Genomic and metabolomic advances in the identification of disease and adverse event biomarkers

Application of metabolomics in diagnostics and differentiation of meningitis: A narrative review with a critical approach to the literature

Due to its high mortality rate associated with various life-threatening sequelae, meningitis poses a vital problem in contemporary medicine. Numerous algorithms, many of which were derived with the aid of artificial intelligence, were brought up in a strive for perfection in predicting the status of sepsis-related survival or exacerbation. This review aims to provide key insights on the contextual utilization of metabolomics. The aim of this the metabolomic approach set of methods can be used to investigate both bacterial and host metabolite sets from both the host and its microbes in several types of specimens - even in one's breath, mainly with use of two methods - Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR). Metabolomics, and has been used to elucidate the mechanisms underlying disease development and metabolic identification changes in a wide range of metabolite contents, leading to improved methods of diagnosis, treatment, and prognosis of meningitis. Mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) are the main analytical platforms used in metabolomics. Its high sensitivity accounts for the usefulness of metabolomics in studies into meningitis, its sequelae, and concomitant comorbidities. Metabolomics approaches are a double-edged sword, due to not only their flexibility, but also - high complexity, as even minor changes in the multi-step methods can have a massive impact on the results. Information on the differential diagnosis of meningitis act as a background in presenting the merits and drawbacks of the use of metabolomics in context of meningeal infections.

An Observation Study of Urinary Biomarkers Exploratory in Alzheimer's Disease using High Resolution Mass Spectrometry

Alzheimer's disease (AD) is regarded as a progressive neurodegenerative dementia, characterized by degeneration of distinct neuronal populations. A case-control study was carried out by using high resolution mass spectrometry to explore AD associated urinary metabolic biomarkers from 30 AD patients and 30 cognitively normal (CN) individuals, respectively. In total, 49 metabolites were determined and validated as known compounds by LC/MS analysis. With two sample t-test statistical analysis (p<0.05), 19 metabolites were shown to be significantly differed from AD to CN. A diagnostic model of receiver-operator characteristic (ROC) curve was constructed with a combination of 9 selected metabolites and yielded a separation with an area under the curve value of 0.976 between two groups. This study indicated urinary metabolites showed a significant expression between AD and CN. AD related metabolites enable to satisfy the diagnostic power of disease discrimination. Additionally, as a non-invasive approach, urine collection provides its convenience in clinical diagnosis of AD.

Tear Metabolomics in Dry Eye Disease: A Review

Dry eye disease (DED) is a multifactorial syndrome that can be caused by alteration in the quality or quantity of the precorneal tear film. It is considered one of the most common ocular conditions leading patients to seek eye care. The current method for diagnostic evaluations and follow-up examinations of DED is a combination of clinical signs and symptoms determined by clinical tests and questionnaires, respectively. The application of powerful omics technologies has opened new avenues toward analysis of subjects in health and disease. Metabolomics is a new emerging and complementary research discipline to all modern omics in the comprehensive analysis of biological systems. The identification of distinct metabolites and integrated metabolic profiles in patients can potentially inform clinicians at an early stage or during monitoring of disease progression, enhancing diagnosis, prognosis, and the choice of therapy. In ophthalmology, metabolomics has gained considerable attention over the past decade but very limited such studies have been reported on DED. This paper aims to review the application of tear metabolomics in DED.

Metabolomics of Pregnancy Complications: Emerging Application of Maternal Hair

In recent years, the study of metabolomics has begun to receive increasing international attention, especially as it pertains to medical research. This is due in part to the potential for discovery of new biomarkers in the metabolome and to a new understanding of the "exposome", which refers to the endogenous and exogenous compounds that reflect external exposures. Consequently, metabolomics research into pregnancy-related issues has increased. Biomarkers discovered through metabolomics may shed some light on the etiology of certain pregnancy-related complications and their adverse effects on future maternal health and infant development and improve current clinical management. The discoveries and methods used in these studies will be compiled and summarized within the following paper. A further focus of this paper is the use of hair as a biological sample, which is gaining increasing attention across diverse fields due to its noninvasive sampling method and the metabolome stability. Its significance in exposome studies will be considered in this review, as well as the potential to associate exposures with adverse pregnancy outcomes. Currently, hair has been used in only two metabolomics studies relating to fetal growth restriction (FGR) and gestational diabetes mellitus (GDM).

An integrated portable system for single chip simultaneous measurement of multiple disease associated metabolites

Metabolites, the small molecules that underpin life, can act as indicators of the physiological state of the body when their abundance varies, offering routes to diagnosis of many diseases. The ability to assay for multiple metabolites simultaneously will underpin a new generation of precision diagnostic tools. Here, we report the development of a handheld device based on complementary metal oxide semiconductor (CMOS) technology with multiple isolated micro-well reaction zones and integrated optical sensing allowing simultaneous enzyme-based assays of multiple metabolites (choline, xanthine, sarcosine and cholesterol) associated with multiple diseases. These metabolites were measured in clinically relevant concentration range with minimum concentrations measured: 25 μM for choline, 100 μM for xanthine, 1.25 μM for sarcosine and 50 μM for cholesterol. Linking the device to an Android-based user interface allows for quantification of metabolites in serum and urine within 2 min of applying samples to the device. The quantitative performance of the device was validated by comparison to accredited tests for cholesterol and glucose.

Serum and urine toxicometabolomics following gentamicin-induced nephrotoxicity in male Sprague-Dawley rats

Gentamicin (GM) is an aminoglycoside antibiotic used in treatment of various types of bacterial infections, but the major adverse effect is drug-induced nephrotoxicity. This study aimed to determine biomarkers that might predict nephrotoxicity initiated by GM using serum or urinary proton nuclear magnetic resonance (¹H NMR) spectral data in male Sprague-Dawley rats. GM (0, 30, or 300 mg/kg/d) was intraperitoneally administered for 3 consecutive days. Animals were sacrificed 2 d (D2) or 8 d (D8) after last administration of GM in order to perform analysis of serum biochemistries and histopathologic examination. Urine samples were collected every 24 h from prior to treatment until sacrifice. Serum and urinary ¹H NMR spectral data revealed apparent differential clustering between control and GM-treated groups as evidenced by principal component analysis (PCA) and orthogonal projections to latent structure-discriminant analysis (OPLS-DA) in global and targeted profiling. The concentrations of endogenous serum metabolites including 3-hydroxybutyrate, alanine, citrate, creatine, glucose, and glycine were increased significantly on D2 or D8. Urinary levels of glucose, glycine, and succinate were significantly elevated on D2 or D8, whereas the concentration of hippurate was significantly decreased on D2 and D8. Correlation of serum and urinary ¹H NMR OPLS-DA with serum biochemistry and renal histopathologic changes suggests that ¹H NMR urinalysis may be used to reliably predict or screen for GM-induced nephrotoxicity. In contrast, Western blot analysis of kidney injury molecule-1 (KIM-1) demonstrated that protein expression was not markedly altered indicating this biomarker was not sensitive to detect GM-mediated renal damage. Data suggest that these altered metabolites might serve as specific and sensitive biomarkers for GM-mediated renal damage.

Toxicological effects of Nux Vomica in rats urine and serum by means of clinical chemistry, histopathology and 1H NMR-based metabonomics approach

ETHNOPHARMACOLOGICAL RELEVANCE

The dried ripe seeds of Nux Vomica (Strychnos nux-vomica L.), a traditional Chinese medicine, have been used to treat multifarious symptoms. However, the clinical applications of Nux Vomica are limited by its severe toxicity. In this study, Nux Vomica was subjected to nuclear magnetic resonance (NMR) metabonomics and pathological examination to determine relevant biomarkers in target organs and to explain the underlying toxicity mechanism.

MATERIALS AND METHOD

Thirty-six male Sprague-Dawley rats were randomly divided into three groups of twelve rats. The control group was oral gavaged with distilled water, and two experiment groups were treated with Nux Vomica at a dose of 0.315 and 0.630g/kg body weight. On days 14 and 21, serum, urine, liver and kidney tissues were collected for histopathological examination, biochemical analysis and ¹H-NMR analysis.

RESULTS

The metabolites changes of rats treated with Nux Vomica are obviously differ from that of controls. In serum, low-dose group compared with control shows the significantly changes included elevated concentration of glucose, TMAO, and creatine, with decreased lipids, 3-HB, lactate, and unsaturated fatty acid. Change in taurine was only observed in the separation comparison of high-dose group and control. In urine, the variation metabolites included elevations in glucose, creatine, and TMAO as well as decreased lactate, succinate, α-ketoglutaric acid, citrate and hippurate in low-dose group compared with control. Only alanine and creatine were decreased significantly in high-dose group compared with control.

CONCLUSION

Nux Vomica induced disruptions in glycolysis, lipid and amino acid metabolism, and toxic effects were aggravated in liver and kidney tissues as dosing time was prolonged. ¹H NMR-based metabonomics combined with biochemical and histopathological methods can be applied to elucidate the toxicity mechanism of Nux Vomica decoction that caused liver and kidney injuries in rats.

Metabolic Adaptations of Uropathogenic E. coli in the Urinary Tract

Escherichia coli ordinarily resides in the lower gastrointestinal tract in humans, but some strains, known as Uropathogenic E. coli (UPEC), are also adapted to the relatively harsh environment of the urinary tract. Infections of the urine, bladder and kidneys by UPEC may lead to potentially fatal bloodstream infections. To survive this range of conditions, UPEC strains must have broad and flexible metabolic capabilities and efficiently utilize scarce essential nutrients. Whole-organism (or "omics") methods have recently provided significant advances in our understanding of the importance of metabolic adaptation in the success of UPECs. Here we describe the nutritional and metabolic requirements for UPEC infection in these environments, and focus on particular metabolic responses and adaptations of UPEC that appear to be essential for survival in the urinary tract.

Identification of potential biomarkers of hepatitis B-induced acute liver failure using hepatic cells derived from human skin precursors

Besides their role in the elucidation of pathogenic processes of medical and pharmacological nature, biomarkers can also be used to document specific toxicological events. Hepatic cells generated from human skin-derived precursors (hSKP-HPC) were previously shown to be a promising in vitro tool for the evaluation of drug-induced hepatotoxicity. In this study, their capacity to identify potential liver-specific biomarkers at the gene expression level was investigated with particular emphasis on acute liver failure (ALF). To this end, a set of potential ALF-specific biomarkers was established using clinically relevant liver samples obtained from patients suffering from hepatitis B-associated ALF. Subsequently, this data was compared to data obtained from primary human hepatocyte cultures and hSKP-HPC, both exposed to the ALF-inducing reference compound acetaminophen. It was found that both in vitro systems revealed a set of molecules that was previously identified in the ALF liver samples. Yet, only a limited number of molecules was common between both in vitro systems and the ALF liver samples. Each of the in vitro systems could be used independently to identify potential toxicity biomarkers related to ALF. It seems therefore more appropriate to combine primary human hepatocyte cultures with complementary in vitro models to efficiently screen out potential hepatotoxic compounds.

Metabolomics approach to serum biomarker for loperamide-induced constipation in SD rats

Loperamide has long been known as an opioid-receptor agonist useful as a drug for treatment of diarrhea resulting from gastroenteritis or inflammatory bowel disease as well as to induce constipation. To determine and characterize putative biomarkers that can predict constipation induced by loperamide treatment, alteration of endogenous metabolites was measured in the serum of Sprague Dawley (SD) rats treated with loperamide for 3 days using ¹H nuclear magnetic resonance (¹H NMR) spectral data. The amounts and weights of stool and urine excretion were significantly lower in the loperamide-treated group than the No-treated group, while the thickness of the villus, crypt layer, and muscle layer was decreased in the transverse colon of the same group. The concentrations of aspartate aminotransferase (AST), lactate dehydrogenase (LDH) and creatinine (Cr) were also slightly changed in the loperamide-treated group, although most of the serum components were maintained at a constant level. Furthermore, pattern recognition of endogenous metabolites showed completely separate clustering of the serum analysis parameters between the No-treated group and loperamide-treated group. Among 35 endogenous metabolites, four amino acids (alanine, glutamate, glutamine and glycine) and six endogenous metabolites (acetate, glucose, glycerol, lactate, succinate and taurine) were dramatically decreased in loperamide-treated SD rats. These results provide the first data pertaining to metabolic changes in SD rats with loperamide-induced constipation. Additionally, these findings correlate the changes in 10 metabolites with constipation.

Pattern recognition analysis for hepatotoxicity induced by acetaminophen using plasma and urinary 1H NMR-based metabolomics in humans

Drug-induced liver injury (DILI) is currently an increasingly relevant health issue. However, available biomarkers do not reliably detect or quantify DILI risk. Therefore, the purpose of this study was to comparatively evaluate plasma and urinary biomarkers obtained from humans treated with acetaminophen (APAP) using a metabolomics approach and a proton nuclear magnetic resonance (NMR) platform. APAP (3 g/day, two 500 mg tablets every 8 h) was administered to 20 healthy Korean males (age, 20-29 years) for 7 days. Urine was collected daily before and during dosing and 6 days after the final dose. NMR spectra of these urine samples were analyzed using principal component analysis (PCA) and partial least-squares-discrimination analysis. Although the activities of aspartate aminotransferase and lactate dehydrogenase were significantly increased 7 days post-APAP treatment, serum biochemical parameters of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, total bilirubin, γ-glutamyl transpeptidase, and lactate dehydrogenase were within normal range of hepatic function. However, urine and plasma (1)H NMR spectroscopy revealed different clustering between predosing and after APAP treatment for global metabolomic profiling through PCA. Urinary endogenous metabolites of trimethylamine-N-oxide, citrate, 3-chlorotyrosine, phenylalanine, glycine, hippurate, and glutarate as well as plasma endogenous metabolites such as lactate, glucose, 3-hydroxyisovalerate, isoleucine, acetylglycine, acetone, acetate, glutamine, ethanol, and isobutyrate responded significantly to APAP dosing in humans. Urinary and plasma endogenous metabolites were more sensitive than serum biochemical parameters. These results might be applied to predict or screen potential hepatotoxicity caused by other drugs using urinary and plasma (1)H NMR analyses.

The human urine metabolome

Urine has long been a "favored" biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca.

Metabolomics as a tool for personalizing medicine: 2012 update

Numerous factors in conjunction with an individual’s genetic make up will determine predisposition to disease, adverse or beneficial effects of drug treatment or therapy, and disease progression. A major limitation of current clinical measures is that the disease phenotype, which is comprised of the genotype and other environmental factors, is underestimated. Rather, each disease is treated similarly even though the disease process is highly complex. Methods that evaluate the interaction of genotype and environmental factors would likely be a better indicator of patients’ response to medical treatments. The omics technologies, specifically metabolomics, will play a major role in the movement towards personalized medicine. Metabolomics is phenotype driven and should provide better clinical biomarkers. Furthermore, recent studies have shown that associations between genetic variants and downstream metabolite changes can provide a unique description of an individual’s genotype and phenotype, which will further enhance the movement towards personalized medicine.

Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity

Circulating microRNAs (miRNAs) have emerged as novel noninvasive biomarkers for several diseases and other types of tissue injury. This study tested the hypothesis that changes in the levels of urinary miRNAs correlate with liver injury induced by hepatotoxicants. Sprague-Dawley rats were administered acetaminophen (APAP) or carbon tetrachloride (CCl(4)) and one nonhepatotoxicant (penicillin/PCN). Urine samples were collected over a 24 h period after a single oral dose of APAP (1250 mg/kg), CCl(4) (2000 mg/kg), or PCN (2400 mg/kg). APAP and CCl(4) induced liver injury based upon increased serum alanine and aspartate aminotransferase levels and histopathological findings, including liver necrosis. APAP and CCl(4) both significantly increased the urinary levels of 44 and 28 miRNAs, respectively. In addition, 10 of the increased miRNAs were in common between APAP and CCl(4). In contrast, PCN caused a slight decrease of a different nonoverlapping set of urinary miRNAs. Cluster analysis revealed a distinct urinary miRNA pattern from the hepatotoxicant-treated groups when compared with vehicle controls and PCN. Analysis of hepatic miRNA levels suggested that the liver was the source of the increased urinary miRNAs after APAP exposure; however, the results from CCl(4) were equivocal. Computational analysis was used to predict target genes of the 10 shared hepatotoxicant-induced miRNAs. Liver gene expression profiling using whole genome microarrays identified eight putative miRNA target genes that were significantly altered in the liver of APAP- and CCl(4)-treated animals. In conclusion, the patterns of urinary miRNA may hold promise as biomarkers of hepatotoxicant-induced liver injury.

A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism

One of the main pathways for the detoxification of reactive metabolites in the liver involves glutathione conjugation. Metabolic profiling studies have shown paradoxical responses in glutathione-related biochemical pathways. One of these is the increase in 5-oxoproline and ophthalmic acid concentrations with increased dosage of paracetamol. Experimental studies have thus far failed to resolve these paradoxes and the robustness of how these proposed biomarkers correlate with liver glutathione levels has been questioned. To better understand how these biomarkers behave in the glutathione system a kinetic model of this pathway was made. By using metabolic control analysis and by simulating biomarker levels under a variety of conditions, we found that 5-oxoproline and ophthalmic acid concentrations may not only depend on the glutathione but also on the methionine status of the cell. We show that neither of the two potential biomarkers are reliable on their own since they need additional information about the methionine status of the system to relate them uniquely to intracellular glutathione concentration. However, when both biomarkers are measured simultaneously a direct inference of the glutathione concentration can be made, irrespective of the methionine concentration in the system.

HPLC-MS/MS methods for the quantitative analysis of ophthalmic acid in rodent plasma and hepatic cell line culture medium

Ophthalmic acid (OA), an endogenous tripeptide analogue of glutathione, has been suggested as a potential biomarker for paracetamol/acetaminophen hepatotoxicity. Here HPLC-MS/MS methods have been developed for the precise, sensitive and specific detection and quantification of OA in in vitro cell culture medium and plasma. For the cell culture medium the LLOQ was found to be 1 ng/ml, with less than 1% between sample carry over at all concentrations and precision below 15% for within day and below 9% for between day analyses. For rat plasma the presence of endogenous OA resulted in the LLOQ being 25 ng/ml (defined as the lowest concentration on the calibration curve where the base peak was less than 20% of the LLOQ). For the plasma assay the percentage carry over was less than 1% for all concentrations and within and between batch precision was below 21%. The methods were linear for both sample types from the LLOQ up to 5 μg/ml. The method was successfully applied to the determination of OA in samples obtained following the chronic administration of the rat hepatotoxin methapyrilene, where plasma OA concentrations were observed to show a weak negative correlation with those of established liver injury biomarkers such as aspartate aminotransferase (AST).

Metabolomics and malaria biology

Metabolomics has ushered in a novel and multi-disciplinary realm in biological research. It has provided researchers with a platform to combine powerful biochemical, statistical, computational, and bioinformatics techniques to delve into the mysteries of biology and disease. The application of metabolomics to study malaria parasites represents a major advance in our approach towards gaining a more comprehensive perspective on parasite biology and disease etiology. This review attempts to highlight some of the important aspects of the field of metabolomics, and its ongoing and potential future applications to malaria research.