{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Huck A"],"funding":["German Research Foundation","CRU 5023","GL 899/1-1","SPP 1656 SI 749/9-1","INST 335/658-1 FUGG","INST 335/453-1 FUGG","German Cancer Consortium","Deutsche Forschungsgemeinschaft","CRC 1449-B04","CRC 1340","CRC 1340-B06","Deutschen Konsortium für Translationale Krebsforschung","CRC-TRR 241-B01","Z02"],"pagination":["e70071"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12501404"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["55(10)"],"pubmed_abstract":["Lymphoid follicles in the human gut are critical immune hubs, yet their role in Crohn's disease pathogenesis remains poorly understood. Here, we apply multiplexed imaging mass cytometry to spatially profile Peyer's patches and lymphoid follicles in biopsies from healthy controls and Crohn's disease patients with ileitis, isolated colonic involvement, or in remission. Despite tissue heterogeneity, our optimized preprocessing pipeline enabled robust tissue annotation, single-cell phenotyping, and neighbourhood-level analysis. While conventional analysis based on cell frequencies did not distinguish disease states, spatial analysis revealed disease-associated remodelling of lymphoid architecture. Biopsies from colonic Crohn's disease patients showed, within follicles, increased frequencies of"],"journal":["European journal of immunology"],"pubmed_title":["Imaging Mass Cytometry-Based Immune Profiling of Human Peyer's Patches in Patients with Crohn's Disease."],"pmcid":["PMC12501404"],"funding_grant_id":["372486779","375876048","445460773","431232613","50474582"],"pubmed_authors":["Bojarski C","Glauben R","Siegmund B","Rodriguez-Sillke Y","Kuhl AA","Huck A","Lehmann M","Bischoff P","Kunkel D","Steinhoff U"],"additional_accession":[]},"is_claimable":false,"name":"Imaging Mass Cytometry-Based Immune Profiling of Human Peyer's Patches in Patients with Crohn's Disease.","description":"Lymphoid follicles in the human gut are critical immune hubs, yet their role in Crohn's disease pathogenesis remains poorly understood. Here, we apply multiplexed imaging mass cytometry to spatially profile Peyer's patches and lymphoid follicles in biopsies from healthy controls and Crohn's disease patients with ileitis, isolated colonic involvement, or in remission. Despite tissue heterogeneity, our optimized preprocessing pipeline enabled robust tissue annotation, single-cell phenotyping, and neighbourhood-level analysis. While conventional analysis based on cell frequencies did not distinguish disease states, spatial analysis revealed disease-associated remodelling of lymphoid architecture. Biopsies from colonic Crohn's disease patients showed, within follicles, increased frequencies of","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-06-04T06:17:05.05Z","creation":"2026-05-06T03:13:33.704Z"},"accession":"S-EPMC12501404","cross_references":{"pubmed":["41054006"],"doi":["10.1002/eji.70071"]}}