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O'Donnell Group

O'Donnell Group
O'Donnell Group
Valerie O'Donnell
Honorary Group Leader
O'Donnell Group

Research Summary

Valerie is an Honorary Group Leader, currently based at the the . She is working with Group Leaders in the Signalling Programme. Valerie’s research is focused on the study of bioactive lipids in circulating blood cells, particularly platelets.  She uses mass spectrometry to identify and characterise new signalling mediators. Since 2007, her group identified large families of lipids made by platelets, neutrophils and monocytes, and demonstrated that these are involved in innate immunity, blood clotting, cardiovascular disease and infection. Translational studies have established a role for these lipids in human thrombotic disease. 

She has developed new methods to quantify aminophospholipids at the platelet surface, for example molecular species of amino-phospholipids and oxidized phospholipids that comprise the pro-coagulant surface, which is essential for blot formation.  She leads/led a programme grant from British Heart Foundation (renewed 2020), and was an ERC Advanced Grant holder (2014-2019). Since 2017, she has been co-lead of LIPID MAPS, a multi-site Biomedical Resource supporting databases, tools, nomenclature and curation of lipids, funded by Wellcome Trust (>66K users, with Edward Dennis and Shankar Subramaniam (UCSD), Simon Andrews and Andrea Lopez, ò, and Bill Griffiths, Swansea).

She was Co-Director of the Systems Immunity Research Institute, Cardiff University from 2016-2020. She is co-investigator on an EU Marie Curie ITN (ArthritisHeal, Leiden), an EU Cost Network (EpiLipidNET) and an MRC Partnership Grant (MAP/UK, Imperial), and an Associate Group Lead at UK Dementia Research Institute (UKDRI) at Cardiff University. 

Latest Publications

Open Access
Conroy MJ, Andrews RM, Andrews S, Cockayne L, Dennis EA, Fahy E, Gaud C, Griffiths WJ, Jukes G, Kolchin M, Mendivelso K, Lopez-Clavijo AF, Ready C, Subramaniam S, O'Donnell VB Signalling , Lipidomics

LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.

+view abstract Nucleic acids research, PMID: 37855672

Sarmad S, Viant MR, Dunn WB, Goodacre R, Wilson ID, Chappell KE, Griffin JL, O'Donnell VB, Naicker B, Lewis MR, Suzuki T, Signalling

Targeted metabolite assays that measure tens or hundreds of pre-selected metabolites, typically using liquid chromatography-mass spectrometry, are increasingly being developed and applied to metabolic phenotyping studies. These are used both as standalone phenotyping methods and for the validation of putative metabolic biomarkers obtained from untargeted metabolomics studies. However, there are no widely accepted standards in the scientific community for ensuring reliability of the development and validation of targeted metabolite assays (referred to here as 'targeted metabolomics'). Most current practices attempt to adopt, with modifications, the strict guidance provided by drug regulatory authorities for analytical methods designed largely for measuring drugs and other xenobiotic analytes. Here, the regulatory guidance provided by the European Medicines Agency, US Food and Drug Administration and International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use are summarized. In this Perspective, we have adapted these guidelines and propose a less onerous 'tiered' approach to evaluate the reliability of a wide range of metabolomics analyses, addressing the need for community-accepted, harmonized guidelines for tiers other than full validation. This 'fit-for-purpose' tiered approach comprises four levels-discovery, screening, qualification and validation-and is discussed in the context of a range of targeted and untargeted metabolomics assays. Issues arising with targeted multiplexed metabolomics assays, and how these might be addressed, are considered. Furthermore, guidance is provided to assist the community with selecting the appropriate degree of reliability for a series of well-defined applications of metabolomics.

+view abstract Nature protocols, PMID: 36828894

Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M Signalling , Bioinformatics , Lipidomics

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

+view abstract Nature methods, PMID: 36543939

Group Members

Valerie O'Donnell

Honorary Group Leader