Germline determinants of humoral immune response to HPV-16 protect against oropharyngeal cancer

Abstract

Although several oropharyngeal cancer (OPC) susceptibility loci have been identified, most previous studies lacked detailed information on human papillomavirus (HPV) status. We conduct a genome-wide analysis by HPV16 serology status in 4,002 oral cancer cases (OPC and oral cavity cancer (OCC)) and 5,256 controls. We detect four susceptibility loci pointing to a distinct genetic predisposition by HPV status. Our most notable finding in the HLA region, that is now confirmed to be specific of HPV(+)OPC risk, reveal two independent loci with strong protective effects, one refining the previously reported HLA class II haplotype association. Antibody levels against HPV16 viral proteins strongly implicate the protective HLA variants as major determinants of humoral response against L1 capsid protein or E6 oncoprotein suggesting a natural immune response against HPV(+)OPC promoted by HLA variants. This indicates that therapeutic vaccines that target E6 and attenuate viral response after established HPV infections might protect against HPV(+)OPC.

Fig. 1. Genome-wide association regional meta-analysis results.

Red line correspond to P = 5 × 10⁻⁸. The y axes show −log10 P values. a HPV(+)OPC cases analysis with 1078 cases and 5256 controls. b HPV(−)OPC cases analysis with 565 cases and 5256 controls. GWAs for each world region were performed using multivariable unconditional logistic regression assuming a log-additive genetic or dosage model with age, sex, and eigenvectors as covariates. P-values are shown from fixed-effect meta-analysis of regional association statistics. HPV human papillomavirus, OPC oropharyngeal cancer.

Fig. 2. Plots of stepwise conditional association in the MHC region for HPV(+)OPC cases.

a–c The association for each locus used for conditioning is shown in each panel: a unconditioned, b conditioned on rs4713462, c conditioned on rs4713462 and HLA-DRB1 amino acid change in position 71 (71-Glu). Detailed association results in Table 2 and Supplementary Fig. 2. Circles represent –log10 (P values) for each binary marker using the imputed allelic dosage (between 0 and 2) and genotyped variants. Multivariable logistic regression assuming a log-additive genetic or dosage model with age, sex, and eigenvectors as covariates was used as baseline model. The dashed black horizontal lines represent the study-wide significant threshold of P = 5 × 10⁻⁸. The physical positions of HLA genes on chromosome 6 are shown at the bottom. The color of the circles indicates the type of marker; light blue—SNPs outside and within HLA genes, green - classical HLA alleles and red—amino acid polymorphisms of the HLA genes. HLA human leukocyte antigen, MHC Major Histocompatibility Complex, HPV human papillomavirus, OPC, oropharyngeal cancer.

Fig. 3. pQTL analysis of plasma antibody levels against HPV proteins of the top two associated HPV(+)OPC HLA variants.

Box plots showing a HPV16 E6 MFI levels and rs4713462 genotypes, and b HPV16 L1 MFI levels and DRB1 (71-Glu) variants in OPC cases. Effect sizes (B, regression coefficient) were adjusted for age, sex, and eigenvectors. For HLA-DRB1 71-Glu, A stands for absence and P stands for presence. Box plots show the medians (center lines) and the 25th and 75th percentiles (box edges), with whiskers extending to 1.5 times the interquartile range. Linear multivariate models were implemented to test associations of genetic variants across the MHC region with HPV16 L1 or E6 log-transformed MFI levels, assuming a dosage model with age, sex and eigenvectors as covariates. HLA human leukocyte antigen, pQTL protein Quantitative Trait Loci, HPV human papillomavirus, OPC oropharyngeal cancer, MFI median fluorescence intensity.