Situation
Dr. Kroon is an outstanding young investigator affiliated with Amsterdam UMC and the University of Amsterdam. His research focuses on vascular metabolism, specifically the role of metabolic alterations in driving blood vessel inflammation. The Kroon lab is particularly interested in the crosstalk between metabolism-driven inflammatory responses of the endothelium under hyperlipidemic conditions. They aim to understand this process to optimize the treatment of atherothrombotic cardiometabolic diseases.
Challenge
In 2022, Dr. Kroon had submitted a starting ERC grant proposal on unravelling how EC metabolism is affected in atherosclerosis, what the impact of this altered EC metabolism is for stem cell function in the bone marrow niche and for macrophage activation in the plaque. Dr. Kroon envisioned to employ multi-omics technologies to answer these questions, on which grant reviewers asked for clarifications.
Solution
Unicle helped Dr. Kroon to prepare a rebuttal to the reviewers and prepare for the final interview with the granting agency. Specifically, we worked out an experimental strategy for the bioinformatics work packages of the grant and generated proof-of-concept preliminary data. We performed data mining of public datasets by searching eight repositories with custom-tailored search filters (GEO, ArrayExpress, PRIDE, PubMed and several single cell data repositories).
In total, we reviewed 30,000+ datasets relevant to atherosclerotic disease, preselected 78 datasets for review by the Dr. Kroon, who ultimately selected 18 bulk and single cell transcriptomics datasets for integrative expression meta-analysis to identify novel therapeutic targets. This preliminary analysis revealed known, previously validated and entirely novel targets, demonstrating the feasibility and power of the proposed approaches of the Kroon lab.
Result
The Kroon lab was successfully awarded a starting ERC grant. Unicle then supported the Kroon lab to prepare for several follow-up grants in similar fashion. Moreover, the way of working with Unicle and the usage of the UniApp inspired Dr. Kroon to select the UniApp as cornerstone application in the newly founded lab. The UniApp is currently used for the various projects in the lab for data management, performing analysis, building publication-ready figures and to integrate results into storylines for (later) publications.
Key results
Successfull ERC grant application
Building bioinformatics capabilities
Stepping stone to follow-up projects
Unicle resources
When reviewing the quality and speeds of the preliminary data analysis ERC application: “This is absolutely amazing and sets ourselves on an even more defined path for the actual research“
Dr. Jeffrey Kroon
Principal Investigator, Vascular and Valve Inflammatory and metabolic responses, Amsterdam UMC
Background client and contact details
