Genomic Analysis of Perianal Fistulizing Crohn's Disease across Ancestries

项目摘要 肛周瘘管性克罗恩病是一种累及直肠的克罗恩病（CD）的衰弱表型。它 通常难以治疗，并与严重残疾和生活质量差有关。瘘管型CD 不成比例地影响非洲裔美国人（AA），表现出更高的患病率， 破坏性病理学除了瘘管CD往往需要一个更积极的组合医疗和 外科手术比管腔疾病更有效。一些证据表明， 直肠上皮、微生物组和免疫系统，驱动肛周瘘的患者特异性发病机制， 但在分子和细胞水平上，特别是在祖先差异方面，人们对这些知之甚少。 肛瘘的复杂性涉及微生物之间的交流和多重免疫和非免疫系统， 免疫细胞类型为需要对疾病进行深入的分子表征提供了强有力的理由。一 一种假说认为，不同的生物学机制部分是由于非洲人和非洲人之间不同的基因组结构造成的， 而欧洲血统的患者导致了健康结果的差异。因此，综合 利用最先进的单细胞基因表达谱的直肠活检和 外周血免疫细胞，将用于探讨肛周病变的本质机制 瘘管性CD，包括非洲和欧洲血统患者组的具体比较。基础上 这些祖先群体之间的整个粘膜的初步转录组分析表明， 代谢和炎症信号的差异，并利用新兴的肠道细胞图谱，我们 对120例病例的分析将确定哪些细胞和基因表达特征与缓解相关， 稳定或疾病进展。目的1：对120例直肠癌患者进行直肠活检， 介绍，并再次在随访时，也与微生物组采样（直肠冲洗液以及粪便），支持由 深层临床表型分析两个祖先群体（欧洲人和AA）具有相同的比较效力 问题研究目的2是使用单细胞RNA测序来分析每种基因的相对丰度的变化， 几十种关键细胞类型，并确定关键基因，这些基因是三种治疗性肿瘤的一致生物标志物。 每个细胞类型内的反应状态。先进的生物信息学方法将用于表征 细胞相互作用网络，并将基因表达的遗传调控与全基因组关联联系起来 通过鉴定细胞类型特异性eQTL进行CD研究。随后，在目标3中，对特定的 将采用患者来源的肠类器官的体外培养物来探索途径，以评估患者特异性 受到相关分子刺激时的反应。这些发现将阐明细胞和分子 导致瘘管化CD中健康差异的主要来源的机制，并支持向 个性化的基因组医学分析，以支持治疗干预。

Project Summary Perianal fistulizing Crohn’s disease is a debilitating phenotype of Crohn’s disease (CD) involving the rectum. It is often refractory to treatment and is associated with severe disability and poor quality of life. Fistulizing CD disproportionately affects African Americans (AA), presenting with much higher prevalence, and more severe with destructive pathology. Besides fistulizing CD often requires a more aggressive combination of medical and surgical intervention than does luminal disease. Several lines of evidence suggest that interactions between the rectal epithelium, the microbiome, and the immune system, drive patent-specific pathogenesis of perianal fistula, but there is very little known about these at the molecular and cellular level, particularly with ancestral differences. The complexity of perianal fistula involving communication between microbes and multiple immune and non- immune cell types provides a strong rationale for a need for deep molecular characterization of the disease. One hypothesis is that different biological mechanisms due in part to divergent genomic architecture between African- and European-ancestry patients contributes to the disparity in health outcomes. Consequently, integrative genomic comparisons utilizing state-of-the-art single cell gene expression profiling of rectal biopsies and of peripheral blood immune cells, will be used to investigate the nature of pathological mechanisms of perianal fistulizing CD including specific comparison of African and European ancestry patient groups. Building on preliminary transcriptome profiling of the whole mucosa between these ancestry groups that implicates differences in metabolic and inflammatory signaling, and taking advantage of the emerging Gut Cell Atlas, our profiling of 120 cases will establish which cellular and gene expression features associate with remission, stabilization, or progression of disease. Aim 1 is to biopsy rectum and take blood samples from 120 patients at presentation, and again at follow-up, also with microbiome sampling (rectal wash as well as stool), supported by deep clinical phenotyping. Two ancestral populations (European and AA) are equally powered for comparison studies. Aim 2 is to use single cell RNA sequencing to profile changes in the relative abundance of each of dozens of key cell types, and to identify key genes that are consistent biomarkers of the three therapeutic response states within each cell type. Advanced bioinformatics approaches will be used to characterize the network of cellular interactions, and to link the genetic regulation of gene expression to genome-wide association studies of CD by identifying cell-type specific eQTL. Subsequently, in Aim 3, mechanistic dissection of specific pathways will be pursued with in vitro cultures of patient-derived intestinal organoids to assess patient specific responses when stimulated by relevant molecules. The findings will both illuminate cellular and molecular mechanisms that contribute to a major source of health disparity in fistulizing CD, and support the transition to personalized genomic medical profiling in support of therapeutic intervention.