Bile Acid Detection Techniques and Bile Acid-Related Diseases

Bile acid is a derivative of cholinergic acid (steroidal parent nucleus) that plays an important role in digestion, absorption, and metabolism. In recent years, bile acids have been identified as signaling molecules that regulate self-metabolism, lipid metabolism, energy balance, and glucose metabolism. The detection of fine changes in bile acids caused by metabolism, disease, or individual differences has become a research hotspot. At present, there are many related techniques, such as enzyme analysis, immunoassays, and chromatography, that are used for bile acid detection. These methods have been applied in clinical practice and laboratory research to varying degrees. However, mainstream detection technology is constantly updated and replaced with the passage of time, proffering new detection technologies. Previously, gas chromatography (GS) and gas chromatography-mass spectrometry (GC-MS) were the most commonly used for bile acid detection. In recent years, high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) has developed rapidly and has gradually become the mainstream bile acid sample separation and detection technology. In this review, the basic principles, development and progress of technology, applicability, advantages, and disadvantages of various detection techniques are discussed and the changes in bile acids caused by related diseases are summarized.

Genes involved in phosphatidylcholine biosynthesis correlate with nuclear factor-κB in biliary tract cancer patients: Evidence from 1H NMR and computational analyses

Gallbladder cancer (GBC) is an aggressive malignancy of gastrointestinal tract. Due to uncontrolled growth, GBC cells rapidly synthesize biomolecules including lipids. The lipids are integral component of cell membrane with a wide range of cellular functions. In this study, we measured the clinicopathological features in 40 cases of histologically confirmed GBC and 16 cases of chronic cholecystitis (CC). The female to male ratio in the GBC and CC groups were 3.44:1 and 2.2:1, respectively. The GBC patients exhibited well to poorly differentiated tumor. In the CC group, all patients showed cholecystitis with no evidence of dysplasia or malignancy. The majority of GBC and CC patients reported pain. Using 1H NMR spectroscopy, we observed 4-folds increase in the level of choline containing phospholipids (CCPLs) in the gallbladder of GBC patients as compared to CC patients. Other lipid metabolites such as cholesterol ester, C18-cholesterol and saturated fatty acids were insignificantly changed between GBC and CC patients. Moreover, the level of CCPLs in the GBC patients with BMI <25 kg/m2 was significantly higher as compared to CC patients. Further, a significant increase in the CCPLs level was observed in GBC female patients in comparison to CC patients. From the computational analyses, we observed that the genes involved in the biosynthesis of phosphatidylcholine (PtdCho) indirectly interact with the RELA, which encodes the NF-κB p65 subunit. The genes involved in the PtdCho biosynthesis were also correlated with the overall and disease-free survival of cholangiocarcinoma patients. The study opens new window for exploring the diagnostic and therapeutic potential of CCPLs in GBC patients.

Identifying unknown metabolites using NMR-based metabolic profiling techniques

Metabolic profiling of biological samples provides important insights into multiple physiological and pathological processes but is hindered by a lack of automated annotation and standardized methods for structure elucidation of candidate disease biomarkers. Here we describe a system for identifying molecular species derived from nuclear magnetic resonance (NMR) spectroscopy-based metabolic phenotyping studies, with detailed information on sample preparation, data acquisition and data modeling. We provide eight different modular workflows to be followed in a recommended sequential order according to their level of difficulty. This multi-platform system involves the use of statistical spectroscopic tools such as Statistical Total Correlation Spectroscopy (STOCSY), Subset Optimization by Reference Matching (STORM) and Resolution-Enhanced (RED)-STORM to identify other signals in the NMR spectra relating to the same molecule. It also uses two-dimensional NMR spectroscopic analysis, separation and pre-concentration techniques, multiple hyphenated analytical platforms and data extraction from existing databases. The complete system, using all eight workflows, would take up to a month, as it includes multi-dimensional NMR experiments that require prolonged experiment times. However, easier identification cases using fewer steps would take 2 or 3 days. This approach to biomarker discovery is efficient and cost-effective and offers increased chemical space coverage of the metabolome, resulting in faster and more accurate assignment of NMR-generated biomarkers arising from metabolic phenotyping studies. It requires a basic understanding of MATLAB to use the statistical spectroscopic tools and analytical skills to perform solid phase extraction (SPE), liquid chromatography (LC) fraction collection, LC-NMR-mass spectroscopy and one-dimensional and two-dimensional NMR experiments.

A review of analytical platforms for accurate bile acid measurement

Bile acids are acidic steroids which help in lipid absorption, act as signaling molecules, and are key intermediate molecules between host and gut microbial metabolism. Perturbations in the circulating bile acid pool can lead to dysregulated metabolic and immunological function which may be associated with liver and intestinal disease. Bile acids have chemically diverse structures and are present in a broad range of concentrations in a wide variety of samples with complex biological matrices. Advanced analytical methods are therefore required to identify and accurately quantify individual bile acids. Though enzymatic determination of total bile acid is most popular in clinical laboratories, these methods provide limited information about individual bile acids. Advanced analytical methods such as gas chromatography- and liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy are highly informative techniques which help in identification and quantification of individual bile acids in complex biological matrices. Here, we review the detection technologies currently used for bile acid identification and quantification. We further discuss the advantages and disadvantages of these analytical techniques with respect to sensitivity, specificity, robustness, and ease of use. Graphical abstract.

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.

Handling Complexity in Animal and Plant Science Research-From Single to Functional Traits: Are We There Yet?

The current knowledge of the main factors governing livestock, crop and plant quality as well as yield in different species is incomplete. For example, this can be evidenced by the persistence of benchmark crop varieties for many decades in spite of the gains achieved over the same period. In recent years, it has been demonstrated that molecular breeding based on DNA markers has led to advances in breeding (animal and crops). However, these advances are not in the way that it was anticipated initially by the researcher in the field. According to several scientists, one of the main reasons for this was related to the evidence that complex target traits such as grain yield, composition or nutritional quality depend on multiple factors in addition to genetics. Therefore, some questions need to be asked: are the current approaches in molecular genetics the most appropriate to deal with complex traits such as yield or quality? Are the current tools for phenotyping complex traits enough to differentiate among genotypes? Do we need to change the way that data is collected and analysed?

Bile Acid Recognition by Mouse Ileal Bile Acid Binding Protein

Ileal bile acid binding protein (I-BABP, gene name FABP6) is a component of the bile acid recycling system, expressed in the ileal enterocyte. The physiological role of I-BABP has been hypothesized to be either an intracellular buffering agent to protect against excess intracellular bile acids or separately as a modulator of bile acid controlled transcription. We investigated mouse I-BABP (mI-BABP) to understand the function of this protein family. Here, we studied energetics and site selectivity of binding with physiological bile acids using a combination of isothermal calorimetric analysis and NMR spectroscopy. We found that the most abundant bile acid in the mouse (β-muricholic acid) binds with weak affinity individually and in combination with other bile acids. Further analysis showed that mI-BABP like human I-BABP (hI-BABP) specifically recognizes the conjugated form of cholic acid:chenodeoxycholic acid (CA:CDCA) in a site-selective manner, displaying the highest affinity of any bile acid combination tested. These results indicate that I-BABP specifically recognizes the ligand combination of CDCA and CA, even in a species such as the mouse where CDCA only represents a trace component of the physiological pool. Specific and conserved recognition of the CDCA and CA ligand combination suggests that I-BABP may play a critical role in the regulation of bile acid signaling in addition to its proposed role as a buffering agent.

Sensitivity enhancement by chromatographic peak concentration with ultra-high performance liquid chromatography-nuclear magnetic resonance spectroscopy for minor impurity analysis

High performance liquid chromatography can be coupled with nuclear magnetic resonance (NMR) spectroscopy to give a powerful analytical method known as liquid chromatography-nuclear magnetic resonance (LC-NMR) spectroscopy, which can be used to determine the chemical structures of the components of complex mixtures. However, intrinsic limitations in the sensitivity of NMR spectroscopy have restricted the scope of this procedure, and resolving these limitations remains a critical problem for analysis. In this study, we coupled ultra-high performance liquid chromatography (UHPLC) with NMR to give a simple and versatile analytical method with higher sensitivity than conventional LC-NMR. UHPLC separation enabled the concentration of individual peaks to give a volume similar to that of the NMR flow cell, thereby maximizing the sensitivity to the theoretical upper limit. The UHPLC concentration of compound peaks present at typical impurity levels (5.0-13.1 nmol) in a mixture led to at most three-fold increase in the signal-to-noise ratio compared with LC-NMR. Furthermore, we demonstrated the use of UHPLC-NMR for obtaining structural information of a minor impurity in a reaction mixture in actual laboratory-scale development of a synthetic process. Using UHPLC-NMR, the experimental run times for chromatography and NMR were greatly reduced compared with LC-NMR. UHPLC-NMR successfully overcomes the difficulties associated with analyses of minor components in a complex mixture by LC-NMR, which are problematic even when an ultra-high field magnet and cryogenic probe are used.

NMR metabolic fingerprints of murine melanocyte and melanoma cell lines: application to biomarker discovery

Melanoma is the most aggressive type of skin cancer and efforts to improve the diagnosis of this neoplasia are largely based on the use of cell lines. Metabolomics is currently undergoing great advancements towards its use to screening for disease biomarkers. Although NMR metabolomics includes both 1D and 2D methodologies, there is a lack of data in the literature regarding heteronuclear 2D NMR assignments of the metabolome from eukaryotic cell lines. The present study applied NMR-based metabolomics strategies to characterize aqueous and lipid extracts from murine melanocytes and melanoma cell lines with distinct tumorigenic potential, successfully obtaining fingerprints of the metabolites from the extracts of the cell lines by means of 2D NMR HSQC correlation maps. Relative amounts of the identified metabolites were compared between the 4 cell lines. Multivariate analysis of ¹H NMR data was able not only to differentiate the melanocyte cell line from the tumorigenic ones but also distinguish among the 3 tumorigenic cell lines. We also investigated the effects of mitogenic agents, and found that they can markedly influence the metabolome of the melanocyte cell line, resembling the pattern of most proliferative cell lines.

Identification and Characterization of Trimethylamine-N-oxide Uptake and Efflux Transporters

Trimethylamine-N-oxide (TMAO) is a recently identified predictor of cardiovascular and chronic kidney disease. TMAO is primarily generated through gut-microbiome mediated conversion of dietary choline and carnitine to TMA, which is converted to TMAO by hepatic flavin monooxygenase 3 (FMO3) and subsequently undergoes renal elimination. We investigated the role of uptake and efflux drug transporters in TMAO disposition in vitro and in vivo. After screening a large array of uptake transporters, we show organic cation transporter 2 (OCT2) is the key transporter for TMAO cellular uptake. In Oct1/2 knockout mice, we observed increased plasma TMAO levels with reduced renal retention, suggesting the importance of Oct2 in facilitating the uptake of TMAO into renal tubular cells in vivo. Multiple transporters of the ATP-binding cassette (ABC) family, including ABCG2 (BCRP) and ABCB1 (MDR1), were capable of TMAO efflux. In human subjects, clinical, dietary, and pharmacogenetic covariates were evaluated for contribution to TMAO levels in a cohort of dyslipidemic patients (n = 405). Interestingly, genetic variation in ABCG2, but not other transporters, appeared to play a role in modulating TMAO exposure.

Characterization of the peak at 2.06 ppm in (31) P magnetic resonance spectroscopy of human liver: phosphoenolpyruvate or phosphatidylcholine?

High field MR scanners can resolve a metabolite resonating at 2.06 ppm in the in vivo proton-decoupled liver (31) P MR spectrum. Traditionally this peak has been assigned to phosphoenolpyruvate (PEP), the key metabolite for gluconeogenesis. However, recent evidence supported the assignment to biliary phosphatidylcholine (PtdCh), which is produced in the liver and stored in the gall bladder. To elucidate the respective contributions of PtdCh and PEP to the in vivo resonance at 2.06 ppm (PEP-PtdCh), we made phantom measurements that confirmed that both biliary PtdCh and PEP resonate approximately at 2 ppm. The absolute quantification of PEP-PtdCh yielded concentrations ranging from 0.6 to 2.0 mmol/l, with mean coefficients of variation of 4.8% for intraday and 7.2% for interday reproducibility in healthy volunteers. The T1 relaxation time of PEP-PtdCh was 0.97 ± 0.30 s in the liver and 0.44 ± 0.11 s in the gallbladder. Ingestion of a mixed meal decreased the concentration of PtdCh-PEP by approximately 12%. In the retrospective analysis, PEP-PtdCh was 68% higher in the liver of subjects with gallbladder infiltration of the volume of interest (VOI) compared with those without gallbladder infiltration. PEP-PtdCh was also significantly higher in the liver of cholecystectomy patients compared with volunteers without gallbladder infiltration, which suggests increased intrahepatic bile fluid as a compensation for gall bladder removal. These results show that liver PtdCh is the major component of the resonance at 2.06 ppm and that careful VOI positioning is mandatory to avoid interference from the gallbladder.

Metabolite characterisation in peritoneal dialysis effluent using high-resolution (1) H and (1) H-(13) C NMR spectroscopy

Metabolite analysis of peritoneal dialysis (PD) effluent may provide information regarding onset and progression of complications associated with prolonged PD therapy. In this context, the nuclear magnetic resonance detectable small metabolites of PD effluent samples were characterised using high-resolution (1) H and (1) H-(13) C NMR spectroscopy. The various spectra were recorded (at 800 MHz proton frequency) on PD effluent samples obtained after 4-h (intraperitoneal) dwell time from patients with end-stage renal failure and continuing normally on PD therapy. In spite of devastating spectral feature of PD effluent due to the presence of intense resonances from glucose and lactate, we were able to identify 53 small endogenous metabolites (including many complex coupled spin systems) and more than 90% of the total CH cross peaks of (1) H-(13) C heteronuclear single-quantum correlation spectrum specific to various metabolites of PD effluent. We foresee that the characteristic fingerprints of various metabolites of control PD effluent samples will be used to identify and distinguish metabolic differences from PD-related complications.

Nutritional modulation of the metabonome: applications of metabolic phenotyping in translational nutritional research

PURPOSE OF REVIEW

Metabolic profiling technologies provide a global overview of complex dietary processes. Metabonomic analytical approaches have now been translated into multiple areas of clinical nutritional research based on the widespread adoption of high-throughput mass spectrometry and proton nuclear magnetic resonance spectroscopy. This has generated novel insights into the molecular mechanisms that shape the microbiome-dietary-chronic disease axis.

RECENT FINDINGS

Metabolome-wide association studies have created a new paradigm in nutritional molecular epidemiology and they have highlighted the importance of gut microbial cometabolic processes in the development of cardiovascular disease and diabetes. Targeted analyses are helping to explain the mechanisms by which high-risk diets (such as red meat) modulate disease risk and they are generating novel biomarkers that will serve to re-define how the efficacy of nutritional interventions is assessed. Nutritional metabonome-microbiome interactions have also been defined in extreme dietary states such as obesity and starvation, and they also serve as important models for understanding how the gut microbiome modifies disease risk. Finally, nutritional systems medicine approaches are creating novel insights into the functional components of our diet, and the mechanisms by which they cause disease.

SUMMARY

Diet is an important modulator of the human metabolic phenotype and the analysis of the nutritional metabolome will drive future development of personalized nutritional interventions.

Two birds with one stone: doing metabolomics with your proteomics kit

Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple ‘-OMICS’ approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC-MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics-based studies. Limitations and requirements are discussed as well as extensions to the LC-MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC-MS, CE-MS or NMR.

Evidence of altered phosphatidylcholine metabolism in Alzheimer's disease

Abberant lipid metabolism is implicated in Alzheimer's disease (AD) pathophysiology, but the connections between AD and lipid metabolic pathways are not fully understood. To investigate plasma lipids in AD, a multiplatform screen (n = 35 by liquid chromatography-mass spectrometry and n = 35 by nuclear magnetic resonance) was developed, which enabled the comprehensive analysis of plasma from 3 groups (individuals with AD, individuals with mild cognitive impairment (MCI), and age-matched controls). This screen identified 3 phosphatidylcholine (PC) molecules that were significantly diminished in AD cases. In a subsequent validation study (n = 141), PC variation in a bigger sample set was investigated, and the same 3 PCs were found to be significantly lower in AD patients: PC 16:0/20:5 (p < 0.001), 16:0/22:6 (p < 0.05), and 18:0/22:6 (p < 0.01). A receiver operating characteristic (ROC) analysis of the PCs, combined with apolipoprotein E (ApoE) data, produced an area under the curve predictive value of 0.828. Confirmatory investigations into the background biochemistry indiciated no significant change in plasma levels of 3 additional PCs of similar structure, total choline containing compounds or total plasma omega fatty acids, adding to the evidence that specific PCs play a role in AD pathology.

Metabolomics view on gut microbiome modulation by polyphenol-rich foods

Health is influenced by genetic, lifestyle, and diet determinants; therefore, nutrition plays an essential role in health management. Still, the substantiation of nutritional health benefits is challenged by the intrinsic macro- and micronutrient complexity of foods and individual responses. Evidence of healthy effects of food requires new strategies not only to stratify populations according to their metabolic requirements but also to predict and measure individual responses to dietary intakes. The influence of the gut microbiome and its interaction with the host is pivotal to understand nutrition and metabolism. Thus, the modulation of the gut microbiome composition by alteration of food habits has potentialities in health improvement or even disease prevention. Dietary polyphenols are naturally occurring constituents in vegetables and fruits, including coffee and cocoa. They are commonly associated to health benefits, although mechanistic evidence in vivo is not yet fully understood. Polyphenols are extensively metabolized by gut bacteria into a complex series of end-products that support a significant effect on the functional ecology of symbiotic partners that can affect the host physiology. This review reports recent nutritional metabolomics inspections of gut microbiota-host metabolic interactions with a particular focus on the cometabolism of cocoa and coffee polyphenols.

NMR spectroscopy for discovery and quantitation of biomarkers of disease in human bile

Human liver synthesizes bile; bile, containing a large number of metabolites, is transported through the canaliculi and bile ducts, and stored in the gallbladder before entering into the intestine. In the intestine, a large number of bile metabolites are reabsorbed and sent back to the liver for recirculation. Owing to close association of the bile with the gastrointestinal system, the bile metabolic profile is highly sensitive to the onset of numerous gastrointestinal disease processes. A growing number of studies suggest that hepatobiliary disease biomarkers are richly populated in human bile. These studies stress the potential of profiling the human bile metabolome for early diagnostics as well as deeper insights into gastrointestinal disease processes. Once the biomarkers are established reliably using human bile, they can be targeted in easily accessible fluids such as blood and urine or targeted in bile itself using noninvasive methods such as in vivo magnetic resonance spectroscopy. NMR spectroscopy is one of the most powerful bioanalytical tools, which promises profiling of human bile metabolome and exploring early biomarkers for hepatobiliary diseases. Comprehensive analysis of human bile using NMR spectroscopy has lead to identification and quantification of major bile metabolites. This review describes the discovery and quantitation of biomarkers of hepatobiliary diseases in human bile using NMR spectroscopy.

A tandem mass spectrometric study of bile acids: interpretation of fragmentation pathways and differentiation of steroid isomers

Bile acids are steroids with a pentanoic acid substituent at C-17. They are the terminal products of cholesterol excretion, and play critical physiological roles in human and animals. Bile acids are easy to detect but difficult to identify by using mass spectrometry due to their poly-ring structure and various hydroxylation patterns. In this study, fragmentation pathways of 18 free and conjugated bile acids were interpreted by using tandem mass spectrometry. The analyses were conducted on ion trap and triple quadrupole mass spectrometers. Upon collision-induced dissociation, the conjugated bile acids could cleave into glycine or taurine related fragments, together with the steroid skeleton. Fragmentations of free bile acids were further elucidated, especially by atmospheric pressure chemical ionization mass spectrometry in positive ion mode. Aside from universally observed neutral losses, eliminations occurred on bile acid carbon rings were proposed for the first time. Moreover, four isomeric 5β-cholanic acid hydroxyl derivatives (3α,6α-, 3α,7β-, 3α,7α-, and 3α,12α-) were differentiated using electrospray ionization in negative ion mode: 3α,7β-OH substituent inclined to eliminate H(2)O and CH(2)O(2) groups; 3α,6α-OH substituent preferred neutral loss of two H(2)O molecules; 3α,12α-OH substituent apt to lose the carboxyl in the form of CO(2) molecule; and 3α,7α-OH substituent exhibited no further fragmentation after dehydration. This study provided specific interpretation for mass spectra of bile acids. The results could contribute to bile acid analyses, especially in clinical assays and metabonomic studies.

Evaluating the transcriptomic and metabolic profile of mice exposed to source drinking water

Transcriptomic and metabonomic methods were used to investigate mice's responses to drinking source water (DSW) exposure. After mice were fed with DSW for 90 days, hepatic transcriptome was characterized by microarray and serum metabonome were determined by (1)H nuclear magnetic resonance (NMR) spectroscopy. A total of 243 differentially expressed genes (DEGs) were identified, among which 141 genes were up-regulated and 102 genes were down-regulated. Metabonomics revealed significant changes in concentrations of creatine, pyruvate, glutamine, lysine, choline, acetate, lipids, taurine, and trimethylamine oxide. Four biological pathways were identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis where both gene expression and metabolite concentrations were altered in response to DSW exposure. These results highlight the significance of combined use of transcriptomic and metabonomic approaches in evaluating potential health risk induced by DSW contaminated with various hazardous materials.

Advances in metabolite identification

One of the central challenges to metabolomics is metabolite identification. Regardless of whether one uses so-called 'targeted' or 'untargeted' metabolomics, eventually all paths lead to the requirement of identifying (and quantifying) certain key metabolites. Indeed, without metabolite identification, the results of any metabolomic analysis are biologically and chemically uninterpretable. Given the chemical diversity of most metabolomes and the character of most metabolomic data, metabolite identification is intrinsically difficult. Consequently a great deal of effort in metabolomics over the past decade has been focused on making metabolite identification better, faster and cheaper. This review describes some of the newly emerging techniques or technologies in metabolomics that are making metabolite identification easier and more robust. In particular, it focuses on advances in metabolite identification that have occurred over the past 2 to 3 years concerning the technologies, methodologies and software as applied to NMR, MS and separation science. The strengths and limitations of some of these approaches are discussed along with some of the important trends in metabolite identification.

Bile UPLC-MS fingerprinting and bile acid fluxes during human liver transplantation

Bile flow restoration is a crucial step in the recovery process post transplantation of the liver. Here, metabolic trajectories based on changes in bile secretion - a known marker of functionality - have been utilised as an approach for discovering bile fluxes during transplantation. A total of ten liver transplants were monitored and from these 68 bile samples from both donors and recipients were collected and analysed using ultra-performance LC-MS in combination with multivariate statistical analysis. Based on the principal component scores constructed from the total bile fingerprint, differentiation of the bile acid concentrations before and after transplantation was detected. A trend was also observed, by constructing metabolic trajectories, whereby the post-transplant profiles approached the position of pre-transplant profiles within 30-60 min of the restoration of bile secretion function. The ten major conjugated bile acid salts were measured and a significant increase in concentrations of taurocholic acid and taurochenodeoxycholic acid were seen after transplantation. In addition, the ratios of secondary bile acids detected in gall bladder and hepatic bile were measured before and after transplantation. This study suggests that bile acid ratios in the donor liver at the pre-transplant and post-transplant stage may be important and that profiling of secreted bile after transplantation may aid clinical assessment and progress post-transplantation.

Lipid profiling of cancerous and benign gallbladder tissues by 1H NMR spectroscopy

Qualitative and quantitative (1) H NMR analysis of lipid extracts of gallbladder tissue in chronic cholecystitis (CC, benign) (n = 14), xanthogranulomatous cholecystitis (XGC, intermediate) (n = 9) and gallbladder cancer (GBC, malignant) (n = 8) was carried out to understand the mechanisms involved in the transformation of benign gallbladder tissue to intermediate and malignant tissue. The results revealed alterations in various tissue lipid components in gallbladder in CC, XGC and GBC. The difference in the nature of lipid components in benign and malignant disease may aid in the identification of the biological pathways involved in the etiopathogenesis of GBC. This is the first study on lipid profiling of gallbladder tissue by (1) H NMR spectroscopy, and has possible implications for the development of future diagnostic approaches.

Simultaneous quantification of glycine- and taurine-conjugated bile acids, total bile acids, and choline-containing phospholipids in human bile using 1H NMR spectroscopy

Bile acids, phospholipids, and cholesterol are the major lipid components in human bile. The composition of bile is altered in various cholestatic diseases, and determining such alterations will be of great clinical importance in understanding the pathophysiology of these diseases. A robust method for the simultaneous quantification of major biliary lipids--glycine-conjugated bile acids (GCBAs), taurine-conjugated bile acids (TCBAs), total bile acids (TBAs) and choline-containing phospholipids (choline-PLs) has been devised using (1)H NMR spectroscopy. Bile samples were obtained from patients with various hepatopancreatobiliary diseases (n=10) during an endoscopic retrograde cholangiopancreatography (ERCP) examination. Peak areas of metabolite-signals of interest were obtained simultaneously by deconvoluting the experimental spectrum, making the present method robust. GCBAs and TCBAs have been quantified using the peak areas of their characteristic methylene (CH(2)) signals resonating at 3.73 and 3.07 ppm, whereas TBA and choline-PLs were quantified using their methyl (CH(3)) and trimethylammonium (-N(+)(CH(3))(3)) signals resonating at 0.65 and 3.22 ppm respectively. The present method was compared with an NMR-based literature method (which involves dissolving bile in DMSO), and a good correlation was observed between the two methods with regression coefficients - 0.97, 0.99, 0.98 and 0.93 for GCBAs, TCBAs, TBAs, and choline-PLs respectively. This method has the potential to be extended to in vivo applications for the simultaneous quantification of various biliary lipids non-invasively.

Human bile as a rich source of biomarkers for hepatopancreatobiliary cancers

Metabolic profiling of biofluids is emerging as an important area with a promising number of applications in clinical medicine, including early diagnosis of numerous diseases that normally remain silent until late in the progress of disease. While blood and urine are more often used to explore biomarkers that distinguish he healthy from disease conditions, human bile is emerging as a rich source of biomarkers specifically for the cancers of the liver (hepatocellular carcinoma), bile ducts (cholangiocarcinoma), gallbladder and pancreas. This is owing to the fact that metabolites linked to the pathways of tumor cell metabolism are rich in bile by virtue of its association or proximity to the pathological source. Recent methodological developments have enabled the identification of a number of bile metabolites that have links with hepatopancreatobiliary diseases. Investigations of human bile are also considered to help the biomarker discovery process in vitro and provide avenues for translational research in detecting and following dynamic variations of biomarkers in clinical settings using noninvasive approaches, such as in vivo magnetic resonance spectroscopy. This article reviews the current status and potential applications of human bile as a source of biomarkers, with emphasis on metabolites, for early detection of cancers associated with the hepatopancreatobiliary system.

Bile salts and cholestasis

Bile salts have a crucial role in hepatobiliary and intestinal homeostasis and digestion. Primary bile salts are synthesized by the liver from cholesterol, and may be modified by the intestinal flora to form secondary and tertiary bile salts. Bile salts are efficiently reabsorbed from the intestinal lumen to undergo enterohepatic circulation. In addition to their function as a surfactant involved in the absorption of dietary lipids and fat-soluble vitamins bile salts are potent signaling molecules in both the liver and intestine. Under physiological conditions the bile salt pool is tightly regulated, but the adaptive capacity may fall short under cholestatic conditions. Elevated serum and tissue levels of potentially toxic hydrophobic bile salts during cholestasis may cause mitochondrial damage, apoptosis or necrosis in susceptible cell types. Therapeutic nontoxic bile salts may restore impaired hepatobiliary secretion in cholestatic disorders. The hydrophilic bile salt ursodeoxycholate is today regarded as the effective standard treatment of primary biliary cirrhosis and intrahepatic cholestasis of pregnancy, and is implicated for use in various other cholestatic conditions. Novel therapeutic bile salts that are currently under evaluation may also prove valuable in the treatment of these diseases.

The role of mass spectrometry-based metabolomics in medical countermeasures against radiation

Radiation metabolomics can be defined as the global profiling of biological fluids to uncover latent, endogenous small molecules whose concentrations change in a dose-response manner following exposure to ionizing radiation. In response to the potential threat of nuclear or radiological terrorism, the Center for High-Throughput Minimally Invasive Radiation Biodosimetry was established to develop field-deployable biodosimeters based, in part, on rapid analysis by mass spectrometry of readily and easily obtainable biofluids. In this review, we briefly summarize radiation biology and key events related to actual and potential nuclear disasters, discuss the important contributions the field of mass spectrometry has made to the field of radiation metabolomics, and summarize current discovery efforts to use mass spectrometry-based metabolomics to identify dose-responsive urinary constituents, and ultimately to build and deploy a noninvasive high-throughput biodosimeter.

Bidirectional correlation of NMR and capillary electrophoresis fingerprints: a new approach to investigating Schistosoma mansoni infection in a mouse model

We demonstrate the statistical integration of nuclear magnetic resonance (NMR) spectroscopy and capillary electrophoresis (CE) data in order to describe a pathological state caused by Schistosoma mansoni infection in a mouse model based on urinary metabolite profiles. Urine samples from mice 53 days post infection with S. mansoni and matched controls were analyzed via NMR spectroscopy and CE. The two sets of metabolic profiles were first processed and analyzed independently and were subsequently integrated using statistical correlation methods in order to facilitate cross assignment of metabolites. Using this approach, metabolites such as 3-ureidopropionate, p-cresol glucuronide, phenylacetylglycine, indoxyl sulfate, isocitrate, and trimethylamine were identified as differentiating between infected and control animals. These correlation analyses facilitated structural elucidation using the identification power of one technique to enhance and validate the other, but also highlighted the enhanced ability to detect functional correlations between metabolites, thereby providing potential for achieving deeper mechanistic insight into the biological process.

Improving metabolite knowledge in stable atherosclerosis patients by association and correlation of GC-MS and 1H NMR fingerprints

The plasma of patients with stable carotid atherosclerosis (n = 9), and healthy subjects (n = 10) have been fingerprinted with both GC-MS and (1)H NMR. Principal component analysis (PCA), partial least-squares-discriminant analysis (PLS-DA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA) have been applied to the profiles from each technique both separately and in combination. These techniques complement each other and enable a clearer picture of the biological samples to be interpreted not only for classification purposes, but also more importantly to define the metabolic state of patients with carotid atherosclerosis. The results showed at least 24 metabolites that were significantly modified in the group of atherosclerotic patients by this nontargeted procedure. Most of the changes can be associated to alterations of the metabolism characteristics of insulin resistance that can be strongly related to the metabolic syndrome. In addition, correlations among variables accounting for the classification show amino acids as variables whose changes showed a high degree of correlation. GC-MS and (1)H NMR fingerprints can provide complementary information in the identification of altered metabolic pathways in patients with carotid atherosclerosis. Moreover, correlations among the results with both techniques, instead of a single study, can provide a deeper insight into the patient state.

MR metabolomics of fecal extracts: applications in the study of bowel diseases

NMR-based metabolomics is becoming a useful tool in the study of body fluids and has a strong potential to contribute to disease diagnosis. While applications on urine and serum have been the focus to date, there are a number of other body fluids that are readily available and could potentially be used for metabolomics-based disease diagnosis. One such body fluid is stool or fecal extract. Given its contact with and transient stay in the colon and rectum, stool carries a lot of useful information regarding the health/disease status of both the colon and the rectum. This could be particularly useful for the non-invasive diagnosis of colorectal cancer and inflammatory bowel disease--the two bowel diseases that are very common and pose significant public health problems. Different methodological considerations including the collection of sample, the storage of sample, the preparation of sample, NMR acquisition parameters, experimental conditions and data analysis methods are discussed. Results obtained in the detection of colorectal cancer and in the differentiation of the two major forms of inflammatory bowel disease (i.e. ulcerative colitis and Crohn's disease) are presented. This is concluded with a brief discussion on the future of MR metabolomics of fecal extracts.

Combining nuclear magnetic resonance spectroscopy and mass spectrometry in biomarker discovery

Metabolic profiling of biological specimens is emerging as a promising approach for discovering specific biomarkers in the diagnosis of a number of diseases. Amongst many analytical techniques, nuclear magnetic resonance spectroscopy and mass spectrometry are the most information-rich tools that enable high-throughput and global analysis of hundreds of metabolites in a single step. Although only one of the two techniques is utilized in a majority of metabolomics applications, there is a growing interest in combining the data from the two methods to effectively unravel the mammoth complexity of biological samples. In this article, current developments in nuclear magnetic resonance, mass spectrometry and multivariate statistical analysis methods are described. While some general applications that utilize the combination of the two analytical methods are presented briefly, the emphasis is laid on the recent applications of nuclear magnetic resonance and mass spectrometry methods in the studies of hepatopancreatobiliary and gastrointestinal malignancies.