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bioRxiv · 10.1101/2025.09.24.678295

Super-Resolved Spatial Transcriptomics Reveals Early Changes in RNA Localization in the 5xFAD Hippocampus

Diamant Karasik, Y.·Eger, H.·Goldberg, T.·Seri, Y.·Schottlender, N.·Ben Mor, T.·Safra, M.·Shenhav, M.·Zak, H.·Danino, M.·Rosenberg, Y.·Glick, A.·Feldman, N.·Slater, N.·Gottfried, I.·Ashery, U.·Alon, S.
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Abstract

Cell-type-specific changes in gene expression and RNA localization are hallmarks of Alzheimers 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 Alzheimers disease research. HighlightsO_LISuper-resolved transcriptomic profiling of the hippocampus at early disease stages C_LIO_LIIdentification of 23 genes with altered spatial localization without changes in abundance C_LIO_LIEarly alterations in single-cell neighborhood organization in the 5xFAD hippocampus C_LIO_LISpatial RNA velocity reveals cell-type-specific cell state differences shaped by cell-cell proximity C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/678295v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1b46cf2org.highwire.dtl.DTLVardef@5cc55eorg.highwire.dtl.DTLVardef@a1ade4org.highwire.dtl.DTLVardef@9f833e_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Diamant Karasik, Y., Eger, H., Goldberg, T., Seri, Y., Schottlender, N., Ben Mor, T., Safra, M., Shenhav, M., Zak, H., Danino, M., Rosenberg, Y., Glick, A., Feldman, N., Slater, N., Gottfried, I., Ashery, U., Alon, S.. 2025-09-26. Super-Resolved Spatial Transcriptomics Reveals Early Changes in RNA Localization in the 5xFAD Hippocampus. https://doi.org/10.1101/2025.09.24.678295

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