Characterization of HLA-DR⁺ non-DC population.

(A) Gating strategy for neutrophils in the blood: Within the lineage (CD3, CD15, CD19, CD20, CD56, CD66b) positive cells neutrophils were gated as CD16⁺ and CD88/89⁺. (B) UMAP clustering of one representative COVID-19 patient. Overlay of gated cDC1 (green, CD141⁺), cDC2 (orange, CD1c⁺, CD5⁺), DC3 (brown, red, dark red, CD1c⁺, CD5^–, CD163^+/–, CD14^+/–), pDC (black, CD123⁺), tDC (blue, CD123⁺, Siglec1⁺, Axl⁺) and non-DC (purple, HLA-DR⁺, Lin-, CD141^–, CD1c^–) populations. (C) Representative histograms of CD11c, CD1c and CD86 expression in cDC1, cDC2, DC3, tDC, pDC and non-DC in a patient with moderate COVID-19. (D) Expression of several surface markers overlayed in the UMAP from (B). Shown is the expression of CD33, CCR2, CD14, CD1c, CD5, CD163, CD86, HLA-DR, CD123, Axl, CD141, XCR1 indicated by color scale (red = high expression, green = intermediate, blue = low expression). (E) Gating strategy for identification of progenitor populations in the blood. Cells are pregated on Lin⁻(CD3, CD15, CD19, CD20, CD56, CD66b, CD88, CD89), HLA-DR⁺ living cells. pDCs and tDCs are excluded via gating on CD123^– cells followed by exclusion of cDCs by gating on CD1c^–, CD141^– cells. These progenitors are then separated into lymphoid cells (CD127⁺) and CD127^– progenitors. Here, cells can be differentiated by their expression of CD117 and CD34 into four quadrants: CD117⁺ CD34^–, CD117⁺ CD34⁺, CD117^– CD34⁺, CD117^– CD34^–. (F) Representative histograms of marker expression of non-DCs, cDCs, pDC/tDCs, lymphoid cells, CD117⁺ CD34⁺, CD117^– CD34^–, CD117⁺ CD34^–, CD117^– CD34⁺ progenitor cells, gated according to (E) of one COVID-19 patient. Expression of CD141, CD14, CD1c, CD33, Ki67, CD115, CD127, CD135, CD45RA, CD163, CD34, CD117, CD123, HLA-DR and Siglec-6 is shown. (G) Percentage of CD117^– CD34^–, CD34⁺ CD117^–, CD117⁺ CD34^–, CD117⁺ CD34⁺ cells of total CD127^– progenitor cells. (H) Percentage of CD127⁺ lymphoid cells of the progenitor cells are shown. Healthy donors (= H, black symbols, n = 12), mild/moderate and severe COVID-19 patients (= M/S, red, n = 9) and recovered patients (= R, orange, n = 9).

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