Deciphering Organ-Specific Lipid Signatures in Zebrafish with a Spatial Lipidomics Pipeline

Author(s): Prateek Arora,Nick Kirschke,Simon Isofort,Mojgan Masoodi,Nadia Mercader

Affiliation(s): Institute of Anatomy, University of Bern, Bern, Switzerland



Spatial lipidomics analysis offers a powerful approach to understanding the lipid composition and distribution within biological tissues. In this study, we present a comprehensive pipeline utilizing Desorption Electrospray Ionization (DESI) mass spectrometry imaging to analyze the lipidomic profiles of zebrafish organs. Our methodology involves seamlessly integrating various R packages, including clustering from Cardinal, to delineate distinct organ regions and identify organ-specific lipid signals. These signals are further processed using the RforMassSpectrometry group of packages, including the MetaboAnnotation package for deisotoping, followed by annotation utilizing LipidMaps and HMDB. Our pipeline incorporates mechanisms to identify common lipid peaks across samples, fostering reproducibility and consistency in lipidomic analyses. Furthermore, by integrating differential analysis capabilities, we can identify significant alterations in lipid composition under varying experimental conditions, offering insights into biological responses and regulatory mechanisms. Using this approach, we have successfully established the first zebrafish heart-specific lipid signature, providing insights into the lipid composition of the organ. This study highlights the utility of spatial lipidomics in unravelling organ-specific lipid profiles and underscores its potential in understanding physiological processes in zebrafish and potentially other model organisms.