Breast cancer is the most common cancer affecting women worldwide1. Several risk factors have been identified, including family history of breast cancer, dense breast tissue, female reproductive factors, alcohol or tobacco use, body mass index, and genetics (e.g. BRCA gene)2,3; however, nearly half of breast cancers develop in women in the absence of these risk factors3, suggesting that additional factors likely contribute to breast cancer risk.The role of viruses in breast cancers is increasingly recognized and is likely underestimated4. As documented elsewhere, human herpes viruses (HHV) including Epstein Barr virus (EBV, HHV4) and cytomegalovirus (CMV, HHV5), mouse mammary tumor virus (MMTV), high risk human papilloma virus (HPVs), bovine leukemia virus (BLV), human polyomavirus JC virus (JCV), and human endogenous retrovirus K (HERVK) have been implicated in human breast cancer4,5,6,7,8,9. Several viruses (e.g., MMTV, HPV, EVB, and BLV) have been identified and shown to co-exist in human breast cancer cells10,11,12, and in benign breast biopsies 1–11 years before developing cancer11. They have also been identified in normal breast tissue samples and in milk of normal lactating women, albeit to a lesser extent10,11. Indeed, viruses linked to human cancers are ubiquitous yet only a small proportion of infected individuals develop cancer, one of many reasons that have made it challenging to identify causal relations between viruses and cancer13. One factor that may moderate the association between viruses and breast cancer is variation in host immunogenetics related to human leukocyte antigen (HLA).HLA genes, located on chromosome 6, code for two main classes of cell-surface proteins involved in the immune response to foreign antigens including viruses and cancer neoantigens14,15. HLA-I molecules of the classical genes A, B and C are expressed on all nucleated cells, bind and present small peptides (8–10 amino acid residues16) from proteolytically degraded foreign antigens to CD8 + cytotoxic T cells, signaling cell destruction. HLA-II molecules of the DPB1, DQB1 and DRB1 genes are expressed on lymphocytes and professional antigen presenting cells, present larger peptides (12–22 amino acid residues17) derived from endocytosed exogenous antigens to CD4 + T cells, facilitating antibody production and adaptive immunity. Each individual carries two of each HLA gene, for a total of 12 classical HLA alleles. The HLA region is the most highly polymorphic region of the human genome18, with most of the variation existing in the binding groove. This variation amounts to tremendous individual variability in the ability to bind and eliminate viruses and other foreign antigens. Specific HLA alleles have been associated with breast cancer protection or susceptibility19,20,21,22,23,24,25,26,27,28. This association is captured in the breast cancer—HLA immunogenetic profile which contains the correlations between the prevalence of breast cancer and HLA allele frequency19. Given the documented involvement of several viruses in breast cancer, discussed above, we investigated, in this study, the possible viral elimination by the HLA system, as a mechanism of preventing the oncogenic effect of those viruses. More specifically, we focused on 7 viruses that have been found in breast cancer tissue (HHV4, HHV5, HPV, JCV, MMTV, BLV, HERVK) and estimated in silico their binding affinity with respect to 69 common HLA-I alleles of the 3 classical genes (A, B, C) and 58 common HLA-II alleles of the 3 classical genes (DPB1, DQB1, DRB1). Since binding affinity is a critical initial step in foreign antigen elimination, it is reasonable to assume that high binding affinity would be more effective in virus elimination, and vice versa for low binding affinity. Thus the objectives of this study were (a) to estimate in silico the predicted binding affinity of specific viruses with respect to specific alleles using the Immune Epitope Database (IEDB) NetMHCpan (ver. 4.1) tool29,30, (b) to identify those viruses whose binding affinities were associated with the breast cancer—HLA immunogenetic profile, and (c) to test the hypothesis that the predicted binding affinity of this set of viruses is lower than that of the viruses unassociated with the breast cancer—HLA profile.
