PROJECT SUMMARY
In response to NOT-AG-23-031, we propose to use the same approach/technique as in the technology-driven
parental application to analyze postmortem dorsolateral prefrontal cortex samples from the spectrum of
Alzheimer’s (AD) subjects. Classical single-cell Omics (RNA-seq, ATAC-seq, Cut&Tag) provide information at
individual gene/locus level, but the sparse coverage of each cell (particularly for histone modifications profiling
using Cut&Tag) limits the predictive power. The imaging approach proposed here, while not resolving
individual loci, captures the integral cellular state and the dominant changes in chromatin and epigenetic
topography (e.g. ImAge captures the dominant aging changes). Although the importance of cellular
heterogeneity in AD has been recognized, most efforts are focused on single cell RNA-sequencing. We
propose to focus on the single cell epigenetic topography, taking advantage of a powerful imaging-based
chromatin and epigenetic analysis technique recently pioneered by the PI laboratory. Preserving the original
framework focused on applying novel imaging-based technology, we will quantitate single cell heterogeneity in
AD spectrum brains and associate trajectories of epigenetic changes in major brain cell types with gene
expression and cognitive decline of AD. Further, we will determine the connection between aging trajectories
during normal brain aging and the pathological progression of AD. We propose to map epigenetic changes
across 150 brain samples of AD spectrum with corresponding gene expression and functional readouts to
reveal the correlations of epigenetic and expression changes with cognitive decline and AD progression. First,
this will enable an accurate assessment of single cell chromatin and epigenetic heterogeneity in the
dorsolateral prefrontal cortex (DLPFC) from the spectrum of AD and normal young adult brains. Second, we
will interrogate unbiased emergence trajectories and examine their correlation with 80 functional readouts
available for each brain sample. Third, we will explore the relationship between the normal aging process and
AD progression. We will deliver the proof of feasibility and a unique single cell level epigenetic dataset that will
advance AD/ADRD research. The available matching skeletal muscle samples and associated omics datasets
could be integrated into the analysis to compare and contrast the trajectories of normal aging and AD
progression. Although this proposal employs bulk RNA-seq data, a powerful single cell RNA-seq approach
becomes increasingly available and will be integrated in future studies. The availability of PBMC from a subset
of the AD cohort enables us in the future to connect the above dependencies to epigenetic signatures in
PBMC, which could be assayed longitudinally and used for early diagnosis of AD.