bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒11‒01
23 papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

  1. Nature. 2020 Oct 28.
    Shang M, Cappellesso F, Amorim R, Serneels J, Virga F, Eelen G, Carobbio S, Rincon MY, Maechler P, De Bock K, Ho PC, Sandri M, Ghesquière B, Carmeliet P, Di Matteo M, Berardi E, Mazzone M.
      Muscle regeneration is sustained by infiltrating macrophages and the consequent activation of satellite cells1-4. Macrophages and satellite cells communicate in different ways1-5, but their metabolic interplay has not been investigated. Here we show, in a mouse model, that muscle injuries and ageing are characterized by intra-tissue restrictions of glutamine. Low levels of glutamine endow macrophages with the metabolic ability to secrete glutamine via enhanced glutamine synthetase (GS) activity, at the expense of glutamine oxidation mediated by glutamate dehydrogenase 1 (GLUD1). Glud1-knockout macrophages display constitutively high GS activity, which prevents glutamine shortages. The uptake of macrophage-derived glutamine by satellite cells through the glutamine transporter SLC1A5 activates mTOR and promotes the proliferation and differentiation of satellite cells. Consequently, macrophage-specific deletion or pharmacological inhibition of GLUD1 improves muscle regeneration and functional recovery in response to acute injury, ischaemia or ageing. Conversely, SLC1A5 blockade in satellite cells or GS inactivation in macrophages negatively affects satellite cell functions and muscle regeneration. These results highlight the metabolic crosstalk between satellite cells and macrophages, in which macrophage-derived glutamine sustains the functions of satellite cells. Thus, the targeting of GLUD1 may offer therapeutic opportunities for the regeneration of injured or aged muscles.
  2. Cancer Cell. 2020 Sep 23. pii: S1535-6108(20)30478-5. [Epub ahead of print]
    Kaymak I, Williams KS, Cantor JR, Jones RG.
      Immune cells' metabolism influences their differentiation and function. Given that a complex interplay of environmental factors within the tumor microenvironment (TME) can have a profound impact on the metabolic activities of immune, stromal, and tumor cell types, there is emerging interest to advance understanding of these diverse metabolic phenotypes in the TME. Here, we discuss cell-extrinsic contributions to the metabolic activities of immune cells. Then, considering recent technical advances in experimental systems and metabolic profiling technologies, we propose future directions to better understand how immune cells meet their metabolic demands in the TME, which can be leveraged for therapeutic benefit.
    Keywords:  immunology; immunometabolism; in vitro modeling; metabolism; metabolomics; physiologic media; stable isotope tracing; tumor microenvironment
  3. J Cell Mol Med. 2020 Oct 26.
    Yelek C, Mignion L, Joudiou N, Terrasi R, Gourgue F, Van Hul M, Delzenne N, Gallez B, Corbet C, Muccioli GG, Feron O, Cani PD, Jordan BF.
      Acetate is reported as a regulator of fat mass but also as lipogenic source for cancer cells. Breast cancer is surrounded by adipose tissue and has been associated with obesity. However, whether acetate contributes to cancer cell metabolism as lipogenic substrate and/or by changing fat storage and eventually obesity-induced breast cancer progression remains unknown. Therefore, we studied the contribution of acetate to breast cancer metabolism and progression. In vitro, we found that acetate is not a bioenergetic substrate under normoxia and did not result in a significant change of growth. However, by using lipidomic approaches, we discovered that acetate changes the lipid profiles of the cells under hypoxia. Moreover, while mice fed a high-fat diet (HFD) developed bigger tumours than their lean counterparts, exogenous acetate supplementation leads to a complete abolishment of fat mass gain without reverting the HFD-induced obesity-driven tumour progression. In conclusion, although acetate protects against diet-induced obesity, our data suggest that it is not affecting HFD-driven tumour progression.
    Keywords:  acetate; high-fat diet; hypoxia; metabolism; obesity; tumour growth
  4. J Biol Chem. 2020 Oct 27. pii: jbc.RA120.015238. [Epub ahead of print]
    Shao W, Hwang J, Liu C, Mukhopadhyay D, Zhao S, Shen MC, Alpergin ESS, Wolfgang MJ, Farber SA, Espenshade PJ.
      Oxygen regulates hypoxia-inducible factor (HIF) transcription factors to control cell metabolism, erythrogenesis, and angiogenesis. While much has been elucidated about how oxygen regulates HIF, whether lipids affect HIF activity is unknown. Here, using cultured cells and two animal models, we demonstrate that lipoprotein-derived fatty acids are an independent regulator of HIF. Decreasing extracellular lipid supply inhibited HIF prolyl hydroxylation, leading to accumulation of the HIFα subunit of these heterodimeric transcription factors comparable to hypoxia with activation of downstream target genes. Addition of fatty acids to culture media suppressed this signal, which required an intact mitochondrial respiratory chain. Mechanistically, fatty acids and oxygen are distinct signals integrated to control HIF activity. Finally, we observed lipid signaling to HIF and changes in target gene expression in developing zebrafish and adult fluorescent reporter mice, and this pathway operates in cancer cells from a range of tissues. This study identifies fatty acids as a physiological modulator of HIF, defining a mechanism for lipoprotein regulation that functions in parallel to oxygen.
    Keywords:  fatty acid; hypoxia-inducible factor (HIF); lipoprotein; low-density lipoprotein (LDL); lysosomal acid lipase; mitochondria
  5. Cancers (Basel). 2020 Oct 27. pii: E3147. [Epub ahead of print]12(11):
    Pellerin L, Carrié L, Dufau C, Nieto L, Ségui B, Levade T, Riond J, Andrieu-Abadie N.
      Metabolic reprogramming contributes to the pathogenesis and heterogeneity of melanoma. It is driven both by oncogenic events and the constraints imposed by a nutrient- and oxygen-scarce microenvironment. Among the most prominent metabolic reprogramming features is an increased rate of lipid synthesis. Lipids serve as a source of energy and form the structural foundation of all membranes, but have also emerged as mediators that not only impact classical oncogenic signaling pathways, but also contribute to melanoma progression. Various alterations in fatty acid metabolism have been reported and can contribute to melanoma cell aggressiveness. Elevated expression of the key lipogenic fatty acid synthase is associated with tumor cell invasion and poor prognosis. Fatty acid uptake from the surrounding microenvironment, fatty acid β-oxidation and storage also appear to play an essential role in tumor cell migration. The aim of this review is (i) to focus on the major alterations affecting lipid storage organelles and lipid metabolism. A particular attention has been paid to glycerophospholipids, sphingolipids, sterols and eicosanoids, (ii) to discuss how these metabolic dysregulations contribute to the phenotype plasticity of melanoma cells and/or melanoma aggressiveness, and (iii) to highlight therapeutic approaches targeting lipid metabolism that could be applicable for melanoma treatment.
    Keywords:  cancer; cholesterol; eicosanoid; fatty acid; glycerophospholipid; lipid droplet; metastasis; obesity; phenotypic switch; pseudo-EMT; sphingolipid
  6. Anal Bioanal Chem. 2020 Oct 27.
    He X, Li Z, Zhang Q.
      Phosphatidylethanolamines (PEs) are targets of non-enzymatic glycation, a chemical process that occurs between glucose and primary amine-containing biomolecules. As the early-stage non-enzymatic glycation products of PE, Amadori-PEs are implicated in the pathogenesis of various diseases. However, only a few Amadori-PE molecular species have been identified so far; a comprehensive profiling of these glycated PE species is needed to establish their roles in disease pathology. Herein, based on our previous work using liquid chromatography-coupled neutral loss scanning and product ion scanning tandem mass spectrometry (LC-NLS-MS and LC-PIS-MS) in tandem, we extend identification of Amadori-PE to the low-abundance species, which is facilitated by using plasma lipids glycated in vitro. The confidence of identification is improved by high-resolution tandem mass spectrometry and chromatographic retention time regression. A LC-coupled multiple reaction monitoring mass spectrometry (LC-MRM-MS) assay is further developed for more sensitive quantitation of the Amadori compound-modified lipids. Using synthesized stable isotope-labeled Amadori lipids as internal standards, levels of 142 Amadori-PEs and 33 Amadori-LysoPEs are determined in the NIST human plasma standard reference material. These values may serve as an important reference for future investigations of Amadori-modified lipids in human diseases.
    Keywords:  Amadori compound; Human plasma; LC-MRM-MS; LPE; NIST SRM-1950; PE
  7. Anal Chem. 2020 Oct 29.
    Ross DH, Cho JH, Zhang R, Hines KM, Xu L.
      Comprehensive profiling of lipid species in a biological sample, or lipidomics, is a valuable approach to elucidating disease pathogenesis and identifying biomarkers. Currently, a typical lipidomics experiment may track hundreds to thousands of individual lipid species. However, drawing biological conclusions requires multiple steps of data processing to enrich significantly altered features and confident identification of these features. Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification) involve performing various steps using different software applications, which imposes a practical limitation and potentially a negative impact on reproducibility. Hydrophilic interaction liquid chromatography-ion mobility-mass spectrometry (HILIC-IM-MS) has shown advantages in separating lipids through orthogonal dimensions. However, there are still gaps in the coverage of lipid classes in the literature. To enable reproducible and efficient analysis of HILIC-IM-MS lipidomics data, we developed an open-source Python package, LiPydomics, which enables performing statistical and multivariate analyses ("stats" module), generating informative plots ("plotting" module), identifying lipid species at different confidence levels ("identification" module), and carrying out all functions using a user-friendly text-based interface ("interactive" module). To support lipid identification, we assembled a comprehensive experimental database of m/z and CCS of 45 lipid classes with 23 classes containing HILIC retention times. Prediction models for CCS and HILIC retention time for 22 and 23 lipid classes, respectively, were trained using the large experimental data set, which enabled the generation of a large predicted lipid database with 145,388 entries. Finally, we demonstrated the utility of the Python package using Staphylococcus aureus strains that are resistant to various antimicrobials.
  8. Cancer Res. 2020 Oct 28. pii: canres.1998.2020. [Epub ahead of print]
    Xiao Y, Rabien A, Buschow R, Amstislavskiy V, Busch J, Kilic E, Villegas SL, Timmermann B, Schütte M, Mielke T, Yaspo ML, Jung K, Meierhofer D.
      Chromophobe renal cell carcinoma (chRCC) accounts for approximately 5% of all renal cancers and around 30% of chRCC cases have mutations in TP53. ChRCC is poorly supported by microvessels and has markably lower glucose uptake than clear cell RCC (ccRCC) and papillary RCC (pRCC). Currently, the metabolic status and mechanisms by which this tumor adapts to nutrient-poor microenvironments remain to be investigated. In this study, we performed proteome and metabolome profiling of chRCC tumors and adjacent kidney tissues and identified major metabolic alterations in chRCC tumors, including the classical Warburg effect, the downregulation of gluconeogenesis and amino acid metabolism, and the upregulation of protein degradation and endocytosis. ChRCC cells depended on extracellular macromolecules as an amino acid source by activating endocytosis to sustain cell proliferation and survival. Inhibition of the PLCG2/IP3/Ca2+/PKC pathway significantly impaired the activation of endocytosis for amino acids uptakes into chRCC cells. In chRCC, whole-exome sequencing revealed that TP53 mutations were not related to expression of PLCG2 and activation of endocytosis. Our study provides novel perspectives on metabolic rewiring in chRCC and identifies the PLCG2/IP3/Ca2+/PKC axis as a potential therapeutic target in chRCC patients.
  9. Minerva Endocrinol. 2020 Oct 26.
    Xu WL, Liu GY, Zhang N, Ren J, Li XY, Li YQ, Chen Y, Liu JY.
      BACKGROUND: Polycystic ovary syndrome (PCOS) is a complex endocrine disorder with well-established metabolic abnormalities. In the present study, untargeted metabolomics technology was applied to analyze the serum and follicular fluid samples from women with polycystic ovary syndrome and healthy controls using 1H nuclear magnetic resonance (NMR).METHODS: 70 samples for PCOS analysis were collected in hospital of Shandong University of Traditional Chinese Medicine, NMR was used as analytical technology and multivariate analysis was applied to analyze metabolomics difference in PCOS and healthy controls.
    RESULTS: Significant metabolic differences were found in both serum and follicular fluid samples with orthogonal partial least-squares discriminant analysis (OPLS-DA). Three discriminated metabolites (1-Methylhistidine, threonine and Citrate) in both serum and follicular fluid were altered in PCOS patients. Abnormal energy metabolism, lipid metabolism and amino acid metabolism were detected in PCOS patients. Furthermore, more significantly changed amino acids were discovered in follicular fluid samples.
    CONCLUSIONS: Our findings would provide a resource for further investigations on metabolic disturbance in PCOS patients.
  10. Cancer Metab. 2020 ;8 23
    Ruiz-Rodado V, Lita A, Dowdy T, Celiku O, Saldana AC, Wang H, Yang CZ, Chari R, Li A, Zhang W, Song H, Zhang M, Ahn S, Davis D, Chen X, Zhuang Z, Herold-Mende C, Walters KJ, Gilbert MR, Larion M.
      Background: Targeting glutamine metabolism in cancer has become an increasingly vibrant area of research. Mutant IDH1 (IDH1 mut ) gliomas are considered good candidates for targeting this pathway because of the contribution of glutamine to their newly acquired function: synthesis of 2-hydroxyglutarate (2HG).Methods: We have employed a combination of 13C tracers including glutamine and glucose for investigating the metabolism of patient-derived IDH1 mut glioma cell lines through NMR and LC/MS. Additionally, genetic loss-of-function (in vitro and in vivo) approaches were performed to unravel the adaptability of these cell lines to the inhibition of glutaminase activity.
    Results: We report the adaptability of IDH1 mut cells' metabolism to the inhibition of glutamine/glutamate pathway. The glutaminase inhibitor CB839 generated a decrease in the production of the downstream metabolites of glutamate, including those involved in the TCA cycle and 2HG. However, this effect on metabolism was not extended to viability; rather, our patient-derived IDH1 mut cell lines display a metabolic plasticity that allows them to overcome glutaminase inhibition.
    Conclusions: Major metabolic adaptations involved pathways that can generate glutamate by using alternative substrates from glutamine, such as alanine or aspartate. Indeed, asparagine synthetase was upregulated both in vivo and in vitro revealing a new potential therapeutic target for a combinatory approach with CB839 against IDH1 mut gliomas.
    Keywords:  13C tracing; AGI5198; CB839; Gliomas; Glutaminase; IDH1-mutant
  11. Cancer Res. 2020 Oct 26. pii: canres.3923.2019. [Epub ahead of print]
    Restall IJ, Cseh O, Richards LM, Pugh TJ, Luchman HA, Weiss S.
      Cancer cells can metabolize glutamine to replenish TCA cycle intermediates, leading to a dependence on glutaminolysis for cell survival. However, a mechanistic understanding of the role that glutamine metabolism has on the survival of glioblastoma (GBM) brain tumor stem cells (BTSC) has not yet been elucidated. Here we report that, across a panel of 19 glioblastoma BTSC lines, inhibition of glutaminase (GLS) showed a variable response from complete blockade of cell growth to absolute resistance. Surprisingly, BTSC sensitivity to GLS inhibition was a result of reduced intracellular glutamate triggering the amino acid deprivation response (AADR) and not due to the contribution of glutaminolysis to the TCA cycle. Moreover, BTSC sensitivity to GLS inhibition negatively correlated with expression of the astrocytic glutamate transporters EAAT1 and EAAT2. Blocking glutamate transport in BTSCs with high EAAT1/EAAT2 expression rendered cells susceptible to GLS inhibition, triggering the AADR and limiting cell growth. These findings uncover a unique metabolic vulnerability in BTSCs and support the therapeutic targeting of upstream activators and downstream effectors of the AADR pathway in GBM. Moreover, they demonstrate that gene expression patterns reflecting the cellular hierarchy of the tissue of origin can alter the metabolic requirements of the cancer stem cell population.
  12. Commun Biol. 2020 Oct 30. 3(1): 638
    Seo J, Jeong DW, Park JW, Lee KW, Fukuda J, Chun YS.
      Hypoxia-inducible factor-1 alpha (HIF-1α) is a transcription factor essential for cancer cell survival. The reprogramming of lipid metabolism has emerged as a hallmark of cancer, yet the relevance of HIF-1α to this process remains elusive. In this study, we profile HIF-1α-interacting proteins using proteomics analysis and identify fatty acid-binding protein 5 (FABP5) as a critical HIF-1α-binding partner. In hepatocellular carcinoma (HCC) tissues, both FABP5 and HIF-1α are upregulated, and their expression levels are associated with poor prognosis. FABP5 enhances HIF-1α activity by promoting HIF-1α synthesis while disrupting FIH/HIF-1α interaction at the same time. Oleic-acid treatment activates the FABP5/HIF-1α axis, thereby promoting lipid accumulation and cell proliferation in HCC cells. Our results indicate that fatty-acid-induced FABP5 upregulation drives HCC progression through HIF-1-driven lipid metabolism reprogramming.
  13. Int J Gynecol Cancer. 2020 Oct 26. pii: ijgc-2020-001862. [Epub ahead of print]
    Ahmed-Salim Y, Galazis N, Bracewell-Milnes T, Phelps DL, Jones BP, Chan M, Munoz-Gonzales MD, Matsuzono T, Smith JR, Yazbek J, Krell J, Ghaem-Maghami S, Saso S.
      Metabolomics, the global analysis of metabolites in a biological specimen, could potentially provide a fast method of biomarker identification for ovarian cancer. This systematic review aims to examine findings from studies that apply metabolomics to the diagnosis, prognosis, treatment, and recurrence of ovarian cancer. A systematic search of English language publications was conducted on PubMed, Science Direct, and SciFinder. It was augmented by a snowball strategy, whereby further relevant studies are identified from reference lists of included studies. Studies in humans with ovarian cancer which focus on metabolomics of biofluids and tumor tissue were included. No restriction was placed on the time of publication. A separate review of targeted metabolomic studies was conducted for completion. Qualitative data were summarized in a comprehensive table. The studies were assessed for quality and risk of bias using the ROBINS-I tool. 32 global studies were included in the main systematic review. Most studies applied metabolomics to diagnosing ovarian cancer, within which the most frequently reported metabolite changes were a down-regulation of phospholipids and amino acids: histidine, citrulline, alanine, and methionine. Dysregulated phospholipid metabolism was also reported in the separately reviewed 18 targeted studies. Generally, combinations of more than one significant metabolite as a panel, in different studies, achieved a higher sensitivity and specificity for diagnosis than a single metabolite; for example, combinations of different phospholipids. Widespread metabolite differences were observed in studies examining prognosis, treatment, and recurrence, and limited conclusions could be drawn. Cellular processes of proliferation and invasion may be reflected in metabolic changes present in poor prognosis and recurrence. For example, lower levels of lysine, with increased cell invasion as an underlying mechanism, or glutamine dependency of rapidly proliferating cancer cells. In conclusion, this review highlights potential metabolites and biochemical pathways which may aid the clinical care of ovarian cancer if further validated.
    Keywords:  ovarian cancer
  14. Cells. 2020 Oct 25. pii: E2352. [Epub ahead of print]9(11):
    Ha NT, Lee CH.
      Farnesyl-diphosphate farnesyltransferase 1 (FDFT1, squalene synthase), a membrane-associated enzyme, synthesizes squalene via condensation of two molecules of farnesyl pyrophosphate. Accumulating evidence has noted that FDFT1 plays a critical role in cancer, particularly in metabolic reprogramming, cell proliferation, and invasion. Based on these advances in our knowledge, FDFT1 could be a potential target for cancer treatment. This review focuses on the contribution of FDFT1 to the hallmarks of cancer, and further, we discuss the applicability of FDFT1 as a cancer prognostic marker and target for anticancer therapy.
    Keywords:  cholesterol synthesis; farnesyl-diphosphate farnesyltransferase 1; lipid rafts; prognostic marker; tumour progression
  15. J Lipid Res. 2020 Oct 30. pii: jlr.RA120001057. [Epub ahead of print]
    Vidal E, Jun B, Gordon WC, Maire MA, Martine L, Grégoire S, Khoury S, Cabaret S, Berdeaux O, Acar N, Bretillon L, Bazan NG.
      Spatial changes of fatty acids in the retina in response to different dietary n-3 formulations have never been explored, although a diet rich in EPA and DHA is recommended to protect the retina against the effects of aging. In this study, Wistar rats were fed for 8 weeks with balanced diet including either EPA-containing phospholipids, EPA-containing triglycerides, DHA-containing phospholipids, or DHA-containing triglycerides. Qualitative changes in fatty acid composition of plasma, erythrocytes and retina were evaluated by gas chromatography-flame ionization detector. Following the different dietary intakes, changes to the quantity and spatial organization of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) species in retina were determined by liquid chromatography coupled to tandem mass spectrometry and MALDI (Matrix Assisted Laser Desorption Ionization) coupled to mass spectrometry imaging. The omega-3 content in the lipids of plasma and erythrocytes suggests that phospholipids as well as triglycerides are good omega-3 carriers for retina. However, a significant increase in DHA content in retina was observed, especially molecular species as di-DHA-containing PC and PE, as well as an increase in very long chain polyunsaturated fatty acids (VLC-PUFAs, more than 28 carbons) following phospholipid-EPA and triglyceride-DHA diets only. All supplemented diets triggered spatial organization changes of DHA in the photoreceptor layer around the optic nerve. Taken together, these findings suggest that dietary omega-3 supplementation can modify the content of fatty acids in the rat retina.
    Keywords:  Diet and dietary lipids; Omega-3 fatty acids; Phospholipids; Phospholipids/Phosphatidylcholine; Triglycerides; docosahexaenoic acid; eicosapentaenoic acid; lipid biochemistry; lipid spatial organisation; very long chain polyunsaturated fatty acids
  16. Metabolites. 2020 Oct 27. pii: E434. [Epub ahead of print]10(11):
    Ćeranić A, Bueschl C, Doppler M, Parich A, Xu K, Lemmens M, Buerstmayr H, Schuhmacher R.
      Stable isotope-assisted approaches can improve untargeted liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomics studies. Here, we demonstrate at the example of chemically stressed wheat that metabolome-wide internal standardization by globally 13C-labeled metabolite extract (GLMe-IS) of experimental-condition-matched biological samples can help to improve the detection of treatment-relevant metabolites and can aid in the post-acquisition assessment of putative matrix effects in samples obtained upon different treatments. For this, native extracts of toxin- and mock-treated (control) wheat ears were standardized by the addition of uniformly 13C-labeled wheat ear extracts that were cultivated under similar experimental conditions (toxin-treatment and control) and measured with LC-HRMS. The results show that 996 wheat-derived metabolites were detected with the non-condition-matched 13C-labeled metabolite extract, while another 68 were only covered by the experimental-condition-matched GLMe-IS. Additional testing is performed with the assumption that GLMe-IS enables compensation for matrix effects. Although on average no severe matrix differences between both experimental conditions were found, individual metabolites may be affected as is demonstrated by wrong decisions with respect to the classification of significantly altered metabolites. When GLMe-IS was applied to compensate for matrix effects, 272 metabolites showed significantly altered levels between treated and control samples, 42 of which would not have been classified as such without GLMe-IS.
    Keywords:  GLMe-IS; abiotic stress of wheat; deoxynivalenol; internal standard; matrix effects; untargeted metabolomics
  17. J Immunother Cancer. 2020 Oct;pii: e001383. [Epub ahead of print]8(2):
    Malczewski AB, Navarro S, Coward JI, Ketheesan N.
      Cancer immunotherapy with checkpoint blockade has become standard of care treatment for numerous cancer types. Despite this, robust predictive biomarkers are lacking. There is increasing evidence that the host microbiome is a predictor of immunotherapy response, although the optimal host microbiome has not been defined. Metabolomics is a new area of medicine that aims to analyze the metabolic profile of a biological system. The microbiome-derived metabolome (fecal and serum) represents the end products of microbial metabolism and these may be functionally more important than the distinct bacterial species that comprise a favorable microbiome. Short-chain fatty acids (SCFA) are metabolites produced by gut microbiota and have a role in T cell homeostasis, including differentiation of regulatory T cells. Recent studies have confirmed differential expression of SCFA for immunotherapy responders compared with non-responders. We propose that the microbiome metabolome, with a focus on SCFA may be a novel predictive biomarker for immunotherapy efficacy.
    Keywords:  biomarkers; immunotherapy; metabolic networks and pathways; tumor
  18. Anal Bioanal Chem. 2020 Oct 29.
    Stricker T, Bonner R, Lisaek F, Hopfgartner G.
      Annotation and interpretation of full scan electrospray mass spectra of metabolites is complicated by the presence of a wide variety of ions. Not only protonated, deprotonated, and neutral loss ions but also sodium, potassium, and ammonium adducts as well as oligomers are frequently observed. This diversity challenges automatic annotation and is often poorly addressed by current annotation tools. In many cases, annotation is integrated in metabolomics workflows and is based on specific chromatographic peak-picking tools. We introduce mzAdan, a nonchromatography-based multipurpose standalone application that was developed for the annotation and exploration of convolved high-resolution ESI-MS spectra. The tool annotates single or multiple accurate mass spectra using a customizable adduct annotation list and outputs a list of [M+H]+ candidates. MzAdan was first tested with a collection of 408 analytes acquired with flow injection analysis. This resulted in 402 correct [M+H]+ identifications and, with combinations of sodium, ammonium, and potassium adducts and water and ammonia losses within a tolerance of 10 mmu, explained close to 50% of the total ion current. False positives were monitored with mass accuracy and bias as well as chromatographic behavior which led to the identification of adducts with calcium instead of the expected potassium. MzAdan was then integrated in a workflow with XCMS for the untargeted LC-MS data analysis of a 52 metabolite standard mix and a human urine sample. The results were benchmarked against three other annotation tools, CAMERA, findMAIN, and CliqueMS: findMAIN and mzAdan consistently produced higher numbers of [M+H]+ candidates compared with CliqueMS and CAMERA, especially with co-eluting metabolites. Detection of low-intensity ions and correct grouping were found to be essential for annotation performance. Graphical abstract.
    Keywords:  Adducts; Electrospray; HRMS; Liquid chromatography; Metabolomics; Software
  19. Redox Biol. 2020 Oct 16. pii: S2213-2317(20)30949-6. [Epub ahead of print]38 101744
    Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky Y, Stockwell BR, He RR, Bahar I, Bayır H, Kagan VE.
      Hydroperoxy-eicosatetraenoyl-phosphatidylethanolamine (HpETE-PE) is a ferroptotic cell death signal. HpETE-PE is produced by the 15-Lipoxygenase (15LOX)/Phosphatidylethanolamine Binding Protein-1 (PEBP1) complex or via an Fe-catalyzed non-enzymatic radical reaction. Ferrostatin-1 (Fer-1), a common ferroptosis inhibitor, is a lipophilic radical scavenger but a poor 15LOX inhibitor arguing against 15LOX having a role in ferroptosis. In the current work, we demonstrate that Fer-1 does not affect 15LOX alone, however, it effectively inhibits HpETE-PE production by the 15LOX/PEBP1 complex. Computational molecular modeling shows that Fer-1 binds to the 15LOX/PEBP1 complex at three sites and could disrupt the catalytically required allosteric motions of the 15LOX/PEBP1 complex. Using nine ferroptosis cell/tissue models, we show that HpETE-PE is produced by the 15LOX/PEBP1 complex and resolve the long-existing Fer-1 anti-ferroptotic paradox.
    Keywords:  15-Lipoxygenase; Ferroptosis; Ferrostatin-1; Hydroperoxy-eicosatetraenoyl-phosphatidylethanolamines; Phospholipid peroxidation
  20. J Mass Spectrom. 2020 Oct 16. e4669
    Taverna D, Gaspari M.
      MS-based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data-dependent methods for protein relative quantification (label-free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole-Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label-based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold-changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field.
    Keywords:  dimethyl labelling; isobaric labelling; label-free proteomics; proteomics benchmarking; quantitative proteomics
  21. Cell Cycle. 2020 Oct 28. 1-3
    Ma Y, Han F, Min J, Lin W.
      Ferroptosis is a newly identified form of cell death that is regulated by many metabolic pathways, including iron, lipid and amino acids. Recent two studies reveal that the mitochondria and energy stress could also mediate ferroptosis. Gao et al. report that mitochondria play an essential role in ferroptosis induced by cysteine deprivation. In addition, Lee et al. show that energy stress depressed ferroptosis partly through activation of AMP-activated protein kinase. These findings provide potential therapeutic strategies for treating ferroptosis-related diseases, such as cancer, tissue injury and neurodegenerative diseases.
    Keywords:  Ferroptosis; energy stress; mitochondria
  22. Metabolites. 2020 Oct 26. pii: E426. [Epub ahead of print]10(11):
    Godfrey WH, Kornberg MD.
      Immune cells undergo dramatic metabolic reprogramming in response to external stimuli. These metabolic pathways, long considered as simple housekeeping functions, are increasingly understood to critically regulate the immune response, determining the activation, differentiation, and downstream effector functions of both lymphoid and myeloid cells. Within the complex metabolic networks associated with immune activation, several enzymes play key roles in regulating inflammation and represent potential therapeutic targets in human disease. In some cases, these enzymes control flux through pathways required to meet specific energetic or metabolic demands of the immune response. In other cases, key enzymes control the concentrations of immunoactive metabolites with direct roles in signaling. Finally, and perhaps most interestingly, several metabolic enzymes have evolved moonlighting functions, with roles in the immune response that are entirely independent of their conventional enzyme activities. Here, we review key metabolic enzymes that critically regulate inflammation, highlighting mechanistic insights and opportunities for clinical intervention.
    Keywords:  immunometabolism; inflammation; metabolism
  23. Molecules. 2020 Oct 22. pii: E4883. [Epub ahead of print]25(21):
    Fujiwara T, Inoue R, Ohtawa T, Tsunoda M.
      Carboxyl-bearing low-molecular-weight compounds such as keto acids, fatty acids, and other organic acids are involved in a myriad of metabolic pathways owing to their high polarity and solubility in biological fluids. Various disease areas such as cancer, myeloid leukemia, heart disease, liver disease, and lifestyle diseases (obesity and diabetes) were found to be related to certain metabolic pathways and changes in the concentrations of the compounds involved in those pathways. Therefore, the quantification of such compounds provides useful information pertaining to diagnosis, pathological conditions, and disease mechanisms, spurring the development of numerous analytical methods for this purpose. This review article addresses analytical methods for the quantification of carboxylic acids, which were classified into fatty acids, tricarboxylic acid cycle and glycolysis-related compounds, amino acid metabolites, perfluorinated carboxylic acids, α-keto acids and their metabolites, thiazole-containing carboxylic acids, and miscellaneous, in biological samples from 2000 to date. Methods involving liquid chromatography coupled with ultraviolet, fluorescence, mass spectrometry, and electrochemical detection were summarized.
    Keywords:  fatty acids; fluorescence; mass spectrometry; perfluorinated carboxylic acids; α-keto acids