AbstractBackgroundDespite significant investment into treatments for AD, little progress has been made in bringing new therapeutics to market. Recent failure of monoclonal antibodies targeting Ab plaques to slow disease progression in phase 3 clinical trials, suggests now more than ever it is imperative to identify early disease signatures before symptom onset whose modification may alter disease trajectory. Our collaborating lab recently identified early dysfunction in the transgenic tri‐synaptic hippocampal circuit using in vivo recordings during awake immobility in the TgF344‐AD rat model (doi: 10.1101/2021.05.10.443512). This dysfunction emerges between 6‐9 months, prior to when TgF344‐AD rat shows overt pathology (including Ab plaques, frank neuronal loss, and endogenous tau pathology) at 16 and 26 mo, but not at 6 mo (Towne, 2013).MethodsThe molecular basis of this trisynpatic circuit dysfunction was explored using 10x Genomics’ v3 gene expression assay to perform snRNA‐seq on freshly dissected hippocampi from 6 mo male and female littermate pairs of Tg and Wt rats (n=16). ∼2000 cells/subject were collected, and cDNA libraries were sequenced (NovaSeq 600) to a depth of ∼120k reads/nuclei. Cell Ranger Pipeline demultiplexed and aligned reads to rat pre‐mRNA reference and generated gene count matrices. A final dataset of 33,079 high quality nuclei were clustered (Louvain graph‐based), and cell‐type specific marke used to determine identity. Identity was collapsed into broad neuronal and glial cell types for differential gene expression (DEG) across genotype (Hurdle Model).ResultsDEGs revealed profound alterations between genotype in cell types important in the trisynaptic circuit, including dentate granule cells (DGCs), and excitatory neurons (ExcNs). (FDR cutoff=0.05, 1111 (DGCs) and 1070 (ExcN’s) DEGs between genotypes). Pathway enrichment revealed dysregulation relevant to memory function: including decreased synaptogenesis, neurite branching, proliferation, and microtubule and cytoskeleton dynamics. DEG’s were enriched for neurological signs including epilepsy, seizures, hyperactivity, and dementia.ConclusionPrior to development of overt pathology or memory deficits, TgF344‐AD rats display transcriptomic alterations in their excitatory neurons, suggestive of impaired ability to form new connections and susceptibility to aberrant, hyperactivity. Electrophysiological detection, followed by intervention targeting these early alterations in gene expression may prevent progression of disease to a symptomatic stage.