Fig. 4 |. Single-cell RNAseq analysis in specific cell clusters from OSCC tumor samples containing a relatively high load of cell-associated bacteria (High_Bac cohort) following data integration.

a, UMAP plots showing the cellular composition of the integrated data from the High_Bac cohort (n = 4 OSCC tumors) and the distribution of total bacteria or Fusobacterium with and without a UMI threshold as it is indicated. Color bars indicate the bacterial UMI transcriptional load. b, Pie charts of the cell-associated microbiome showing the most dominant bacterial genera in the single cells from the integrated data from the High_Bac cohort with and without a ≥4 UMI threshold as it is indicated. See also Supplementary Table 4. c, Volcano plots showing the differentially expressed genes in the macrophage and epithelial cell clusters when comparing Fusobacterium-positive single cells (Fuso.+) against total bacteria-negative single cells (Total Bac.−) with and without a UMI threshold of ≥4 as indicated. Dashed lines indicate the threshold of significant gene expression defined as the log₂ fold change ≤−0.58 and ≥0.58 with a −log₁₀ P value ≥1.301. Fold changes and P values were calculated by using a LMM, followed by a Benjamini-Hochberg multiple correction test. See also Supplementary Table 5. d, GSEA analysis showing the signaling pathways that are differentially regulated comparing Fuso.+ versus Total Bac.–single cells in the epithelial and macrophage cell cluster from the High_Bac cohort applying a UMI threshold of ≥4 for positive cells. A Wilcoxon rank sum test was implemented to calculate the normalized enrichment score. The data used to generate this figure have been published previously⁸.