CAREER: Reverse engineering the inflammatory signaling network from single-cell data

1454301 Miller-Jensen，Kathryn先天免疫系统是一组细胞及其产物，保护人类和其他生物体免受入侵病原体的侵害。当先天免疫细胞功能异常时，它们可以通过向邻近细胞分泌不正确的信号而导致自身免疫性疾病和癌症。然而，如果药物可以特异性地靶向先天免疫细胞，使它们恢复健康状态，那么就有可能利用它们来治疗这些疾病。与许多其他生物系统一样，先天免疫反应也很复杂，因为并非所有细胞都以完全相同的方式对相同的刺激做出反应，即使这些细胞在遗传上是相同的。这个CAREER奖项的目标是通过测量单细胞中的噪声信号和分泌来更好地了解先天免疫系统，以发现它们如何共同产生保护性免疫反应。这项研究将使用新的实验工具，如微流体装置，允许测量来自单细胞的许多生物信号。计算建模将用于解释这些复杂的单细胞数据集，并开发关于先天免疫系统调节的新假设和修改先天免疫系统以治疗疾病的新方法。有效的免疫应答需要先天性和适应性免疫系统的细胞之间的广泛沟通。巨噬细胞在调节免疫应答中起主要作用，其通过在微生物产物（例如脂多糖（LPS））刺激时执行分泌的促炎细胞因子和抗炎细胞因子的精心策划的级联。最近，已经发现先天免疫细胞内信号传导和分泌应答中存在显著的细胞间异质性。该CAREER奖的目标是测试以下假设：1）信号传导动力学调节分泌异质性; 2）细胞间异质性通过旁分泌转化为群体中快速可靠的反应（即，小区到相邻小区）信令。为了探索这些假设，研究人员将使用最先进的实验工具进行单细胞分析，包括集成的微流体装置，用于同一单细胞中信号传导，转录动力学和分泌的活细胞成像。这些数据将用于对异质性“分泌程序”进行分类（具体目标1），识别差异运输细胞因子从转录到分泌的异质性来源（具体目标2），并开发信号传导、细胞因子分泌和扩散的数学模型，以拟合单细胞数据，从而预测紧急群体行为（具体目标3）。这些结果将对免疫学、癌症及其他领域产生重大影响，并可能为特异性调节先天免疫反应以治疗疾病提供改进的策略。像这项研究中使用的微流体工具不仅能够发现新的生物机制，而且还提供了有趣和切实的方式来学习生物学和工程学的基础技能。因此，这个职业奖将支持一项教育计划，通过为大纽黑文地区的高中生提供暑期外展计划，增加工程的多样性和参与度。具体来说，研究人员将使用微流体设备吸引高中生，并通过开发暑期教学模块（通过耶鲁大学的科学课程途径）和暑期实验室实习来教授他们免疫学，生物学和工程学的基本概念。这种实践方法对于招聘和留住更多样化的科学，技术，工程和数学（STEM）大学毕业生群体至关重要。

1454301Miller-Jensen, Kathryn The innate immune system is the group of cells and their products that protect humans and other organisms against invading pathogens. When innate immune cells function abnormally, they can contribute to autoimmune diseases and cancer by secreting incorrect signals to neighboring cells. However, if drugs could specifically target the innate immune cells to return them to a healthy state, then it may be possible to harness them to treat these diseases. The innate immune response - like many other biological systems - is complicated by the fact that not all cells respond exactly the same way to the same stimulus, even though the cells are genetically identical. The goal of this CAREER award is to better understand the innate immune system by measuring noisy signals and secretion in single cells to discover how they work together to produce a protective immune response. This research will use novel experimental tools such as microfluidic devices, that permit measurement of many biological signals from single cells. Computational modeling will be used to interpret these complex single-cell data sets and develop new hypotheses about innate immune system regulation and new ways to modify the innate immune system to treat disease. An effective immune response requires extensive communication between cells of the innate and adaptive immune systems. Macrophages play a major role in regulating the immune response by executing a well-orchestrated cascade of secreted pro- and anti-inflammatory cytokines upon stimulation by microbial products, such as lipopolysaccharide (LPS). Recently, it has been discovered that there is significant cell-to-cell heterogeneity in innate immune intracellular signaling and secretion responses. The goal of this CAREER award is to test the hypotheses that 1) signaling dynamics regulate secretion heterogeneity; and 2) intercellular heterogeneity is converted to rapid and reliable responses in the population via paracrine (i.e., cell-to-neighbor cell) signaling. To explore these hypotheses, the researchers will use state-of-the-art experimental tools for single-cell analysis, including an integrated microfluidic device for live-cell imaging of signaling, transcriptional dynamics and secretion in the same single cells. These data will be used to classify heterogeneous 'secretion programs' (Specific Objective 1), identify sources of heterogeneity from transcription to secretion across differentially trafficked cytokines (Specific Objective 2), and to develop a mathematical model of signaling, cytokine secretion, and diffusion fit to single-cell data to make predictions about emergent population behavior (Specific Objective 3). The results will have significant implications for immunology, cancer, and beyond, and may suggest improved strategies for specifically modulating the innate immune response to treat disease. Microfluidic tools like the ones used in this research not only enable discovery of new biological mechanisms, but also provide fun and tangible ways to learn foundational skills in biology and engineering. Therefore, this CAREER award will support an educational initiative to increase diversity and participation in engineering through a summer outreach program for high school students in the greater New Haven area. Specifically, the researchers will use microfluidic devices to engage high school students and teach them basic concepts in immunology, biology and engineering through development of a summer teaching module (run through Yale's Pathways to Science Program) and summer lab internships. Such hands-on approaches are critical to recruit and retain a more diverse group of science, technology, engineering and mathematics (STEM) college graduates.