Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis

Vulvar squamous cell carcinoma (VSCC) and precancerous vulvar intraepithelial neoplasia (VIN) can develop through human papillomavirus (HPV)‐dependent and ‐independent pathways, indicating a heterogeneous disease. Only a minority of VIN progress, but current clinicopathological classifications are insufficient to predict the cancer risk. Here we analyzed copy number alterations (CNA) to assess the molecular heterogeneity of vulvar lesions in relation to HPV and cancer risk. HPV‐status and CNA by means of whole‐genome next‐generation shallow‐sequencing were assessed in VSCC and VIN. The latter included VIN of women with associated VSCC (VIN(VSCC)) and women who did not develop VSCC during follow‐up (VIN (no) (VSCC)). HPV‐testing resulted in 41 HPV‐positive (16 VIN(VSCC), 14 VIN (no) (VSCC), and 11 VSCC) and 24 HPV‐negative (11 VIN(VSCC) and 13 VSCC) lesions. HPV‐positive and ‐negative VSCC showed a partially overlapping pattern of recurrent CNA, including frequent gains of 3q and 8q. In contrast, amplification of 11q13/cyclinD1 was exclusively found in HPV‐negative lesions. HPV‐negative VIN(VSCC) had less CNA than HPV‐negative VSCC (P = .009), but shared chromosome 8 alterations. HPV‐positive VIN (no) (VSCC) had less CNA than VIN(VSCC) (P = .022). Interestingly, 1pq gain was detected in 81% of HPV‐positive VIN(VSCC) and only in 21% of VIN (no) (VSCC) (P = .001). In conclusion, HPV‐dependent and ‐independent vulvar carcinogenesis is characterized by distinct CNA patterns at the VIN stage, while more comparable patterns are present at the cancer stage. Cancer risk in VIN seems to be reflected by the extent of CNA, in particular chromosome 1 gain in HPV‐positive cases.