Metabolomic pathway visualization tool outsourcing editing function

Sugimoto, Masahiro

doi:10.1109/embc.2015.7320166

Cited by 3 publications

(3 citation statements)

References 45 publications

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“…Differences were considered significant at p 0.05. The data processing and pathway visualization were conducted by our proprietary software, MasterHands and Pathway Visualization [ 19 , 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

Metabolomic Alteration of Oral Keratinocytes and Fibroblasts in Hypoxia

Kato

Sugimoto

Enomoto

et al. 2021

JCM

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The oxygen concentration in normal human tissue under physiologic conditions is lower than the atmospheric oxygen concentration. The more hypoxic condition has been observed in the cells with wound healing and cancer. Somatic stem cells reside in a hypoxic microenvironment in vivo and prefer hypoxic culture conditions in vitro. Oral mucosa contains tissue-specific stem cells, which is an excellent tissue source for regenerative medicine. For clinical usage, maintaining the stem cell in cultured cells is important. We previously reported that hypoxic culture conditions maintained primary oral keratinocytes in an undifferentiated and quiescent state and enhanced their clonogenicity. However, the metabolic mechanism of these cells is unclear. Stem cell biological and pathological findings have shown that metabolic reprogramming is important in hypoxic culture conditions, but there has been no report on oral mucosal keratinocytes and fibroblasts. Herein, we conducted metabolomic analyses of oral mucosal keratinocytes and fibroblasts under hypoxic conditions. Hypoxic oral keratinocytes and fibroblasts showed a drastic change of metabolite concentrations in urea cycle metabolites and polyamine pathways. The changes of metabolic profiles in glycolysis and the pentose phosphate pathway under hypoxic conditions in the oral keratinocytes were consistent with those of other somatic stem cells. The metabolic profiles in oral fibroblasts showed only little changes in any pathway under hypoxia except for a significant increase in the antioxidant 2-oxoglutaric acid. This report firstly provides the holistic changes of various metabolic pathways of hypoxic cultured oral keratinocytes and fibroblasts.

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Section: Methodsmentioning

confidence: 99%

Metabolomic Alteration of Oral Keratinocytes and Fibroblasts in Hypoxia

Kato

Sugimoto

Enomoto

et al. 2021

JCM

Self Cite

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“…5.04, GraphPad Software Inc., San Diego, CA, USA) was used for statistical tests. Metabolites were visualized in our proprietary pathway visualization tool (Keio University, Yamagata, Japan) [35].…”

Section: Data Analysis and Statistical Analysismentioning

confidence: 99%

Metabolomic profiling of tumor-infiltrating macrophages during tumor growth

Umemura

Sugimoto

Kitoh

et al. 2020

Cancer Immunol Immunother

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Myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) are both key immunosuppressive cells that contribute to tumor growth. Metabolism and immunity of tumors depend on the tumor microenvironment (TME). However, the intracellular metabolism of MDSCs and TAMs during tumor growth remains unclear. Here, we characterized CD11b+ cells isolated from a tumor-bearing mouse model to compare intratumoral TAMs and intrasplenic MDSCs. Intratumoral CD11b+ cells and intrasplenic CD11b+ cells were isolated from tumor-bearing mice at early and late stages (14 and 28 days post-cell transplantation, respectively). The cell number of intrasplenic CD11b+ significantly increased with tumor growth. These cells included neutrophils holding segmented leukocytes or monocytes with an oval nucleus and Gr-1hi IL-4Rαhi cells without immunosuppressive function against CD8 T cells. Thus, these cells were classified as MDSC-like cells (MDSC-LCs). Intratumoral CD11b+ cells included macrophages with a round nucleus and were F4/80hi Gr-1lo IL-4Rαhi cells. Early stage intratumoral CD11b+ cells inhibited CD8 T cells via TNFα. Thus, this cell population was classified as TAMs. Metabolomic analyses of intratumoral TAMs and MDSC-LCs during tumor growth were conducted. Metabolic profiles of intratumoral TAMs showed larger changes in various metabolic pathways, e.g., glycolysis, TCA cycle, and glutamic acid pathways, during tumor growth compared with MDSL-LCs. Our findings demonstrated that intratumoral TAMs showed an immunosuppressive capacity from the early tumor stage and underwent intracellular metabolism changes during tumor growth. These results clarify the intracellular metabolism of TAMs during tumor growth and contribute to our understanding of tumor immunity.

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“…Accordingly, newer generation visualization tools are needed to assist with the analyses and interpretation of these increasingly high-dimensional and complex data sets. Several resources now offer a variety of techniques for visualizing metabolomics data structure and exploring the inter-relations between individual and groups of metabolites [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21].…”

Section: Introductionmentioning

confidence: 99%

A Single Visualization Technique for Displaying Multiple Metabolite–Phenotype Associations

et al. 2019

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To assist with management and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity, we need better visualization tools. Using a dataset of several hundred metabolite measures profiled in a cohort of ~1500 individuals sampled from a population-based community study, we performed association analyses with eight demographic and clinical traits and outcomes. We compared frequently used existing graphical approaches with a novel ‘rain plot’ approach to display the results of these analyses. The ‘rain plot’ combines features of a raindrop plot and a conventional heatmap to convey results of multiple association analyses. A rain plot can simultaneously indicate effect size, directionality, and statistical significance of associations between metabolites and several traits. This approach enables visual comparison features of all metabolites examined with a given trait. The rain plot extends prior approaches and offers complementary information for data interpretation. Additional work is needed in data visualizations for metabolomics to assist investigators in the process of understanding and convey large-scale analysis results effectively, feasibly, and practically.

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Metabolomic pathway visualization tool outsourcing editing function

Cited by 3 publications

References 45 publications

Metabolomic Alteration of Oral Keratinocytes and Fibroblasts in Hypoxia

Metabolomic Alteration of Oral Keratinocytes and Fibroblasts in Hypoxia

Metabolomic profiling of tumor-infiltrating macrophages during tumor growth

A Single Visualization Technique for Displaying Multiple Metabolite–Phenotype Associations

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