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 免疫治疗中的问题。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翻译免疫基因组实验室(TIGL)的创建是为了扩展技术 和在WU实验室内开发的计算能力，并提供专用资源 用于不同癌症类型的免疫基因组分析。我目前的项目组合是 专注于设计单细胞/基因组学技术的开发，以了解 肿瘤微环境中肿瘤细胞和免疫细胞群之间的串扰 以及他们相互施加的选择性压力。特别是：(I)我已开发出 检测成对α和β-TCR克隆型的灵敏而可靠的重组人TCRseq 以及在批量RNA样本中进行TCR谱带分析。它已经做到了 揭示了关于免疫疗法的影响的新见解，如癌症疫苗 抗原特异性免疫的产生，并被广泛应用于监测 其他免疫疗法试验。(2)对于平板单细胞分析和散装RNA样品，i 已经开发出一种新的策略来执行qPCR和转录组测序。此外，我 已经实现了一个基于Droplet的10x基因组学平台来研究单细胞转录组 和表面蛋白在相同的单个细胞中的表达。(Iii)我具有生成 靶向多重RNA检测，旨在同时检测基因和转录组 单细胞级别的信息。总而言之，这些不同的方法过去和现在都是 被应用于NCI资助的几个吴实验室项目。我们的新举措侧重于 单细胞基因组学新技术及其应用的进一步发展和实施 申请。

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.