BART-spatial unravels biologically significant transcriptional regulators from spatial omics data

Transcriptional regulators (TRs) are crucial regulators of cell fate decisions by activating or repressing lineage-specific genes and integrating environmental signals with intrinsic networks. Identifying functional TRs is essential for understanding development, tissue organization, and disease. Emerging spatial transcriptomics and epigenomics technologies now provide near-single-cell resolution mapping of genomic features while preserving information of each cell's physical location and microenvironment which influence TR activity. Despite these advances, identifying active TRs in spatial data remains challenging due to low TR expression and the fact that TR activity often does not correlate directly with mRNA levels. Moreover, existing tools mainly designed for non-spatial single-cell data overlook spatial heterogeneity. To bridge this gap, we developed BART-spatial (Binding Analysis for Regulation of Prediction for spatial omics), an innovative computational method to infer functional TRs from spatial omics data. BART-spatial integrates spatial variability and pseudo-temporal information with publicly available TR binding profiles. Applied to multiple spatial datasets from diverse platforms, including 10X Visium, Visium HD, Atera, and spatial RNA-ATAC-seq, BART-spatial consistently outperforms existing methods, identifying stage-specific TRs and revealing regulators undetectable by expression alone. Its compatibility with spatial epigenomics data further strengthens its utility and enables cross-validation. Overall, BART-spatial provides a powerful and robust tool for decoding spatially resolved gene regulatory programs.