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Background/Aims: The regulation of tissue boundaries plays a critical role across all stages of an organism’s development. These boundaries ensure structural integrity, proper cell differentiation, directional guidance of cell migration, and the preservation of distinct tissue domains. Dysregulation of tissue boundaries is implicated in a range of pathological conditions, including developmental diseases and cancer. Loss or malfunction of boundary signals can result in craniofacial malformations, improper segregation of inner ear structures, tumor invasion, and metastasis. Building on recent advances in spatial transcriptomics sequencing, we developed a computational workflow to delineate gene expression patterns specifically across tissue boundaries. This workflow is designed for the identification of boundaries, quantification of gene expression gradients across these boundaries, and the detection of shared gene expression patterns. We applied our workflow to StereoSeq spatial transcriptomic data from the dorsal pallium - meninges boundary in E16.5 mouse embryos.
Conclusions: Our analysis revealed diverse gene expression patterns, including clusters of genes that are upregulated or inhibited directly at the boundary, and more complex spatial regulatory patterns. Further, genes with similar expression patterns were assessed for functional enrichment, exposing spatially confined biological processes such as neural development, regulation of angiogenesis, modulation of synaptic transmission, and extracellular matrix organization.