Although a strong association of HLA genotype and HCV viral clearance has been reported by our group and others, prior studies relating HLA with HCV viral load and with liver disease have had inconsistent findings. Few of these prior studies, however, conducted HLA class I genotyping. Most studies of HCV-related liver disease were also cross-sectional. In the current investigation, therefore, we conducted high-resolution HLA class I and II genotyping in a large prospective cohort of HCV viremic women at elevated risk of HCV disease progression due to a high prevalence of HIV coinfection.
Our data analysis identified 6 alleles and allele groups that were significantly associated with HCV viral load. Interestingly, 5 of these were HLA class II. The strongest relationship was the association of DQB1*0301 with low HCV viral load (β = −.4; P
< .00001). This finding is noteworthy, because DQB1*0301 is also one of the alleles that has been most consistently associated with clearance of HCV viremia (reviewed in [3
]). At least 5 prior studies reported data regarding HCV viral load and HLA [5
]. However, there was no agreement among these studies, or with the findings of the current study. The main advantage to the current investigation was statistical power, this study being 3-fold larger than prior studies.
Our data additionally suggested a possible association of DQB1*0301 with reduced risk of FIB-4 and APRI diagnosed fibrosis. This included a statistically significant 40%–50% reduction in risk of FIB-4–defined liver fibrosis detected at any visit and an association of similar strength but of borderline statistical significance with APRI-defined liver fibrosis at any visit. Though the effect estimates in 4 other models did not approach statistical significance, they showed the same 40%–50% decreased risk of fibrosis. Thus, the consistency of the DQB1*0301 findings across these several analyses—inverse associations like the one observed in its relation with HCV viral load—made these results notable. Further, 2 small independent studies reported similar results regarding DQB1*0301 and liver disease [14
]. Whereas our study did not demonstrate the inverse association between DRB1*11 and liver fibrosis reported elsewhere (reviewed in [8
]), it is interesting to note that DQB1*0301 and DRB1*11 are in linkage disequilibrium [39
]. In the current study, excluding women with the DQB1*0301-DRB1*1101 haplotype did not meaningfully change the results (data not shown), suggesting that our findings related specifically to DQB1*0301.
Several additional HLA alleles were also associated with FIB-4– and APRI-defined fibrosis in ≥1 of our analyses, but none were significant in all 6 models. B*1503 was notable because it had associations with increased risk of fibrosis that reached statistical significance or borderline significance in 5 of the 6 analyses. Although no prior studies have observed an association of B*1503 with HCV disease progression, we note that this allele has been associated elsewhere with poor prognosis after HIV-2 infection [40
]. In contrast, A*3303 and homozygosity at the A locus showed consistent inverse associations across analyses. Interestingly, most of the alleles associated with FIB-4–and APRI-defined fibrosis were HLA class I, whereas most of those related to HCV viral load were class II alleles. If correct, the data could be interpreted to mean that CD4+
T cell responses are important for controlling HCV viral load, whereas CD8+
T cell responses play a larger role in determining the rate of disease progression.
This study had several limitations. First, most of our significant findings did not retain significance after adjustment for multiple comparisons and the results await confirmation. The major finding regarding DQB1*0301 and HCV viral load, however, remained highly significant after Bonferroni correction. Furthermore, DQB1*0301, B*1503, A*3303, and the A homozygous group had consistent associations across multiple if interrelated fibrosis end points that reduced the possibility that they occurred by chance. A second concern was the unavailability of histologic data, the reference standard for diagnosis of liver fibrosis. Nonetheless, there are advantages to prospective observational cohorts involving noninvasive follow-up, in that large numbers of participants can be studied and repeated testing with long follow-up is possible—as in the current study. A third concern was that our study population was racially heterogeneous, and we cannot exclude the possibility of confounding by population substructure. We did, however, control for self-reported race/ethnicity, and in the US, these self-reported categories have been shown to correlate well with genetically determined ancestry [41
]. Fourth, we did not conduct haplotype analyses (except as noted for DQB1*0301-DRB1*1101); haplotype frequencies vary considerably by race/ethnicity, and in a multiracial population such as ours it would require larger numbers of subjects within each racial group to study haplotype associations adequately. Finally, because of the extensive linkage disequilibrium in the HLA region, it is possible that the alleles identified in our analyses are markers for other, causal, genetic variants that affect HCV pathogenesis.
Because most of the women in our study population were coinfected with HCV and HIV, we took several steps to minimize the possibility that the associations we observed might be due to the relation of HLA alleles with HIV, and not to their relationship with HCV. Specifically, each of our analyses adjusted for HIV serostatus, CD4+ T-cell count, and HIV RNA level. We further examined each of our significant associations for interaction by HIV serostatus and CD4+ T-cell count, but few significant interactions were observed.
In summary, we found that DQB1*0301 was associated with low HCV viral load and also possibly with a low risk of liver fibrosis, as measured using 2 noninvasive indexes of liver fibrosis, FIB-4 and APRI. Similar results regarding DQB1*0301 and liver disease progression had been noted in other studies, and DQB1*0301 is in linkage disequilibrium with DRB1*11, which some prior studies associated with disease progression. Prior data have additionally suggested DQB1*0301 may play a role in HCV clearance. Although most other associations with HCV load in our study involved HLA class II alleles, additional associations with fibrosis primarily involved class I alleles. Overall, although the findings of this study await confirmation, they add to the growing evidence that HLA genotype, and DQB1*0301 in particular, influence both the early and late stages of HCV-related liver disease.