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Taking control of cancer-associated splicing switches

   Department of Eye and Vision Science

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  Dr K Hamill  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

In cancer, numerous changes to protein expression occur. Some of these are the result of changes to gene transcription or mRNA degradation rates, however, it has increasingly apparent that changes to alternative splicing profile are a key driver of cancer progression. Alternative splicing leads to different protein isoforms being generated from the same parent gene. In many cases the alternative isoform has opposing functions to that of the isoform that is predominantly expressed, therefore cancer associated dysregulation of gene splicing can lead to increased proliferation, invasion, migration, evasion from apoptosis and remodelling of the tumour microenvironment. Alternative splicing can also be one the reasons behind changes to mRNA stability and therefore can directly affect protein abundance.
Of particular interest to our research group is a specific type of alternative splicing termed alternative polyadenylation. Most mRNAs end at a polyA site at their 3’ untranslated region. However, recent data suggest that polyadenylation can happen at more than one site depending on conditions in the cell at the time of production. Changes to where a mRNA is polyadenylated can have dramatic effects. Using different polyA site can lead to the loss or gain of micro RNA (miRNA) seed regions or protein binding sites which in turn changes the amount of protein produced from the transcript or where that protein is produced.

The interest in alternative polyadenylation doesn’t end at the 3’ end of mRNAs. An increasing body of work, including our own, point toward an important role for intronic polyadenylation as a mechanism to either destabilise a gene (i.e. turn it off) or to generate short protein fragments which can have dominant negative effects.

In this project we will use a combination of unbiased transcriptomic approaches and hypothesis-driven molecular biology experiments to better understand the regulation of these cancer-associated splicing switches, focusing on the role of alternative polyadenylation in head and neck cancer progression.

The University of Liverpool is a world-leader in head and neck cancer. Using our extensive resource of patient samples and in collaboration with clinical and pathology experts in squamous cell carcinoma, we will carefully select a panel of patient material and perform 3’ sequencing to provide a comprehensive map of alternative polyadenylation and how that relates to patient outcome. We will cross-correlate these data with differential expressed gene analyses to identify how known and putative regulators of alternative polyadenylation correlate with the observed changes.

With our correlative data in hand, we will progress to a mechanistic understanding of the process. A subset of the transcripts identified as being alternatively polyadenylated will be selected for follow up in vitro. Again, using the wealth of resources available to us locally, we will characterise the changes in cells in a dish to identify the appropriate model system then perform systematic modification to candidate regulatory proteins and determine their effect. At the same time, we will make minigene and/or reporter constructs to further our understanding of the regulatory mechanism.

By understanding how the switches are regulated, we will be in a position to begin proof-of-concept analysis of potential RNA therapeutic interventions. These could take different forms depending on the outcomes of the initial results but are likely to involve morpholinos to change splicing/polyadenylation, miRNA mimics and inhibitors, and short-activating RNAs to regulate promoter activity.

Completion of these studies will represent a major advancement of our understanding of a deadly disease and a step toward a new treatment. They will also fundamentally improve our understanding of genetic regulation.

The techniques in which you will train in are highly transferrable and sought after in academia and industry. You will join a team of researchers working not only in molecular biology but also biochemistry, cell biology, transgenic and pre-clinical models, and you, therefore, will have support and guidance to develop the project in the direction the data suggest we should go and in the direction that best suits your personal development needs and career aspirations.

We are looking to appoint a highly motivated student with an undergraduate or Masters degree ideally with a strong genetics or genomics component, further training will be provided in all relevant areas.
Informal enquiries are encouraged.

Note that this is a non-funded studentship, students will be required to secure their own funding, however, we will help you with the application processes.

If you are interested in apply for this opportunity, then please contact Dr Kevin Hamill on [Email Address Removed]

Funding Notes

There is NO funding attached to this project.

The successful applicant will be expected to provide the funding for tuition fees and living expenses as well as research costs of £8,000 per year.

Further details of current fees can be found on the University of Liverpool website.
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