KIR in adaptive immunity: in vivo relevance for human disease

BACKGROUND
This project capitalises on our recent work on killer cell immunoglobulin-like receptors (KIRs). KIRs are expressed predominantly on natural killer cells where they play an important role in innate immunity. There are few studies elucidating the impact of KIRs on the T cell response in human disease.

WORK WHICH HAS LED UP TO THIS PROJECT
Our research has revealed a novel and unexpected way in which immunity can be enhanced. We have found that a particular KIR (KIR2DL2) enhances both protective and detrimental HLA class I disease associations in two chronic virus infections (hepatitis C virus and human T lymphotropic virus) and is an important determinant of clinical outcome. Strikingly, although KIRs are primarily associated with innate immunity, we believe our observations suggest that they also have a major impact on the adaptive immune response.

A NEW ROLE FOR KIR?
Many associations between disease outcome and pairs of KIR-HLA genes have been reported. In every case the KIR-HLA pair consisted of a KIR and the HLA molecule that it binds and the effect was attributed to direct NK killing; i.e. NK cells express the KIR which binds its HLA ligand, this modulates the NK killing of virus-infected cells and thus affects disease outcome.

What we have observed is quite different.

We report that associations between HLA class I molecules and disease outcome are weak in the absence of KIR2DL2 but are enhanced in the presence of KIRDL2, more so if there are two copies of the KIR2DL2 gene. This is true for multiple HLA-A, B and C alleles, most of which do not bind KIR2DL2. We see this effect for two different virus infections and for both protective and detrimental HLA associations. Both clinical outcome and, independently, viral burden are affected. Additionally, the protective effect of HLA binding of many different viral peptides is also enhanced by KIR2DL2. In contrast KIR2DL2 with its C1 ligand (not in the context of protective or detrimental HLA molecules) has absolutely no detectable impact on any measure for either virus. We think that this KIR2DL2-enhancement of HLA class I associations cannot be explained by NK killing of virus-infected cells. Instead we postulate a novel interaction between KIRs and adaptive immunity that is having a significant impact on clinical outcome.

HYPOTHESIS
We suggest KIR2DL2 enhances adaptive immunity by increasing T cell survival during chronic infection and thus enhances the strength of the CD8+ T cell response. If the CD8+ T cell is restricted by a protective HLA class I molecule then, in a KIR2DL2+ person, the CD8+ T cell response will be stronger and protective associations will be enhanced, but equally if CD8+ T cells are restricted by a detrimental HLA molecule then the detrimental associations will be enhanced.


OBJECTIVES
We will test the hypothesis that KIR2DL2 enhances adaptive immunity and investigate how general this effect is. Specifically, we will test if the CD8+ T cell response to hepatitis C virus and human T lymphotropic virus is stronger in individuals with KIR2DL2 and we will investigate if KIR2DL2 also impacts on the risk of developing virus-associated leukemia.

IMPORTANCE
Our data are consistent with an unexpected and clinically important interaction between innate and adaptive immunity. Understanding how the CD8+ T cell response can be enhanced would represent a significant advance in our basic knowledge and would be a major step towards combating the dysfunctions associated with weakened immunity.

APPROACH
We take a multidisciplinary systems approach in which we combine mathematical modelling and sequencing of the host and pathogen genomes with more "traditional" cellular immunology. Investigating the human immune response is challenging; by using this combined approach we gain unique insight.

We have clear and consistent evidence that the presence of a host gene, namely KIR2DL2, enhances both protective and detrimental HLA class I associations in two unrelated chronic viral infections. What is much less clear is the underlying mechanism of action. Epistatic HLA-KIR associations are typically attributed to direct NK-mediated lysis of virus-infected cells. We believe direct NK killing is not compatible with our observations and instead hypothesise that the downstream effectors of KIR2DL2-dependent enhancement are CD8+ T cells. We wish to test this hypothesis and to explore the generality of this KIR2DL2-enhancement by investigating whether KIR2DL2 also impacts on the probability of developing virus-associated malignancy. Importantly, we suggest that KIR2DL2 consistently enhances the efficiency of the CD8+ T cell response; this does not imply that KIR2DL2 is consistently beneficial to human health as KIR2DL2 also enhances the efficiency of CD8+ T cells restricted by detrimental HLA alleles.


Approach. We will take an integrated theoretical and experimental approach. We will study 3 patient cohorts. 1) HCV: 60 HCV-HIV coinfected individuals with acute HCV. 2) HTLV-1 (UK): 30 individuals chronically infected with HTLV-1. 3) HTLV-1 (Japan): 240 adult T cell leukemia/lymphoma (ATLL) cases and 200 HTLV-I-infected healthy controls.

To compare the strength of the CD8+ T cell response between KIR2DL2+ and KIR2DL2- individuals we will use next generation sequencing of the HCV genome (Illumina HiSeq), mathematical modelling of host-pathogen dynamics including parameter inference and model selection, ex vivo CTL and NK killing assays and HLA class I epitope prediction. To assess the impact of KIR2DL2 in adult T cell leukemia/lymphoma we will use HLA and KIR genotyping, epitope prediction, logistic regression and Monte Carlo methods in a case-control cohort.

Chronic viral infections, virus-associated malignancies and the age-related decline in immunity are increasingly important challenges facing the UK. Enhancing the adaptive immune response is likely to be key to addressing these challenges. Although our project is basic science it investigates fundamental questions regarding human health and the enhancement of adaptive immunity and will have clear implications for the health of the UK and the global population.