Multi-Omic Single-Cell System for Improved Combination Cancer Immunotherapy Monitoring and Implementation

Isoplexis建议提供一种新的多组学方法，用于靶向分析TCR序列和 从1000个单细胞阵列中提取蛋白质组。具体地说，我们将提供单细胞，TCR测序和 蛋白捕获试验用于识别反应性抗原特异性TCR并同时评估这些T细胞 对该抗原的功能性反应。挑战仍然是将静止嵌入的T细胞的激活联系起来 在肿瘤中通过联合免疫疗法来影响患者的预后。确定治疗方法的组合 每个患者的最佳反应表明了最佳的治疗过程。单细胞的质量 这些免疫细胞的多功能反应与阳性结果的相关性远远好于传统的批量 分析。例如，PD-1在T细胞激活时上调，而PD-L1由一系列细胞表达 类型。由于PD-1/PD-L1相互作用负向调节T细胞免疫功能，PD-1/PD-L1阻断可以 救援效应器T细胞功能。分析TIL的关键是评估(1)这些T细胞在肿瘤中的功能 环境，以使试验领导人能够预测应答者和非应答者，这是 免疫肿瘤学，以及(2)了解最高功能细胞的TCR序列。单等联体- 细胞分泌分析在产生和定量高度多元化的、单一的和 单元格数据。来自TCR序列的额外单细胞数据将有助于将抗原特异性与多功能联系起来 T细胞参与患者的反应，用于改进生物标记物和靶向T细胞疗法的开发。我们 提出了以下具体目标：(1)发展SCBC流式细胞，用于双重捕获多个蛋白质和 转录组在设备上。(2a)生产现有的小型和台式自动化仪器 用于多组学应用的仪器。2b)开发用于自动数据处理和直观的软件套件 多功能和转录组数据的综合信息学。3)建立耐心的表型学习和 多个试验中的基因信息，与大量患者基因/表型数据的机器学习一起应用。 在我们的第二阶段拨款结束时，我们将在全自动的TCR/蛋白质组分析上演示双重TCR/蛋白质组分析 小型化的SCBC仪器、IsoMini和软件套件将在三个方面成功使用 耶鲁大学、斯坦福大学和弗雷德·哈奇的联合疗法试验。

IsoPlexis proposes to deliver a novel multi-omic method for targeted profiling of both the TCR sequence and proteome from an array of 1000+ single cells. Specifically, we will deliver a single-cell, TCR sequencing and protein capture assay for identifying responsive antigen specific TCRs, and concurrently evaluate these T-cells for functional response to that antigen. The challenge remains to link the activation of quiescent T-cell embedded in tumors by combination immunotherapies to patient outcome. Determining the combination of therapies to which each individual patient best responds indicates the best course of treatment. The quality of single-cell polyfunctional response of these immune cells correlates to positive outcomes far better than traditional bulk analysis. For example, PD-1 is upregulated upon T-cell activation while PD-L1 is expressed by a range of cell types. Since PD-1/PD-L1 interactions negatively regulate T cell immune function, PD-1/PD-L1 blockade can rescue effector T cell function. Critical to analyzing TILs is to assess (1) these T-cells’ function in the tumor environment in order to enable trial leaders to predict responders vs non-responders, a critical problem in immuno-oncology, and (2) to understand the TCR Sequence of the highest functioning cells. IsoPlexis single- cell secretion analysis exceeds its competition in the generation and quantitation of highly-multiplexed, single- cell data. Additional single-cell data from the TCR sequence would help to link antigen specificity to polyfunctional T cells involved in patient response, for improved biomarkers and targeted T-cell therapy development. We propose the following specific aims: (1) develop SCBC flow cell for the dual capture of multiplexed proteins and transcriptome on-device. (2a) produce a miniaturized and benchtop automated instrument of the existing instrument for multi-omic applications. 2b) develop a software suite for automated data processing and intuitive integrated informatics of polyfunctional and transcriptome data. 3) Establish patient learning of phenotype & genotype information in multiple trials, applied with machine learning of large patient genotype/phenotype data. At the end of our Phase II grant, we will demonstrate a dual TCR/proteomic assay on a fully-automated miniaturized SCBC instrument, the IsoMini, and software suite that will be successfully used across three combination therapy trials at Yale, Stanford and Fred Hutch.