Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model
Detecting and understanding Alzheimer's disease (AD) in its early stages is essential for uncovering the initial mechanisms behind its neuropathology and devising effective interventions. In this study, we leveraged the humanized AppNL-G-F mouse which exhibits early-onset amyloid pathology along a predictable timeline, to investigate molecular changes in the hippocampus and blood before the onset of severe neuropathology and independent of aging. Employing a multi-omics approach, we identified alterations in chromatin accessibility, gene expression, and DNA methylation associated with early amyloidosis. Chromatin accessibility changes were prominent in excitatory neurons during early pathology, with a later shift to inhibitory neurons, potentially reflecting compensatory mechanisms to mitigate excitatory neuron dysregulation. Despite broadly comparable hippocampal cell composition, transcriptomic comparisons between wild-type and AppNL-G-F mice revealed major gene expression differences, particularly in pathways related to mitochondrial function and protein biosynthesis, preceding severe amyloid plaque deposition. In later stages, upregulation of immune and neuroinflammatory pathways was observed, aligning with established neuroinflammatory processes in AD. Additionally, we identified extensive DNA methylation differences in both the blood and hippocampus of AppNL-G-F mice during early and late stages of pathology. Many differentially methylated regions in the blood, even at early pathology stages, were associated with cis-regulatory elements in the brain and were located near differentially expressed genes in the hippocampus. These regions were enriched in pathways related to brain function, such as neuron development and synaptic processes, indicating a link between blood methylation patterns and brain function. This suggests the potential utility of blood methylation as a biomarker for early amyloidosis detection. Notably, we identified five candidate biomarker genes, including Rbfox1 and Camta1, with epigenetic dysregulation detectable in both the brain and blood prior to severe amyloid accumulation. Our study, leveraging a unique AD mouse model and a multi-omics approach, highlights epigenetic signatures of AD before the onset of clinical symptoms, providing a foundation for future research into early diagnosis and therapeutic strategies, as well as potential biomarkers. Overall design: scATAC-seq libraries were prepared after pooling of n=5 biological replicates per genotype (wildtype and APP_nlgf), age (postnatal week 3, week 8, and week 24) and sex (male and female). For each tissue and time point, regions of significant differential methylation (DMRs) were identified by comparing the two genotypes, with sex included as a covariate in the analysis.