Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis

Abstract

Purpose: A significant barrier to adoption of de-escalated treatment protocols for human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is that few predictors of poor prognosis exist. We conducted the first large whole-genome sequencing (WGS) study to characterize the genetic variation of the HPV type 16 (HPV16) genome and to evaluate its association with HPV-OPC patient survival.

Patients and methods: A total of 460 OPC tumor specimens from two large United States medical centers (1980-2017) underwent HPV16 whole-genome sequencing. Site-specific variable positions [single nucleotide polymorphisms (SNPs)] across the HPV16 genome were identified. Cox proportional hazards model estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival by HPV16 SNPs. Harrell C-index and time-dependent positive predictive value (PPV) curves and areas under the PPV curves were used to evaluate the predictive accuracy of HPV16 SNPs for overall survival.

Results: A total of 384 OPC tumor specimens (83.48%) passed quality control filters with sufficient depth and coverage of HPV16 genome sequencing to be analyzed. Some 284 HPV16 SNPs with a minor allele frequency ≥1% were identified. Eight HPV16 SNPs were significantly associated with worse survival after false discovery rate correction (individual prevalence: 1.0%-5.5%; combined prevalence: 15.10%); E1 gene position 1053 [HR for overall survival (HR_os): 3.75, 95% CI 1.77-7.95; P_fdr = 0.0099]; L2 gene positions 4410 (HR_os: 5.32, 95% CI 1.91-14.81; P_fdr = 0.0120), 4539 (HR_os: 6.54, 95% CI 2.03-21.08; P_fdr = 0.0117); 5050 (HR_os: 6.53, 95% CI 2.34-18.24; P_fdr = 0.0030), and 5254 (HR_os: 7.76, 95% CI 2.41-24.98; P_fdr = 0.0030); and L1 gene positions 5962 (HR_os: 4.40, 95% CI 1.88-10.31; P_fdr = 0.0110) and 6025 (HR_os: 5.71, 95% CI 2.43-13.41; P_fdr = 0.0008) and position 7173 within the upstream regulatory region (HR_os: 9.90, 95% CI 3.05-32.12; P_fdr = 0.0007). Median survival time for patients with ≥1 high-risk HPV16 SNPs was 3.96 years compared with 18.67 years for patients without a high-risk SNP; log-rank test P < 0.001. HPV16 SNPs significantly improved the predictive accuracy for overall survival above traditional factors (age, smoking, stage, treatment); increase in C-index was 0.069 (95% CI 0.019-0.119, P < 0.001); increase in area under the PPV curve for predicting 5-year survival was 0.068 (95% CI 0.015-0.111, P = 0.008).

Conclusions: HPV16 genetic variation is associated with HPV-OPC prognosis and can improve prognostic accuracy.

Keywords: HPV16; HPV16 sublineages; HPV16 variants; OPC; oropharyngeal cancer; viral genome sequencing.

Figure 1:

Individual HPV16 SNP associations with overall survival Cox proportional hazards models were used to generate hazard ratios and 95% confidence intervals for the risk of death (overall survival) for each minor HPV16 SNP. The major allele at each SNP position was used as the referent group. A total of 284 SNPs varied between the 384 HPV16 genomes sequenced and were included in the analysis. The Y-axis denotes the false discovery rate (FDR) corrected Ps for the hazard ratio of each outcome. The X-axis denotes the position of each SNP in the HPV16 genome; each gene is identified with a different color. URR, upstream regulatory region (grey); E6, early gene 6 (purple); E7, early gene 7 (magenta); E1, early gene 1 (green); E2, early gene 2 (light blue); E4, early gene 4 (dark blue); E5, early gene 5 (pink); NC, non-coding region (black); L2, late gene 2 (orange); L1, late gene 1 (yellow). Dotted line denotes the FDR cutoff of 0.05.

Figure 2:

Kaplan Meier plots for overall survival by individuals high-risk HPV16 SNPs Overall survival probability comparing the minor allele (blue) to the major allele (red) for the following SNP positions within the HPV16 genome: A) 1053; B) 4410; C) 4539; D) 5050; E) 5254; E) 5962; G) 6025 and H) 7173.

Figure 3.

Kaplan Meier plots for overall survival comparing patients with and without at least 1 high-risk HPV16 SNP Overall survival probability comparing patients with at least 1 high-risk HPV16 SNP (blue) to patients with no high-risk HPV16 SNPs (red).

Figure 4.

Positive Predictive Value (PPV) Curves Time-dependent PPV curves comparing the predictive accuracy of the Cox model using traditional factors (age, stage, smoking, treatment) to predict survival compared (black) to the Cox model with the addition of high-risk HPV16 SNPs (red). Panel A depicts PPV curve for predicting 3-year overall survival; Panel B for predicting 5-year overall survival and Panel C for predicting 8-year overall survival.