Date of Award

Fall 2023

Project Type

Thesis

Program or Major

Genetics

Degree Name

Master of Science

First Advisor

Matthew D MacManes

Second Advisor

David C Plachetzki

Third Advisor

William K Thomas

Abstract

Arid environments continue to increase their global coverage yearly due to climate change, and leaves harsh environmental effects in their wake. Of these effects—which include high UV radiation, extreme temperatures, and sparse food sources —lack of free water poses the greatest challenge to the ecosystem as a whole. Water resources are predicted to continue to decrease with the rise in desertification, increasing the threat of dehydration and its harmful effects on bodily function. Dehydration-related kidney injury has been linked to the onset of chronic kidney disease in humans, which has become a leading cause of mortality worldwide . Therefore, studies focusing on dehydration and its effects on the kidney are pertinent to human health in the midst of global warming. Desert-adapted mammals provide an excellent model for studying dehydration, as their environment often forces them to survive on minimal extrinsic water. Peromyscus eremicus, commonly known as the cactus mouse, have been known to go their entire life without water intake, but seemingly do not incur excessive kidney damage. Additionally, they are able to be studied in a laboratory setting and have publicly available genomic information, making them an ideal research candidate. While multiple studies outlining their physiology and kidney function exist, none include spatial relevance of their findings. The research outlined here serves as preliminary work for future studies by utilizing the 10X Genomics Visium platform to generate a spatial atlas of genes expressed in the kidney of Peromyscus eremicus. The specific objectives of this research were to (1) explore cell type distribution across the kidney using previously defined cell type markers, (2) to define spatially resolved clusters by cell type, gene expression, and location, (3) to explore location and expression values of previously significant genes, and (4) to explore differential gene expression patterns across the kidney tissue. Spatial libraries were generated from four kidney slices of wildtype mice using 10X Visium guidelines. Preliminary processing was performed using their publicly available pipeline called Spaceranger. Further analysis was completed using the R packages Seurat and BayesSpace, which allowed us to identify and define spatial clusters. Major cell types were defined from previously discovered cell marker genes and visualized using BayesSpace’s advanced subspot resolution. Specifically, the proximal tubules and the loop of Henle were described with high levels of certainty with regard to location and gene expression. Exploration of expression level and locations of genes previously studied in relation to dehydration revealed that genes involved with epithelial sodium channels (ENaC) and sodium-potassium-chloride cotransporters (NKCC2) were highly expressed, while the aquaporin gene family as a whole was not expressed (excluding AQP7) compared to previous literature. Finally, GO term analyses of highly variable genes per cluster were performed to further assign functionality and features to the defined spatial clusters. Overall, the results from this study lay the groundwork for understanding how desert- adapted mammals may cope with lack of water in their environment and provide insight to how humans may one day be able to treat and prevent dehydration- related disease states. These results also provide preliminary information to further investigate spatially relevant information in future dehydrated P. eremicus studies.

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