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To examine these relationships in eosinophilic gastrointestinal diseases, we developed a protocol using Ce3D (clearing-enhanced 3D) 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 imaging. Tissues were fixed, permeabilized, and immunolabeled for mucosal nerves (Protein Gene Product 9.5), sensory neurons (substance P), eosinophils (eosinophil peroxidase), mast cells (tryptase), and epithelial cells (pan-cytokeratin). Vacuum-microwave\u2013assisted staining was employed to enhance antibody penetration and protocol efficiency. Samples were cleared with Ce3D and imaged using confocal microscopy. Machine learning\u2013enhanced 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 3-dimensional 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 interactions in human GI mucosal biopsies.<\/jats:p>","DOI":"10.1093\/jleuko\/qiag058","type":"journal-article","created":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T12:21:46Z","timestamp":1777638106000},"source":"Crossref","is-referenced-by-count":0,"title":["Three-dimensional modeling of sensory nerve architecture and eosinophil and mast cell interactions in eosinophilic gastrointestinal disease"],"prefix":"10.1093","volume":"118","author":[{"given":"Ari M","family":"Levine","sequence":"first","affiliation":[{"name":"Human Eosinophil Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health , 9000 Rockville Pike, Bethesda, MD20892 ,","place":["United 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Rockville Pike, Bethesda, MD20892 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6867-7569","authenticated-orcid":false,"given":"Alla","family":"Turshudzhyan","sequence":"additional","affiliation":[{"name":"National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , 9000 Rockville Pike, Bethesda, MD20892 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0549-7768","authenticated-orcid":false,"given":"Sheila","family":"Kumar","sequence":"additional","affiliation":[{"name":"National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , 9000 Rockville Pike, Bethesda, MD20892 ,","place":["United 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