Fig 2: Activation of the TLR4 signaling pathway after H. suis infection(A) Tlr4 mRNA levels in the stomachs of H. suis-infected WT, Myd88 KO, Trif KO, and Myd88/Trif DKO mice 6 months after infection were determined with qRT-PCR.(B) Immunohistology of TLR4-expressing cells analyzed with confocal microscopy. Magnification, 100×.(C) Immunohistology of EpCAM-positive cells in the stomachs of H. suis-infected WT mice. Magnification, 100×. Formation of gastric lymphoid follicles is indicated by dotted lines. Representative images are shown.(D–H) C57BL/6J WT mice were infected with H. suis for 6 months and gastric cells were analyzed with flow cytometry. (D) Staining with B220 and CD19 antibodies, followed by staining for TLR4. Right panels show TLR4 staining among B220 + CD19 + cells. (E) Staining with CD4 and TCRβ antibodies, followed by staining for TLR4. Right panels show TLR4 staining among CD4+ TCRβ+ cells. (F) Staining for CD11c and MHC class antibodies, followed by staining for TLR4. Right panels show TLR4 staining among CD11c + MHC class + cells.(G) Staining for FDC M1, followed by staining for TLR4. Right panels show TLR4 staining among FDC M1+ cells. (H) Staining for EpCAM, followed by staining for TLR4. Right panels show TLR4 staining among EpCAM + cells.Ifna (I) and Ifnb (J) mRNA levels in the stomach after H. suis infection were determined with qRT-PCR. (A, I, and J) Data were normalized to β-actin levels.Data are shown as the mean ± SD (n = 5) of three independent experiments. ∗∗p < 0.01, N.S., no significant difference (ANOVA). Ab, antibody; DKO, double knockout. Scale bar, 100 μm.

Fig 3: Paclitaxel response activates canonical interferon response genes.3A) UMAP showing the scRNA-seq landscape for ligand perturbations. IFNB = Interferon-Beta, OSM = Oncostatin-M, NOTCHi_IFNB = Notch inhibitor + Interferon-Beta, NOTCHi = Notch inhibitor, TGFB = Transforming Growth Factor Beta, IFNG = Interferon-Gamma, LTA = Lymphotoxin-Alpha, PBS = Phosphate Buffered Saline (control). 3B) Heatmap showing the Pearson correlation for all gene log2 fold-change between perturbation versus time-matched control. Inset number and color indicate correlation. 3C,D) Gene enrichment map for Paclitaxel uniquely upregulated (3C) and Paclitaxel+Interferon shared upregulated (3D) genes. Color indicates significance, size indicates number of upregulated genes, and lines connect ontologies with shared elements. 3E) ChEA3 transcription factor enrichment ranks computed from 140 Paclitaxel uniquely upregulated genes (x axis) versus 120 Paclitaxel-Interferon shared upregulated genes (y axis). Lower rank indicates higher imputed activity. TFs to the lower right of the diagonal have higher imputed activity within the PTX+IFN shared upregulated gene set, and TFs to the upper left of the diagonal have higher imputed activity within the PTX uniquely upregulated gene set. 3F) Bar plot showing Average Log2FC from paclitaxel treated scRNA-seq data for the 24 top ranked transcription factors (intersect of top 15 ranked for PTX unique or PTX shared individually). Transcription factor names in red had differential upregulation (average log2 fold-change > 0.25, FDR < 0.01) at either 24 or 72 hours of paclitaxel treatment compared to vehicle control.

Fig 4: Paclitaxel response activates canonical interferon response genes. (A) UMAP showing the scRNA-seq landscape after ligand perturbations. IFNB = Interferon-Beta, OSM = Oncostatin-M, NOTCHi_IFNB = Notch inhibitor + Interferon-Beta, NOTCHi = Notch inhibitor, TGFB = Transforming Growth Factor Beta, IFNG = Interferon-Gamma, LTA = Lymphotoxin-Alpha, PBS = Phosphate Buffered Saline (control). (B) Heatmap showing the Pearson correlation for log2 fold-change values for each perturbation versus time-matched control. (C,D) Gene enrichment map for Paclitaxel uniquely upregulated (3C) and Paclitaxel + Interferon shared upregulated (3D) genes. Color indicates significance, size indicates number of upregulated genes, and lines connect ontologies with shared elements. (E) ChEA3 transcription factor enrichment ranks computed from 140 Paclitaxel uniquely upregulated genes (x axis) versus 120 Paclitaxel-Interferon shared upregulated genes (y axis). Lower rank indicates higher imputed activity, and named TFs with red dots were within the top 15 ranks for either geneset. TFs to the lower right of the diagonal have higher imputed activity within the PTX + IFN shared upregulated gene set, and TFs to the upper left of the diagonal have higher imputed activity within the PTX uniquely upregulated gene set. (F) Bar plot showing Average Log2FC from paclitaxel treated scRNA-seq data for the 24 top ranked transcription factors (intersect of top 15 ranked for PTX unique or PTX shared individually). Red font indicates TFs significantly upregulated (average log2 fold-change > 0.25, FDR < 0.01) at either 24 or 72 h of paclitaxel treatment compared to vehicle control.