metabolome profiling analysis  (MetWare Ltd)

Journal: NPJ Systems Biology and Applications

Article Title: Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy

doi: 10.1038/s41540-025-00545-7

Figure Lengend Snippet: a Rates of electron flow in the electron transport chain from different metabolic substrates that produce NADH and FADH2. Slopes of MitoPlate S-1 substrate utilization indicating the relative amount of reduced cytochrome c subjected to different treatments (colors) and added substrates (x-axis). The colors of the dots represent the pathways in which the substrates are involved. The data are presented as the means ± standard deviations. P values were obtained via t tests to compare the DOX and control samples following a significant two-tailed one-way ANOVA result ( P < 0.05). Significance levels: * P < 0.05. b Cellular respiration and oxygen consumption rates. Mitochondrial metabolic parameters were inferred from the oxygen consumption rates measured by O2K high-resolution respirometry. The parameters were normalized on the basis of estimated cell volume (top), cell dry weight (middle) and cell number (bottom). While AC16 cells treated with DOX presented a greater OCR than the controls did, a different trend was observed for the parameters normalized by the dry weight of the cells. This observation suggests that DOX may impede the aerobic respiration ability of cells. Notably, the cells treated with DOX were enlarged, particularly those subjected to prolonged DOX treatment. Each data point shown is an estimated value inferred from an OCR experiment. c Gene expression levels, metabolite concentrations, and predicted fluxes. This figure illustrates the genes, metabolites, and reactions involved in oxidative phosphorylation (top) and the TCA cycle (bottom). The colored rectangles represent metabolic genes: light green indicates downregulated genes (adjusted P < 0.05 and −1 < log2FC < −0.3), pink indicates upregulated genes (adjusted P < 0.05 and 1 > log2FC > 0.3), dark green indicates downregulated DEGs, white indicates genes with minimal expression values (base mean < 30 or one sample has zero value), and gray indicates unchanged genes (none of the above conditions are met). All P values and log2FC values were derived from DGE analysis of the DOX-D2 samples compared with the controls. The plots with violin graphs display the sampled fluxes, with flux values in μmol/gram of protein/hour. The arrows below these plots indicate the reaction directions. The bar plots show substrate concentrations obtained and normalized from CE-MS metabolomics data (unit: nmol/gram of protein). The colors of the violin and bar plots represent different groups: blue for the control, orange for DOX-D2, green for DOX-D4, and red for DOX-D6. d Bubble plot presenting the metabolic pathway analysis results. The bubble sizes indicate -log10 (adjusted P values), and the colors denote the DAR ratio, which is the ratio of DARs to all reactions in the given pathways (Y-axis). The left column shows pathway results using DARs between the DOX-D2 and control samples, the middle column compares the DOX-D4 and control samples, and the right column displays pathway results using the DARs between the DOX-D6 and control samples. e Predicted metabolic fluxes for biomass and NADPH production. The violin plots (top) show sampled fluxes normalized by protein weight, whereas the bar plots (bottom) display fluxes normalized by cell number ( n = 1500 per group). The error bars represent 95% confidence intervals. These results suggest that the metabolic capacity per protein weight may differ from that per cell.

Article Snippet: The absolute concentrations of the AC16 cells were determined via a targeted quantitative metabolomics profiling technique conducted by Human Metabolome Technologies, Inc. (HMT).

Techniques: Control, Two Tailed Test, Gene Expression, Phospho-proteomics, Expressing, Derivative Assay

Journal: NPJ Systems Biology and Applications

Article Title: Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy

doi: 10.1038/s41540-025-00545-7

Figure Lengend Snippet: a Seahorse analyzer-measured OCR values (left) and the mitochondrial parameters (right) inferred from the data. N = 4 or 5. The error bars represent the standard deviations. b A bar chart showing the proportions of cells in the G1, G2, and S phases in the control and DOX-treated groups. A lower proportion of cells in the G2 and S phases was observed in the DOX-D2 (G2: 2.71 ± 0.25%, S-phase: 4.53 ± 0.79%), DOX-D4 (G2: 3.47 ± 0.34%, S-phase: 7.25 ± 2.34%), and DOX-D6 conditions (G2: 13.18 ± 0.10%, S-phase: 20.59 ± 1.84%) than in the control conditions (G2: 19.29 ± 0.85%, S-phase: 28.00 ± 1.40%). Each data point represents the cells in one culture plate ( n = 3 per group). The P value in the figure was obtained from Tukey’s test of the proportions of cells in the S phase following a significant two-tailed mixed-design one-way ANOVA ( P < 0.05). c Nontargeted metabolomic profiling results showing the relative carnitine concentrations in the DOX-treated and control samples. d Percentages of positive senescent cells detected in ( e ). Data points represent the mean percentages of positive cells in the three confocal images of the culture plates. CT: control; D2: DOX-D2; D4: DOX-D4; and D6: DOX-D6. In the figure, P values were obtained from Tukey’s multiple comparison tests following a significant two-tailed mixed-design one-way ANOVA test result ( P < 0.05). e Images of senescent cells. The blue area indicates β-galactosidase activity, which is present in senescent cells.

Article Snippet: The absolute concentrations of the AC16 cells were determined via a targeted quantitative metabolomics profiling technique conducted by Human Metabolome Technologies, Inc. (HMT).

Techniques: Control, Two Tailed Test, Comparison, Activity Assay

Journal: NPJ Systems Biology and Applications

Article Title: Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy

doi: 10.1038/s41540-025-00545-7

Figure Lengend Snippet: a Randomly sampled OXPHOS fluxes in GEMs normalized to the number of cells in the control (blue), DOX-D2 (orange), DOX-D4 (green), and DOX-D6 (red) groups. b Venn diagram showing the intersections of important metabolic genes predicted via sample-specific GEMs. The yellow boxes indicate some of the genes that are exclusively important for DOX-D2 (left) and DOX-D4&D6 (right). The gray boxes list the metabolic pathways in which these genes are involved. The percentages are the proportions of how many genes are associated with the pathways. In this figure, DOX-D4 & DOX-D6 represent the merged gene data from these two groups, reflecting the effects of mid- to long-term DOX toxicity on cardiac cells (Supplementary Fig. ). c Volcano plots showing metabolite fold changes and adjusted p values of the DOX-D2 (left) or DOX-D4 and DOX-D6 (right) samples compared with the control samples. The green circles indicate significantly decreased metabolites, and the yellow circles indicate significantly increased metabolites. Similar to ( b ), the DOX-D4 and DOX-D6 data were merged to represent their combined metabolomic profiles, as these two groups presented similar metabolite concentrations. d Pathway analysis performed using the significantly changed metabolites identified in ( c ). Pathway impact, the x-axis, was assessed by calculating the ratio of the summed importance measures of the matched metabolites to the total importance measures of all the metabolites in the pathway. Importance was determined using MetaboAnalyst , which uses the relative betweenness centrality and out-degree centrality in directed metabolic pathway networks. The y-axis is the −log( P value) obtained from a hypergeometric test. The left image shows the perturbed DOX-D2 substrates (increased and decreased), and the right image shows the altered DOX-D4 and DOX-D6 substrates.

Article Snippet: The absolute concentrations of the AC16 cells were determined via a targeted quantitative metabolomics profiling technique conducted by Human Metabolome Technologies, Inc. (HMT).

Techniques: Control

Journal: NPJ Systems Biology and Applications

Article Title: Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy

doi: 10.1038/s41540-025-00545-7

Figure Lengend Snippet: a Heatmap and hierarchical clustering of the measured metabolite concentrations in the AC16 samples ( n = 3 per group) subjected to different treatments. The heatmap colors represent the z scores calculated for the substrates. The bottom colors are the groups of the samples (blue: control; orange: DOX-D2; green: DOX-D4; red: DOX-D6). b Metabolic parameters derived from raw metabolomics data. The data are presented as the means ± SDs. P values were obtained from multiple comparison t tests following a significant two-tailed one-way ANOVA result ( P < 0.05). Significance levels: **** P < 0.0001, *** P < 0.001, ** P < 0.01, and * P < 0.05. c Absolute concentration (nmol/gram protein dry weight) of energy transfer cofactors and redox cofactors measured by capillary electrophoresis mass spectrometry. The data are presented as the means ± SDs. The data points were measurements of the samples ( n = 3 per group). P values were obtained from t tests as multiple comparison tests following a significant two-tailed one-way ANOVA result ( P < 0.05). d Pentose phosphate pathway (PPP) and e glycolysis pathway. The subplots in ( d ) and ( e ) illustrate metabolite concentrations measured by capillary electrophoresis mass spectrometry (bar plots), metabolic fluxes predicted by pipeGEM (violin plots), and gene expression changes from the RNA-seq data (rectangular boxes). Bar plots display absolute substrate concentrations (nmol/gram protein dry weight), with bar heights representing the mean and error bars indicating SDs. Sample groups are color-coded (blue: control; orange: DOX-D2; green: DOX-D4; and red: DOX-D6). Unmeasured substrates such as glucose, 6-PGDL (D-Glucono-1,5-lactone 6-phosphate), and 1,3-BPG are depicted as white rounded rectangles. The arrows on the edges represent chemical reactions and their directions. Violin plots indicate the predicted fluxes of these reactions, with the flux units (μmol/gram protein dry weight/hour) labeled. Negative values signify reversed reaction directions because of their bidirectional nature. The colored rectangles linking the flux plots correspond to the subunits or isozymes that regulate the reactions. Dark red and dark green indicate upregulated and downregulated DEGs, respectively, in the DOX-D2-treated group compared with the control group. Pink and light green indicate genes with P < 0.05 and logFCs between 1 and 0.3 (pink) or between −1 and −0.3 (green), respectively. White indicates genes with nearly absent raw counts (base mean < 30), whereas gray indicates none of the above.

Article Snippet: The absolute concentrations of the AC16 cells were determined via a targeted quantitative metabolomics profiling technique conducted by Human Metabolome Technologies, Inc. (HMT).

Techniques: Control, Derivative Assay, Comparison, Two Tailed Test, Concentration Assay, Electrophoresis, Mass Spectrometry, Gene Expression, RNA Sequencing, Labeling

Journal: Horticulture Research

Article Title: Tea polyphenol mediated CsMYB77 regulation of CsPOD44 to promote tea plant ( Camellia sinensis ) root drought resistance

doi: 10.1093/hr/uhaf048

Figure Lengend Snippet: Transcriptome and metabolome analyses of tea plant roots under different treatments. (A) Principal Component Analysis (PCA) score plot depicting gene expression differences in tea plant roots across four treatment groups. (B) Bubble chart illustrating Gene Ontology (GO) enrichment of differentially expressed genes (DEGs) across various pathways in DS group vs TPDS group. (C) Gene Set Enrichment Analysis (GSEA) of phenylpropanoid biosynthesis-related genes, with the highest enrichment observed in the TPDS-R group. (D) Metabolomic analysis of phenylpropanoid biosynthesis pathway (Ko00940) related metabolites under four treatments. Metabolites are divided into 19 types. The upward and downward lines indicate increases or decreases in metabolite content, respectively. (E) Classification of metabolites related to phenylpropanoid biosynthesis pathway (Ko00940) into four main categories: phenolic acids, amino acids and their derivatives, lignans and coumarins, and alkaloids. Changes in their contents across the four treatments are depicted. (F) Modular hierarchical clustering tree from the Weighted Gene Co-expression Network Analysis (WGCNA). (G) Heatmap illustrating the relationship between gene expression modules and sample traits, with numbers indicating correlation coefficients (R) and corresponding p -values (in parentheses). (H) Co-expression network of candidate genes within key co-expression modules identified by WGCNA analysis. Treatment details: CK group received 100 mL of water every 5 days; TP group received 100 mL of tea polyphenols (100 mg/L) every 5 days; DS group received 100 mL of water every 15 days; TPDS group received 100 mL of tea polyphenols (100 mg/L) every 15 days.

Article Snippet: The metabolomic profiling of tea plant roots from the four treatments was conducted by Metware Biotechnology Co., Ltd. (China) ( ).

Techniques: Gene Expression, Expressing