In this preliminary experiment, we used spatial transcriptomics to assess the gene expression profiles of microglia or astrocytes in relation to their distance from plaques. We compared 18-month-old APPKI mice (APPNL-F) which carry 2 mutations for familial Alzheimer’s disease to APPNL-F crossed with mice with the Trem2R47H mutation knocked in (APPTREM2KI; n=4 each genotype). In addition, we included Wild Type (WT) and Trem2R47H KI mice (n=2-3). The APPKI mice start to show amyloid plaques at about 9 months of age and by 18 months have a heavy plaque load. To do spatial transcriptomics with the GeoMx® Mouse Whole Transcriptome Atlas, microglia (Iba1 positive cells) areas of interest (AOIs) were divided into 3 groups: those touching plaques; those within an area of heavy plaque load (periplaque) and those far from plaques. Periplaque astrocytes (S100b positive cells) or away from plaque astrocytes were also analyzed. Several of the “disease-associated microglial” (DAM) genes that do not show significant differences in an RNAseq study showed clear and significant increases in the microglia on plaques, with the differences in some cases dropping off already in the periplaque region, which was rather remarkable. This steep spatial gradient strongly suggests that these genes are upregulated due to contact with the plaque, rather than being involved in the migration of microglia towards plaques. Moreover, we could distinguish which of these genes were influenced by the alteration in Trem2 and its decreased expression. There were also some genes strongly decreased in the vicinity of plaques and microglia and astrocytes that frequently behaved differently.
1. Understand how spatial transcriptomics can be used to study the whole mouse transcriptome in CNS samples
2. Learn how the Trem2R47H mutation affects the expression profiles of microglia and astrocytes in an Alzheimer's Disease model
3. Understand the relationship between distance from plaques and gene expression for microglia and astrocytes