Three-dimensional modeling of sensory nerve architecture and eosinophil and mast cell interactions in eosinophilic gastrointestinal disease

Increased sensory nerve density has been described in type II inflammatory conditions and is linked to eosinophil and mast cell infiltration and neuropathic pain. To examine these relationships in eosinophilic gastrointestinal diseases (EGIDs), we developed a protocol using Clearing-enhanced 3D (Ce3D) tissue clearing to evaluate mucosal gastrointestinal (GI) nerve remodeling and interactions with eosinophils and mast cells in whole mount GI biopsies. Human gastric and esophageal biopsies were processed for 3-dimensional (3D) imaging. Tissues were fixed, permeabilized and immunolabeled for mucosal nerves (PGP9.5), sensory neurons (substance P), eosinophils (EPX), mast cells (tryptase), and epithelial cells (pan-cytokeratin). Vacuum-microwave-assisted staining was employed to enhance antibody penetration and protocol efficiency. Samples were cleared with Ce3D and imaged using confocal microscopy. Machine learning-enhanced quantitative analysis and modeling of nerve morphology and cellular interactions, including nerve length, branching, and spatial relationships between eosinophils, mast cells, and sensory neurons were performed. We established a 3D imaging method for whole mount GI biopsies to characterize nerve architecture and eosinophil and mast cell interactions in the human esophagus and stomach. This approach enables high resolution and volumetric analyses and can be modified to assess other spatial neuroimmune in human GI mucosal biopsies.