Nuclear magnetic resonance-based serum metabolomic analysis reveals different disease evolution profiles between septic shock survivors and non-survivors.

BACKGROUND: Septic shock is the most severe phase of sepsis and is associated with high rates of mortality. However, early stage prediction of septic shock outcomes remains difficult. Metabolomic techniques have emerged as a promising tool for improving prognosis. METHODS: Orthogonal projections to latent structures-discriminant analysis (OPLS-DA) models separating the serum metabolomes of survivors from those of non-survivors were established with samples obtained at the intensive care unit (ICU) admission (H0) and 24 h later (H24). For 51 patients with available H0 and H24 samples, multi-level modeling was performed to provide insight into different metabolic evolutions that occurred between H0 and H24 in the surviving and non-surviving patients. Relative quantification and receiver operational characteristic curves (ROC) were applied to estimate the predictability of key discriminatory metabolites for septic shock mortality. RESULTS: Metabolites that were involved in energy supply and protein breakdown were primarily responsible for differentiating survivors from non-survivors. This was not only seen in the H0 and H24 discriminatory models, but also in the H0-H24 paired models. Reanalysis of extra H0-H24 paired samples in the established multi-level model demonstrated good performance of the model for the classification of samplings. According to the ROC results, nine discriminatory metabolites defined consistently from the unpaired model and the H0-H24 time-trend change (ΔH24-H0) show good prediction of mortality. These results suggest that NMR-based metabolomic analysis is useful for a better overall assessment of septic shock patients. CONCLUSIONS: Dysregulation of the metabolites identified by this study is associated with poor outcomes for septic shock. Evaluation of these compounds during the first 24 h after ICU admission in the septic shock patient may be helpful for estimating the severity of cases and for predicting outcomes. TRIAL REGISTRATION: All human serum samples were collected and stored, provided by the "center of biologic resources for liver disease", in Jean Verdier Hospital, Bondy, France (BB-0033-00027).

Nuclear magnetic resonance metabolomics and human liver diseases: The principles and evidence associated with protein and carbohydrate metabolism.

During the last decade, metabolomics has become widely used in the field of human diseases. Numerous studies have demonstrated that this is a powerful technique for improving the understanding, diagnosis and management of various types of liver disease, such as acute and chronic liver diseases, and liver transplantation. Nuclear magnetic resonance (NMR) spectroscopy is one of the two most commonly applied methods for metabolomics. The aim of the present review was to investigate the results from recent key publications focusing on aspects of protein and carbohydrate metabolism. The review includes existing procedures, which are currently used for NMR data acquisition and statistical analysis. In addition, notable results obtained by these studies on protein and carbohydrate metabolism concerning human liver diseases are presented.

Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR.

Mucin 1 is a well-established target for the early diagnosis of epithelial cancers. The nucleotides of the S1.3/S2.2 DNA aptamer involved in binding to variable number tandem repeat mucin 1 peptides have been identified using footprinting experiments. The majority of these binding nucleotides are located in the 25-nucleotide variable region of the total aptamer. Imino proton and 2D NMR spectra of truncated and total aptamers in supercooled water reveal common hydrogen-bonding networks and point to a similar secondary structure for this 25-mer sequence alone or embedded within the total aptamer. NMR titration experiments confirm that the TTT triloop structure is the primary binding site and show that the initial structure of the truncated aptamers is conserved upon interaction with variable number tandem repeat peptides. The thermal dependence of the NMR chemical shift data shows that the base-paired nucleotides melt cooperatively at 47 ± 4°C. The structure of the 25-mer oligonucleotide was determined using a new combined mesoscale molecular modeling, molecular dynamics and NMR spectroscopy investigation. It contains three Watson-Crick pairs, three consecutive mispairs and four Watson-Crick pairs capped by a TTT triloop motif. The 3D model structures (PDB 2L5K) and biopolymer chain elasticity molecular models are consistent with both NMR and long unconstrained molecular dynamics (10 ns) in explicit water, respectively. Database Structural data are available in the Protein Data Bank and BioMagResBank databases under the accession numbers 2L5K and 17129, respectively.

Deuteration of water enables self-organization of phospholipid-based reverse micelles.

Phospholipid-based reverse micelles are composed of branched cylinders. Their branching points are known to attract themselves and to slide along branches. The rate of this sliding is governed by the lifetime of H(D)-bonded water bridges between phospholipid molecules. This lifetime is increased when the water is deuterated. On condition that the water contains at least 40 D atoms%, water/dipalmitoylphosphatidylcholine (DPPC)/deuterated pyridine reverse micelles with the composition 1.1:1:250 (v/v) have been shown to self-organize into a liquid crystal in the 310-316 K temperature range. The mechanism of this self-organization is unraveled by following the FTIR and (1)H NMR spectra of more concentrated micelles upon heating. During the preparation of micelles, pyridine-(D(+))H(+) ions are formed. They give rise to hydron transfers, under the influence of the DPPC electric charges, evidenced by two broad FTIR absorptions above (BB1) and below (BB2) the nu(C-O) stretch. These hydron transfers occur along strong (D(+))H(+) bonds of pyridinium ions with pyridine (BB1) and DPPC C=O groups (BB2). The proton transfers at the interface of micelles, relayed in the continuous pyridine medium, create a tenuous link between separated micelles, thus facilitating their organization. Upon heating, DPPC heads shrink and DPPC chains expand to make wedge-shaped DPPC molecules. The micelles then change in shape: cylinders constrict and enclosed water drifts towards branching points, which swell. Branching points of neighboring micelles come into contact. Due to the deuteration of water these contacts are prolonged and H bonds are formed between DPPC molecules located in each branching point. Upon storage at 39 degrees C, these branching points fuse. The lateral diffusion of DPPC molecules becomes free, as evidenced by a narrowing of all (1)H NMR resonances. Upon further heating, reorganization into a liquid crystal occurs.

The DNA structure responds differently to physiological concentrations of K(+) or Na(+).

The influence of monovalent cations on DNA conformation and readout is an open question. This NMR study of DNA with either Na(+) or K(+) at physiological concentrations shows that the nature of the cation affects the (31)P chemical shifts (deltaP) and the sequential distances H2'(i)-H6/8(i+1), H2"(i)-H6/8(i+1), and H6/8(i)-H6/8(i+1). The deltaP and distance variations ascertain that the nature of the cation affects the DNA overall structure, i.e. both the conformational equilibria between the backbone BI (epsilon-zeta <0 degrees ) and BII (epsilon-zeta >0 degrees ) states and the helical parameters, via their strong mechanical coupling. These results reveal that Na(+) and K(+) interactions with DNA are different and sequence-dependent. These ions modulate the overall intrinsic properties of DNA, and possibly its packaging and readout.

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.

A preferential target of antisense oligonucleotides directed against human PGY/MDR1 mRNA is a hairpin containing a stem with a G*U wobble pair, capped by the purine-rich 5'r(GGGAUG)3' hexaloop. This hairpin is studied by multidimensional NMR and restrained molecular dynamics, with special emphasis on the conformation of south sugars and non-standard phosphate linkages evidenced in both the stem and the loop. The hairpin is found to be highly structured. The G*U wobble pair, a strong counterion binding site, displays structural particularities that are characteristic of this type of mismatch. The upper part of the stem undergoes distortions that optimize its interactions with the beginning of the loop. The loop adopts a new fold in which the single-stranded GGGA purine tract is structured in A-like conformation stacked in continuity of the stem and displays an extensive hydrogen bonding surface for recognition. The remarkable hairpin stability results from classical inter- and intra-strand interactions reinforced by numerous hydrogen bonds involving unusual backbone conformations and ribose 2'-hydroxyl groups. Overall, this work emphasizes numerous features that account for the well-ordered structure of the whole hairpin and highlights the loop properties that facilitate interaction with antisense oligonucleotides.

Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition.

The backbone states of B-DNA influence its helical parameters, groove dimensions, and overall curvature. Therefore, detection and fine characterization of these conformational states are desirable. Using routine NMR experiments on a nonlabeled B-DNA oligomer and analyzing high-resolution X-ray structures, we investigated the relationship between interproton distances and backbone conformational states. The three H2'i-H6/8i+1, H2' 'i-H6/8i+1, and H6/8i-H6/8i+1 sequential distances were found cross-correlated and linearly coupled to epsilon-zeta values in X-ray structures and 31P chemical shifts (deltaP) in NMR that reflect the interconversion between the backbone BI (epsilon-zeta < 0 degrees ) and BII (epsilon-zeta > 0 degrees) states. These relationships provide a detailed check of the NMR data consistency and the possibility to extend the set of restraints for structural refinement through various extrapolations. Furthermore, they allow translation of deltaP in terms of BI/BII ratios. Also, comparison of many published deltaP in solution to crystal data shows that the impact of sequence on the BI/BII propensities is similar in both environments and is therefore an intrinsic and general property of B-DNA. This quantification of the populations of BI and BII is of general interest because these sequence-dependent backbone states act on DNA overall structure, a key feature for DNA-protein-specific recognition.

Different properties of H2O- and D2O-containing phospholipid-based reverse micelles near a critical temperature.

Dipalmitoylphosphatidylcholine (DPPC)/water/pyridine reverse micelles have been found to transform from a clear liquid into a glass when the DPPC-to-water volume fraction is in the 0.78-0.89 range at 28 or 26 degrees C depending on whether water is H2O or D2O. Their study by SANS, FT-IR, and 1H NMR for this composition has shown remarkable effects of the isotopic nature of water on their structural and dynamic properties. By SANS, between 38 and 43.5 degrees C, micelles appear as either flexible polymer-like cylinders or short rods depending on whether water is H2O or D2O. On the basis of this dual aspect, micelles have been visualized as branched cylinders whose quasi-spherical branching points would be prone to assemble into short rods. In addition, when water contains more than 40% of D2O, a Bragg reflection emerges at 0.12 A(-1) on SANS spectra, evidencing an organization of micelles. In addition, FT-IR spectra show that DPPC phosphate groups are D bonded only when water is D2O. Consequently, we assumed that forces prone to organize the D2O-containing micelles are D-bonded water bridges between neighboring micelles at the level of their branching points. In fact, ab initio calculations have shown that water dimers are more stable when the bridging atom is D rather than H. These water bridges could be formed due to the fact that branching points, able to slide along micelles, keep close for a longer time when water is D2O than when it is H2O. Indeed, it has been shown experimentally that the lateral diffusion of phospholipid molecules in any layer is slower in the first case. Formation of such bridges triggers a deuteron migration between micelles evidenced by the 1/T1 relaxation rate of deuterons of water in D2O-containing micelles measured at 43 degrees C by 1H NMR.

Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin.

Hairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. To investigate the intrinsic properties of a backbone submitted to a hexaloop fold, we present here a molecular dynamics study of an abasic hexaloop closed by an A-form 6 basepair stem. The analysis of the 23 ns trajectory made in explicit solvent shows that both the sugars and the torsion angles in the loop undergo numerous conformational transitions. The south sugars, although not in a majority, are the major actors of the loop stretching. The five torsion angles, epsilon, zeta, alpha, beta, and gamma, are unequally variable, and only zeta and alpha exhibit trimodal distributions. The analysis of the phosphate linkages in terms of epsilonzeta'-alpha'-beta'-gamma-combinations allows us to define five conformational families, each one composed of one major substate in equilibrium with several less populated ones. The transitions between the substates within a family follow specific pathways involving the angles epsilon, zeta, and alpha. Thus, this work reveals that the backbone conformational space is both reduced and ordered even in a hexaloop devoid of bases.

Serum 1H-nuclear magnetic spectroscopy followed by principal component analysis and hierarchical cluster analysis to demonstrate effects of statins on hyperlipidemic patients.

Use of statins for prevention of coronary heart disease is based on the decrease of serum cholesterol and LDL cholesterol. To better investigate the changes in lipid profile after statin treatment, we propose here to use an analysis of serum by proton nuclear magnetic resonance (NMR) spectroscopy associated with a multivariate analysis of the main spectral components. Sera were obtained from 60 male patients treated for 6 weeks with simvastatin (30 patients) or atorvastatin (30 patients) for who LDL cholesterol decreased by over 45% in all selected patients. Proton nuclear magnetic resonance spectra were obtained and the region of methyl resonance from lipids was separated into six consecutive lines attributed to lipids which were analyzed by principal component analysis (PCA) and clustering by hierarchical cluster analysis (HCA) based on Euclidian distance coupled with the Ward's minimum variance method. PCA and HCA gave a map discriminating the 120 samples into five clusters, three clusters containing samples obtained at baseline and two others containing samples obtained after treatment. Both statins produced a decrease in lower-density lipoprotein components and an increase in higher density lipoprotein components. Patients with a coronary heart disease history could be discriminated after treatment by the increase in the component containing the highest proportion of HDL. Proton NMR spectroscopy of sera coupled with a PCA and an HCA was able to detect variations in the metabolism of lipids resulting from statin treatments.

Impact of exogenous lysolipids on sensitive and multidrug resistant K562 cells: 1H NMR studies.

The ability of lysolipids to enter into a membrane bi-layer and disturb the membrane structure was used to study the behavior of K562 erythroleukemic cells, K562 wild type (K562wt) as well as the multidrug resistant cells K562adr. Both types of cells, when analyzed by proton NMR spectroscopy exhibit the high resolution signals assigned to so-called "mobile lipid" signals, which, in most cases, are located outside the lipid bi-layer as lipid droplets. In order to perform these studies, the K562wt and K562adr cells were treated for 48h with lysophosphatidylcholine oleoyl (LPC18), lysophosphatidylcholine palmitoyl (LPC16) and L-alpha-lysophosphatidyslerine (LPS). After evaluating toxicity of lysolipids, proton NMR of whole treated cells was used to analyze the mobile lipid content. Nile red staining and fluorescence microscopy were used to detect the presence of intracellular lipid droplets. Membrane lipid asymmetry perturbation was estimated by annexin V staining with use of flow cytometry. Using fluorescence spectroscopy the functioning of P-glycoprotein (P-gp) responsible for multidrug resistance was also evaluated after the treatment with lysolipids. Lysolipids were found to be more toxic for K562wt than for K562adr cells. LPS and LPC16 produced an increased of a mobile lipid NMR signal and amount of lipid droplets in K562wt cells only. LPC18, with the lowest toxicity, has shown more intense effects on NMR spectra with a large increase of lipid NMR signal without changes in lipid droplet staining. The functioning of the P-gp pump and membrane asymmetry were not modified by any of the lysolipids used.

Aminoglycoside and glycopeptide renal toxicity in intensive care patients studied by proton magnetic resonance spectroscopy of urine.

OBJECTIVE: Aminoglycoside and glycopeptide antibiotics are responsible for renal toxicity. In most cases, the nephrotoxicity is limited to a reversible tubular injury, but an acute and sustained renal failure may occur. The aim of our study was to explore the renal function of patients given these antimicrobial agents with proton magnetic resonance spectroscopy of urine. This technique is able to detect, in urine samples, a wide range of metabolites reflecting renal tubular function. The variables assessed by magnetic resonance spectroscopy were compared with the routine markers of renal function: creatinine, urea, and 24-hr urine volume. DESIGN: Prospective clinical study. SETTING: Intensive care unit. PATIENTS: All patients in an intensive care unit receiving an aminoglycoside and/or a glycopeptide were included in the study if they presented with signs of renal dysfunction. All experiments were performed on urine samples collected for the routine follow-up of these patients. INTERVENTION: Proton spectra were acquired with water suppression, and the peak intensity of each metabolite was reported in relationship to the intensity of the creatinine peak. MEASUREMENTS AND MAIN RESULTS: The ratio values obtained by magnetic resonance spectroscopy were compared with the values of creatininemia and blood urea obtained routinely by biochemistry and with the value of the 24-hr urine volume by logistic regression and general linear models. This statistical analysis showed that the ratio of dimethylamine to creatinine was highly correlated with creatininemia. CONCLUSIONS: Dimethylamine is an osmolyte released from the medullar region of the kidney. Thus, our study demonstrated that nephrotoxicity from aminoglycosides and glycopeptides is not limited to proximal tubular toxicity but also may involve the medullar region (Henle loop and collecting duct) of the nephron.