Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum

Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.

Automated summary

Omics study, including proteomics, lipidomics, and metabolomics, allows us to understand the molecular modifications in living organisms in response to contaminants or in different physiological conditions. However, individual omics only provides a partial image of the biological complexity. To obtain comprehensive omics information from a single sample, a specific sample preparation method needs to be optimized. This study developed a biphasic extraction procedure using a MTBE/Methanol mixture to simultaneously extract polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses. The method was applied to study the reproductive cycle of female amphipod Gammarus fossarum, and multivariate data analyses were used to integrate the multi-omics datasets and identify molecular signatures specific to different stages.