Data modeling the interplay between single-cell shape, single-cell protein expression, and tissue state

While cell shape fundamentally governs tissue function, the underlying links between single-cell shape and protein expression have been difficult to resolve due to limitations in imaging multiplexing and population averaging. Here, we use multiplexed imaging and machine learning to investigate the coupling of cell shape and protein expression in heterogeneous human tissues. Our analysis establishes a universal, bi-directional link between a cell's shape and its protein expression across cell types, diseases, and disease states, amplified for cell state markers. Machine learning interpretability shows that shape features can potentially generate hypotheses of protein functions. Screening all protein-cell type pairs identified a subpopulation of large, p53-positive tumor cells across two cancers. Shape properties further enhanced graph neural network disease state prediction. Our results open the door to unraveling the intricate connections between protein expression, cell shape, tissue organization, and tissue state in a physiological context.