Liquid biopsy-based toolkits for neoantigen and cognate TCR discovery for cancer immunotherapy

基于液体活检的工具包，用于癌症免疫治疗的新抗原和同源 TCR 发现

• 批准号: 10684704
• 负责人: Wei Wei
• 金额: $ 44.27万
• 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: 2021-09-05 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10684704
• 关键词: Address; Adoption; Advanced Development; Alleles; Antigens; Autologous; Bar Codes; Binding; Biological Assay; Biopsy; Biopsy Specimen; Blood; Blood specimen; Cancer Vaccines; Cell Separation; Cells; Cellular immunotherapy; Clinical; Cytomegalovirus; Data; Diagnosis; Disease Progression; Ecosystem; Engineering; Evolution; Exclusion; Freezing; Human; Human Herpesvirus 4; Image Cytometry; Immune; Immunotherapy; Kinetics; Lesion; Libraries; Lymphocyte; Malignant Neoplasms; Medical center; Molecular Profiling; Monitor; Mutation; Neoplasm Circulating Cells; Oncologist; Operative Surgical Procedures; Paraffin Embedding; Pathologic; Patients; Peptide/MHC Complex; Peripheral; Peripheral Blood Lymphocyte; Pharmacotherapy; Population; Procedures; Reference Standards; Resistance; Resolution; Sampling; Specimen; T cell clonality; T-Cell Receptor Genes; T-Lymphocyte; T-cell receptor repertoire; Time; Tumor Immunity; Tumor Tissue; Tumor-Infiltrating Lymphocytes; Validation; WT1 gene; Work; anti-tumor immune response; antigen-specific T cells; cancer immunotherapy; cellular transduction; checkpoint therapy; clinical translation; driving force; dynamical evolution; immune checkpoint blockade; immunogenic; insight; liquid biopsy; melanoma; minimally invasive; nanoparticle; neoantigen vaccine; neoantigens; neoplastic cell; novel; overtreatment; personalized immunotherapy; programs; recruit; response; screening; single molecule; tool; transcriptome; tumor; tumor exome

Project Summary/Abstract Neoantigens derived from tumor-specific mutations are a major driving force behind the current cancer immunotherapies. The interactions between neoantigens and antigen-specific T cells enable T cell recognition and tumor killing. Resolving neoantigens and antigen-reactive T cells normally requires fresh (or snap frozen) tumor materials from which the tumor tissue can be sequenced and tumor-infiltrating lymphocytes can be isolated and expanded. Unfortunately, the availability of fresh (or snap frozen) tumor tissue biopsies is a significant limiting factor for personalized immunotherapy. Sequencing quality of paraffin-embedded pathological specimen is often suboptimal for neoantigen discovery. Sequencing data of a small biopsy from a single tumor lesion may not be representative of the tumor's full clonal spectrum. More importantly, the molecular profile of tumors evolves dynamically over time. But repeated biopsy sampling is seldom feasible for patients with many cancers that require invasive biopsy procedures. Circulating tumor cells (CTCs) and match blood lymphocytes are good surrogates for neoantigen and cognate TCR discovery. They enable clinicians to repeatedly and non-invasively interrogate the mutational landscape and dynamic evolution of the anti-tumor immunity via serially collected blood samples. A major technical challenge here is to develop high-throughput, low sample volume, minimally invasive tools to resolve the neoantigen and cognate TCR dynamics and to match the TCR genes with specific neoantigens. We propose to develop a toolkit for liquid biopsy-based neoantigen and cognate TCR discovery through a strategic integration of a novel on-chip image cytometry platform and a highly modular nanoparticle-barcoded single-molecule peptide-MHC tetramer cell sorting assay. We will perform advanced development and rigorous validation of the toolkit in this proposed work. We will investigate the dynamic evolution of neoantigen and TCR repertoires during immune checkpoint blockade using serially collected blood samples from melanoma patients. Upon successful completion, it will deliver a simple and noninvasive approach for liquid biopsy-based neoantigen and cognate TCR discovery for patients whose surgical biopsies are not available or not attainable, with transformative potentials on personalized neoantigen vaccines and T-cell based immunotherapies. The neoantigen and cognate TCR dynamics will provide critical insights into the understanding of immunotherapy response and resistance.

项目摘要/摘要 源自肿瘤特异性突变的新抗原是当前癌症背后的主要驱动力 免疫疗法。新抗原和抗原特异性T细胞之间的相互作用使T细胞识别 和杀死肿瘤。解决新抗原和抗原反应性T细胞通常需要新鲜（或捕捉） 可以从中可以对肿瘤组织进行测序并分离肿瘤组织的肿瘤材料 并扩展。不幸的是，新鲜（或捕捉）肿瘤组织活检的可用性是重要的 个性化免疫疗法的限制因素。石蜡包裹的病理标本的测序质量 通常是新抗原发现的次优。从单个肿瘤病变中进行小型活检的测序数据可能 不代表肿瘤的全克隆光谱。更重要的是，肿瘤的分子谱 随着时间的推移动态发展。但是重复的活检采样很少是许多癌症患者 这需要侵入性的活检程序。 循环肿瘤细胞（CTC）和匹配血液淋巴细胞是新抗原和同源的良好替代物 TCR发现。它们使临床医生能够反复和非侵入性询问突变景观 通过串行收集的血液样本对抗肿瘤免疫的动态演变。主要技术 这里的挑战是开发高通量，样本量低，微创工具来解决 新抗原和同源TCR动力学，并与特定的新抗原相匹配。我们建议 通过战略整合开发用于基于液体活检的新抗原和同源TCR发现的工具包 新型片上图像细胞仪平台和高度模块化的纳米粒子 - 核模型的单分子 肽-MHC四聚体细胞分类测定法。我们将对先进的开发和严格验证 在这项拟议的工作中工具包。我们将研究新抗原和TCR曲目的动态演变 免疫检查点阻断了黑色素瘤患者的血液样本。成功 完成，它将为基于液体活检的新抗原和同源提供一种简单且无创的方法 对于无法获得或无法实现的手术活检的患者的TCR发现，具有变革性 个性化新抗原疫苗和基于T细胞的免疫疗法的潜力。新抗原和同源 TCR动力学将为理解免疫疗法反应和抗性提供关键的见解。