Fig. 4: Activated lung adventitial niches host CCR7⁺ exhausted T cell aggregates in prolonged COVID-19.

a Immunofluorescence (IF) overlay depicts CCR7 (yellow), CD3 (cyan), αSMA (blue) and CD31 (magenta) in a prolonged COVID-19 lung. White square depicts region of interest (ROI), where enlarged single channels are shown, together with PD1, Ki67 and DAPI (n = 8 FOVs). See also Supplementary Fig. 4a. b Dot plot representation of absolute counts of CD4⁺ and CD8⁺ T cells and NK cells analyzed by multiplex microscopy. Data (M ± SD) are analyzed by two-way ANOVA with Fisher’s LSD test, F (3, 84) = 29.56, p ˂ 0.0001. See also Supplementary Fig. 2a–c, Supplementary Movie 4 and 5. c Dot plot showing protein expression of CD4⁺ and CD8⁺ T cells in lungs and lymph nodes of COVID-19 donors and controls. Color code indicates average mean fluorescence intensity (MFI) for each marker and dot size indicates percent expressed. d Violin plots show expression level of relevant markers in CD4⁺ and CD8⁺ T cells in lymph node and lungs for each disease group. See also Supplementary Fig. 4A–C. c–d (n = 41 FOVs). e Violin plots show expression level of relevant markers in myeloid cells of lymph nodes for each disease group. See also Supplementary Fig. 4c. (n = 9 FOVs). d–e Data analyzed by one-way ANOVA with Wilcoxon test, comparing each group to the prolonged, where * p ˂ 0.05, ** p ˂ 0.01, *** p ˂ 0.001 and **** p ˂ 0.0001. f IF overlays depict DAPI (blue), HLA-DR-DQ (cyan), CD3 (magenta) and CD141 (yellow) in a control and a chronic lymph node. White square depicts the ROI, where orange arrows indicate direct cell contacts between T cells and CD141⁺HLA-DR-DQ⁺ dendritic cells. Scale bar: 20 µm (n = 9 FOVs). g Heat map display (z-score) of the MFI for each marker of CD4⁺ and CD8⁺ T cells within lung perivascular and epithelial niches in the prolonged group analyzed by multiplex microscopy. (n = 32 FOVs). Source data are provided as a Source Data file. See also Supplementary Figs. 2a–c and 4a.