Super-resolved spatial transcriptomics reveals early hippocampal RNA localization changes in a mouse model of Alzheimer’s disease

Summary Cell-type-specific changes in gene expression and RNA localization are hallmarks of Alzheimer’s disease (AD) and other neurodegenerative disorders, yet spatial dysregulation in early disease stages remains poorly defined. Here, we applied Expansion Sequencing (ExSeq) to map the spatial distribution of 101 genes at super-resolution in the hippocampus of 4-week-old 5xFAD and wild-type (WT) mice, prior to overt pathology. We uncovered early alterations in RNA spatial organization and gene expression, including 23 genes showing altered localization without changes in abundance in the 5xFAD hippocampus. Using spatial expression analysis and single-cell neighborhood analysis, we identified cell-type- and region-specific molecular programs associated with synaptic function, neuroinflammation, and metabolic stress that differed between 5xFAD and WT mice. Spatial RNA velocity further revealed state differences influenced by local cell to cell interactions. Together, these results suggest that RNA positioning and transcriptional programs are perturbed at early disease stages. Finally, we provide the full super-resolution ExSeq dataset as an open resource for spatial and cell-type-specific analyses in early Alzheimer’s disease research. Highlights Super-resolved transcriptomic profiling of the hippocampus at early disease stages Identification of 23 genes with altered spatial localization without changes in abundance Early alterations in single-cell neighborhood organization in the 5xFAD hippocampus Spatial RNA velocity reveals cell-type-specific cell state differences shaped by cell-cell proximity Competing Interest Statement The authors have declared no competing interest. Footnotes The text was revised, and changes were made to the analysis