Single Cell and Immunogenomics

项目摘要 为这项赠款申请提出的项目寻求测试基于移植(Hct)的新型免疫调节剂。 AML和MDS的联合治疗，解剖白血病细胞及其周围免疫细胞 群体共同进化与allo-HCT课程的关系(目的是获得对 合理设计有效的联合治疗AML和MDS)，并了解供者如何克隆 干细胞群中的造血(CHIP)影响免疫细胞亚群的重建。堆芯 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 这些研究的最新计算和实验工具。核心3将分析整个外显子组测序数据 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差异 并使用匹配的RNA测序数据来确定这些变体中的哪些是 表达。最近开发的复杂算法将被实施来使用这些信息来预测 构成个体化白血病新抗原和造血祖细胞系的个人化HLA结合肽 限制性次要组织相容抗原(目标1)。为了确定对HCT的免疫应答，单项- 非肿瘤免疫细胞群体的细胞转录组测序将被用来识别与 免疫细胞功能(目标2)。有针对性的RNA分析将被用来确定如何发现这些 表型与单个细胞的基因型有关，并将被用来定义芯片如何影响对 HCT。T细胞对HCT的反应将通过使用靶向批量的TCR谱系分析进一步表征 和单细胞测序以评估T细胞克隆性(目标3)。成对的α/βTCR链单细胞 序列信息将被用来按顺序重建表达单个富含TCR的细胞系(目标4 从功能上准确地确定哪种TCR与哪种抗原相互作用。此分析将直接评估是否 新抗原或mHAg诱导的T细胞反应有助于临床治疗反应。

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.