In our evaluation of selected immune response and DNA repair gene variants and their association with HPV persistence and progression to cervical cancer, we report that common variants in genes influencing DNA damage were associated with both HPV persistence and progression to CIN3 or cervical cancer and genes influencing immune response were associated with HPV persistence.
Most notably, polymorphisms within the DNA repair gene FANCA
were associated with CIN3 or cervical cancer but not with HPV persistence. FANCA
is 1 of 12 groups of genes within the Fanconi anemia pathway and is thought to play a role in the recognition of DNA damage and the repair of DNA damage by homologous recombination. FANCA
is the major gene implicated in Fanconi anemia (FA) with FANCA
mutations accounting for ~70% of all FA cases. FA patients are characterized by increased apoptosis in hematopoietic cells, chromosome instability, sensitivity to DNA cross-linking damage, DNA damage from oxidative stress and/or reactive oxygen species, and telomere shortening [27
]. FA patients are susceptible to cancer, including cervical cancer and other HPV-associated tumors [28
], and our results, which implicate variants in FANCA
with disease progression, add to the current understanding of FA and cervical cancer. Our data suggest that, in addition to FA mutations, FA variants may be an important host event involved in susceptibility to cervical cancer.
We also identified associations for DNA repair genes EXO1
with progression to CIN3 or cervical cancer and associations for XRCC1
with HPV persistence. The association we observed between EXO1
and disease progression supports the involvement of DNA repair in cervical pathogenesis and progression to CIN3 or cervical cancer [29
plays a role in base-excision repair of spontaneous and induced DNA damage [31
], and its association with HPV persistence (both overall and of oncogenic HPV strains) was not expected. Although it is possible that the increased susceptibility to DNA damage among women with the XRCC1
R399Q variant facilitates HPV persistence, our findings require replication and further investigation.
Of the immune response genes evaluated, a variant in the innate immunity gene IRF3
was associated with HPV persistence, and a TLR2
variant was associated with progression to CIN3 or cervical cancer. Our results for IRF3
are consistent with our hypothesis about immune response genes involved in persistent infection and consistent with the growing literature on IRF3
in viral infections, including herpes simplex virus 1 infection and hepatitis C persistence [35
]. We note that the association with HPV persistence was further pronounced when persistence was limited to women persistently infected for ≥2 years, but the associations were equally significant for persistence for ≥2 years of infection with either oncogenic or nononcogenic HPV strains, consistent with IRF3
’s role in innate immunity. Finally, Toll-like receptors are essential for response to bacterial infections and inflammatory response [38
], and our observed association between the TLR2
S450S variant and CIN3 or cervical cancer support the potential role of innate immune response genes and inflammatory response in progression from HPV persistence to CIN3 and cervical cancer.
Study limitations include potential survival bias, as supplemental case patients diagnosed outside the Guanacaste cohort were retrospectively ascertained, and DNA could not be obtained from deceased individuals. However, since half of supplemental case patients had CIN3, survival bias is unlikely to affect our results. Because of our limited number of patients with invasive cancer, the use of CIN3 or cancer as a case group may have obscured associations specific to invasion. Finally, although we targeted predefined genes and intended for our evaluation to be hypothesis generating, we cannot exclude the possibility that some of our results are false-positives (or false-negatives). Although we did not find FDR values above our predefined notable threshold of 0.2 after taking into account all SNPs tested, we note that the association between FANCA G501S and CIN3 or cervical cancer (assigning a prior probability of .05) was notable by FPRP (0.17), indicating a <20% chance of being a false-positive, given our prior probability. Finally, study limitations also include our evaluation of a relatively small proportion of these genes, as permitted by our candidate SNP selection process, which was based largely on available biological evidence and validated assays. For example, full coverage of the FANCA gene using tag SNPs would require an additional 18 SNPs. Thus, the fact that we did not select tag SNPs or conduct other, more comprehensive analyses within each candidate gene may have decreased our ability to identify significant SNPs related to disease. We therefore cannot discount the possibility that some of the genes evaluated could be associated with disease but are not thus identified in our analyses because of the limited number of SNPs evaluated.
Study strengths include our population-based study design, which approximated a case-cohort design because the proportion of women in the cohort with evidence of CIN3 or cancer was small. In our analysis, we have excluded women with a CIN2 diagnosis from both the case and control groups, because it is frequently misclassified. The final 3 comparison groups (women with CIN3 or cervical cancer, women with HPV persistence, and random control subjects) allowed evaluation of both HPV persistence and disease progression.
In summary, our results require replication but, to our knowledge, we are the first to report potential host genetic variants relevant for HPV persistence and those relevant for progression to CIN3 or cervical cancer. If replicated, functional studies to determine the biological relevance of confirmed variants should be pursued. Improved gene coverage of the implicated genes (e.g., FANCA and IRF3) and evaluation of additional genes within these DNA repair and immune response pathways can help refine and develop the findings reported here, if real. Finally, future efforts should include evaluating the interplay between viral and host genetics along with HPV cofactors in determining the risk of HPV persistence and of progression to CIN3 or cervical cancer.