Defining the cistrome and quantitative transcriptome of virus-transformed cells using massively parallel sequencing
Lead Research Organisation:
The Pirbright Institute
Department Name: Avian Infectious Diseases
Abstract
As in humans, many animals including chickens, develop cancer. However, unlike in humans, most of the cancers in chickens are caused by viruses. Marek's disease (MD) is a common disease of chickens involving paralysis and commonly death from the growth of highly malignant T lymphomas (cancers of white blood cells). MD is caused by a transmissible agent, Marek's disease virus (MDV). MDV is very contagious and is a major threat to the poultry industry worldwide. The estimated total loss from this disease worldwide is up to £ 2 billion. Presently, it is controlled by vaccination, and nearly 22 billion vaccine doses a year are used in an attempt to control the disease. Despite widespread vaccination, the threat from this disease is on the increase, and more fundamental studies to understand the mechanisms by which this virus cause cancer is needed to develop more effective control programmes. Another cancer inducing virus of chickens less common in the UK called Reticuloendotheliosis virus (REV) is a very good model for cancer. The advantage of using this virus for studying the mechanisms of cancer is that the experiments to induce cancer can be done on chicken cells collected from birds. We have used this model and examined the molecular changes to the cells while it is transformed into cancer cells. We have identified very important changes in the expression of genes and small 22-nucleotide microRNAs molecules between normal cancer cells, suggesting that these changes contribute to cancer. In this new grant proposal, to be carried out jointly between the Institute for Animal Health (Compton) and ARK-Genomics (Roslin Institute), we want to extend these studies to obtain detailed information on the changes in the expression of genes using the new RNA-Seq technology that will provide a much detailed comprehensive picture on the expression of genes during the transformation process. Similarly, we will also examine the sequences in the genomes where viral oncoproteins can directly bind to the DNA to change the gene expression to cause cancer. We aim to use this excellent model system and Marek's disease cancer model to obtain detailed gene expression data to understand and predict the molecular pathways to cancer. The study is very important to understand the mechanisms by which these viruses induce cancer, some of which are valuable in understanding cancer in other species including humans. Finally, the findings from the project will be very valuable in developing new approaches for the control of cancers caused by oncogenic viruses.
Technical Summary
The objectives of this work are to define the interactions between virus-encoded transcription factors, the host genomic DNA, microRNAs and mRNA expression during transformation by two avian oncogenic viruses, Reticuloendotheliosis virus (REV) and Marek's disease virus (MDV). Our preliminary data show that both MDV and REV encode transcription factors that bind to host DNA and upregulate important mRNA and microRNA genes, and that the miR-155/miR-M4 pathway is incredibly important to both viruses. We will dissect the exact relationship between virus-encoded transcription factors, microRNAs and gene expression using the latest next-generation sequencing technologies. Specifically, in REV we will simultaneously measure the temporal expression of mRNAs and microRNAs using mRNA-Seq and miRNA-Seq. We will combine this data with ChIP-Seq data to define the binding sites of vRel (the oncogenic transcription factor of REV) within the host genome, both at infection and at full transformation. These data will be integrated within a statistical and bioinformatics framework to provide an incredibly rich dataset on how proteins, microRNAs and mRNAs interact in this system. We will repeat the above with Marek's disease virus (MDV); however, we can only assay MDV at uninfected and tumour cells due to a lack of models of in vitro transformation. Finally, we will define the differential targetome of miR-155 and miR-M4 using an RCAS vector system, providing us with fine-grained data on the effects of miR-155 and miR-M4 on gene expression, their similarities and differences. These data combined will allow us to build a model of virus-induced transformation, and to compare and contrast the pathways used by REV and MDV.
Planned Impact
The beneficiaries of this research will include academic scientists, the poultry industry sector including the poultry breeding companies (e.g. Aviagen) and vaccine production companies (Pfizer Animal Health), farmers and the general public. Global demand for food is rising, both as a result of population growth and due to dietary changes in developing countries. A UN FAO report on this issue forecasts that food production will need to increase by over 40% by 2030 and by over 70% by 2050. With close to 55 billion chickens reared annually, poultry meat and eggs dominate animal protein products for human consumption world-wide. In the UK, the poultry sector is thought to contribute around £3.4 billion to the economy. Compared to the other livestock sectors, the modern poultry production methods have the most efficient feed-to-meat conversion ratios with lowest global warming potential. Because of these attributes, the poultry production sector is likely to expand significantly to meet the global demand for food in the coming years. Marek's disease (MD) is also one of the major diseases of poultry which causes serious economic losses and the global estimate of losses from Marek's disease is approximately $2,000 million annually. Detailed understanding of the molecular basis of tumours induced by these viruses, as the current proposal aims to achieve, will benefit development of new strategies for control. Rapid-onset lymphomas induced by MD and REV are also good models for studying virus-induced lymphomas in other species including humans. For example, the pathways of B-cell transformation occur through the CtBP interaction, both in MDV and Epstein-Barr virus (EBV)-induced tumours. Similarly, both MDV and the human pathogen KSHV encode functional miR-155 homologues, and since there are no human models of KSHV-induced tumours, MDV system will be valuable.
Organisations
People |
ORCID iD |
Venugopal Nair (Principal Investigator) |
Publications
Yao Y
(2012)
Novel microRNAs encoded by duck enteritis virus.
in The Journal of general virology
Yao Y
(2013)
MicroRNA expression profiles in avian haemopoietic cells.
in Frontiers in genetics
Yao Y
(2014)
An avian retrovirus uses canonical expression and processing mechanisms to generate viral microRNA.
in Journal of virology
Yao Y
(2014)
Role of virus-encoded microRNAs in Avian viral diseases.
in Viruses
Yao Y
(2017)
Activation of gga-miR-155 by reticuloendotheliosis virus T strain and its contribution to transformation.
in The Journal of general virology
Mwangi WN
(2017)
Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling.
in The Journal of general virology
Description | Extensive data on transcriptome and the methylome of cell lines transformed by oncogenic viruses have been generated. The data on the molecular changes during reactivation of Marek's disease virus-transformed cells and virus replication in the feather follicle epithelium were determined by transcriptome and pathway analysis tools. |
Exploitation Route | The extensive set of data are being analysed for publication and deposition in the public databases. These data will be useful for further research and submitting grant applications. |
Sectors | Agriculture Food and Drink |
Description | Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development |
Amount | £440,000 (GBP) |
Funding ID | BB/R007896/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2018 |
End | 03/2021 |
Description | AN INTERVIEW WITH PROFESSOR VENUGOPAL NAIR |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Professor Venugopal Nair is a Research Group Leader at The Pirbright Institute, a visiting Professor of Avian Virology at the Department of Zoology, and a Jenner Investigator at the Jenner Institute, University of Oxford. He is also a member of the Microbiology Society, and in this interview, he tells us more about his research into viral diseases of livestock. |
Year(s) Of Engagement Activity | 2020 |
URL | https://microbiologysociety.org/membership/meet-our-members/focus-area-viruses/an-interview-with-pro... |
Description | Chaired the Poultry Disease group meeting |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Poultry Disease group is a forum of veterinary practitioners to discuss the advances in poultry diseases that could be translated from research labs to the farms |
Year(s) Of Engagement Activity | 2017 |
Description | Poultry Health Course (Pirbright) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The course is organised for participants from Brazil to understand the current advances in poultry diseases. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.poultryhealthcourse.com/ |
Description | Presentation on the effects on oncogenic virus infection at the Veterinarian's Forum, Namakkal, India on 29 Dec 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | The purpose of the engagement was to update the practicing poultry veterinarians on the problems with oncogenic virus diseases and methods of control. The meeting attended by nearly 100 veterinarians was very informative and ended with a long discussion on the challenges and innovations |
Year(s) Of Engagement Activity | 2018 |
Description | UK-Malaysia Vaccinology Workshop (Malaysia) |
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 | This workshop aimed to build long-term and sustainable links between scientists in the UK and Malaysia working on/have interests in veterinary vaccines. This workshop has encouraged early career researchers from veterinary, biological and social sciences to understand the ever-increasing threats to global food security from infectious animal diseases and their control using next generation vaccine strategies. |
Year(s) Of Engagement Activity | 2016 |
URL | http://ukmalaysiaworkshop.co.uk/ |
Description | V Nair invited to talk on 'Cell type- and disease stage-specific interactions of Marek's disease virus & the host' at the International Symposium on Marek's disease and avain herpesiviruses at Yangzhou, China during 29th July to 2nd Aug 2018 |
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 | Most recent updates in the field of avian herpesvirus research was discussed and active engagements for future collaborations discussed |
Year(s) Of Engagement Activity | 2018 |