Dahye Yoon

1H-NMR-based metabolomic studies of bisphenol A in zebrafish (Danio rerio)

ABSTRACT Proton nuclear magnetic resonance (1H-NMR) spectroscopy was used to study the response of zebrafish (Danio rerio) to increasing concentrations of bisphenol A (4,4′-(propane-2,2-diyl)diphenol, BPA). Orthogonal partial least squares discriminant analysis (OPLS-DA) was applied to detect aberrant metabolomic profiles after 72 h of BPA exposure at all levels tested (0.01, 0.1, and 1.0 mg/L). The OPLS-DA score plots showed that BPA exposure caused significant alterations in the metabolome. The metabolomic changes in response to BPA exposure generally exhibited nonlinear patterns, with the exception of reduced levels of several metabolites, including glutamine, inosine, lactate, and succinate. As the level of BPA exposure increased, individual metabolite patterns indicated that the zebrafish metabolome was subjected to severe oxidative stress. Interestingly, ATP levels increased significantly at all levels of BPA exposure. In the present study, we demonstrated the applicability of 1H-NMR-based metabolomics to identify the discrete nature of metabolic changes.

Metabolomics of Breast Cancer Using High-Resolution Magic Angle Spinning Magnetic Resonance Spectroscopy: Correlations with 18F-FDG Positron Emission Tomography-Computed Tomography, Dynamic Contrast-Enhanced and Diffusion-Weighted Imaging MRI.

Purpose Our goal in this study was to find correlations between breast cancer metabolites and conventional quantitative imaging parameters using high-resolution magic angle spinning (HR-MAS) magnetic resonance spectroscopy (MRS) and to find breast cancer subgroups that show high correlations between metabolites and imaging parameters. Materials and methods Between August 2010 and December 2013, we included 53 female patients (mean age 49.6 years; age range 32–75 years) with a total of 53 breast lesions assessed by the Breast Imaging Reporting and Data System. They were enrolled under the following criteria: breast lesions larger than 1 cm in diameter which 1) were suspicious for malignancy on mammography or ultrasound (US), 2) were pathologically confirmed to be breast cancer with US-guided core-needle biopsy (CNB) 3) underwent 3 Tesla MRI with dynamic contrast-enhanced (DCE) and diffusion-weighted imaging (DWI) and positron emission tomography-computed tomography (PET-CT), and 4) had an attainable immunohistochemistry profile from CNB. We acquired spectral data by HR-MAS MRS with CNB specimens and expressed the data as relative metabolite concentrations. We compared the metabolites with the signal enhancement ratio (SER), maximum standardized FDG uptake value (SUV max), apparent diffusion coefficient (ADC), and histopathologic prognostic factors for correlation. We calculated Spearman correlations and performed a partial least squares-discriminant analysis (PLS-DA) to further classify patient groups into subgroups to find correlation differences between HR-MAS spectroscopic values and conventional imaging parameters. Results In a multivariate analysis, the PLS-DA models built with HR-MAS MRS metabolic profiles showed visible discrimination between high and low SER, SUV, and ADC. In luminal subtype breast cancer, compared to all cases, high SER, ADV, and SUV were more closely clustered by visual assessment. Multiple metabolites were correlated with SER and SUV in all cases. Multiple metabolites showed correlations with SER and SUV in the ER positive, HER2 negative, and Ki-67 negative groups. Conclusion High levels of PC, choline, and glycine acquired from HR-MAS MRS using CNB specimens were noted in the high SER group via DCE MRI and the high SUV group via PET-CT, with significant correlations between choline and SER and between PC and SUV. Further studies should investigate whether HR-MAS MRS using CNB specimens can provide similar or more prognostic information than conventional quantitative imaging parameters.

Discrimination of Basal Cell Carcinoma from Normal Skin Tissue Using High-Resolution Magic Angle Spinning 1H NMR Spectroscopy.

High-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy is a useful tool for investigating the metabolism of various cancers. Basal cell carcinoma (BCC) is the most common skin cancer. However, to our knowledge, data on metabolic profiling of BCC have not been reported in the literature. The objective of the present study was to investigate the metabolic profiling of cutaneous BCC using HR-MAS 1H NMR spectroscopy. HR-MAS 1H NMR spectroscopy was used to analyze the metabolite profile and metabolite intensity of histopathologically confirmed BCC tissues and normal skin tissue (NST) samples. The metabolic intensity normalized to the total spectral intensities in BCC and NST was compared, and multivariate analysis was performed with orthogonal partial least-squares discriminant analysis (OPLS-DA). P values < 0.05 were considered statistically significant. Univariate analysis revealed 9 metabolites that showed statistically significant difference between BCC and NST. In multivariate analysis, the OPLS-DA models built with the HR-MAS NMR metabolic profiles revealed a clear separation of BCC from NST. The receiver operating characteristic curve generated from the results revealed an excellent discrimination of BCC from NST with an area under the curve (AUC) value of 0.961. The present study demonstrated that the metabolite profile and metabolite intensity differ between BCC and NST, and that HR-MAS 1H NMR spectroscopy can be a valuable tool in the diagnosis of BCC.

Metabolic responses in zebrafish (Danio rerio) exposed to zinc and cadmium by nuclear magnetic resonance -based metabolomics

ABSTRACT Heavy metals are common marine and soil pollutants that are mainly the result of industrial activity, and are a threat to the environment and human health. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomics was applied to adult Danio rerio to monitor the metabolic change as a response to ZnCl2 and CdCl2 exposure at different concentrations for 72 h. NMR spectroscopy was used to identify and quantify the metabolites extracted from D. rerio. The metabolite profiles of the control and heavy metal exposed group were classified by partial least squares – discriminant analysis (PLS-DA) analysis, and potential contaminant-specific biomarkers were suggested. For the ZnCl2-exposed zebrafish, the levels of ATP, aspartate and NAD+ were increased, whereas the levels of formate, inosine, hypoxanthine and succinate decreased. In addition, the CdCl2-exposed zebrafish showed an increase in the levels of ATP and formate and a decrease in the levels of glutamate, inosine and glutathione. Overall, Zn and Cd may lead to neurotoxicity, disturbances in the energy metabolism and oxidative stress. Our finding demonstrated that the application of NMR-based metabolomics might be useful for detecting the toxicity caused by sub-lethal concentrations of heavy metal contaminants in the environment.

Applications of NMR spectroscopy based metabolomics: a review

Metabolomics is the study which detects the changes of metabolites level. Metabolomics is a terminal view of the biological system. The end products of the metabolism, metabolites, reflect the responses to external environment. Therefore metabolomics gives the additional information about understanding the metabolic pathways. These metabolites can be used as biomarkers that indicate the disease or external stresses such as exposure to toxicant. Many kinds of biological samples are used in metabolomics, for example, cell, tissue, and bio fluids. NMR spectroscopy is one of the tools of metabolomics. NMR data are analyzed by multivariate statistical analysis and target profiling technique. Recently, NMR-based metabolomics is a growing field in various studies such as disease diagnosis, forensic science, and toxicity assessment.

Induction of p53-Independent Apoptosis and G1 Cell Cycle Arrest by Fucoidan in HCT116 Human Colorectal Carcinoma Cells

It is well known that fucoidan, a natural sulfated polysaccharide present in various brown algae, mediates anticancer effects through the induction of cell cycle arrest and apoptosis. Nevertheless, the role of tumor suppressor p53 in the mechanism action of fucoidan remains unclear. Here, we investigated the anticancer effect of fucoidan on two p53 isogenic HCT116 (p53+/+ and p53−/−) cell lines. Our results showed that inhibition of cell viability, induction of apoptosis and DNA damage by treatment with fucoidan were similar in two cell lines. Flow cytometric analysis revealed that fucoidan resulted in G1 arrest in the cell cycle progression, which correlated with the inhibition of phosphorylation of retinoblastoma protein (pRB) and concomitant association of pRB with the transcription factor E2Fs. Furthermore, treatment with fucoidan obviously upregulated the expression of cyclin-dependent kinase (CDK) inhibitors, such as p21WAF1/CIP1 and p27KIP1, which was paralleled by an enhanced binding with CDK2 and CDK4. These events also commonly occurred in both cell lines, suggesting that fucoidan triggered G1 arrest and apoptosis in HCT116 cells by a p53-independent mechanism. Thus, given that most tumors exhibit functional p53 inactivation, fucoidan could be a possible therapeutic option for cancer treatment regardless of the p53 status.

Intratumoral Agreement of High-Resolution Magic Angle Spinning Magnetic Resonance Spectroscopic Profiles in the Metabolic Characterization of Breast Cancer.

AbstractHigh-resolution magic angle spinning (HR-MAS) magnetic resonance (MR) spectroscopy data may serve as a biomarker for breast cancer, with only a small volume of tissue sample required for assessment. However, previous studies utilized only a single tissue sample from each patient. The aim of this study was to investigate whether intratumoral location and biospecimen type affected the metabolic characterization of breast cancer assessed by HR-MAS MR spectroscopyThis prospective study was approved by the institutional review board and informed consent was obtained. Preoperative core-needle biopsies (CNBs), central, and peripheral surgical tumor specimens were prospectively collected under ultrasound (US) guidance in 31 patients with invasive breast cancer. Specimens were assessed with HR-MAS MR spectroscopy. The reliability of metabolite concentrations was evaluated and multivariate analysis was performed according to intratumoral location and biospecimen type.There was a moderate or higher agreement between the relative concentrations of 94.3% (33 of 35) of metabolites in the center and periphery, 80.0% (28 of 35) of metabolites in the CNB and central surgical specimens, and 82.9% (29 of 35) of metabolites between all 3 specimen types. However, there was no significant agreement between the concentrations of phosphocholine (PC) and phosphoethanolamine (PE) in the center and periphery. The concentrations of several metabolites (adipate, arginine, fumarate, glutamate, PC, and PE) had no significant agreement between the CNB and central surgical specimens.In conclusion, most HR-MAS MR spectroscopic data do not differ based on intratumoral location or biospecimen type. However, some metabolites may be affected by specimen-related variables, and caution is recommended in decision-making based solely on metabolite concentrations, particularly PC and PE. Further validation through future studies is needed for the clinical implementation of these biomarkers based on data from a single tissue sample.

The difference of metabolic profile between male and female zebrafish

Various experiments using zebrafish have been highlighted recently in the scientific community. Because it is possible to conduct practical experiment from various neurological research to area of genetic study or toxicity experiment. However, gender difference effects are nearly not considered. If the gender differences of zebrafish are considered it is possible to obtain more accurate data. In this study, zebrafish which have different genders were compared each other with NMR-based metabolomics. The extracts of male and female zebrafish were measured by 600 MHz NMR spectrometer. Statistical analysis and target profiling were conducted. As a result, muscle related metabolites were observed in male zebrafish and nerve related metabolites were observed in female zebrafish.

JAK/STAT and TGF-ß activation as potential adverse outcome pathway of TiO 2 NPs phototoxicity in Caenorhabditis elegans

Titanium dioxide nanoparticles (TiO2NPs) are widely used nanoparticles, whose catalytic activity is mainly due to photoactivation. In this study, the toxicity of TiO2NPs was investigated on the nematode Caenorhabditis elegans, with and without UV activation. Comparative analyses across the four treatments revealed that UV-activated TiO2NPs led to significant reproductive toxicity through oxidative stress. To understand the underlying molecular mechanism, transcriptomics and metabolomics analyses were conducted, followed by whole-genome network-based pathway analyses. Differential expression analysis from microarray data revealed only 4 DEGs by exposure to TiO2NPs alone, compared to 3,625 and 3,286 DEGs by UV alone and UV-activated TiO2NPs, respectively. Pathway analyses suggested the possible involvement of the JAK/STAT and TGF-ß pathways in the phototoxicity of TiO2NPs, which correlated with the observation of increased gene expression of those pathways. Comparative analysis of C. elegans response across UV activation and TiO2NPs exposure was performed using loss-of-function mutants of genes in these pathways. Results indicated that the JAK/STAT pathway was specific to TiO2NPs, whereas the TGF-ß pathway was specific to UV. Interestingly, crosstalk between these pathways was confirmed by further mutant analysis. We consider that these findings will contribute to understand the molecular mechanisms of toxicity of TiO2NPs in the natural environment.

Metabolomics and mitochondrial dysfunction in Alzheimer’s disease

Alzheimer’s disease (AD) is characterized by cognitive impairment, progressive neurodegeneration, and Aβ accumulation. Aβ oligomers can lead to synaptic damage via alterations in glutamate receptors and excitotoxicity, as well as mitochondrial dysfunction. AD is associated with various biological indicators, including (1) predisposing factors such as genetic risk factors, (2) laboratory markers such as Aβ and tau protein, and (3) diagnostic markers such as MRI and PET findings. However, these markers are not confirmed, invasive, or expensive. In the present study, we employed nuclear magnetic resonance (NMR) methods that are inexpensive, time-efficient, and can be performed using samples obtained from various easily accessible sources such as cerebrospinal fluid, plasma, and peripheral tissue, thus highlighting the clinical utility of this approach. NMR analyses of blood metabolites showed that glutamine, glutamate, leucine, oxaloacetate, aspartate, isoleucine, and 3-hydroxyisovalerate are increased in patients with AD compared with control individuals. These metabolites seem to be related to mitochondrial dysfunction. Our data indicated that 3-hydroxyisovalerate, which is linked to known pathologic processes associated with mitochondrial dysfunction and accelerated neurodegeneration, was increased in the blood samples of patients with AD.