Journal: Cell

Article Title: TREM2 maintains microglial metabolic fitness in Alzheimer’s disease

doi: 10.1016/j.cell.2017.07.023

Figure Lengend Snippet: (A) Top most changed metabolites between WT and Trem2−/− BMDM cultured overnight in 10% LCCM. Defined as p≤0.01 and identified in the mouse metabolic network analysis in B.

Article Snippet: Polar metabolites were extracted according to General Metabolics protocol for extraction of polar metabolites from adherent mammalian cell culture.

Techniques: Cell Culture

Journal: Frontiers in Endocrinology

Article Title: Multiomics signatures of type 1 diabetes with and without albuminuria

doi: 10.3389/fendo.2022.1015557

Figure Lengend Snippet: Differentially abundant circulating metabolites and microbiome origin and functionality assessment. Summary of the circulating metabolites and lipids data integrated with gut microbiome origin and functionality in the T1D vs healthy controls comparison. The two heatmaps display significantly contrasted (FDR < 10%) polar metabolites (left) and lipid clusters (right) between T1D and healthy individuals. Column 1 (red green of each of the two heatmaps shows the Cliff’s Delta effect size for the clinical group comparison, ordered from higher to lower abundance in T1D individuals and colored from red (higher) to green (lower) gradient depending on its relative abundance in T1D individuals. Column 2 (black-white) shows the usefulness of the metabolite for discrimination between T1D and healthy individuals based on Area Under the Curve (AUC) analyses. The black-to-white-to-black gradient for AUC depicts assessment ability with 50% being uninformative AUC, 0% being the limit for the identification of healthy individuals and 100% being the limit for identification of T1D individuals. Column 3 (purple white) depicts relationship between the metabolites and bacterial QMP counts (absolute MGS abundance). Cells are colored if there is any significant association with metabolite levels (based on LASSO modelling) and the white-to-purple color gradient depicts the explained variance by the microbiome. Column 4 (purple white) depicts the relationship between the circulating metabolites and functional abundance of GMMs. Cells are colored if there is any significant association with metabolite levels (based on LASSO modelling) and the white-to-purple color gradient depicts the explained variance by the microbiome metabolic potential (or functionality).

Article Snippet: From the factorization results, we observed that the lipidomics dataset explained a major part of the factors composition (~50% variance), followed by the polar metabolites, bioclinical variables, and the functional bacterial profiling (GMM) of the gut microbiome (~30% of factor’s variance) ( ).

Techniques: Comparison, Functional Assay

Journal: Cancers

Article Title: Space- and Time-Resolved Metabolomics of a High-Grade Serous Ovarian Cancer Mouse Model

doi: 10.3390/cancers14092262

Figure Lengend Snippet: Metabolite annotations for the 14 selected features in the HILIC dataset. Proposed metabolite annotation, experimental monoisotopic m / z value, elemental formula, chromatographic retention time (min), mass error (ppm), main adduct type detected, abundance log-transformed fold changes, and metabolite annotation confidence level are shown. Fold changes were calculated as the base 2 logarithm of the average abundance ratios between TKO and TKO controls in the 37–60 %lifetime group. Positive values indicate higher levels in TKO serum samples and negative values indicate lower levels in TKO serum samples compared to TKO controls. The confidence level for metabolite annotation was assigned as (1) exact mass, isotopic pattern, retention time, and MS/MS spectrum of a chemical standard matched to the feature. (2) exact mass, isotopic pattern, retention time, and MS/MS spectrum matched to an in-house spectral database or literature spectra (3) putative ID assignment based only on elemental formula match. (4) unknown compound. Compound classes are provided for features with low annotation confidence levels.

Article Snippet: Isotopically labeled polar metabolite standards ( ) were purchased from Cambridge Isotope Laboratories (Tewksbury, MA, USA) and were used to prepare the internal standard mixture for HILIC experiments.

Techniques: Hydrophilic Interaction Liquid Chromatography

Journal: Cancers

Article Title: Space- and Time-Resolved Metabolomics of a High-Grade Serous Ovarian Cancer Mouse Model

doi: 10.3390/cancers14092262

Figure Lengend Snippet: Optimized discriminant lipid panel for early stage HGSC. Variables were selected using a genetic algorithm (GA) for optimum discrimination of 37–60 %lifetime TKO and TKO control samples. Proposed metabolite annotation, experimental monoisotopic m / z value, elemental formula, chromatographic retention time (min), mass error (ppm), main adduct type detected, abundance log-transformed fold changes, and metabolite annotation confidence level are shown. Fold changes were calculated as the base 2 logarithm of the average abundance ratios between TKO and TKO controls in the 37–60 %lifetime group. Positive values indicate higher levels in TKO serum samples and negative values indicate lower levels in TKO serum samples compared to TKO controls. The confidence level for metabolite annotation was assigned as (1) exact mass, isotopic pattern, retention time, and MS/MS spectrum of a chemical standard matched to the feature. (2) exact mass, isotopic pattern, retention time, and MS/MS spectrum matched to an in-house spectral database or literature spectra (3) putative ID assignment based only on elemental formula match. (4) unknown compound. Abbreviations: DG: Diacylglycerols, TG: Triacylglycerols, FA: Fatty acids, HexCer: Hexosylceramides, LPC: Lysophosphatidylcholines, LPE: Lysophosphatidylethanolamines, PC: Phosphatidylcholines, PC-O: Ether phosphatidylcholines, PE: Phosphatidylethanolamines, PE-O: Ether phosphatidylethanolamines, PI: Phosphatidylinositols, PS: Phosphatidylserines, SiE: Stigmasterol ester, Cer: Ceramides, and SM: Sphingomyelins.

Article Snippet: Isotopically labeled polar metabolite standards ( ) were purchased from Cambridge Isotope Laboratories (Tewksbury, MA, USA) and were used to prepare the internal standard mixture for HILIC experiments.

Techniques: Control

Journal: Cancers

Article Title: Space- and Time-Resolved Metabolomics of a High-Grade Serous Ovarian Cancer Mouse Model

doi: 10.3390/cancers14092262

Figure Lengend Snippet: Pathway analysis showing key metabolic alterations observed in TKO mice. Metabolites and lipid classes associated with HGSC development are represented as solid symbols and colored based on their corresponding pathway. Intermediates connecting the pathways are shown in grey text. Blue arrows pointing downwards indicate the metabolite showed an overall decrease in TKO animals compared to TKO controls while the red arrows pointing upwards indicate the metabolite increased in TKO animals. Pathway information was derived from the Kyoto Encyclopedia of Genes and Genomes, MetaboAnalyst, Lipid Pathway Enrichment Analysis, and existing scientific literature. Abbreviations: DG: Diacylglycerols, TG: Triacylglycerols, PC: Phosphatidylcholines, PC O-: Ether phosphatidylcholines, PE: Phosphatidylethanolamines, PE O-: Ether phosphatidylethanolamines, LPE: Lysophosphatidylethanolamines and LPC: Lysophosphatidylcholines.

Article Snippet: Isotopically labeled polar metabolite standards ( ) were purchased from Cambridge Isotope Laboratories (Tewksbury, MA, USA) and were used to prepare the internal standard mixture for HILIC experiments.

Techniques: Derivative Assay

Journal: Archives of Toxicology

Article Title: Discovering a predictive metabolic signature of drug-induced structural cardiotoxicity in cardiac microtissues

doi: 10.1007/s00204-025-04074-4

Figure Lengend Snippet: Magnitude of perturbation in cardiac microtissues induced by 72 different exposure conditions. Bar charts display the number of m / z features measured in intracellular a , b polar metabolite, and c , d lipid extracts of cardiac microtissues exposed to one of the twelve xenobiotics at either a low (blue bars) or high (red bars) concentration for 6, 48 or 72 h, with significantly different intensity relative to batch- and time-matched controls. Also shown, e , f , are the number of m / z -RT features measured in spent culture media of exposed cardiac microtissues with significantly different intensity relative to controls. Data were measured by a DIMS polar positive, b DIMS polar negative, c DIMS lipids positive, d DIMS lipids negative, e HILIC positive UHPLC-MS and f HILIC negative UHPLC-MS analytical assays. Significance was defined as p < 0.01, as determined by two-tailed Welch’s t-test (Color figure online)

Article Snippet: Bar charts display the number of m / z features measured in intracellular a , b polar metabolite, and c , d lipid extracts of cardiac microtissues exposed to one of the twelve xenobiotics at either a low (blue bars) or high (red bars) concentration for 6, 48 or 72 h, with significantly different intensity relative to batch- and time-matched controls.

Techniques: Concentration Assay, Hydrophilic Interaction Liquid Chromatography, Two Tailed Test