Fig. 1.

HPV integrations at PD-L1 and PD-L2. a–c Structural analysis of HPV integration events at PD-L1 or PD-L2 for three different HNSC tumors. The dots in the plot show the coordinates in HPV genome (X) and human chromosome (Y) of the breakpoints⁶⁷. The vertical line represents a series of breakpoints clustered together by Pindel⁶⁶. In the figure, e1 represents exon 1. HPV integrates intron 4 and 5′ UTR of PD-L1 in tumor TCGA-CV-5443 and TCGA-T2-A6X0, respectively. In tumor TCGA-HL-7533, HPV can integrate multiple locations in or after intron 3 of PD-L2. The bottom panel shows the number of mapped HPV reads (log₂ ratio) along with HPV coordinates and E6, E7, E1, E2, E4, E5, L2, and L1 are different genes in HPV genome. d The expression of PD-L1 or PD-L2 for HPV-positive samples with and without HPV integrations and virus-negative tumors