Stable isotope resolved metabolomics analysis of ribonucleotide and RNA metabolism in human lung cancer cells

We have developed a simple NMR-based method to determine the turnover of nucleotides and incorporation into RNA by stable isotope resolved metabolomics (SIRM) in A549 lung cancer cells. This method requires no chemical degradation of the nucleotides or chromatography. During cell growth, the free ribonucleotide pool is rapidly replaced by de novo synthesized nucleotides. Using [U-¹³C]-glucose and [U-¹³C,¹⁵N]-glutamine as tracers, we showed that virtually all of the carbons in the nucleotide riboses were derived from glucose, whereas glutamine was preferentially utilized over glucose for pyrimidine ring biosynthesis, via the synthesis of Asp through the Krebs cycle. Incorporation of the glutamine amido nitrogen into the N3 and N9 positions of the purine rings was also demonstrated by proton-detected ¹⁵N NMR. The incorporation of ¹³C from glucose into total RNA was measured and shown to be a major sink for the nucleotides during cell proliferation. This method was applied to determine the metabolic action of an anti-cancer selenium agent (methylseleninic acid or MSA) on A549 cells. We found that MSA inhibited nucleotide turnover and incorporation into RNA, implicating an important role of nucleotide metabolism in the toxic action of MSA on cancer cells.     

Stable isotope resolved metabolomics of lung cancer in a SCID mouse model

We have determined the time course of [U-¹³C]-glucose utilization and transformations in SCID mice via bolus injection of the tracer in the tail vein. Incorporation of ¹³C into metabolites extracted from mouse blood plasma and several tissues (lung, heart, brain, liver, kidney, and skeletal muscle) were profiled by NMR and GC–MS, which helped ascertain optimal sampling times for different target tissues. We found that the time for overall optimal ¹³C incorporation into tissue was 15–20 min but with substantial differences in ¹³C labeling patterns of various organs that reflected their specific metabolism. Using this stable isotope resolved metabolomics (SIRM) approach, we have compared the ¹³C metabolite profile of the lungs in the same mouse with or without an orthotopic lung tumor xenograft established from human PC14PE6 lung adenocarcinoma cells. The ¹³C metabolite profile shows considerable differences in [U-¹³C]-glucose transformations between the two lung tissues, demonstrating the feasibility of applying SIRM to investigate metabolic networks of human cancer xenograft in the mouse model.     

Effects of decomposition and storage conditions on the δ13C and δ15N isotope values of killer whale (Orcinus orca) skin and blubber tissues

Several different factors in the collection and preservation of whale skin and blubber samples were examined to determine their effect on the results obtained by stable nitrogen and carbon isotope (δ¹⁵N and δ¹³C) analysis. Samples of wet killer whale skin retained their original stable isotope values for up to 14 d at 4°C or lower. However, decomposition significantly changed the δ¹⁵N value within 3 d at 20°C. Storage at ?20°C was as effective as ?80°C for the preservation of skin and blubber samples for stable isotope analysis for at least a year. By contrast, once a skin sample had been freeze‐dried and lipid extracted, the stable isotope values did not change significantly when it was stored dry at room temperature for at least 12 mo. Preservation of whale skin samples for a month in DMSO‐salt solution, frozen or at room temperature, did not significantly change the δ¹⁵N and δ¹³C values of lipid extracted tissues, although the slight changes seen could influence results of a study if only small changes are expected.     

Differentiation between unlabeled and very-low-level fully 15N,13C-labeled nucleotides for resonance assignments in nucleic acids

Based on different characteristics between unlabeled and fully ¹⁵N,¹³C-labeled nucleotides, we develop a method for unambiguous resonance assignments in nucleic acids following site-specific fully ¹⁵N,¹³C isotope incorporation at very low levels¹. The J-couplings between heteronuclei provide for distinction between the NMR signals of the fully labeled nucleotides and those of the natural abundance nucleotides. The method is demonstrated for DNA oligonucleotides², in the dimeric G-quadruplex [d(GGGTTCAGG)]₂and in the 22-nucleotide human telomeric fragment d[AG₃(TTAG₃)₃]. We expect this approach to be useful for selective monitoring of important functional domains and of their interactions in large nucleic acids.     

Getting to the fat of the matter: models,methods and assumptions for dealing with lipids in stable isotope analyses

Within an organism, lipids are depleted in ¹³C relative to proteins and carbohydrates (more negative δ¹³C), and variation in lipid content among organisms or among tissue types has the potential to introduce considerable bias into stable isotope analyses that use δ¹³C. Despite the potential for introduced error, there is no consensus on the need to account for lipids in stable isotope analyses. Here we address two questions: (1) If and when is it important to account for the effects of variation in lipid content on δ¹³C? (2) If it is important, which method(s) are reliable and robust for dealing with lipid variation? We evaluated the reliability of direct chemical extraction, which physically removes lipids from samples, and mathematical normalization, which uses the carbon-to-nitrogen (C:N) ratio of a sample to normalize δ¹³C after analysis by measuring the lipid content, the C:N ratio, and the effect of lipid content on δ¹³C (Δδ¹³C) of plants and animals with a wide range of lipid contents. For animals, we found strong relationships between C:N and lipid content, between lipid content and Δδ¹³C, and between C:N and Δδ¹³C. For plants, C:N was not a good predictor of lipid content or Δδ¹³C, but we found a strong relationship between carbon content and lipid content, lipid content and Δδ¹³C, and between and carbon content and Δδ¹³C. Our results indicate that lipid extraction or normalization is most important when lipid content is variable among consumers of interest or between consumers and end members, and when differences in δ¹³C between end members is <10–12‰. The vast majority of studies using natural variation in δ¹³C fall within these criteria. Both direct lipid extraction and mathematical normalization reduce biases in δ¹³C, but mathematical normalization simplifies sample preparation and better preserves the integrity of samples for δ¹⁵N analysis.     

Biomass production of site selective 13C/15N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR

Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large scale production of useful nucleotides. These nucleotides are site specifically labeled in C1′ and C5′ with minimal scrambling within the ribose ring. To demonstrate the utility of this labeling approach, the new site-specific labeled and the uniformly labeled nucleotides were used to synthesize a 36-nt RNA containing the catalytically essential domain 5 (D5) of the brown algae group II intron self-splicing ribozyme. The D5 RNA was used in binding and relaxation studies probed by NMR spectroscopy. Key nucleotides in the D5 RNA that are implicated in binding Mg²⁺ ions are well resolved. As a result, spectra obtained using selectively labeled nucleotides have higher signal-to-noise ratio compared to those obtained using uniformly labeled nucleotides. Thus, compared to the uniformly ¹³C/¹⁵N-labeled nucleotides, these specifically labeled nucleotides eliminate the extensive ¹³C–¹³C coupling within the nitrogenous base and ribose ring, give rise to less crowded and more resolved NMR spectra, and accurate relaxation rates without the need for constant-time or band-selective decoupled NMR experiments. These position selective labeled nucleotides should, therefore, find wide use in NMR analysis of biologically interesting RNA molecules.     

Stable isotope-resolved metabolomics (SIRM) in cancer research with clinical application to nonsmall cell lung cancer

Metabolomics provides a readout of the state of metabolism in cells or tissue and their responses to external perturbations. For this reason, the approach has great potential in clinical diagnostics. Clinical metabolomics using stable isotope resolved metabolomics (SIRM) for pathway tracing represents an important new approach to obtaining metabolic parameters in human cancer subjects in situ. Here we provide an overview of the technology development of labeling from cells in culture and mouse models. The high throughput analytical methods NMR and mass spectrometry, especially Fourier transform ion cyclotron resonance, for analyzing the resulting metabolite isotopomers and isotopologues are described with examples of applications in cancer biology. Special technical considerations for clinical applications of metabolomics using stable isotope tracers are described. The whole process from concept to analysis will be exemplified by our on-going study of nonsmall cell lung cancer (NSCLC) metabolomics. This powerful new approach has already provided important new insights into metabolic adaptations in lung cancer cells, including the upregulation of anaplerosis via pyruvate carboxylation in NSCLC.     

Regeneration of Mycelial Protoplasts from Lyophyllum shimeji

A new HPLC system for simultaneous analysis of NAD⁺, NADH, NADP⁺, and NADPH was developed and used to measure the transhydrogenase activity of spinach ferredoxin-N ADP ⁺ reductase (EC 1.18.1.2, FNR). The system is based on a reverse-phase HPLC with isocratic elution on an ODS column (4.6 × 50 mm). The four nucleotides were completely separated by developing the column with 0.15 m sodium phosphate/citrate buffer (pH 6.8) containing 1 mm EDTA at 40°C with a flow rate of 1 ml/min. The four nucleotides can be simultaneously assayed within 13 min by monitoring the effluents with a UV detector. It was also indicated that the transhydrogenase activity of spinach FNR can be advantageously assayed by measuring the nucleotides by this method.     

Synthesis of Stable Isotope Labeled Analogs of the Anti-Hepatitis C Virus Nucleotide Prodrugs PSI-7977 and PSI-352938

In order to support bioanalytical LC/MS method development and plasma sample analysis in preclinical and clinical studies of the anti-hepatitis C-virus nucleotides, PSI-7977 and PSI-352938, the corresponding stable isotope labeled forms were prepared. These labeled compounds were prepared by addition reaction of the freshly prepared Grignard reagent ¹³CD₃MgI to the corresponding 2 ′-ketone nucleosides followed by fluorination of the resulting carbinol with DAST. As expected, these 2 ′-C-(trideuterated-¹³C-methyl) nucleotide prodrugs showed similar anti-HCV activity to that of the corresponding unlabeled ones.     

A skew in poo: Biases in primate fecal isotope analysis and recommendations for standardized sample preparation

Feces are a treasure trove in the study of animal behavior and ecology. Stable carbon and nitrogen isotope analysis allows to assess the dietary niches of elusive primate species and primate breastfeeding behavior. However, some fecal isotope data may unwillingly be biased toward the isotope ratios of undigested plant matter, requiring more consistent sample preparation protocols. We assess the impact of this potential data skew in 114 fecal samples of wild bonobos (Pan paniscus) by measuring the isotope differences (Δ¹³C, Δ¹⁵N) between bulk fecal samples containing larger particles (>1 mm) and filtered samples containing only small particles (<1 mm). We assess the influence of fecal carbon and nitrogen content (ΔC:N) and sample donor age (subadult, adult) on the resulting Δ¹³C, Δ¹⁵N values (n = 228). Additionally, we measure the isotope ratios in three systematically sieved fecal samples of chimpanzees (Pan troglodytes verus), with particle sizes ranging from 20 μm to 8 mm (n = 30). We found differences in fecal carbon and nitrogen content, with the smaller fecal fraction containing more nitrogen on average. While the Δ¹³C values were small and not affected by age or ΔC:N, the Δ¹⁵N values were significantly influenced by fecal ΔC:N, possibly resulting from the differing proportions of undigested plant macroparticles. Significant relationships between carbon stable isotope ratios (δ¹³C) values and %C in large fecal fractions of both age groups corroborated this assessment. Δ¹⁵N values were significantly larger in adults than subadults, which should be of concern in isotope studies comparing adult females with infants to assess breastfeeding. We found a random variation of up to 3.0‰ in δ¹³C and 2.0‰ in nitrogen stable isotope ratios within the chimpanzee fecal samples separated by particle sizes. We show that particle size influences isotope ratios and propose a simple, cost-effective filtration method for primate feces to exclude larger undigested food particles from the analysis, which can easily be adopted by labs worldwide.     

Freezing and chemical preservatives alter the stable isotope values of carbon and nitrogen of the Asiatic clam (Corbicula fluminea)

We tested the impacts of most common sample preservation methods used for aquatic sample materials on the stable isotope ratios of carbon and nitrogen in clams, a typical baseline indicator organism for many aquatic food web studies utilising stable isotope analysis (SIA). In addition to common chemical preservatives ethanol and formalin, we also assessed the potential impacts of freezing on δ¹³C and δ¹⁵N values and compared the preserved samples against freshly dried and analysed samples. All preservation methods, including freezing, had significant impacts on δ¹³C and δ¹⁵N values and the effects in general were greater on the carbon isotope values (1.3–2.2‰ difference) than on the nitrogen isotope values (0.9–1.0‰ difference). However, the impacts produced by the preservation were rather consistent within each method during the whole 1 year experiment allowing these to be accounted for, if clams are intended for use in retrospective stable isotope studies.     

DeltaMS: a tool to track isotopologues in GC- and LC-MS data

Introduction

Stable isotopic labeling experiments are powerful tools to study metabolic pathways, to follow tracers and fluxes in biotic and abiotic transformations and to elucidate molecules involved in metal complexing.

Objective

To introduce a software tool for the identification of isotopologues from mass spectrometry data.

Methods

DeltaMS relies on XCMS peak detection and X¹³CMS isotopologue grouping and then analyses data for specific isotope ratios and the relative error of these ratios. It provides pipelines for recognition of isotope patterns in three experiment types commonly used in isotopic labeling studies: (1) search for isotope signatures with a specific mass shift and intensity ratio in one sample set, (2) analyze two sample sets for a specific mass shift and, optionally, the isotope ratio, whereby one sample set is isotope-labeled, and one is not, (3) analyze isotope-guided perturbation experiments with a setup described in X¹³CMS.

Results

To illustrate the versatility of DeltaMS, we analyze data sets from case-studies that commonly pose challenges in evaluation of natural isotopes or isotopic signatures in labeling experiment. In these examples, the untargeted detection of sulfur, bromine and artificial metal isotopic patterns is enabled by the automated search for specific isotopes or isotope signatures.

Conclusion

DeltaMS provides a platform for the identification of (pre-defined) isotopologues in MS data from single samples or comparative metabolomics data sets.

Graphical Abstract

Open image in new window

     

Kangaroo tooth enamel oxygen and carbon isotope variation on a latitudinal transect in southern Australia: implications for palaeoenvironmental reconstruction

Tooth enamel apatite carbonate carbon and oxygen isotope ratios of modern kangaroos (Macropus spp.) collected on a 900-km latitudinal transect spanning a C₃–C₄ transition zone were analysed to create a reference set for palaeoenvironmental reconstruction in southern Australia. The carbon isotope composition of enamel carbonate reflects the proportional intake of C₃ and C₄ vegetation, and its oxygen isotope composition reflects that of ingested water. Tooth enamel forms incrementally, recording dietary and environmental changes during mineralisation. Analyses show only weak correlations between climate records and latitudinal changes in δ¹³C and δ¹⁸O. No species achieved the δ¹³C values (~?1.0 ‰) expected for 100 % C₄ grazing diets; kangaroos at low latitudes that are classified as feeding primarily on C₄ grasses (grazers) have δ¹³C of up to ?3.5 ‰. In these areas, δ¹³C below ?12 ‰ suggests a 100 % C₃ grass and/or leafy plant (browse) diet while animals from higher latitude have lower δ¹³C. Animals from semi-arid areas have δ¹⁸O of 34–40 ‰, while grazers from temperate areas have lower values (~28–30 ‰). Three patterns with implications for palaeoenvironmental reconstruction emerge: (1) all species in semi-arid areas regularly browse to supplement limited grass resources; (2) all species within an environmental zone have similar carbon and oxygen isotope compositions, meaning data from different kangaroo species can be pooled for palaeoenvironmental investigations; (3) relatively small regional environmental differences can be distinguished when δ¹³C and δ¹⁸O data are used together. These data demonstrate that diet–isotope and climate–isotope relationships should be evaluated in modern ecosystems before application to the regional fossil record.     

DFT study of a series of crown-4 ethers and their selectivity trend for alkali metal cations: Li+ and Na+

The molecular and electronic structures for 12- to 16-crown-4 (named 12C4, 13C4, 14C4, 15C4, 16C4, respectively) and 2,3,5,6,8,9-hexahydrobenzo[b][1,4,7,10]tetraoxacyclododecine (B12C4) 3,5,6,7,9,10-hexahydro -2H-benzo[e][1,4,7,10]tetraoxacyclotridecine (B13C4) and their complexes with alkali metal cations Li⁺ and Na⁺ have been explored using the density functional theory (DFT) with B3LYP/ 6–31G* method. The nucleophilicity of crown-4 ethers has been investigated by the Fukui function. Their selectivity trend shows that of all the crown-4 ethers, 14C4 shows the highest cation selectivity for Li⁺ over Na⁺, has been achieved on the basis of thermodynamic analysis. In addition, Li⁺/crown-4 series are more stable than Na⁺/crown-4 series in the gas phase. The calculated results are in good agreement with the experimental observation.     

Seasonal and daily time course of the 13C composition in soil CO2 efflux recorded with a tunable diode laser spectrophotometer (TDLS)

Temporal variations of carbon isotope composition of soil CO₂ efflux (F_S and δ¹³C_FS) at different time scales should reflect both temporal variations of the climate conditions that affect canopy functioning and temporal changes in the relative contribution of autotrophic respiration to total F_S. A tunable diode laser spectrophotometer (TDLS) was installed in the Hesse forest (northeast of France) early during the 2007 growing season to determine the seasonal and daily variability in δ¹³C_FS. This method, based on the measurement of the absorption of an infrared laser emission at specific wave lengths of the ¹³CO₂ and ¹²CO₂, allows the continuous monitoring of the two isotopologues. The concentrations of the two isotopologues in F_S were continuously monitored from June to November 2007 using chamber method and Keeling plots drawn from nocturnal accumulation of CO₂ below the canopy. These TDLS measurements and isotope ratio mass spectrometer based Keeling plots gave very similar values of δ¹³C_FS, showing the reliability of the TDLS system in this context. Results were analysed with regard to seasonal and daily changes in climatic and edaphic variables and compared with the δ¹³C of CO₂ respired by roots, litter and soil incubated under controlled conditions. Pronounced daily as well as seasonal variations in δ¹³C_FS were recorded (up to 1.5‰). The range of variation of δ¹³C_FS was of the same order of magnitude at both diurnal and seasonal scales. δ¹³C_FS observed in the field fluctuated between values of litter and of root respiration recorded during incubation, suggesting that temporal (and probably spatial) variations were associated with changes in the relative contribution of the two compartments during the day and during the season.     

Anthranilic acid,the new player in the ensemble of aromatic residue labeling precursor compounds

The application of metabolic precursors for selective stable isotope labeling of aromatic residues in cell-based protein overexpression has already resulted in numerous NMR probes to study the structural and dynamic characteristics of proteins. With anthranilic acid, we present the structurally simplest precursor for exclusive tryptophan side chain labeling. A synthetic route to ¹³C, ²H isotopologues allows the installation of isolated ¹³C–¹H spin systems in the indole ring of tryptophan, representing a versatile tool to investigate side chain motion using relaxation-based experiments without the loss of magnetization due to strong ¹J_CC and weaker ²J_CH scalar couplings, as well as dipolar interactions with remote hydrogens. In this article, we want to introduce this novel precursor in the context of hitherto existing techniques of in vivo aromatic residue labeling.     

Carbon and sulfur isotopic signatures of ancient life and environment at the microbial scale: Neoarchean shales and carbonates

An approach to coordinated, spatially resolved, in situ carbon isotope analysis of organic matter and carbonate minerals, and sulfur three‐ and four‐isotope analysis of pyrite with an unprecedented combination of spatial resolution, precision, and accuracy is described. Organic matter and pyrite from eleven rock samples of Neoarchean drill core express nearly the entire range of δ¹³C, δ³⁴S, Δ³³S, and Δ³⁶S known from the geologic record, commonly in correlation with morphology, mineralogy, and elemental composition. A new analytical approach (including a set of organic calibration standards) to account for a strong correlation between H/C and instrumental bias in SIMS δ¹³C measurement of organic matter is identified. Small (2–3 μm) organic domains in carbonate matrices are analyzed with sub‐permil accuracy and precision. Separate 20‐ to 50‐μm domains of kerogen in a single ~0.5 cm³ sample of the ~2.7 Ga Tumbiana Formation have δ¹³C = ?52.3 ± 0.1‰ and ?34.4 ± 0.1‰, likely preserving distinct signatures of methanotrophy and photoautotrophy. Pyrobitumen in the ~2.6 Ga Jeerinah Formation and the ~2.5 Ga Mount McRae Shale is systematically ¹³C‐enriched relative to co‐occurring kerogen, and associations with uraniferous mineral grains suggest radiolytic alteration. A large range in sulfur isotopic compositions (including higher Δ³³S and more extreme spatial gradients in Δ³³S and Δ³⁶S than any previously reported) are observed in correlation with morphology and associated mineralogy. Changing systematics of δ³⁴S, Δ³³S, and Δ³⁶S, previously investigated at the millimeter to centimeter scale using bulk analysis, are shown to occur at the micrometer scale of individual pyrite grains. These results support the emerging view that the dampened signature of mass‐independent sulfur isotope fractionation (S‐MIF) associated with the Mesoarchean continued into the early Neoarchean, and that the connections between methane and sulfur metabolism affected the production and preservation of S‐MIF during the first half of the planet's history.     

Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein

Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise ²H isotope shift measurements for ¹³C^??, ¹³C^??, ¹³C??, ¹⁵N, and ¹H^N have been obtained by using a mixed sample of protonated and uniformly perdeuterated ??-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil ²H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.     

Metabolomic profiling of bronchoalveolar lavage fluids by isotope labeling liquid chromatography mass spectrometry: a promising approach to studying experimental asthma

Metabolomic analysis of bronchoalveolar lavage fluid (BALF) may help understand the pathophysiology of pulmonary diseases such as asthma. However, a major analytical challenge is that most metabolites in BALF are in low abundance and further diluted by the collection procedure. Here we report a sensitive metabolomic profiling method based on ¹²C-/¹³C-differential isotope dansylation that targets amine- and phenol-containing metabolites, solid phase extraction for analyte enrichment, and liquid chromatography Fourier transform ion cyclotron resonance-mass spectrometry (LC–FTICR-MS). This method detected 250 ion pairs or putative metabolites in rat BALF and 36 of them were positively identified. The majority were not reported in previous studies using NMR or conventional LC–MS. The developed isotope labeling method was then applied to investigate metabolomic changes in BALF samples from a model of allergic asthma in rats. Statistical analysis of the resultant data showed that there was distinct separation between normal and inflamed rats. Metabolic pathway analysis indicated that the arginine-proline metabolic pathway was dysregulated in rats with experimental asthma.     

Otoliths speak out: why the Pacific halibut in Puget sound are different

Pacific halibut, Hippoglossus stenolepis, is one of the most important commercial groundfish and is managed as a single coast-wide population from Alaska to northern California. Nevertheless, genetic investigations did not show success in detecting the population structure of the species. Here I report stable oxygen and carbon isotope analyses (δ¹⁸O and δ¹³C) in otoliths to discriminate the stock differences from two sample locations between the Washington coast (WC) and the northern Puget Sound (PS), and two sample years in 2007 and 2008. In general the δ¹⁸O values of halibut otoliths from WC ranged from ?0.2 to 1.8‰, higher than the PS samples from ?0.5 to 1.4‰. In contrast, the δ¹³C values from WC ranged from ?3.6 to ?1.0‰, lower than the PS samples from ?3.2 to ?1.2‰. Results from the otolith nuclei (age-0 halibut) and the 8^th (the earliest maturity age for male halibut) and edge otolith rings (the latest location where the fish lived) showed significant differences between halibut samples from PS and WC. In particular, the sample location difference (between PS and WC) in both δ¹³C and δ¹⁸O data was significant and markedly larger than the sample year difference (between 2007 and 2008). These isotopic signatures provide evidence that the PS halibut may belong to a distinct stock that is significantly different from WC halibut.