Certain host genetic variants have been shown to exert their effects on HIV-induced disease at specific times after infection22,23
, including certain alleles of the HLA-B
. Using two independent, non-overlapping cohorts, we show that the -35
variant associates strongly with HIV outcomes during the early phase of infection by influencing steady-state viral load, and to a weaker extent with the very late phase of infection by influencing time to death. These temporal data implicate two at least partially distinct mechanisms of HIV restriction associated with the -35
variant. In support of this model, a preliminary analysis suggests that the early effect on viral load is not modulated by the presence or absence of activating KIR2DS
, whereas the late effect might be dependent on the presence or absence of KIR2DS
(Supplementary Tables 4a,b
). Very few well-powered natural history cohorts of seroincident patients before initiation of highly active antiretroviral therapy are available for study, and we have not been able to replicate in an independent cohort our findings regarding the potential modulating effect of KIR2DS
in late chronic disease. Thus, these data remain intriguing, but unsubstantiated.
We have shown that surface expression of HLA-C varies significantly across -35
genotypes and that the HLA-C
alleles that are in positive LD with -35C
are expressed at a higher level than those that are in LD with -35T
. However, the level of HLA-C expression is not bimodal; rather there is a continuum of expression that cannot be attributed completely to zygosity of -35
genotypes (). It will be necessary to probe further into expression levels of the different HLA-C allotypes, for example by studying expression on cells from HLA-C
homozygotes, to determine precisely the order of expression levels among the HLA-C allotypes. The expression data argue against the -35
variant having a sole, direct effect on HLA-C expression, but rather indicates a more complex regulatory mechanism of HLA-C expression in which -35
might simply mark by LD the true regulatory variant(s). Nevertheless, viral load analysis of 43 SNPs in the coding region of exons 2–3 and three more SNPs in the 5′UTR region show that -35
is still the variant that best associates with both viral load control and HLA-C expression (Supplementary Table 5
). The most parsimonious model from the data presented in this report is that the level of HLA-C expression is responsible for the genetic effects on early viral load outcomes to HIV infection and that -35
is serving as a reliable proxy for HLA-C expression levels in European American individuals.
High levels of HLA-C expression during early HIV infection may provide protection by enhancing antigen presentation to CTLs in an acquired immune response. Another possible mechanism to explain the protective effect of high HLA-C expression relates to the interactions between inhibitory KIR2DLs and their HLA-C ligands. Several studies have shown that high expression of MHC class I–specific inhibitory receptors on an NK cell during its maturation is necessary for arming the cell to respond to aberrant targets when it matures25–28
. Accordingly, higher surface expression of inhibitory KIRs that recognize self–MHC class I augments the activity of mature NK cells27
, so it is likely that higher expression of ligands for KIRs during NK cell maturation also better arms the effector cell for stronger activity when faced with an appropriate target cell. The inhibitory KIR2DL1 and KIR2DL2/L3 receptors recognize the dimorphic C1 and C2 HLA-C allotypes, and these inhibitory KIRs are present in the genomes of nearly all individuals29
. Thus, the differential effect of low- versus high-expressing HLA-C types on mVL might relate to greater KIR2DL recognition of highly expressed HLA-C molecules during NK cell maturation, preparing the NK cell for a more effective response against aberrant target cells. That is, more interaction between inhibitory KIRs and their self–MHC class I ligands during NK cell development (which would occur when class I is present at a high level) would result in stronger responses upon the loss or alteration of cognate ligands associated with viral infection. This scenario cannot be tested in a genetic association study, as the genes for the inhibitory KIRs for both HLA-C
groupings are present in nearly all individuals, but functional approaches could appropriately address whether protection conferred by high HLA-C expression involves enhanced activity of NK cells through a licensing process25,26
. Regardless of the mechanism through which high HLA-C provides protection, HIV Nef variants derived from patients with the protective -35CC
genotype seem indirectly to counteract an enhanced HLA-C–mediated immune control by manipulating MHC class II antigen presentation and helper T-cell function (F. Kirchhoff, personal communication). These data suggest that high levels of HLA-C expression exert selection pressure on the virus.
Our results strongly implicate HLA-C as a major determinant in both early and late outcomes of HIV infection. No individual HLA-C allotype appears to be clearly better than others in terms of controlling HIV through antigen presentation to CTLs, unlike HLA-B allotypes8
. However, higher levels of HLA-C on target cell surfaces might generally result in more effective antigen presentation to CTLs or enhance NK cell activity, thus boosting the immune system and leading to better viral control by the host.