Understanding human cytomegalovirus latency as a means to target the latent reservoir

Lead Research Organisation: University of Cambridge
Department Name: Medicine

Abstract

Human cytomegalovirus (HCMV) is a type of herpesvirus which is carried without symptoms by the majority of the population. However, it can cause serious disease in infants born to mothers who acquire the infection in pregnancy. Similarly, in people whose immune systems are suppressed, for instance when they undergo organ transplantation or stem cell grafts, HCMV can be life threatening. There has been a continual call for increases in the number of transplants in the UK (see http://www.bbc.co.uk/news/health-40564329 and http://www.bbc.co.uk/news/health-11688102); this means that HCMV disease is likely to become more and more of a problem, particularly, in transplant patients.
Unlike many other viruses, HCMV is never cleared after its initial infection but persists for the life-time of the individual. At least in part, this is due to the ability of HCMV to avoid the immune system by expression of virus genes which help it avoid immune responses. However, the life-long persistence of this virus is also a biological property of all herpesviruses because the virus is able to undergo a so-called latent infection. During latency, the virus hides in the cell without making new virus particles but is still able to reawaken, generating new infectious virus which can cause disease and can also be passed on to other uninfected people.
Understanding how the virus succeeds in maintaining itself as a latent infection in people without causing disease and how this relationship breaks down to cause disease should help develop better methods of treating the virus and for designing a vaccine (there is currently no vaccine available).
Our research is aimed at determining (i) the mechanisms by which the virus maintains a silent infection (latency) in specialised cells of the immune system (ii) how the virus re-awakens (reactivation) and (ii) how the immune system is prevented from eliminating the virus from the body. This will help us understand how the virus is able to hijack the cell in order for the virus to be carried latently and will inform us of novel therapies to target latently infected cells to prevent disease in transplant patients. In addition to advancing our understanding of HCMV, in particular, this research may also lead to a better understanding of other virus infections which persist in the body, how the human host controls them as well as help identify common strategies for their elimination.

Technical Summary

HCMV primary infection of the immunocompetent is asymptomatic. However, infection of individuals with compromised or immature immune systems can be life threatening. Furthermore, HCMV persists for the lifetime of the host which, due to its ability to avoid immunesurveillance and, ultimately, establish a latent infection. Cellular latency is defined maintenance of viral genomes in the absence of infectious virus production. Consequently, current therapies targeting HCMV replication will not target the latent virus; yet reactivation from latency is a major cause of disease in immune suppressed transplant patients. Work from our laboratory has been instrumental in identifying some of the viral genes expressed during latency, the host immune responses to these antigens and how these genes modify the latently infected cell. However, the viral transcriptome is likely far more complex than initially thought and how latent virus modifies the latently infected cell will be a result of a complex array of interactions between multiple latency-associated viral gene products and a multitude of host cell functions. On this basis, we have now made considerable efforts to try to analyse changes in the total cell proteome resulting from latent infection by unbiased approaches which has helped identify important phenotypic changes resulting from latent infection. We also have developed unbiased screening technologies to identify viral and cellular factors necessary for the establishment and maintenance of latency, as well as reactivation, in the myeloid lineage. Such analyses will allow a more comprehensive understanding of how this human pathogen persists for the lifetime of the host and will also help us to exploit the phenotypic changes in the latently infected cell for chemotherapeutic and immunological targets to lead to credible strategies aimed at eliminating latent virus in vivo and in solid organ donor tissue.

Planned Impact

HCMV is universally distributed in human populations and, like all herpesviruses, persists throughout life after primary infection. HCMV remains an important human pathogen, particularly in the settings of congenital infection; it is the commonest infective cause of congenital central nervous system damage and is also a major cause of disease in immunocompromised subjects, especially in the context of organ and stem cell allografting. Whilst antiviral therapy is available, side effects and drug resistance occur. Additionally, current antivirals do not target the latent reservoir and so do not eliminate virus which can reactivate and cause morbidity, particularly in transplant patients receiving tissue from HCMV seropositive donors or in recipients who are already seropositive for the virus. Consequently, HCMV headed the list of needed vaccines in the US Institute of Medicine on Priorities for Vaccines report (Arvin Clin Infect Dis 2004), in part reflecting the weighting given to quality life years saved.
Understanding virus pathogenesis at a molecular level during lytic infection and latency, and how viral gene products interact with host immune responses, is crucial for design of novel antiviral strategies and approaches to vaccines. For HCMV, this is increasingly important not least because of the increasing calls for transplant organs by the BMA and Government but also because there is opinion that long-term persistence of HCMV, underpinned by virus reactivation, is associated with long-term diseases such as atherosclerosis and neoplasias.
This research will directly benefit UK and international research academics in the herpesvirus community as well as those interested in immunity and immune evasion. Similarly, the National Institute of Health Research (NIHR) community clearly benefits from any successful outcomes of the proposed research programme through decreased transplantation-mediated HCMV disease. Cambridge University and Cambridge University Hospitals NHS Foundation Trust, as one of the 20 NIHR Comprehensive Biomedical Research Centres (BRC) in the UK, are ideally placed to adopt new technologies, techniques and treatments for improving health and to translate fundamental biomedical research into clinical research that benefits patients: Antimicrobial resistance and Transplantation and regenerative medicine are two of the themes in our BRC, which will help facilitate the translational research associated with this application. Our research should also inform industrial partners interested in vaccine/drug development as it will provide key information both for vaccine design and drug targeting. For instance, a successful vaccine program will have clear health impacts through the prevention of congenital infections and subsequent long-term associated health care costs and the ability to target the latent viral would have far-reaching clinical benefits in transplant recipients.
Our proposed programme will support 2 technicians and 2 postdoctoral scientists, all are supported by our present programme of work. Long-term funding has allowed, and will continue to allow, our research technicians to become highly skilled laboratory workers. Their in-house training will also enable them to move into higher roles vital for the effective running of research groups and University Departments. The training that our post-doctoral researchers receive, not only in laboratory based research but also in student teaching will enable them to move on to academic posts to develop their own research programs as well as to become well trained scientists who would also be highly valued by industry.

Publications

10 25 50
 
Title Caco-2 epithelial cells were infected with human cytomegalovirus for 4 days, before being infected with ZsGreen-tagged SARS-CoV-2 for a further 2 days. 
Description Cover image on Journal of Infectious Diseases (https://doi.org/10.1093/infdis/jiac452) 
Type Of Art Image 
Year Produced 2023 
Impact Cover image to journal 
 
Description Development of a robust T cell assay to retrospectively diagnose SARS-CoV-2 infection and IFN-? release assay as diagnostic and monitoring assay in Long COVID patients
Amount £372,684 (GBP)
Funding ID COV-LT2-0004 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 10/2021 
End 06/2023
 
Description MRC DTP Doctoral Training Award
Amount £80,000 (GBP)
Funding ID RG86932 
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description Wellcome Infection Immunity and Inflammation PhD Programme
Amount £110,000 (GBP)
Funding ID 109075/Z/15/A 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2016 
End 09/2019
 
Title Assessment of anti-viral activity by Cytomegalovirus dissemination assay 
Description We have developed an assay system to allow the assessment of antiviral activity of T cells and NK cells against human cytomegalovirus using autologous fibroblasts and dendritic cells. This assay is a significant advance on measuring specific cell frequencies and effector measure as it allows a quantitative measure of anti viral activity and can be used to compare the ability to control HCMV between eg different patient groups. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact This assay was first developed to examine anti-cytomegalovirus activity of CD8+ T cells and we have subsequently used it to examine CD4+ T cells (doi: 10.1128/JVI.02128-16) and NK cells doi: 10.1128/JVI.02614-15. As part of a successful Welcome Trust collaborative award we will be using this assay to examine cytomegalovirus vireamia in the context of solid organ transplantation. 
 
Title Novel immunotoxin to target HCMV latently infected cells 
Description We have developed a novel fusion-toxin protein to target and kill HCMV latently infected cells 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact We have been approached by a number of international organ transplant centres to determine whether this novel immunotoxin could be used to clear latently infected cells from solid organs. 
URL http://www.med.cam.ac.uk/blog/novel-therapeutic-make-stem-cell-transplants-safer/
 
Title Transient activation of human cytomegalovirus lytic gene expression during latency allows cytotoxic T cell killing of latently infected cells 
Description This approach of transiently inducing viral lytic gene expression by HDAC inhibition, in otherwise latently infected cells, offers a window of opportunity to target and purge the latent myeloid cell reservoir by making these normally immunologically undetectable cells visible to pre-existing host immune responses to viral lytic antigens. 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact We are presently investigating the possibility of using such an approach to reduce the latent load of HCMV in stem cell grafts prior to engraftment 
 
Description Analysis of LUNA 
Organisation University College London
Department Department of Infection and Population Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Analysis of the control of the HCMV latency-associated LUNA gene product of HCMV
Collaborator Contribution co-analysers of the LUNA gene product
Impact Reeves et al 2010. Human cytomegalovirus IE72 protein interacts with the transcriptional repressor hDaxx to regulate LUNA gene expression during lytic infection J. Virol 84:7185
Start Year 2013
 
Description Analysis of latency-associated transcripts 
Organisation Cleveland Clinic
Department Cleveland Clinic Foundation
Country United States 
Sector Charity/Non Profit 
PI Contribution Our research led to the detection of certain viral genes during latent infection
Collaborator Contribution Our collaborators helped us to define latent transcripts further work on which was funded by an MRC Programme Grant renewal
Impact Betty Lau, Emma Poole, Ellen Van Damme, Lieve Bunkens, Madeleine Sowash, Harry King, Eain Murphy, Mark Wills, Marnix Van Loock, John Sinclair 2016. Human cytomegalovirus miR-UL112-1 promotes the down-regulation of viral immediate early gene expression during latency to prevent T cell recognition of latently infected cells Published ahead of print 10.1099/jgv.0.000546 Betty Lau, Emma Poole, Benjamin Krishna, Immaculada Sellart, Mark R. Wills, Eain Murphy, and¬ John Sinclair (2016) The Expression of Human Cytomegalovirus MicroRNA MiR-UL148D during Latent Infection in Primary Myeloid Cells Inhibits Activin A-triggered Secretion of IL-6. Sci Rep. 6 :31205, doi:10.1038/srep31205
Start Year 2013
 
Description Analysis of nanobodies targeting viral US28 to reactivate HCMV 
Organisation University of Amsterdam
Country Netherlands 
Sector Academic/University 
PI Contribution Analysis of the ability of nanobodies targeting US28, provided by our collaborators, to reactivate HCMV in the myeloid lineage
Collaborator Contribution Provision of the US28-specific nanobodies
Impact Multidisciplinary - Medicinal chemistry and virology
Start Year 2017
 
Description Coordinating COVID-19 asymptomatic testing programmes in university settings: providing insight on acquired immunity across the student population. 
Organisation Cardiff University
Country United Kingdom 
Sector Academic/University 
PI Contribution University of Cambridge Have enrolled >200 participants and biobanked sera, saliva and PBMC were are currently performing experimental work on this material and samples from University of Nottingham according to our particular expertise, Cambridge is performing virus neutralisation assays again COVID variants, T cell assay and examining saliva for antiviral activity The beginning of the 2020/2021 academic year across UK universities was followed by a sharp increase in the COVID-19 infection rates in a largely asymptomatic student population, which could only be monitored thanks to the decision of some Higher Education providers to establish in-house asymptomatic testing facilities. These services ran in parallel to UK Government's surveillance efforts, which in turn relied mostly on self-referred symptomatic cases. Appreciating the untapped potential contained in these highly controlled cohorts, the University of Nottingham, The University of Cambridge and Cardiff University created asymptomatic services with consent to research and future contact embedded in the sample collection workflow. Given the regional, demographic and living arrangements differences within and across these three universities, this consortium provides a unique opportunity to systematically collect samples and data that will prove invaluable in understanding the development of immunity against SARS-CoV2, through past and future immunological profile in this population. It will also enable studies on still underappreciated aspects of the infection, such as the impact of virus mutation on the development of the immune response. Our aim is to create a national data asset that adds value to existing activities that is underpinned by consent and that adds value to existing national activities in this space. This new, diverse and rich collection will be constructed by coordinating existing programmes across the University of Nottingham, University of Cambridge and Cardiff University, bringing consistency to data collection and generation.
Collaborator Contribution The beginning of the 2020/2021 academic year across UK universities was followed by a sharp increase in the COVID-19 infection rates in a largely asymptomatic student population, which could only be monitored thanks to the decision of some Higher Education providers to establish in-house asymptomatic testing facilities. These services ran in parallel to UK Government's surveillance efforts, which in turn relied mostly on self-referred symptomatic cases. Appreciating the untapped potential contained in these highly controlled cohorts, the University of Nottingham, The University of Cambridge and Cardiff University created asymptomatic services with consent to research and future contact embedded in the sample collection workflow. Given the regional, demographic and living arrangements differences within and across these three universities, this consortium provides a unique opportunity to systematically collect samples and data that will prove invaluable in understanding the development of immunity against SARS-CoV2, through past and future immunological profile in this population. It will also enable studies on still underappreciated aspects of the infection, such as the impact of virus mutation on the development of the immune response. Our aim is to create a national data asset that adds value to existing activities that is underpinned by consent and that adds value to existing national activities in this space. This new, diverse and rich collection will be constructed by coordinating existing programmes across the University of Nottingham, University of Cambridge and Cardiff University, bringing consistency to data collection and generation.
Impact None at present still in the investigation stage
Start Year 2020
 
Description Coordinating COVID-19 asymptomatic testing programmes in university settings: providing insight on acquired immunity across the student population. 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution University of Cambridge Have enrolled >200 participants and biobanked sera, saliva and PBMC were are currently performing experimental work on this material and samples from University of Nottingham according to our particular expertise, Cambridge is performing virus neutralisation assays again COVID variants, T cell assay and examining saliva for antiviral activity The beginning of the 2020/2021 academic year across UK universities was followed by a sharp increase in the COVID-19 infection rates in a largely asymptomatic student population, which could only be monitored thanks to the decision of some Higher Education providers to establish in-house asymptomatic testing facilities. These services ran in parallel to UK Government's surveillance efforts, which in turn relied mostly on self-referred symptomatic cases. Appreciating the untapped potential contained in these highly controlled cohorts, the University of Nottingham, The University of Cambridge and Cardiff University created asymptomatic services with consent to research and future contact embedded in the sample collection workflow. Given the regional, demographic and living arrangements differences within and across these three universities, this consortium provides a unique opportunity to systematically collect samples and data that will prove invaluable in understanding the development of immunity against SARS-CoV2, through past and future immunological profile in this population. It will also enable studies on still underappreciated aspects of the infection, such as the impact of virus mutation on the development of the immune response. Our aim is to create a national data asset that adds value to existing activities that is underpinned by consent and that adds value to existing national activities in this space. This new, diverse and rich collection will be constructed by coordinating existing programmes across the University of Nottingham, University of Cambridge and Cardiff University, bringing consistency to data collection and generation.
Collaborator Contribution The beginning of the 2020/2021 academic year across UK universities was followed by a sharp increase in the COVID-19 infection rates in a largely asymptomatic student population, which could only be monitored thanks to the decision of some Higher Education providers to establish in-house asymptomatic testing facilities. These services ran in parallel to UK Government's surveillance efforts, which in turn relied mostly on self-referred symptomatic cases. Appreciating the untapped potential contained in these highly controlled cohorts, the University of Nottingham, The University of Cambridge and Cardiff University created asymptomatic services with consent to research and future contact embedded in the sample collection workflow. Given the regional, demographic and living arrangements differences within and across these three universities, this consortium provides a unique opportunity to systematically collect samples and data that will prove invaluable in understanding the development of immunity against SARS-CoV2, through past and future immunological profile in this population. It will also enable studies on still underappreciated aspects of the infection, such as the impact of virus mutation on the development of the immune response. Our aim is to create a national data asset that adds value to existing activities that is underpinned by consent and that adds value to existing national activities in this space. This new, diverse and rich collection will be constructed by coordinating existing programmes across the University of Nottingham, University of Cambridge and Cardiff University, bringing consistency to data collection and generation.
Impact None at present still in the investigation stage
Start Year 2020
 
Description Single Cell RNAseq of latently infected cells 
Organisation Weizmann Institute of Science
Country Israel 
Sector Academic/University 
PI Contribution We provide sorted latently infected CD34 and CD14 positive cells for RNAseq
Collaborator Contribution RNA sequencing of latently infected cells
Impact None, yet
Start Year 2015
 
Description Targeting the latent HCMV reservoir using novel fusion toxin proteins that bind to viral US28 
Organisation University Health Network (UHN)
Country Canada 
Sector Academic/University 
PI Contribution We have provided expertise to analyse the latent HCMV reservoir in human lung
Collaborator Contribution They have delivered a novel antiviral that targets the HCMV latent reservoir using a model of ex vivo lung perfusion
Impact Ribeiro et al 2022
Start Year 2018
 
Description Targeting the latent HCMV reservoir using novel fusion toxin proteins that bind to viral US28 
Organisation University of Cambridge
Department Department of Surgery
Country United Kingdom 
Sector Academic/University 
PI Contribution We have analysed the targeting of latently infected cells using reagents supplied by Synklino
Collaborator Contribution Synklino have provided the novel fusion toxin protein The Department of Surgery collaborate with us on using ex vivo perfusion of transplant kidneys as a model to analyse targeting of the HCMV latent reservoir in the kidney
Impact none, yet
Start Year 2018
 
Description US28 as a therapeutic target of latent HCMV infection 
Organisation University of Copenhagen
Country Denmark 
Sector Academic/University 
PI Contribution We are providing the latent model for analysis
Collaborator Contribution Provisions of reagents
Impact Targeting the latent cytomegalovirus reservoir with an antiviral fusion toxin protein; Nature Communications NCOMMS-16-15473C, 2017, B. A. Krishna, K. Spiess, E. L. Poole, B. Lau, S. Voigt, T. N. Kledal, M. M. Rosenkilde, J. H. Sinclair
Start Year 2013
 
Description proteomics analyses of latency-associated HCMV genes 
Organisation University of Cambridge
Department Cambridge Institute for Medical Research (CIMR)
Country United Kingdom 
Sector Academic/University 
PI Contribution Analysis of the role of US28 and UL138-interacting proteins in HCMV latency
Collaborator Contribution Proteomic analysis to identify interaction partners with latency-associated HCMV genes
Impact Weekes, M.P, Tan SY, Poole E, Talbot S, Antrobus R, Smith DL, Montag C, Gygi SP, Sinclair JH, Lehner PJ. (2013) Latency-associated degradation of the MRP1 drug transporter during latent human cytomegalovirus infection. Science 340, 199-202. Karniely S, Weekes MP, Antrobus R, Rorbach J, van Haute L, Umrania Y, Smith DL, Stanton RJ, Minczuk M, Lehner PJ, Sinclair JH. 2016. Human Cytomegalovirus Infection Upregulates the Mitochondrial Transcription and Translation Machineries. MBio 7
Start Year 2013
 
Title IDENTIFICATION AND ELIMINATION OF HCMV-INFECTED CELLS 
Description The invention relates to the use of a single heavy chain variable domain antibody against human cytomegalovirus protein US28, which antibody binds to the extracellular region including, for example, the N-terminal extracellular region and/or the extracellular loops of US28, for isolation of cells that are infected with cytomegalovirus and/or for ex vivo reactivation of cytomegalovirus in latently infected cells. The invention further relates to the anti-US28 antibody for use in a method of reactivating cytomegalovirus in infected cells, or in a method of eliminating infected cells. The invention further relates to a tissue, organ, or cells such as bone marrow stem cells, from which cells that were infected with CMV have been removed with the use of the anti-US28 antibody. 
IP Reference WO2021025556 
Protection Patent application published
Year Protection Granted 2021
Licensed No
Impact This work has led to the possibility of developing novel ways to target the latent HCMV reservoir in live donors (prior to graft donation) or recipients (also prior to engraftment).
 
Title Ex vivo Treatment of Cytomegalovirus in Human Donor Lungs Using a Novel Chemokine-Based Immunotoxin 
Description Transmission of latent human cytomegalovirus (CMV) via organ transplantation with post-transplant viral reactivation is extremely prevalent and results in substantial adverse impact on outcomes. Therapies targeting the latent reservoir within the allograft and mitigating viral transmission would represent a major advance. F49A-FTP is a pseudomonas exotoxin A-based immunotoxin that targets latent CMV. Here, we used a clinically established normothermic ex-vivo lung perfusion (EVLP) platform to deliver F49A-FTP aiming at reducing latent CMV reservoir from donor lungs. First, we successfully developed an assay that reactivates latent CMV from human lung tissue to be able to evaluate efficacy of the immunotoxin delivered ex-vivo. We were then able to show that CMV seropositive human donor lungs treated ex-vivo with F49A-FTP had significant reduction in CMV reactivation when compared to controls, suggesting successful targeting of latent virus (76% median reduction vs. 15% increase, respectively, p=0.0087). Safety of this treatment was demonstrated by stable ex vivo lung function over 6 hours and absence of off target effects as demonstrated by comparable cell death and inflammation as compared to controls. Our experiments demonstrate the first approach targeting latent CMV in a donor organ with promising results towards clinical translation. 
Type Support Tool - For Medical Intervention
Current Stage Of Development Refinement. Non-clinical
Year Development Stage Completed 2020
Development Status Under active development/distribution
Impact None yet 
 
Title Ex vivo Treatment of Cytomegalovirus in Human Donor kidneys Using a Novel Chemokine-Based Immunotoxin 
Description Developing the delivery of a novel fusion toxin protein to kills cells latently infected with HCMV in kidney organ donations 
Type Support Tool - For Medical Intervention
Current Stage Of Development Refinement. Non-clinical
Year Development Stage Completed 2020
Development Status Under active development/distribution
Impact None as yet 
 
Description Invited Chair and member of the International Scientific Advisory Board for the 45th International Herpesvirus Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion of research work by International researchers in the herpesvirus field leading enabling post-doctoral and postgraduate student career development
Year(s) Of Engagement Activity 2021
 
Description Invited Chairperson and member of the Scientific Advisory Committee at the 17th International CMV Workshop Alabama 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact International Workshop
Year(s) Of Engagement Activity 2019
 
Description Member of the Scientific Advisory Committee at the 44th International Herpesvirus Workshop, Knoxville USA, July 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact International Workshop
Year(s) Of Engagement Activity 2019
 
Description School Visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Visit to local primary school as part of Cambridge Science Week
Year(s) Of Engagement Activity 2019