Extended Data Fig. 6: Bacteria-associated single cells correlate with upregulation of cell inflammation and cancer progression pathways in patients with OSCC.

a, Dot plot showing the relative expression of gene markers for the T cell, myeloid and epithelial / mesenchymal cell compartment from single-cell data from patients with OSCC (n = 7 patients) as it is indicated in the cell clusters annotated in the UMAP plot from Fig. 3c. Colour bars indicate the average expression level, and the dots represent the percentage of expression for each gene marker. b, UMAP plot indicates the distribution of aneuploid and euploid cells in samples from patients with OSCC. c, Heat map shows the copy number variations (CNV) across 41,723 cells from the epithelial cell cluster as it is indicated. d, Percentage of aneuploid cells for each cell type annotated in Fig. 3c. Insert tables indicate the percentage of aneuploid cells and bacterial transcripts (UMIs) for each sub-cell clusters in the epithelial cell cluster as it is indicated. e, GSEA analysis showing the signalling pathways that are differentially regulated in cells from the sub-cell cluster 3, which contains the majority of aneuploid cancer cells, relative to other sub-cell clusters (All others) from the epithelial cell cluster. f, UMAP plot highlighting the epithelial sub-clusters that are contained in the epithelial cell cluster detected in Fig. 3c. g, Volcano plot showing the gene-expression profile in cancer cells from sub-cell cluster 3 in comparison to other sub-cell clusters from the epithelial cell cluster. 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. h, GSEA analysis showing the signalling pathways that are differentially regulated comparing total bacteria-associated cells (Total Bac+) vs bacteria-negative cells (Total Bac-) in the epithelial single cells as described in Fig. 3c. I, UMAP plot highlighting the transcriptional cellular group that is associated with bacterial invasion (Total Bac+; red cells) along with the bacteria-negative cell population (Total Bac-; grey cells). j, Volcano plot indicates the gene-expression profile in total bacteria-associated cell (Total Bac+) relative to total bacteria-negative cells (Total Bac-) in the epithelial single-cell cluster described in Fig. 3c. k, GSEA analysis showing the signalling pathways that are differentially regulated comparing total bacteria-associated cells (Total Bac+) vs bacteria-negative cells (Total Bac-) in the macrophage single cells as described in Fig. 3c. l, Volcano plot indicates the gene-expression profile in total bacteria-associated cell (Total Bac+) relative to total bacteria-negative cells (Total Bac-) in the macrophage cell cluster described in Fig. 3c. 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. Wilcoxon Rank Sum test was implemented to calculate the normalized enrichment score (NES) in panels (e), (h) and (k). A LMM analysis followed by Benjamini–Hochberg multiple-correction test was used to calculate the fold change and p-values for each gene in panels (g), (j) and (l).