Nano and biomolecular engineered technologies for neoantigen-specific T cell capture and characterization

用于新抗原特异性 T 细胞捕获和表征的纳米和生物分子工程技术

• 批准号: 10489832
• 负责人: James R. Heath
• 金额: $ 54.79万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-16 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10489832
• 关键词: Address; Algorithms; Antigen Presentation; Antigens; Antitumor Response; Artificial nanoparticles; Binding; Blood; Bypass; CCNE1 gene; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; COVID-19 patient; Cells; Clinic; Clinical; Clone Cells; Community Clinical Oncology Program; Cost Savings; Data; Data Set; Disadvantaged; Engineering; Exhibits; Funding; Genes; Genetic; Genetic Engineering; Grant; Haplotypes; Heart; Histocompatibility Antigens Class II; Immunooncology; Immunotherapy; Infusion procedures; KRAS2 gene; Length; Libraries; MHC Class II Genes; MHC antigen; Malignant neoplasm of ovary; Methodology; Methods; Mutate; Mutation; Nanotechnology; Oncogenes; Patients; Peptides; Peripheral Blood Mononuclear Cell; Population; Preparation; Protein Engineering; Proteins; Protocols documentation; Reagent; Reporting; Resources; Specificity; T cell response; T cell therapy; T-Cell Receptor; T-Cell Receptor Genes; T-Lymphocyte; T-Lymphocyte Subsets; TP53 gene; Technology; Therapeutic; Time; Tumor Antigens; Validation; Work; antigen-specific T cells; antitumor effect; base; cancer cell; cancer immunotherapy; colon cancer patients; cost; design; design and construction; innovation; invention; microchip; mutant; nano; neoantigens; pandemic disease; prediction algorithm; public database; tool; tumor

Project summary Much of cancer immunotherapy is focused on engineering or activating tumor-antigen specific CD8+ T cells and, to a lesser extent, CD4+ T cells. In particular, neoantigen-specific T cells are attractive because they can kill cancer cells with high specificity. 1 A general approach starts with identifying T cells that recognize neoantigens broadly expressed within the tumor, isolating the T cells and determining their T cell receptor (TCR) sequences. These TCRs can then be transfected into patient T cells, perhaps with additional genetic engineering2 to promote more durable anti-tumor effects, and expanded into an infusion product for patient treatment. 3 In fact, this approach has recently entered the clinic, with one trial (NCT03970382) drawing from inventions from an NCI- funded CCNE U54 grant led by the PI of this proposal. 4,5 However, there are still a number of fundamental and technological challenges associated with advancing neoantigen-specific TCR-engineered therapies. First, the discovery of neoantigen-specific TCRs relies on guidance from algorithms, such as NET MHCpan 4.1, to predict antigen/MHC presentation (based upon binding and other considerations), and many neoantigens arising from truncal mutations, such as mutant KRAS or mutant TP53, are predicted as unlikely, yet have been reported as clinically effective targets. 6,7,8 Second, neoantigen-specific CD4+ T cells and their class II restricted neoantigens, while identified as important for immunotherapy-induced anti-tumor responses, 9,10 remain a largely untapped therapeutic resource, with prediction algorithms 11,12 for Class II antigen/MHC binding less developed. A third challenge is that analysis of a patient blood for neoantigen-specific T cells typically requires upwards of 20M peripheral blood mononuclear cells (PBMCs), and so isn't particularly efficient. Here we propose 3 specific Aims designed to address these outstanding issues. At the heart of the technology solutions are combinations of engineered nanoparticles (NPs) and biomolecular engineered constructs designed for efficient and selective capture, analysis, and validation of truncal neoantigen-specific CD4+ and CD8+ T cell populations. Significant preliminary data is presented for all 3 Aims, some of which uses COVID-19 patient data generated by our work during the current pandemic. 13,14 The result of this work will be a powerful toolset designed for a minimally-biased search for CD4+ and CD8+ T cell populations against truncal neoantigens (independent of patient HLA haplotype), a toolset designed for the rapid validation and characterization of those neoantigen-specific T cell clonotypes, and a public data base of Class I and Class II truncal neoantigens and T cell receptor genes specific to those neoantigens.

项目概要 许多癌症免疫疗法都集中于改造或激活肿瘤抗原特异性 CD8+ T 细胞， 在较小程度上，CD4+ T 细胞。特别是新抗原特异性 T 细胞很有吸引力，因为它们可以杀死 癌细胞具有高度特异性。 1 一般方法从识别识别新抗原的 T 细胞开始 在肿瘤内广泛表达，分离 T 细胞并确定其 T 细胞受体 (TCR) 序列。 然后可以将这些 TCR 转染到患者 T 细胞中，或许还需要额外的基因工程2来促进 更持久的抗肿瘤作用，并扩展为输液产品用于患者治疗。 3 事实上，这 该方法最近已进入临床，其中一项试验 (NCT03970382) 借鉴了 NCI 的发明 资助了由本提案的 PI 领导的 CCNE U54 赠款。 4,5 然而，仍然存在一些基本的和 与推进新抗原特异性 TCR 工程疗法相关的技术挑战。首先， 新抗原特异性 TCR 的发现依赖于算法（例如 NET MHCpan 4.1）的指导来预测 抗原/MHC 呈递（基于结合和其他考虑因素），以及许多由 躯干突变，例如突变型 KRAS 或突变型 TP53，被预测为不太可能发生，但已被报道为 临床上有效的目标。 6,7,8 其次，新抗原特异性 CD4+ T 细胞及其 II 类限制性新抗原， 虽然 9,10 被认为对于免疫疗法诱导的抗肿瘤反应很重要，但它在很大程度上仍然是一个尚未开发的领域 治疗资源，II 类抗原/MHC 结合的预测算法 11,12 尚未开发。第三个 挑战在于，分析患者血液中的新抗原特异性 T 细胞通常需要超过 20M 外周血单核细胞 (PBMC)，因此效率不是特别高。在这里我们提出3个具体目标 旨在解决这些突出问题。技术解决方案的核心是以下组合： 工程纳米颗粒 (NP) 和生物分子工程结构，旨在实现高效和选择性 捕获、分析和验证躯干新抗原特异性 CD4+ 和 CD8+ T 细胞群。重要的 提供了所有 3 个目标的初步数据，其中一些目标使用我们工作生成的 COVID-19 患者数据 当前疫情期间。 13,14 这项工作的结果将是一个强大的工具集，专为最小偏差而设计 搜索针对躯干新抗原的 CD4+ 和 CD8+ T 细胞群（独立于患者 HLA） 单倍型），旨在快速验证和表征这些新抗原特异性 T 细胞的工具集 克隆型，以及 I 类和 II 类树干新抗原和 T 细胞受体基因特异性的公共数据库 那些新抗原。