Extended Data Fig. 7: NK cell responses to fibrin stimulation.

a, Volcano plots of DEGs from bulk RNA-seq of fibrin-stimulated mouse primary NK cells for four days. n = 3 mice per group. The cutoffs were Log2 fold change > 0.25, adjusted P (FDR) < 0.1 by two-sided quasi-likelihood F-test in edgeR with the Benjamini-Hochberg method. b, Differential phosphorylation site intensities between Fibrin- and IL-15-treated NK cells isolated from PBMCs. Phosphorylation sites grouped based on upstream kinases annotated in the OmniPath network database of kinase-substrate relationships. Red boxes indicate a significant shift in kinase-specific substrate regulation. Unadjusted P < 0.05 calculated from log2 fold changes of n = 8,054 phosphorylation sites between conditions derived from 2 (mock), 3 (fibrin) and 2 (IL-15) biologically independent experiments (two-tailed z-test, Methods). Box indicates the interquartile range (IQR) and whiskers denote the 1.5 × IQR. c, Downregulated network of phosphoproteomic interaction in fibrin-treated human NK cells for 1 h compared to IL-15. Colour of kinase represents z-score of kinase activity and colour of substrates represents log2FC (Methods). d, Flow cytometry of mouse NK cells fibrin-stimulated for four days. Ki-67 (%), granzyme B (MFI) and IFN-γ (MFI), n = 8 mice per group. Two-tailed paired Student’s t-test. e, Flow cytometry of fibrin-stimulated mouse NK cells for four days at concentrations indicated. NKp46 (MFI), NKG2D (MFI). n = 4 mice per group. One-way ANOVA with post-hoc analysis by Sidak’s multiple comparisons. Data are mean ± s.e.m. f, Flow cytometry of NK cells fibrin-stimulated for 1, 2, and 4 days. NKG2D (MFI), CD54 (MFI), NKp46 (MFI), and granzyme B (%). n = 4 mice per group. Two-tailed paired Student’s t-test. g, Kinase activities inferred from global mass spectrometry phosphoproteomics of NK cells and macrophages (data from Mendiola et al.²¹) unstimulated (Mock) or Fibrin-treated for 1 h. Gating strategy is shown in Supplementary Fig. 2.

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