PEPSI: Polarity measurements from spatial proteomics imaging suggest immune cell engagement

Subcellular protein localization is important for understanding functional states of cells. However, measuring and quantifying this information can be difficult and typically requires high-resolution microscopy. We develop a metric PEPSI to define surface protein polarity from immunofluorescence IF imaging data and use it to identify distinct immune cell states within tumor microenvironments. We apply this metric to characterize over two million cells across 600 patient samples and find that cells identified as having polar expression exhibit characteristics relating to tumor-immune cell engagement. We show that incorporating these polarity-defined cell subtypes improves the performance of deep learning models trained to predict patient survival outcomes.