Revealing Molecular Difference Between MOL5 and MOL6 in Mouse Brain Using Spatial Transcriptomics

This study investigates the molecular and functional distinctions between two adjacent layers of the mouse motor cortex, MOL5 and MOL6, using spatial transcriptomics (ST). The spatial transcriptomics data were analyzed using GraphST, a graph convolutional network-based method, to identify spatially variable genes and delineate distinct spatial domains. Differential gene expression analysis, conducted with DEsingle, revealed 464 differentially expressed genes between MOL5 and MOL6. These genes were further analyzed using Gene Ontology (GO) enrichment to identify key biological processes, such as synaptic transmission, neuron projection development, and regulation of membrane potential, which are crucial for motor control and neuronal excitability. Additionally, TRRUST analysis identified transcription factors Myc and Mycn as key regulators of these processes, highlighting their roles in neuronal growth and differentiation. Protein-protein interaction analysis using the MCODE algorithm identified clusters associated with mitochondrial function and synaptic organization, further emphasizing the specialized roles of MOL5 and MOL6 in motor function. This study demonstrates the power of spatial transcriptomics in uncovering molecular differences between brain regions and offers insight into the potential of future spatial sequencing techniques, such as spatiotemporal sequencing, for exploring dynamic gene expressions in complex tissues.