Engineered Probiotics for Closed-Loop Control of Disease-Associated Gut Metabolites in Gut-On-Chip Models

用于闭环控制芯片肠道模型中疾病相关肠道代谢物的工程益生菌

• 批准号: 10572700
• 负责人: Benjamin Michael Woolston
• 金额: $ 15.7万
• 依托单位: NORTHEASTERN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-15 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10572700
• 关键词: Anti-Inflammatory Agents; Architecture; Biological Assay; Butyrates; Chemicals; Clinical; Complex; Consensus; Consumption; Crohn' s disease; Data; Directed Molecular Evolution; Disease; Electron Transport; Engineered Probiotics; Engineering; Ensure; Environment; Enzymes; Epithelial; Equilibrium; Escherichia coli; Gel; Genetic; Health; Human; Hydrogen Sulfide; In Situ; In Vitro; Individual; Inflammation; Integration Host Factors; Intestines; Kinetics; Link; Logic; Measurement; Metabolic Pathway; Metabolism; Microbe; Mitochondria; Modality; Modeling; Mucous Membrane; Mucous body substance; Organ; Output; Oxygen; Pathway interactions; Patients; Performance; Physiological; Physiology; Play; Probiotics; Production; Property; Publishing; Reactive Oxygen Species; Research; Resolution; Rheology; Role; Structure; Sulfides; System; Technology; Testing; Therapeutic; Thick; Transcriptional Regulation; Tube; Ulcerative Colitis; Validation; Work; base; commensal microbes; design; design-build-test; disorder control; genotoxicity; gut microbiota; high reward; high risk; human tissue; inflammatory marker; interest; mathematical model; microbial; mucosal microbiota; novel; novel therapeutics; operation; oxidation; promoter; response; sensor; small molecule; spatiotemporal; synthetic biology; therapy outcome; transcription factor

PROJECT SUMMARY Engineered commensal microbes represent a promising platform for controlling microbial metabolism in the gut microbiota for therapeutic outcomes. While strains have been successfully engineered to either reduce the concentration of a toxic metabolite or produce a therapeutic one, strains capable of controlling the level of a metabolite within a narrow window have not been developed. Such ‘smart probiotics’, able to dynamically respond to the environment and either produce or consume a compound based on the local concentration, would be particularly useful for stabilizing metabolites which play a concentration-dependent role in host health and disease. For example, ulcerative colitis and Crohn’s disease have been linked to microbially produced hydrogen sulfide (H2S), with a growing consensus that low levels of this molecule have anti-inflammatory properties and support a healthy epithelium, whereas high concentrations of H2S are genotoxic, inhibit mitochondrial function and butyrate oxidation, and potentially weaken the mucosal barrier. Given that H2S concentration varies spatially and temporally throughout the mucosa, controlling H2S within a tight range is not possible with current small- molecule sulfide donors, which release sulfide regardless of local concentration. We propose a new synthetic biology-based approach to controlling microbial metabolites in situ, in which the engineered microbe uses a transcription factor responsive to the metabolite of interest to dynamically balance the expression of metabolic pathways for production and consumption of the metabolite. This will produce a stable, titratable concentration in a manner analogous to a thermostat. In this proposal, we will demonstrate this technology by developing engineered strains of E. coli Nissle to dynamically control the level of H2S in situ, incorporating mathematical modeling and a human organ-chip platform into the design-built-test cycle to achieve robust and stable operation in the complex gut environment. If successful, the proposed research will establish the design rules for a novel synthetic biology control strategy applicable to many gut metabolites with concentration-dependent roles in disease, identify and mitigate host factors that impact engineered strain performance, and facilitate greater translatability of synthetic probiotics.

项目概要 工程共生微生物代表了控制微生物代谢的有前途的平台 肠道微生物群对治疗结果的影响。虽然菌株已被成功改造以减少 有毒代谢物的浓度或产生治疗性代谢物，能够控制有毒代谢物水平的菌株 狭窄窗口内的代谢物尚未开发出来。这种“智能益生菌”能够动态地 响应环境并根据当地浓度产生或消耗化合物，将 对于稳定代谢物特别有用，这些代谢物在宿主健康中发挥浓度依赖性作用 疾病。例如，溃疡性结肠炎和克罗恩病与微生物产生的氢气有关 硫化物 (H2S)，越来越多的人认为低水平的这种分子具有抗炎特性，并且 支持健康的上皮细胞，而高浓度的 H2S 具有遗传毒性，会抑制线粒体功能 和丁酸氧化，并可能削弱粘膜屏障。鉴于 H2S 浓度随空间变化 并在整个粘膜中暂时控制 H2S 在较小的范围内是不可能的 硫化物分子供体，无论局部浓度如何，都会释放硫化物。我们提出了一种新的合成 基于生物学的原位控制微生物代谢物的方法，其中工程微生物使用 转录因子对感兴趣的代谢物作出反应，动态平衡代谢物的表达 代谢物的生产和消耗途径。这将产生稳定的、可滴定的浓度 以类似于恒温器的方式。在本提案中，我们将通过开发来演示这项技术 工程化的大肠杆菌 Nissle 菌株能够在原位动态控制 H2S 水平，并结合数学 将建模和人体器官芯片平台纳入设计构建测试周期，以实现稳健稳定的运行 在复杂的肠道环境中。如果成功，拟议的研究将为小说建立设计规则 合成生物学控制策略适用于许多具有浓度依赖性作用的肠道代谢物 疾病，识别和减轻影响工程菌株性能的宿主因素，并促进更大的 合成益生菌的可翻译性。