Fig. 4: IgA plasma cells in human airways colocalize with SMGs.

a, UMAP of scRNA-seq and snRNA-seq data from epithelial cells (excluding alveolar AT1 and AT2) colored by cell type, with a dot plot for the marker genes of SMG duct cells. b, smFISH staining of mucous (MUC5B), serous (LPO) and duct (ALDH1A3/RARRES1) cells in human bronchus. c, UMAP plots of myeloid, T/NK and B lineage cells, colored by cell type. d, Number of B lineage cells with different Ig isotypes in airway (trachea and bronchi) from the analysis of VDJ amplified libraries. e, Visium ST results show IgA plasma cells specifically localize in the glands. Normalized average cell abundance (dot size and color) are shown from cell2location for SMG and B lineage cell types across the manually annotated micro-anatomical tissue environments. H&E section of bronchi with manually annotated glands shown in blue (top panel), cell2location density scores for IgA plasma cells and SMG serous cells shown in lower panels. Cell type loadings are represented by both dot size and color. f, Unsupervised NMF analysis of Visium ST cell2location results for 11 factors, showing NMF factor loadings normalized per cell type (dot size and color). Factors 3 and 6 identify two separated factors in the SMG colocalizing IgA plasma cells, specifically with SMG serous cells (factor 3), but less with other SMG cell types (factor 6). Other factors and cell types are shown in Supplementary Fig. 4. g, Multiplex IHC staining of human trachea for the SMG structure (Hoechst for nuclei, EpCAM for epithelium, Phalloidin for actin, CD31 for vessels), B lineage markers (IgD, IgA2 and IgG) and CD4 T cells (CD45, CD3 and CD4). Arrowheads point to CD45⁺ CD3⁺ CD4⁺ cells. Scale bar 100 µm. h, Percentages of different isotypes of 470 B plasma cells from nasal, tracheal and bronchial brushes of two COVID-19 positives and three healthy control patients⁷¹. Patients with over 20 plasma cells were considered. Donors used for replicas in b and g are shown in Supplementary Table 9. Macro, macrophage; CM, central memory; EM, effector memory; EMRA, effector memory re-expressing CD45RA.