Cell shapes decode molecular phenotypes in image-based spatial proteomics

Cellular and tissue structures arise from a few cell shapes, which undergo transformations based on biophysical constraints. Despite links between signaling pathways and cellular geometry, whole-proteome orchestration in association with cell shape is underexplored. In this study, over 1 million single cells stained for 11,998 proteins across 11 cell lines in the Human Protein Atlas were analyzed for organelle, pathway, and single-protein levels in association with cellular shapespace. We found that cell and nuclear shapes across cell lines exist in a shared continuum. The subcellular organelle topology varies across cell lines but remains consistent within each cell line's shapespace. At the single-protein level, cells of different shapes in the same cell-cycle phase might be preparing for different fates, and many non-cell-cycle proteins expressed shape-based abundance variation. Using a shape-based coordinate framework, we analyzed the distribution shift of protein spatial localization under drug perturbation.