Mutant Density and Chromatin Dynamics in Intestinal Tumorigenesis

Abstract

Colon cancer with the fourth highest incidence among cancers and fourth leading cause of cancer deaths often arises due to mutations in APC, Adenomous polyposis coli, mutated in ~80% cases. Loss of the tumor suppressor is sufficient for crypt hyperplasia and adenoma, a pre-cancerous tumor, formation. The identity of the tumor-initiating cell has been debated along with the effect of the mutation on the chromatin as the tumors remain dependent on the APC null state. In chapter 2, I explore the cell of origin of intestinal epithelial cancers. In mouse models of intestinal tumorigenesis, stem cell specific Cre drivers readily produce tumors while Cre drivers targeting differentiated cells fail to do so; however, the mechanism restricting the tumor-initiating capabilities has not been elucidated. Using stem cell and secretory specific Cre drivers, I identify a non-cell autonomous role for clustering of Apc null crypts in tumorigenesis, where elimination of clustering in the stem cell specific Cre reduced tumorigenesis. Furthermore, a distinct chromatin state exists in the Lgr5+ Apc null tumor cells and not the inert Apc null stem cells regardless of the Cre driver, demonstrating that Apc loss in a stem cell does not create a unique chromatin state underlying their tumor initiating capabilities. These results challenge the stem cell as the cell of origin of epithelial intestinal tumors as altering tamoxifen administration in the stem cell specific Cre generated inert Apc null clones that lacked significant chromatin differences with the clones from the secretory Cre. In chapter 3, I examine the effect of the Vogelgram mutational series on the chromatin landscape. In intestinal tumors, the progression of adenomas to more advanced tumors correlates with the successive accumulation of mutations as described in the Vogelgram mutational series, comprising of APC, KRAS, TP53, and SMAD4. ATAC-seq was employed on organoid and mouse models to explore the effects of the mutational series on the chromatin landscape. The initial Apc mutation that dysregulated Wnt signaling had the greatest impact on the chromatin accessibility relative to the previous state in both organoids and mice with minimal changes in cis-regulatory elements through the Vogelgram series.