In this large-scale study, over 1400 SNPs in 112 gene regions that are candidates for playing a role in HCV clearance were genotyped. We found 18 SNPs in African-Americans and 20 SNPs in European-Americans with an empirical p < 0.01. Interestingly, we identified 4 gene regions that had an empirical p-value < 0.01 in both of the major races studied: TNFSF18, TANK, HAVCR1 and IL18BP. Two of the SNPs tested, HAVCR1 (rs1553316) and IL18BP (rs5743673), are coding SNPs, however, neither is known to have functional consequences. The replication of four gene regions in two independent populations is encouraging and suggests that these gene regions should be considered leading candidates for a role in HCV clearance. Although the exact SNPs were not necessarily replicated in each population this may be due to differences in allele frequencies, LD structure, or true allelic heterogeneity.
The TNFSF18 (Tumor Necrosis Factor (ligand) Superfamily, member 18), also known as GITRL, gene region is found on chromosome 1. TNFSF18 is expressed on CD4+CD28+ Regulatory T-cells (TRegs). TRegs can suppress other immune responses, providing a negative feedback on the immune system and preventing autoimmune responses. The binding of TNFSF18 to its receptor results in a down-regulation of TReg regulatory function and thus can lead to an increase in immune response, which would be favorable for HCV clearance (19
The TANK (TRAF family member-associated NFKB activator) region is located on chromosome 2. TANK has been found to be important in type 1 interferon production through its interaction with both the RIG-I and toll-like receptor dependent (TLR) pathways (20
), both of which are important in the innate immune response to HCV. TANK also plays a role in inducing a cellular response to tumor necrosis factor-alpha (21
), and it has been described as an adaptor protein that is required for IRF3 activation (22
). Thus, if a SNP alters the function of TANK, then either the innate or adaptive immune response to HCV could be affected.
The HAVCR1 (Hepatitis A Virus Cellular Receptor 1), also known as TIM1, gene region is found on chromosome 5. It belongs to a family of cell surface glycoproteins and appears to act as a costimulatory molecule in vitro leading to enhancement of T cell proliferation as well as Th1 and Th2 cytokine production. Interestingly, polymorphisms in HAVCR1 including a six-amino-acid insertion at residue 157 (157insMTTTVP), are linked to asthma and autoimmune diseases suggesting that these variants may affect HAVCR1 function (23
). Thus, it is also possible that such functional variants could alter the immune response to HCV
The IL18BP (Interleukin-18 Binding Protein) gene region is found on chromosome 11. IL18BP is a secreted protein that can bind to and neutralize IL18, which prevents IL18-induced IFN-gamma production (24
). Polymorphisms in both IFN-gamma and IL18 have been implicated in HCV infection outcome (25
), and IL18 is up regulated in persons with chronic HCV infection (27
). It is possible variants in IL18BP could affect the activity or production of IL18 and IFN gamma altering HCV outcome.
In addition to these four gene regions, one of the top-scoring SNPs in the EA group, rs1804027, was also significant in a study (listed as IMS-JST013416) investigating natural clearance of HCV in a Japanese population (28
). This SNP results in a non-synonymous mutation in nuclear body protein SP110. The function of SP110 has not been well described, but it has been shown that HCV core protein can bind an isoform of SP110, SP110b, which results in the activation of Retinoic Acid Receptor (RARα)-mediated transcription (29
It is important to consider the limitations of this study when interpreting the results. First, the size of the study makes it difficult to detect weak associations in frequent polymorphisms and any associations in rare variants. Second, deletion or insertion polymorphisms that may alter function are unlikely to be discovered unless they are tightly linked to one of the tested SNPs. Third, SNPs were selected for coverage of genes and not for specific function therefore this study was not designed to identify causal alleles, but genes that may influence HCV clearance. Fourth, this study included many of the leading candidate gene regions potentially associated with HCV clearance at the time it was designed. However, since it was not intended to be an exhaustive survey of all interesting gene regions, additional studies based on these data should also consider the most recent data in HCV pathogenesis and include other relevant gene regions. For example, recently we and others reported a polymorphism in Il28B associated with HCV clearance and treatment response (30
). Lastly, epistatic interactions between variants in different genes (such as ligand-receptor pairs) were not considered, because this study did not have enough power for such a large number of comparisons. Such interactions can be important in HCV pathogenesis as has been demonstrated for HLA and KIR genes (3
By providing data on over 1400 SNPs in 112 candidate gene regions for HCV clearance or persistence, this study is an important first step since it reveals SNPs in four gene regions that warrant further investigation as a possible genetic basis for the natural clearance of HCV in multiple populations. Furthermore, this study provides the stimulus for confirmatory studies of our top scoring SNPs in other large, independent cohorts in order to determine the causal gene regions involved in the outcome of an acute HCV infection. These gene regions then need to be further dissected in order to determine the specific polymorphisms involved in HCV clearance.