Spatial transcriptomics profiling across tissue boundaries in the developing mouse brain

Tissue boundaries preserve structural integrity and guide cell differentiation during development, despite constant stress from proliferation, cell death, and tissue deformation. To study gene regulation in these regions we developed REBOSEP, a workflow for analyzing spatial transcriptomics data to detect tissue boundaries and measure gene expression relative to boundary distance. REBOSEP uses hierarchical clustering to uncover shared regulatory patterns among genes, revealing highly diverse expression changes that can shift sharply across just a few cell layers. Using this approach, the study generated the first resource of gene expression across tissue boundaries, covering five brain-meninges boundaries in the developing mouse brain. Analysis of the dorsal pallium-meninges boundary showed specific regulatory patterns in outer brain and meningeal layers, with strong links to developmental processes and distance-dependent regulation in major pathways, including those involved in neurodevelopmental disease and cancer. Overall, REBOSEP provides a systematic framework for studying gene expression regulation at tissue boundaries.