This study examines the effects of genetic diversity in the human MHC on the dynamics of viral decline in subjects treated with peginterferon for chronic HCV. We utilized data from a large, well-characterized cohort of AAs and CAs with genotype 1 HCV infections who underwent a standard treatment protocol. We genotyped the A, B, and C class I loci, as well as the DRB1, DQA1, DQB1, DPA1, and DPB1 class II loci, and observed significant associations of two class I alleles and two class II alleles with the dynamics of the viral decline.
We also observed that the carriage of DQA1*04 or DQB1*0402 alleles was associated with slower rates of viral decline. Interestingly, the frequencies of these alleles are greater among AAs than among CAs (Table ). In addition, carriage of each of these alleles is associated with a greater difference in the level of viral decline among CAs than among AAs. The frequency of DQA1*04 is 10.1% among AAs and 2.8% among CAs; the frequency of DQB1*0402 is 8.1% among AAs and 2.8% among CAs. Differential distribution of the frequencies of these alleles by race may contribute to the observed population differences in response to peginterferon by race on the population level.
The DQA1*04 and DQB1*04 alleles have been previously implicated as a risk for Crohn's disease (31
) and cirrhosis (10
) in chronic HCV infections. The DQB1*0401/*0402 alleles are associated with viral persistence in several Japanese studies (1
). Previous studies that have examined the structure of DQB1*04 have shown that a leucine substitution exists at position 56 (21
), which is located in the antigen-binding groove of the DQ molecule and probably contributes to the ability to present HCV peptides. The leucine substitution is present only in the DQB1*0401 and DQB1*0402 alleles. All other DQB1 alleles have a proline at this position. Future studies are needed to specifically examine HCV antigen presentation in the context of these two class II MHC alleles.
In addition, the DQB1*0402 and DQA1*04 alleles exist as a haplotype and, therefore, our findings of similar magnitude and direction of effects for the individual alleles are not surprising. Because the DQA1*04 and DQB1*0402 alleles often exist on a haplotype with DRB1*03 or DRB1*08, we examined whether carriage of the DRB1*08-DQA1*04-DQB1*0402 or DRB1*03-DQA1*04-DQB1*0402 haplotypes was associated with viral dynamics. However, due to the relatively low frequency of individuals with DRB1*08-DQA1*04-DQB1*0402 (4 AA and 10 CA patients) and DRB1*03-DQA1*04-DQB1*0402 (24 AA and 0 CA patients) in the cohort overall and the extreme distributions within each race, we were not able to obtain meaningful results with our longitudinal analyses (data not shown) and, therefore, are not able to exclude the possibility that another allele in linkage disequilibrium with the DQA1*04 or DQB1*0402 may negatively affect viral decline during therapy. Extended haplotypes involving DQB1*0401/*0402 have also been associated with greater HCV-induced liver injury (15
), although the immediate functional relevance with respect to viral dynamics is not clear.
CA noncarriers of the class I allele A*03 had greater rates of viral decline than CA carriers. In contrast, AA noncarriers had slower rates of viral decline than AA carriers (Fig. ), unlike the effect within CAs. The effects of allele carriage appear to be greater among CA noncarriers and carriers than among AA noncarriers and carriers. Overall, the frequency of the A*03 allele is slightly lower among AAs than CAs (11.2% among AAs and 14.2% among CAs). It is possible that the main effects of this allele are seen among CAs, and that the smaller differences in viral dynamics among AA noncarriers and carriers is due to other undetermined genetic and/or nongenetic factors. It is also possible that AA and CA haplotype differences may contribute to the observed differences. Alternatively, it is possible that our observations are due to chance. Larger studies are needed to evaluate the potential effects of extended haplotypes within each race.
Carriers of Cw*03 had more pronounced viral dynamic declines than CA noncarriers (Fig. ). Viral declines among AA carriers and noncarriers were similar. Class I alleles are important in CD8+
T cells responses, which have been shown to play a role in the clearance of HCV during therapy (28
). Future studies are needed to understand the role of Cw*03 in HCV antigen presentation. Overall, the frequency of the Cw*03 allele is similar among AAs and CAs (10.9% among AAs and 10.3% among CAs).
In summary, our observations suggest that carriage of DQA1*04 and DQB1*0402, or another allele in linkage disequilibrium with these alleles, may represent a risk for slower rates of viral decline during peginterferon therapy. With both DQA1*04 and DQB1*0402, CA noncarriers had better rates of viral decline during the course of therapy compared to CA carriers, AA noncarriers, and AA carriers, respectively (Fig. ).
The 28-day viral response represents a critical biological point for the study of the response to therapy due to its prognostic potential (16
). Unlike SVR, early viral responses are less likely to be affected by dose adjustments and patient compliance and may therefore represent a more purely biologic picture of the role of host genetics in the interferon response. It is likely that in a complex process such as the response to peginterferon treatment for chronic HCV infection, multiple genes are involved, with different genes possibly operating at different time points during the course of therapy. Therefore, it is possible that the alleles that we describe here play an important role, either independently, as a haplotype, or in combination with other unidentified genetic markers during the early period after the start of therapy, while other markers may exert a more influential role at subsequent time points during the course of therapy. In the future, larger studies are needed to refine the potential influence of extended MHC haplotypes on HCV viral dynamics during treatment.
Previous mathematical models using differential equations have suggested that the shape of the viral decline with standard alpha interferon or peginterferon is nonlinear. For example, biphasic and triphasic declines have been reported (9
). However, these models are based on very frequent sampling of viral levels spaced only hours apart, as opposed to days apart as with our study, meaning that the frequency and spacing of viral level measurements are critical to the modeling of viral kinetics. In the absence of intensive sampling of viral levels, we used a square root transformation of the time scale to linearize the trajectory of the viral decline for our statistical modeling. This approach allowed us to focus our analysis on the linear relationship of MHC allele carriage on the overall dynamics of the viral decline, rather than the smaller fluctuations in the viral decline after each administration of interferon. Consequently, these linear individual change trajectories were modeled, and the effects of allele and race on the rate of change were examined. This analysis allowed a more simplified summary measure of the relationship between MHC allele carriage and the trajectories of viral levels over time.
A key factor in genetic association studies is the potential for confounding from population stratification. We have previously utilized recently developed techniques in mathematical genetics to infer individual admixture and found self-reported race to be highly correlated with individual admixture. Consequently, we have utilized self-reported race in our study (30
). In addition, due to the hypothesis-generating nature of the present study, we have deliberately elected to not adjust for the number of comparisons made rather than reject an association solely based on statistical grounds (29
). Although it is possible that the associations that we have observed are false positives, the consistent patterns within each race provide additional evidence of potential biological effects (Fig. ).
Our study offers an important first picture of the role of diversity in the human MHC on the dynamics of viral decline during the first 28 days of therapy. Future studies are needed to confirm our observations, as well as expand our understanding of the biological mechanisms of these alleles in the context of HCV therapy. We have previously reported that the A*02, B*58, and DPB1*1701 alleles are associated with the SVR to alpha peginterferon-plus-ribavirin therapy (25
). The response to therapy is likely a complex process that occurs over the course of time. Most likely, different combinations of genes are involved at different time points to clear viremia. For example, studies of Caucasian populations have consistently shown that the class II alleles DRB1*11 and DQB1*0301 are associated with natural clearance of HCV viremia (11
). However, a clear understanding of the biological mechanisms of these alleles is still lacking. Additional research, particularly with understanding of the differences in the presentation of HCV peptides by different HLA alleles, is needed to better understand the differences that we have observed between early viral dynamics and SVR. Additional nongenetic factors, such as decreased immune function through coinfections, may also play a role. Further research is needed to help evaluate these factors, as well as the functional characteristics of these alleles on HCV elimination.