Ian James

NK cell receptors and HLA molecules are intimately involved in the immune response against viral infections. The killer immunoglobulin-like receptors (KIRs) on NK cells regulate NK cell responses via the recognition of their particular HLA class I ligands. At the genomic level, both genetic systems are polymorphic and have recognised haplotypes, which adds complexity to their interaction. Previously, we and others have shown the association of HLA class I with HIV progression. Recently, the Carrington group observed a synergistic effect involving the activating KIR3DS1 gene and HLA-B Bw4-80Ile on the rate of depletion of CD4+ T cells. To further investigate the relationship between the two genetic systems, we examined changes in viral load in 249 pre-treatment patients from the Western Australia HIV cohort. Genetic variants known to affect HIV progression including HLA-Bw4-80Ile but not KIR3DS1 were associated with differences in HIV-1 viral load set point. When we examined only those patients with known seroconversion dates, we found that the presence of the KIR3DS1 gene was associated with more rapid decline in the proportion of CD4+ T cells (p=0.01) but were unable to show a KIR3DS1 and Bw4-80Ile interaction. The presence of other KIR genes (viz KIR2DS2, KIR2DL2 and KIR2DS1), all found on KIR B group haplotypes, were also associated with a more rapid progression, whilst some KIR genes found the A haplotype with delayed progression We suggest that multiple KIR genes influence outcome in HIV infection. Further analyses of KIR haplotypes is needed to understand the complex interactions between KIR genes and their ligands in driving NK cell responses to HIV.

OBJECTIVES: To investigate a possible role for functional promoter polymorphisms in tumour necrosis factor (TNF) alpha and beta loci, in modifying the risk of progression to lipodystrophy in HIV-infected patients. Additionally, to investigate whether the effect of antiretroviral therapy-specific factors on lipodystrophy progression may depend on, or interact with, the presence of predisposing host factors. METHODS: Stored DNA samples of 220 participants in the Western Australian HIV Cohort were typed for promoter polymorphisms at TNF-α (-238G/A and -308G/A), and TNF-β (-250G/C) loci. Results were incorporated into Cox proportional hazards regression analyses (SAS statistical package, SAS Institute, Cary, North Carolina, USA), to assess the effect of variant alleles on the development of clinically apparent lipodystrophy, with adjustment for predictive host and treatment variables. Carriage of the -238G/A TNF-α polymorphism was found in 11.4% of the cohort, all of whom were of white racial origin. Analyses were therefore performed in a limited dataset of 191 white Caucasian participants, to exclude potential confounding attributable to the role of the TNF-α -238G/A polymorphism as a surrogate marker of white racial origin. RESULTS: Carriage frequency of the TNF-α promoter polymorphism -238G/A was 13.1%. Risk of progression to lipodystrophy was significantly increased in heterozygotes compared with carriers of the wild-type allele (P=0.014, log rank). Cox proportional hazards analyses demonstrated a significant independent effect of TNF-α -238G/A heterozygosity (RR=1.73, P=0.041), which was independent of the effects of age (RR=1.053/year), duration of dual nucleoside reverse transcriptase inhibitor therapy pre-highly active antiretroviral therapy (RR=1.025/month), and time on stavudine (RR=1.081/month). Promoter polymorphisms at TNF-α -308G/A and TNF-β -250G/C were found to not contribute significantly to the Cox proportional hazards regressions. Analyses combining TNF-α -238G/A heterozygosity and treatment-related variables as interaction terms did not suggest synergistic effects of TNF polymorphism and antiretroviral therapy on lipodystrophy progression. DISCUSSION: In this study, carriage of the TNF-α -238G/A promoter polymorphism independently increased the risk of lipodystrophy progression in a cohort of 191 white Caucasian HAART recipients. The influence of other host and treatment-related variables on lipodystrophy progression were not altered after adjustment for the effect of TNF-α -238G/A polymorphism, indicating that effects of treatment are not contingent on the presence of this host factor.

The selection in vivo of mutations in HIV-1 that allow viral escape from host HLA class I restricted cytotoxic T lymphocyte (CTL) responses has been documented in individuals. Recently we showed that the many HLA-A and -B allele-specific polymorphisms in HIV-1 reverse transcriptase (RT) suggested extensive CTLescape mutation at a population level. HLA class II restricted CD4 T helper responses have a central role in HIV-1 immunity and associations between HLA class II alleles and HIV-1 disease progression have been reported. However, CD4 T cell escape mutation in HIV-1 has not been proven. We sought to determine whether, as for CTLescape, CD4 T cell escape in HIV-1 was evident at a population level as HLA-DRB1 associated polymorphisms. We analysed the diversity of HIV-1 RT sequences in a large, well characterised cohort of HIV-1 infected patients over 2210 person-years of observation. We examined the relationship between the HLA-A, -B and -DRB1 alleles present in the cohort (as covariates) and polymorphism in HIV-1 RT (as the outcome) in multivariate logistic regression models. Each single residue in HIV-1 RT (positions 20-227) was examined in separate models sequentially. Power calculations and model selection steps were carried out to limit the number of comparisons, and final Bonferroni correction was made to mark out the most significant associations. Polymorphism in HIV-1 RT occurred at sites with least functional constraint against mutation. At these sites, we identified 64 characteristic polymorphisms associated with specific HLA-A or -B alleles (OR > 1, p < 0.05). These polymorphisms were often within or proximate to known or putative CTLepitopes, and correlated with the known HLA allele restriction of these epitopes. There were also 13 polymorphisms that were independently associated with specific HLA-DRB1 alleles (OR > 1, p < 0.05). Four of the 5 known T helper cell epitopes in HIV-1 RT encompassed sites of HLA-DRB1 allele-specific polymorphism found in our study. There were also 'negative associations' between polymorphism and common HLA alleles, suggesting that the HIV-1 consensus sequence could have been selected by the host population's dominant HLA. This novel, population-based approach shows that polymorphisms in HIV-1 sequence are characteristic for specific HLA class I and II alleles, in keeping with viral adaptation to both the CTLand CD4 T helper cell responses of a human host population. These findings suggest that HLA has a central role in HIV-1 primordial and contemporary evolution and has implications for epitope mapping and predicting HIV-1 dynamics in individuals.