Single cell investigation of co-evolution in cancer cells and host cell immune microenvironment

项目摘要 癌细胞如何与宿主微环境免疫细胞共同进化仍然是一个关键问题。 免疫治疗的问题。吴实验室专注于抗原特异性相互作用的研究 以及它们参与抗肿瘤免疫的细胞和分子途径。 DFCI翻译免疫基因组学实验室（TIGL）的创建是为了扩大技术 和计算能力，并提供专门的资源 用于不同癌症类型的免疫基因组学分析。我目前的项目组合是 专注于设计单细胞/基因组学技术的发展，以了解 肿瘤微环境中肿瘤细胞和免疫细胞群之间的串扰 以及它们相互施加的选择性压力。具体而言：（i）我已制定了 rhTCRseq用于确定人T细胞中成对的α和β-TCR克隆型的灵敏性和稳健性 单细胞以及在大量RNA样品中进行TCR库分析。它已经 揭示了关于免疫疗法（如癌症疫苗）对 抗原特异性免疫的产生，并被广泛应用于监测 其他免疫治疗试验(ii)对于基于平板的单细胞分析和批量RNA样品， 已经开发了一种新的策略来执行qPCR和转录组测序。另外我 已经实施了基于液滴的10 x基因组学平台来研究单细胞转录组 和表面蛋白的表达。(iii)我有专门的技术 靶向多重RNA检测，旨在同时检测基因型和转录组 单细胞水平的信息。总之，这些不同的方法一直是， 正在应用于吴实验室的几个国家癌症研究所资助的项目。我们的新措施集中于 进一步开发和实施新的单细胞基因组学技术及其 应用.

Project Summary How cancer cells co-evolve with their host microenvironment immune cells remains a critical question in immunotherapy. The Wu lab focuses on the study of antigen-specific interactions and their involvement in the cellular and molecular pathways underlying anti-tumor immunity. The DFCI Translational Immunogenomics Laboratory (TIGL) was created to expand technology and computational capabilities developed within the Wu Lab and provide a dedicated resource for immunogenomic analysis across different cancer types. My current portfolio of projects is focused on designing the development of single cell/genomics techniques to understand the crosstalk between tumor cells and immune cell populations within the tumor microenvironment and the selective pressure they mutually exert on each other. In particular: (i) I have developed the sensitive and robust rhTCRseq to determine paired alpha and beta-TCR clonotypes in single cells as well as to perform TCR repertoire analysis in bulk RNA samples. It has already revealed novel insights regarding the impact of immunotherapies, such as cancer vaccines, on the generation of antigen-specific immunity, and is being widely applied to the monitoring of other immunotherapy trials. (ii) For plate-based single-cell analysis and for bulk RNA samples, I have developed a novel strategy to perform qPCR and transcriptome sequencing. In addition, I have implemented a droplet-based 10x Genomics platform to study single cell transcriptome and surface protein expression in the same single cells. (iii) I have expertise in generating targeted multiplex RNA assays, aimed at simultaneous detection of genotype and transcriptome information at the single cell level. Altogether these diverse approaches have been and are being applied to several NCI-funded projects in the Wu Lab. Our new initiatives focus on the further development and implementation of novel single cell genomics technologies and their applications.