Virus-host interactions in hepatitis C virus infection

At least 250,000 people in the UK are thought to be infected with hepatitis C virus (HCV), which can cause severe liver damage in up to 20 per cent of patients. HCV is much easier to contract than HIV, with prisoners and drug users particularly vulnerable to infection. While there has been considerable progress in the scientific understanding of the disease in recent years, it is extremely difficult to effectively track the spread of HCV and to understand the biological roots of the illness. The lack of surveillance of the disease in the UK has also made it harder for doctors to determine why some patients can develop symptoms as soon as they are infected, while others only go onto develop cirrhosis of the liver after many years. Treatments that can cure patients of infection are available but they are not always successful. By collecting and then analysing clinical samples taken from patients, along with use of laboratory-based methods for studying the virus, the projects in this programme will help us to understand why some people develop disease more rapidly than others and also why certain patients fail to respond to treatment.

Chronic hepatitis C virus (HCV) infection causes liver disease, with those developing end-stage liver disease and hepatocellular carcinoma expected to double over the next decade. Whereas HCV infection can be cured in a proportion of patients, the determinants for treatment response are incompletely described. Characterising the complexity of virus/host interactions is essential for a complete understanding of the mechanisms underlying disease progression and treatment response. The programme combines clinical studies on the natural course of HCV infection with fundamental research that enables examination of the virus using in vitro models. Major elements of the programme are:
Patient Cohorts for Clinical and Fundamental Research – I am principal grant holder for HCV Research UK, a consortium funded by the Medical Research Foundation to recruit 10,000 infected patients from centres across the UK. Funding has established a clinical database and biorepository for research studies into natural infection. We have also created a local cohort, HCV Outcomes, for specific research projects.
Gene Expression Changes in HCV Genotype 1 and 3 Infection - There are 6 HCV genotypes (gts), two of which, gts1 and 3, are the most prevalent in the UK. The pattern of pathogenesis for these genotypes is not identical and they have different responses to pegylated interferon-alpha and ribavirin. Our transcriptomic and microarray studies have found alterations in gene expression between gt1 and gt3 in liver biopsies and PBMCs. This could identify genetic signatures related to disease progression and treatment response. Samples have also been analysed for markers of senescence since T-cell exhaustion occurs during chronic HCV infection. Such an approach aims to link HCV and enhanced biological ageing in infected patients.
The Effect of Infection on the T-cell Receptor Repertoire – T-cells are crucial for combating HCV. We are developing the technology to explore the T-cell receptor repertoire by high-throughput sequence methods to analyse T-cell populations that temporally change in different population groups (e.g. chronic vs cleared infection) and that recognise specific HCV antigens. These studies will be important for developing possible T-cell based vaccines.
Development of Systems to Examine HCV Infection - Model systems for studying HCV isolates have been restricted to HCV gts1 and 2 (strain JFH-1). Given the high prevalence of gt3 in the UK, we are creating gt3/gt2 chimeric constructs with the JFH-1 strain. This enables studies on gt3 isolates to examine i) the properties of quasispecies in natural infection, ii) sequences involved in evading intrinsic immune responses and iii) resistance to antiviral therapies.
Host Factors and Processes that Regulate Productive Infection - Host factors and processes are intimately involved in maintaining and regulating HCV infection in vivo. We are conducting studies that examine ISG15, an interferon-regulated factor and the effect of HCV infection on the cell ubiquitinome. For ISG15, our studies examine the mechanism through which ISG15 reduces HCV RNA replication and whether its activity requires ISGylation of cellular or viral substrates. Both cell biology and proteomic approaches are being applied to determine whether HCV infection alters disrtibution of ubiquitinylated proteins and the cell ubiquitinome. Presently, the group has shown that infection induces novel polyubiquitin foci that are being characterised.