A Mechanistic Model of Chimeric Antigen Receptor (CAR) Signaling Predicts the Effects of Co-Stimulatory Signaling on T cell Activation

描述（由申请人提供）：过继细胞疗法（ACT）是癌症免疫治疗研究的一个令人兴奋的领域，它将患者自身的免疫细胞从体内取出，在体外修饰，然后重新注射以攻击癌症。最成功的修饰形式是用嵌合抗原受体（CAR）蛋白改造患者的T细胞，这种蛋白在识别癌细胞时触发免疫反应。为了激活T细胞，car由(1)来自抗体的细胞外结构域和(2)来自内源性T细胞受体的细胞内信号域组成，它们可以与肿瘤相关抗原结合。目前已经开发了三代CAR，每一代都增加了CAR上存在的细胞内共刺激结构域的数量。含有CD3ζ信号结构域与CD28或41BB共刺激结构域结合的car在B细胞淋巴瘤的临床试验中显示出一些希望；然而，一些患者对治疗没有反应，而另一些患者则经历免疫系统的过度激活，这可能是致命的。目前尚不清楚进一步增加共刺激结构域的数量将如何影响T细胞活化，或者这种增加是否能够改善对CAR治疗的控制。因此，需要更深入地了解导致CAR - T细胞活化的细胞信号通路，以描述信号域通路如何整合以影响T细胞活化的各种功能。系统生物学，特别是计算机制建模，为理解和优化CAR工程T细胞的激活提供了一个独特的平台。本研究旨在通过开发一套能够预测由不同CAR介导的T细胞活化的机制计算模型，探索不同CAR信号域（单独或联合）的作用。这些模型将描述单个信号域的激活机制，这些机制以前没有被建模，影响与T细胞激活的特定特性相关的下游蛋白质，如细胞因子产生、T细胞存活和细胞增殖。这些模型将由文献中已知相互作用的常微分方程组成。他们将接受关于蛋白质结合和激活的流式细胞术数据的训练，以便这些模型能够预测CAR刺激的效果。我们将进行硅实验来预测单个CAR共刺激域的信号如何整合以影响T细胞反应的特定方面。例如，我们可以通过使用该模型来确定最佳信号域组合来优化对治疗无反应的患者的CAR治疗，以增加与细胞因子产生相关的蛋白质，而不影响与生存相关的蛋白质。这些假设将在体外实验中得到验证。因此，拟议的研究将为提高CAR工程T细胞的安全性和有效性提供有价值的信息，使这种疗法的益处扩大到更广泛的患者群体。

DESCRIPTION (provided by applicant): Adoptive cell therapy (ACT) is an exciting area of cancer immunotherapy research in which a patient's own immune cells are removed from their body, modified in vitro, and re-injected to attack the cancer. The most successful form of modification is to engineer T cells from the patient with chimeric antigen receptor (CAR) proteins, which trigger an immune response upon recognition of a cancer cell. To activate the T cells, CARs are composed of (1) an extracellular domain, derived from an antibody, that can bind to a tumor associated antigen and (2) several intracellular signaling domains, derived from endogenous T cell receptors that can activate an immune response. Currently three generations of CARs have been developed, each increasing the number of intracellular co-stimulatory domains present on the CAR. CARs containing the CD3ζ signaling domain in combination with either CD28 or 41BB co-stimulatory domains have shown some promise in clinical trials of B cell lymphoma; however, some patients do not respond to therapy, while others experience over activation of the immune system, which can be deadly. It is not clear how further increasing the number of co-stimulatory domains will affect T cell activation or if the increase will be able to improve the control over CAR therapy. Therefore, a deeper understanding of the cell signaling pathways that lead to CAR T cell activation is needed to describe how signaling domain pathways integrate to affect the various fucntions of T cell activation. Systems biology, specifically computational mechanistic modeling, provides a unique platform to understand and optimize the activation of CAR engineered T cells. This proposal aims to explore the effects of different CAR signaling domains, individually and in combination, by developing a set of mechanistic computational models that can predict T cell activation mediated by different CARs. The models will describe the mechanisms by which activation of individual signaling domains, which have not been previously modeled, affect downstream proteins that correlate to specific properties of T cell activation, such as cytokine production, T cell survival, and cell proliferatin. The models will be comprised of ordinary differential equations derived from known interactions in the literature. They will be trained on flow cytometry data of protein binding and activation such that the models are able to predict the effects of CAR stimulation. We will perform in silico experiments to predict how signaling of individual CAR co-stimulatory domains is integrated to affect particular aspects of the T cell response. For example, we can optimize CAR therapy for patients that do not respond to treatment by using the model to determine the optimal signaling domain combination to increase proteins that correlate to cytokine production without affecting those that correlate to survival. These hypotheses will then be validated by in vitro experiments. Thus, the proposed research will provide valuable information to improve the safety and efficacy of CAR engineered T cells, enabling the benefits of this therapy to be expanded to a wider patient population.