Early Onset Alzheimer’s Disease Markers in Mouse Hippocampus Unveiled by Single-Cell Transcriptomic Analysis Following Cranial Radiotherapy

Author

Tuba AksoyFollow

Author ORCID Identifier

https://orcid.org/0000-0002-2287-6199

Date of Graduation

8-2024

Document Type

Dissertation (PhD)

Program Affiliation

Neuroscience

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

David Grosshans, M.D, Ph.D.

Committee Member

Pavel Sumazin, Ph.D.

Committee Member

Kimberley Tolias, Ph.D.

Committee Member

Gabriel Fries, Ph.D.

Committee Member

Yin Liu, Ph.D.

Committee Member

Gabriel Sawakuchi, Ph.D.

Abstract

Cranial radiation therapy plays an integral role in the treatment of brain tumors but can lead to progressive cognitive deficits in survivors by mechanisms that are poorly understood. To develop preventive or mitigative strategies, it is crucial to better understand the underlying pathogenesis of radiation-induced cognitive impairments. The study investigated single-cell transcriptomics and DNA methylation changes as potential drivers of persistent cellular dysfunction after radiation exposure, specifically concentrating on the CA1-3 regions of the hippocampus and the prefrontal cortex due to their role in cognitive functions. Thirteen-week-old mice underwent whole-brain radiation at clinically relevant doses. Following whole-brain radiation, an assessment of memory, attention, and problem-solving skills using the Puzzle Box and Novel Object Place Recognition tests revealed a decline in cognitive abilities among irradiated mice. Accompanying the deterioration of cognitive skills, transcriptional shifts identified multiple sex, region and cell type specific altered pathways following radiation, including synaptic transmission, chromatin remodeling and pathways associated with early-onset Alzheimer’s disease. The Ttr gene was consistently downregulated across all cell types in the hippocampal CA1-3 regions, along with other alterations in Amyloid beta (Aβ) clearance markers such as CST3, APOE, APOE, APOJ/CLU, TREM2 and PIEZO1. We also identified downregulation of several ribosomal genes in pyramidal cells of the hippocampal CA1-3 regions in radiated mice. Comparisons between the observed transcriptional changes and markers of Alzheimer’s disease (PMID: 31042697, 31768052) affirmed that the transcriptional alterations induced by radiation closely resemble those seen in early-onset Alzheimer’s disease, rather than late-onset. Furthermore, radiation exposure led to alterations in the DNA methylation states of regulatory regions in the profiled cells. These changes were significantly correlated with the observed dysregulation of gene expression within each region, suggesting that cranial radiation induced transcriptional changes in numerous brain cell types, at least partially through dysregulation of DNA methylation.

Keywords

neuroscience, radiation, neurodegeneration, Alzheimer's, single cell rna sequencing, wgbs, methylation, epigenetics, integrative analysis, bioinformatics