Integrating Genomics and Experimental Models to Uncover Mechanisms of Liver Pathobiology

Date of Award

Fall 1-1-2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Genetics

First Advisor

Vilarinho, Silvia

Abstract

Liver disease is one of the leading causes of morbidity and mortality, yet much about the shared pathobiology of common liver disease remains unknown. In order to investigate shared mechanisms in disease, this dissertation uses in silico, in vitro, and in vivo approaches to interrogate liver biology through the lens of rare disease. Firstly, we created an integrated single cell RNA sequencing (scRNA-seq) atlas of 28 human livers incorporating the RNA of 36,188 cells. We discovered that liver cells show overall little variation in the transcriptomic profile of non-diseased individuals, demonstrating the robustness of the liver to perturbation. Furthermore, this atlas provides a baseline dataset for interrogation in both common and rare genetic liver disorders. Second, we employed an in vitro induced pluripotent stem cell (iPSC)-derived cholangiocyte model to interrogate the cellular mechanisms of kinesin family-member 12 (KIF12)-mediated high-GGT cholestasis. We used the previously generated scRNA-seq atlas to determine KIF12 is largely expressed in cholangiocytes. By using genome editing to introduce patient mutations into iPSCs and inducing cholangiocyte differentiation, we were able to determine that biallelic KIF12 mutations interrupt normal intracellular trafficking of lysosomes, mitochondria and cilia. This phenotype was able to be rescued via viral delivery of wild-type KIF12. Finally, we used in vivo conditional mouse models to investigate the role of the gene Gimap5 in regulating liver sinusoidal endothelial cell (LSEC) identity and portal hypertension. Prior work in our laboratory determined that Gimap5 deficiency leads to LSEC capillarization and portal hypertension. We deleted Gimap5 in LSECs and lymphatic endothelial cells (LyECs) and determined it was not sufficient to induce LSEC capillarization. In summation, this dissertation broadens our understanding of liver disease by using various approaches to better disentangle mechanisms regulating both common and rare liver disorders. This work sets the stage for not only understanding mechanisms but developing improved diagnostics and treatments for liver disease.

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