Development of Biomarkers for IBD Using Protein Chips

描述（由申请人提供）：炎症性肠病（IBD），包括溃疡性结肠炎（UC）和克罗恩病（CD），是一种慢性且经常致残的肠道炎症性疾病，在美国影响超过100万人。UC和克罗恩结肠炎最可怕的并发症之一是患结直肠癌（CRC）的风险大大增加，约占IBD患者死亡总数的15%。到目前为止，虽然内窥镜检查仍然是IBD诊断/预后的唯一确定和重要工具，但它是一种侵入性和高度资源密集型的手术。因此，需要一种更便宜、更省力、侵入性更小的IBD诊断/预后工具。在这里，我们提出了一种新的高通量蛋白质组学方法来筛选和鉴定IBD的新的血清学生物标志物。我们假设IBD患者的血清中存在疾病特异性抗体，无论是抗肠道微生物还是抗人内源性蛋白（自身抗体），这些特异性抗体可以作为IBD诊断的血清学生物标志物，或作为疾病预后和/或治疗反应性的指示物。随着对大量正常受试者和IBD患者血清的完全获取，血清抗体将直接用于筛选高密度蛋白芯片（也称为蛋白质阵列），以鉴定IBD特异性蛋白抗原。我们的酵母蛋白芯片覆盖了整个酵母蛋白质组（5800种独特的蛋白质），由约翰霍普金斯大学机器人生产，将用于我们提议的筛选的初始阶段。目前正在开发大肠杆菌蛋白质组芯片（含有4288种独特蛋白质）和人类蛋白质芯片（含有4000种独特蛋白质），预计在3 ~ 5个月内完成。大肠杆菌和人类蛋白芯片将用于第二阶段的生物标志物筛选。目标是确定CD和uc特异性血清学生物标志物，并使用这些生物标志物开发临床可靠、全面的一步诊断蛋白质芯片/试剂盒，用于IBD诊断和分型。此外，鉴定IBD特异性抗体不仅可能揭示新的IBD致病机制，还可能为IBD的治疗干预提供潜在的分子靶点。

DESCRIPTION (provided by applicant): Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic and frequently disabling intestinal inflammatory disorders that affect more than a million individuals in the US. One of the most dreaded complications of UC and Crohn's colitis is the greatly increased risk of developing colorectal cancer (CRC), which accounts for approximately 15% of all deaths in IBD patients. So far, while endoscopy remains as the only established and vital tool for IBD diagnosis/prognosis, it is an invasive and highly resource-intensive procedure. Therefore, a less expensive, less laborious, less invasive tool is needed for IBD diagnosis/prognosis. Here, we propose a novel high-throughput proteomic approach to screen and identify new serological biomarkers for IBD. We hypothesize that disease- specific antibodies, either anti-intestinal microorganisms or anti-human endogenous proteins (autoantibodies), are present in the sera of IBD patients, and these specific antibodies can be used as serological biomarkers for either IBD diagnosis, or as indicative of disease prognosis and/or responsiveness to therapy. With a complete access to a large number of sera from normal subjects and IBD patients, serum antibodies will be used directly to screen high-density protein chips (also called protein arrays) to identify IBD-specific protein antigens. Our yeast protein chips that cover the entire yeast proteome (with 5,800 unique proteins) and robotically produced at Johns Hopkins will be used in the initial stage of our proposed screening. We are currently in the developing phase of generating E. coli proteome chips (with 4288 unique proteins) and human protein chips (4,000 unique proteins), which are expected to be ready in 3- 5 months. E. coli and human protein chips will be used in the second phase of biomarker screening. The goal is to identify CD- and UC-specific serological biomarkers and to use these biomarkers to develop a clinically reliable, comprehensive one-step diagnostic protein chip/kit for IBD diagnosis and subtyping. Moreover, identification of IBD-specific antibodies might not only reveal new pathogenic mechanisms of IBD, but also provide potential molecular targets for therapeutic intervention of IBD.