Mount Sinai NYC Genetics Research Center: Multi-omic integration across data-types, cell niches and populations

项目摘要 本提案是应FOA RFA-DK-21-022的要求提交的，作为遗传学研究中心(GRC)， 在NIDDK炎症性肠病(IBD)遗传学联合会(IBDGC)内，在伊坎医学院 纽约西奈山医学中心。在本期间，我们在界定 回肠克罗恩病抗肿瘤坏死因子无反应的机制及NOD2突变在回肠疾病中的作用 改变血液单核细胞分化，导致异常的髓系基质生态位。在这项提案中，我们寻求 对血液中单核细胞分化的作用进行了扩大，但新近关注的是肛周瘘，一大未见 克隆氏病的医疗需求，对非裔美国人的影响不成比例。单细胞转录组有 为IBD的分子机制提供了巨大的洞察力；我们的实验室在这方面拥有丰富的专业知识，并将 利用新的方法，包括多组ATAC+转录组和更高分辨率的空间 转录学平台即将推出。目标1将专注于涉及肛周的直接体外单细胞分析 瘘管包括非裔美国人和欧洲血统的克罗恩病患者。AIM 2将在体外扩增 分析的重点是直肠来源的肠样病变和系列的血液白细胞和血小板分析。都是上皮性的 细胞和单核细胞可分化为间充质样细胞。茎和其他的程度 多能细胞带有慢性炎症的印记，在急性炎症发作与缓解期间将进行评估。 通过多组ATAC+转录组和系列血白细胞和血小板分析。比较分析两种方法 这些跨欧洲和非裔美国人队列的多组数据将被执行，这些数据集中在GWAS基因座上， 重点研究WNT、AP-1和活性氧自由基的作用。在直接体外数据(目标1)和 体外系统(目标2)将提供最大的洞察力。目标3描述了我们对IBDGC的建议贡献 大体上说。我们一直是全联盟临床招募工作的主要贡献者(回肠切除， 溃疡性结肠炎)，以及最近招募非裔美国人和西班牙裔IBD患者。 我们已经报道了非洲裔美国人病例对照参考数据对这两个共同 (改善多基因风险评分)和罕见(与极早发病的IBD基因重叠)遗传变异。超越 肛周克罗恩病，新招募的溃疡性结肠炎患者因急性症状住院； 系列血液分析是可行的，具有关键的短期结果。对机理的完整解释 潜在的IBD基因座关联将需要在人群中进行更深层次的基因组询问，以及数据 跨空间(细胞定位、疾病程度)、关键临床场景和时间的集成。

PROJECT ABSTRACT This proposal is submitted in response to FOA RFA-DK-21-022, to serve as a Genetics Research Center (GRC), within the NIDDK Inflammatory Bowel Disease (IBD) Genetics Consortium (IBDGC), at the Icahn School of Medicine at Mount Sinai, New York. During the present period, we made substantive progress in defining mechanisms of anti-TNF non-response in ileal Crohn’s disease and defined the role of NOD2 mutations in altering blood monocyte differentiation to result in an aberrant myeloid-stromal niche. In this proposal, we seek to expand on the role of blood monocyte differentiation, but newly-focused on perianal fistulae, a major unmet medical need in Crohn’s disease, disproportionately affecting African-Americans. Single cell transcriptomics has provided enormous insight into molecular mechanisms in IBD; our lab has substantial expertise in this and will leverage new approaches including multiome ATAC + transcriptome and higher resolution spatial transcriptomics platforms available soon. Aim 1 will focus on direct ex-vivo single cell analyses involving perianal fistulae including African-American and European ancestry Crohn’s disease patients. Aim 2 will expand in vitro analyses focusing on rectal-derived enteroids and serial blood leukocyte and platelet analyses. Both epithelial cells and monocytes can differentiate into mesenchymal-type cells. The extent to which stem- and other pluripotent cells are imprinted with chronic inflammation and during acute flares vs. remission will be evaluated via multiome ATAC + transcriptome and serial blood leukocyte and platelet analyses. Comparative analyses of these multi-omic data across European vs. African-American cohorts focused on GWAS loci will be performed, focusing on WNT, AP-1 and reactive oxygen species’ effects. Iterating between direct ex-vivo data (Aim 1) and in vitro systems (Aim 2) will provide maximal insight. Aim 3 describes our proposed contributions to the IBDGC broadly. We have been major contributors to Consortium-wide clinical recruitment efforts (ileal resection, ulcerative colitis demarcation), and more recently, recruitment of African-American and Hispanic IBD patients. We have reported on the particular value of African-American case-control reference data for both common (improving polygenic risk scores) and rare (overlap with very-early onset IBD genes) genetic variants. Beyond perianal Crohn’s disease, new recruitment of ulcerative colitis patients hospitalized with acute flares is proposed; serial blood analyses are feasible, with key short-term outcomes. A complete explication of mechanisms underlying IBD locus associations will require deeper genomic interrogation across populations, as well as data integration across space (cellular niches, disease extent), key clinical scenarios and time.