A novel strategy to eliminate solid cancers by combining oncolytic adenoviruses and epigenetic drugs to activate the host anti-tumour immune-responses.

Background: Late-stage pancreatic ductal adenocarcinoma (PDAC) and triple-negative breast cancer (TNBC) are aggressive cancers of unmet medical needs. Major reasons for the poor treatment outcomes are the development of resistance to all current treatments including immune-checkpoint inhibitors. A promising therapeutic approach is oncolytic adenoviruses (OAds) that kill cells through unique mechanisms. Our cancer selective replicating OAd mutants specifically kill cancer cells by lysis in turn recruiting and re-activating host anti-tumour immune responses. In our preclinical models, intratumoural delivery efficiently inhibited tumour growth while systemic delivery was less efficacious due to neutralization by blood factors. To eliminate distant metastatic lesions, administration directly into the blood-stream is necessary and further engineering of the OAds to resist blood factor interference are underway. We found that retargeting of the viruses to specific tumour antigens in combination with enhancers of viral replication resulted in high uptake at distant tumour sites. We previously demonstrated that OAds re-sensitised treatment-resistant PDAC cells to apoptosis inducing chemotherapeutics resulting in elimination of resistant tumours. Currently, we have found that less toxic drugs such as those altering the epigenome significantly increased viral activity and cancer cell killing in response to the OAds.

The PhD project will focus on identifying epigenetic compounds that enhance viral efficacy and delineating the mechanisms. The overall goal is to develop improved therapies for patients afflicted by PDAC and TNBC. During infection with adenovirus, viral proteins reprogram the host cell epigenetics to change the distribution of specific host histone marks (e.g. histone acetylation) across the genome. This redistribution alters the genes expressed in the infected cell to shut off host genes that respond to limit infection and activate genes that cause the cell to enter the cell cycle. These events are absolute requirements for adenovirus propagation and occur during specific stages of the viral life cycle by regulated expression of viral genes. One example is the viral E1A protein that directly binds to host p300/CBP, facilitating the redistribution of histone marks to silence some groups of genes and switch others on.

In this project, genome-wide profiles of these marks and how they are altered soon after infection with the OAds will be generated using a cutting edge high-throughput sequencing based approach called ‘cut and run.’ This will provide insight into how viral proteins manipulate the host genome and identify key genes and pathways involved in the setting of therapeutic OAds. This data will be combined with a screen to determine which epigenome-targeting drugs are most effective at promoting viral replication, specifically in cancer cells. Collectively, this will provide the basis to select target pathways for functional validation (e.g. siRNA/viral mutants/small molecules). Understanding these pathways will pave the way towards developing even more specific drugs to enhance the anti-tumour activity of the oncolytic viruses. The findings will be validated in preclinical tumour models in healthy mice or those with a compromised immune response.

We are looking for an enthusiastic hard-working student with a BSc or MSc in biology, virology, molecular biology or similar. A strong interest to learn and apply bioinformatics to genomics, oncology and virology is desirable.


Potential research placements

1. Training in molecular biological techniques, including extraction of DNA/RNA, QC and preparation of high-throughput sequencing libraries. This will be in parallel to training in both R/python and analysis of publicly available ChIP-seq data following adenoviral infection for comparison for self-generated data in the later stages of the project. Dr Holland, KCL.

2. Training in basic laboratory techniques such as mammalian cell culture, flow cytometry, immunohistochemistry and PCR. Thorough training in all virus-related techniques including mutant construction, production and characterisation. Design of in vivo studies and evaluation using small animal imaging will be an essential part of the training. Dr Halldén and Dr Tizong Miao, BCI, QMUL.

3. Basic computerised programming for complex analysis of data derived from own experiments and from databases. The student will be exposed to working as part of big multidisciplinary team focused on bioinformatics, developing databases for PDAC and mining of data networks for validation in wet labs. Prof Claude Chelala, BCI, QMUL.


For further details on how to apply please visit the CRUK CoL PhD training programme web page: https://www.colcc.ac.uk/phd-studentships/