Defining the role of Death Associated Protein Kinase 1 in cell fate using genomic and proteomic analysis

Lead Research Organisation: University of Reading
Department Name: Pharmacy

Abstract

Project Overview: Death associated protein kinase 1 (DAPK1) is key regulator of cell fate in human cells, acting as a control point for autophagic cell death, and has been implicated in cancer and neurodegneration. Despite two decades of research, the molecular pathways coordinated by DAPK1 remain poorly defined.

The aim of this project is to use new advances in genomic and proteomic technology, coupled with novel insights into the enzymatic function of DAPK1, to dissect the pathways downstream of this protein. This will, in turn, help define the cellular role of this important protein and aid in the development of new drugs to modulate DAPK1.

This four year studentship, funded by an Industrial CASE award from the BBSRC, will be based partly at the University of Reading School of Pharmacy and partly at BC platforms, a leader in the field of bioinformatics. The student will use cellular and biochemical methods to characterise DAPK1, leading on to genomic and proteomic analysis of the cellular impact of modulating the enzymes activity. Bioinformatic investigation of the latter will be carried out with BC platforms, providing industry experience. During the course of the PhD, the student will have the opportunity to register for a Certificate in Business Administration at Henley Business School, part of the University of Reading.

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M017222/1 01/10/2015 30/09/2019
1644051 Studentship BB/M017222/1 01/10/2015 30/09/2019 James Tomkins
 
Description Current progress from this studentship has included the further development of a bioinformatic pipeline to utilise protein-protein interaction data that is already available in the public domain for constructing protein interaction networks. This approach has been complemented by integration of novel data to prioritise interactors for further validation. We have identified numerous common and distinct protein interactors of the human ROCO proteins and provided functional associations.
Exploitation Route We are aiming for the pipeline we've developed to be become a publicly available resource for others to use. The results we have presented in our recent publication will provide the foundation for other researchers interest in the ROCO protein interaction network, more also more broadly, researchers interested in data integration approaches for explore protein interaction landscapes.
Sectors Pharmaceuticals and Medical Biotechnology

URL http://onlinelibrary.wiley.com/doi/10.1002/pmic.201700444/abstract
 
Title PINOT 
Description PINOT (Protein Interaction Network Online Tool) is an open access we resource for querying protein interaction data curated into molecular interaction repositories. The pipeline processes data and provides confidence scoring for each protein protein interaction. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact Ongoing analysis for several projects 
URL https://doi.org/10.1101/788000
 
Description Eva Kevei 
Organisation University of Reading
Department School of Biological Sciences Reading
Country United Kingdom 
Sector Academic/University 
PI Contribution Developing C. elegans models for investigating DAPK-1
Collaborator Contribution Provided lab environment and expertise for C. elegans research
Impact Thesis chapter
Start Year 2018