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. 2024 Nov 20;635(8039):699–707. doi: 10.1038/s41586-024-07571-1

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 10 — a) Protein expression in CD ileum (representative of n = 2) of HLA-DR (MHC-II) in INFLAREs (MUC6) along with localisation of CD3+ T cells and regulatory T cells (FoxP3+CD3+). b) Expression per donor of genes involved in IFNGR to MHC-II signalling pathway in INFLAREs and MGN cells in small intestine, as summarised in Fig. 5f. c) Additional protein staining for INFLAREs (MUC6) in CD disease ileum (as in Fig. 5g, n = 4) with various T cell subsets (CD4+CD3+, CD8+CD3+, TCRγδ+CD3+T cells). d) Protein staining as in (c) in Celiac disease duodenum tissue (n = 2). e) Quantitation of T cell densities for the T cell subsets indicated in MUC6+ glands and adjacent control epithelium across 5 sections from 3 donors as represented in (c). P-values calculated based on ROIs as replicates (n = 126 MUC6+ ROIs and 59 adjacent control ROIs) using negative binomial linear regression, adjusting for log area, two-sided Wald test. f) Protein staining as in (c) and (d) in healthy proximal duodenum (n = 2) showing abundance and localisation of T cell subsets in Brunner’s glands.