Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming.

Measurement of metabolic flux levels using stable isotope labeling has been successfully used to investigate metabolic redirection and reprogramming in living cells or tissues. The metabolic flux ratio between two reactions can be estimated from the 13C-labeling patterns of a few metabolites combined with the knowledge of atom mapping in the complicated metabolic network. However, it remains unclear whether an observed change in the labeling pattern of the metabolites is sufficient evidence of a shift in flux ratio between two metabolic states. In this study, a data analysis method was developed for the quantitative assessment of metabolic reprogramming. The Metropolis-Hastings algorithm was used with an in silico metabolic model to generate a probability distribution of metabolic flux levels under a condition in which the 13C-labeling pattern was observed. Reanalysis of literature data demonstrated that the developed method enables analysis of metabolic redirection using whole 13C-labeling pattern data. Quantitative assessment by Cohen's effect size (d) enables a more detailed read-out of metabolic reprogramming information. The developed method will enable future applications of the metabolic isotopomer analysis to various targets, including cultured cells, whole tissues, and organs.

Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells.

Precise measurement of sugar phosphates in glycolysis and the pentose phosphate (PP) pathway for 13C-metabolic flux analysis (13C-MFA) is needed to understand cancer-specific metabolism. Although various analytical methods have been proposed, analysis of sugar phosphates is challenging because of the structural similarity of various isomers and low intracellular abundance. In this study, gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) is applied to sugar phosphate analysis with o-(2,3,4,5,6-pentafluorobenzyl) oxime (PFBO) and trimethylsilyl (TMS) derivatization. Optimization of the GC temperature gradient achieved baseline separation of sugar phosphates in 31 min. Mass spectra showed the predominant generation of fragment ions containing all carbon atoms in the sugar phosphate backbone. The limit of detection of pentose 5-phosphates and hexose 6-phosphates was 10 nM. The method was applied to 13C-labeling measurement of sugar phosphates for 13C-MFA of the MCF-7 human breast cancer cell line. 13C-labeling of sugar phosphates for 13C-MFA improved the estimation of the net flux and reversible flux of bidirectional reactions in glycolysis and the PP pathway.

Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells.

Cancer cells often respond to chemotherapeutic inhibitors by redirecting carbon flow in the central metabolism. To understand the metabolic redirections of inhibitor treatment on cancer cells, this study established a 13C-metabolic flux analysis (13C-MFA)-based method to evaluate metabolic redirection in MCF-7 breast cancer cells using mass spectrometry. A metabolic stationary state necessary for accurate 13C-MFA was confirmed during an 8-24 h window using low-dose treatments of various metabolic inhibitors. Further 13C-labeling experiments using [1-13C]glucose and [U-13C]glutamine, combined with gas chromatography-mass spectrometry (GC-MS) analysis of mass isotopomer distributions (MIDs), confirmed that an isotopic stationary state of intracellular metabolites was reached 24 h after treatment with paclitaxel (Taxol), an inhibitor of mitosis used for cancer treatment. Based on these metabolic and isotopic stationary states, metabolic flux distribution in the central metabolism of paclitaxel-treated MCF-7 cells was determined by 13C-MFA. Finally, estimations of the 95% confidence intervals showed that tricarboxylic acid cycle metabolic flux increased after paclitaxel treatment. Conversely, anaerobic glycolysis metabolic flux decreased, revealing metabolic redirections by paclitaxel inhibition. The gap between total regeneration and consumption of ATP in paclitaxel-treated cells was also found to be 1.2 times greater than controls, suggesting ATP demand was increased by paclitaxel treatment, likely due to increased microtubule polymerization. These data confirm that 13C-MFA can be used to investigate inhibitor-induced metabolic redirection in cancer cells. This will contribute to future pharmaceutical developments and understanding variable patient response to treatment.

E-cadherin prolongs the moment for interaction between intestinal stem cell and its progenitor cell to ensure Notch signaling in adult Drosophila midgut.

Intestinal stem cells (ISCs) are required for maintenance of the proper cell composition in the adult intestine. To ensure permanent recruitment of newly differentiated cells, the ISC undergoes asymmetric cell division that generates an ISC itself and a progenitor cell. In the Drosophila midgut, cell fate for the absorptive cell is determined by Notch (N) signal in the progenitor cells that receive a ligand Delta (Dl) produced by the ISCs. Although most of the ISCs and progenitor cells are distantly located, they should retain their attachment when N is activated because the Dl-N interaction requires cell adhesion. Furthermore, N cannot be activated before completion of cell division. Thus, the moment after cell division and before cell separation should be prolonged for certain N activation, although the mechanism for this remains unclear. Here, we demonstrate that E-cadherin (E-cad) is required for stable attachment between the two cells. When E-cad does not function, N is not activated and cell differentiation is attenuated. We also show that the ISC tumor by N inactivation is assisted by a defect in E-cad down-regulation. These findings reveal one of the normal N functions used to inhibit tumorigenesis through lowering of E-cad for proper midgut cell turnover.

Drosophila T-box transcription factor Optomotor-blind prevents pathological folding and local overgrowth in wing epithelium through confining Hh signal.

Aberration of morphogen signaling leads directly to inappropriate cell differentiation and secondarily causes various pathological phenotypes such as abnormal morphogenesis and tumorigenesis. However, mechanisms for linking morphogen signaling and the higher order phenotypes have not been fully elucidated. Here we focus on the Drosophila T-box gene optomotor-blind (omb), a transcriptional target of a long-range morphogen Decapentaplegic (Dpp). Genetic analyses of omb function revealed that a negative feedback loop, where omb plays a crucial role, exists between Dpp and its upstream regulator Hedgehog (Hh), a short-range morphogen. Consequently, dysfunction of omb elicits hyperactivation of Hh signaling that causes an ectopic folding and local overgrowth in the wing columnar epithelium, neither of which are the direct results of reduced Dpp response. In the case of the local overgrowth, it was never seen in mutants for thick veins (tkv) encoding a Dpp receptor, suggesting that the Dpp signaling pathway is divided into two antagonistic branches, one of which contains Omb. Thus defect in feedback between the two morphogens explains both phenotypes, and disruption of a balance between the morphogen targets further accounts for the local overgrowth. These are the mechanisms for generating secondary phenotypes when a single signaling factor Omb fails to function.