Natural Isotope Abundance in Metabolites: Techniques and Kinetic Isotope Effect Measurement in Plant, Animal, and Human Tissues

Understanding natural isotopic variations in cultured cancer cells

RATIONALE

Natural variations in the abundance of the stable isotopes of nitrogen (δ15N) and carbon (δ13C) offer valuable insights into metabolic fluxes. In the wake of strong interest in cancer metabolism, recent research has revealed δ15N and δ13C variations in cancerous compared to non-cancerous tissues and cell lines. However, our understanding of natural isotopic variations in cultured mammalian cells, particularly in relation to metabolism, remains limited. This study aims to start addressing this gap using metabolic modulations in cells cultured under controlled conditions.

METHODS

Prostate cancer cells (PC3) were cultured in different conditions and their δ15N and δ13C were measured using isotope ratio mass spectrometry. Isotopic variations during successive cell culture passages were assessed and two widely used cell culture media (RPMI and DMEM) were compared. Metabolism was modulated through glutamine deprivation and hypoxia.

RESULTS

Successive cell culture passages generally resulted in reproducible δ15N and δ13C values. The impact of culture medium composition on δ15N and δ13C of the cells highlights the importance of maintaining a consistent medium composition across conditions whenever possible. Glutamine deprivation and hypoxia induced a lower δ13C in bulk cell samples, with only the former affecting δ15N. Gaps between theory and experiments were bridged and the lessons learned throughout the process are provided.

CONCLUSIONS

Exposing cultured cancer cells to hypoxia allowed us to further investigate the relation between metabolic modulations and natural isotopic variations, while mitigating the confounding impact of changing culture medium composition. This study highlights the potential of natural δ13C variations for studying substrate fluxes and nutrient allocation in reproducible culture conditions. Considering cell yield and culture medium composition is pivotal to the success of this approach.

Position-specific carbon stable isotope analysis of glyphosate: isotope fingerprinting of molecules within a mixture

Glyphosate [N-(phosphonomethyl) glycine] is a widely used herbicide and a molecule of interest in the environmental sciences, due to its global use in agriculture and its potential impact on ecosystems. This study presents the first position-specific carbon isotope (13C/12C) analyses of glyphosates from multiple sources. In contrast to traditional isotope ratio mass spectrometry (IRMS), position-specific analysis provides 13C/12C ratios at individual carbon atom positions within a molecule, rather than an average carbon isotope ratio across a mixture or a specific compound. In this work, glyphosate in commercial herbicides was analyzed with only minimal purification, using a nuclear magnetic resonance (NMR) spectroscopy method that detects 1H nuclei with bonds to either 13C or 12C, and isolates the signals of interest from other signals in the mixture. Results demonstrate that glyphosate from different sources can have significantly different intramolecular 13C/12C distributions, which were found to be spread over a wide range, with δ13C Vienna Peedee Belemnite (VPDB) values of -28.7 to -57.9‰. In each glyphosate, the carbon with a bond to the phosphorus atom was found to be depleted in 13C compared to the carbon at the C2 position, by 4 to 10‰. Aminomethylphosphonic acid (AMPA) was analyzed for method validation; AMPA contains only a single carbon position, so the 13C/12C results provided by the NMR method could be directly compared with traditional isotope ratio mass spectrometry. The glyphosate mixtures were also analyzed by IRMS to obtain their average 13C/12C ratios, for comparison with our position-specific results. This comparison revealed that the IRMS results significantly disguise the intramolecular isotope distribution. Finally, we introduce a 31P NMR method that can provide a position-specific 13C/12C ratio for carbon positions with a C-P chemical bond, and the results obtained by 1H and 31P for C3 carbon agree with one another within their analytical uncertainty. These analytical tools for position-specific carbon isotope analysis permit the isotopic fingerprinting of target molecules within a mixture, with potential applications in a range of fields, including the environmental sciences and chemical forensics.

Guamara and Cocuixtle: Source of Proteases for the Transformation of Shrimp By-Products into Hydrolysates with Potential Application

Since the fruits of Bromelia pinguin and Bromelia karatas are rich in proteases, the aim of this research was to optimize the hydrolysis process of cooked white shrimp by-products due to the effect of these proteases. A robust Taguchi L_16' design was used to optimize the hydrolysis process. Similarly, the amino acid profile by GC-MS and antioxidant capacity (ABTS and FRAP) were determined. The optimal conditions for hydrolysis of cooked shrimp by-products were pH 8.0, 30 °C, 0.5 h, 1 g of substrate and 100 µg/mL of B. karatas, pH 7.5, 40 °C, 0.5 h, 0.5 g substrate and 100 µg/mL enzyme extract from B. pinguin and pH 7.0, 37 °C, 1 h, 1.5 g substrate and 100 µg/mL enzyme bromelain. The optimized hydrolyzates of B. karatas B. pinguin and bromelain had 8 essential amino acids in their composition. The evaluation of the antioxidant capacity of the hydrolyzates under optimal conditions showed more than 80% inhibition of in ABTS radical, B. karatas hydrolyzates had better higher ferric ion reduction capacity with 10.09 ± 0.02 mM TE/mL. Finally, the use of proteolytic extracts from B. pinguin and B. karatas to optimize hydrolysis process allowed obtaining hydrolyzates of cooked shrimp by-products with potential antioxidant capacity.

13C Natural Isotope Abundance in Urothelium as a New Marker in the Follow-Up of Patients with Bladder Cancer

Bladder cancer (BC) is the most common urological malignancy and has a high incidence of recurrence. BC cells alter their nutrient uptake and metabolic pathways in order to continue the production of sufficient levels of ATP and metabolic intermediates for proliferation and survival. Changes in metabolic pathways regarding the rate of the enzymatic reaction and transport lead to differences in the content of natural isotopes (13C, 15N, 34S) between normal and cancerous tissues. The assessment of the stable isotopes of carbon, nitrogen, and sulfur in normal urothelium and bladder cancer samples was performed using Isotope Ratio Mass Spectrometry (IRMS). The natural abundance of 15N and 13C was decreased in bladder cancer samples when compared to normal urothelium. No significant correlation was observed in BC specimens depending on the tumor grade and stage. Samples derived from bladder tumors and normal urothelium had a different pattern of 15N and 13C isotope abundance. Decreased 13C natural isotopes in the normal urothelium of BC patients were significantly associated with a shorter DFS. Our results suggest that isotopic analysis of normal urothelium of BC patients can be used to predict bladder cancer recurrence.

Compound-Specific 14N/15N Analysis of Amino Acid Trimethylsilylated Derivatives from Plant Seed Proteins

Isotopic analyses of plant samples are now of considerable importance for food certification and plant physiology. In fact, the natural nitrogen isotope composition (δ¹⁵N) is extremely useful to examine metabolic pathways of N nutrition involving isotope fractionations. However, δ¹⁵N analysis of amino acids is not straightforward and involves specific derivatization procedures to yield volatile derivatives that can be analysed by gas chromatography coupled to isotope ratio mass spectrometry (GC-C-IRMS). Derivatizations other than trimethylsilylation are commonly used since they are believed to be more reliable and accurate. Their major drawback is that they are not associated with metabolite databases allowing identification of derivatives and by-products. Here, we revisit the potential of trimethylsilylated derivatives via concurrent analysis of δ¹⁵N and exact mass GC-MS of plant seed protein samples, allowing facile identification of derivatives using a database used for metabolomics. When multiple silylated derivatives of several amino acids are accounted for, there is a good agreement between theoretical and observed N mole fractions, and δ¹⁵N values are satisfactory, with little fractionation during derivatization. Overall, this technique may be suitable for compound-specific δ¹⁵N analysis, with pros and cons.

Stable Isotope Abundance and Fractionation in Human Diseases

The natural abundance of heavy stable isotopes (¹³C, ¹⁵N, ¹⁸O, etc.) is now of considerable importance in many research fields, including human physiology. In fact, it varies between tissues and metabolites due to isotope effects in biological processes, that is, isotope discriminations between heavy and light isotopic forms during enzyme or transporter activity. The metabolic deregulation associated with many diseases leads to alterations in metabolic fluxes, resulting in changes in isotope abundance that can be identified easily with current isotope ratio technologies. In this review, we summarize the current knowledge on changes in natural isotope composition in samples (including various tissues, hair, plasma, saliva) found in patients compared to controls, caused by human diseases. We discuss the metabolic origin of such isotope fractionations and highlight the potential of using isotopes at natural abundance for medical diagnosis and/or prognostic.

N uptake, assimilation and isotopic fractioning control δ 15N dynamics in plant DNA: A heavy labelling experiment on Brassica napus L

In last decades, a large body of evidence clarified nitrogen isotope composition (δ¹⁵N) patterns in plant leaves, roots and metabolites, showing isotopic fractionation along N uptake and assimilation pathways, in relation to N source and use efficiency, also suggesting ¹⁵N depletion in plant DNA. Here we present a manipulative experiment on Brassica napus var. oleracea, where we monitored δ ¹⁵N of purified, lyophilized DNA and source leaf and root materials, over a 60-days growth period starting at d 60 after germination, in plants initially supplied with a heavy labelled (δ ¹⁵N_Air-N2 = 2100 mUr) ammonium nitrate solution covering nutrient requirements for the whole observation period (470 mg N per plant) and controlling for the labelled N species (ṄH₄, ṄO₃ and both). Dynamics of Isotopic Ratio Mass Spectrometry (IRMS) data for the three treatments showed that: (1) leaf and root δ ¹⁵N dynamics strictly depend on the labelled chemical species, with ṄH₄, ṄO₃ and ṄH₄ṄO₃ plants initially showing higher, lower and intermediate values, respectively, then converging due to the progressive NH₄⁺ depletion from the nutrient solution; (2) in ṄH₄ṄO₃, where δ¹⁵N was not affected by the labelled chemical species, we did not observe isotopic fractionation associated to inorganic N uptake; (3) δ¹⁵N values in roots compared to leaves did not fully support patterns predicted by differences in assimilation rates of NH₄⁺ and NO₃^-; (4) DNA is depleted in ¹⁵N compared to the total N pools of roots and leaves, likely due to enzymatic discrimination during purine biosynthesis. In conclusion, while our experimental setup did not allow to assess the fractionation coefficient (ε) associated to DNA bases biosynthesis, this is the first study specifically reporting on dynamics of specific plant molecular pools such as nucleic acids over a long observation period with a heavy labelling technique.

Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes

Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.

Intramolecular distribution of 13C/12C isotopes in amino acids of diverse origins

Carbon stable isotope analysis can provide information about the origin and synthetic pathways that produce organic molecules, with applications in chemical, medical and (bio)geochemical sciences. The ¹³C/¹²C isotope ratios of organics such as amino acids are most commonly obtained as whole molecule averages. In this study, we apply proton nuclear magnetic resonance spectroscopy to conduct position-specific carbon isotope analyses of L-/D-alanine, L-threonine and L-histidine from different sources, in addition to molecule average stable isotope analyses obtained via mass spectrometry. Our results demonstrate that carbon isotope ratios can vary significantly between the individual carbon positions within an amino acid. For example, the β- and γ- carbons of L-threonine can differ in ¹³C/¹²C ratio by > 20 ‰. Comparisons of the position-specific and whole molecule average stable isotope abundances show that whole molecule analyses can mask the intramolecular isotope variation. These results provide the first experimentally measured position-specific isotope ratios for alpha and side chain carbons of alanine, threonine and histidine. Comparison with previous ab initio calculations of intramolecular equilibrium fractionation shows that the carbon isotope distributions are not at equilibrium, thus kinetic isotope effects play a significant role in amino acid synthesis. We hypothesize that position-specific ¹³C/¹²C isotope ratios provide an "isotopic fingerprint" that can give insight into the origin or synthesis pathway that formed an amino acid, and that this emerging analytical field will be a valuable addition to traditional stable isotope analysis.

Site-specific peak intensity ratio (SPIR) from 1D 2H/1H NMR spectra for rapid distinction between natural and synthetic nicotine and detection of possible adulteration

¹H and ²H NMR spectra of 4 natural and synthetic nicotine samples were collected in a non-quantitative way and site-specific ²H/¹H peak intensity ratio (SPIR) was calculated for 12 distinct sites of nicotine. Experimental results illustrated that the SPIRs at sites of 6, 2', and 5'β of natural nicotine were significantly different from those of the synthetic nicotine, and could be used for nicotine authentication as the measured SPIRs were indicative of the site-specific natural isotope fractionation. We demonstrated that this method could be applied to detect adulteration of natural nicotine with as low as 20% synthetic nicotine, without the need to measure the site-specific δD values, which usually required time-consuming quantitative ²H NMR and additional IRMS for the overall ²H/¹H isotopic ratio determination. The distinguishable ²H/¹H SPIRs of nicotine, which can be quickly measured by NMR in non-quantitative way, can serve as an attractive alternative tool for tobacco authentication. Graphical abstract.

Position-specific 13 C/12 C analysis of amino acid carboxyl groups - automated flow-injection analysis based on reaction with ninhydrin

RATIONALE

The fundamental level of stable isotopic knowledge lies at specific atomic positions within molecules but existing methods of analysis require lengthy off-line preparation to reveal this information. An automated position-specific isotope analysis (PSIA) method is presented to determine the stable carbon isotopic compositions of the carboxyl groups of amino acids (δ¹³ C_CARBOXYL values). This automation makes PSIA measurements easier and routine.

METHODS

An existing high-performance liquid chromatography (HPLC) gas handling interface/stable isotope ratio mass spectrometry system was modified by the addition of a post-column derivatisation unit between the HPLC system and the interface. The post-column reaction was optimised to yield CO₂ from the carboxyl groups of amino acids by reaction with ninhydrin.

RESULTS

The methodology described produced δ¹³ C_CARBOXYL values with typical standard deviations below ±0.1 ‰ and consistent differences (Δ¹³ C_CARBOXYL values) between amino acids over a 1-year period. First estimates are presented for the δ¹³ C_CARBOXYL values of a number of internationally available amino acid reference materials.

CONCLUSIONS

The PSIA methodology described provides a further dimension to the stable isotopic characterisation of amino acids at a more detailed level than the bulk or averaged whole-molecule level. When combined with on-line chromatographic separation or off-line fraction collection of protein hydrolysates the technique will offer an automated and routine way to study position-specific carboxyl carbon isotope information for amino acids, enabling more refined isotopic studies of carbon uptake and metabolism.