Development of a LH-PCR Based Diagnostic for Inflammatory Bowel Disease

基于 LH-PCR 的炎症性肠病诊断方法的开发

• 批准号: 7272260
• 负责人: Patrick M Gillevet
• 金额: $ 10.14万
• 依托单位: BIOSPHEREX, LLC
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-06-15 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7272260
• 关键词: Address; Adverse effects; Affect; American; Animal Model; Animals; Antibiotic Therapy; Antibiotics; Area; Attention; Bacteria; Bacterial Counts; Bioinformatics; Biopsy; Biopsy Specimen; Case Series; Cecum; Celiac Disease; Chemicals; Chronic; Class; Clinical; Cluster Analysis; Colitis; Colon; Colorectal; Communities; Complex; Complication; Control Groups; Crohn' s disease; Custom; Data; Data Set; Databases; Development; Diagnosis; Diagnostic; Diagnostic tests; Diarrhea; Disease; Disease remission; Disruption; Distal part of ileum; Elemental Diets; Enterobacteriaceae; Enterocolitis; Environment; Environmental Microbiology; Epithelial; Escherichia coli; Excision; Feces; Fingerprint; Flare; Gastrointestinal tract structure; Genetic; Genus Cola; Germ-Free; Goals; Hand; Health; Healthcare Systems; Heterogeneity; Human; Human body; Ileostomy; Immune system; Immunosuppressive Agents; Incidence; Individual; Infection; Inflammation; Inflammatory; Inflammatory Bowel Diseases; Intestines; Invasive; Irritable Bowel Syndrome; Ischemic Colitis; Knock-out; Knowledge; Laboratories; Lead; Length; Libraries; Mails; Methods; Microbial Biofilms; Molecular Profiling; Monitor; Mucous Membrane; Numbers; Operative Surgical Procedures; Pathogenesis; Patient Monitoring; Patients; Pattern; Pharmaceutical Preparations; Physicians; Pilot Projects; Polymerase Chain Reaction; Population; Pouchitis; Primary Care Physician; Probiotics; Quality of life; Radiation Colitis; Rate; Reaction; Rectum; Recurrence; Relapse; Reporting; Research Ethics Committees; Ribosomal RNA; Rodent; Running; Sampling; Screening procedure; Site; Soil; Statistically Significant; Swab; Symptoms; T-Lymphocyte; Techniques; Technology; Testing; Thinking; Time; Tissues; Toxic effect; Ulcerative Colitis; Variant; analytical tool; attenuation; base; carcinogenesis; clinical application; cost; cost effective; data mining; design; disorder control; enema administration; follow-up; gastrointestinal; germ free condition; healthy volunteer; ileum; improved; insight; microbial; microbial community; novel diagnostics; pathogen; prebiotics; prevent; rectal; repository; restoration; satisfaction; success; time use; tool; treatment effect

DESCRIPTION (provided by applicant): Inflammatory Bowel Diseases (IBDs), namely ulcerative colitis (UC) and Crohn's disease (CD), are chronic, lifelong, relapsing illnesses, affecting close to 1 million Americans and costing approximately 2 billion dollars/year to the US healthcare system. IBDs are of unknown cause, have no cure and are increasing in incidence. We have found that the diversity of the mucosa associated or luminal wall adherent microbial populations is decreased in IBD. We also identified putative peaks in LH-PCR fingerprints that may indicate patterns associated with IBD. Furthermore, linkage of our LH-PCR fingerprints to clone sequences show that certain bacterial groups are present in the mucosal flora of IBD patients. These findings have led us to hypothesize that there is a protective biofilm of bacteria adhering to the Ileocolonic wall and an invasion of this protective biofilm by lumen bacteria in IBD (dysbiosis). Our initial results indicate that there is little variation in this protective biofilm along the colon and ileum. Our initial observations also indicate that the lumen/stool microflora may be indicative of the disease state. Our goal is to determine the feasibility of monitoring dysbiosis by fingerprinting rectal swabs and stool samples collected by the patient. Our second aim is to fully characterize these microflora communities by pyrosequencing mucosal, lumen, rectal swab, and stool samples. If we demonstrate that stool cards and rectal swabs are a reliable representation of the lumen and mucosal bacterial patterns, then our diagnostic test will be the most feasible, noninvasive and easy test to assess dysbiosis. Patients can place their stool on the cards (or physicians can place the stool on the card after rectal examination) and mail them to our central laboratory for bacterial fingerprinting. The goal is to identify flare up before it becomes clinically apparent and thus prevent the symptomatic flare-ups with damage to the intestinal track. This could clearly improve quality of life and prevent the complication of surgery. Studies that characterize microflora in humans using powerful techniques from environmental microbiology can bring about significant advances in the understanding of these illnesses. There is a growing recognition of the importance of microflora in health and disease not limited to IBD but also in other areas such as colorectal carcinogenesis, intestinal infections, celiac disease, irritable bowel syndrome, prebiotic and probiotic therapies. This proposal involves the first time use of a sophisticated and highly reproducible bacterial fingerprinting tool, LH-PCR, in the study of microflora in the GI tract. The team assembled for this proposal is interdisciplinary and combines three very valuable sets of expertise to address the complexity of the GI microflora, namely clinical IBD expertise, environmental microbiology expertise, and bioinformatics expertise to analyze complex sets of data. New diagnostic tools based on LH-PCR can be utilized for routine real-time clinical use as direct result of this proposal. Such a tool can then be used to help determine the absence/presence of disease; and predict the various phenotypic presentations of the disease, the disease course, and treatment effects. If distinct differences between the microflora of controls and IBD are defined as proposed, it would be also feasible to implement a clinical diagnostic for IBD with major commercial potential. If we demonstrate that stool card is a reliable representation of the mucosal attached bacterial pattern and rectal swabs are a surrogate for mucosal biopsies, then our diagnostic test will be the most feasible, noninvasive and easy test to assess dysbiosis. Patients can place their stool on the cards (or physicians can place the stool on the card after rectal examination) and mail them to our central laboratory for bacterial fingerprinting. Furthermore, patients (or primary care physicians) can safely insert the swab in the rectum and rub it against the rectal mucosa and obtain the sample and then send it to our central laboratory for bacterial fingerprinting.

描述（由申请人提供）：炎症性肠病 (IBD)，即溃疡性结肠炎 (UC) 和克罗恩病 (CD)，是慢性、终生、复发性疾病，影响近 100 万美国人，每年给美国医疗保健系统造成约 20 亿美元的损失。 IBD 的原因不明，无法治愈，而且发病率正在增加。我们发现 IBD 中粘膜相关或腔壁粘附微生物种群的多样性降低。我们还确定了 LH-PCR 指纹中的推定峰，这些峰可能表明与 IBD 相关的模式。此外，我们的 LH-PCR 指纹与克隆序列的联系表明 IBD 患者的粘膜菌群中存在某些细菌群。这些发现使我们推测，IBD（生态失调）的回结肠壁上附着有一层细菌保护性生物膜，并且腔内细菌侵入了这种保护性生物膜。我们的初步结果表明，沿结肠和回肠的保护性生物膜几乎没有变化。我们的初步观察还表明，管腔/粪便微生物群落可能表明疾病状态。我们的目标是确定通过对患者收集的直肠拭子和粪便样本进行指纹识别来监测生态失调的可行性。我们的第二个目标是通过对粘膜、管腔、直肠拭子和粪便样本进行焦磷酸测序来全面表征这些微生物群落。如果我们证明粪便卡和直肠拭子是管腔和粘膜细菌模式的可靠代表，那么我们的诊断测试将是评估生态失调的最可行、无创且简单的测试。患者可以将粪便放在卡上（或者医生可以在直肠检查后将粪便放在卡上）并将其邮寄到我们的中心实验室进行细菌指纹识别。目标是在临床症状变得明显之前识别出症状，从而防止症状发作并损害肠道。这可以明显提高生活质量并预防手术并发症。利用环境微生物学的强大技术来表征人类微生物群落的研究可以为对这些疾病的理解带来重大进展。人们越来越认识到微生物群在健康和疾病中的重要性，不仅限于 IBD，还包括结直肠癌、肠道感染、乳糜泻、肠易激综合征、益生元和益生菌疗法等其他领域。该提案涉及首次在胃肠道微生物群研究中使用复杂且高度可重复的细菌指纹识别工具 LH-PCR。为该提案组建的团队是跨学科的，结合了三组非常有价值的专业知识来解决胃肠道微生物区系的复杂性，即临床 IBD 专业知识、环境微生物学专业知识和分析复杂数据集的生物信息学专业知识。作为该提案的直接结果，基于 LH-PCR 的新诊断工具可用于常规实时临床应用。然后可以使用这样的工具来帮助确定是否存在疾病；并预测疾病的各种表型表现、病程和治疗效果。如果对照和 IBD 之间的微生物区系之间的明显差异按照建议进行定义，那么对 IBD 实施具有重大商业潜力的临床诊断也是可行的。如果我们证明粪便卡是粘膜附着细菌模式的可靠代表，并且直肠拭子是粘膜活检的替代品，那么我们的诊断测试将是评估生态失调的最可行、无创且简单的测试。患者可以将粪便放在卡上（或者医生可以在直肠检查后将粪便放在卡上）并将其邮寄到我们的中心实验室进行细菌指纹识别。此外，患者（或初级保健医生）可以安全地将拭子插入直肠并在直肠粘膜上摩擦并获取样本，然后将其发送到我们的中心实验室进行细菌指纹识别。