ESPRESSO: spatiotemporal omics based on organelle phenotyping

Omics technologies such as genomics, transcriptomics, proteomics and metabolomics methods, have been instrumental in improving our understanding of complex biological systems by providing high-dimensional phenotypes of cell populations and single cells. Despite fast-paced advancements, these methods are limited in their ability to include a temporal dimension. Here, we introduce ESPRESSO (Environmental Sensor Phenotyping RElayed by Subcellular Structures and Organelles), a technique that provides single-cell, high-dimensional phenotyping resolved in space and time. ESPRESSO combines fluorescent labeling, advanced microscopy and image and data analysis methods to extract morphological and functional information from organelles at the single-cell level. We validate ESPRESSO's methodology and its application across numerous cellular systems for the analysis of cell type, stress response, differentiation and immune cell polarization. We show that ESPRESSO can correlate phenotype changes with gene expression, and demonstrate its applicability to 3D cultures, offering a path to improved spatially and temporally resolved biological exploration of cellular states.