AbstractExtracellular vesicles have emerged as crucial components in the advancement of liquid biopsy. However, the efficient isolation of molecularly defined subpopulations remains challenging, limiting the performance of liquid chromatography−tandem mass spectrometry (LC−MS/MS)-based metabolomic analysis. In this study, HER2-targeting peptides were identified via phage display screening against the extracellular domain of HER2 and used to construct a peptide-directed magnetic separation platform (SA@HER2-2-MPMs) for the rapid and selective enrichment of HER2-positive extracellular vesicles. The biotinylated peptide enabled the specific recognition of HER2-enriched EVs’ membranes, while streptavidin-functionalized magnetic polystyrene microspheres facilitated their efficient capture and magnetic separation. The enriched extracellular vesicles were subjected to subsequent metabolite extraction and LC−MS/MS analysis, forming the basis of an integrated workflow for subtype-specific extracellular vesicles isolation and metabolomic profiling. Compared with UC preparations, the peptide-directed workflow yielded lower measured concentrations of selected plasma-associated contaminants and supported downstream LC−MS/MS profiling. Metabolomic analysis revealed disease-associated alterations, and an exploratory predictive reanalysis using nested cross-validation and a held-out internal subset showed high within-cohort discrimination. This study establishes a peptide-directed strategy for isolating molecularly defined EV subpopulations and provides a platform for exploratory metabolic biomarker discovery in HER2-positive breast cancer; independent external validation remains required.

Advancements in in vivo stable isotope tracing have revolutionized our understanding of cancer metabolism, transitioning the field from static metabolomic snapshots to dynamic metabolic pathway activities. However, interpreting raw fractional enrichment data presents significant biological and analytical challenges. This review systematically examines the methodological landscape of in vivo tracing, addressing the interpretive gap created by clinical constraints, such as single-timepoint surgical sampling. We dissect how secondary circulating tracers and the inherent heterogeneity of the tumor microenvironment can confound metabolic signals. We highlight the critical transition to metabolic flux analysis as the requisite computational step to overcome these challenges and to identify targetable metabolic vulnerabilities in precision oncology.

The Mediterranean diet (MedDiet) reduces cardiovascular disease, type 2 diabetes, and other chronic diseases. Adherence has mainly been assessed using self-reported questionnaires, and no previous stu...

Microbial inoculants reshape cherry tomato fruit metabolome and boost quality traits · Subject of Research: Metabolomic profiling of cherry tomato

Microbial inoculants reshape cherry tomato fruit metabolome and boost quality traits · Subject of Research: Metabolomic profiling of cherry tomato

Compost produced from biowaste has a defined microbiota, and some bacterial species may represent promising resources for low-input crop systems. However, their effects on plant physiology are poorly investigated and remain difficult to predict from standard bacterial traits alone. We isolated several bacterial strains (Bacillus sonorensis, Glutamicibacter arilaitensis, and Kocuria rhizophila) from biowaste compost and examined their early effects on tomato seedlings under controlled in vitro conditions. Responses were assessed by root phenotyping, root and shoot transcriptomics, and mass spectrometry-based profiling of primary metabolites in plant tissues, root exudates and bacterial culture filtrates. B. sonorensis induces the broadest response, reducing primary root length and lateral root number and density and triggering broad transcriptional changes related to metabolism, redox balance, hormone signalling and defence-associated pathways. G. arilaitensis elicits a more selective, tissue-dependent response, whereas K. rhizophila has limited phenotypic and transcriptional effects at this stage. All isolates reshape primary metabolism, with recurrent effects on amino acid-, carbohydrate- and lipid-related pathways, together with isolate-specific changes in root exudate composition. This study characterises the early molecular and metabolic responses of tomato to compost-derived bacteria and identifies common and strain-specific physiological signatures that provide a foundation for future studies under biotic and abiotic stress.

A metabolomic and 16S rRNA study of captive Amur tigers found 169 metabolites differing significantly across subadult, adult and old animals fed an identical diet.

The Mediterranean diet (MedDiet) reduces cardiovascular disease, type 2 diabetes, and other chronic diseases. Adherence has mainly been assessed using…

Read the full paper: Optimization and Metabolomic Profiling of Wolffia globosa Extract Reveal Multitarget Neuroprotective Activity Against Alzheimer’s Disease with In Vitro, In Silico, and In Vivo Validation

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Targeted metabolomics of gill and mantle tissues from five marine bivalve species spanning lifespans from approximately 30 to over 500 years revealed longevity-associated metabolic signatures. Longer....