bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒06‒09
nineteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research

  1. Analyst. 2019 Jun 06.
      Methylation of components involved in one-carbon metabolism is extremely important in cancer; comprehensive studies on methylation are essential and may provide us with a better understanding of tumorigenesis, and lead to the discovery of potential biomarkers. Here, we present an improved methodology for methylated metabolite profiling and its relative quantification in breast cancer cell lines by isotope dilution mass spectrometry based on 13CD3-methionine metabolic labeling using ultra-high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UPLC-HRMS/MS). First, all the methylated metabolites related to methionine were first screened and profiled by introducing 13CD3-methionine as the only medium into breast cancer cell growth cultures for both cellular polar metabolites and lipids. In total, we successfully found 20 labeled methylated metabolites and most of them were identified, some of which have not been reported before. We also developed a relative quantification method for all identified methylated metabolites based on isotope dilution mass spectrometry assays. Finally, the developed method was used for different breast cancer cells and mammary epithelial cells. Most methylated metabolites were disrupted in cancer cells. 1-Methyl-nicotinamide was decreased significantly, while trimethylglycine-glutamic acid-lysine and trimethyl-lysine were increased more than five times. This method offers a new insight into the methylation process, with several key pathways and important new metabolites being identified. Further investigation with biological assays should help to reveal the overall methylation metabolic network.
  2. Lab Invest. 2019 Jun 03.
      Metabolomic profiling can aid in understanding crucial biological processes in cancer development and progression and can also yield diagnostic biomarkers. Desorption electrospray ionization coupled to mass spectrometry imaging (DESI-MSI) has been proposed as a potential adjunct to diagnostic surgical pathology, particularly for prostate cancer. However, due to low resolution sampling, small numbers of mass spectra, and little validation, published studies have yet to test whether this method is sufficiently robust to merit clinical translation. We used over 900 spatially resolved DESI-MSI spectra to establish an accurate, high-resolution metabolic profile of prostate cancer. We identified 25 differentially abundant metabolites, with cancer tissue showing increased fatty acids (FAs) and phospholipids, along with utilization of the Krebs cycle, and benign tissue showing increased levels of lyso-phosphatidylethanolamine (PE). Additionally, we identified, for the first time, two lyso-PEs with abundance that decreased with cancer grade and two phosphatidylcholines (PChs) with increased abundance with increasing cancer grade. Importantly, we developed and internally validated a multivariate metabolomic classifier for prostate cancer using 534 spatial regions of interest (ROIs) in the training cohort and 430 ROIs in the test cohort. With excellent statistical power, the training cohort achieved a balanced accuracy of 97% and validation on testing data set demonstrated 85% balanced accuracy. Given the validated accuracy of this classifier and the correlation of differentially abundant metabolites with established patterns of prostate cancer cell metabolism, we conclude that DESI-MSI is an effective tool for characterizing prostate cancer metabolism with the potential for clinical translation.
  3. J Gerontol A Biol Sci Med Sci. 2019 Jun 04. pii: glz141. [Epub ahead of print]
      Omega-3 polyunsaturated fatty acids (n3-PUFA) are well-recognized for their potent triglyceride-lowering effects, but the potential influence of these bioactive lipids on other biological processes, particularly in the context of healthy aging, remains unknown. With the goal of gaining new insight into some less well-characterized biological effects of n3-PUFAs in healthy older adults, we performed metabolomics of fasting peripheral blood plasma collected from 12 young adults and 12 older adults before and after an open-label intervention of n3-PUFA (3.9g/day, 2.7g EPA, 1.2g DHA). Proton nuclear magnetic resonance (1H-NMR) based lipoprotein subclass analysis revealed the expected reduction in total TG, but also demonstrated that n3-PUFA supplementation reduced VLDL particle number, modestly increased HDL cholesterol, and shifted the composition of HDL subclasses. Further metabolite profiling by 1H-NMR and mass spectrometry revealed pronounced changes in phospholipids, cholesterol esters, diglycerides, and triglycerides following n3-PUFA supplementation. Furthermore, significant changes in hydroxyproline, kynurenine, and 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid (CMPF) following n3-PUFA supplementation provide further insight into some less well-recognized biological effects of n3-PUFA supplementation, including possible effects on protein metabolism, the kynurenine pathway, and glucose metabolism.
    Keywords:  DHA; EPA; lipoproteins; metabolomics; n3-PUFA
  4. Nat Protoc. 2019 Jun 05.
      Identification of previously unreported metabolites (so-called 'unknowns') in untargeted metabolomic data has become an increasingly active area of research. Considerably less attention, however, has been dedicated to identifying unknown metabolic pathways. Yet, for each unknown metabolite structure, there is potentially a yet-to-be-discovered chemical transformation. Elucidating these biochemical connections is essential to advancing our knowledge of cellular metabolism and can be achieved by tracking an isotopically labeled precursor to an unexpected product. In addition to their role in mapping metabolic fates, isotopic labels also provide critical insight into pathway dynamics (i.e., metabolic fluxes) that cannot be obtained from conventional label-free metabolomic analyses. When labeling is compared quantitatively between conditions, for example, isotopic tracers can enable relative pathway activities to be inferred. To discover unexpected chemical transformations or unanticipated differences in metabolic pathway activities, we have developed X13CMS, a platform for analyzing liquid chromatography/mass spectrometry (LC/MS) data at the systems level. After providing cells, animals, or patients with an isotopically enriched metabolite (e.g., 13C, 15N, or 2H), X13CMS identifies compounds that have incorporated the isotopic tracer and reports the extent of labeling for each. The analysis can be performed with a single condition, or isotopic fates can be compared between multiple conditions. The choice of which metabolite to enrich and which isotopic label to use is highly context dependent, but 13C-glucose and 13C-glutamine are often applied because they feed a large number of metabolic pathways. X13CMS is freely available.
  5. Cell Rep. 2019 Jun 04. pii: S2211-1247(19)30619-9. [Epub ahead of print]27(10): 3062-3080.e11
      Extracellular vesicles (EVs), including exosomes, modulate multiple aspects of cancer biology. Tumor-associated macrophages (TAMs) secrete EVs, but their molecular features and functions are poorly characterized. Here, we report methodology for the enrichment, quantification, and proteomic and lipidomic analysis of EVs released from mouse TAMs (TAM-EVs). Compared to source TAMs, TAM-EVs present molecular profiles associated with a Th1/M1 polarization signature, enhanced inflammation and immune response, and a more favorable patient prognosis. Accordingly, enriched TAM-EV preparations promote T cell proliferation and activation ex vivo. TAM-EVs also contain bioactive lipids and biosynthetic enzymes, which may alter pro-inflammatory signaling in the cancer cells. Thus, whereas TAMs are largely immunosuppressive, their EVs may have the potential to stimulate, rather than limit, anti-tumor immunity.
    Keywords:  T cell response; exosome; extracellular vesicle; inflammation; lipid metabolism; lipidomics; proteomics; tumor microenvironment; tumor-associated macrophage
  6. Chem Phys Lipids. 2019 May 29. pii: S0009-3084(19)30047-7. [Epub ahead of print]
      Fat is historically associated with poor health and obesity. However, the continuous use of lipidomics and genetic studies in model organisms revealed that specific lipid profiles and signals might delay aging. In order to identify and quantify the lipid species, researchers are taking advantage of the recent developments in the area of lipidomics that is mainly done by mass spectrometry and further techniques, such as NMR spectroscopy and chromatographic separations. This review will emphasize the role of lipid composition and metabolism during aging. We review the molecular and physiological changes during the progression of aging with a special focus on the role of lipids. Interventions to modulate life span in a variety of organisms such caloric restriction, show a significant extension of their maximum life-span and a decrease in the onset of age-related diseases. In particular, the influence of dietary restriction in lipid metabolism will be a major point of this review.
    Keywords:  Aging, mass spectrometry; odd chain fatty acids; oxidized lipids; polyunsaturated fatty acids; vinyl-ether lipids
  7. Nutr Metab (Lond). 2019 ;16 37
      Background: Proliferative diabetic retinopathy (PDR), a sight-threatening retinopathy, is the leading cause of irreversible blindness in adults. Despite strict control of systemic risk factors, a fraction of patients with diabetes develop PDR, suggesting the existence of other potential pathogenic factors underlying PDR. This study aimed to investigate the plasma metabotype of patients with PDR and to identify novel metabolite markers for PDR. Biomarkers identified from this study will provide scientific insight and new strategies for the early diagnosis and intervention of diabetic retinopathy.Methods: A total of 1024 patients with type 2 diabetes were screened. To match clinical parameters between case and control subjects, patients with PDR (PDR, n = 21) or those with a duration of diabetes of ≥10 years but without diabetic retinopathy (NDR, n = 21) were assigned to the present case-control study. Distinct metabolite profiles of serum were examined using liquid chromatography-mass spectrometry (LC-MS).
    Results: The distinct metabolites between PDR and NDR groups were significantly enriched in 9 KEGG pathways (P < 0.05, impact > 0.1), namely, alanine, aspartate and glutamate metabolism, caffeine metabolism, beta-alanine metabolism, purine metabolism, cysteine and methionine metabolism, sulfur metabolism, sphingosine metabolism, and arginine and proline metabolism. A total of 63 altered metabolites played important roles in these pathways. Finally, 4 metabolites were selected as candidate biomarkers for PDR, namely, fumaric acid, uridine, acetic acid, and cytidine. The area under the curve for these biomarkers were 0.96, 0.95, 1.0, and 0.95, respectively.
    Conclusions: This study suggested that impairment in the metabolism of pyrimidines, arginine and proline were identified as metabolic dysregulation associated with PDR. And fumaric acid, uridine, acetic acid, and cytidine might be potential biomarkers for PDR. Fumaric acid was firstly reported as a novel metabolite marker with no prior reports of association with diabetes or diabetic retinopathy, which might provide insights into potential new pathogenic pathways for diabetic retinopathy.
    Keywords:  LC-MS; Metabolic profiling; Metabolomics; Proliferative diabetic retinopathy; Type 2 diabetes
  8. SLAS Discov. 2019 Jun 05. 2472555219850082
      Biomarkers that indicate the presence or severity of organ damage caused by diseases and toxicities are useful diagnostic tools. Metabolomics platforms using chromatography coupled with mass spectrometry (MS) have been widely used for biomarker screening. In this study, we aimed to establish a novel metabolomics platform using ion chromatography coupled with MS (IC-MS) for human biofluids. We found that ethylenediaminetetraacetic acid (EDTA) plasma is not suitable for IC-MS metabolomics platforms because of the desensitization of MS. IC-MS enabled detection of 131 polar metabolites in human serum and urine from healthy volunteers. Pathway analysis demonstrated that the metabolites detectable using our platform were composed of a broad spectrum of organic acids with carboxylic moieties. These metabolites were significantly associated with pathways such as the tricarboxylic acid (TCA) cycle; glyoxylate and dicarboxylate metabolism; alanine, aspartate, and glutamate metabolism; butanoate metabolism; and the pentose phosphate pathway. Moreover, comparison of serum and urine samples showed that four metabolites (4-hydroxybutyric acid, aspartic acid, lactic acid, and γ-glutamyl glutamine) were abundant in serum, whereas 62 metabolites, including phosphoric acid, vanillylmandelic acid, and N-tiglylglycine, were abundant in urine. In addition, allantoin and uric acid were abundant in male serum, whereas no gender-associated differences were found for polar metabolites in urine. Our results demonstrate that the present established IC-MS metabolomics platform can be applied for analysis of human serum and urine as well as detection of a broad spectrum of polar metabolites in human biofluids.
    Keywords:  human biofluids; ion chromatography–mass spectrometry; nontargeted metabolomics; polar metabolites
  9. Biochim Biophys Acta Rev Cancer. 2019 May 29. pii: S0304-419X(19)30015-0. [Epub ahead of print]
      Cancer cells constantly face a fluctuating nutrient supply and interference with adaptive responses might be an effective therapeutic approach. It has been discovered that in the absence of glucose, cancer cells can synthesize crucial metabolites by expressing phosphoenolpyruvate carboxykinase (PEPCK, PCK1 or PCK2) using abbreviated forms of gluconeogenesis. Gluconeogenesis, which in essence is the reverse pathway of glycolysis, uses lactate or amino acids to feed biosynthetic pathways branching from glycolysis. PCK1 and PCK2 have been shown to be critical for the growth of certain cancers. In contrast, fructose-1,6-bisphosphatase 1 (FBP1), a downstream gluconeogenesis enzyme, inhibits glycolysis and tumor growth, partly by non-enzymatic mechanisms. This review sheds light on current knowledge of cancer cell gluconeogenesis and its role in metabolic reprogramming, cancer cell plasticity, and tumor growth.
    Keywords:  Adaptation; Gluconeogenesis; Metabolic plasticity; Starvation; Tumor
  10. Toxics. 2019 Jun 04. pii: E32. [Epub ahead of print]7(2):
      Human exposure to aldehydes is implicated in multiple diseases including diabetes, cardiovascular diseases, neurodegenerative disorders (i.e., Alzheimer's and Parkinson's Diseases), and cancer. Because these compounds are strong electrophiles, they can react with nucleophilic sites in DNA and proteins to form reversible and irreversible modifications. These modifications, if not eliminated or repaired, can lead to alteration in cellular homeostasis, cell death and ultimately contribute to disease pathogenesis. This review provides an overview of the current knowledge of the methods and applications of aldehyde exposure measurements, with a particular focus on bioanalytical and mass spectrometric techniques, including recent advances in mass spectrometry (MS)-based profiling methods for identifying potential biomarkers of aldehyde exposure. We discuss the various derivatization reagents used to capture small polar aldehydes and methods to quantify these compounds in biological matrices. In addition, we present emerging mass spectrometry-based methods, which use high-resolution accurate mass (HR/AM) analysis for characterizing carbonyl compounds and their potential applications in molecular epidemiology studies. With the availability of diverse bioanalytical methods presented here including simple and rapid techniques allowing remote monitoring of aldehydes, real-time imaging of aldehydic load in cells, advances in MS instrumentation, high performance chromatographic separation, and improved bioinformatics tools, the data acquired enable increased sensitivity for identifying specific aldehydes and new biomarkers of aldehyde exposure. Finally, the combination of these techniques with exciting new methods for single cell analysis provides the potential for detection and profiling of aldehydes at a cellular level, opening up the opportunity to minutely dissect their roles and biological consequences in cellular metabolism and diseases pathogenesis.
    Keywords:  aldehydes; biological fluids; cancer; data-dependent profiling; derivatization; diseases; exposure biomarkers; genotoxicity; high-resolution mass spectrometry; isotope labeling; oxidative stress
  11. Metabolomics. 2019 Jun 06. 15(6): 88
      INTRODUCTION: The mitochondrial-derived peptides (MDPs) are a novel group of natural occurring peptides that have important signaling functions and biological activity. Both humanin and small-humanin-like peptide 2 (SHLP2) have been reported to act as insulin sensitizers and modulate metabolism.OBJECTIVES: By using a metabolomic approach, this study explores how the plasma metabolite profile is regulated in response to humanin and SHLP2 treatment in a diet-induced obesity (DIO) mouse model. The results also shed light on the potential mechanism underlying MDPs' insulin sensitization effects.
    METHODS: Plasma samples were obtained from DIO mice subjected to vehicle (water) treatment, or peptide treatment with either humanin analog S14G (HNG) or SHLP2 (n = 6 per group). Vehicle or peptides were given as intraperitoneal (IP) injections twice a day at dose of 2.5 mg/kg/injection for 3 days. Metabolites in plasma samples were comprehensively identified and quantified using UPLC-MS/MS.
    RESULTS: HNG and SHLP2 administration significantly altered the concentrations of amino acid and lipid metabolites in plasma. Among all the metabolic pathways, the glutathione and sphingolipid metabolism responded most strongly to the peptide treatment.
    CONCLUSIONS: The present study indicates that humanin and SHLP2 can lower several markers associated with age-related metabolic disorders. With the previous understanding of the effects of humanin and SHLP2 on cardiovascular function, insulin sensitization, and anti-inflammation, this metabolomic discovery provides a more comprehensive molecular explanation of the mechanism of action for humanin and SHLP2 treatment.
    Keywords:  Aging; Insulin resistance; Mitochondrial-derived peptide; Obesity; Sphingolipids; UPLC-MS/MS
  12. Cancer Res. 2019 Jun 06.
      The extracellular milieu of tumors is generally assumed to be immunosuppressive due in part to metabolic factors. Here, we review methods for probing the tumor metabolic microenvironment. In parallel, we consider the resulting available evidence, with a focus on lactate, which is the most strongly increased metabolite in bulk tumors. Limited microenvironment concentration measurements suggest depletion of glucose and modest accumulation of lactate (less than 2-fold). Isotope tracer measurements show rapid lactate exchange between the tumor and circulation. Such exchange is catalyzed by MCT transporters, which cotransport lactate and protons (H+). Rapid lactate exchange seems at odds with tumor lactate accumulation. We propose a potential resolution to this paradox. Because of the high pH of tumor cells relative to the microenvironment, H+-coupled transport by MCTs tends to drive lactate from the interstitium into tumor cells. Accordingly, lactate may accumulate preferentially in tumor cells, not the microenvironment. Thus, although they are likely subject to other immunosuppressive metabolic factors, tumor immune cells may not experience a high lactate environment. The lack of clarity regarding microenvironmental lactate highlights the general need for careful metabolite measurements in the tumor extracellular milieu.
  13. Cancers (Basel). 2019 Jun 04. pii: E770. [Epub ahead of print]11(6):
      Metabolic programs are known to be altered in cancers arising from various tissues. Malignant transformation can alter signaling pathways related to metabolism and increase the demand for both energy and biomass for the proliferating cancerous cells. This scenario is further complexed by the crosstalk between transformed cells and the microenvironment. One of the most common metabolic alterations, which occurs in many tissues and in the context of multiple oncogenic drivers, is the increased demand for the amino acid glutamine. Many studies have attributed this increased demand for glutamine to the carbon backbone and its role in the tricarboxylic acid (TCA) cycle anaplerosis. However, an increasing number of studies are now emphasizing the importance of glutamine functioning as a proteogenic building block, a nitrogen donor and carrier, an exchanger for import of other amino acids, and a signaling molecule. Herein, we highlight the recent literature on glutamine's versatile role in cancer, with a focus on nitrogen metabolism, and therapeutic implications of glutamine metabolism in cancer.
    Keywords:  cancer; glutamate; glutamate ammonia ligase (GLUL); glutaminase (GLS); glutamine; glutamine synthetase (GS); glutaminolysis; metabolism
  14. Cell Signal. 2019 May 29. pii: S0898-6568(19)30119-6. [Epub ahead of print]
      EphA2, which belongs to the Eph family of receptor tyrosine kinases, is overexpressed in a variety of human cancers. Serine 897 (S897) phosphorylation of EphA2 is known to promote cancer cell migration and proliferation in a ligand-independent manner. In this study, we show that glucose deprivation induces S897 phosphorylation of EphA2 in glioblastoma cells. The phosphorylation requires the activity of the cystine/glutamate antiporter xCT and reactive oxygen species (ROS)-dependent ERK and RSK activation. Furthermore, depletion of EphA2 in glioblastoma cells leads to decreased cell viability under glucose starvation. Our results suggest a role of EphA2 in glioblastoma cell viability under glucose-limited conditions.
    Keywords:  Amino acid transporter; EphA2; Glioblastoma; Glucose; RSK; xCT
  15. Methods Enzymol. 2019 ;pii: S0076-6879(19)30056-4. [Epub ahead of print]622 431-448
      Dysregulated cellular metabolism is an emerging hallmark of cancer. Improved methods to profile aberrant metabolic activity thus have substantial applications as tools for diagnosis and understanding the biology of malignant tumors. Here we describe the utilization of a bioorthogonal ligation to fluorescently detect the TCA cycle oncometabolite fumarate. This method enables the facile measurement of fumarate hydratase activity in cell and tissue samples, and can be used to detect disruptions in metabolism that underlie the genetic cancer syndrome hereditary leiomyomatosis and renal cell cancer (HLRCC). The current method has substantial utility for sensitive fumarate hydratase activity profiling, and also provides a foundation for future applications in diagnostic detection and imaging of cancer metabolism.
    Keywords:  Bioorthogonal; Bioorthogonal oncometabolite ligation: HLRCC; Click chemistry; Cycloaddition; Fluorogenic; Fumarate; Fumarate hydratase; Hereditary cancer; Profiling; Sensor; Tetrazole
  16. Cell. 2019 May 20. pii: S0092-8674(19)30501-X. [Epub ahead of print]
      RLR-mediated type I IFN production plays a pivotal role in elevating host immunity for viral clearance and cancer immune surveillance. Here, we report that glycolysis, which is inactivated during RLR activation, serves as a barrier to impede type I IFN production upon RLR activation. RLR-triggered MAVS-RIG-I recognition hijacks hexokinase binding to MAVS, leading to the impairment of hexokinase mitochondria localization and activation. Lactate serves as a key metabolite responsible for glycolysis-mediated RLR signaling inhibition by directly binding to MAVS transmembrane (TM) domain and preventing MAVS aggregation. Notably, lactate restoration reverses increased IFN production caused by lactate deficiency. Using pharmacological and genetic approaches, we show that lactate reduction by lactate dehydrogenase A (LDHA) inactivation heightens type I IFN production to protect mice from viral infection. Our study establishes a critical role of glycolysis-derived lactate in limiting RLR signaling and identifies MAVS as a direct sensor of lactate, which functions to connect energy metabolism and innate immunity.
    Keywords:  MAVS; RLR signaling; glucose metabolism; interferon; lactate
  17. Trends Cell Biol. 2019 May 31. pii: S0962-8924(19)30084-4. [Epub ahead of print]
      Acetate and the related metabolism of acetyl-coenzyme A (acetyl-CoA) confer numerous metabolic functions, including energy production, lipid synthesis, and protein acetylation. Despite its importance as a nutrient for cellular metabolism, its source has been unclear. Recent studies have provided evidence to support the existence of a de novo pathway for acetate production derived from pyruvate, the end product of glycolysis. This mechanism of pyruvate-derived acetate generation could have far-reaching implications for the regulation of central carbon metabolism. In this Opinion, we discuss our current understanding of acetate metabolism in the context of cell-autonomous metabolic regulation, cell-cell interactions, and systemic physiology. Applications relevant to health and disease, particularly cancer, are emphasized.
    Keywords:  acetate metabolism; alcoholism; cancer; lipogenesis; nutrition
  18. Front Cell Neurosci. 2019 ;13 212
      Until recently, glial cells have been considered mainly support cells for neurons in the mammalian brain. However, many studies have unveiled a variety of glial functions including electrolyte homeostasis, inflammation, synapse formation, metabolism, and the regulation of neurotransmission. The importance of these functions illuminates significant crosstalk between glial and neuronal cells. Importantly, it is known that astrocytes secrete signals that can modulate both presynaptic and postsynaptic function. It is also known that the lipid compositions of the pre- and post-synaptic membranes of neurons greatly impact functions such as vesicle fusion and receptor mobility. These data suggest an essential lipid-mediated communication between glial cells and neurons. Little is known, however, about how the lipid metabolism of both cell types may interact. In this review, we discuss neuronal and glial lipid metabolism and suggest how they might interact to impact neurotransmission.
    Keywords:  CNS; communication; glial; lipids; neurons
  19. Methods Protoc. 2018 Jun 19. pii: E23. [Epub ahead of print]1(2):
      Ionic liquids (ILs) have advanced a variety of applications, including matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). ILs can be used as matrices and solvents for analyte extraction and separation prior to analysis using laser desorption/ionization-mass spectrometry (LDI-MS). Most ILs show high stability with negligible sublimation under vacuum, provide high ionization efficiency, can be used for qualitative and quantitative analyses with and without internal standards, show high reproducibility, form homogenous spots during sampling, and offer high solvation efficiency for a wide range of analytes. Ionic liquids can be used as solvents and pseudo-stationary phases for extraction and separation of a wide range of analytes, including proteins, peptides, lipids, carbohydrates, pathogenic bacteria, and small molecules. This review article summarizes the recent advances of ILs applications using MALDI-MS. The applications of ILs as matrices, solvents, and pseudo-stationary phases, are also reviewed.
    Keywords:  extraction; ionic liquid matrices; ionic liquids; matrix-assisted laser desorption/ionization–mass spectrometry; separation