Figure 2. Human transcriptome differences between HPV⁺ C1 and HPV⁺ C2 groups.

Volcano plot showing log₂ fold-change (horizontal axis) and –log₁₀FDR (vertical axis) values from the whole transcriptome analysis between HPV^– (n = 28) and HPV⁺ C1 (n = 19) OPSCC (A) and between HPV^– (n = 28) and HPV⁺ C2 (n = 33) OPSCC groups (B). Genes were considered differentially expressed at a significance level of 0.05 (n = 4366 in A and n = 8724 in B). Green dots represent differentially expressed genes with lower expression in HPV^– cases than in HPV⁺ C1 cases (n = 2537 in A and n = 5268 in B). Purple dots represent differentially expressed genes with higher expression in HPV^– cases than in HPV⁺ C1 cases (n = 1829 in A and n = 3456 in B). Black dots represent genes whose expression was not significantly different between groups. (C) 7760 differentially expressed genes between HPV⁺ (n = 52) and HPV^– (n = 28) OPSCC cases and their corresponding log₂ fold-change values when their expression was compared between HPV^– (n = 28) and HPV⁺ C1 cases (n = 19) (vertical axis) and between HPV^– (n = 28) and HPV⁺ C2 cases (n = 33) (horizontal axis). The red line represents the best-fit calculated by linear regression. The black line represents the 45° line. The line of best-fit slope was lower than 1 (0.72 ± 0.004), indicating greater log₂ fold-change values in the horizontal axis (HPV^– vs. HPV⁺ C2) than in the vertical axis (HPV^– vs. HPV⁺ C1). This suggests that differences in expression levels of HPV-related genes were smaller between HPV⁺ C1 and HPV^– cases than between HPV⁺ C2 and HPV^– cases. (D) PCA using expression of 319 genes from the HPV-KEGG pathway database among all 80 TCGA OPSCC cases. All 3 groups (HPV⁺C1, n = 19; HPV⁺C2, n = 33; HPV^–, n = 28) showed distinct expression profiles of HPV-related genes. (E) Venn diagram representing HPV-KEGG pathway genes differentially expressed between HPV⁺ C1 (n = 19) and HPV^– cases (n = 28) and between HPV⁺ C2 (n = 33) and HPV^– (n = 28) cases. A greater number of HPV-related genes was differentially expressed between HPV⁺ C2 and HPV^– cases. This suggests that the HPV⁺ C1 group exhibited expression of some HPV-related genes similar to that in HPV^– cases. (F) Mean expression of 61 HPV-KEGG pathway genes among HPV⁺ C1 (n = 19), HPV⁺ C2 (n = 33), and HPV^– (n = 28) cases. These 61 genes were differentially expressed between HPV⁺ C1 and HPV⁺ C2 but not between HPV⁺ C1 and HPV^– cases, suggesting that HPV⁺C1 cases lost part of their HPV characteristics.