bims-mascan 2020-02-09 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2020‒02‒09
twenty-four papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research

Metabolic and amino acid alterations of the tumor microenvironment.
Glutamine and asparagine activate mTORC1 independently of Rag GTPases.
Energy-stress-mediated AMPK activation inhibits ferroptosis.
Development of a sensitive and quantitative method for the identification of two major furan fatty acids in human plasma.
Dietary Methionine in T Cell Biology and Autoimmune Disease.
Metabolomic Analysis of the Effects of Leptin Replacement Therapy in Patients with Lipodystrophy.
MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS.
Impaired lipid metabolism by age-dependent DNA methylation alterations accelerates aging.
Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia.
Metabolome and proteome changes in skeletal muscle and blood of pre-weaning calves fed leucine and threonine supplemented diets.
Spatially Controlled Molecular Analysis of Biological Samples Using Nanodroplet Arrays and Direct Droplet Aspiration.
Crosstalk between autophagy and metabolic regulation of cancer stem cells.
EGFR activates GDH1 transcription to promote glutamine metabolism through MEK/ERK/ELK1 pathway in glioblastoma.
Stable Isotope Analysis of Intact Oxyanions Using Electrospray Quadrupole-Orbitrap Mass Spectrometry.
Enhanced lipid accumulation and metabolism are required for the differentiation and activation of tumor-associated macrophages.
Itaconate modulates tricarboxylic acid and redox metabolism to mitigate reperfusion injury.
Alcohol effects on hepatic lipid metabolism.
Mass Spectrometry for Identification, Monitoring, and Minimal Residual Disease Detection of M-Proteins.
Mass Spectrometry Search Tool (MASST).
Lipid droplets: platforms with multiple functions in cancer hallmarks.
Phosphoinositides in cell proliferation and metabolism.
Application of CE-MS for the analysis of histones and histone modifications.
Preferential uptake of polyunsaturated fatty acids by colorectal cancer cells.

Curr Med Chem. 2020 Feb 06.

Metabolic and amino acid alterations of the tumor microenvironment.

Petr Stepka, Vit Vsiansky, Martina Raudenska, Jaromir Gumulec, Vojtech Adam, Michal Masarik.

  Metabolic changes driven by the hostile tumor microenvironment surrounding cancer cells and effect of these changes on tumorigenesis and metastatic potential have been known for a long time. The usual point of interest is glucose and changes in its utilization by cancer cells, mainly in the form of the Warburg effect. However, amino acids, both intra- and extracellular, also represent an important aspect of tumour microenvironment, which can have a significant effect on cancer cell metabolism and overall development of the tumor. Namely alterations in metabolism of amino acids glutamine, sarcosine, aspartate, methionine and cysteine have been previously connected to the tumor progression and aggressivity of prostate cancer. The aim of this review is to pinpoint current gaps in our knowledge of the role of amino acids as a part of the tumor microenvironment and to show effect of various amino acids on cancer cell metabolism and metastatic potential. This review shows limitations and exceptions from the traditionally accepted model of Warburg effect in some cancer tissues, with the emphasis on prostate cancer, because the traditional definition of Warburg effect as a metabolic switch to aerobic glycolysis does not always apply. Prostatic tissue both in healthy and transformed state significantly differs in many metabolic aspects, including the metabolisms of glucose and amino acids, from metabolism of other tissues. Findings from different tissues are therefore not always interchangeable and have to be taken into account during experimentation modifying the environment of tumor tissue by amino acid supplementation or depletion, which could potentially serve as a new therapeutic approach.

Keywords:  Cancer metabolism ; aspartate; glutamine ; metastasis; methionine; sarcosine

DOI:  https://doi.org/10.2174/0929867327666200207114658
J Biol Chem. 2020 Feb 04. pii: jbc.AC119.011578. [Epub ahead of print]

Glutamine and asparagine activate mTORC1 independently of Rag GTPases.

Delong Meng, Qianmei Yang, Huanyu Wang, Chase H Melick, Rishika Navlani, Anderson R Frank, Jenna L Jewell.

  Nutrient sensing by cells is crucial, and when this sensing mechanism is disturbed human disease can occur. mTOR complex 1 (mTORC1) senses amino acids to control cell growth, metabolism and autophagy. Leucine, arginine, and methionine signal to mTORC1 through the well-characterized Rag GTPase signaling pathway. In contrast, glutamine activates mTORC1 through a Rag GTPase-independent mechanism that requires ADP-ribosylation factor 1 (Arf1). Here, using several biochemical and genetic approaches, we show that eight amino acids filter through the Rag GTPase pathway. Like glutamine, asparagine signals to mTORC1 through Arf1 in the absence of the Rag GTPases. Both the Rag-dependent and Rag-independent pathways required the lysosome and lysosomal function for mTORC1 activation. Our results show that mTORC1 is differentially regulated by amino acids through two distinct pathways.

Keywords:  Arf1; Rag GTPase; amino acid; asparagine; glutamine; mTOR complex (mTORC); mTORC1; metabolism; signal transduction

DOI:  https://doi.org/10.1074/jbc.AC119.011578
Nat Cell Biol. 2020 Feb;22(2): 225-234

Energy-stress-mediated AMPK activation inhibits ferroptosis.

Hyemin Lee, Fereshteh Zandkarimi, Yilei Zhang, Jitendra Kumar Meena, Jongchan Kim, Li Zhuang, Siddhartha Tyagi, Li Ma, Thomas F Westbrook, Gregory R Steinberg, Daisuke Nakada, Brent R Stockwell, Boyi Gan.

Energy stress depletes ATP and induces cell death. Here we identify an unexpected inhibitory role of energy stress on ferroptosis, a form of regulated cell death induced by iron-dependent lipid peroxidation. We found that ferroptotic cell death and lipid peroxidation can be inhibited by treatments that induce or mimic energy stress. Inactivation of AMP-activated protein kinase (AMPK), a sensor of cellular energy status, largely abolishes the protective effects of energy stress on ferroptosis in vitro and on ferroptosis-associated renal ischaemia-reperfusion injury in vivo. Cancer cells with high basal AMPK activation are resistant to ferroptosis and AMPK inactivation sensitizes these cells to ferroptosis. Functional and lipidomic analyses further link AMPK regulation of ferroptosis to AMPK-mediated phosphorylation of acetyl-CoA carboxylase and polyunsaturated fatty acid biosynthesis. Our study demonstrates that energy stress inhibits ferroptosis partly through AMPK and reveals an unexpected coupling between ferroptosis and AMPK-mediated energy-stress signalling.

DOI: https://doi.org/10.1038/s41556-020-0461-8
J Lipid Res. 2020 Feb 06. pii: jlr.D119000514. [Epub ahead of print]

Development of a sensitive and quantitative method for the identification of two major furan fatty acids in human plasma.

Long Xu, Changfeng Hu, Yongguo Liu, Siming Li, Walter Vetter, Huiyong Yin, Yonghua Wang.

  This paper focuses on the establishment of an accurate and sensitive quantitation method for analysis of furan fatty acids. Particularly, the sensitivity of GC-MS and UPLC-ESI-MS/MS was compared for the identification and quantification of furan fatty acids. Different methylation methods were tested with respect to GC-MS analysis. Special attention needs to be paid to the methylation of furan fatty acids as acidic catalysts might lead to the degradation of furan ring. GC-MS analysis in full scan mode demonstrated that the limit-of-quantitation (LOQ) was 10 μM. UPLC-ESI-MS/MS in multiple reaction monitoring (MRM) mode displayed a higher detection sensitivity than GC-MS. Moreover, identification of furan fatty acids with charge-reversal derivatization was tested in positive mode with two widely used pyridinium salts. Unexpectedly, significant oxidation was observed using N-(4-aminomethylphenyl) pyridinium (AMPP) as a derivatization agent. The formed 3-acyl-oxymethyl-1-methylpyridinium iodide (AMMP) derivatized by 2-bromo-1-methylpyridinium iodide and 3-carbinol-1-methylpyridinium iodide improved the sensitivity more than 2000 fold, compared with non-derivatization in negative mode by UPLC-ESI-MS/MS. This charge reversal derivatization enabled the targeted quantitation of furan fatty acids in human plasma. Thus, it is anticipated that this protocol could greatly contribute to the clarification of pathological mechanisms related to furan fatty acids and their metabolites.

Keywords:  Charge-reversal derivatization; Diabetes; Fatty acid; Furan fatty acids; Lipidomics; Lipids; Mass spectrometry; Multiple reaction monitoring; Precursor ion scan; UPLC-ESI-MS/MS

DOI:  https://doi.org/10.1194/jlr.D119000514
Cell Metab. 2020 Feb 04. pii: S1550-4131(20)30007-3. [Epub ahead of print]31(2): 211-212

Dietary Methionine in T Cell Biology and Autoimmune Disease.

Shuang Tang, Xiaoling Li, Jason W Locasale.

Dietary methionine and its subsequent metabolism have profound effects on metabolic disease, cancer, and healthspan. In this issue of Cell Metabolism, Roy et al. (2020) report methionine as a nutritional factor for activated T cells that maintains H3K4 methylation and mediates functions that affect autoimmune disease.

DOI: https://doi.org/10.1016/j.cmet.2020.01.007
J Endocr Soc. 2020 Jan 01. 4(1): bvz022

Metabolomic Analysis of the Effects of Leptin Replacement Therapy in Patients with Lipodystrophy.

Shivraj Grewal, Sriram Gubbi, Andin Fosam, Caroline Sedmak, Shanaz Sikder, Harsha Talluru, Rebecca J Brown, Ranganath Muniyappa.

  Context and Objective: Leptin treatment has dramatic clinical effects on glucose and lipid metabolism in leptin-deficient patients with lipodystrophy. Further elucidation of metabolic effects of exogenous leptin therapy will shed light on understanding leptin physiology in humans. Our objective was to utilize metabolomic profiling to examine the changes associated with administration of short-term metreleptin therapy in patients with lipodystrophy.Study Design: We conducted a pre-post-treatment study in 19 patients (75% female) with varying forms of lipodystrophy (congenital generalized lipodystrophy, n = 10; acquired generalized lipodystrophy, n = 1; familial partial lipodystrophy, n = 8) who received daily subcutaneous metreleptin injections for a period of 16 to 23 weeks. A 3-hour oral glucose tolerance test and body composition measurements were conducted before and after the treatment period, and fasting blood samples were used for metabolomic profiling. The study outcome aimed at measuring changes in physiologically relevant metabolites before and after leptin therapy.
Results: Metabolomic analysis revealed changes in pathways involving branched-chain amino acid metabolism, fatty acid oxidation, protein degradation, urea cycle, tryptophan metabolism, nucleotide catabolism, vitamin E, and steroid metabolism. Fold changes in pre- to post-treatment metabolite levels indicated increased breakdown of fatty acids, branched chain amino acids proteins, and nucleic acids.
Conclusions: Leptin replacement therapy has significant effects on important metabolic pathways implicated in patients with lipodystrophy. Continued metabolomic studies may provide further insight into the mechanisms of action of leptin replacement therapy and provide novel biomarkers of lipodystrophy.Abbreviations: 1,5-AG, 1,5-anhydroglucitol; 11βHSD1, 11-β hydroxysteroid dehydrogenase 1; BCAA, branched-chain amino acid; FFA, free fatty acid; GC-MS, gas chromatography mass spectrometry; IDO, indoleamine 2,3-dioxygenase; IFN-γ, interferon-γ; m/z, mass to charge ratio; OGTT, oral glucose tolerance test; TDO, tryptophan 2,3-dioxygenase; TNF-α, tumor necrosis factor-α; UPLC-MS/MS, ultra-performance liquid chromatography-tandem mass spectrometry.

Keywords:  leptin; lipodystrophy; metabolomics; metreleptin

DOI:  https://doi.org/10.1210/jendso/bvz022
Mass Spectrom Rev. 2020 Feb 04.

MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS.

Na Li, Xianquan Zhan.

  The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 Wiley Periodicals, Inc. Mass Spec Rev.

Keywords:  biomarkers; diagnostic targets; individualized patient profiling; mitochondria; molecular network; multiomics; ovarian cancer; patient stratification; quantitative phosphoproteomics; quantitative proteomics; therapeutic targets

DOI:  https://doi.org/10.1002/mas.21618
Proc Natl Acad Sci U S A. 2020 Feb 06. pii: 201919403. [Epub ahead of print]

Impaired lipid metabolism by age-dependent DNA methylation alterations accelerates aging.

Xin Li, Jiaqiang Wang, Leyun Wang, Guihai Feng, Gen Li, Meixin Yu, Yufei Li, Chao Liu, Xuewei Yuan, Guangxi Zang, Zhihuan Li, Ling Zhao, Hong Ouyang, Qingli Quan, Guangyu Wang, Charlotte Zhang, Oulan Li, Junkai Xiang, Jian-Kang Zhu, Wei Li, Qi Zhou, Kang Zhang.

  Epigenetic alterations and metabolic dysfunction are two hallmarks of aging. However, the mechanism of how their interaction regulates aging, particularly in mammals, remains largely unknown. Here we show ELOVL fatty acid elongase 2 (Elovl2), a gene whose epigenetic alterations are most highly correlated with age prediction, contributes to aging by regulating lipid metabolism. Impaired Elovl2 function disturbs lipid synthesis with increased endoplasmic reticulum stress and mitochondrial dysfunction, leading to key accelerated aging phenotypes. Restoration of mitochondrial activity can rescue age-related macular degeneration (AMD) phenotypes induced by Elovl2 deficiency in human retinal pigmental epithelial (RPE) cells. We revealed an epigenetic-metabolism axis contributing to aging and potentially to antiaging therapy.

Keywords:  ER stress; aging; epigenetic alteration; lipid metabolism; mitochondrial dysfunction

DOI:  https://doi.org/10.1073/pnas.1919403117
Cell Rep. 2020 Feb 04. pii: S2211-1247(20)30020-6. [Epub ahead of print]30(5): 1542-1552.e7

Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.

Jayne Louise Wilson, Thomas Nägele, Monika Linke, Florian Demel, Stephanie D Fritsch, Hannah Katharina Mayr, Zhengnan Cai, Karl Katholnig, Xiaoliang Sun, Lena Fragner, Anne Miller, Arvand Haschemi, Alexandra Popa, Andreas Bergthaler, Markus Hengstschläger, Thomas Weichhart, Wolfram Weckwerth.

  Mechanistic or mammalian target of rapamycin complex 1 (mTORC1) is an important regulator of effector functions, proliferation, and cellular metabolism in macrophages. The biochemical processes that are controlled by mTORC1 are still being defined. Here, we demonstrate that integrative multiomics in conjunction with a data-driven inverse modeling approach, termed COVRECON, identifies a biochemical node that influences overall metabolic profiles and reactions of mTORC1-dependent macrophage metabolism. Using a combined approach of metabolomics, proteomics, mRNA expression analysis, and enzymatic activity measurements, we demonstrate that Tsc2, a negative regulator of mTORC1 signaling, critically influences the cellular activity of macrophages by regulating the enzyme phosphoglycerate dehydrogenase (Phgdh) in an mTORC1-dependent manner. More generally, while lipopolysaccharide (LPS)-stimulated macrophages repress Phgdh activity, IL-4-stimulated macrophages increase the activity of the enzyme required for the expression of key anti-inflammatory molecules and macrophage proliferation. Thus, we identify Phgdh as a metabolic checkpoint of M2 macrophages.

Keywords:  Phgdh; Tsc2; biochemical Jacobian; cancer; mTOR; macrophage polarization; macrophage proliferation; metabolic modeling; metabolomics; serine/glycine pathway; tumor-associated macrophages

DOI:  https://doi.org/10.1016/j.celrep.2020.01.011
Cell Death Dis. 2020 Feb 06. 11(2): 102

Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia.

Yang Li, Joshua J Gruber, Ulrike M Litzenburger, Yiren Zhou, Yu Rebecca Miao, Edward L LaGory, Albert M Li, Zhen Hu, Michaela Yip, Lori S Hart, John M Maris, Howard Y Chang, Amato J Giaccia, Jiangbin Ye.

Despite the fact that Otto H. Warburg discovered the Warburg effect almost one hundred years ago, why cancer cells waste most of the glucose carbon as lactate remains an enigma. Warburg proposed a connection between the Warburg effect and cell dedifferentiation. Hypoxia is a common tumor microenvironmental stress that induces the Warburg effect and blocks tumor cell differentiation. The underlying mechanism by which this occurs is poorly understood, and no effective therapeutic strategy has been developed to overcome this resistance to differentiation. Using a neuroblastoma differentiation model, we discovered that hypoxia repressed cell differentiation through reducing cellular acetyl-CoA levels, leading to reduction of global histone acetylation and chromatin accessibility. The metabolic switch triggering this global histone hypoacetylation was the induction of pyruvate dehydrogenase kinases (PDK1 and PDK3). Inhibition of PDKs using dichloroacetate (DCA) restored acetyl-CoA generation and histone acetylation under hypoxia. Knocking down PDK1 induced neuroblastoma cell differentiation, highlighting the critical role of PDK1 in cell fate control. Importantly, acetate or glycerol triacetate (GTA) supplementation restored differentiation markers expression and neuron differentiation under hypoxia. Moreover, ATAC-Seq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, which can be restored by acetate supplementation. In addition, hypoxia-induced histone hypermethylation by increasing 2-hydroxyglutarate (2HG) and reducing α-ketoglutarate (αKG). αKG supplementation reduced histone hypermethylation upon hypoxia, but did not restore histone acetylation or differentiation markers expression. Together, these findings suggest that diverting pyruvate flux away from acetyl-CoA generation to lactate production is the key mechanism that Warburg effect drives dedifferentiation and tumorigenesis. We propose that combining differentiation therapy with acetate/GTA supplementation might represent an effective therapy against neuroblastoma.

DOI: https://doi.org/10.1038/s41419-020-2303-9
J Proteomics. 2020 Feb 03. pii: S1874-3919(20)30045-2. [Epub ahead of print] 103677

Metabolome and proteome changes in skeletal muscle and blood of pre-weaning calves fed leucine and threonine supplemented diets.

Kuai Yu, Manolis Matzapetakis, Anita Horvatić, Marta Terré, Alex Bach, Josipa Kuleš, Natalia Yeste, Néstor Gómez, Laura Arroyo, Elisabet Rodríguez-Tomàs, Raquel Peña, Nicolas Guillemin, André M de Almeida, Peter David Eckersall, Anna Bassols.

  In pre-weaning calves, both leucine and threonine play important roles in growth and muscle metabolism. In this study, metabolomics, proteomics and clinical chemistry were used to assess the effects of leucine and threonine supplementation added to milk replacer on 14 newborn Holstein male calves: 7 were fed a control diet (Ctrl) and 7 were fed the Ctrl diet supplemented with 0.3% leucine and 0.3% threonine (LT) from 5.6 days of age to 53.6 days. At this time, blood and semitendinosus muscle biopsies were collected for analysis. Integrated metabolomics and proteomics showed that branched-chain amino acids (BCAA) degradation and mitochondrial oxidative metabolism (citrate cycle and respiratory chain) were the main activated pathways in muscle because of the supplementation. BCAA derivatives and metabolites related to lipid mobilization showed the major changes. The deleterious effects of activated oxidative phosphorylation were balanced by the upregulation of antioxidant proteins. An increase in protein synthesis was indicated by elevated aminoacyl-tRNA biosynthesis and increased S6 ribosomal protein phosphorylation in skeletal muscle. In conclusion, LT group showed greater BCAA availability and mitochondrial oxidative activity; as the muscle cells undergo greater aerobic metabolism, antioxidant defenses were activated to compensate for possible cell damage. Data are available via ProteomeXchange (PXD016098). SIGNIFICANCE: Leucine and threonine are essential amino acids for the pre-weaning calf, being of high importance for growth. In this study, we found that leucine and threonine supplementation of milk replacer to feed pre-weaning calves led to differences in the proteome, metabolome and clinical chemistry analytes in skeletal muscle and plasma, albeit no differences in productive performance were recorded. This study extends our understanding on the metabolism in dairy calves and helps optimizing their nutritional status.

Keywords:  Amino acid; Calf; Metabolomics; Muscle; Plasma; Proteomics

DOI:  https://doi.org/10.1016/j.jprot.2020.103677
J Am Soc Mass Spectrom. 2020 Feb 05. 31(2): 418-428

Spatially Controlled Molecular Analysis of Biological Samples Using Nanodroplet Arrays and Direct Droplet Aspiration.

Marta Sans, Anna Krieger, Bryan R Wygant, Kyana Y Garza, C Buddie Mullins, Livia S Eberlin.

Mass spectrometry (MS) has emerged as a valuable technology for molecular and spatial evaluation of biological samples. Ambient ionization MS techniques, in particular, allow direct analysis of tissue samples with minimal pretreatment. Here, we describe the design and optimization of an alternative ambient liquid extraction MS approach for metabolite and lipid profiling and imaging from biological samples. The system combines a piezoelectric picoliter dispenser to form solvent nanodroplets onto the sample surface with controlled and tunable spatial resolution and a conductive capillary to directly aspirate/ionize the nanodroplets for efficient analyte transmission and detection. Using this approach, we performed spatial profiling of mouse brain tissue sections with different droplet sizes (390, 420, and 500 μm). MS analysis of normal and cancerous human brain and ovarian tissues yielded rich metabolic profiles that were characteristic of disease state and enabled visualization of tissue regions with different histologic composition. This method was also used to analyze the lipid profiles of human ovarian cell lines. Overall, our results demonstrate the capabilities of this system for spatially controlled MS analysis of biological samples.

DOI: https://doi.org/10.1021/jasms.9b00077
Mol Cancer. 2020 Feb 06. 19(1): 27

Crosstalk between autophagy and metabolic regulation of cancer stem cells.

Mouradi El Hout, Emma Cosialls, Maryam Mehrpour, Ahmed Hamaï.

  Cancer is now considered as a heterogeneous ecosystem in which tumor cells collaborate with each other and with host cells in their microenvironment. As circumstances change, the ecosystem evolves to ensure the survival and growth of the cancer cells. In this ecosystem, metabolism is not only a key player but also drives stemness. In this review, we first summarize our current understanding of how autophagy influences cancer stem cell phenotype. We emphasize metabolic pathways in cancer stem cells and discuss how autophagy-mediated regulation metabolism is involved in their maintenance and proliferation. We then provide an update on the role of metabolic reprogramming and plasticity in cancer stem cells. Finally, we discuss how metabolic pathways in cancer stem cells could be therapeutically targeted.

Keywords:  Autophagy; Cancer stem cells; Lipid metabolism; Metabolic heterogeneity; Therapeutic target

DOI:  https://doi.org/10.1186/s12943-019-1126-8
Oncogene. 2020 Feb 07.

EGFR activates GDH1 transcription to promote glutamine metabolism through MEK/ERK/ELK1 pathway in glioblastoma.

Rui Yang, Xiuxiu Li, Yanan Wu, Guanghui Zhang, Xiaoran Liu, Yanping Li, Yonghua Bao, Wancai Yang, Hongjuan Cui.

Cancer metabolism research has recently been revived and its focus expanded from glucose and the Warburg's effects on other nutrients, such as glutamine. The underlying mechanism of oncogenic alterations of glutaminolysis remains unclear. Genetic alterations of EGFR are observed in ~50% of glioblastoma (GBM) patients, and have been found to play important roles in the metabolic abnormalities of GBM. In this study, we found that glutamine metabolism was upregulated after EGFR activation in a GDH1 (glutamate dehydrogenase 1)-dependent manner. Knockdown of GDH1 significantly reduced the cell proliferation, colony formation and tumorigenesis abilities of glioblastoma cells. Furthermore, we showed that GDH1-mediated glutaminolysis was involved in EGF-promoted cell proliferation. EGFR triggered the phosphorylation of ELK1 at Ser 383 through activating MEK/ERK signaling. Phosphorylated ELK1 enriched in the promoter of GDH1 to activate the transcription of GDH1, which then promoted glutamine metabolism. In addition, EGFR activation did not accelerate glutaminolysis in ELK1 knockdown or ELK1 Ser383-mutated cells. Collectively, our findings indicate that EGFR phosphorylates ELK1 to activate GDH1 transcription and glutaminolysis through MEK/ERK pathway, providing new insight into oncogenic alterations of glutamine metabolism.

DOI: https://doi.org/10.1038/s41388-020-1199-2
Anal Chem. 2020 Feb 03.

Stable Isotope Analysis of Intact Oxyanions Using Electrospray Quadrupole-Orbitrap Mass Spectrometry.

Cajetan Neubauer, Antoine Crémière, Xingchen T Wang, Nivedita Thiagarajan, Alex L Sessions, Jess F Adkins, Nathan F Dalleska, Alexandra V Turchyn, Josephine A Clegg, Annie Moradian, Michael J Sweredoski, Spiros D Garbis, John M Eiler.

The stable isotopes of sulfate, nitrate, and phosphate are frequently used to study geobiological processes of the atmosphere, ocean, as well as land. Conventionally, the isotopes of these and other oxyanions are measured by isotope-ratio sector mass spectrometers after conversion into gases. Such methods are prone to various limitations on sensitivity, sample throughput, or precision. In addition, there is no general tool that can analyze several oxyanions or all the chemical elements they contain. Here, we describe a new approach that can potentially overcome some of these limitations based on electrospray hyphenated with Quadrupole Orbitrap mass spectrometry. This technique yields an average accuracy of 1-2‰ for sulfate δ34S and δ18O and nitrate δ15N and δ18O, based on in-house and international standards. Less abundant variants such as δ17O, δ33S, and δ36S, and the 34S-18O "clumped" sulfate can be quantified simultaneously. The observed precision of isotope ratios is limited by the number of ions counted. The counting of rare ions can be accelerated by removing abundant ions with the quadrupole mass filter. Electrospray mass spectrometry (ESMS) exhibits high-throughput and sufficient sensitivity. For example, less than 1 nmol sulfate is required to determine 18O/34S ratios with 0.2‰ precision within minutes. A purification step is recommended for environmental samples as our proposed technique is susceptible to matrix effects. Building upon these initial provisions, new features of the isotopic anatomy of mineral ions can now be explored with ESMS instruments that are increasingly available to bioanalytical laboratories.

DOI: https://doi.org/10.1021/acs.analchem.9b04486
Cancer Res. 2020 Feb 03. pii: canres.2994.2019. [Epub ahead of print]

Enhanced lipid accumulation and metabolism are required for the differentiation and activation of tumor-associated macrophages.

Pan Su, Qiang Wang, Enguang Bi, Xingzhe Ma, Lintao Liu, Maojie Yang, Jianfei Qian, Qing Yi.

Tumor-associated macrophages (TAMs) are important tumor-promoting cells. However, the mechanism underlying how tumor and its microenvironment reprogram these cells remains elusive. Here we report that lipids play a crucial role in TAM generation in tumor microenvironment. Macrophages from both human and murine tumor tissues are enriched with lipids as a result of increased lipid uptake by macrophages. TAMs expressed elevated levels of the scavenger receptor CD36, accumulated lipids, and used fatty acid oxidation (FAO) instead of glycolysis for energy. High levels of FAO promoted mitochondrial oxidative phosphorylation, production of reactive oxygen species, phosphorylation of JAK1 and dephosphorylation of SHP1, leading to STAT6 activation and transcription of genes regulating TAM generation and function. These processes were critical for TAM polarization and activity in vitro and in vivo. In summary, we describe a novel mechanism underlying lipid metabolism-initiated process that promotes the differentiation and function of the protumor TAMs in TME.

DOI: https://doi.org/10.1158/0008-5472.CAN-19-2994
Mol Metab. 2020 Feb;pii: S2212-8778(19)30951-2. [Epub ahead of print]32 122-135

Itaconate modulates tricarboxylic acid and redox metabolism to mitigate reperfusion injury.

Thekla Cordes, Alfredo Lucas, Ajit S Divakaruni, Anne N Murphy, Pedro Cabrales, Christian M Metallo.

  OBJECTIVES: Cerebral ischemia/reperfusion (IR) drives oxidative stress and injurious metabolic processes that lead to redox imbalance, inflammation, and tissue damage. However, the key mediators of reperfusion injury remain unclear, and therefore, there is considerable interest in therapeutically targeting metabolism and the cellular response to oxidative stress.METHODS: The objective of this study was to investigate the molecular, metabolic, and physiological impact of itaconate treatment to mitigate reperfusion injuries in in vitro and in vivo model systems. We conducted metabolic flux and bioenergetic studies in response to exogenous itaconate treatment in cultures of primary rat cortical neurons and astrocytes. In addition, we administered itaconate to mouse models of cerebral reperfusion injury with ischemia or traumatic brain injury followed by hemorrhagic shock resuscitation. We quantitatively characterized the metabolite levels, neurological behavior, markers of redox stress, leukocyte adhesion, arterial blood flow, and arteriolar diameter in the brains of the treated/untreated mice.
RESULTS: We demonstrate that the "immunometabolite" itaconate slowed tricarboxylic acid (TCA) cycle metabolism and buffered redox imbalance via succinate dehydrogenase (SDH) inhibition and induction of anti-oxidative stress response in primary cultures of astrocytes and neurons. The addition of itaconate to reperfusion fluids after mouse cerebral IR injury increased glutathione levels and reduced reactive oxygen/nitrogen species (ROS/RNS) to improve neurological function. Plasma organic acids increased post-reperfusion injury, while administration of itaconate normalized these metabolites. In mouse cranial window models, itaconate significantly improved hemodynamics while reducing leukocyte adhesion. Further, itaconate supplementation increased survival in mice experiencing traumatic brain injury (TBI) and hemorrhagic shock.
CONCLUSIONS: We hypothesize that itaconate transiently inhibits SDH to gradually "awaken" mitochondrial function upon reperfusion that minimizes ROS and tissue damage. Collectively, our data indicate that itaconate acts as a mitochondrial regulator that controls redox metabolism to improve physiological outcomes associated with IR injury.

Keywords:  Brain injury; Cerebral ischemia/reperfusion (IR); Itaconate; Mitochondrial metabolism; Redox stress; Succinate dehydrogenase (SDH)

DOI:  https://doi.org/10.1016/j.molmet.2019.11.019
J Lipid Res. 2020 Feb 06. pii: jlr.R119000547. [Epub ahead of print]

Alcohol effects on hepatic lipid metabolism.

Sookyoung Jeon, Rotonya Carr.

  Alcoholic liver disease (ALD) is the most prevalent type of chronic liver disease with significant morbidity and mortality worldwide. ALD begins with simple hepatic steatosis and progresses to alcoholic steatohepatitis, fibrosis, and cirrhosis. The severity of hepatic steatosis is highly associated with the development of later stages of ALD. This review explores the disturbances of alcohol-induced hepatic lipid metabolism through altered hepatic lipid uptake, de novo lipid synthesis, fatty acid oxidation, hepatic lipid export, and lipid droplet formation and catabolism. In addition, we review emerging data on the contributions of genetics and bioactive lipid metabolism in alcohol-induced hepatic lipid accumulation.

Keywords:  Alcohol; Fatty acid/Biosynthesis; Fatty acid/Oxidation; Fatty acid/Transport; Lipid droplets; Liver; Sphingolipids; VLDL

DOI:  https://doi.org/10.1194/jlr.R119000547
Clin Chem. 2020 Feb 07. pii: hvz041. [Epub ahead of print]

Mass Spectrometry for Identification, Monitoring, and Minimal Residual Disease Detection of M-Proteins.

M Zajec, P Langerhorst, M M VanDuijn, J Gloerich, H Russcher, A J van Gool, T M Luider, I Joosten, Y B de Rijke, J F M Jacobs.

  BACKGROUND: Monoclonal gammopathies (MGs) are plasma cell disorders defined by the clonal expansion of plasma cells, resulting in the characteristic excretion of a monoclonal immunoglobulin (M-protein). M-protein detection and quantification are integral parts of the diagnosis and monitoring of MGs. Novel treatment modalities impose new challenges on the traditional electrophoretic and immunochemical methods that are routinely used for M-protein diagnostics, such as interferences from therapeutic monoclonal antibodies and the need for increased analytical sensitivity to measure minimal residual disease.CONTENT: Mass spectrometry (MS) is ideally suited to accurate mass measurements or targeted measurement of unique clonotypic peptide fragments. Based on these features, MS-based methods allow for the analytically sensitive measurement of the patient-specific M-protein.
SUMMARY: This review provides a comprehensive overview of the MS methods that have been developed recently to detect, characterize, and quantify M-proteins. The advantages and disadvantages of using these techniques in clinical practice and the impact they will have on the management of patients with MGs are discussed.

Keywords:  Clonotypic Peptide; M-protein; MASS-FIX; MASS-SCREEN; Mass spectrometry; Minimal Residual Disease; Monoclonal Gammopathy; Therapeutic Monoclonal Antibodies; miRAMM

DOI:  https://doi.org/10.1093/clinchem/hvz041
Nat Methods. 2020 Feb;17(2): 128

Mass Spectrometry Search Tool (MASST).

Arunima Singh.

DOI: https://doi.org/10.1038/s41592-020-0743-x
Cell Death Dis. 2020 Feb 06. 11(2): 105

Lipid droplets: platforms with multiple functions in cancer hallmarks.

André L S Cruz, Ester de A Barreto, Narayana P B Fazolini, João P B Viola, Patricia T Bozza.

Lipid droplets (also known as lipid bodies) are lipid-rich, cytoplasmic organelles that play important roles in cell signaling, lipid metabolism, membrane trafficking, and the production of inflammatory mediators. Lipid droplet biogenesis is a regulated process, and accumulation of these organelles within leukocytes, epithelial cells, hepatocytes, and other nonadipocyte cells is a frequently observed phenotype in several physiologic or pathogenic situations and is thoroughly described during inflammatory conditions. Moreover, in recent years, several studies have described an increase in intracellular lipid accumulation in different neoplastic processes, although it is not clear whether lipid droplet accumulation is directly involved in the establishment of these different types of malignancies. This review discusses current evidence related to the biogenesis, composition and functions of lipid droplets related to the hallmarks of cancer: inflammation, cell metabolism, increased proliferation, escape from cell death, and hypoxia. Moreover, the potential of lipid droplets as markers of disease and targets for novel anti-inflammatory and antineoplastic therapies will be discussed.

DOI: https://doi.org/10.1038/s41419-020-2297-3
Adv Biol Regul. 2020 Jan 20. pii: S2212-4926(20)30004-X. [Epub ahead of print] 100693

Phosphoinositides in cell proliferation and metabolism.

Emilio Hirsch, Federico Gulluni, Miriam Martini.

  Phosphoinositides (PI) are key players in many trafficking and signaling pathways. Recent advances regarding the synthesis, location and functions of these lipids have improved our understanding of how and when these lipids are generated and what their roles are in physiology and disease. In particular, PI play a central role in the regulation of cell proliferation and metabolism. Here, we will review recent advances in our understanding of PI function, regulation, and importance in different aspects of proliferation and energy metabolism.

Keywords:  Cell metabolism; PI3K; Phosphoinositides; Proliferation; mTOR

DOI:  https://doi.org/10.1016/j.jbior.2020.100693
Methods. 2020 Jan 31. pii: S1046-2023(19)30134-3. [Epub ahead of print]

Application of CE-MS for the analysis of histones and histone modifications.

Klaus Faserl, Bettina Sarg, Herbert H Lindner.

The analysis, identification and quantification of histones and their post-translational modifications plays a central role in chromatin research and in studying epigenetic regulations during physiological processes. In the last decade analytical strategies based on mass spectrometry have been greatly improved for providing a global view of single modification abundances or to determine combinatorial patterns of modifications. Presented here is a newly developed strategy for histone protein analysis and a number of applications are illustrated with an emphasis on PTM characterization. Capillary electrophoresis is coupled to mass spectrometry (CE-MS) and has proven to be a very promising concept as it enables to study intact histones (top-down proteomics) as well as the analysis of enzymatically digested proteins (bottom-up proteomics). This technology combines highly efficient low-flow CE separations with ionization in a single device and offers an orthogonal separation principle to conventional LC-MS analysis, thus expanding the existing analytical repertoire in a perfect manner.

DOI: https://doi.org/10.1016/j.ymeth.2020.01.017
Sci Rep. 2020 Feb 06. 10(1): 1954

Preferential uptake of polyunsaturated fatty acids by colorectal cancer cells.

Adriana Mika, Jaroslaw Kobiela, Alicja Pakiet, Aleksandra Czumaj, Ewa Sokołowska, Wojciech Makarewicz, Michał Chmielewski, Piotr Stepnowski, Antonella Marino-Gammazza, Tomasz Sledzinski.

Although a growing body of evidence suggests that colorectal cancer (CRC) is associated with alterations of fatty acid (FA) profiles in serum and tumor tissues, available data about polyunsaturated fatty acid (PUFA) content in CRC patients are inconclusive. Our study showed that CRC tissues contained more PUFAs than normal large intestinal mucosa. However, serum levels of PUFAs in CRC patients were lower than in healthy controls. To explain the mechanism of PUFA alterations in CRC, we measured FA uptake by the colon cancer cells and normal colon cells. The levels of PUFAs in colon cancer cell culture medium decreased significantly with incubation time, while no changes were observed in the medium in which normal colon cells were incubated. Our findings suggest that the alterations in tumor and serum PUFA profiles result from preferential uptake of these FAs by cancer cells; indeed, PUFAs are essential for formation of cell membrane phospholipids during rapid proliferation of cancer cells. This observation puts into question potential benefits of PUFA supplementation in CRC patients.

DOI: https://doi.org/10.1038/s41598-020-58895-7