Analysis of DC and monocyte subpopulations by phenograph clustering.

(A, B) Results of phenograph reclustering of HLA-DR⁺/intermediate Lin^- cells (DCs and monocytes) after exclusion of all undefined cells. (A) Heatmap of marker expression in phenograph clusters and (B) UMAP of pooled data from healthy controls (H) and COVID-19 patients with mild disease are shown with phenograph clusters indicated by colors and annotation of monocyte and DC subpopulations indicated. Color overlays show the scaled marker expression for CD88/CD89 and Siglec-1. (C) Heatmap of marker expression in phenograph clusters of reclustered monocytes and (D) of reclustered DCs. (E) Monocyte UMAPs with phenograph clusters indicated by colors are shown separately for the indicated patient groups with annotation of monocyte subpopulations indicated in the UMAP of healthy controls. (F) Monocyte UMAP with color overlay indicating scaled Siglec-1 expression in pooled data from COVID-19 patients with moderate disease. (G and I) Frequencies of phenograph clusters derived from reclustering of monocytes (G) and DCs (I) in individual patients grouped by disease severity and controls. Letters indicate patients, numbers indicate consecutive sampling timepoints. Healthy donors (HD) were numbered. (H, J) Frequency of monocytes in the Siglec-1⁺ mo 1 cluster (H) and of DCs in the Siglec-1⁺ DC3 cluster (J) at the indicated grouped time points. Red symbols: mild/moderate COVID-19; blue symbols: severe COVID-19; orange symbols: recovered. Connected lines represent multiple measurements of the same donor at different time points. Columns indicate the mean. Kruskal-Wallis test with Dunn’s correction. * p<0.05, ** p<0.01, *** p<0.001.

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