Fig. 5: Adventitial niches aim at the formation of ectopic lymphoid structures in prolonged COVID-19 lungs.

a Immunofluorescence (IF) image depicting CD45 (yellow), DAPI (magenta), Collagen IV (cyan) and Collagen I (blue). White square represents a region of interest (ROI), shown as an enlargement and depicting a highly infiltrated bronchus with a dense immune cell aggregate adjacent to it in the lower left corner. b The spatial distribution of ectopic lymphoid structure-related transcripts is shown in a color-coded fashion as normalized enrichment scores (NES) in overlay with relevant tissue landmarks: intermediate-to-large vessels (yellow line), airway structures (black line) and lymphoid structure (orange line). a, b (n = 2 prolonged lung samples). See also Supplementary Fig. 5. c IF images from the same area of a prolonged lung, where DAPI (blue), CD3 (red), PNAd (green) and Collagen IV (Col. IV, white) are shown in the left panel, while DAPI (blue), Pax5 (magenta) and CD4 (cyan) are shown in the right (n = 9 FOVs). d Dot plot representation of the absolute counts of B cells / plasma cells per field of view analyzed by multiplex microscopy. Data (M ± SD) are analyzed by one-way ANOVA with Fisher´s LSD test, F (3, 28) = 8.332, p = 0.0004 (n = 32 FOVs). Source data are provided as a Source Data file. See also Supplementary Fig 2a–c. e Heat map display of the correlation between relevant clinical parameters, donor stratification and fibrosis score with the presence of large immune aggregates. See also Supplementary Fig 1c. Pearson r values are shown in the plot with additional color code for positive (blue) or negative (red) correlations. Statistical significance (two-sided) is depicted with * for p = 0.039 and ** for p = 0.007.