Renewed interest in metabolic research over the last two decades has inspired an explosion of technological developments for studying metabolism. At the forefront of methodological innovation is an ...approach referred to as “untargeted” or “discovery” metabolomics. The experimental objective of this technique is to comprehensively measure the entire metabolome, which constitutes a largely undefined set of molecules. Given its potential comprehensive coverage, untargeted metabolomics is often the first choice of experiments for investigators pursuing a metabolic research question. It is important to recognize, however, that untargeted metabolomics may not always be the optimal experimental approach. Conventionally, untargeted metabolomics only provides information about relative differences in metabolite pool sizes. Therefore, depending on the specific scientific question at hand, a complementary approach involving stable isotopes (such as metabolic flux analysis) may be better suited to provide biological insights. Unlike untargeted metabolomics, stable-isotope methods can provide information about differences in reaction rates.
Metabolism studies are complicated by the unknown number of compounds composing the metabolome, the chemical diversity of metabolites, and the complex dynamics of pathway regulation. Zamboni, Saghatelian, and Patti discuss cutting-edge metabolomics and metabolic flux technologies to address these challenges.
Metabolites, the chemical entities that are transformed during metabolism, provide a functional readout of cellular biochemistry. With emerging technologies in mass spectrometry, thousands of ...metabolites can now be quantitatively measured from minimal amounts of biological material, which has thereby enabled systems-level analyses. By performing global metabolite profiling, also known as untargeted metabolomics, new discoveries linking cellular pathways to biological mechanism are being revealed and are shaping our understanding of cell biology, physiology and medicine.
Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly the inception of ...the field, compound identification has been widely recognized as the rate-limiting step of the experimental workflow. In spite of exponential increases in the size of metabolomic databases, which now contain experimental MS/MS spectra for over a half a million reference compounds, chemical structures still cannot be confidently assigned to many signals in a typical LC/MS dataset. The purpose of this Perspective is to consider why identification rates continue to be low in untargeted metabolomics. One rationalization is that many naturally occurring metabolites detected by LC/MS are true “novel” compounds that have yet to be incorporated into metabolomic databases. An alternative possibility, however, is that research data do not provide database matches because of informatic artifacts, chemical contaminants, and signal redundancies. Increasing evidence suggests that, for at least some sample types, many unidentifiable signals in untargeted metabolomics result from the latter rather than new compounds originating from the specimen being measured. The implications of these observations on chemical discovery in untargeted metabolomics are discussed.
Recently, interest in untargeted metabolomics has become prevalent in the general scientific community among an increasing number of investigators. The majority of these investigators, however, do ...not have the bioinformatic expertise that has been required to process metabolomic data by using command-line driven software programs. Here we introduce a novel platform to process untargeted metabolomic data that uses an intuitive graphical interface and does not require installation or technical expertise. This platform, called XCMS Online, is a web-based version of the widely used XCMS software that allows users to easily upload and process liquid chromatography/mass spectrometry data with only a few mouse clicks. XCMS Online provides a solution for the complete untargeted metabolomic workflow including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be browsed online in an interactive, customizable table showing statistics, chromatograms, and putative METLIN identities for each metabolite. Additionally, all results and images can be downloaded as zip files for offline analysis and publication. XCMS Online is available at https://xcmsonline.scripps.edu.
A long-standing question in cancer biology has been why oxygenated tumors ferment the majority of glucose they consume to lactate rather than oxidizing it in their mitochondria, a phenomenon known as ...the 'Warburg effect.' An abundance of evidence shows not only that most cancer cells have fully functional mitochondria but also that mitochondrial activity is important to proliferation. It is therefore difficult to rationalize the metabolic benefit of cancer cells switching from respiration to fermentation. An emerging perspective is that rather than mitochondrial metabolism being suppressed in tumors, as is often suggested, mitochondrial activity increases to the level of saturation. As such, the Warburg effect becomes a signature of excess glucose being released as lactate due to mitochondrial overload.
Bacterial biofilms in the colon alter the host tissue microenvironment. A role for biofilms in colon cancer metabolism has been suggested but to date has not been evaluated. Using metabolomics, we ...investigated the metabolic influence that microbial biofilms have on colon tissues and the related occurrence of cancer. Patient-matched colon cancers and histologically normal tissues, with or without biofilms, were examined. We show the upregulation of polyamine metabolites in tissues from cancer hosts with significant enhancement of N1, N12-diacetylspermine in both biofilm-positive cancer and normal tissues. Antibiotic treatment, which cleared biofilms, decreased N1, N12-diacetylspermine levels to those seen in biofilm-negative tissues, indicating that host cancer and bacterial biofilm structures contribute to the polyamine metabolite pool. These results show that colonic mucosal biofilms alter the cancer metabolome to produce a regulator of cellular proliferation and colon cancer growth potentially affecting cancer development and progression.
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•Colonic mucosal biofilms alter the cancer metabolome•N1, N12-diacetylspermine was significantly upregulated in tissues with biofilms•Biofilms create conditions conducive to oncogenic transformation in colon cells•Global isotope metabolomics reveals the metabolite fate of N1, N12-diacetylspermine
Johnson et al. examine the metabolomics of bacterial communities called biofilms and human colon cancers. The host and bacterial polyamine metabolites are proposed to act together to promote biofilm formation and cancer growth, creating conditions conducive for normal to cancer cell transformation.
When using liquid chromatography/mass spectrometry (LC/MS) to perform untargeted metabolomics, it is now routine to detect tens of thousands of features from biological samples. Poor understanding of ...the data, however, has complicated interpretation and masked the number of unique metabolites actually being measured in an experiment. Here we place an upper bound on the number of unique metabolites detected in Escherichia coli samples analyzed with one untargeted metabolomics method. We first group multiple features arising from the same analyte, which we call “degenerate features”, using a context-driven annotation approach. Surprisingly, this analysis revealed thousands of previously unreported degeneracies that reduced the number of unique analytes to ∼2961. We then applied an orthogonal approach to remove nonbiological features from the data using the 13C-based credentialing technology. This further reduced the number of unique analytes to less than 1000. Our 90% reduction in data is 5-fold greater than previously published studies. On the basis of the results, we propose an alternative approach to untargeted metabolomics that relies on thoroughly annotated reference data sets. To this end, we introduce the creDBle database (http://creDBle.wustl.edu), which contains accurate mass, retention time, and MS/MS fragmentation data as well as annotations of all credentialed features.
Mass spectrometry-based metabolomics is the comprehensive study of naturally occurring small molecules collectively known as the metabolome. Given the vast structural diversity and chemical ...properties of endogenous metabolites, biological extraction and chromatography methods bias the number, property, and concentration of metabolites detected by mass spectrometry and creates a challenge for global untargeted studies. In this work, we used Escherichia coli bacterial cells to explore the influence of solvent polarity, temperature, and pH in extracting polar and nonpolar metabolites simultaneously. In addition, we explored chromatographic conditions involving different stationary and mobile phases that optimize the separation and ionization of endogenous metabolite extracts as well as a mixture of synthetic standards. Our results reveal that hot polar solvents are the most efficient in extracting both hydrophilic and hydrophobic metabolites simultaneously. In addition, ammonium fluoride in the mobile phase substantially improved ionization efficiency in negative electrospray ionization mode by an average increase in signal intensity of 5.7 and over a 2-fold increase in the total number of features detected. The improvement in sensitivity with ammonium fluoride resulted in 3.5 times as many metabolite hits in databases compared to ammonium acetate or formic acid enriched mobile phases and allowed for the identification of unique metabolites involved in fundamental cellular pathways.
Metabolites, which are typically recognized as small molecules that are involved in cellular reactions, provide a functional signature of phenotype that is complementary to the upstream biochemical ...information obtained from genes, transcripts and proteins. The high correlation between metabolites and phenotype has created a surge of interest in the field that is reflected in the number of metabolomic publications growing from just a few articles in 1999 to over 5,000 in 2011. Although relatively new compared with its genomic and proteomic predecessors, research in the field of metabolomics has already led to the discovery of biomarkers for disease, fundamental insights into cellular biochemistry and clues related to disease pathogenesis.
Durable antibody production after vaccination or infection is mediated by long-lived plasma cells (LLPCs). Pathways that specifically allow LLPCs to persist remain unknown. Through bioenergetic ...profiling, we found that human and mouse LLPCs could robustly engage pyruvate-dependent respiration, whereas their short-lived counterparts could not. LLPCs took up more glucose than did short-lived plasma cells (SLPCs) in vivo, and this glucose was essential for the generation of pyruvate. Glucose was primarily used to glycosylate antibodies, but glycolysis could be promoted by stimuli such as low ATP levels and the resultant pyruvate used for respiration by LLPCs. Deletion of Mpc2, which encodes an essential component of the mitochondrial pyruvate carrier, led to a progressive loss of LLPCs and of vaccine-specific antibodies in vivo. Thus, glucose uptake and mitochondrial pyruvate import prevent bioenergetic crises and allow LLPCs to persist. Immunizations that maximize these plasma cell metabolic properties might thus provide enduring antibody-mediated immunity.
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•LLPCs import more glucose than do short-lived plasma cells (SLPCs)•LLPCs primarily use glucose to glycosylate antibodies•Under metabolic stress, LLPCs but not SLPCs divert glucose to form pyruvate•Genetic ablation of mitochondrial pyruvate import shortens the lifespan of LLPCs
Durable antibody production after vaccination or infection is mediated by long-lived plasma cells (LLPCs), but specific pathways that allow LLPC persistence are unknown. Bhattacharya and colleagues show that LLPCs import and use glucose for antibody glycosylation, but in times of metabolic stress, they divert glucose to generate pyruvate for survival.
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