Fig. 7: Recurrent CNAs and heterozygous mutations in downregulated TSGs and signaling-related genes.

a Histograms showing cumulative fractions of tumors with CNA gain (red) and loss (blue) in 100-kb bins for 26 tumors with clonal integration (positive) and 25 without (negative). Fractions (y-axis) were calculated as tumors with TCN > ploidy × 2^0.8 (gain) or TCN < ploidy × 2^−0.8 (loss), divided by total. Dark-colored bins indicate significantly higher fractions than expected using the G-test of goodness of fit (BH-adjusted P < 0.05 and odds ratio > 1). Proto-oncogenes in significant gain bins are in red. Among the genes in significant loss bins, TSGs with two hits in multiple tumors, mutated in ≥21 tumors along with TRAF3 and CYLD (in Supplementary Fig. 11), and mutated in ≥5 tumors exclusively in either group are in blue. Genes exclusive to one group are in bold and underlined. b Schematic of scRNA-seq analysis using publicly available datasets: 12 tumors from 11 patients with HPV⁺ OPSCC versus three normal tissues. QC, quality control; PC, principal component; DE, differential expression. c Volcano plot from pseudobulk differential expression analysis using a two-sided Wald test. Significantly upregulated (shrunken log₂ fold change > 1) and downregulated (shrunken log₂ fold change < −1) genes (BH-adjusted P < 0.05) in HPV⁺ OPSCC malignant cells are in red and blue, respectively. Among TSGs and signaling-related genes listed in Supplementary Fig. 11, the upregulated and downregulated genes are labeled. d Heat map showing mutations, including heterozygous deletions, in the seven downregulated TSGs and the four downregulated signaling-related genes. Upper bar plot and heat maps show the mutation counts, HPV types, HPV physical states, and prognosis. HOMDEL, homozygous deletion (TCN < 0.5, no alleles); MUT + HETDEL, nonsynonymous mutation and heterozygous deletion (TCN < 1.5; no wild-type alleles); HETDEL, heterozygous deletion (only one wild-type allele); MUT, nonsynonymous mutation (only one wild-type allele). e ATM immunohistochemistry showing lower expression in a tumor with a heterozygous deletion of ATM (OU08) compared to the epithelial cells in a healthy tonsil or a tumor with wild-type ATM (OU04), similar to homozygous deletion (OU13). Representative results were obtained from four groups, with samples from each. Scale bars, 50 μm. IHC, immunohistochemistry. Source data are provided as a Source Data file.