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.
We hypothesize that a comprehensive genetic survey of human inflammatory bowel disease (IBD)-associated neoplasia (IBDN), with detailed mathematical mapping and testing at discrete developmental stages, can be used to identify genetic alterations that drive neoplastic progression in IBD (Aim 1). To better characterize the order of these alterations and their causal impact on colon cancer arising in IBD patients, we will generate a porcine model. We further hypothesize that by performing longitudinal analyses of genetic alterations in this porcine model, we will identify characteristic genetic trajectories tat drive cancer progression (Aim 2). 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.