaborations; Combined Modality Therapy; DNA analysis; DNA sequencing; Data; Data Analyses; Detection; Genomics; Genotype; Goals; Hematopoiesis; Hematopoietic; Immune; Immune response; Immunogenomics; Immunologics; Individual; Institutes; Laboratories; Leukemic Cell; Malignant Neoplasms; Minor Histocompatibility Antigens; Non-Malignant; Outcome; Pathway interactions; Patients; Peptides; Phenotype; Population; RNA analysis; Resistance; Sampling; Single Nucleotide Polymorphism; Somatic Mutation; Specimen; Stem cell transplant; T cell clonality; T cell response; T-Cell Immunologic Specificity; T-Cell Receptor; T-Lymphocyte; T-cell receptor repertoire; Testing; Therapeutic; Transplantation; Tumor-infiltrating immune cells; Variant; alpha-beta T-Cell Receptor; base; beta Chain Antigen T Cell Receptor; computerized tools; exome sequencing; graft vs leukemia effect; immune reconstitution; immunogenic; immunogenicity; immunoregulation; insertion/deletion mutation; insight; leukemia; neoantigens; novel; novel vaccines; predicting response; rational design; response; single cell sequencing; stem cell population; targeted treatment; tool; transcriptome; transcriptome sequencing; treatment response; vaccine strategy

Project Summary The projects proposed for this grant application seek to test novel transplant (HCT)-based immunomodulatory combination treatments for AML and MDS, to dissect how leukemia cells and their surrounding immune cell populations co-evolve in relationship to allo-HCT course (with the aim of gaining essential insights into the rational design of effective combination therapy for AML and MDS), and to understand how donor clonal hematopoiesis (CHIP) in the stem cell population impacts the reconstitution of immune cell subpopulations. Core 3 will support the single cell- and immunogenomics-related goals of these projects by focusing on applying the latest computational and experimental tools to these studies. Core 3 will analyze whole exome sequencing data from leukemia and normal samples to identify cancer-specific somatic mutations and polymorphic differences between donor and recipient, and use matched RNA sequencing data to determine which of these variants are expressed. Recently developed sophisticated algorithms will be implemented to use this information to predict personal HLA-binding peptides that compose personal leukemia neoantigens and hematopoietic-lineage restricted minor histocompatibility antigens (Aim 1). In order to determine the immune response to HCT, single- cell transcriptome sequencing of non-tumor immune cell populations will be used to identify pathways related to immune cell functions (Aim 2). Targeted RNA analysis will be used to determine how these discovered phenotypes relate to the genotype of individual cells and will be used to define how CHIP affects response to HCT. Response of T cells to HCT will be further characterized by TCR repertoire analysis using targeted bulk and single-cell sequencing to assess T cell clonality (Aim 3). The paired alpha/beta TCR chain single-cell sequence information will be used to reconstruct cell lines expressing individual enriched TCRs (Aim 4) in order to functionally determine exactly which TCR interacts with which antigen. This analysis will directly assess if neoantigen- or mHAg-directed T cell responses contribute to clinical responses to therapy.

项目概要 本次拨款申请提出的项目旨在测试基于新型移植（HCT）的免疫调节剂 AML 和 MDS 的联合治疗，剖析白血病细胞及其周围的免疫细胞如何 人群与异体 HCT 过程相关的共同进化（目的是获得对异基因 HCT 过程的重要见解） 合理设计针对 AML 和 MDS 的有效联合疗法），并了解供体克隆如何 干细胞群中的造血作用 (CHIP) 会影响免疫细胞亚群的重建。核 3 将通过重点应用以下方法来支持这些项目的单细胞和免疫基因组学相关目标 这些研究的最新计算和实验工具。 Core 3 将分析全外显子组测序数据 从白血病和正常样本中识别癌症特异性体细胞突变和多态性差异 供体和受体之间进行比较，并使用匹配的 RNA 测序数据来确定这些变异中的哪些是 表示。最近开发的复杂算法将被实施，以使用这些信息来预测 构成个人白血病新抗原和造血谱系的个人 HLA 结合肽 限制性次要组织相容性抗原（目标 1）。为了确定 HCT 的免疫反应，单 非肿瘤免疫细胞群的细胞转录组测序将用于识别与 免疫细胞功能（目标 2）。靶向 RNA 分析将用于确定这些是如何发现的 表型与单个细胞的基因型相关，将用于定义 CHIP 如何影响对 血细胞CT。 T 细胞对 HCT 的反应将通过使用靶向批量的 TCR 库分析来进一步表征 以及单细胞测序来评估 T 细胞克隆性（目标 3）。配对的α/β TCR链单细胞 序列信息将用于重建表达个体富集 TCR 的细胞系（目标 4） 功能上准确确定哪个 TCR 与哪个抗原相互作用。该分析将直接评估是否 新抗原或 mHAg 导向的 T 细胞反应有助于临床治疗反应。