Fig. 2: Single-cell characterization of the acute hyperinflammatory response to LPS administration.

a, UMAP representation of all single cells obtained from bone marrow and peripheral blood of LPS-challenged healthy volunteers (n = 3 for each compartment at BL: bone marrow, 7 d before the LPS challenge; blood, immediately before the LPS challenge) and at 4 h and d7 post-LPS challenge, colored based on cell type. b, UMAP of all blood and bone marrow cells (n = 3) as in a, colored based on acquisition time point (top) and collected compartment (bottom). c, UMAP of blood and bone marrow HSCs and myeloid lineage cells at BL and 4 h (n = 3) as in a, colored based on cell type. d, UMAP of blood (PB) and bone marrow (BM) HSCs and myeloid lineage cells at BL and 4 h (n = 3) as in c, colored based on time point (top) and compartment (bottom). e, Heatmap representation of pro-monocyte and mature monocyte genes in myeloid cells from the bone marrow and blood of LPS-challenged healthy volunteers (n = 3) at BL and 4 h. f, NMF-inferred gene program enriched in blood and bone marrow infMonos from bone marrow and blood of LPS-challenged healthy volunteers (n = 3) as in d. g, UMAP of blood and bone marrow T and NK cells at BL and 4 h (n = 3) as in a, colored based on cell type. h, UMAP of blood and bone marrow T and NK cells at BL and 4 h (n = 3) as in g, colored based on time point (top) and compartment (bottom). i, NMF-inferred gene program enriched in T_inf cells from bone marrow and blood of LPS-challenged healthy volunteers (n = 3) as in h. j, Normalized expression profile of several IFN pathway genes in blood and bone marrow HSCs and myeloid lineage cells, T cells and NK cells, and B cells and pDCs of LPS-challenged healthy volunteers at BL and 4 h (n = 3). Max, maximum; min, minimum; Cycl, cycling; T_N, naive T cell; T_CM, central memory T cell; T_EM, effector memory T cell; MAIT, mucosal-associated invariant T cell.