Modelling the acid/base H-1 NMR chemical shift limits of metabolites in human urine

INTRODUCTION: Despite the use of buffering agents the 1H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. OBJECTIVES: To investigate the acid, base and metal ion dependent 1H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. METHODS: Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl2, MgCl2, NaCl or KCl, and their 1H NMR spectra were acquired. RESULTS: Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na+, K+, Ca2+ and Mg2+, were also measured. CONCLUSION: These data will be a valuable resource for 1H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1H NMR spectra

convISA: A simple, convoluted method for isotopomer spectral analysis of fatty acids and cholesterol

Isotopomer spectral analysis (ISA) is a simple approach for modelling the cellular synthesis of fatty acids and cholesterol in a stable isotope labelling experiment. In the simplest model, fatty acid biosynthesis is described by two key parameters: the fractional enrichment of acetyl-CoA from the labelled substrate, D, and the fractional de novo synthesis of the fatty acid during the exposure to the labelled substrate, g(t). The model can also be readily extended to include synthesis via elongation of unlabelled shorter fatty acids. This modelling strategy is less complex than metabolic flux analysis and only requires the measurement of the mass isotopologues of a single metabolite. However, software tools to perform these calculations are not freely available. We have developed an algorithm (convISA), implemented in MATLAB™, which employs the convolution (Cauchy product) of mass isotopologue distributions (MIDs) for ISA of fatty acids and cholesterol. In our method, the MIDs of each molecule are constructed as a single entity rather than deriving equations for individual isotopologues. The flexibility of this method allows the model to be applied to raw data as well as to data that has been corrected for natural isotope abundance. To test the algorithm, convISA was applied to 238 MIDs of methyl palmitate available from the literature, for which ISA parameters had been calculated via other methods. A very high correlation was observed between estimates of the D and g(t) parameters from convISA with both published values, and estimates generated by our own metabolic flux analysis using a simplified stoichiometric model (r=0.981 and 0.944, and 0.996 and 0.942). We also demonstrate the application of the convolution ISA approach to cholesterol biosynthesis; the model was applied to measurements made on MCF7 cells cultured in U-13C-glucose. In conclusion, we believe that convISA offers a convenient, flexible and transparent framework for metabolic modelling that will help facilitate the application of ISA to future experiments

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine

Introduction Despite the use of buffering agents the 1H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. Objectives To investigate the acid, base and metal ion dependent 1H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Methods Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl2, MgCl2, NaCl or KCl, and their 1H NMR spectra were acquired. Results Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na+, K+, Ca2+ and Mg2+, were also measured. Conclusion These data will be a valuable resource for 1H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1H NMR spectra

Rapid screening of cellular stress responses in recombinant Pichia pastoris strains using metabolite profiling

Heterologous protein production in the yeast Pichia pastoris can be limited by biological responses to high expression levels; the unfolded protein response (UPR) is a key determinant of the success of protein production in this organism. Here, we used untargeted NMR metabolic profiling (metabolomics) of a number of different recombinant strains, carried out in a miniaturized format suitable for screening-level experiments. We identified a number of metabolites (from both cell extracts and supernatants) which correlated well with UPR-relevant gene transcripts, and so could be potential biomarkers for future high-throughput screening of large numbers of P. pastoris clones

Metabolomic characterisation of the effects of oncogenic PIK3CA transformation in a breast epithelial cell line

Somatic mutations in PIK3CA are frequently found in a number of human cancers, including breast cancer, altering cellular physiology and tumour sensitivity to chemotherapy. This renders PIK3CA an attractive molecular target for early detection and personalised therapy. Using 1H Nuclear Magnetic Resonance spectroscopy (NMR) and Gas Chromatography – Mass Spectrometery (GC-MS) together with 13C stable isotope-labelled glucose and glutamine as metabolic tracers, we probed the phenotypic changes in metabolism following a single copy knock-in of mutant PIK3CA (H1047R) in the MCF10A cell line, an important cell model for studying oncogenic transformation in breast tissues. We observed effects in several metabolic pathways, including a decrease in glycerophosphocholine level together with increases in glutaminolysis, de novo fatty acid synthesis and pyruvate entry into the tricarboxylic acid cycle. Our findings highlight altered glyceroplipid metabolism and lipogenesis, as key metabolic phenotypes of mutant PIK3CA transformation that are recapitulated in the MCF10A cellular model

99mTc-radiolabeled composites enabling in vivo imaging of arterial dispersal and retention of microspheres in the vascular network of rabbit lungs, liver, and liver tumors

Ross W Stephens,1 Gregory D Tredwell,1 Karen J Knox,1 Lee A Philip,1 David W King,1 Kelly M Debono,2 Jessica L Bell,1 Tim J Senden,1 Marcel R Tanudji,3 Jillean G Winter,3 Stephanie A Bickley,3 Michael J Tapner,3 Stephen K Jones3 1The Biomedical Radiochemistry Laboratory, Department of Applied Mathematics, Research School of Physics and Engineering, Australian National University, Canberra, ACT, Australia; 2Animal Services Division, Research School of Biology, Australian National University, Canberra, ACT, Australia; 3Research and Development, Sirtex Medical Limited, Sydney, NSW, Australia Purpose: Selective internal radiation therapy (SIRT) is an effective treatment option for liver tumors, using Y-90-loaded polymer microspheres that are delivered via catheterization of the hepatic artery. Since Y-90 is a beta emitter and not conveniently imaged by standard clinical instrumentation, dosimetry is currently evaluated in each patient using a surrogate particle, 99mTechnetium-labeled macroaggregated albumin (99mTc-MAA). We report a new composite consisting of 99mTc-labeled nanoparticles attached to the same polymer microspheres as used for SIRT, which can be imaged with standard SPECT.Methods: Carbon nanoparticles with an encapsulated core of 99mTc were coated with the polycation protamine sulfate to provide electrostatic attachment to anionic polystyrene sulfonate microspheres of different sizes (30, 12, and 8 µm). The in vivo stability of these composites was determined via intravenous injection and entrapment in the capillary network of normal rabbit lungs for up to 3 hours. Furthermore, we evaluated their biodistribution in normal rabbit livers, and livers implanted with VX2 tumors, following intrahepatic artery instillation. Results: We report distribution tests for three different sizes of radiolabeled microspheres and compare the results with those obtained using 99mTc-MAA. Lung retention of the radiolabeled microspheres ranged from 72.8% to 92.9%, with the smaller diameter microspheres showing the lowest retention. Liver retention of the microspheres was higher, with retention in normal livers ranging from 99.2% to 99.8%, and in livers with VX2 tumors from 98.2% to 99.2%. The radiolabeled microspheres clearly demonstrated preferential uptake at tumor sites due to the increased arterial perfusion produced by angiogenesis.Conclusion: We describe a novel use of radiolabeled carbon nanoparticles to generate an imageable microsphere that is stable in vivo under the shear stress conditions of arterial networks. Following intra-arterial instillation in the normal rabbit liver, they distribute in a distinct segmented pattern, with the smaller microspheres extending throughout the organ in finer detail, while still being well retained within the liver. Furthermore, in livers hosting an implanted VX2 tumor, they reveal the increased arterial perfusion of tumor tissue resulting from angiogenesis. These novel composites may have potential as a more representative mimic of the vascular distribution of therapeutic microspheres in patients undergoing SIRT. Keywords: liver cancer, SIRT, radiolabeled microspheres, medical imagin

Persistence of epigenomic effects after recovery from repeated treatment with two nephrocarcinogens

The discovery of the epigenetic regulation of transcription has provided a new source of mechanistic understanding to long lasting effects of chemicals. However, this information is still seldom exploited in a toxicological context and studies of chemical effect after washout remain rare. Here we studied the effects of two nephrocarcinogens on the human proximal tubule cell line RPTEC/TERT1 using high-content mRNA microarrays coupled with miRNA, histone acetylation (HA) and DNA methylation (DM) arrays and metabolomics during a 5-day repeat-dose exposure and 3 days after washout. The mycotoxin ochratoxin A (OTA) was chosen as a model compound for its known impact on HA and DM. The foremost effect observed was the modulation of thousands of mRNAs and histones by OTA during and after exposure. In comparison, the oxidant potassium bromate (KBrO3) had a milder impact on gene expression and epigenetics. However, there was no strong correlation between epigenetic modifications and mRNA changes with OTA while with KBrO3 the gene expression data correlated better with HA for both up- and down-regulated genes. Even when focusing on the genes with persistent epigenetic modifications after washout, only half were coupled to matching changes in gene expression induced by OTA, suggesting that while OTA causes a major effect on the two epigenetic mechanisms studied, these alone cannot explain its impact on gene expression. Mechanistic analysis confirmed the known activation of Nrf2 and p53 by KBrO3, while OTA inhibited most of the same genes, and genes involved in the unfolded protein response. A few miRNAs could be linked to these effects of OTA, albeit without clear contribution of epigenetics to the modulation of the pathways at large. Metabolomics revealed disturbances in amino acid balance, energy catabolism, nucleotide metabolism and polyamine metabolism with both chemicals. In conclusion, the large impact of OTA on transcription was confirmed at the mRNA level but also with two high-content epigenomic methodologies. Transcriptomic data confirmed the previously reported activation (by KBrO3) and inhibition (by OTA) of protective pathways. However, the integration of omic datasets suggested that HA and DM were not driving forces in the gene expression changes induced by either chemical