Fig. 3: Immunosuppression operates on NK cells and T cells but not on myeloid cells. | Nature Communications

Fig. 3: Immunosuppression operates on NK cells and T cells but not on myeloid cells.

From: Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation

Fig. 3

a Representative CD3+ (n = 29) and CD68+ (n = 31) lung regions profiled by DSP. b Normalized gene expression of immunosuppression-related genes in CD3+ rich and CD68+ rich ROIs (n = 60 ROIs from n = 7 decedents, men = 2, women = 5) of lung. Z -scale from −1.5 to 1.5. c Comparison of selected genes expression in CD3+ rich regions between sexes from lung tissues. Each point represents one ROI. Colored dots represent different samples. Blue (n = 21), red (n = 8). Data are shown as mean ± s.e.m. p (PDCD1) = 0.049; p (SLAMF7) = 0.001; p (CD33) = 0.03; p (KLRK1) = 0.02; p (GZMB) = 0.049; p (FCGR3B) = 0.009; p (IL15) = 0.007; p (CD83) = 0.04; p (IL6) = 0.02; p (SIGLEC5) = 0.04;Unpaired two-tailed Student’s t tests, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns: not significant. d, f mIHC staining of GZMB+ CD3+ T cells (d, left), CD56+ NK cells (d, right), or CD80+/CD83+ BATF3+/BDCA2+ DCs (d) Number of cells depicted/total observed: SARS-CoV-2 NP+ (Lung 5/1923, Liver 3/702, Heart 1/374); GZMB+CD3+ (Lung 1/723, Liver 7/695); CD56+ (Lung 13/8783, Liver 3/3802, Heart 4/1077). (f) in the neighborhood of SARS-CoV2-NP+ cells in various organs and corresponding spatial annotations. Number of cells depicted/total observed: SARS-CoV-2 NP+ (Lung 4/2701, Liver 3/1034, Kidney 1/103, Heart 4/638); CD80,CD83+ BATF3,BDCA2+ (Lung 3/796, Liver 6/2792, Kidney 1/4, Heart 2/374). Scalebars: 10 μm. e, g Odds ratios of GZMB+ CD3+ T cells (e, left) (Lung: 0.027 ± 0.295; Liver: 1.085 ± 0.195; Kidney: −0.243 ± 1.977; Heart: −0.014 ± 1.430; Spleen: −0.026 ± 0.188), CD56+ NK cells (e, middle) (Lung: −0.227 ± 0.101; Liver: 0.405 ± 0.125; Kidney: −0.209 ± 0.704; Heart: 0.745 ± 0.248; Spleen: −0.364 ± 0.064), CD8+ cells (e, right) (Lung: −0.276 ± 0.177; Liver: 0.090 ± 0.075; Kidney: 0.850 ± 0.459; Heart: 0.477 ± 0.215; Spleen: −0.077 ± 0.039), activated macrophages (g, left) (Lung: 1.037 ± 0.303; Liver: 1.048 ± 0.134; Spleen: 0.361 ± 0.366), or activated DCs (g, right) (Lung: 0.844 ± 0.243; Liver: 0.736 ± 0.104; Kidney: 1.364 ± 0.706; Heart: 1.242 ± 0.273; Spleen: −0.162 ± 0.039) in NP-proximal compared to NP-distal regions in various organs. h Odds ratios of CD80/CD83 positivity in NP-proximal CD206+ cells compared to NP-distal CD206+ cells (Lung: 0.844 ± 0.339; Liver: 0.796 ± 0.165; Spleen: −0.083 ± 0.403) and in NP-proximal BATF3/BDCA2+ cells compared to NP-distal BATF3/BDCA2+ cells (Lung: 0.652 ± 0.257; Liver: 0.786 ± 0.119; Kidney: 1.170 ± 0.820; Heart: 1.126 ± 0.341; Spleen: −0.376 ± 0.047). Odds ratios of CD80/83 positivity defined as (N(p)CD80/CD83+/n(d) CD80/CD83+)/(n(p) CD80/CD83−/n(d) CD80/CD83−), where (p) and (d) refer to CD206+ or BATF3/BDCA2+ cells proximal or distal from viral NP. e, g, h Circles indicate sample odds ratios, squares with error bars indicate aggregated odds ratios and confidence intervals. Proximity is as defined by a distance cut-off of 15 µm from viral NP. Data are shown as Odds Ratio ± 95% CI. Source data are provided as a Source Data file.

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