Mouse Forebrain Region Features and Cholinergic Neurons Subtyping: Integrated Analysis with Spatial Multi-omics

The forebrain regions display distinct yet under-characterized gene expression patterns. In this study, we analyzed region-specific feature genes in forebrain regions and Isocortex subregions at both the transcriptomic and proteomic levels. The key finding was the observation of a low correlation but high functional similarity between mRNA and protein expression, providing new insights into the relationship between gene expression forms in neuronal pathways and the neuronal activity states. Cholinergic neurons (CNs) play a vital role in forebrain sensory and motor regulation. With Spatial-transcriptome and immunofluorescence joint analysis (STIF), which overcomes the resolution limitations of the 10X Visium system, we identified CNs and CN-subtypes specific feature genes in the striatum and basal forebrain, providing crucial insights into the heterogeneity and functional diversity of these neuronal populations. The spatial distribution and expression patterns of the identified feature genes were validated using either external datasets or rolling circle amplification fluorescence in situ hybridization (RCA-FISH), coincident results were revealed.