Fig. 1

Multilevel omics integration reveals high expression of FOXO1 in the acute stage following TBI. a UMAP embedding of the entire dataset colored by orthogonally generated clusters labeled by manual cell type annotation, which were the scRNA-seq data analysis for peripheral blood samples from healthy donors and TBI patients (n = 3 in each group). b Dot plot showing the top 10 changed genes in every cell cluster of the human scRNA-seq. c UMAP plot depicting the subpopulation of human neutrophils by scRNA-seq, with each cell color-coded for clusters. d Dot plot showing the expression of the top 10 changed genes in each human neutrophil cluster. e GO analysis depicting the detailed gene of positive regulation of transcription, DNA-templated. f GO analysis depicting the detailed gene of positive regulation of protein metabolic process. g Representative regulatory network of target genes by FOXO1 in each neutrophil cluster. The same color represents the gene from the same cluster. h Heatmap showing the differential metabolites in neutrophils between the sham and TBI groups in mice. Higher expression levels are indicated by red and lower by green. i Bubble chart showing the pathway activities through the differential metabolites of neutrophils from mice (sham group vs. TBI group). Each group had 7 repeated samples of neutrophils per group. j Western blotting showing the expression of FOXO1 in neutrophils from humans or mice. Human: TBI patients vs. healthy donors; mice: TBI group vs. sham group, n = 3 for each group. k The relative mRNA expressions of FOXO1 in neutrophils from human or mice detected by qRT-PCR. Human: TBI patients vs. healthy donors; mice: TBI group vs. sham group, n = 5 for each group. Data are represented as the mean ± SEM. ^*P < 0.05, ^**P < 0.01, ns non-significant. FOXO1 forkhead box protein O1, TBI traumatic brain injury, UMAP uniform manifold approximation and projection, GO Gene Ontology, qRT‑PCR quantitative real‑time PCR, MAIT mucosal-associated invariant T, NK natural killer cell, DC dendritic cellsDC, ILC innate lymphoid cell, CSF3R granulocyte colony-stimulating factor receptor, SOD2 superoxide dismutase [Mn], mitochondrial, MEAT1 Terminal uridylyltransferase 7, NAMPT Nicotinamide Phosphoribosyltransferase, CXCL8 C-X-C Motif Chemokine Ligand 8, S100A9 S100 calcium binding protein A9, PLAUR plasminogen activator, urokinase receptor, S100A8 S100 calcium binding protein A8, ATP2B1-AS1 ATP2B1 antisense RNA 1, NKG7 natural killer cell granule protein 7, CCL5 C–C motif chemokine ligand 5, GNLY granulysin, HSPA5 heat shock protein family A (Hsp70) member 5, PPP2R5C protein phosphatase 2 regulatory subunit B'gamma, RPL3 ribosomal protein L3, CD247 CD247 molecule, RPL23A, ribosomal protein L23a, PSA ribosomal protein sa, HCST hematopoietic cell signal transducer, FCGR3A A fc gamma receptor iiia, CDKN1C cyclin dependent kinase inhibitor 1c, LST1 leukocyte specific transcript 1, RHOC ras homolog family member, IFITM3 interferon induced transmembrane protein 3, MTSS1 MTSS I-BAR domain containing 1, SMIM25 plaque enriched lncRNA in atherosclerotic and inflammatory bowel macrophage regulation, NAP1L1 nucleosome assembly protein 1 like 1, MS4A7 membrane spanning 4-domains a7, LRRC25 LRRC25 leucine rich repeat containing 25, IER5 immediate early response 5, KMT2C lysine methyltransferase 2c, TBL1X transducin beta like 1 x-linked, PICALM phosphatidylinositol binding clathrin assembly protein, WWOX ww domain containing oxidoreductase, ZNF609 zinc finger protein 609, JUNB JunB proto-oncogene, AP-1 transcription factor subunit, ATF3 activating transcription factor 3, TLR4 toll like receptor 4, NME2 nme/nm23 nucleoside diphosphate kinase 2, MAFF maf bzip transcription factor f, IER2 immediate early response 2, TFDP2 transcription factor dp-2, GLI3 gli family zinc finger 3, CDK8 cyclin dependent kinase 8, TNFSF11 TNF superfamily member 11, TNFAIP3 TNF α induced protein 3, TNF tumor necrosis factor, IL1B interleukin 1 β, NFKB1A nuclear factor kappa b subunit 1, SMURF1 smad specific e3 ubiquitin protein ligase 1, WWP2 WW domain containing E3 ubiquitin protein ligase 2, ATG2 autophagy related 2, SMURF2 smad specific e3 ubiquitin protein ligase 2, TGFB1 transforming growth factor β 1, PANBP9, MAPK8 mitogen-activated protein kinase 8, GSK3B glycogen synthase kinase 3 β. RAB7A member RAS oncogene family, RAB1A member RAS oncogene family, RAN binding protein 9