A Spatially Resolved Atlas of Alternative Polyadenylation Across 18 Human Tissues and 76 Disease States

ABSTRACT Alternative polyadenylation (APA) is a key regulator of gene expression and cellular dynamics, yet systematic investigations of spatially resolved APA across diverse human tissues remain limited. Here, we developed SpatialAPA ( https://github.com/Omicslab-Zhang/spatialAPA ), a framework that benchmarks multiple APA identification methods and integrates spatial APA data with gene expression and cellular dynamics at spatial resolution. Applying SpatialAPA to 363 spatial transcriptomic data from 56 projects across 18 human tissues and 76 diseases, we constructed a spatially resolved APA atlas comprising 346,932 APA events across 52,175 genes. This atlas reveals organ–specific APA patterns and provides new insights into how APA regulates tissue homeostasis and disease progression beyond transcriptional control. To ensure cross–sample comparability, we applied batch correction, while spatial cell deconvolution uncovered cell–type–specific dynamics and interactions. In triple–negative breast cancer, integrated spatial and single–cell analyses identified TSPAN8 –positive epithelial subpopulations whose distinct APA regulation and transcriptional programs drive differentiation and malignant progression. To facilitate community access, we developed an online platform ( http://www.biomedical-web.com/spatialAPAdb/home ) for exploring APA, gene expression, and cellular dynamics in health and disease. Together, this study establishes the first comprehensive spatial APA atlas, providing a valuable resource and analytical framework for investigating molecular mechanisms and therapeutic targets.