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. 2020 Dec 26;2(1):100166. doi: 10.1016/j.xcrm.2020.100166

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© 2020 The Authors

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMC Copyright notice

In-depth characterization of the myeloid cells in the peripheral blood of COVID-19 patients

(A) t-SNE plots of normalized expression of the indicated markers across a maximum of 1,000 neutrophils per patient (n = 22 healthy controls, 27 mild COVID-19 patients, and 29 severe COVID-19 patients).

(B) t-SNE plot generated as indicated in (A) and colored by disease severity.

(C) Left: t-SNE plot generated as indicated in (A) and colored by CD16 expression level based on manual assignment of PhenoGraph clusters. Right: boxplot showing the frequency of CD16^low neutrophils in COVID-19 patients and healthy controls. Statistical analyses were performed with a Mann-Whitney-Wilcoxon test corrected for multiple testing using the Holm method, and p values are shown if the results were significant (p < 0.05).

(D) t-SNE plots of normalized expression of the indicated markers across a maximum of 1,000 monocytes per patient.

(E) t-SNE plots generated as indicated in (D) colored by disease severity (top) and by clusters identified with the PhenoGraph algorithm (bottom).

(F) Contour plots showing the distribution of a subset of 10,000 cells from the indicated clusters for a selected set of markers. For this analysis, classical monocytes M1–M7 were merged in a single cluster.

(G) Heatmap of the normalized marker expression in PhenoGraph monocyte clusters. The frequency of each cluster in patients with mild and severe disease and in healthy controls is indicated as a stacked histogram to the right of the heatmap. Cell numbers for each cluster are plotted to the right of the stacked histogram.

(H) Overlaid histograms showing arcsinh transformed counts on a linear axis for selected markers for the CD169⁺-activated monocyte clusters.

(I) Overlaid histograms showing arcsinh transformed counts on a linear axis for the indicated markers for the classical monocyte clusters. Values in the plot indicate median untransformed count intensities.

In (H) and (I), values on the plot indicate the median raw ion count intensity for each cluster and marker indicated.