Journal: Gut Microbes
Article Title: Phenotypic profiling of neutrophils in acute Clostridioides difficile infection identifies a TNF-induced activation signature associated with epithelial damage
doi: 10.1080/19490976.2026.2659430
Figure Lengend Snippet: cNeu3-like neutrophils share a transcriptomic profile with TNF-polarized neutrophils during acute CDI, and TNF treatment induces this phenotype in vitro . (A) Monocle pseudotime trajectory analysis of bone marrow and blood neutrophil clusters from uninfected and infected mouse. (B) Cell fate analysis performed using Monocle3 by analyzing genes upregulated as cells transition from Neu5 to Neu6 along the pseudotime trajectory. Each point represents a cell in UMAP space, and cells are colored by the gene module upregulated as cells transition from Neu5 to Neu6. (C) Metascape KEGG pathway enrichment analysis of genes upregulated as cells transition from Neu5 to Neu6. (D) Neutrophil cytokine-induced polarization cellular state plots of bone marrow, blood, and colon neutrophils from uninfected and C. difficile -infected mouse. DEGs from neutrophils polarized with TNF, type I/II interferons, IL-1α/β, or GM-CSF were utilized to define neutrophil transcriptomic states induced by the corresponding cytokines. For this analysis, gene lists were obtained from Cui et al. 2023. (E) Cui 2023 TNF-polarized neutrophil gene signature and KEGG TNF signaling pathway signature for Neu6, Neu8, and cNeu3 plotted against pseudotime. (F) Amount of TNF (pg/mg of protein) collected from uninfected and C. difficile -infected mice during acute CDI (i.e., day 2 after challenge). (G) Experimental plan: Neutrophils were isolated from the bone marrow of WT mice and enriched by MACS bead-based negative selection. Neutrophils were plated at 1 × 10 6 cells/well in 96-well plates and then treated with recombinant murine TNF (50 ng/ml) or control (PBS) for 2 h. Cells were incubated at 37 °C and then stained for flow cytometry. (H) Representative flow cytometry plot showing CD11b and IL-1β staining in untreated and TNF-treated samples. (I) Percent distribution of CD11b hi IL-1β hi in untreated and TNF-treated samples. (J) Comparison of MALT1, MIP1α, and CD63 gMFI in gate 1 vs. gate 2 populations in untreated and TNF-treated samples. Panels (F) and (J and K) are presented as box-and-whisker plots (boxes = interquartile range, whiskers = minimum and maximum, line = median). Panel (F) shows data combined from 4 independent experiments, n = 14 (control) and 18 (CDI) (F); panels (H) and (J) are representative of 2 independent experiments, n = 3 per group; panel I is combined data points from two independent experiments, total n = 6 per group. Stats: Mann–Whitney test (F); Spearman correlation (G); unpaired t -test with Welch's correction (I and J); * p < 0.05; ** p < 0.01; *** p < 0.001; and **** p < 0.0001.
Article Snippet: Neutrophils were enriched using MACS MS columns (Miltenyi #130-097-658) and stained with antibodies for Ly6G (BioLegend #127654 or #563978), CD11b (BioLegend #101259 or Thermo Fisher #12-0112-82), and viability dye (Thermo Fisher # L10120 ).
Techniques: In Vitro, Infection, Isolation, Selection, Recombinant, Control, Incubation, Staining, Flow Cytometry, Comparison, Whisker Assay, MANN-WHITNEY