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. 2022 Dec 21;55(1):66–77. doi: 10.1038/s41588-022-01243-4

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© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, Expression of PIGR and CCL28 in epithelial cells by violin plot. b, CellChat cell–cell interaction analysis pathways for CCL chemokines produced by SMG epithelial cells and received by B cells (memory, naive and IgA/IgG/plasmablast combined) or CD4 T cells (CD4-naive/CM, CD4-EM/Effector and CD4-TRM combined) within airway tissue (trachea and bronchi). Arrow direction denotes chemokine-receptor pairs on specific cell types, arrowhead thickness reflects the relative expression of chemokine signal from each cell type. c,d, Expression dot plot of relevant chemokines and corresponding receptors as shown in b. e, smFISH (CCL28) and IHC (IgA2) staining in tracheal SMG. f, CellChat analysis as in b showing signaling of TNFSF13/APRIL and IL-6 from SMG epithelial cells to relevant B cell subsets and CD4-naive/CM. The proportion of the circle for each gene/cell type reflects the relative expression. g, smFISH (IL-6, TNFSF13/APRIL) and IHC (IgA2) staining in tracheal SMG. h, CellChat analysis as in f showing signaling from HLA genes expressed by SMG epithelial cells, signaling to CD4 on CD4 T cells. i, RNA expression of HLA-DRA, HLA-DRB1 and CD40 in B cells (as professional antigen-presenting cells for comparison) on violin plot, ciliated and SMG epithelial cells from scRNA-seq/snRNA-seq. j, IHC of HLA-DR and EpCAM in human airways showing strong expression of HLA-DR in the SMG (white dashed line) compared to the surface epithelium (yellow dashed line). k, IHC staining of CD4, CD45RO, HLA-DR and EpCAM, as indicated, in the airway SMG showing localization and close contact of CD4⁺ CD45RO⁺ T cells with HLA-DR⁺ glands as shown in the enlargement. Dotted lines enclose HLA-DR negative or low regions of glands, yellow arrowheads denote CD4⁺ CD45RO⁺ T cells, white arrowheads in the zoom-in show CD4⁺ CD45RO⁺ cells interacting with HLA-DR⁺ gland epithelial cells. Donors used for replicas in e, g, j and k are shown in Supplementary Table 9.