HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women

Abstract

Background: HPV16 is a common sexually transmitted infection although few infections lead to cervical precancer/cancer; we cannot distinguish nor mechanistically explain why only certain infections progress. HPV16 can be classified into four main evolutionary-derived variant lineages (A, B, C, D) that have been previously suggested to have varying disease risks.

Methods: We used a high-throughput HPV16 whole-genome sequencing assay to investigate variant lineage risk among 3215 HPV16-infected women. Using sublineages A1/A2 as the reference, we assessed all variant lineage associations with infection outcome over three or more years of follow-up: 1107 control subjects (<CIN2), 906 CIN2, 1008 CIN3, 69 squamous cell carcinomas (SCC), 85 adenocarcinomas in situ (AIS), and 40 adenocarcinomas. Logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). All statistical tests were two-sided.

Results: A4 sublineage was associated with an increased risk of cancer, specifically adenocarcinoma (OR = 9.81, 95% CI = 2.02 to 47.69, P = 4.7x10(-03)). Lineage B had a lower risk of CIN3 (OR = 0.51, 95% CI = 0. 28 to 0.91, P = 02) while lineage C showed increased risk (OR = 2.06, 95% CI = 1.09 to 3.89, P = 03). D2/D3 sublineages were strongly associated with an increased risk of CIN3 and cancer, particularly D2 (OR for cancer = 28.48, 95% CI = 9.27 to 87.55, P = 5.0x10(-09)). D2 had the strongest increased risk of glandular lesions, AIS (OR = 29.22, 95% CI = 8.94 to 95.51, P = 2.3x10(-08)), and adenocarcinomas (OR = 137.34, 95% CI = 37.21 to 506.88, P = 1.5x10(-13)). Moreover, the risk of precancer and cancer for specific variant lineages varied by a women's race/ethnicity; those women whose race/ethnicity matched that of the infecting HPV16 variant had an increased risk of CIN3 + (P < 001).

Conclusions: Specific HPV16 variant sublineages strongly influence risk of histologic types of precancer and cancer, and viral genetic variation may help explain its unique carcinogenic properties.

Figure 1.

Phylogenetic tree and sublineage-specific nucleotide and amino acid changes in HPV16 sublineages. The x-axis shows the HPV16 genome positions and gene regions, aligned according to sublineage in the phylogenetic tree on the y-axis . Sublineage-specific single-nucleotide polymorphisms (SNPs) were determined from an alignment of 63 complete-genome nucleotide sequences by selecting the nucleotides that occurred only in members of a given sublineage. The nucleotide of each SNP is color-coded as shown at the top figure legend , and the open circles represent nonsynonymous changes. Amino acid changes in the E2/E4 gene region are changes observed in E2. SNPs for a given lineage are cumulative as the tree is traversed from deepest node out to finer sublineage branches. For example, A ( underlined, first row ) changes are found in all A sublineage genomes plus the changes on each specific A sublineage row; and the D4 sublineage ( last row ) contains all changes shown on the BCD ( underlined, row 6 ), CD ( underlined, row 8 ), D ( underlined, row 10 ), and D4 ( row 14 ) lines. E1 = early gene 1; E2 = early gene 2; E4 = early gene 4; E5 = early gene 5; E6 = early gene 6; E7 = early gene 7; L1 = late gene 1; L2 = late gene 2; NA/AA = North American/Asian-American; URR = upstream regulatory region.

Figure 2.

HPV16 variant lineage associations with squamous and glandular precancer/cancer subtypes. Squamous lesions include CIN3 ( green ) and SCC ( blue ); glandular lesions include AIS ( red ) and Adeno ( black ). Y-axis shows the odds ratios and 95% confidence intervals ( colored bars ) on a log scale. Adeno = adenocarcinoma; AIS = adenocarcinoma in situ; CI = confidence interval; CIN3 = cervical intraepithelial neoplasia grade 3; SCC = squamous cell carcinoma.