Single-cell Spatial Transcriptomics Analysis of Alzheimer's Disease Pathogenesis in Mouse Models

Understanding molecular mechanisms of Alzheimer’s disease (AD) has proven challenging as disease effects occur at multiple scales in different brain regions. We apply multiplexed error-robust fluorescence in situ hybridization (MERFISH) to generate spatially resolved single-cell RNA atlases from multiple cortical and subcortical brain regions in 5xFAD and age-matched C57 wild-type mice. We also investigate the effect of the TREM2R47H mutation, a strong risk factor for the development of AD in humans, producing similar atlases for Trem2R47H and Trem2R47H-5xFAD mice. We identify amyloid- beta plaque proximal molecular alterations in microglia and astrocytes, but also in five neuronal cell types. Spatial analysis of microglia and astrocyte concentrations reveals Trem2R47H -dependent regional variations, as well as regional transcriptional variation independent of either 5xFAD or Trem2R47H mutations. Cortical excitatory neurons exhibit a consistent Trem2R47H -induced expression increase in Ntrk2, and other MAPK signaling- associated genes, and thalamic excitatory neurons exhibit both 5xFAD and Trem2R47H induced gene program alterations. Additionally, nearly every neuronal cell type exhibits subclusters with decreased 5xFAD populations. Taken together, our MERFISH analysis of 5xFAD and Trem2R47H Alzheimer’s mouse models reveals spatially localized, cell-type-specific, plaque and Trem2R47H induced transcriptome dysregulations in cortical and subcortical brain regions.