Biochemical analysis using high-resolution magic angle spinning NMR spectroscopy distinguishes lipoma-like well-differentiated liposarcoma from normal fat

Rapid and Precise Diagnosis of Retroperitoneal Liposarcoma with Deep-Learned Label-Free Molecular Microscopy

The retroperitoneal liposarcoma (RLPS) is a rare malignancy whose only curative therapy is surgical resection. However, well-differentiated liposarcomas (WDLPSs), one of its most common types, can hardly be distinguished from normal fat during operation without an effective margin assessment method, jeopardizing the prognosis severely with a high recurrence risk. Here, we combined dual label-free nonlinear optical modalities, stimulated Raman scattering (SRS) microscopy and second harmonic generation (SHG) microscopy, to image two predominant tissue biomolecules, lipids and collagen fibers, in 35 RLPSs and 34 normal fat samples collected from 35 patients. The produced dual-modal tissue images were used for RLPS diagnosis based on deep learning. Dramatically decreasing lipids and increasing collagen fibers during tumor progression were reflected. A ResNeXt101-based model achieved 94.7% overall accuracy and 0.987 mean area under the ROC curve (AUC) in differentiating among normal fat, WDLPSs, and dedifferentiated liposarcomas (DDLPSs). In particular, WDLPSs were detected with 94.1% precision and 84.6% sensitivity superior to existing methods. The ablation experiment showed that such performance was attributed to both SRS and SHG microscopies, which increased the sensitivity of recognizing WDLPS by 16.0 and 3.6%, respectively. Furthermore, we utilized this model on RLPS margins to identify the tumor infiltration. Our method holds great potential for accurate intraoperative liposarcoma detection.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Multiexponential T2 relaxometry of benign and malignant adipocytic tumours

Background

We investigated a recently proposed multiexponential (Mexp) fitting method applied to T2 relaxometry magnetic resonance imaging (MRI) data of benign and malignant adipocytic tumours and healthy subcutaneous fat. We studied the T2 distributions of the different tissue types and calculated statistical metrics to differentiate benign and malignant tumours.

Methods

Twenty-four patients with primary benign and malignant adipocytic tumours prospectively underwent 1.5-T MRI with a single-slice T2 relaxometry (Carr-Purcell-Meiboom-Gill sequence, 25 echoes) prior to surgical excision and histopathological assessment. The proposed method adaptively chooses a monoexponential or biexponential model on a voxel basis based on the adjusted R² goodness of fit criterion. Linear regression was applied on the statistical metrics derived from the T2 distributions for the classification.

Results

Healthy subcutaneous fat and benign lipoma were better described by biexponential fitting with a monoexponential and biexponential prevalence of 0.0/100% and 0.2/99.8% respectively. Well-differentiated liposarcomas exhibit 17.6% monoexponential and 82.4% biexponential behaviour, while more aggressive liposarcomas show larger degree of monoexponential behaviour. The monoexponential/biexponential prevalence was 47.6/52.4% for myxoid tumours, 52.8/47.2% for poorly differentiated parts of dedifferentiated liposarcomas, and 24.9/75.1% pleomorphic liposarcomas. The percentage monoexponential or biexponential model prevalence per patient was the best classifier distinguishing between malignant and benign adipocytic tumours with a 0.81 sensitivity and a 1.00 specificity.

Conclusions

Healthy adipose tissue and benign lipomas showed a pure biexponential behaviour with similar T2 distributions, while decreased adipocytic cell differentiation characterising aggressive neoplasms was associated with an increased rate of monoexponential decay curves, opening a perspective adipocytic tumour classification.

Advances in lung cancer biomarkers: The role of (metal-) metabolites and selenoproteins

Lung cancer (LC) is the second most common cause of death in men after prostate cancer, and the third most recurrent type of tumor in women after breast and colon cancers. Unfortunately, when LC symptoms begin to appear, the disease is already in an advanced stage and the survival rate only reaches 2%. Thus, there is an urgent need for early diagnosis of LC using specific biomarkers, as well as effective therapies and strategies against LC. On the other hand, the influence of metals on more than 50% of proteins is responsible for their catalytic properties or structure, and their presence in molecules is determined in many cases by the genome. Research has shown that redox metal dysregulation could be the basis for the onset and progression of LC disease. Moreover, metals can interact between them through antagonistic, synergistic and competitive mechanisms, and for this reason metals ratios and correlations in LC should be explored. One of the most studied antagonists against the toxic action of metals is selenium, which plays key roles in medicine, especially related to selenoproteins. The study of potential biomarkers able to diagnose the disease in early stage is conditioned by the development of new analytical methodologies. In this sense, omic methodologies like metallomics, proteomics and metabolomics can greatly assist in the discovery of biomarkers for LC early diagnosis.

Serum lipidomic biomarkers for non-small cell lung cancer in nonsmoking female patients

Lung cancer (Lca) is one of the malignant tumors with the fastest morbidity and mortality increase and the greatest threat to human health and life. The incidence of non-small cell lung cancer (NSCLC) in the nonsmoking female has increased recently. However, its pathogenesis is still unclear, and there is an urgent need for clinical diagnostic biomarkers, especially for early diagnosis. A nontargeted lipidomic approach based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS), as well as two machine learning approaches (genetic algorithm and binary logistic regression) was used to screen candidate discriminating lipids and define a combinational lipid biomarker in serum samples to distinguish female patients with NSCLC from healthy controls. Moreover, the candidate biomarkers were verified by using an external validation sample set. Our result revealed that fatty acid (FA) (20:4), FA (22:0) and LPE (20:4) can serve as a combinational biomarker for distinguishing female patients with NSCLC from healthy control with good sensitivity and specificity. Furthermore, this combinational biomarker also showed good performance in distinguishing early-stage NSCLC female patients from a healthy control. We observed that levels of unsaturated fatty acids clearly decreased, while saturated fatty acids and lysophosphatidylethanolamines pronouncedly increased in Lca patients, compared with the healthy controls, which revealed significant disturbance of lipid metabolism in NSCLC females. Our results not only provide hints to the pathological mechanism of NSCLC in nonsmoking female but also supply a combinational lipid biomarker to aid the diagnosis of NSCLC at early-stage.

Biomarker identification and pathway analysis by serum metabolomics of lung cancer

Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top altered pathways for analysis and visualization. We constructed a diagnostic model using potential serum biomarkers from patients with lung cancer. We assessed their specificity and sensitivity according to the area under the curve of the receiver operator characteristic (ROC) curves, which could be used to distinguish patients with lung cancer from normal subjects. The pathway analysis indicated that sphingolipid metabolism was the top altered pathway in lung cancer. ROC curve analysis indicated that glycerophospho-N-arachidonoyl ethanolamine (GpAEA) and sphingosine were potential sensitive and specific biomarkers for lung cancer diagnosis and prognosis. Compared with the traditional lung cancer diagnostic biomarkers carcinoembryonic antigen and cytokeratin 19 fragment, GpAEA and sphingosine were as good or more appropriate for detecting lung cancer. We report our identification of potential metabolic diagnostic and prognostic biomarkers of lung cancer and clarify the metabolic alterations in lung cancer.

Identification of potential erythrocyte phospholipid fatty acid biomarkers of advanced lung adenocarcinoma, squamous cell lung carcinoma, and small cell lung cancer

New biomarkers for lung cancer would be valuable. Our aim was to analyze the fatty acid profiles of the main phospholipid species in erythrocytes from patients with advanced squamous cell lung carcinoma (SCC), lung adenocarcinoma (ADC), and small cell lung cancer (SCLC) and benign lung diseases (chronic obstructive pulmonary disease (COPD) and asthma) to determine the fatty acids that could be use as lung cancer markers. Twenty-eight, 18, 14, 16, and 15 patients with, respectively, SCC, ADC, SCLC, asthma, and COPD and 50 healthy subjects were enrolled in the study. Fatty acid profiles were investigated using gas chromatography/mass spectrometry followed by receiver operating characteristic (ROC) curve analysis. The fatty acid profiles changed significantly in the different pathologies analyzed. Based on the diagnostic yields and operating characteristics, the most significant fatty acids that might be used as biomarkers were as follows: ADC--arachidonic acid (20:4n6) in phosphatidylcholine and oleic acid (18:1n9) in phosphatidylethanolamine (PE); SCC--eicosapentaenoic acid (20:5n3) in PE and palmitic acid (16:0) in phosphatidylserine + phosphatidylinositol (PS+PI); SCLC--eicosadienoic acid (20:2n6) in PS+PI and lignoceric acid (24:0) in sphingomyelin. In conclusion, fatty acids from erythrocyte phospholipid species might serve as biomarkers in the diagnosis, and probably in other aspects related to clinical disease management, of ADC, SCC, and SCLC.

Metabolomic profiling of human serum in lung cancer patients using liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry and gas chromatography/mass spectrometry

PURPOSE

Lung cancer is one of the most common causes of death from cancer. Serum markers that enable diagnosis of the disease in the early stage have not been found.

METHODS

Serum samples were collected from 30 healthy volunteers and from 30 lung cancer patients preoperatively and postoperatively. Samples were subjected to metabolomic analysis using liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry and gas chromatography/mass spectrometry. Differences in metabolomic profiles among the three groups were characterized by multivariate statistical techniques such as principal components analysis and partial least squares discriminant analysis (PLS-DA). An independent t test was used to determine whether levels of biomarker candidates identified using PLS-DA modeling were significantly different among groups at the univariate analysis level (p < 0.05).

RESULTS

Based on pattern recognition results and univariate analysis, we showed that levels of ten potential biomarkers in serum were significantly different in the preoperative lung cancer patients compared with healthy volunteers and/or the postoperative lung cancer patients. The levels of sphingosine, phosphorylcholine, glycerophospho-N-arachidonoyl ethanolamine, γ-linolenic acid, 9,12-octadecadienoic acid, oleic acid, and serine were significantly different in preoperative lung cancer patients compared to healthy volunteers and to postoperative lung cancer patients. For prasterone sulfate, α-hydroxyisobutyric acid, 2,3,4-trihydroxybutyric acid, the levels were statistically different in preoperative and postoperative lung cancer patients compared with the healthy volunteers.

CONCLUSIONS

Our study identified potential metabolic biomarkers for diagnosis of lung cancer.

Plasma metabolome analysis by integrated ionization rapid-resolution liquid chromatography/tandem mass spectrometry

RATIONALE

Acquiring global information on plasma-endogenous metabolites challenges metabolomics. This study has been designed to investigate the suitability of integrated ionization rapid-resolution liquid chromatography/tandem mass spectrometry (RRLC/MS/MS) for different kinds of metabolites in complex plasma, and provides an approach for plasma metabolomics in acquiring more comprehensive data of metabolites.

METHODS

Integrated ionization of electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photoionization (APPI) combined with RRLC/MS/MS has been carried out to perform analysis on the global plasma metabolome of healthy volunteers. The contributions to the total numbers of ion features by RRLC/MS with ESI, APCI, and APPI in positive and negative ion modes were calculated. Representative unique and identical ions were identified. The intensities of identical ions were compared.

RESULTS

Each of ESI, APCI, and APPI coupled with RRLC/MS has its own advantage over the other two techniques for certain types of metabolites in plasma. LC/ESI-MS is very sensitive for detecting glycerophosphocholines, glycerophosphoethanolamines, acyl carnitines, bile acids, sulfate, etc. LC/APCI-MS is suitable for analyzing cyclic alcohols, fatty acids, and linoleic acids. LC/APPI-MS proves to be appropriate in detecting steroids, sphingolipids, some amino acids, nucleosides, and purines in plasma.

CONCLUSIONS

It is suggested that the integrated ionization LC/MS approach should be applied for global plasma metabolomics. Moreover, the results obtained demonstrate that it is preferable to choose certain techniques from LC/ESI-MS, LC/APCI-MS, and LC/APPI-MS for metabolite target analysis.

Metabonomic studies of pancreatic cancer response to radiotherapy in a mouse xenograft model using magnetic resonance spectroscopy and principal components analysis

AIM: To investigate the metabolic profiles of xenograft pancreatic cancer before and after radiotherapy by high-resolution magic angle spinning proton magnetic resonance spectroscopy (HRMAS ¹H NMR) combined with principal components analysis (PCA) and evaluate the radiotherapeutic effect.

METHODS: The nude mouse xenograft model of human pancreatic cancer was established by injecting human pancreatic cancer cell SW1990 subcutaneously into the nude mice. When the tumors volume reached 800 mm³, the mice received various radiation doses. Two weeks later, tumor tissue sections were prepared for running the NMR measurements. ¹H NMR and PCA were used to determine the changes in the metabolic profiles of tumor tissues after radiotherapy. Metabolic profiles of normal pancreas, pancreatic tumor tissues, and radiation- treated pancreatic tumor tissues were compared.

RESULTS: Compared with ¹H NMR spectra of the normal nude mouse pancreas, the levels of choline, taurine, alanine, isoleucine, leucine, valine, lactate, and glutamic acid of the pancreatic cancer group were increased, whereas an opposite trend for phosphocholine, glycerophosphocholine, and betaine was observed. The ratio of phosphocholine to creatine, and glycerophosphocholine to creatine showed noticeable decrease in the pancreatic cancer group. After further evaluation of the tissue metabolic profile after treatment with three different radiation doses, no significant change in metabolites was observed in the ¹H NMR spectra, while the inhibition of tumor growth was in proportion to the radiation doses. However, PCA results showed that the levels of choline and betaine were decreased with the increased radiation dose, and conversely, the level of acetic acid was dramatically increased.

CONCLUSION: The combined methods were demonstrated to have the potential for allowing early diagnosis and assessment of pancreatic cancer response to radiotherapy.

Metabolomics in lung inflammation:a high-resolution (1)h NMR study of mice exposedto silica dust

ABSTRACT Here we report the first (1)H NMR metabolomics studies on excised lungs and bronchoalveolar lavage fluid (BALF) from mice exposed to crystalline silica. High-resolution (1)H NMR metabolic profiling on intact excised lungs was performed using slow magic angle sample spinning (slow-MAS) (1)H PASS (phase-altered spinning sidebands) at a sample spinning rate of 80 Hz. Metabolic profiling on BALF was completed using fast magic angle spinning at 2 kHz. Major findings are that the relative concentrations of choline, phosphocholine (PC), and glycerophosphocholine (GPC) were statistically significantly increased in silica-exposed mice compared to sham controls, indicating an altered membrane choline phospholipids metabolism (MCPM). The relative concentrations of glycogen/glucose, lactate, and creatine were also statistically significantly increased in mice exposed to silica dust, suggesting that cellular energy pathways were affected by silica dust. Elevated levels of glycine, lysine, glutamate, proline, and 4-hydroxyproline were also increased in exposed mice, suggesting the activation of a collagen pathway. Furthermore, metabolic profiles in mice exposed to silica dust were found to be spatially heterogeneous, consistent with regional inflammation revealed by in vivo magnetic resonance imaging (MRI).

[Preliminary results of metabolite in serum and urine of lung cancer patients detected by metabolomics]

背景与目的

肺癌是当今世界各国最常见的恶性肿瘤之一。目前尚没有寻找到理想的用于肺癌诊断的肿瘤标志物，因而尝试用各种新方法来探索新的生物学标志物已成为肺癌研究的热点。本研究采用代谢组学技术对肺癌患者和其它肺部疾病患者血清及尿液中的小分子代谢物质进行分析，以寻求潜在的肺癌肿瘤标志物。

方法

运用气相色谱/质谱法（gas chromatography/mass spectrometry, GC/MS）对19例肺癌与15例其它肺部疾病患者的血清及尿液样本进行代谢组学分析，采用正交偏最小二乘判别分析法（orthogonal to partial least squares discriminant analysis, OPLS-DA）进行建模，运用两样本的t检验寻找两组间差异性代谢产物。

结果

检测到血清中代谢产物共57种，尿液中代谢产物共38种，多变量统计结果显示肺癌患者与其它肺部疾病患者的代谢谱有明显差异，根据t检验结果寻找到血清相关的差异代谢产物13种，尿液相关的差异代谢产物7种。

结论

利用代谢组学方法能区分肺癌与其它肺部疾病患者，其结果在分子水平辅助肺癌的诊断、未来作为新技术应用于肺癌的诊断有一定的前景。

Metabolomics in the fields of oncology: a review of recent research

The study of all endogenously produced metabolites, known as metabolomics, is the youngest of the "omics" sciences. It is becoming increasingly clear that, of all of the "omics" techniques, metabolomic approaches will become increasingly useful in disease diagnosis and have potential power to improve our understanding of the underlying mechanisms of cancer. The primary aim of the review is to discuss the relationship between metabolomics and tumors are elucidated in detail. Then the review is also to introduce the technologies of metabolomics, especially emphasizing the application of metabolomics in the fields of oncology.

Longitudinal profiling of articular cartilage degradation in osteoarthritis by high-resolution magic angle spinning 1H NMR spectroscopy: experimental study in the meniscectomized guinea pig model

This study assessed the 1H HRMAS NMR spectroscopic profile of articular cartilage in both physiological and osteoarthitic situations. One-dimensional and two-dimensional 1H HRMAS NMR spectra were obtained from the tibial plateau cartilage of healthy and operated (unilateral medial meniscectomy and sham surgery) guinea pigs at different stages of disease, over a 6-month period. The major osteoarthritis-induced 1H HRMAS NMR changes were an increase of the N-acetyl peak of proteoglycans (at day 20 after meniscectomy) and a decrease after day 60 as the pathology evolved. These proteoglycan changes revealed by 1H HRMAS NMR analysis were validated by proteoglycan biochemistry assays. 1H HRMAS NMR analysis also evidenced a sharp increase in methylene resonances of chondrocyte membrane lipids from day 90 as a marker of apoptosis. There was an increase of the mobile methyl group of collagen at day 120, which was associated with collagen breakdown. 1H HRMAS NMR analysis provided a multifactorial and sequential picture of cartilage degradation at the extracellular matrix and chondrocyte levels.

An isotropic chemical shift-chemical shift anisotropic correlation experiment using discrete magic angle turning

An isotropic-anisotropic shift 2D correlation spectroscopy is introduced that combines the advantages of both magic angle turning (MAT) and magic angle hopping (MAH) technologies. In this new approach, denoted DMAT for "discrete magic angle turning", the sample rotates clockwise followed by an anticlockwise rotation of exactly the same amount with each rotation less or equal than 360 degrees but greater than 240 degrees , with the rotation speed being constant only for times related to the evolution dimension. This back and forth rotation is repeated and synchronized with a special radio frequency (RF) pulse sequence to produce an isotropic-anisotropic shift 2D correlation spectrum. For any spin-interaction of rank-2 such as chemical shift anisotropy, isotropic magnetic susceptibility interaction, and residual homo-nuclear dipolar interaction in biological fluid samples, the projection along the isotropic dimension is a high resolution spectrum. Since a less than 360 degrees sample rotation is involved, the design potentially allows for in situ control over physical parameters such as pressure, flow conditions, feed compositions, and temperature so that true in situ NMR investigations can be carried out.

Metabonomics: a useful tool for the future surgeon

BACKGROUND

In the past decade or so, a range of technologies have emerged that have shown promise in increasing our understanding of disease processes and progression. These advances are referred to as the "omics" technologies; genomics, transcriptomics, and proteomics. More recently, another "omics" approach has come to the fore: metabonomics, and this technology has the potential for significant clinical impact. Metabonomics refers to the analysis of the metabolome, that is, the metabolic profile of a system. The advantage of studying the metabolome is that the end points of biological events are elucidated.

RESULTS

Although still in its infancy, the metabonomics approach has shown immense promise in areas as diverse as toxicology studies to the discovery of biomarkers of disease. It has also been applied to studies of both renal and hepatic transplants. Metabolome analysis may be conducted on a variety of biological fluids and tissue types and may utilize a number of different technology platforms, mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being the most popular. In this review, we cover the background to the evolution of metabonomics and its applications with particular emphasis on clinical applications.

CONCLUSIONS

We conclude with the suggestion that metabonomics offers a platform for further biomarker development, drug development, and in the field of medicine.

Metabonomics and its application in oncobiology research

The primary aim of this review is to introduce the research status of metabonomics/metabolomics and the application of metabonomics in oncobiology research. At first, the concept of metabonomics and the relationship between metabonomics and tumors are elucidated in detail. Then the research technologies of metabonomics in oncobiology are introduced. Finally, the latest advances in the application of metabonomics in early diagnosis, treatment and prognosis of tumors are summarized.

Benign and atypical meningioma metabolic signatures by high-resolution magic-angle spinning molecular profiling

Meningiomas are neoplasms that arise from the leptomeningeal covering of the brain and spinal cord, accounting for 15%-20% of CNS tumors. The WHO classifies meningiomas into three histological grades: benign, atypical, and anaplasic in accordance with the clinical prognosis. Atypical and anaplasic meningiomas tend to recur. Sometimes, meningiomas with histological diagnosis of benign meningioma show clinical characteristics of atypical meningioma. In this context, high-resolution magic-angle spinning (HR-MAS) spectroscopy of intact tissue from brain tumor biopsies has shown great potential as a support diagnostic tool. In this work, we show differences between benign and atypical meningiomas in HR-MAS molecular profiles of meningioma biopsies. Metabolic differences between meningioma grades include changes in the levels of glutathione. Glutathione role in cancer is still unclear, as it may act both as protective and pathogenic factor. Glutamine and glutamate, which are related to glutathione metabolism and have been associated with tumor recurrence, are also increased in atypical meningiomas. Other metabolites associated with tumor malignancy that show statistically significant differences between benign and atypical meningiomas include phosphocholine and phosphoethanolamine. Overall, this work suggests that the additional information obtained by NMR metabolomics applied to biopsies of human meningiomas may be useful for assessing tumor grade and determining optimum treatment strategies.

Technology insight: metabonomics in gastroenterology-basic principles and potential clinical applications

Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function. Metabonomics, especially when based on nuclear magnetic resonance spectroscopy, has the potential to identify biomarkers and prognostic factors, enhance clinical diagnosis, and expand hypothesis generation. As a consequence, the use of metabonomics has been extensively explored in the past decade, and applied successfully to the study of human diseases, toxicology, microbes, nutrition, and plant biology. This Review introduces the basic principles of nuclear magnetic resonance spectroscopy and commonly used tools for multivariate data analysis, before considering the applications and future potential of metabonomics in basic and clinical research, with emphasis on applications in the field of gastroenterology.

Characterization of bovine patellar cartilage by NMR

Metabolic and structural changes in cartilage tissue are thought to be at the root of degenerative joint disease. We identify here the NMR resonances in bovine patellar cartilage tissue by static and high-resolution magic angle spinning (HRMAS) NMR spectroscopy, (1)H-(13)C heteronuclear single-quantum correlation (HSQC) spectroscopy, total correlation spectroscopy (TOCSY), and saturation transfer experiments. Some differences between the patellar cartilage samples studied here and earlier nasal cartilage and intervertebrate disc studies were found. In addition, we show assignments downfield of the water signal, which also includes the assignment of amide and hydroxy protons on the basis of their exchangeability with water. These results will allow an identification of spectroscopic markers of cartilage degradation using techniques such as chemical exchange saturation transfer imaging.

A developmental model of sarcomagenesis defines a differentiation-based classification for liposarcomas

The importance of adult stem cells in the development of neoplastic diseases is becoming increasingly well appreciated. We hypothesized that sarcomas of soft tissue could be categorized by their developmental/differentiation status from stem cell to mature tissue, similar to the hematological malignancies. We conducted gene expression analyses during in vitro differentiation of human mesenchymal stem cells into adipose tissue, as a representative mature connective tissue, and identified genes whose expression changed significantly during adipogenesis. Gene clustering and distance correlation analysis allowed the assignment of a unique time point during adipogenesis that strongly correlates to each of the four major liposarcoma subtypes. Using a novel gene expression strategy, in which liposarcomas are compared to their corresponding adipocytic maturing cells, we identified a group of genes overexpressed in liposarcomas that indicate the stage of differentiation arrest, ie, sharing a similar expression profile to adipocytic cells at a corresponding stage of differentiation, and a distinct set of genes overexpressed in liposarcomas that are not found in the corresponding stage of differentiation. We propose that the latter set is enriched for candidate transformation-associated genes. Our results indicate that a degree of developmental maturity can be quantitatively assigned to solid tumors, supporting the notion that transformation of a solid tumor stem cell can occur at distinct stages of maturation.

Discrimination of metabolic profiles of pancreatic cancer from chronic pancreatitis by high-resolution magic angle spinning 1H nuclear magnetic resonance and principal components analysis

The metabolic profiles of Sprague-Dawley rat pancreases were investigated by high-resolution magic angle spinning proton magnetic resonance spectroscopy ((1)H NMR) combined with principal components analysis (PCA) to discriminate pancreatic cancer from chronic pancreatitis. Intact pancreatic tissue samples were obtained from Sprague-Dawley rats with histologically proven pancreatic cancer (n = 5), chronic pancreatitis (n = 5), and two matched controls (n = 5 per group). Two (1)H NMR experiments, single-pulse and Carr-Purcell-Meiboom-Gill, were carried out separately. Increases in phosphocholine and glycerophosphocholine levels and decreases in leucine, isoleucine, valine, lactate and alanine levels were observed in chronic pancreatitis, whereas the opposite trends were observed in pancreatic cancer. Increasing taurine and decreasing betaine were found both in chronic pancreatitis and in pancreatic cancer. Additionally, the lipid content in pancreatic cancer was higher than that in chronic pancreatitis. PCA was carried out for the single-pulse and Carr-Purcell-Meiboom-Gill (1)H NMR spectra, respectively, to visualize separation among the samples and to extract characteristic metabolites of pancreatic cancer and chronic pancreatitis. Decreased phosphocholine and glycerophosphocholine were suggested as unique metabolite indicators of pancreatic cancer. Furthermore, even with the disturbance of various quantities of lipid contents pancreatic cancer and chronic pancreatitis could be differentiated well by the combination of high-resolution magic angle spinning (1)H NMR and PCA. Thus this combination was demonstrated to have the potential to improve magnetic resonance spectroscopy for positive early diagnosis of pancreatic cancer in clinical settings.

The Cinderella story of metabolic profiling: does metabolomics get to go to the functional genomics ball?

To date most global approaches to functional genomics have centred on genomics, transcriptomics and proteomics. However, since a number of high-profile publications, interest in metabolomics, the global profiling of metabolites in a cell, tissue or organism, has been rapidly increasing. A range of analytical techniques, including 1H NMR spectroscopy, gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), Fourier Transform mass spectrometry (FT-MS), high performance liquid chromatography (HPLC) and electrochemical array (EC-array), are required in order to maximize the number of metabolites that can be identified in a matrix. Applications have included phenotyping of yeast, mice and plants, understanding drug toxicity in pharmaceutical drug safety assessment, monitoring tumour treatment regimes and disease diagnosis in human populations. These successes are likely to be built on as other analytical and bioinformatic approaches are developed to fully exploit the information obtained in metabolic profiles. To assist in this process, databases of metabolomic data will be necessary to allow the passage of information between laboratories. In this prospective review, the capabilities of metabolomics in the field of medicine will be assessed in an attempt to predict the impact this 'Cinderella approach' will have at the 'functional genomic ball'.

(1)H relaxation times of metabolites in biological samples obtained with nondestructive ex-vivo slow-MAS NMR

Methods suitable for measuring (1)H relaxation times such as T(1), T(2) and T(1rho) of metabolites in small, intact biological objects including live cells, excised organs and tissues, oil seeds etc. are developed in this work. This was achieved by combining inversion-recovery, spin-echo, or a spin-lock segment with the phase-adjusted spinning sideband (PASS) technique, which was applied at low sample-spinning rates. Here, PASS was used to produce high-resolution (1)H spectra in a nondestructive way so that the relaxation parameters of individual metabolite could be determined. The methodologies were demonstrated by measuring (1)H T(1), T(2), and T(1rho) of metabolites in excised rat liver at a spinning rate of 40 Hz.

Metabolite identification in human liver needle biopsies by high-resolution magic angle spinning 1H NMR spectroscopy

High-resolution magic angle spinning (HR-MAS) 1H NMR spectroscopy of intact human liver needle biopsies has not been previously reported. HR-MAS NMR spectra collected on 17 specimens with tissue amounts between approximately 0.5 and 12 mg showed very good spectral resolution and signal-to-noise ratios. One-dimensional 1H spectra revealed many intense signals corresponding to cellular metabolites. In addition, some high molecular weight metabolites, such as glycogen and mobile fatty acids, could be observed in some spectra. Resonance assignments for 22 metabolites were obtained by combining the analysis of three different types of 1D 1H spectral editing, such as T2 filtering or the nuclear Overhauser effect and 2D TOCSY and 13C-HSQC spectra. Biochemical stability of the liver tissue during up to 16 h of magic angle spinning at 277 K was studied. Biochemical trends corresponding to the different pathologies were observed, involving free fragments of lipids among other metabolites. NMR signal intensity ratios can be useful for discrimination among non-pathological, hepatitis C affected and cirrhotic liver tissues. Overall, this work demonstrates the applicability of HR-MAS NMR spectroscopy to the biochemical characterization of needle biopsies of the human liver.

Metabonomics and the endocrine system

Proton-NMR-based metabonomics offers a rare opportunity as a definitive screening technique for biofluids and tissue biopsies. The procedure is extraordinary in that it allows the 'complete biochemical picture' to be examined at one time and is able to detect subtle but repeatedly consistent disparities that may be occurring in different, and perhaps unrelated, biochemical pathways. Such metabolic responses to an initial perturbation in homeostasis may be followed over a sequential time-course to their eventual dissipation or consequent sequelae. The application of this technique is beginning slowly to filter into the area of endocrine research and has been used to examine long-term and diffuse physiological alterations that may occur following such events as anabolic steroid treatment of cattle and the exposure of endometrial cells to tamoxifen. Although only modest inroads have been made so far, this technique promises immense potential for future researches within the endocrine field.

Reduction of spinning sidebands in proton NMR of human prostate tissue with slow high-resolution magic angle spinning

High-resolution magic angle spinning (HRMAS) NMR spectroscopy has proven useful for analyzing intact tissue and permitting correlations to be made between tissue metabolites and disease pathologies. Extending these studies to slow-spinning methodologies helps protect tissue pathological structures from HRMAS centrifuging damage and may permit the study of larger objects. Spinning sidebands (SSBs), which are produced by slow spinning, must be suppressed to prevent the complication of metabolic spectral regions. In this study human prostate tissues, as well as gel samples of a metabolite mixture solution, were measured with continuous-wave (CW) water presaturation on a 14.1T spectrometer, with HRMAS spinning rates of 250, 300, 350, 600, and 700 Hz, and 3.0 kHz. Editing the spectra by means of a simple minimum function (Min(A, B, ..., N) for N spectra acquired at different but close spinning rates) produced SSB-free spectra. Statistically significant linear correlations were observed for metabolite concentrations quantified from the Min(A, B, ..., N)-edited spectra generated at low spinning rates, with concentrations measured from the 3 kHz spectra, and also with quantitative pathology. These results indicate the empirical utility of this scheme for analyzing intact tissue, which also may be used as an adjunct tool in pathology for diagnosing disease.

Water suppression without signal loss in HR-MAS 1H NMR of cells and tissues

In cell and tissue samples, water is normally three orders of magnitude more abundant than other metabolites. Thus, water suppression is required in the acquisition of NMR spectra to overcome the dynamic range problem and to recover metabolites that overlap with the broad baseline of the strong water resonance. However, the heterogeneous cellular environment often complicates water suppression and the strong coupling of water to membrane lipids interferes with the NMR detection of membrane associated lipid components. The widely used water suppression techniques including presaturation and double pulsed field gradient selective echo result in more than a 70% reduction in membrane associated lipid components in proton spectra of cells and tissues compared to proton spectra acquired in the absence of water suppression. A water suppression technique based on the combination of selective excitation pulses and pulsed field gradients is proposed to use in the acquisition of high resolution MAS NMR spectra of tissue specimens and cell samples. This pulse sequence methodology enables efficient water suppression for intact cells and tissue samples and eliminates signal loss from cellular metabolites.

High-resolution1H NMR spectroscopy in a live mouse subjected to 1.5 Hz magic angle spinning

It is demonstrated that the resolution of the (1)H NMR metabolite spectrum in a live mouse can be significantly enhanced by an ultraslow magic angle spinning of the animal combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. Proton NMR spectra were measured of the torso and the top part of the belly of a female BALBc mouse in a 2 T field while spinning the animal at a speed of 1.5 Hz. It was found that even in this relatively low field, with PHORMAT an isotropic spectrum is obtained with line widths that are a factor of 4.6 smaller than those obtained in a stationary mouse. It is concluded that in vivo PHORMAT has the potential to significantly increase the utility of (1)H NMR spectroscopy for biochemical and biomedical animal research.

High-resolution diffusion and relaxation-edited magic angle spinning1H NMR spectroscopy of intact liver tissue

High-resolution magic angle spinning (HRMAS) (1)H NMR spectroscopy is ideal for monitoring the metabolic environment within tissues, particularly when spectra are weighted by physical properties such as T(1) and T(2) relaxation times and apparent diffusion coefficients (ADCs). In this study, spectral-editing using T(1) and T(2) relaxation times and ADCs at variable diffusion times was used in conjunction with HRMAS (1)H NMR spectroscopy at 14.1 T in liver tissue. To enhance the sensitivity of ADC measurements to low molecular weight metabolites a T(2) spin echo was included in a standard stimulated gradient spin-echo sequence. Fatty liver induced in rats by chronic orotic acid feeding was investigated using this modified sequence. An increase in the combined ADC for the co-resonant peaks glucose, betaine, and TMAO during fatty liver disease was detected (ADCs = 0.60 +/- 0.11 and 0.35 +/- 0.1 * 10(-9) m(2)s(-1) (n = 3) for rats fed with and without orotic acid), indicative of a reduction in glucose and betaine and an increase in TMAO.

High-resolution magic angle spinning proton NMR analysis of human prostate tissue with slow spinning rates

The development of high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for intact tissue analysis and the correlations between the measured tissue metabolites and disease pathologies have inspired investigations of slow-spinning methodologies to maximize the protection of tissue pathology structures from HR-MAS centrifuging damage. Spinning sidebands produced by slow-rate spinning must be suppressed to prevent their complicating the spectral region of metabolites. Twenty-two human prostatectomy samples were analyzed on a 14.1T spectrometer, with HR-MAS spinning rates of 600 Hz, 700 Hz, and 3.0 kHz, a repetition time of 5 sec, and employing various rotor-synchronized suppression methods, including DANTE, WATERGATE, TOSS, and PASS pulse sequences. Among them, DANTE, as the simplest scheme, has shown the most potential in suppression of tissue water signals and spinning sidebands, as well as in quantifying metabolic concentrations.

Isotropic susceptibility shift under MAS: the origin of the split water resonances in 1H MAS NMR spectra of cell suspensions

Bulk susceptibility variations in a multiphase system such as cultured cells and tissue have two manifestations: a dipolar field component outside the regular heterogenous region which introduces linebroadening, and an isotropic field part which results in a frequency shift. Previous NMR studies have emphasized the utility of magic angle spinning for averaging the dipolar component, particularly if the spins of interest are limited to one phase of a multiphase system such as a sample of liquid with air pockets or glass beads. However, in analyzing spectra from complex multiphase systems, such as cell suspensions and tissues, etc., the isotropic part is often neglected, leading to questionable interpretation of experimental results. The present study demonstrates that under magic angle spinning, the water resonance in NMR experiments of cell suspensions is split into two resolved peaks due to the isotropic susceptibility shift. These two peaks are assigned to a central core of cell free water and an outer cylindrical ring of tightly packed cells in close association with water. A comprehensive theory for this splitting is provided based on a coaxis cylinder model with different susceptibilities. The frequency difference is shown to be dependent on the susceptibility difference and also on the angle of the rotor in the magnetic field. The splitting distance of the two water peaks can be used to measure the susceptibility difference of water in these two phases. The susceptibility difference was measured for three different cell types: 3T3 F442A preadipocyte cells, mouse embryonic stem cells, and human red blood cells.

Cellular environment of metabolites and a metabonomic study of tamoxifen in endometrial cells using gradient high resolution magic angle spinning 1H NMR spectroscopy

High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy was used to metabolically characterise Ishikawa cells, a human cell line derived from endometrial adenocarcinoma. The spectra obtained had well-resolved resonances from the nucleotide derivatives of uridine and adenosine. Using a combination of diffusion- and relaxation-weighted spectroscopy, the cellular environment of key metabolites previously identified as related to cell growth was also investigated. As Ishikawa cells are hormone-responsive, the metabolic action of tamoxifen, a selective estrogen receptor modulator (SERM), was also investigated. Cells were exposed to 5, 1 and 0.1 microM tamoxifen. Using the statistical regression technique of prediction to latent structures by partial least squares, a predictive model was built modelling the metabolic profile of the cells against exposure to tamoxifen. These spectral changes were characterised by increased resonance intensities from ethanolamine (3.26 ppm), glucose (3.34-3.94 ppm), glutamate (2.14, 2.32 ppm), tyrosine (7.24 ppm), uridine (7.85 ppm) and adenosine (8.20 ppm), and a relative decrease in contributions from myo-inositol resonances (3.30, 3.62, 3.55 ppm). The nucleotide changes suggest that tamoxifen affects RNA transcription, while the changes in ethanolamine and myo-inositol concentrations are indicative of cell membrane turnover.

The evaluation of different MAS techniques at low spinning rates in aqueous samples and in the presence of magnetic susceptibility gradients

It was recently demonstrated that the nuclear magnetic resonance (NMR) linewidths for stationary biological samples are dictated mainly by magnetic susceptibility gradients, and that phase-altered spinning sideband (PASS) and phase-corrected magic angle turning (PHORMAT) solid-state NMR techniques employing slow and ultra-slow magic angle spinning (MAS) frequencies can be used to overcome the static susceptibility broadening to yield high-resolution, spinning sideband (SSB)-free 1H NMR spectra [Magn. Reson. Med. 46 (2001) 213; 47 (2002) 829]. An additional concern is that molecular diffusion in the presence of the susceptibility gradients may limit the minimum useful MAS frequency by broadening the lines and reducing SSB suppression at low spinning frequencies. In this article the performance of PASS, PHORMAT, total sideband suppression (TOSS), and standard MAS techniques were evaluated as a function of spinning frequency. To this end, 300MHz (7.05T) 1H NMR spectra were acquired via PASS, TOSS, PHORMAT, and standard MAS NMR techniques for a 230-microm-diameter spherical glass bead pack saturated with water. The resulting strong magnetic susceptibility gradients result in a static linewidth of about 3.7kHz that is larger than observed for a natural biological sample, constituting a worst-case scenario for examination of susceptibility broadening effects.

RESULTS

(I) TOSS produces a distorted centerband and fails in suppressing the SSBs at a spinning rate below approximately 1kHz. (II) Standard MAS requires spinning speeds above a few hundred Hz to separate the centerband from the SSBs. (III) PASS produces nearly SSB-free spectra at spinning speeds as low as 30Hz, and is only limited by T(2)-induced signal losses. (IV) With PHORMAT, a SSB-free isotropic projection is obtained at any spinning rate, even at an ultra-slow spinning rate as slow as 1Hz. (V) It is found empirically that the width of the isotropic peak is proportional to F(-x), where F is the spinning frequency, and x=2 for MAS, 0.84 for PASS, and 0.5 for PHORMAT.

Biochemical correlates of thiazolidinedione-induced adipocyte differentiation by high-resolution magic angle spinning NMR spectroscopy

Thiazolidinediones, a class of synthetic ligands to the peroxisome proliferator-activated receptor-gamma, induce terminal adipocyte differentiation of 3T3 F442A cells, and have already been used as alternative therapeutic agents for the treatment of liposarcoma in clinical trials. The biochemical changes occurring in the 3T3 F442A cell line and well-differentiated liposarcoma following induction of adipocyte differentiation with the thiazolidinedione troglitazone were measured using high-resolution magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. 3T3 F442A cell differentiation was characterized by a large accumulation of intracellular triglyceride and withdrawal from the cell cycle. Phosphatidylcholine (PTC), phosphocholine (PC), myo-inositol, and glycerol were found to be possible biochemical markers for adipocyte differentiation induced by thiazolidenediones. The molar ratio of PTC to PC increased fourfold in differentiated 3T3 F442A cells compared to undifferentiated cells, suggesting a substantial increase in CTP:phosphocholine cytidylyltransferase activity with differentiation. A 2.8-fold increase in the PTC:PC ratio was observed in the lipoma-like well-differentiated liposarcoma of three patients who were treated with troglitazone when compared to liposarcoma from patients not treated with this drug. Thus, this ratio may be an NMR-detectable marker of troglitazone efficacy and response to differentiation therapy for liposarcoma.

High-resolution 1H NMR spectroscopy in rat liver using magic angle turning at a 1 Hz spinning rate

It is demonstrated that a high-resolution (1)H NMR spectrum of excised rat liver can be obtained using the technique of magic angle turning (MAT) at a sample spinning rate of 1 Hz. A variant of the phase-corrected MAT (PHORMAT) pulse sequence that includes a water suppression segment was developed for the investigation. The spectral resolution achieved with PHORMAT approaches that obtained from a standard magic angle spinning (MAS) experiment at a spinning rate of several kHz. With such ultra-slow spinning, tissue and cell damage associated with the standard MAS experiment is minimized or eliminated. The technique is potentially useful for obtaining high-resolution (1)H spectra in live animals.