Host factors required for human polyomavirus replication and spread

Polyomaviruses are ubiquitous viruses that infect virtually everyone on the planet. We currently know of thirteen different polyomaviruses that infect humans, which are mainly contracted during childhood. These viruses can persist within us for life and they can cause serious problems in immune-suppressed patients, including at least one type of cancer. One of the most significant medical problems that is caused by polyomavirus infection is in kidney transplantation, where a virus known as BK polyomavirus causes extensive damage to the kidneys and bladder. The only available drugs to treat infections with polyomaviruses are either ineffective or can damage the kidneys and so they are not viable options for use in kidney transplant patients, and as a consequence BK polyomavirus infection leads to an unacceptably high risk losing the transplanted kidney. Therefore, we have an urgent need to develop new therapeutics to combat the diseases caused by BK polyomavirus and related viruses. However, there is insufficient knowledge of the basic biology of these viruses.

Polyomaviruses express only a handful of their own proteins and so they are particularly reliant on processes within our cells to successfully replicate and spread. We have recently developed large scale genetic screens to identify the genes in our cells that are crucial for BK polyomavirus infection. The proposed research will use state-of-the-art techniques to provide a detailed understanding of what factors within our cells BK polyomavirus needs. This knowledge will identify new ways that we can develop medicines to inhibit these viruses, which could have far reaching benefits for kidney transplant recipients and for treating other diseases caused by polyomaviruses.

Polyomaviruses are ubiquitous viral pathogens that establish life-long persistent infections in their hosts and can cause serious problems in immune-suppressed patients. Of all the human polyomaviruses BKPyV has the biggest clinical impact due to causing BK polyomavirus-associated nephropathy (BKVAN) in up to 10% of renal transplant patients, and this disease can lead to allograft loss in a high proportion of such patients. Due to a lack of effective antiviral therapies for treating BKVAN, there is a pressing need to understand the basic biology of BKPyV to develop novel therapeutics against this virus. To address this gap in understanding, we have established a CRISPR genome-wide screen for host factors required in early stages of BKPyV infection. This has uncovered specific host factors involved in endocytosis, transcription and splicing. This research will determine the importance and mechanisms of action of the identified host factors during BKPyV infection. Furthermore, these genetic screens will be expanded to encompass the entire replication cycle of this virus within renal epithelial cells to identify and characterise host pathways required for viral late gene expression, virion assembly and virus egress. Additionally, we will characterise the changes to the plasma membrane proteome of BKPyV infected cells, to gain further understanding of how this virus alters cellular secretion pathways to promote its own release, and to define biomarkers of infection. This programme of work will provide the most complete understanding of host factors required for BKPyV to establish infection, replicate and spread in primary renal cells. In addition to providing new therapeutic targets for the treatment of life threatening diseases in the immunocompromised, our work will have wide reaching implications beyond the field of polyomavirus biology as we expect to uncover new insights into cellular biological processes.

This research will identify and characterise host factors necessary for polyomaviruses to successfully replicate and spread. The immediate impacts of this work will be advancing our understanding of the fundamental biology of BK polyomavirus as well as other clinically important polyomaviruses. In addition, this work will have impacts on research into kidney epithelial cell biology and associated diseases.

Beyond these short-term impacts, this research has potential for long-term impact in the following areas:

Healthcare
BK polyomavirus is a significant problem for renal transplant patients and haematopoietic stem cell transplant patients where it can cause nephropathy or haemorrhagic cystitis respectively. Our research has the potential to identify novel host targets that can be targeted by small molecular inhibitors to prevent BK polyomavirus disease. This would help prevent serious allograft dysfunction due to BK polyomavirus-associated nephropathy in renal transplant recipients. Our research may also aid development of new antiviral treatments against closely related human pathogens such as JC polyomavirus, which causes progress multifocal leukoencephalopathy, and more distantly related viruses such as papillomavirus, which cause a range of cancers.

Commercial Sector
Development and testing of any new antiviral therapeutics would require commercialisation by the biotechnology and/or pharmaceutical sectors. This would involve UK-based companies and consequent positive impacts for these businesses finances and employment opportunities.

Knowledge Economy
Postdoctoral researchers and postgraduate students directly involved with this research will gain a plethora of new skills, including experience in state-of-the art high content screening and proteomics techniques. This will significantly enhance the future impact of these scientists in academic or non-academic biosciences research. In addition, this research will expand the intellectual and practical training opportunities for current and future undergraduate students during their laboratory research projects at the University of Cambridge.