mutation is associated with tumor HPV status and promotes poor disease outcomes with a higher mutation count in HPV-related cervical carcinoma and head & neck squamous cell carcinoma.

Human papillomavirus (HPV) infection and gene mutations were reputed as key factors in cervical carcinoma (CC) and head and neck squamous cell carcinoma (HNSCC). However, the associations of HPV status and gene mutations remain to be determined. This study aims to identify molecular patterns of mutation and HPV status via rewiring tumor samples of HNSCC (n=1478) and CC (n=178) from the TCGA dataset. Here, we found that mutation was associated with HPV status in CC (=0.040) and HNSCC (=0.044), especially in HPV 16 integrated CC (=0.036). Cancer survival analysis demonstrated that samples with mutation showed poor disease outcomes in CC (=0.013) and HNSCC (=0.0124). In addition, the expression status of was more favorable for prediction than or in CC and HNSCC. Mutation clustering analysis showed that samples with mutation showed higher mutation count in CC (=1.76e-67) and HNSCC (<10e-10). Further analysis identified 289 co-occurrence genes in these two cancer types, which were enriched in PI3K signaling, cell division process, and chromosome segregation process, et al. The 289-co-occurrence gene signature identified a cluster of patients with a higher portion of copy number variation (CNV) lost in the genome, different tumor HPV status (<10e-10), higher mutation count (<10e-10), higher fraction genome altered value (=2.078e-4), higher aneuploidy score (=3.362e-4), and earlier started the smoking year (=2.572e-4), which were associated with shorter overall survival (=0.0103) in CC and HNSCC samples. Overall, mutation was associated with tumor HPV status and was an unfavorable prognostic biomarker for CC and HNSCC.