Decode and design T cell induction by a complex gut microbial community

项目摘要/摘要 免疫调节为癌症、自身免疫性疾病、代谢疾病的治疗带来了巨大的希望 疾病和传染病。产生抗原特异性T和B细胞的新方法 最小的反应性是迫切需要的。肠道微生物群中的某些细菌菌株能诱导出一种有效的、 特异性适应性免疫反应。潜在的机制可以指导新的治疗策略 哪些细菌特异的免疫反应被合理地改变或重新定向。肠子是一块很宽的地方 微生物-微生物和微生物-宿主相互作用的多样性。然而，之前的论文描述了 微生物菌群在人工条件下的单定植。这种方法可以识别 能够调节免疫细胞的菌株，但目前尚不清楚菌株在存在 复合微生物区系的其他成员。这种知识鸿沟阻碍了微生物的逻辑设计 有治疗作用。 我的长期研究目标是开发新的技术来理解“生理”的肠道 在分子机制水平上的生态系统，使我可以识别免疫调节细菌从 微生物组和建立新的治疗方法。在这项提议中，我将通过殖民建立一种“生理”的内脏 具有复杂定义肠道群落的无菌小鼠(104个菌株)和对每个菌株的T细胞反应谱 单独的。在Aim1中，我将通过单细胞鉴定一组细菌反应性TCR及其刺激菌株 技术，这样我就可以在单个TCR水平上提供菌株-T细胞相互作用的总体图景。在……里面 AIM2，我将鉴定和鉴定一种对多种菌株通用的细菌抗原。在Aim3，T细胞的结果 分析将被用来“设计”治疗细菌群落，在其中炎性菌株将 在IBD小鼠模型中建立耐受性社区来治疗结肠炎而辍学。成功者 该项目的完成将“破译”肠道微生物群对免疫调节的一株一株的观点。 并为“设计”合理调节免疫反应的新疗法提供了分子基础 治疗IBD和其他破坏性的全身性疾病。 来自K99和导师的支持将用最先进的技术补充我在免疫学方面的专业知识 微生物学和单细胞生物学技术。我将通过迈克尔博士的培训来实现这一点 Fischbach(主要导师，细菌遗传学)，Daniel Mucida博士(单细胞生物学和T细胞共同导师) 生物学)，Justin Sonnenburg博士(咨询委员会，元基因组分析)，KC Huang博士，(咨询 委员会，合成微生物群落)。我在K99/R00大奖期间接受的培训和指导 将为我实现我的学术目标--建立一个充满活力的独立的 研究计划，可以回答肠道生态系统中的一个重要问题，以建立一个新的 有治疗作用。

Project Summary/Abstract Immune modulation holds tremendous promise for the treatment of cancer, autoimmune disease, metabolic disease, and infectious disease. New ways to generate antigen-specific T and B cells inexpensively and with minimal reactogenicity are badly needed. Certain bacterial strains from the gut microbiome elicit a potent, specific adaptive immune response. The underlying mechanisms could guide new therapeutic strategies in which bacteria-specific immune responses are rationally altered or re-directed. The gut is the site of a wide variety of microbe-microbe and microbe-host interactions. However previous papers have characterized microbial strains of the microbiome under artificial conditions of mono-colonization. This approach can identify strains that are capable of modulating immune cells, but it is unknown how a strain functions in the presence of other members of the complex microbiota. This knowledge gap hinders a logical design of a microbial therapeutic. My long-term research objective is to develop new technologies to understand the “physiological” gut ecosystem at the level of molecular mechanisms so that I can identify immune modulatory bacteria from the microbiome and build new therapeutics. In this proposal, I will establish a “physiological” gut by colonizing germ-free mice with a complex defined gut community (104 strains) and profile T cell responses to each strain individually. In Aim1, I will identify a set of bacteria-reactive TCRs and their stimulatory strain by single cell technologies, so that I can provide a big picture of the strain-T-cell interactions at the single TCR level. In Aim2, I will identify and characterize a bacterial antigen common to multiple strains. In Aim3, the result of T cell profiling will be used to “design” therapeutic bacterial communities in which inflammatory strains will be dropped out for building a tolerogenic community to treat colitis in an IBD mouse model. The successful completion of this project will “decode” a strain-by-strain view of immune modulation by the gut microbiome and provide a molecular basis for “designing” the new therapy that logically modulates immune response to treat IBD and other devastating systemic disorders. Support from the K99 and mentors will complement my expertise in immunology with state-of-art technologies in microbiology and single cell biology. I will accomplish this with training from Dr. Michael Fischbach (primary mentor, bacterial genetics), Dr. Daniel Mucida (co-mentor, single-cell biology and T cell biology), Dr. Justin Sonnenburg (advisory committee, metagenomic analysis), and Dr KC Huang, (advisory committee, a synthetic microbial community). The training and mentorship I receive during my K99/R00 award will provide a critical stepping stone for me to achieve my academic goal of establishing a vibrant independent research program that can answer an important question in the gut ecosystem for establishing a new therapeutic.