Interferon lambda polymorphisms: validation and characterisation

2017-03-03T03:58:01Z (GMT) by Bonanzinga, Sara
Polymorphisms in the interferon lambda (IFNλ) gene cluster have been shown to influence spontaneous and treatment induced clearance of hepatitis C virus (HCV) infection. The most studied single nucleotide polymorphism (SNP), rs12979860, lies within the first intron of IFNλ4, though is still commonly referred to as IFNλ3. Several association studies have been performed, with little insight into the mechanisms behind the observations. Assay validation provided clear evidence that plasma samples provide sufficient genomic DNA to detect IFNλ3 genotypes, as well as being robust under lengthy storage conditions allowing retrospective testing. Association studies previously performed have focused on individuals infected with HCV genotype 1. To explore this further, the relationship between IFNλ3 genotype and HCV subtypes 1a and 1b was investigated, and it was determined that the benefit of having a CC genotype was greater in individuals infected with HCV 1b. Nationwide distribution of IFNλ3 genotype was determined, and it was found that the predominant rs12979860 genotype was CT, followed by CC, then TT. This profile is similar to that in North America and Western European countries, likely a reflection of migration and ethnic diversification. In Queensland, Tasmania, and South Australia, the CT genotype accounts for more than 50% of individuals. In contrast, the predominant genotype in New South Wales was CC (50%), and in both the Northern Territory and Victoria, CC and CT were roughly equal in distribution. The structure of the IFNλ gene cluster and its products was studied in an attempt to find why multiple copies of very similar genes have been retained. It was found that substitution of C for the ancestral T at rs12979860 changes the predicted local DNA structure and creates a potential binding site for the transcription factor E2F, which can act as both a repressor and activator. In addition, a tyrosine residue (Y160) found only in the IFNλ2 amino acid sequence, may be functionally significant because it confers the potential for additional post-transcriptional regulation. It was predicted that differences in local DNA structure produced by rs12979860 alleles might affect transcription. Enzyme linked Immunosorbent Assays (ELISAs) were used to measure the plasma concentrations of IFNλ2 and IFNλ3. A difference in the IFNλ2:IFNλ3 ratio was observed: the T allele correlated with a decrease (CC > CT > TT) due mainly to a decrease in IFNλ2. Thymidine phosphorylase (TP) is an enzyme that is known to be induced by interferons, suggesting that its activity may be influenced by IFNλ genotype. It was found that the presence of the T allele correlated with an increase (CC