Metabolite assignment of ultrafiltered synovial fluid extracted from knee joints of reactive arthritis patients using high resolution NMR spectroscopy.

Currently, there are no reliable biomarkers available that can aid early differential diagnosis of reactive arthritis (ReA) from other inflammatory joint diseases. Metabolic profiling of synovial fluid (SF)-obtained from joints affected in ReA-holds great promise in this regard and will further aid monitoring treatment and improving our understanding about disease mechanism. As a first step in this direction, we report here the metabolite specific assignment of 1 H and 13 C resonances detected in the NMR spectra of SF samples extracted from human patients with established ReA. The metabolite characterization has been carried out on both normal and ultrafiltered (deproteinized) SF samples of eight ReA patients (n = 8) using high-resolution (800 MHz) 1 H and 1 H─13 C NMR spectroscopy methods such as one-dimensional 1 H CPMG and two-dimensional J-resolved1 H NMR and homonuclear 1 H─1 H TOCSY and heteronuclear1 H─13 C HSQC correlation spectra. Compared with normal SF samples, several distinctive 1 H NMR signals were identified and assigned to metabolites in the 1 H NMR spectra of ultrafiltered SF samples. Overall, we assigned 53 metabolites in normal filtered SF and 64 metabolites in filtered pooled SF sample compared with nonfiltered SF samples for which only 48 metabolites (including lipid/membrane metabolites as well) have been identified. The established NMR characterization of SF metabolites will serve to guide future metabolomics studies aiming to identify/evaluate the SF-based metabolic biomarkers of diagnostic/prognostic potential or seeking biochemical insights into disease mechanisms in a clinical perspective.

Developing and Standardizing a Protocol for Quantitative Proton Nuclear Magnetic Resonance (1H NMR) Spectroscopy of Saliva.

Metabolic profiling by 1H NMR spectroscopy is an underutilized technology in salivary research, although preliminary studies have identified promising results in multiple fields (diagnostics, nutrition, sports physiology). Translation of preliminary findings into validated, clinically approved knowledge is hindered by variability in protocol for the collection, storage, preparation, and analysis of saliva. This study aims to evaluate the effects of differing sample pretreatments on the 1H NMR metabolic profile of saliva. Protocol considerations are highly varied in the current literature base, including centrifugation, freeze-thaw cycles, and different NMR quantification methods. Our findings suggest that the 1H NMR metabolite profile of saliva is resilient to any change resulting from freezing, including freezing of saliva prior to centrifuging. However, centrifugation was necessary to remove an unidentified broad peak between 1.24 and 1.3 ppm, the intensity of which correlated strongly with saliva cellular content. This peak obscured the methyl peak from lactate and significantly affected quantification. Metabolite quantification was similar for saliva centrifuged between 750 g to 15 000 g. Quantification of salivary metabolites was similar whether quantified using internal phosphate-buffered sodium trimethylsilyl-[2,2,3,3-2H4]-propionate (TSP) or external TSP in a coaxial NMR tube placed inside the NMR tube containing the saliva sample. Our results suggest that the existing literature on salivary 1H NMR will not have been adversely affected by variations of the common protocol; however, use of TSP as an internal standard without a buffered medium appears to affect metabolite quantification, notably for acetate and methanol. We include protocol recommendations to facilitate future NMR-based studies of saliva.

MultiNet PyGRAPPA: Multiple neural networks for reconstructing variable density GRAPPA (a 1H FID MRSI study).

Magnetic resonance spectroscopic imaging (MRSI) is a powerful tool for mapping metabolite levels across the brain, however, it generally suffers from long scan times. This severely hinders its application in clinical settings. Additionally, the presence of nuisance signals (e.g. the subcutaneous lipid signals close to the skull region in brain metabolite mapping) makes it challenging to apply conventional acceleration techniques to shorten the scan times. The goal of this work is, therefore, to increase the overall applicability of high resolution metabolite mapping using 1H MRSI by introducing a novel GRAPPA acceleration acquisition/reconstruction technique. An improved reconstruction method (MultiNet) is introduced that uses machine learning, specifically neural networks, to reconstruct accelerated data. The method is further modified to use more neural networks with nonlinear hidden layers and is then combined with a variable density undersampling scheme (MultiNet PyGRAPPA) to enable higher in-plane acceleration factors of R = 5.6 and R = 7 for a non-lipid suppressed ultra-short TR and TE 1H FID MRSI sequence. The proposed method is evaluated for high resolution metabolite mapping of the human brain at 9.4T. The results show that the proposed method is superior to conventional GRAPPA: there is no significant residual lipid aliasing artifact in the images when the proposed MultiNet method is used. Furthermore, the MultiNet PyGRAPPA acquisition/reconstruction method with R = 5.6 results in reproducible high resolution metabolite maps (with an in-plane matrix size of 64 × 64) that can be acquired in 2.8 min on 9.4T. In conclusion, using multiple neural networks to predict the missing points in GRAPPA reconstruction results in a more reliable data recovery while keeping the noise levels under control. Combining this high fidelity reconstruction with variable density undersampling (MultiNet PyGRAPPA) enables higher in-plane acceleration factors even for non-lipid suppressed 1H FID MRSI, without introducing any structured aliasing artifact in the image.

MR Spectroscopy-derived Proton Density Fat Fraction Is Superior to Controlled Attenuation Parameter for Detecting and Grading Hepatic Steatosis.

Purpose To prospectively compare the diagnostic accuracy of controlled attenuation parameter (CAP) obtained with transient elastography and proton density fat fraction (PDFF) obtained with proton magnetic resonance (MR) spectroscopy with results of liver biopsy in a cohort of adult patients suspected of having nonalcoholic fatty liver disease (NAFLD). Materials and Methods The institutional review board approved this study. Informed consent was obtained from all patients. The authors evaluated 55 patients suspected of having NAFLD (40 men, 15 women). Patients had a median age of 52.3 years (interquartile range [IQR], 43.7-57.6 years) and a median body mass index of 27.8 kg/m2 (IQR, 26.0-33.1 kg/m2). CAP and PDFF measurements were obtained on the same day, within 27 days of biopsy (IQR, 7-44 days). CAP and PDFF were compared between steatosis grades by using the Jonckheere-Terpstra test. Diagnostic accuracies of CAP and PDFF for grading steatosis were assessed with receiver operating characteristic (ROC) analysis. Within-weeks reproducibility (CAP and PDFF) and within-session repeatability were assessed with linear regression analyses, intraclass correlation coefficients, and coefficients of variation. Results Steatosis grades at liver biopsy were distributed as follows: S0, five patients; S1, 24 patients; S2, 17 patients; and S3, nine patients. Both PDFF and CAP helped detect histologically proven steatosis (≥S1), but PDFF showed better diagnostic accuracy than CAP in terms of the area under the ROC curve (0.99 vs 0.77, respectively; P = .0334). PDFF, but not CAP, enabled the grading of steatosis (P < .0001). For within-weeks reproducibility, the intraclass correlation coefficient with PDFF was higher than that with CAP (0.95 vs 0.65, respectively; P = .0015); coefficients of variation were similar (19% vs 11%, P = .55). Within-session repeatability of CAP was good, with a coefficient of variation of 4.5%. Conclusion MR spectroscopy-derived PDFF is superior to CAP in detecting and grading liver steatosis in human NAFLD. © RSNA, 2017 Online supplemental material is available for this article.

Improved localization, spectral quality, and repeatability with advanced MRS methodology in the clinical setting.

PURPOSE: To investigate the utility of an advanced magnetic resonance spectroscopy (MRS) protocol in the clinical setting, and to compare the localization accuracy, spectral quality, and quantification repeatability between this advanced and the conventional vendor-provided MRS protocol on a clinical 3T platform. METHODS: Proton spectra were measured from the posterior cingulate cortices in 30 healthy elderly subjects by clinical MR technologists using a vendor-provided (point resolved spectroscopy with advanced 3D gradient-echo B0 shimming) and an advanced (semi-LASER with FAST(EST)MAP shimming) protocol, in random order. Spectra were quantified with LCModel using standard pipelines for the clinical and research settings, respectively. RESULTS: The advanced protocol outperformed the vendor-provided protocol in localization accuracy (chemical-shift-displacement error: 2.0%/ppm, semi-LASER versus 11.6%/ppm, point resolved spectroscopy), spectral quality (water linewidth: 6.1 ± 1.8 Hz, FAST(EST)MAP versus 10.5 ± 3.7 Hz, 3D gradient echo; P < 7e-6; residual water: 0.08 ± 0.12%, VAPOR versus 0.45 ± 0.50%, WET; P < 2e-5) and within-session repeatability of metabolite concentrations, particularly of low signal-to-noise ratio data with two to eight averages (test-retest coefficients of variance of metabolite concentrations, P < 0.01). Concentrations of J-coupled metabolites such as γ-aminobutyric acid and glutamate were biased when using the default pipeline with simulated macromolecules. CONCLUSIONS: The quality of MRS data can be improved using advanced acquisition and analysis protocols on standard 3T hardware in the clinical setting, which can facilitate robust applications in central nervous system diseases. Magn Reson Med 79:1241-1250, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

rDolphin: a GUI R package for proficient automatic profiling of 1D 1H-NMR spectra of study datasets.

INTRODUCTION: Adoption of automatic profiling tools for 1H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices. OBJECTIVES: To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process. METHODS: rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality. RESULTS: The information and quality achieved in two public datasets of complex matrices are maximized. CONCLUSION: rDolphin is an open-source R package ( http://github.com/danielcanueto/rDolphin ) able to provide the best balance between accuracy, reproducibility and ease of use.

Quantitative determination and validation of octreotide acetate using 1 H-NMR spectroscopy with internal standard method.

Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated 1 H-qNMR method for assay of octreotide acetate, a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard. Experimental conditions, including relaxation delay time, the numbers of scans, and pulse angle, were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision, and robustness. The assay result was compared with that by means of high performance liquid chromatography, which is provided by Chinese Pharmacopoeia. The statistical F test, Student's t test, and nonparametric test at 95% confidence level indicate that there was no significant difference between these two methods. qNMR is a simple and accurate quantitative tool with no need for specific corresponding reference standards. It has the potential of the quantitative analysis of other peptide drugs and standardization of the corresponding reference standards.

Toward Reliable Lipoprotein Particle Predictions from NMR Spectra of Human Blood: An Interlaboratory Ring Test.

Lipoprotein profiling of human blood by 1H nuclear magnetic resonance (NMR) spectroscopy is a rapid and promising approach to monitor health and disease states in medicine and nutrition. However, lack of standardization of measurement protocols has prevented the use of NMR-based lipoprotein profiling in metastudies. In this study, a standardized NMR measurement protocol was applied in a ring test performed across three different laboratories in Europe on plasma and serum samples from 28 individuals. Data was evaluated in terms of (i) spectral differences, (ii) differences in LPD predictions obtained using an existing prediction model, and (iii) agreement of predictions with cholesterol concentrations in high- and low-density lipoproteins (HDL and LDL) particles measured by standardized clinical assays. ANOVA-simultaneous component analysis (ASCA) of the ring test spectral ensemble that contains methylene and methyl peaks (1.4-0.6 ppm) showed that 97.99% of the variance in the data is related to subject, 1.62% to sample type (serum or plasma), and 0.39% to laboratory. This interlaboratory variation is in fact smaller than the maximum acceptable intralaboratory variation on quality control samples. It is also shown that the reproducibility between laboratories is good enough for the LPD predictions to be exchangeable when the standardized NMR measurement protocol is followed. With the successful implementation of this protocol, which results in reproducible prediction of lipoprotein distributions across laboratories, a step is taken toward bringing NMR more into scope of prognostic and diagnostic biomarkers, reducing the need for less efficient methods such as ultracentrifugation or high-performance liquid chromatography (HPLC).

Workflow for Integrated Processing of Multicohort Untargeted 1H NMR Metabolomics Data in Large-Scale Metabolic Epidemiology.

Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robust processing pipelines that can ensure reliable data for statistical analysis. The COMBI-BIO project incorporates serum from ∼8000 individuals, in three cohorts, profiled by six assays in two phases using both 1H NMR and UPLC-MS. Here we present the COMBI-BIO NMR analysis pipeline and demonstrate its fitness for purpose using representative quality control (QC) samples. NMR spectra were first aligned and normalized. After eliminating interfering signals, outliers identified using Hotelling's T2 were removed and a cohort/phase adjustment was applied, resulting in two NMR data sets (CPMG and NOESY). Alignment of the NMR data was shown to increase the correlation-based alignment quality measure from 0.319 to 0.391 for CPMG and from 0.536 to 0.586 for NOESY, showing that the improvement was present across both large and small peaks. End-to-end quality assessment of the pipeline was achieved using Hotelling's T2 distributions. For CPMG spectra, the interquartile range decreased from 1.425 in raw QC data to 0.679 in processed spectra, while the corresponding change for NOESY spectra was from 0.795 to 0.636, indicating an improvement in precision following processing. PCA indicated that gross phase and cohort differences were no longer present. These results illustrate that the pipeline produces robust and reproducible data, successfully addressing the methodological challenges of this large multifaceted study.

SpinCouple: Development of a Web Tool for Analyzing Metabolite Mixtures via Two-Dimensional J-Resolved NMR Database.

A new Web-based tool, SpinCouple, which is based on the accumulation of a two-dimensional (2D) (1)H-(1)H J-resolved NMR database from 598 metabolite standards, has been developed. The spectra include both J-coupling and (1)H chemical shift information; those are applicable to a wide array of spectral annotation, especially for metabolic mixture samples that are difficult to label through the attachment of (13)C isotopes. In addition, the user-friendly application includes an absolute-quantitative analysis tool. Good agreement was obtained between known concentrations of 20-metabolite mixtures versus the calibration curve-based quantification results obtained from 2D-Jres spectra. We have examined the web tool availability using nine series of biological extracts, obtained from animal gut and waste treatment microbiota, fish, and plant tissues. This web-based tool is publicly available via http://emar.riken.jp/spincpl.

Nuclear magnetic relaxation by the dipolar EMOR mechanism: General theory with applications to two-spin systems.

In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. We have embarked on a systematic program to develop, from the stochastic Liouville equation, a general and rigorous theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole coupling strengths, and Larmor frequencies. Here, we present a general theoretical framework applicable to spin systems of arbitrary size with symmetric or asymmetric exchange. So far, the dipolar EMOR theory is only available for a two-spin system with symmetric exchange. Asymmetric exchange, when the spin system is fragmented by the exchange, introduces new and unexpected phenomena. Notably, the anisotropic dipole couplings of non-exchanging spins break the axial symmetry in spin Liouville space, thereby opening up new relaxation channels in the locally anisotropic sites, including longitudinal-transverse cross relaxation. Such cross-mode relaxation operates only at low fields; at higher fields it becomes nonsecular, leading to an unusual inverted relaxation dispersion that splits the extreme-narrowing regime into two sub-regimes. The general dipolar EMOR theory is illustrated here by a detailed analysis of the asymmetric two-spin case, for which we present relaxation dispersion profiles over a wide range of conditions as well as analytical results for integral relaxation rates and time-dependent spin modes in the zero-field and motional-narrowing regimes. The general theoretical framework presented here will enable a quantitative analysis of frequency-dependent water-proton longitudinal relaxation in model systems with immobilized macromolecules and, ultimately, will provide a rigorous link between relaxation-based magnetic resonance image contrast and molecular parameters.

(1) H and (13) C NMR spectral assignment of N,N'-disubstituted thiourea and urea derivatives active against nitric oxide synthase.

The (1) H and (13) C NMR resonances of seventeen N-alkyl and aryl-N'-[3-hydroxy-3-(2-nitro-5-substitutedphenyl)propyl]-thioureas and ureas (1-17), and seventeen N-alkyl or aryl-N'-[3-(2-amino-5-substitutedphenyl)-3-hydroxypropyl]-thioureas and ureas (18-34), designed as NOS inhibitors, were assigned completely using the concerted application of one- and two-dimensional experiments (DEPT, HSQC and HMBC). NOESY studies confirm the preferred conformation of these compounds. Copyright © 2016 John Wiley & Sons, Ltd.

Chiral Recognition of Diketopiperazine Cyclo(Pro-Gly) and Propranolol Using (-)-Epigallocatechin-3-O-gallate.

In the (1)H-NMR spectrum of a solution containing an equimolecular amount of cyclo(L-Pro-Gly), cyclo(D-Pro-Gly) and (-)-epigallocatechin-3-O-gallate (EGCg) in a D2O, a difference in the chemical shift of (1)H-NMR signal for H7α, H7ß,8α of the Pro residue was observed. Judging from the crystal structures of the 2 : 2 complexes of EGCg and cyclo(L-Pro-Gly), cyclo(D-Pro-Gly), the difference in the chemical shift resulted mainly from a magnetic anisotropic shielding effect by the ring current from the B ring of EGCg. Therefore, it was considered that chirality of cyclo(Pro-Gly) was recognized by EGCg in the D2O solution. Furthermore, in the (1)H-NMR spectrum of a solution containing an equimolecular amount of racemic propranolol ((R)- and (S)-propranolols) and EGCg in D2O, the (1)H-NMR signal for H2 of the naphthalene group was observed as two doublets, suggesting that the racemic propranolol formed diastereomers of complexes with EGCg; as a result, chirality of propranolol was recognized by EGCg in the D2O solution.

[Prostate cancer]. / Prostatakarzinom.

For many clinical issues regarding prostate cancer magnetic resonance imaging (MRI) is gaining increasing importance for prostate diagnostics. The high morphological resolution of T2-weighted sequences is unsurpassed compared to other imaging modalities. It enables not only the detection and localization of prostate cancer but also allows the evaluation of extracapsular extensions. Functional MRI methods, such as diffusion-weighted imaging (DWI), dynamic contrast-enhanced (DCE) MRI and proton magnetic resonance spectroscopy ((1)H-MRS) increase the specificity and to a lesser extent, the sensitivity of diagnostics. In accordance with the interdisciplinary S3 guidelines, prostate MRI is recommended for patients with at least one negative biopsy for cancer detection. According to the guidelines areas suspected of being cancerous should be selectively biopsied in addition to the systematic biopsy. The transmission of findings about the suspected tumor areas according to the structured PI-RADS classification system has proven its worth. The localization and staging of prostate carcinoma is best achieved with the help of MRI and is recommended in the S3 guidelines especially for tumors with a clinical stage cT3/4 or with a Gleason grading system score ≥8. In addition to these applications MRI is mainly used under study conditions for local recurrence or active surveillance.

Analysis of Scotch Whisky by 1H NMR and chemometrics yields insight into its complex chemistry.

Scotch Whisky has been analysed as a complex mixture in its raw form using high resolution Nuclear Magnetic Resonance (NMR) and previously developed water and ethanol suppression techniques. This has allowed for the positive identification of 25 compounds in Scotch Whisky by means of comparison to reference standards, spike-in experiments, and advanced 1D and 2D NMR experiments. Quantification of compounds was hindered by signal overlap, though peak alignment strategies were largely successful. Statistical total correlation spectroscopy (STOCSY) yielded information on signals arising from the same compound or compounds of similar origin. Statistical analysis of the spectra was performed using Independent and Principal Components Analysis (ICA, PCA) as well as Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Several whisky production parameters were successfully modelled, including blend or malt status, use of peated malt, alcohol strength, generic authentication and maturation wood type, whilst age and geographical origin could not be modelled.

Using proton magnetic resonance spectroscopic imaging to study glutamatergic alterations in patients with schizophrenia: A systematic review.

The glutamate hypothesis of schizophrenia posits aberrant glutamatergic activity in patients with schizophrenia. Levels of glutamate and glutamine can be detected and quantified in vivo by proton magnetic resonance spectroscopy. A related technique, proton magnetic resonance spectroscopic imaging (1H-MRSI), is particularly useful as it simultaneously collects multiple spectra, across multiple voxels, from a single acquisition. The primary aim of this study was to review and discuss the use of 1H-MRSI to measure levels of glutamate and glutamine in patients with schizophrenia. Additionally, the advantages and disadvantages of using 1H-MRSI to examine schizophrenia pathophysiology are discussed. A literature search was conducted through Ovid. English language studies utilizing 1H-MRSI to measure glutamate and glutamine in patients with schizophrenia were identified. Six studies met the inclusion criteria. The included studies provide inconclusive support for glutamatergic elevations within frontal brain regions in patients with schizophrenia. The key benefit of employing 1H-MRSI to examine schizophrenia pathophysiology appears to be its broader spatial coverage. Future 1H-MRSI studies utilizing large sample sizes and longitudinal study designs are necessitated to further our understanding of glutamatergic alterations in patients with schizophrenia.