Metabolomics:Open Access

Mathematics- or physics-majored students are disciplinary, sensitive to numbers and mathematical imagination. They play unique roles in biomedical science now. This editorial offers new insights in this matter and possible future perspectives.

Carcinoma of the thyroid gland is the most common cancer of the endocrine system. It accounts for approximately 10% of thyroid focal lesions, and the incidence of this cancer is increasing. A valuable technique for differentiating cancerous from benign nodules is fine-needle aspiration biopsy (FNA) with cytological verification. Unfortunately, in 30% of cases, FNA results are not sufficient to determine the proper method of treatment. Therefore, many patients are referred for diagnostic surgery and histopathologic examination. Despite the development of new imaging and molecular diagnostic techniques, no universal marker for pre-surgery identification of malignant changes in the thyroid is available. Modern measuring techniques, such as nuclear magnetic resonance spectroscopy - NMR - and mass spectrometry – MS, in combination with chemometric analysis led to the development of a new field of biology – metabolomics. Metabolomics allows for the analysis of biochemical processes in biological systems by assessing the metabolome (set of all metabolites - small molecular compounds with a molecular weight <1000 Da - contained in measured biological material). The metabolite profile quantitatively and qualitatively changes in response to disturbances of homeostasis. The promising results of the use of metabolomics methods as diagnostic tools for certain cancers and our experience with using metabolomics methods to differentiate benign from malignant thyroid tumors suggest that this field of science, which has been growing for several years, will improve the diagnosis and differentiation of thyroid cancer.

Lectin was isolated and purified from the endophytic fungi Aspergillus flavus of Viscum album and it was a D-galactose and N-acetylgalactoseamine specific lectin capable of agglutinating A+ve blood group tested in hemeagglutination method. The lectin was confirmed a glycoprotein PAS staining on NATIVE-PAGE and it is having single band of 64 kDa protein (in SDS-PAGE) similar to plant lectin. The peptide sequences were identified from purified lectin 64 kDa protein band is shown. NVRFDLSGATSSSYK similar to Cucurbia pepo protein peptide sequence and it is a ribosome inactivating protein. Apoptotic activity was tested on human breast adenocarcinoma cancer (MCF-7) cell line and it is a time and dose dependent manner. Dose dependent inhibition of cancer cells was observed with IC50 values of 0.02 μg/ ml from Aspergillus flavus. MCF-7 cell death elicited by the lectin extract was found to be apoptotic in nature based the indication of nucleus condensation, shrinkage of nucleus membrane; membrane bebbling and also DNA fragmentation are the hallmark of apoptosis was observed in MCF-7 cells after staining with Hoechst 33342. Caspase mediated apoptosis was observed in lectin treated MCF-7 cells by cleaving fluorogenic peptide substrates, Ac-DEVD-AMC. The caspase-7 was observed as an effector in cleaving other caspases, further inhibition of caspase with an inhibitor provide clear evidence of caspase-7 mediated apoptosis in MCF-7 treated cells.

Microvascular inflammation is considered as a trigger for vasculopathy and early atherosclerosis development in diabetes mellitus. However, activated mononuclears/macrophages/neutrophils play a pivotal role in pathogenesis of vascular complications among individuals with diabetes mellitus. The neutrophil extracellular traps (NETs) have been known as a component of innate immune system for the last few decades. NETosis is induced by pathogens as well as other stimuli such as activated platelets, metabolic triggers, and oxidative stress components. In diabetes, neutrophils are primed to release NETs and die by NETosis. The objective of the mini review is to highlight the possible role of NETosis in early diabetes-related vasculopathy beyond cardiovascular complications.

Metabolomics is a valuable tool to gain mechanistic insight into biological processes. It is frequently used to obtain complementary details to other ‘omics technologies such as transcriptomics or proteomics. For knowledge generation, reproducible measurements of physiological, intact, and artifact-free metabolite levels are imperative necessitating further standardization of best practices to improve reliability of research outcomes. Here we report a novel cell sample preparation method (MxP® CellCollect) for metabolomics applications using adherent mammalian cells, which reduces the time consumption and physiological stress of conventional methods such as trypsinization or cell scraping. The most common sampling procedures to detach cells from their growth surface, trypsinization and scraping were compared to the MxP® CellCollect method investigating metabolite profiles of two breast cancer cell lines (MDA-MB-231 and MCF7). Metabolite levels as well as direction of metabolite changes differed tremendously revealing issues with trypsinization and scraping risking non-physiological or misleading results in contrast to MxP® CellCollect. Differences in metabolic profiles of cells harvested by trypsinization as compared to MxP® CellCollect or scraping can be directly attributed to prolonged, medium-free incubation time during cell detachment leading to a severely energy-depleted intracellular state. Labile metabolites or metabolites with fast intracellular turnover rates such as glycolysis and TCA cycle intermediates were strongly and significantly decreased by trypsinization. The same was true for amino acids and nucleoside triphosphates. Results obtained with scraping using methanol as solvent were multifaceted. Even mild evaporation of methanol prior metabolite extraction led to temperature- and/or light-dependent degradation of labile metabolites such as nucleoside triphosphates into di- and monophosphates liberating pyrophosphate. Furthermore, lipid metabolites, in particular cell membrane lipids, were found to have significantly lower levels than measured by trypsinization or MxP® CellCollect, indicating that lipid metabolites are insufficiently detached and/or unspecifically adsorb to the hydrophobic dish and scraping tool.

Due to the potential risk of accidental exposure to gamma radiation, it’s critical to identify the biomarkers of radiation exposed creatures. In the present study, NMR based metabolomics combined with multivariate data analysis to evaluate the metabolites changed in the C57BL/6 mouse spleen after 4 days whole body exposure to 3.0 Gy and 7.8 Gy gamma radiations. Principal component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS) are employed for classification and identification potential biomarkers associated with gamma irradiation. Two different strategies for NMR spectral data reduction (i.e., spectral binning and spectral deconvolution) are combined with normalize to constant sum and unit weight before multivariate data analysis, respectively. The combination of spectral deconvolution and normalization to unit weight is the best way for identifying discriminatory metabolites between the irradiation and control groups. Normalized to the constant sum may achieve some pseudo biomarkers. PCA and OPLS results shown that the exposed groups can be well separated from the control group. Leucine, 2-aminobutyrate, valine, lactate, arginine, glutathione, 2-oxoglutarate, creatine, tyrosine, phenylalanine, π-methylhistidine, taurine, myoinositol, glycerol and uracil are significantly elevated while ADP is decreased significantly. These significantly changed metabolites are associated with multiple metabolic pathways and may be potential biomarkers in the spleen exposed to gamma irradiation.

Both genetic and environmental factors play roles in hyperuricemia and susceptibility may be modified by functional polymorphisms in folate metabolic genes, such as methylenetetrahydrofolate reductase (MTHFR). Several case control studies investigated association between C677T polymorphism with hyperuricemia but the sample size was small in these studies and the association power was weak. The aim of the present meta-analysis was to evaluate association between MTHFR C677T polymorphism and hyperuricemia. This meta-analysis recruited 6 published studies which were selected by search of electronic databases up to August 2013, including 558 hyperuricemic cases and 912 healthy controls. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association between MTHFR C677T polymorphism and hypeuricemia susceptibility using fixed effect models. Statistically significant relationship was found between C677T polymorphism and hyperuricemia with all genetic models (Additive model T vs. C: OR=1.8401, 95% CI=1.55-2.18, p<0.0001; Homozygote model TT vs. CC: OR=2.9873, 95% CI=2.06-4.33, p<0.0001; Co-dominant CT vs. CC: OR=2.3785, 95 % CI=1.85-3.04, p<0.0001; Dominant model TT+CT vs. CC: OR=2.5233, 95% CI=1.99-3.19, p<0.0001; Recessive model TT vs. CT+CC: OR=2.2628, 95% CI=1.61-3.17, p<0.0001). In conclusion, the MTHFR C677T polymorphism was associated with an increased risk of hyperuricemia.

Objective: To investigate the change of glycometabolism in the offspring from in vitro fertilization through fresh embryo and vitrified embryo transplantation, and evaluate the effect of vitrification technology on the health of offspring. Materials and method: Offspring mice from fresh embryo transfer (FET) and vitrified embryo transfer (VET) were divided into two groups. Natural mating mice were used as the control. Introperitoneal glucose tolerance (IPGTT) and insulin tolerance test (IPITT) were performed in the adulthood offsprings. Total RNA was extracted from 14.5dpc fetus and neonate livers, and glycometabolism-related genes were detected by quantitative RT-PCR. Results: The glucose levels of IPGTT at 30 min and 120 min in offspring mice from VET were significantly higher than control, and the glucose level at 120 min was significantly higher than that in FET. In liver tissues from 14.5 dpc embryos, the mRNA expression of Igf1 and Igf2 in FET and VET groups, the mRNA expression of Glut8 in VET was significantly higher than that in the control. In livers of newly born mice, the mRNA expression of Igf1 and Igf2 in FETï¼ÃƒÂ¯Ã‚¿Â½Glut1 and Glut2 in FET and VET was significantly lower than that in the control.VET and FET, especially VET, may affect the glycometabolism of offspring mice.

Aim: Chronic inflammation of adipose tissues plays a key role in obesity-induced metabolic disorders. We examined effects of sera from obese patients with or without different compositions of metabolic disorders on the activation of Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) signaling pathway in the human monocytic leukemia cell line (THP-1), which have never been reported. Method: With or without pretreatment of TLR4 monoclonal antibody, THP-1 cells were incubated for 48h by sera from 45 obese patients with or without metabolic disorders and 15 controls. The level of TLR4 in THP-1 cells, intracellular level of phosphorylated NF-κB p65, IL-1β and TNF-α levels in cell culture supernatants were measured. Results: Compared with controls, the expression level of TLR4, NF-κB p65, IL-1β and TNF-α were significantly increased (p < 0.05) after cells were incubated with sera from obese patients. The more compositions of metabolic disorders, the higher increase of these factors. Pretreatment with TLR4 monoclonal antibody suppressed the degree of increase in these factors (p < 0.05). Conclusion: Sera from obese patients could induce the activation of TLR4/NF-κB signaling pathway in THP-1 monocytes by different degrees. The TLR4/NF-κB signaling pathway plays an important role in the proinflammatory effect of obese patient-derived sera.

Dunaliella salina is a model chlorophyte microalga in studying carotenoid metabolism and osmoregulation. Nitrogen depletion plays an important role in inducing β-carotene accumulation of D. salina cells. However, the underlying mechanism is still unclear. In this study, the metabolic profiling of D. salina cells during the process of nitrogen deprivation was performed by gas chromatography-mass spectrometry. A total of 78 metabolites were identified and quantified, including 16 amino acids, 19 sugars, 13 organic acids, 11 alcohols, 11 fatty acids, 4 amines and 4 others. Nitrogen deprivation induced changes in saturation of fatty acids by increasing saturated fatty acids and decreasing polyunsaturated fatty acids in D. salina. The relative levels of metabolites such as sucrose, maltose and organic acids, which act as carbon skeleton, were increased, in contrast, glycerol, myo-inositol which are related to the osmoregulatory mechanism, kept constant under nitrogen deprivation condition. The levels of proline, glutamic acid and other metabolites, which were involved in protective function, were increased in nitrogen deprivation condition. The precursors of these metabolites are the intermediates of the Calvin cycle and the TCA cycle. The results of this research might be applicable to the interpretation of metabolic synthesis and fatty acid production during process of nitrogen deprivation and provide a new method for accumulating high amounts of carotenoids in D. salina.