(PQC-1) Driver Events In IBD-Associated Neoplastic Progression

描述(申请人提供)：炎症性肠病(IBD)患者的护理是复杂的。一个关键的临床难题是如何管理结肠癌风险的增加。不幸的是，目前的知识不能准确地确定肿瘤风险和最好的量身定做的治疗方法。这一挑战的部分原因是缺乏有关IBD患者结肠癌中发生的体细胞突变的遗传信息。此外，突变的顺序和顺序突变在肿瘤转化过程中的意义目前还没有被探索。我们假设，对人类IBD相关肿瘤(IBDN)进行全面的基因调查，并在离散的发育/时间阶段进行详细的数学作图和测试，可以用来识别推动IBD肿瘤进展的基因改变。我们进一步假设，通过对我们的IBDN猪模型中的基因变化进行纵向分析，我们将识别出驱动癌症进展的特有的遗传“致癌轨迹”。随着肿瘤在每只动物体内的发展和演变，将通过连续结肠镜采样获得反复活检标本，并进行遗传分析。通过整合这些人类和动物数据集，我们将了解哪些分子事件驱动和/或预测IBD早期病变进展为更晚期的恶性疾病。在整个赠款中，我们将使用完整外显子组测序(WES)和SNP阵列来表征小规模外显子组改变(点突变，INDELs)和拷贝数改变。我们将通过追求以下具体目标来研究这些假说：目标1-识别和排序人类IBD相关肿瘤进展中的基因改变。A)对100例IBD-Ca的横断面队列进行外显子组测序和SNP阵列分析。B)使用多种算法的组合，识别最有可能的驱动因素改变并推断致癌轨迹。C)通过Sanger测序和SNP排列30个LGD、30个HGD和30个IBD-Ca来测试致癌轨迹。目的2-在猪IBDN模型中描述结肠癌基因改变的时间顺序和功能影响。A)确定目标1.b)中确定的致癌轨迹的表型影响，以确定纵向活检中基因改变的时间分布，并与人类IBDN改变的顺序进行比较。总而言之，这一新颖的综合策略很可能提供对早期和预测性分子事件的洞察，因为我们将能够以精细的细节绘制这些事件的时间图，以及在它们发生时立即“捕捉到它们”。最终，该项目的成功完成将转化为更好地为IBD患者量身定做治疗性和预防性治疗。

DESCRIPTION (provided by applicant): The care of patients with inflammatory bowel disease (IBD) is complex. One crucial clinical dilemma is the management of the increased risk for colon cancer. Unfortunately, current knowledge does not allow for accurate determination of neoplastic risk and the best tailored management. This challenge is due, in part, to the lack of genetic information regarding somatic mutations occurring in colon cancer arising in IBD patients. Furthermore, the order of mutations and the significance of sequential mutations in regards to the course of neoplastic transformation are currently unexplored. We hypothesize that a comprehensive genetic survey of human IBD-associated neoplasia (IBDN), with detailed mathematical mapping and testing at discrete developmental/temporal stages, can be used to identify genetic alterations that drive neoplastic progression in IBD. We further hypothesize that by performing longitudinal analyses of genetic alterations in our IBDN porcine model, we will identify characteristic genetic "oncogenic trajectories" that drive cancer progression. Iterative biopsy specimens from neoplasia, as it develops and evolves within each animal, will be obtained via serial colonoscopic sampling, and genetic analyses will be performed. By integrating these human and animal datasets, we will learn which molecular events drive and/or predict the progression of early lesions to more advanced malignant disease in IBD. Throughout this grant, we will characterize small-scale exome alterations (point mutations, indels) and copy number alterations, using both whole-exome sequencing (WES) and SNP arrays. We will investigate these hypotheses by pursuing the following Specific Aims: Aim 1 - To identify and order genetic alterations in human IBD-associated neoplastic progression. A) Perform exome sequencing and SNP-array assays on a cross-sectional cohort of 100 IBD-Ca. B) Using a combination of algorithms, identify the most likely driver alterations and infer oncogenic trajectories. C) Test oncogenic trajectories by Sanger-sequencing and SNP-arraying 30 LGD, 30 HGD, & 30 IBD-Ca. Aim 2 - To characterize the temporal order and functional impact of genetic alterations in colon cancer arising in a porcine IBDN model. A) To determine the phenotypic impact of oncogenic trajectories determined in Aim 1. B) To identify temporal profiles of genetic alterations in longitudinal biopsies and compare to ordering of alterations in human IBDN. In toto, this novel integrated strategy is likely to provide insight into early and predictiv molecular events, since we will be able to temporally map these events in exquisite detail, as well as to "catch them in the act" as soon as they occur. Ultimately, the successful completion of this project will translate in better tailoring of curative and preventative treatments for IBD patients.