SUPER-RESOLVED SPATIAL TRANSCRIPTOMICS REVEALS EARLY HIPPOCAMPAL RNA LOCALIZATION CHANGES IN A MOUSE MODEL OF ALZHEIMER’S DISEASE

Alzheimer’s disease (AD) is characterized by progressive neurodegeneration, yet the earliest molecular events preceding overt pathology remain poorly understood. In particular, early disruptions in RNA spatial organization remain poorly defined.
Here, we applied Expansion Sequencing (ExSeq) to generate a super-resolution spatial transcriptomic map of the hippocampus in 4-week-old 5xFAD mice and wild-type controls, prior to amyloid plaque deposition. ExSeq enabled in situ profiling of over 100 genes at nanoscale resolution, allowing simultaneous analysis of gene expression and RNA spatial localization at the single-cell level.
Our analysis uncovered early, cell-type- and region-specific changes in RNA spatial organization that occurred independently of changes in overall gene expression. We further identified cell-type- and region-specific molecular programs associated with synaptic function, neuroinflammation, and metabolic stress that differed between 5xFAD and WT mice. Notably, we identified a subset of genes exhibiting altered subcellular localization without changes in transcript abundance in the 5xFAD hippocampus. Leveraging ExSeq’s spatial resolution, we further detected early differences in neuronal state and local cellular neighborhoods, revealed through spatial RNA velocity analysis.
Together, these findings demonstrate that disrupted RNA localization is an early molecular feature of AD, preceding classical pathological hallmarks. This work highlights the power of super-resolution spatial transcriptomics to uncover subtle, spatially resolved molecular changes at disease onset and provides a framework for identifying early biomarkers in neurodegenerative disorders.