Mapping epidermal growth factor receptor-1 sorting domains in endosomes with a calibrated three-dimensional expansion microscopy toolkit

Endosomes are nanoscale intracellular compartments that sort and recycle cell-surface receptors such as epidermal growth factor receptor-1 (EGFR1). Nanometer-scale interactions and coclustering of signaling proteins, cargo, and the membrane are critical to this process, yet direct 3D visualization has been hindered by the limited resolution of conventional and super-resolution microscopies. Here, we adapt expansion microscopy (ExM) to visualize and quantify nanoclusters of endosomal proteins in human retinal pigment epithelial (RPE-1) cells. We developed a 3D distortion analysis leveraging the Farneback optical-flow principle to detect anisotropies in hydrogel expansion, revealing under-expansion of cytoplasmic regions within ExM hydrogels and overestimation of size and distance measurements of small compartments such as endosomes. To calibrate ExM images of cytoplasmic regions containing endosomes, we introduced a self-assembling protein nanocage that reports the true local nanoscale expansion factor. To stimulate and visualize EGFR1 internalization and sorting, we applied a pulse-chase protocol with fluorescently tagged epidermal growth factor (EGF), fixed cells at 15 and 30 min, and subjected samples to 10-fold ExM and multiplexed 3D Airyscan microscopy to map cargo and EGFR1 relative to other endosomal proteins. A volume tracing pipeline was developed to visualize the changes in the labeled EGF and EGFR1 densities at the limiting membrane of the endosomes. These changes included enrichment of EGF and EGFR1 in the endosomal interior and accumulation of Rab5a near the limiting membrane during early endosome maturation. Together, this multiplexed 3D ExM toolkit provides a quantitative framework for visualizing and measuring small subcellular organelles at true molecular-scale resolution.