Phosphorylation is a vital cellular regulatory mechanism. Alterations in phosphorylation are major contributors to disease, and numerous clinically-important drugs target kinases to treat cancer and other disorders. Acquired resistance to these therapies can arise by rewiring of kinase pathways. Characterising signalling networks is therefore crucial to delineate changes in disease, to improve predictions of drug efficacy and patient response to targeted therapies, to understand resistance, and to identify biomarkers and diagnostics. To this end, Kinomica offers mass-spectrometry-based and computational services that interrogate thousands of phosphorylation sites and elucidate large phosphoproteomic networks.
Although thousands of phosphorylation sites are known, identifying the kinases for particular phosphorylation events is a major roadblock. This hinders understanding of signalling changes in disease and, for Kinomica, means that the depth of their phosphoproteomic datasets cannot be fully exploited. To address these problems, we recently developed a method (“KiPIK”) to identify kinases for specific phosphorylation sites that uses libraries of kinase inhibitors that have been profiled on near-kinome-wide panels of protein kinases. The inhibition profile for each kinase provides a ‘fingerprint’ that allows unknown kinases acting on target phosphosites in cell extracts to be identified. The method has clear advantages over in silico and genetic screening, and we have validated it on diverse kinase-phosphosite pairs (Watson et al. 2020). It has potential reveal kinase pathway rewiring in disease, particularly cancer, and perhaps to reveal therapeutic targets in individual patients. However, a remaining question is whether KiPIK can unambiguously identify kinases for phosphorylation sites of kinases with related consensus motifs.
This is a collaborative project supervised by Prof Jonathan Higgins (Newcastle), Prof Pedro Cutillas (Kinomica and Queen Mary University of London), and Dr David Britton (Kinomica). You will identify suitable known phosphorylation sites (eg target motifs of basophilic kinases; R/K-x-x-x-x-S/T, R/K-x-x-S/T and R/K-x-R/K-x-x-S/T) and test whether KiPIK can distinguish kinases for related consensus sites. You will use KiPIK to identify candidate kinases for phosphorylation sites commonly present in Kinomica’s datasets for which the corresponding kinase(s) are unknown, and validate them using cell biological approaches. You will visit Kinomica within year 1 to learn about their technology and business, and to identify additional targets for study, and then later for an extended period to integrate knowledge from the CASE project.
The project provides training in both bench science and quantitative skills, allowing you to develop interdisciplinary skills essential for a career in academia, industry, and beyond. You will learn human cell culture; kinase assays and high-throughput inhibitor screening assays; mass spectrometry and proteomics; cell biological approaches such as RNA interference, CRISPR, inhibition studies, and live and fixed cell microscopy; statistical analysis and the basics of AI/machine learning.
Success will validate KiPIK as a platform for fundamental and disease-based research, allowing the elucidation kinase signalling and pathway rewiring in disease, and will increase the information provided by Kinomica’s technologies.
Lab links:
Jonathan Higgins: https://www.ncl.ac.uk/medical-sciences/people/profile/jonathanhiggins.html
Pedro Cutillas and David Britton: https://kinomica.com/about-kinomica/meet-the-team/
Pedro Cutillas: https://www.bartscancer.london/staff/professor-pedro-cutillas/
Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme and how to apply can be found on our website:
http://www.dimen.org.uk/how-to-apply/application-overview
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