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和克罗恩氏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患者所有死亡的15%。到目前为止，虽然内窥镜检查仍然是IBD诊断/预后的唯一既定和重要工具，但它是一种侵入性和高度资源密集型的手术。因此，IBD诊断/预后需要一种更便宜、更省力、更少侵入性的工具。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，抗肠道微生物或抗人内源性蛋白（自身抗体），并且这些特异性抗体可用作IBD诊断的血清学生物标志物，或作为疾病预后和/或对治疗的反应性的指示。在完全获取大量正常人和IBD患者血清的情况下，将直接使用血清抗体筛选高密度蛋白芯片（也称蛋白阵列），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（具有5，800种独特的蛋白质），并在约翰霍普金斯机器人生产，将用于我们提出的筛选的初始阶段。我们目前正处于开发阶段，产生E。大肠杆菌蛋白质组芯片（含4288种独特蛋白质）和人类蛋白质芯片（含4,000种独特蛋白质），预计3- 5个月内完成。E.大肠杆菌和人类蛋白质芯片将用于生物标志物筛选的第二阶段。目的是鉴定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用于IBD诊断和分型的临床可靠的、全面的一步诊断蛋白芯片/试剂盒。IBD特异性抗体的鉴定不仅可以揭示IBD的新的致病机制，而且可以为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.