MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
biorxiv(2023)
Abstract
Interactions between proteins and metabolites are key for cellular function, from the catalytic breakdown of nutrients to signaling. An important case is cell-cell communication, where cellular metabolites are secreted into the microenvironment and initiate a signaling cascade by binding to an intra- or extracellular receptor of another cell. While protein-protein mediated cell-cell communication is routinely inferred from transcriptomic data, for metabolite-protein interactions this is challenging due to the limitations of high-throughput single-cell and spatial metabolomics technologies, together with the absence of comprehensive prior knowledge resources that include metabolites. Here we report MetalinksDB, a comprehensive and flexible database of intercellular metabolite-protein interactions that is a magnitude larger than existing ones. MetalinksDB can be tailored to specific biological contexts such as diseases, pathways, or tissue/cellular locations by querying subsets of interactions using the web interface ( ) or the knowledge graph adapters. We showcase the use of MetalinksDB by identifying deregulated processes in renal cancer patients from multi-omics data as well as inferring metabolite-mediated cell-cell communication events driving acute kidney injury from spatial transcriptomic data. We anticipate that MetalinksDB will facilitate the study of metabolite-mediated communication processes.
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### Competing Interest Statement
J.S.R. reports funding from GSK, Pfizer, and Sanofi, and fees/honoraria from Travere Therapeutics, Stadapharm, Astex, Pfizer, and Grunenthal.
[1]: pending:yes
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