Microbiome Driven Proteolysis as a Contributing Factor to Severity of Ulcerative Colitis Disease Activity

微生物组驱动的蛋白水解是溃疡性结肠炎疾病活动严重程度的影响因素

• 批准号: 10673152
• 负责人: David J Gonzalez
• 金额: $ 54万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10673152
• 关键词: Address; Animals; Bacteria; Bacteroides; Basic Science; Biochemical; Blood; Cell Culture Techniques; Chronic; Chronic Disease; Clinical; Colitis; Collagen; Colon; Colonic inflammation; Coupled; Crohn' s disease; Data Set; Development; Diagnosis; Disease; Disease Management; Epithelium; Feces; Functional disorder; Genetic; Genomics; Germ-Free; Goals; Histologic; Human; Immune response; In Vitro; Individual; Inflammatory; Inflammatory Bowel Diseases; Integration Host Factors; Interleukin-10; Intestinal permeability; Investigation; Link; Mediating; Metagenomics; Microbiology; Modeling; Mucins; Mucositis; Mus; Nature; North America; Pathway interactions; Patients; Peptide Fragments; Peptide Hydrolases; Persons; Play; Prevalence; Protease Inhibitor; Proteins; Proteolysis; Publishing; Regulation; Role; Sampling; Serine Proteinase Inhibitors; Serum; Severities; Severity of illness; Shotguns; Stress; Structure; Taxonomy; Testing; Therapeutic; Tight Junctions; Translational Research; Transplantation; Ulcerative Colitis; Validation; Work; bacterial genetics; cohort; data integration; design; effective therapy; gut microbiome; gut microbiota; host microbiome; host microbiota; improved; in vitro Model; in vivo; in vivo Model; inhibitor; intestinal barrier; metaproteomics; microbial; microbiome; microbiome research; microbiota; mutant; novel; novel strategies; novel therapeutic intervention; prevent; tool

Ulcerative colitis (UC) is a chronic disease characterized by inflammation of the mucosa of the colon. UC has a significant global burden, and is characterized by an aberrant immune response directed towards the gut microbiota. Current treatment options exclusively target host inflammatory pathways and are often ineffective in managing disease. Nearly 1 million individuals in North America are currently living with UC and its prevalence in humans continues to grow worldwide. The considerable number of growing cases, coupled with the lack of an effective therapy, stresses the need for investigation into new therapeutic interventions against UC. Our group recently characterized host-microbiome interactions governing UC through six fecal or serum based –omic datasets from 40 UC patients displaying a wide range of clinical, endoscopic, and histologic disease activity. After broad-scale analyses, the six datasets provided powerful evidence towards a central hypothesis: Bacteroides vulgatus proteases can drive UC disease severity. Metaproteomics pinpointed B. vulgatus proteases as a distinguishing feature of severity. Shotgun metagenomics guided taxonomic inferences and revealed that the B. vulgatus association was driven primarily by protein regulation as opposed to microbial abundances. An abundance of serine protease inhibitors found in the patient serum suggested the importance of proteases. The metapeptidome showed increased peptide fragments correlated with UC disease severity. An independent 210-person cohort validated the strong connection between B. vulgatus proteases and UC disease severity. Testing our hypothesis, we demonstrate B. vulgatus can disrupt intestinal epithelial permeability in vitro, and protease inhibition was sufficient to restore epithelial barrier. Monocolonization of B. vulgatus into germfree IL-10 deficient mice demonstrated colonization induces colitis in these animals and protease inhibition is sufficient to prevent colitis development. Furthermore, transplantation of feces from UC patients with over-abundant B. vulgatus proteases into germ-free mice induced colitis dependent on protease activity (Mills et al., Nature Microbiology 2021). Based on our published work, we have formulated two testable hypotheses to further build on these new findings: 1) proteolysis is a central mechanism utilized by B. vulgatus to induce colitis in vitro and in vivo relevant to UC and 2) B. vulgatus proteases degrade key components of the intestinal barrier. The specific aims of this application are to define the genomic context, roles, and develop specific inhibitors against B. vulgatus proteases in UC (Aim 1), characterize the targets and dynamics of B. vulgatus mediated proteolysis in UC (Aim 2). To complete this proposal, we will use a multifaceted approach of state-of-the-art biochemical, cell culture, bacterial genetics, and in vivo models. Ultimately, this work has the potential to break new ground in UC basic and translational research.

溃疡性结肠炎(UC)是一种以结肠粘膜炎症为特征的慢性疾病。UC具有显著的全球性负担，其特征是针对肠道微生物区系的异常免疫反应。目前的治疗方案只针对宿主炎症途径，在管理疾病方面往往无效。北美目前有近100万人患有UC，其在全球人类中的流行率继续上升。数量不断增加的病例，加上缺乏有效的治疗方法，强调了对UC新的治疗干预措施进行调查的必要性。我们小组最近通过来自40名UC患者的6个基于粪便或血清的基因组数据集描述了宿主-微生物组相互作用对UC的控制作用，这些数据集显示了广泛的临床、内窥镜和组织学疾病活动。经过广泛的分析，这六个数据集为一个中心假设提供了强有力的证据：普通拟杆菌蛋白水解酶可以驱动UC疾病的严重性。总蛋白质组学将普通芽孢杆菌的蛋白水解酶确定为严重程度的一个显著特征。鸟枪式元基因组学指导了分类学推断，并揭示了普通芽孢杆菌的相关性主要是由蛋白质调节驱动的，而不是微生物的丰度。在患者血清中发现了大量的丝氨酸蛋白酶抑制剂，这表明了蛋白酶的重要性。Metapeptidome显示与UC疾病严重程度相关的多肽片段增加。一项由210人组成的独立队列证实了普通芽胞杆菌蛋白水解酶与UC疾病严重程度之间的密切联系。为了验证我们的假设，我们证明了普通芽孢杆菌在体外可以破坏肠上皮细胞的通透性，而抑制蛋白酶足以恢复上皮屏障。在无菌IL-10缺陷小鼠体内的单一定植表明，在这些动物中定植可以诱导结肠炎，而抑制蛋白酶足以阻止结肠炎的发展。此外，将UC患者的粪便移植到无菌小鼠中，这些患者的粪便中含有过多的芽孢杆菌蛋白酶，可依赖于蛋白酶的活性诱导结肠炎(Mills等人，《自然微生物学》，2021)。在我们已发表的工作的基础上，我们提出了两个可检验的假说，以进一步建立在这些新发现的基础上：1)蛋白分解是普通芽孢杆菌在体外和体内诱导与UC相关的结肠炎的中心机制；2)普通芽孢杆菌蛋白酶降解肠道屏障的关键成分。本申请的具体目的是确定UC中的基因组背景、作用，并开发针对普通芽胞杆菌蛋白水解酶的特异性抑制剂(目标1)，表征普通芽胞杆菌在UC中介导的蛋白分解的靶点和动力学(目标2)。为了完成这项提议，我们将使用最先进的生化、细胞培养、细菌遗传学和体内模型的多方面方法。最终，这项工作有可能在UC基础和翻译研究方面开辟新的天地。