Single cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2 R47H Alzheimer's risk gene mutation.

Introduction: The R47H missense mutation of the TREM2 gene is a strong risk factor for development of Alzheimer's Disease. We investigate cell-type-specific spatial transcriptomic changes induced by the Trem2 ^R47H mutation to determine the impacts of this mutation on transcriptional dysregulation.
Methods: We profiled 15 mouse brain sections consisting of wild-type, Trem2 ^R47H , 5xFAD and Trem2 ^R47H ; 5xFAD genotypes using MERFISH spatial transcriptomics. Single-cell spatial transcriptomics and neuropathology data were analyzed using our custom pipeline to identify plaque and Trem2 ^R47H induced transcriptomic dysregulation.
Results: The Trem2 ^R47H mutation induced consistent upregulation of Bdnf and Ntrk2 across many cortical excitatory neuron types, independent of amyloid pathology. Spatial investigation of genotype enriched subclusters identified spatially localized neuronal subpopulations reduced in 5xFAD and Trem2 ^R47H ; 5xFAD mice.
Conclusion: Spatial transcriptomics analysis identifies glial and neuronal transcriptomic alterations induced independently by 5xFAD and Trem2 ^R47H mutations, impacting inflammatory responses in microglia and astrocytes, and activity and BDNF signaling in neurons.
Competing Interests: CONFLICT OF INTEREST STATEMENT The authors declare no competing interests for this project.