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

描述（由申请人提供）：炎性肠病（IBD）患者的护理是复杂的。一个关键的临床难题是结肠癌风险增加的管理。不幸的是，目前的知识还不能准确确定肿瘤风险和最佳的定制管理。这一挑战部分是由于缺乏IBD患者结肠癌中发生的体细胞突变的遗传信息。此外，突变的顺序和序列突变在肿瘤转化过程中的意义目前尚未探索。我们假设，对人类IBD相关肿瘤（IBDN）进行全面的遗传调查，并在离散的发育/时间阶段进行详细的数学制图和测试，可用于识别驱动IBD肿瘤进展的遗传改变。我们进一步假设，通过对IBDN猪模型的遗传改变进行纵向分析，我们将确定驱动癌症进展的特征遗传“致癌轨迹”。随着肿瘤在每只动物体内的发展和演变，将通过连续结肠镜取样获得肿瘤的反复活检标本，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早期病变向更晚期恶性疾病的进展。在整个资助过程中，我们将使用全外显子组测序（WES）和SNP阵列来表征小规模外显子组改变（点突变，索引）和拷贝数改变。我们将通过以下具体目标来研究这些假设：目的1 -识别和排序人类ibd相关肿瘤进展的遗传改变。A)对100 IBD-Ca的横断面队列进行外显子组测序和snp阵列分析。B)使用算法组合，确定最可能的驱动改变并推断致癌轨迹。C)通过sanger测序和snp阵列检测30个LGD， 30个HGD和30个IBD-Ca的致癌轨迹。目的2 -表征猪IBDN模型中结肠癌基因改变的时间顺序和功能影响。A)确定Aim 1中确定的致癌轨迹的表型影响。B)确定纵向活检中遗传改变的时间谱，并与人类IBDN的改变顺序进行比较。总的来说，这种新颖的综合策略很可能提供对早期和可预测的分子事件的洞察，因为我们将能够以精细的细节绘制这些事件的时间图，并在它们发生时“当场捕获”。最终，该项目的成功完成将为IBD患者提供更好的治疗和预防治疗。

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.