Regulation of protein stability by lysine hydroxylation

Cells control the rates and extent to which 'worker' proteins are produced and eliminated as a means to control physiological processes, including development and ageing. To distinguish proteins to be retained from those to be disposed of, cells use a code of alterations to proteins known as post-translational modifications (PTMs). When something goes wrong in such a complex and intricate set of processes it can lead to disease. While a number of PTMs have been characterized, many others remain to be discovered and their biological functions remain elusive. In the Fellowship, I will use a combination of biochemical, biophysical and cellular studies to shine light on an unprecedented and recently-identified PTM involving atmospheric oxygen. The results will help us to understand how cells determine protein lifetimes as a function of their environment.

Cells regulate protein homeostasis, i.e. synthesis and degradation rates, in response to external stimuli. Because of their central role in healthy human development and emerging relevance as therapeutic targets, it is important to understand such regulatory mechanisms at the molecular level. I propose to carry out research which will illuminate novel mechanistic links between dioxygen mediated posttranslational modifications (PTMs) and protein homeostasis. Investigations will focus initially on the replication stress response regulator SDE2, which is involved in pre-mRNA splicing and DNA damage response. SDE2 undergoes proteolytic cleavage at a strictly conserved GGKGG motif immediately downstream of its ubiquitin-like domain, likely catalysed by a deubiquitinase enzyme. This processing reveals a C-terminal domain (SDE2-C) that is rapidly degraded inside cells. Notably, SDE2-C contains features of an N-degron, including the presence of destabilizing N-terminal lysine residue. I hypothesize a mechanistic link between dioxygen mediated PTMs of N-end rule processed proteins and protein homeostasis. The proposed fellowship work involves fundamental studies to test this hypothesis and hence define new regulatory pathways of protein stability and function.

I am committed to ensuring that taxpayer-funded research as in the work proposed here achieves maximal impact both in terms of translating fundamental research to the benefit of public health and improving the UK economy. I see my work as early-stage fundamental research in biosciences with potential to reveal new targets and mechanisms and discoveries with unforeseen future applications to advance benefits for society e.g. in drug discovery. My approach is therefore to maximize opportunities to exploit such benefits. In some cases securing IP on inventions arising from this research may enable wider exploitation of the outputs of my work in the most efficient and productive ways. In other circumstances it may be that not filing a patent application will best enable impact onto the wider community.

Targeting protein homeostasis through modulation of ubiquitin-mediated post-translational protein degradation is currently being investigated as one of most exciting therapeutic area. For example, proteasome inhibitors and the cereblon-modulator lenalidomide are frontline drugs in hematological malignancies such as multiple myeloma. While efficacious, they have limitations (including lack of activity in solid tumours; development of resistance to treatment in patience, leading to relapse), thus creating an unmet need for alternative therapeutic agents with equal or superior efficacy that target post-translational protein homeostasis pathways. Given the current spur of interest in targeting protein degradation pathways e.g. using DUB inhibitors and degraders (also known as PROTACs), revealing new targets and mechanisms for intervention to control intracellular protein levels will be of wide interest. There is therefore the potential for the outlined research to lead directly to patentable or otherwise commercially exploitable reagents, tools, concepts and targets, which may form the basis for the development of new therapeutic strategies, ultimately impacting patients in future.

Specific tasks I will carry out to enable and maximize impacts are (see also academic beneficiaries):
1. Publish original research papers in leading academic journals
2. Disseminate findings at multiple appropriate academic conferences
3. Explore opportunities for new intellectual property of commercial value
4. Develop solid skills in multi-disciplinary research, communication and collaborative skills that will help me and colleagues, in the long run, to become a better independent research and contribute to scientific and economic progress
5. Communicate findings to the public at regular public engagement events held within the University of Oxford science departments. I will also actively participate in "Open Doors" activities, where my research can be showcased to people in the community, and where I can provide "hands-on" activities for children (and adults) and give tours of the laboratories.
6. I will alert the University and the BBSRC Press Offices, where appropriate, to disseminate key findings arising from my research to a lay audience, nationally and internationally.

In summary, my proposed research will likely benefit a wide range of academic and industrial scientists, the biopharma industry in the UK and beyond, and potentially patients in the long run.