Genomic Analysis of Perianal Fistulizing Crohn's Disease across Ancestries

跨血统肛周瘘管克罗恩病的基因组分析

• 批准号: 10461837
• 负责人: SUBRA KUGATHASAN
• 金额: $ 38.56万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-16 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10461837
• 关键词: Affect; African; African American population; American; Architecture; Atlases; Bioinformatics; Biological; Biological Markers; Biological Models; Biopsy; Blood; Blood specimen; Cells; Communication; Complex; Complication; Crohn' s disease; Data; Disease; Disease Outcome; Disease Progression; Disease model; Disease remission; Dissection; Enrollment; Epithelial; Epithelial Cells; European; Feces; Fistula; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genomics; Growth Factor; High Prevalence; Hospitals; Immune; Immune system; In Vitro; Individual; Inflammatory; Intestines; Lamina Propria; Legal patent; Link; Maps; Matched Group; Medical; Metabolic; Microbe; Modeling; Molecular; Mucous Membrane; Nature; Operative Surgical Procedures; Organoids; Outcome; Pathogenesis; Pathologic; Pathology; Pathway interactions; Patients; Phenotype; Population; Quality of life; Rectum; Refractory; Reporting; Resistance; Resolution; Risk; Role; Sampling; Severity of illness; Signal Transduction; Skin; Source; Staging; Suspensions; TNF gene; Testing; Therapeutic Intervention; Time; base; bioinformatics pipeline; causal variant; cell type; clinical phenotype; comparative; comparison intervention; cost; cytokine; design; disability; dysbiosis; follow-up; genome wide association study; healing; health disparity; insight; microbiome; multiple omics; novel; patient response; peripheral blood; personalized intervention; predictive modeling; recruit; rectal; response; single-cell RNA sequencing; transcriptome; transcriptomics; treatment response

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.

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 往往难以治疗，并与严重残疾和较低的生活质量有关。发泡CD 不成比例地影响非裔美国人(AA)，呈现出更高的患病率和更严重的 具有破坏性的病理性。此外，对CD进行瘘管治疗通常需要更积极的医疗和 手术干预比腔内疾病更有效。有几条证据表明， 直肠上皮、微生物组和免疫系统驱动了肛周瘘管的特殊发病机制， 但在分子和细胞水平上对此知之甚少，尤其是与祖先的差异。 肛周瘘的复杂性涉及微生物和多种免疫和非免疫之间的沟通 免疫细胞类型为深入研究该病的分子特征提供了强有力的依据。一 假说认为，不同的生物机制部分是由于非洲和非洲之间不同的基因组结构 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对直肠活检组织和直肠组织进行基因组比较 外周血免疫细胞，将用于研究肛周本质的病理机制 瘘管化CD包括非洲血统和欧洲血统患者群体的具体比较。在基础上建设 这些祖先群体之间的整个粘膜的初步转录组图谱表明 代谢和炎症信号的差异，并利用新出现的肠道细胞图谱，我们的 对120例患者的分析将确定哪些细胞和基因表达特征与缓解有关， 病情稳定，或病情恶化。目标1是对120名患者的直肠进行活检并采集血样 介绍，并在后续行动中再次进行微生物群采样(直肠洗涤和大便)，由 深入的临床表型。两个祖先群体(欧洲人和AA人)同样有能力进行比较 学习。目标2是使用单细胞RNA测序来描绘每一个相对丰度的变化 数十种关键细胞类型，并确定与三种治疗方法一致的生物标志物的关键基因 每个单元格类型中的响应状态。先进的生物信息学方法将被用来表征 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 识别细胞型特异性eQTL研究慢性萎缩性胃病。随后，在目标3中，机械地剖析了具体的 将通过患者来源的肠道器官的体外培养来评估患者的特异性 在相关分子刺激下的反应。这一发现将同时阐明细胞和分子 促成CD瘘管病健康差距的一个主要来源的机制，并支持向 支持治疗干预的个性化基因组医学图谱。