Single Cell and Immunogenomics

单细胞和免疫基因组学

• 批准号: 10218095
• 负责人: Kenneth James Livak
• 金额: $ 28.84万
• 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/10218095
• 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; design; exome sequencing; graft vs leukemia effect; immune reconstitution; immunogenic; immunogenicity; immunoregulation; insertion/deletion mutation; insight; leukemia; neoantigens; novel; novel vaccines; predicting response; response; single cell sequencing; stem cell population; targeted treatment; tool; transcriptome; transcriptome sequencing

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.

项目摘要 该资助申请的项目旨在测试基于新移植（HCT）的免疫调节剂。 AML和MDS的联合治疗，以剖析白血病细胞及其周围的免疫细胞 人群在与allo-HCT过程的关系中共同进化（目的是获得对Allo-HCT过程的基本见解）。 合理设计AML和MDS的有效联合治疗），并了解供体克隆 干细胞群中的造血（CHIP）影响免疫细胞亚群的重建。核心 3将支持这些项目的单细胞和免疫基因组学相关目标，重点是应用 最新的计算和实验工具，这些研究。核心3将分析全外显子组测序数据 从白血病和正常样本中鉴定癌症特异性体细胞突变和多态性差异 在供体和受体之间，并使用匹配的RNA测序数据来确定这些变体中的哪一个是 表达。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（目的1）。为了确定对HCT的免疫应答， 非肿瘤免疫细胞群的细胞转录组测序将用于鉴定与以下相关的途径： 免疫细胞功能（目标2）。有针对性的RNA分析将用于确定这些发现是如何发生的。 表型与单个细胞的基因型有关，并将用于定义CHIP如何影响对 HCT。T细胞对HCT的应答将进一步通过使用靶向原液的TCR库分析来表征。 和单细胞测序以评估T细胞克隆性（Aim 3）。配对的α/β TCR链单细胞 序列信息将用于重建表达单个富集TCR的细胞系（Aim 4）， 以在功能上准确地确定哪个TCR与哪个抗原相互作用。该分析将直接评估， 新抗原或mHAg导向的T细胞应答有助于对治疗的临床应答。