A selective NMR method for detecting choline containing compounds in liver tissue: the 1H-14N HSQC experiment

Zero-field J-spectroscopy of quadrupolar nuclei

Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) allows molecular structure elucidation via measurement of electron-mediated spin-spin J-couplings. This study examines zero-field J-spectra from molecules with quadrupolar nuclei, exemplified by solutions of various isotopologues of ammonium cations. The spectra reveal differences between various isotopologues upon extracting precise J-coupling values from pulse-acquire measurements. A primary isotope effect, △ J = γ 14 N / γ 15 N J 15 N H - J 14 N H ≈ - 58 mHz, is deduced by analysis of the proton-nitrogen J-coupling ratios. This study points toward further experiments with symmetric cations containing quadrupolar nuclei, promising applications in biomedicine, energy storage, and benchmarking quantum chemistry calculations.

Application of 15N-Edited 1H-13C Correlation NMR Spectroscopy─Toward Fragment-Based Metabolite Identification and Screening via HCN Constructs

Many key building blocks of life contain nitrogen moieties. Despite the prevalence of nitrogen-containing metabolites in nature, 15N nuclei are seldom used in NMR-based metabolite assignment due to their low natural abundance and lack of comprehensive chemical shift databases. However, with advancements in isotope labeling strategies, 13C and 15N enriched metabolites are becoming more common in metabolomic studies. Simple multidimensional nuclear magnetic resonance (NMR) experiments that correlate 1H and 15N via single bond 1JNH or multiple bond 2-3JNH couplings using heteronuclear single quantum coherence (HSQC) or heteronuclear multiple bond coherence are well established and routinely applied for structure elucidation. However, a 1H-15N correlation spectrum of a metabolite mixture can be difficult to deconvolute, due to the lack of a 15N specific database. In order to bridge this gap, we present here a broadband 15N-edited 1H-13C HSQC NMR experiment that targets metabolites containing 15N moieties. Through this approach, nitrogen-containing metabolites, such as amino acids, nucleotide bases, and nucleosides, are identified based on their 13C, 1H, and 15N chemical shift information. This approach was tested and validated using a [15N, 13C] enriched Daphnia magna (water flea) metabolite extract, where the number of clearly resolved 15N-containing peaks increased from only 11 in a standard HSQC to 51 in the 15N-edited HSQC, and the number of obscured peaks decreased from 59 to just 7. The approach complements the current repertoire of NMR techniques for mixture deconvolution and holds considerable potential for targeted metabolite NMR in 15N, 13C enriched systems.

Linking research of biomedical datasets

Biomedical data preprocessing and efficient computing can be as important as the statistical methods used to fit the data; data processing needs to consider application scenarios, data acquisition and individual rights and interests. We review common principles, knowledge and methods of integrated research according to the whole-pipeline processing mechanism diverse, coherent, sharing, auditable and ecological. First, neuromorphic and native algorithms integrate diverse datasets, providing linear scalability and high visualization. Second, the choice mechanism of different preprocessing, analysis and transaction methods from raw to neuromorphic was summarized on the node and coordinator platforms. Third, combination of node, network, cloud, edge, swarm and graph builds an ecosystem of cohort integrated research and clinical diagnosis and treatment. Looking forward, it is vital to simultaneously combine deep computing, mass data storage and massively parallel communication.

Harnessing Water to Enhance Quadrupolar NMR Spectroscopy and Imaging

¹⁷ O and ¹⁴ N are attractive targets for in vivo NMR spectroscopy and imaging, but low gyromagnetic ratios γ and fast spin relaxation complicate observations. This work explores indirect ways of detecting some of these sites with the help of proton-detected double resonance techniques. As standard coherence transfer methods are of limited use for such indirect detection, alternative routes for probing the quadrupolar spectra on ¹ H were tested. These centered on modulating the broadening effects imparted onto protons adjacent to the low-γ species through J couplings through either continuous wave or spin-echo double-resonance decoupling/recoupling sequences. As in all cases, the changes imparted by these double-resonance strategies were small due to the fast relaxation undergone by the quadrupoles, the sensitivity of these approaches was amplified by transferring their effects onto the abundant water ¹ H signal. These amplifications were mediated by the spontaneous exchanges that the labile ¹ Hs bound to ¹⁷ O or ¹⁴ N undergo with the water protons. In experiments designed on the basis of double-resonance spin echoes, these enhancements were imparted by looping the transverse encodings together with multiple longitudinal storage periods, leading to decoupling-recoupling with exchange (D-REX) sequences. In experiments designed on the basis of continuous on/off quadrupolar decoupling, these solvent exchanges were incorporated into chemical-exchange saturation transfer schemes, leading to decoupling-recoupling with saturation transfer (D-REST) sequences. Both of these variants harnessed sizable proportions of the easily detectable water signals, in order to characterize the NMR spectra and/or to image with atomic-site specificity the ¹⁷ O and ¹⁴ N species.

Untargeted 2D NMR Metabolomics of [13C-methyl]Methionine-Labeled Tumor Models Reveals the Non-DNA Methylome and Provides Clues to Methyl Metabolism Shift during Tumor Progression

For more than a decade, DNA and histone methylations have been the focus of extensive work, although their relationship with methyl group metabolism was overlooked. Recently, it has emerged that epigenetic methylations are influenced by methyl donor nutrient availability, cellular levels of S-adenosyl-methionine (SAM), and cytoplasmic methyltransferase activities. SAM-dependent methyltransferases methylate a wide range of targets, from small molecules to proteins and nucleic acids. However, few investigations of the global methylome of tumors have been performed. Here, untargeted NMR metabolomics of two mouse tumor models labeled with [¹³C-methyl]methionine were used to search for the NMR-visible set of cellular methyl acceptors denoted the global methylome. Tumor models were B16 melanoma cell cultures and B16 melanoma tumors, which may be considered as two stages of B16 tumor development. Based on 2D ¹H-¹³C NMR spectra and orthogonal partial least squares discriminant analysis of spectra, our study revealed markedly different global methylomes for melanoma models. The methylome of B16 melanoma cell cultures was dominated by histone methylations, whereas that of B16 melanoma tumors was dominated by cytoplasmic small-molecule methylations. Overall, the technique gave access to the non-DNA methylome. Comparison of tumor models also exhibiting differential expression of aerobic glycolysis provided clues to a methyl metabolism shift during tumor progression.

A Crosstalk- and Interferent-Free Dual Electrode Amperometric Biosensor for the Simultaneous Determination of Choline and Phosphocholine

Choline (Ch) and phosphocholine (PCh) levels in tissues are associated to tissue growth and so to carcinogenesis. Till now, only highly sophisticated and expensive techniques like those based on NMR spectroscopy or GC/LC- high resolution mass spectrometry permitted Ch and PCh analysis but very few of them were capable of a simultaneous determination of these analytes. Thus, a never reported before amperometric biosensor for PCh analysis based on choline oxidase and alkaline phosphatase co-immobilized onto a Pt electrode by co-crosslinking has been developed. Coupling the developed biosensor with a parallel sensor but specific to Ch, a crosstalk-free dual electrode biosensor was also developed, permitting the simultaneous determination of Ch and PCh in flow injection analysis. This novel sensing device performed remarkably in terms of sensitivity, linear range, and limit of detection so to exceed in most cases the more complex analytical instrumentations. Further, electrode modification by overoxidized polypyrrole permitted the development of a fouling- and interferent-free dual electrode biosensor which appeared promising for the simultaneous determination of Ch and PCh in a real sample.

Monitoring alkaline transitions of yeast iso-1 cytochrome c at natural isotopic abundance using trimethyllysine as a native NMR probe

Spectral overlap makes it difficult to use NMR for mapping the conformational profile of heterogeneous conformational ensembles of macromolecules. Here, we apply a 1H-14N HSQC experiment to monitor the alkaline conformational transitions of yeast iso-1 cytochrome c (ycyt c) at natural isotopic abundance. Trimethylated Lys72 of ycyt c is selectively detected by a 1H-14N HSQC experiment, and used as a probe to trace conformational transitions of ycyt c under alkaline conditions. It was found that at least four different conformers of ycyt c coexisted under alkaline conditions. Besides the native structure, Lys73 or Lys79 coordinated conformers and a partially unfolded state with exposed heme were observed. These results indicate that the method is powerful at simplifying spectra of a trimethylated protein, which makes it possible to study complex conformational transitions of naturally extracted or chemically modified trimethylated protein at natural isotopic abundance.

Assessment of MR-based R2* and quantitative susceptibility mapping for the quantification of liver iron concentration in a mouse model at 7T

PURPOSE

To assess the feasibility of quantifying liver iron concentration (LIC) using R2* and quantitative susceptibility mapping (QSM) at a high field strength of 7 Tesla (T).

METHODS

Five different concentrations of Fe-dextran were injected into 12 mice to produce various degrees of liver iron overload. After mice were sacrificed, blood and liver samples were harvested. Ferritin enzyme-linked immunosorbent assay (ELISA) and inductively coupled plasma mass spectrometry were performed to quantify serum ferritin concentration and LIC. Multiecho gradient echo MRI was conducted to estimate R2* and the magnetic susceptibility of each liver sample through complex nonlinear least squares fitting and a morphology enabled dipole inversion method, respectively.

RESULTS

Average estimates of serum ferritin concentration, LIC, R2*, and susceptibility all show good linear correlations with injected Fe-dextran concentration; however, the standard deviations in the estimates of R2* and susceptibility increase with injected Fe-dextran concentration. Both R2* and susceptibility measurements also show good linear correlations with LIC (R2  = 0.78 and R2  = 0.91, respectively), and a susceptibility-to-LIC conversion factor of 0.829 ppm/(mg/g wet) is derived.

CONCLUSION

The feasibility of quantifying LIC using MR-based  R2* and QSM at a high field strength of 7T is demonstrated. Susceptibility quantification, which is an intrinsic property of tissues and benefits from being field-strength independent, is more robust than R2* quantification in this ex vivo study. A susceptibility-to-LIC conversion factor is presented that agrees relatively well with previously published QSM derived results obtained at 1.5T and 3T.

(1)H- (31)P soft-HSQC pulse sequence specifically for detecting phosphomono- and diesters in biological samples

PURPOSE

Phosphomono- and diesters (PME and PDE) are important metabolites that are potential biomarkers for a number of cancers. We designed a new NMR pulse sequence, i.e., (1)H-(31)P soft-heteronuclear single quantum correlation (HSQC), specifically for noninvasively detecting PME and PDE in biological samples.

PROCEDURE

The nonselective (1)H refocusing π pulses in the conventional heteronuclear single quantum correlation pulse sequence are replaced by selective π pulses. When the selective pulses are offset on the CH2O resonances, the homonuclear couplings between the NCH2 and CH2O protons are effectively removed, and the spectrum of PME and PDE is significantly enhanced.

RESULTS

The sensitivity of this pulse sequence has been demonstrated with milk and mouse brain samples. A soft-HSQC spectrum, where only PME and PDE signals appear, can be recorded from these biological samples in minutes with remarkably high signal-to-noise ratio.

CONCLUSION

This pulse sequence provides a new and quick method for in vivo studies of phosphorus metabolite in the human brain and other tissues for medical purposes.

Fast detection of choline-containing metabolites in liver using 2D ¹H-¹⁴N three-bond correlation (HN3BC) spectroscopy

Detection and quantification of total choline-containing metabolites (CCMs) in tissues by magnetic resonance spectroscopy (MRS) has received considerable attention as a biomarker of cancer. Tissue CCMs are mainly choline (Cho), phosphocholine (PCho), and glycerophosphocholine (GPCho). Because the methyl (1)H resonances of tissue CCMs exhibit small chemical shift differences and overlap significantly in 1D (1)H MRS, quantification of individual components is precluded. Development of a MRS method capably of resolving individual components of tissue CCMs would be a significant advance. Herein, a modification of the 2D (1)H-(14)N HSQC technique is targeted on the two methylene (1)H in the CH(2)O group ((3)J(1H14N)=2.7 Hz) and applied to ex vivo mouse and human liver samples at physiological temperature (37°C). Specifically, the (1)H-(14)N HSQC technique is modified into a 2D (1)H-(14)N three-bond correlation (HN3BC) experiment, which selectively detects the (1)H of CH(2)O coupled to (14)N in CCMs. Separate signals from Cho, PCho, and GPCho components are resolved with high detection sensitivity. A 2D HN3BC spectrum can be recorded from mouse liver in only 1.5 min and from human carcinoma liver tissue in less than 3 min with effective sample volume of 0.2 ml at 14.1T.