Dr Clare Davies

Supervisor Details

Contact Details

Institute of Cancer and Genomic Sciences, University of Birmingham

Scientific Background

Arginine methylation – a new player in cancer pathogenesis

Protein modifications expand the functional diversity of the proteome enabling dynamic modulation of cellular processes, but are often deregulated during cancer pathogenesis. Arginine methylation, catalysed by protein arginine methyltransferases (PRMTs), was identified over 45 years ago, however the significance of this modification for oncogenesis and malignant progression is only just becoming apparent. In particular, expression of many PRMTs correlates with a poorer cancer prognosis and has thus attracted significant attention as a novel drug target. Despite this potential, the mechanisms by which PRMTs contribute to cancer progression is largely unknown. The Davies lab aims to increase our understanding into the biology of PRMTs and arginine methylation. Using breast cancer as a model, the questions we are currently addressing are:

How is PRMT5 regulating the DNA damage response?
What is the mechanism by which PRMT5 controls the function of breast cancer stem cells?
Do PRMTs initiate and/or facilitate cancer progression and can a cancer arginine methylome be identified?

To address all of these questions, the Davies lab takes a multidisciplinary approach that includes molecular and cell biology, flow cytometry, quantitative proteomics, protein biochemistry (methylation assays, immunoprecipitations), genomic analysis (RNA-Seq and ChIP-Seq), single cell analysis, analysis of patient sample by IHC and functional assays, microscopy and animal models of cancer (genetically engineered, cell line xenografts and patient-derived xenografts (PDXs)).

Research Groups

The Davies Laboratory

Supervision Style

In three words or phrases: supportive, organised, goal-driven.

Provision of Training

Technical training will be supervised by a member of the team who is an expert on that technique. We follow the 3-step approach: (1) demonstrate the assay; (2) watch you do the assay; (3) let you have a go independently with team members at hand. As time progresses, I would expect you to be able to troubleshoot methodology and think independently, all part of the training process!

Progression Monitoring and Management

We will have a weekly one to one meeting on a Monday. At the start, I will help you plan your week, but as time goes on your will come with your planner and we will discuss what has been completed and what needs to be the next step. The one-to-one meetings are also an opportunity for you to describe your results to me (I can see if this is correct, and what has been missed), so this helps with training into data interpretation. We can also discuss your own ideas and ways in which to approach the question. I also have high expectations, and will try and develop you to your full potential.

Communication

The team has a Slack group chat with which we regularly communicate during the week. Whilst I expect you to keep up with my/ team communications I will expect you to manage your work/life balance. I am known to email my team/PhD students at all hours of the day and night, however I will not expect you to do the same or respond immediately. I take mentorship seriously, and I am happy to discuss any issues that are impacting your ability to fulfil your potential or my/our expectations.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once a week

In year 1 of PhD study

At least once a week

In year 2 of PhD study

At least once a week

In year 3 of PhD study

At least once a fortnight

These meetings will usually be face to face. I am usually contactable for an instant response on every working day.

Working Patterns

The timing of work in my lab is flexible, and other than attending pre-arranged meetings, I expect students to manage their own time. However, it is recommended that the student is in the lab during core hours as to be able to interact with other lab members. Working at weekend and late at night may also be required, depending on the experiments.

Notice Period for Feedback

I need at least 2 week’s notice to provide feedback on written work of up to 5000 words.

Project Details

Dr Davies is the supervisor on the below project:

Functional and mechanistic investigations into the importance of PADI enzymes for DNA repair

Secondary Supervisor(s): Prof Jo Morris

University of Registration: University of Birmingham

BBSRC Research Themes:

Understanding the Rules of Life (Structural Biology)
Integrated Understanding of Health (Ageing, Pharmaceuticals)

No longer accepting applications

Project Outline

The ability for a cell to repair damaged DNA is incredibly important for maintaining genome stability. An inability to do so leads to mutagenic events that can predispose individuals to neurological disease and cancer. Whilst our knowledge into the key proteins plays in various DNA repair pathways has increased dramatically, it is becoming apparent that protein post-translational modifications play an integral role. Current thinking is that these modifications act as a platform, promoting protein complex assembly and disassembly, modulating enzymatic activity, and signaling pathway choice.

The amino acid arginine is targeted for methylation by the PRMT family of enzymes, and the Davies lab has recently described a role for PRMT5 in the DNA damage response (Clarke et al., Molecular Cell, 2017). Interestingly, arginine is also targeted by a second family of enzymes called PADIs (peptidylarginine demininases). Here, PADIs post-translationally convert positively charged arginine in substrate proteins to the neutral nonessential amino acid citrulline, a process referred to as citrullination. Surprisingly, very little is known about PADI enzymes for DNA repair even though PADI2 and PADI4 levels are elevated in cancer possibly leading to chemoresistance. Top-down mass spectrometry screens for the protein citrullinome has identified an enrichment of DNA repair proteins. Supporting this, we now have data that PADI enzymes are indeed important for maintain genome stability. However, the mechanisms by which this occurs, the specific type of DNA repair pathway that required PADI activity, or the substrates they citrullinate are still unknown.

In this PhD studentship, we will address the following important questions:

Are PADI2/PADI4 driving a specific DNA repair pathway? Achieved thought specific PADI2 and PADI4 inhibitors, in parallel with CRISPR-mediated PADI2/PADI4 knockout and overexpression studies after ionising radiation (double strand breaks), MMC (interstrand crosslinks/FA pathway), HU/Aphidicolin (replication stress) and campothecin (Top1 cleavage complex). Methodologies include colony survival assays, DNA damage induction as measure by gH2AX and 53BP1 foci, DNA fibre analysis, signalling pathway activation (western blotting).
Which DNA repair proteins are citrullinated after DNA damage? Using probes that specifically detect citrullinated proteins, we will conduct Mass Spectrometry after DNA damage in wildtype or PADI2 or PAD4 knockout cells.
How does how citrullination of a DNA repair protein affects its function? Taking proteins identified from question 2, we will map the citrullination sites (by mass spec) and conduct in silico structural analysis to understand how arginine-citrulline conversion affects structure. Genetic engineering of mammalian cells to express a photo-activated site-specific incorporation of citrulline will establish in vivo relevance.

Given that PADI inhibitors are currently being explored for the treatment of inflammatory disease, understanding how PADIs contribute to DNA repair and genome stability could lead to drug repurposing in combination with conventional DNA damaging chemotherapies, in PADI2/4 overexpressing cancers

References

Protein Arginine Deiminases (PADs): Biochemistry and Chemical Biology of Protein Citrullination. Mondal S, Thompson PR.Acc Chem Res. 2019 Mar 19;52(3):818-832. doi: 10.1021/acs.accounts.9b00024. Epub 2019 Mar 7.PMID: 30844238
Insights into peptidylarginine deiminase expression and citrullination pathways.Yu K, Proost P.Trends Cell Biol. 2022 Sep;32(9):746-761. doi: 10.1016/j.tcb.2022.01.014. Epub 2022 Feb 21.PMID: 35197210

Techniques

Cell culture, siRNA knockdown, drug treatments.
Molecular cloning including site-directed mutagenesis.
CRISPR-Cas9-mediated gene editing.
Lentiviral infections to generate cell lines.
Colony survival assays.
Immunofluorescene of DNA damage foci.
DNA fibre analysis.
Western blotting.
Immunoprecipitations.
Mass Spectrometry and associated analysis.
In silico structural analysis.
Photoactivatable citrulline incorporation in mammalian cells.
In silico structure analysis.