Virus-host interactions in hepatitis C virus infection

Lead Research Organisation: MRC Virology Unit

Abstract

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.

Technical Summary

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.

Publications

10 25 50

 
Description EC Collaborative Project
Amount £268,538 (GBP)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start  
 
Description MRC Developmental Pathway Funding Scheme (DPFS)
Amount £327,361 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start  
 
Description Marie Curie Intra-European Fellowship
Amount £126,000 (GBP)
Organisation Marie Sklodowska-Curie Actions 
Sector Academic/University
Country Global
Start 01/2006 
End 12/2008
 
Description Studies on Liver Disease
Amount £1,924,918 (GBP)
Funding ID C0365 
Organisation Medical Research Council (MRC) 
Department Medical Research Foundation
Sector Charity/Non Profit
Country United Kingdom
Start 01/2011 
End 03/2019
 
Title HCV materials 
Description My group has produced antibodies, constructs and developed biophysical approaches that have been utilised by a wide number of international groups. Characterisation of the antibodies and constructs has been completed and we continue to develop the biophysical methods. Other researchers are aware of our materials through publication of papers and presentations at conferences. A considerable number of man-years has been devoted to this area and the benefits have been acknowledged in publications from those who have received our materials. 
Type Of Material Technology assay or reagent 
Year Produced 2006 
Provided To Others? Yes  
Impact Our materials have facilitated the ongoing development of systems for studying HCV biology and also influenced the field related to lipid disorders. 
 
Description C McCormick, University of Southampton 
Organisation University of Southampton
Country United Kingdom 
Sector Academic/University 
PI Contribution Studies on the mechanism of HCV RNA replication
Collaborator Contribution Partner developed a novel system for examining HCV RNA replication using subgenomic replicons
Impact Collaboration has given rise to 1 publication with more in the pipeline. Collaborator also submitted a grant application to MRC (unsuccessful).
Start Year 2011
 
Description Collaboration on apoE 
Organisation National Institute of Health and Medical Research (INSERM)
Department INSERM U748 (Virus Host Interactions and Liver Diseases)
Country France 
Sector Public 
PI Contribution My group conducted imaging studies for the collaboration.
Collaborator Contribution The group at Strasbourg broadened our research interests to include studies on the role of apolipoproteins on assembly and release of infectious HCV.
Impact The collaboration resulted in 1 publication [PMID: 20014138].
Start Year 2009
 
Description Heidelberg - Virology 
Organisation Heidelberg University
Country Germany 
Sector Academic/University 
PI Contribution My group has developed biophysical assays that have given a unique perspective on the properties of HCV proteins. This expertise was incorporated into our collaboration.
Collaborator Contribution The group at Heidelberg provided key reagents and knowledge that enhanced our programme of work.
Impact The collaboration involved a member of the team from Heidelberg visiting Glasgow to obtain training in biophysical methods. It also led to one publication (PubMed ID 17942391) with others in the process of nearing completion for submission.
Start Year 2006
 
Description Impact of TRC8 on HCV RNA replication 
Organisation University of Cambridge
Department Cambridge Institute for Medical Research (CIMR)
Country United Kingdom 
Sector Academic/University 
PI Contribution My group provides the systems for analysis of HCV RNA replication and production of infectious virus.
Collaborator Contribution We have established a collaboration with a group at CIMR in Cambridge who study the role of ubiquitin ligases in virus infection. The link has expanded the range of studies in which we are engaged on interactions between HCV and cellular processes.
Impact As yet there are no publications arising from the collaboration but the preliminary data are potentially exciting and could lead to longer term links with Prof Lehner's group in Cambridge.
Start Year 2008
 
Description Institut Pasteur 
Organisation Pasteur Institute, Paris
Country France 
Sector Academic/University 
PI Contribution My group has provided considerable expertise to the group at Pasteur by way of methods in cell biology.
Collaborator Contribution Along with the group at the Pasteur Institute, we have built cell biology studies on certain aspects of HCV infection. The group at Pasteur have not provided us with reagents etc.
Impact This collaboration has led to the publication of 2 papers (PubMed IDs - 18489704, 19269968). It has also facilitated the French group to obtain further funding for their part in the studies.
Start Year 2006
 
Description LipidomicNet Consortium 
Organisation University Hospital Regensburg
Country Germany 
Sector Hospitals 
PI Contribution The consortium is a partnership of about 25 groups from across Europe involved in examining the relationship between human disease and lipid storage. My group is examing this relationship in the context of hepatitis C virus infection.
Collaborator Contribution Access to facilities for lipid analysis at the Babraham Institute in Cambridge. The institute is also providing back-up by way of training.
Impact Inclusion in the consortium has allowed us access to state-of-the-art technology and expert on lipid profiling and cell biology imaging. For the consortium, we add a unique dimension as no other groups studying viruses are part of LipidomicNet.
Start Year 2008
 
Description Provision of antibodies 
Organisation AstraZeneca
Department Arrow Therapeutics
Country United Kingdom 
Sector Private 
PI Contribution The antibodies were unique reagents that were to be used in screening assays to identify unique compounds with anti-HCV activity.
Impact The company has not divulged any data from their screens.
Start Year 2007
 
Description Structural studies on the IFNL4 protein 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution We have provided data on the antiviral activities of natural variants of the human IFNL4 protein (both partners).
Collaborator Contribution The team at Stanford has modelled predictive structures of IFNL4 and natural variants based on their previous publications on other IFNL proteins. The group in Aarhus has created constructs aimed at producing authentically folded IFNL4 proteins for structural studies.
Impact A manuscript describing the findings of the collaboration will be submitted imminently and a pre-publication version of the paper has been published in Bioarchive.
Start Year 2016
 
Description Structural studies on the IFNL4 protein 
Organisation Howard Hughes Medical Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution We have provided data on the antiviral activities of natural variants of the human IFNL4 protein (both partners).
Collaborator Contribution The team at Stanford has modelled predictive structures of IFNL4 and natural variants based on their previous publications on other IFNL proteins. The group in Aarhus has created constructs aimed at producing authentically folded IFNL4 proteins for structural studies.
Impact A manuscript describing the findings of the collaboration will be submitted imminently and a pre-publication version of the paper has been published in Bioarchive.
Start Year 2016
 
Description Studies on Lipid Metabolism in HCV-Infected Patients 
Organisation Newcastle University
Department Institute of Cellular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution My group has provided the tissue culture systems that produce infectious HCV to correlate effects of a high fat supplement in natural HCV infection with effects on virus infectivity seen in vitro.
Collaborator Contribution Interaction with the group at Newcastle University has enabled us to establish a link with studies on human subjects in the area of lipid metabolism and HCV infection.
Impact The collaboration has given rise to 1 paper (PMID: 20682323).
Start Year 2009
 
Description UTMB, Institut Pasteur 
Organisation University of Texas
Country United States 
Sector Academic/University 
PI Contribution My group produced all of the mutants and performed all of the cell-based analysis for the study.
Collaborator Contribution The group at UTMB, along with a group at the Pasteur Institute, provided animals for key parts of a study on GB virus-B, whichis a close genetic relative of HCV.
Impact The collaboration yielded a publication (PubMed ID 16882659).
 
Description Interviews 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I have given interviews to journalists for newspapers.

There was no further contact with the journalists and so it is difficult to judge any impact.
Year(s) Of Engagement Activity 2006,2007
 
Description Invited speaker at UK Clinical Pharmacists Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was the third workshop by the UK Clinical Pharmacists to which I had been invited. The group wished to learn about the new therapies for treating hepatitis C virus infection and the success achieved by these therapies.
Year(s) Of Engagement Activity 2018
 
Description PCR workshop - Glasgow Science Centre 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact The workshop was organised by Dr D Bhella from the Unit and he will no doubt provide more comprehensive details. Both of the CDFs employed on the project volunteered their time and expertise for the workshop.

As noted above, Dr D Bhella will most likely address this question on behalf of the Unit.
Year(s) Of Engagement Activity 2009
 
Description presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I have given a presentation to a HepC support group and been involved in fund-raising activities.

Support groups are more aware of the activities funded by MRC to study HCV infection
Year(s) Of Engagement Activity 2006
 
Description presentations 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I have given practical demonstrations and talks at open days for schools.

There are now well-established contacts with local schools and teachers. Students have expressed a greater interest in pursuing a scientific career after the open day events.
Year(s) Of Engagement Activity 2006,2007,2008