Date of Award

Winter 12-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department


Degree Name

Doctor of Philosophy (PhD)

Degree Type



The small intestine in homeostasis is capable of regular regeneration, but in cases of massive injury like Short Bowel Syndrome, the innate human response often fails to fully compensate for the loss of nutrient absorptive surface area that accompanies bowel resection. Murine models display an active compensatory reaction deemed “adaptation” in which the surface area of the bowel is increased to accommodate nutrient absorptive needs. This observation has highlighted several gaps in knowledge regarding bowel adaptation. Firstly, what occurs on a molecular level in murine models during adaptation? Secondly, how can the findings in mice be applied to humans in an accurate modeling system? Using a murine model of bowel resection, single cell RNA sequencing was employed to analyze the molecular changes accompanying adaptation of the intestinal epithelium. We identify a process we deem “regional reprogramming” through which distal enterocytes upregulate genes associated with proximal intestinal nutrient transport during adaptation. In silico analysis indicates the importance of region-specific diffusible signals, notably Vitamin A, in driving this process through activation of transcription factors and signaling cascades. We further apply these findings to build an in vitro model of regional reprogramming utilizing chimerization of proximal and distal intestinal organoids. The chimeric organoid model, when analyzed using single cell RNA-seq, indicates proximalization of distal organoid tissue upon exposure to the proximal organoid signaling environment—potentially related to changes in Guanylate Cyclase-C signaling. Finally, we utilize direct reprogramming to investigate the ability potential upstream transcription factor Gata4 to induce regional reprogramming in vitro in organoids. We find that the use of Gata4 alone is not sufficient to induce regional reprogramming in vitro, necessitating further study of the role of transcription factor signaling in regional reprogramming. This work concludes that regional reprogramming occurs during adaptation in mice, introduces a novel preliminary model of regional reprogramming due to diffusible signals—the chimera, and lays the groundwork for use of direct reprogramming to study regional reprogramming related to transcription factor activation in vitro.


English (en)

Chair and Committee

Samantha A. Morris

Committee Members

Helen McNeill