Date of Award
2024
Document Type
Thesis
Degree Name
Master of Science (MS)
Department
Complex Systems and Data Science
First Advisor
Seth Frietze
Second Advisor
Alice Patania
Abstract
Viruses have been well-documented to invade and proliferate within the brain, precipitating neurodegeneration and functional impairment in affected regions. Microglia are the brain's primary immune cells essential for maintaining neuronal homeostasis and defending against pathogenic infiltration. In their homeostatic state, microglia ensure neuronal and glial integrity, facilitate blood vessel formation, and aid in debris clearance. However, microglial activation occurs in response to neuronal damage or pathogen detection. Prolonged or excessive activation can lead to a cascade of neuroinflammation characterized by sustained release of proinflammatory mediators, contributing to neurodegeneration and subsequent diseases. Therefore, understanding the regulatory mechanisms of microglia is crucial for mitigating their overactivation and preserving brain health.
In this study, we employed a multiscale genetic analysis to elucidate regulatory changes in virally activated microglia. We first utilized spatial transcriptomics and spatial proteomics alongside high-resolution imaging on one Mock mouse brain and HSV-1 infected mouse brain. Analysis revealed region-specific expression of inflammatory response proteins/genes such as Ifit and Irf genes upregulated. To further classify virally activated microglia, we performed 10X Chromium single-cell multiome sequencing in microglia isolated from HSV-1-infected and Mock mice. snRNAseq identified marker genes per cluster via differential analysis, revealing microglial population heterogeneity. Within-cluster analysis pinpointed differentially expressed genes between Mock and HSV1 cells, some of which overlapped with the differentially express genes from the spatial omic analysis such as Sp100, Ifit, and Irf genes. scATACseq unveiled unique peaks between clusters, reinforcing cellular diversity and indicating differential region accessibility across Mock and HSV-1 cells. Integrating scATACseq and snRNAseq together showed differential regulon enrichment between clusters and cluster-specific regulatory landscapes. Regulons in virus-activated microglia were Sp100, Irf7, Irf1, and Klf13.
Broadly, this project furthers our understanding of the regional immune system responses to HSV-1 infection of the brain. Additionally, we have shown differential regulon enrichment between mock and HSV-1 cells and across cell state clusters, providing a novel TF-gene regulatory network characterization for microglial heterogeneity and activation signatures induced by HSV-1 infection.
Language
en
Number of Pages
85 p.
Recommended Citation
Lunn, Cameron, "Integrative Omic Analyses Reveal Activated Microglial Signatures in Response to HSV1 Brain Infections" (2024). Graduate College Dissertations and Theses. 1930.
https://scholarworks.uvm.edu/graddis/1930