bims-mascan 2021-01-03 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–01–03
33 papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

Metabolic Dynamics of In Vitro CD8+ T Cell Activation.
Distinctive Metabolomics Patterns Associated With Insulin Resistance and Type 2 Diabetes Mellitus.
Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MSn.
Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format.
Integration of Lipidomics and Transcriptomics Reveals Reprogramming of the Lipid Metabolism and Composition in Clear Cell Renal Cell Carcinoma.
Amino Acid Transporters Are a Vital Focal Point in the Control of mTORC1 Signaling and Cancer.
Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labeling in Metabolomics.
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification.
Reductive TCA cycle metabolism fuels glutamine- and glucose-stimulated insulin secretion.
Abrogating GPT2 in triple negative breast cancer inhibits tumor growth and promotes autophagy.
Identification and initial characterization of a potent inhibitor of ferroptosis.
The role of Data-Independent Acquisition for Glycoproteomics.
Non-canonical Glutamate-Cysteine Ligase Activity Protects against Ferroptosis.
High Coverage Profiling of Carboxylated Metabolites in HepG2 Cells Using Secondary Amine-Assisted Ultrahigh-Performance Liquid Chromatography Coupled to High-Resolution Mass Spectrometry.
Critical role of mTOR in regulating aerobic glycolysis in carcinogenesis (Review).
Increased demand for NAD+ relative to ATP drives aerobic glycolysis.
Single cell metabolomics using mass spectrometry: Techniques and data analysis.
The role of metabolism in chondrocyte dysfunction and the progression of osteoarthritis.
High Fructose Drives the Serine Synthesis Pathway in Acute Myeloid Leukemic Cells.
Liquid Chromatography-High-Resolution Mass Spectrometry-Based In Vitro Toxicometabolomics of the Synthetic Cathinones 4-MPD and 4-MEAP in Pooled Human Liver Microsomes.
Identification of novel diagnostic biomarkers in endometrial cancer using targeted metabolomic profiling.
Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview.
Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism.
Coenzyme Q Depletion Reshapes MCF-7 Cells Metabolism.
Profiling of mouse macrophage lipidome using direct infusion shotgun mass spectrometry.
A preliminary study procedure for detection of polyamines in plasma samples as a potential diagnostic tool in prostate cancer.
Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma.
How Autophagy Shapes the Tumor Microenvironment in Ovarian Cancer.
ER stress-induced adipocytes secrete-aldo-keto reductase 1B7-containing exosomes that cause nonalcoholic steatohepatitis in mice.
Eicosanoids in Cancer: New Roles in Immunoregulation.
NAD+ metabolism and its roles in cellular processes during ageing.
Hepatic synthesis of triacylglycerols containing medium-chain fatty acids is dominated by diacylglycerol acyltransferase 1 and efficiently inhibited by etomoxir.
Simultaneous determination of methionine cycle metabolites, urea cycle intermediates and polyamines in serum, urine and intestinal tissue by using UHPLC-MS/MS.

Metabolites. 2020 Dec 28. pii: E12. [Epub ahead of print]11(1):

Metabolic Dynamics of In Vitro CD8+ T Cell Activation.

Joy Edwards-Hicks, Michael Mitterer, Erika L Pearce, Joerg M Buescher.

  CD8+ T cells detect and kill infected or cancerous cells. When activated from their naïve state, T cells undergo a complex transition, including major metabolic reprogramming. Detailed resolution of metabolic dynamics is needed to advance the field of immunometabolism. Here, we outline methodologies that when utilized in parallel achieve broad coverage of the metabolome. Specifically, we used a combination of 2 flow injection analysis (FIA) and 3 liquid chromatography (LC) methods in combination with positive and negative mode high-resolution mass spectrometry (MS) to study the transition from naïve to effector T cells with fine-grained time resolution. Depending on the method, between 54% and 98% of measured metabolic features change in a time-dependent manner, with the major changes in both polar metabolites and lipids occurring in the first 48 h. The statistical analysis highlighted the remodeling of the polyamine biosynthesis pathway, with marked differences in the dynamics of precursors, intermediates, and cofactors. Moreover, phosphatidylcholines, the major class of membrane lipids, underwent a drastic shift in acyl chain composition with polyunsaturated species decreasing from 60% to 25% of the total pool and specifically depleting species containing a 20:4 fatty acid. We hope that this data set with a total of over 11,000 features recorded with multiple MS methodologies for 9 time points will be a useful resource for future work.

Keywords:  FIA-MS; LC-MS; T cell; activation; lipidomics; metabolic reprogramming; metabolomics; time course

DOI:  https://doi.org/10.3390/metabo11010012
Front Mol Biosci. 2020 ;7 609806

Distinctive Metabolomics Patterns Associated With Insulin Resistance and Type 2 Diabetes Mellitus.

Xinyun Gu, Mohammed Al Dubayee, Awad Alshahrani, Afshan Masood, Hicham Benabdelkamel, Mahmoud Zahra, Liang Li, Anas M Abdel Rahman, Ahmad Aljada.

  Obesity is associated with an increased risk of insulin resistance (IR) and type 2 diabetes mellitus (T2DM) which is a multi-factorial disease associated with a dysregulated metabolism and can be prevented in pre-diabetic individuals with impaired glucose tolerance. A metabolomic approach emphasizing metabolic pathways is critical to our understanding of this heterogeneous disease. This study aimed to characterize the serum metabolomic fingerprint and multi-metabolite signatures associated with IR and T2DM. Here, we have used untargeted high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) to identify candidate biomarkers of IR and T2DM in sera from 30 adults of normal weight, 26 obese adults, and 16 adults newly diagnosed with T2DM. Among the 3633 peak pairs detected, 62% were either identified or matched. A group of 78 metabolites were up-regulated and 111 metabolites were down-regulated comparing obese to lean group while 459 metabolites were up-regulated and 166 metabolites were down-regulated comparing T2DM to obese groups. Several metabolites were identified as IR potential biomarkers, including amino acids (Asn, Gln, and His), methionine (Met) sulfoxide, 2-methyl-3-hydroxy-5-formylpyridine-4-carboxylate, serotonin, L-2-amino-3-oxobutanoic acid, and 4,6-dihydroxyquinoline. T2DM was associated with dysregulation of 42 metabolites, including amino acids, amino acids metabolites, and dipeptides. In conclusion, these pilot data have identified IR and T2DM metabolomics panels as potential novel biomarkers of IR and identified metabolites associated with T2DM, with possible diagnostic and therapeutic applications. Further studies to confirm these associations in prospective cohorts are warranted.

Keywords:  chemical isotope labeling liquid chromatography; clinical metabolic panel; insulin resistance; obesity; type 2 diabetes mellitus; untargeted metabolomics profiling

DOI:  https://doi.org/10.3389/fmolb.2020.609806
Mol Cell Proteomics. 2020 Dec 29. pii: mcp.RA120.002266. [Epub ahead of print]

Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MSn.

Simone Kurz, M Osman Sheikh, Shan Lu, Lance Wells, Michael Tiemeyer.

  High performance liquid chromatography has been employed for decades to enhance detection sensitivity and quantification of complex analytes within biological mixtures. Among these analytes, glycans released from glycoproteins and glycolipids have been characterized as underivatized or fluorescently tagged derivatives by HPLC coupled to various detection methods. These approaches have proven extremely useful for profiling the structural diversity of glycoprotein and glycolipid glycosylation but require the availability of glycan standards and secondary orthogonal degradation strategies to validate structural assignments. A robust method for HPLC separation of glycans as their permethylated derivatives, coupled with in-line MSn fragmentation to assign structural features independent of standards, would significantly enhance the depth of knowledge obtainable from biological samples. Here, we report an optimized workflow for LC-MS analysis of permethylated glycans that includes sample preparation, mobile phase optimization, and MSn method development to resolve structural isomers on-the-fly. We report baseline separation and MSn fragmentation of isomeric N- and O-glycan structures, aided by supplementing mobile phases with Li+, which simplifies adduct heterogeneity and facilitates cross-ring fragmentation to obtain valuable monosaccharide linkage information. Our workflow has been adapted from standard proteomics-based workflows and, therefore, provides opportunities for laboratories with expertise in proteomics to acquire glycomic data with minimal deviation from existing buffer systems, chromatography media, and instrument configurations. Furthermore, our workflow does not require a mass spectrometer with high-resolution/accurate mass capabilities. The rapidly evolving appreciation of the biological significance of glycans for human health and disease requires the implementation of high-throughput methods to identify and quantify glycans harvested from sample sets of sufficient size to achieve appropriately powered statistical significance. The LC-MSn approach we report generates glycan isomeric separations, robust structural characterization, and is amenable to auto-sampling with associated throughput enhancements.

Keywords:  Glycomics; HPLC; Mass Spectrometry; N-Glycosylation; O-glycosylation; Separation Technologies

DOI:  https://doi.org/10.1074/mcp.RA120.002266
Anal Chim Acta. 2021 Jan 25. pii: S0003-2670(20)31143-0. [Epub ahead of print]1143 189-200

Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format.

Theresa L Pedersen, Ira J Gray, John W Newman.

  The goal of this research was to develop a high-throughput, cost-effective method for metabolic profiling of lipid mediators and hormones involved in the regulation of inflammation and energy metabolism, along with polyunsaturated fatty acids and common over-the-counter non-steroidal anti-inflammatory drugs (NSAIDs). We describe a 96-well plate protein precipitation and filtration procedure for 50 μL of plasma or serum in the presence of 37 deuterated analogs and 2 instrument internal standards. Data is acquired in two back-to-back UPLC-MS/MS analyses using electrospray ionization with positive/negative switching and scheduled multiple reaction monitoring for the determination of 145 compounds, including oxylipins, endocannabinoids and like compounds, bile acids, glucocorticoids, sex steroids, polyunsaturated fatty acids, and 3 NSAIDs. Intra- and inter-batch variability was <25% for >70% of metabolites above the LOQ in both matrices, but higher inter-batch variability was observed for serum oxylipins and some bile acids. Results for NIST Standard Reference Material 1950, compared favorably with the 20 certified metabolite values covered by this assay, and we provide new data for oxylipins, N-acylethanolamides, glucocorticoids, and 17-hydroxy-progesterone in this material. Application to two independent cohorts of elderly men and women showed the routine detection of 86 metabolites, identified fasting state influences on essential fatty acid-derived oxylipins, N-acylethanolamides and conjugated bile acids, identified rare presence of high and low testosterone levels and the presence of NSAIDs in ∼10% of these populations. The described method appears valuable for investigations in large cohort studies to provide insight into metabolic cross-talk between the array of mediators assessed here.

Keywords:  High-throughput; Lipid mediators; Metabolic profiling; NIST SRM 1950

DOI:  https://doi.org/10.1016/j.aca.2020.11.019
Metabolites. 2020 Dec 13. pii: E509. [Epub ahead of print]10(12):

Integration of Lipidomics and Transcriptomics Reveals Reprogramming of the Lipid Metabolism and Composition in Clear Cell Renal Cell Carcinoma.

Giuseppe Lucarelli, Matteo Ferro, Davide Loizzo, Cristina Bianchi, Daniela Terracciano, Francesco Cantiello, Lauren N Bell, Stefano Battaglia, Camillo Porta, Angela Gernone, Roberto A Perego, Eugenio Maiorano, Ottavio de Cobelli, Giuseppe Castellano, Leonardo Vincenti, Pasquale Ditonno, Michele Battaglia.

  Clear cell renal cell carcinoma (ccRCC) is fundamentally a metabolic disease. Given the importance of lipids in many cellular processes, in this study we delineated a lipidomic profile of human ccRCC and integrated it with transcriptomic data to connect the variations in cancer lipid metabolism with gene expression changes. Untargeted lipidomic analysis was performed on 20 ccRCC and 20 paired normal tissues, using LC-MS and GC-MS. Different lipid classes were altered in cancer compared to normal tissue. Among the long chain fatty acids (LCFAs), significant accumulations of polyunsaturated fatty acids (PUFAs) were found. Integrated lipidomic and transcriptomic analysis showed that fatty acid desaturation and elongation pathways were enriched in neoplastic tissue. Consistent with these findings, we observed increased expression of stearoyl-CoA desaturase(SCD1) and FA elongase 2 and 5 in ccRCC. Primary renal cancer cells treated with a small molecule SCD1 inhibitor (A939572) proliferated at a slower rate than untreated cancer cells. In addition, after cisplatin treatment, the death rate of tumor cells treated with A939572 was significantly greater than that of untreated cancer cells. In conclusion, our findings delineate a ccRCC lipidomic signature and showed that SCD1 inhibition significantly reduced cancer cell proliferation and increased cisplatin sensitivity, suggesting that this pathway can be involved in ccRCC chemotherapy resistance.

Keywords:  SCD1; cholesterol; lipidomics; lipids; renal cell carcinoma

DOI:  https://doi.org/10.3390/metabo10120509
Int J Mol Sci. 2020 Dec 22. pii: E23. [Epub ahead of print]22(1):

Amino Acid Transporters Are a Vital Focal Point in the Control of mTORC1 Signaling and Cancer.

Yann Cormerais, Milica Vučetić, Scott K Parks, Jacques Pouyssegur.

  The mechanistic target of rapamycin complex 1 (mTORC1) integrates signals from growth factors and nutrients to control biosynthetic processes, including protein, lipid, and nucleic acid synthesis. Dysregulation in the mTORC1 network underlies a wide array of pathological states, including metabolic diseases, neurological disorders, and cancer. Tumor cells are characterized by uncontrolled growth and proliferation due to a reduced dependency on exogenous growth factors. The genetic events underlying this property, such as mutations in the PI3K-Akt and Ras-Erk signaling networks, lead to constitutive activation of mTORC1 in nearly all human cancer lineages. Aberrant activation of mTORC1 has been shown to play a key role for both anabolic tumor growth and resistance to targeted therapeutics. While displaying a growth factor-independent mTORC1 activity and proliferation, tumors cells remain dependent on exogenous nutrients such as amino acids (AAs). AAs are an essential class of nutrients that are obligatory for the survival of any cell. Known as the building blocks of proteins, AAs also act as essential metabolites for numerous biosynthetic processes such as fatty acids, membrane lipids and nucleotides synthesis, as well as for maintaining redox homeostasis. In most tumor types, mTORC1 activity is particularly sensitive to intracellular AA levels. This dependency, therefore, creates a targetable vulnerability point as cancer cells become dependent on AA transporters to sustain their homeostasis. The following review will discuss the role of AA transporters for mTORC1 signaling in cancer cells and their potential as therapeutic drug targets.

Keywords:  ASCT2; LAT1; SNAT2; amino acid transporters; cancer; growth factors; mTORC1; nutrients; xCT

DOI:  https://doi.org/10.3390/ijms22010023
Anal Chem. 2020 Dec 28.

Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labeling in Metabolomics.

Jordi Capellades, Alexandra Junza, Sara Samino, Julia S Brunner, Gernot Schabbauer, Maria Vinaixa, Oscar Yanes.

Isotopic-labeling experiments have been valuable to monitor the flux of metabolic reactions in biological systems, which is crucial to understand homeostatic alterations with disease. Experimental determination of metabolic fluxes can be inferred from a characteristic rearrangement of stable isotope tracers (e.g., 13C or 15N) that can be detected by mass spectrometry (MS). Metabolites measured are generally members of well-known metabolic pathways, and most of them can be detected using both gas chromatography (GC)-MS and liquid chromatography (LC)-MS. In here, we show that GC methods coupled to chemical ionization (CI) MS have a clear advantage over alternative methodologies due to GC's superior chromatography separation efficiency and the fact that CI is a soft ionization technique that yields identifiable protonated molecular ion peaks. We tested diverse GC-CI-MS setups, including methane and isobutane reagent gases, triple quadrupole (QqQ) MS in SIM mode, or selected ion clusters using optimized narrow windows (∼10 Da) in scan mode, and standard full scan methods using high resolution GC-(q)TOF and GC-Orbitrap systems. Isobutane as a reagent gas in combination with both low-resolution (LR) and high-resolution (HR) MS showed the best performance, enabling precise detection of isotopologues in most metabolic intermediates of central carbon metabolism. Finally, with the aim of overcoming manual operations, we developed an R-based tool called isoSCAN that automatically quantifies all isotopologues of intermediate metabolites of glycolysis, TCA cycle, amino acids, pentose phosphate pathway, and urea cycle, from LRMS and HRMS data.

DOI: https://doi.org/10.1021/acs.analchem.0c02998
Beilstein J Org Chem. 2020 ;16 3038-3051

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification.

Steffen Lippold, Arnoud H de Ru, Jan Nouta, Peter A van Veelen, Magnus Palmblad, Manfred Wuhrer, Noortje de Haan.

  Glycoproteomic data are often very complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were developed to facilitate and improve both the identification and quantification of glycopeptides. Here, a selection of these tools was combined and evaluated with the aim of establishing a robust glycopeptide detection and quantification workflow targeting enriched glycoproteins. For this purpose, a tryptic digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography-tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and quantification.

Keywords:  bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry

DOI:  https://doi.org/10.3762/bjoc.16.253
Cell Metab. 2020 Dec 08. pii: S1550-4131(20)30655-0. [Epub ahead of print]

Reductive TCA cycle metabolism fuels glutamine- and glucose-stimulated insulin secretion.

Guo-Fang Zhang, Mette V Jensen, Sarah M Gray, Kimberley El, You Wang, Danhong Lu, Thomas C Becker, Jonathan E Campbell, Christopher B Newgard.

  Metabolic fuels regulate insulin secretion by generating second messengers that drive insulin granule exocytosis, but the biochemical pathways involved are incompletely understood. Here we demonstrate that stimulation of rat insulinoma cells or primary rat islets with glucose or glutamine + 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (Gln + BCH) induces reductive, "counter-clockwise" tricarboxylic acid (TCA) cycle flux of glutamine to citrate. Molecular or pharmacologic suppression of isocitrate dehydrogenase-2 (IDH2), which catalyzes reductive carboxylation of 2-ketoglutarate to isocitrate, results in impairment of glucose- and Gln + BCH-stimulated reductive TCA cycle flux, lowering of NADPH levels, and inhibition of insulin secretion. Pharmacologic suppression of IDH2 also inhibits insulin secretion in living mice. Reductive TCA cycle flux has been proposed as a mechanism for generation of biomass in cancer cells. Here we demonstrate that reductive TCA cycle flux also produces stimulus-secretion coupling factors that regulate insulin secretion, including in non-dividing cells.

Keywords:  NADPH; anaplerosis; insulin secretion; isocitrate dehydrogenase-2; metabolic flux; pancreatic islet β cells; reductive TCA cycle; stable isotopes

DOI:  https://doi.org/10.1016/j.cmet.2020.11.020
Int J Cancer. 2020 Dec 24.

Abrogating GPT2 in triple negative breast cancer inhibits tumor growth and promotes autophagy.

Devina Mitra, Silvia Vega-Rubin-de-Celis, Nadine Royla, Stephan Bernhardt, Heike Wilhelm, Nooraldeen Tarade, Gernot Poschet, Michael Buettner, Ilona Binenbaum, Simone Borgoni, Martina Vetter, Eva Johanna Kantelhardt, Christoph Thomssen, Aristotelis Chatziioannou, Rüdiger Hell, Stefan Kempa, Karin Müller-Decker, Stefan Wiemann.

  Uncontrolled proliferation and altered metabolic reprogramming are hallmarks of cancer. Active glycolysis and glutaminolysis are characteristic features of these hallmarks and required for tumorigenesis. A fine balance between cancer metabolism and autophagy is a prerequisite of homeostasis within cancer cells. Here we show that glutamate pyruvate transaminase 2 (GPT2), which serves as a pivot between glycolysis and glutaminolysis, is highly upregulated in aggressive breast cancers, particularly the triple negative breast cancer (TNBC) subtype. Abrogation of this enzyme results in decreased TCA cycle intermediates, which promotes the rewiring of glucose carbon atoms and alterations in nutrient levels. Concordantly, loss of GPT2 results in an impairment of mechanistic target of rapamycin complex 1 (mTORC1) activity as well as the induction of autophagy. Furthermore, in vivo xenografts studies have shown that autophagy induction correlates with decreased tumor growth and that markers of induced autophagy correlate with low GPT2 levels in patient samples. Taken together, these findings indicate that cancer cells have a close network between metabolic and nutrient sensing pathways necessary to sustain tumorigenesis, and that aminotransferase reactions play an important role in maintaining this balance.

Keywords:  Autophagy; Breast Cancer; Cancer metabolism; GPT2; mTORC1

DOI:  https://doi.org/10.1002/ijc.33456
J Cell Biochem. 2020 Dec 29.

Identification and initial characterization of a potent inhibitor of ferroptosis.

Nishanth Kuganesan, Samkeliso Dlamini, Jade McDaniel, Viranga L M Tillekeratne, William R Taylor.

  Ferroptosis is a form of iron-dependent cell death characterized by elevated lipid peroxides and reactive oxygen species (ROS). Glutathione (GSH) plays an essential role in scavenging ROS to maintain cell viability and acts as a cofactor of GSH peroxidase 4 (GPX4) that protects lipids from oxidation. We have previously described a novel class of small molecules that induce ferroptosis in certain types of cancer cells. These compounds induce ferroptosis by blocking the uptake of cystine required for GSH synthesis. Even though ferroptosis is a well-established form of cell death, signaling pathways that modulate this process are not known. Therefore, we used a panel of growth factors/kinase inhibitors to test effects on ferroptosis induced by our lead compound. We discovered that BMS536924, a dual inhibitor of insulin-like growth and insulin receptors, is a potent inhibitor of ferroptosis. Further investigation indicated that the anti-ferroptotic activity of BMS536924 does not lie in its ability to inhibit insulin signal transduction. Instead, we provide evidence that BMS536924 binds iron, an essential cofactor in ferroptosis. Our results suggest caution in interpreting the effects of BMS536924 in investigations of insulin signaling and uncover a novel ferroptosis inhibitor.

Keywords:  ROS; Xc-; cysteine; cystine; insulin; iron

DOI:  https://doi.org/10.1002/jcb.29870
Mol Cell Proteomics. 2020 Dec 28. pii: mcp.R120.002204. [Epub ahead of print]

The role of Data-Independent Acquisition for Glycoproteomics.

Zilu Ye, Sergey Y Vakhrushev.

  Data independent acquisition (DIA) is now an emerging method in bottom-up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications (PTM), such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O- glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA is briefly introduced. DIA based glycoproteomics is then summarized and described into four aspects based on the actual samples. Lastly, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics.

Keywords:  Data Independent Acquisition; Glycoproteomics; Glycosylation; HCD MS/MS; Mass Spectrometry; OrbiTrap; Post-translational modifications*; SWATH-MS

DOI:  https://doi.org/10.1074/mcp.R120.002204
Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30662-8. [Epub ahead of print]

Non-canonical Glutamate-Cysteine Ligase Activity Protects against Ferroptosis.

Yun Pyo Kang, Andrea Mockabee-Macias, Chang Jiang, Aimee Falzone, Nicolas Prieto-Farigua, Everett Stone, Isaac S Harris, Gina M DeNicola.

  Cysteine is required for maintaining cellular redox homeostasis in both normal and transformed cells. Deprivation of cysteine induces the iron-dependent form of cell death known as ferroptosis; however, the metabolic consequences of cysteine starvation beyond impairment of glutathione synthesis are poorly characterized. Here, we find that cystine starvation of non-small-cell lung cancer cell lines induces an unexpected accumulation of γ-glutamyl-peptides, which are produced due to a non-canonical activity of glutamate-cysteine ligase catalytic subunit (GCLC). This activity is enriched in cell lines with high levels of NRF2, a key transcriptional regulator of GCLC, but is also inducible in healthy murine tissues following cysteine limitation. γ-glutamyl-peptide synthesis limits the accumulation of glutamate, thereby protecting against ferroptosis. These results indicate that GCLC has a glutathione-independent, non-canonical role in the protection against ferroptosis by maintaining glutamate homeostasis under cystine starvation.

Keywords:  GCLC; NRF2; cysteine; cystine; ferroptosis; glutamate; γ-glutamyl

DOI:  https://doi.org/10.1016/j.cmet.2020.12.007
Anal Chem. 2020 Dec 27.

High Coverage Profiling of Carboxylated Metabolites in HepG2 Cells Using Secondary Amine-Assisted Ultrahigh-Performance Liquid Chromatography Coupled to High-Resolution Mass Spectrometry.

Jie Zheng, Ge-Ge Gong, Shu-Jian Zheng, Yu Zhang, Yu-Qi Feng.

Carboxylic metabolites are an important class of metabolites, which widely exist in mammals with various types. Chemical isotope labeling liquid chromatography-mass spectrometry (CIL-LC-MS) has been widely used for the detection of carboxylated metabolites. However, high coverage analysis of carboxylated metabolites in biological samples is still challenging due to improper reactivity and selectivity of labeling reagents to carboxylated metabolites. In this study, we used N-methylphenylethylamine (MPEA) to label various types of carboxylated metabolites including short-chain fatty acids (SCFAs), medium-chain fatty acids (MCFAs), long-chain fatty acids (LCFAs), polycarboxylic acids (polyCAs), amino acids (AAs), and aromatic acids. Additionally, metabolites containing other functional groups, such as phenol, sulfhydryl, and phosphate groups, could not be labeled under the conditions of MPEA labeling. After MPEA labeling, the detection sensitivity of carboxylic acids was increased by 1-2 orders of magnitude, and their chromatographic retention on a reversed-phase (RP) column was enhanced (RT > 3 min). Under optimized labeling conditions, we used MPEA and d3-N-methylphenylethylamine (d3-MPEA) for high coverage screening of carboxylated metabolites in HepG2 cells by ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS). As a result, a total of 403 potential carboxylated metabolites were obtained of which 68 were confirmed based on our established in-house chemically labeled metabolite database (CLMD). SCFAs, MCFAs, LCFAs, polyCAs, AAs, and aromatic acids were all detected in HepG2 cell extracts. Due to the successful identification of AAs, the current method increased the coverage of carboxylated metabolites compared with our previous work. Moreover, 133 and 109 carboxylated metabolites with changed contents were obtained in HepG2 cells incubated with curcumin and R-3-hydroxybutyric acid, respectively. In general, our established method realized high coverage analysis of carboxylated metabolites in HepG2 cells.

DOI: https://doi.org/10.1021/acs.analchem.0c04048
Int J Oncol. 2020 Nov 25.

Critical role of mTOR in regulating aerobic glycolysis in carcinogenesis (Review).

Hui Fan, Yuanyuan Wu, Suyun Yu, Xiaoman Li, Aiyun Wang, Shijun Wang, Wenxing Chen, Yin Lu.

Mammalian target of rapamycin (mTOR) serves an important role in regulating various biological processes, including cell proliferation, metabolism, apoptosis and autophagy. Among these processes, energy metabolism is the dominant process. The metabolism of not only amino acids, fatty acids and lipids, but also that of nucleotides and glucose has been indicated to be regulated by mTOR. Aerobic glycolysis, which is a specific form of glucose metabolism, is prevalent in carcinomas, and it has been considered to be a potential target for cancer therapy. In reviewing the complexity of the mTOR pathway, it is important to elucidate the central role and detailed pathway via which mTOR regulates glycolysis. In the present study, the complex mechanisms via which mTOR regulates aerobic glycolysis were comprehensively reviewed to highlight the potential of drug development via targeting the molecules associated with mTOR and glycolysis and to further provide strategies for the clinical treatment of cancer.

DOI: https://doi.org/10.3892/ijo.2020.5152
Mol Cell. 2020 Dec 22. pii: S1097-2765(20)30904-7. [Epub ahead of print]

Increased demand for NAD+ relative to ATP drives aerobic glycolysis.

Alba Luengo, Zhaoqi Li, Dan Y Gui, Lucas B Sullivan, Maria Zagorulya, Brian T Do, Raphael Ferreira, Adi Naamati, Ahmed Ali, Caroline A Lewis, Craig J Thomas, Stefani Spranger, Nicholas J Matheson, Matthew G Vander Heiden.

  Aerobic glycolysis, or preferential fermentation of glucose-derived pyruvate to lactate despite available oxygen, is associated with proliferation across many organisms and conditions. To better understand that association, we examined the metabolic consequence of activating the pyruvate dehydrogenase complex (PDH) to increase pyruvate oxidation at the expense of fermentation. We find that increasing PDH activity impairs cell proliferation by reducing the NAD+/NADH ratio. This change in NAD+/NADH is caused by increased mitochondrial membrane potential that impairs mitochondrial electron transport and NAD+ regeneration. Uncoupling respiration from ATP synthesis or increasing ATP hydrolysis restores NAD+/NADH homeostasis and proliferation even when glucose oxidation is increased. These data suggest that when demand for NAD+ to support oxidation reactions exceeds the rate of ATP turnover in cells, NAD+ regeneration by mitochondrial respiration becomes constrained, promoting fermentation, despite available oxygen. This argues that cells engage in aerobic glycolysis when the demand for NAD+ is in excess of the demand for ATP.

Keywords:  Aerobic Glycolysis; Cell Metabolism; Fermentation; NAD+; PDK; Warburg Effect

DOI:  https://doi.org/10.1016/j.molcel.2020.12.012
Anal Chim Acta. 2021 Jan 25. pii: S0003-2670(20)31144-2. [Epub ahead of print]1143 124-134

Single cell metabolomics using mass spectrometry: Techniques and data analysis.

Renmeng Liu, Zhibo Yang.

  Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.

Keywords:  Biological variance vs technical variance; Machine learning; Single cell mass spectrometry; Single cell metabolomics; Univariate and multivariate analysis; Vacuum-based and ambient mass spectrometry

DOI:  https://doi.org/10.1016/j.aca.2020.11.020
Ageing Res Rev. 2020 Dec 28. pii: S1568-1637(20)30384-6. [Epub ahead of print] 101249

The role of metabolism in chondrocyte dysfunction and the progression of osteoarthritis.

Linli Zheng, Ziji Zhang, Puyi Sheng, Ali Mobasheri.

  Osteoarthritis (OA) is a degenerative joint disease characterized by low-grade inflammation and high levels of clinical heterogeneity. Aberrant chondrocyte metabolism is a response to changes in the inflammatory microenvironment and may play a key role in cartilage degeneration and OA progression. Under conditions of environmental stress, chondrocytes tend to adapt their metabolism to microenvironmental changes by shifting from one metabolic pathway to another, for example from oxidative phosphorylation to glycolysis. Similar changes occur in other joint cells, including synoviocytes. Switching between these pathways is implicated in metabolic alterations that involve mitochondrial dysfunction, enhanced anaerobic glycolysis, and altered lipid and amino acid metabolism. The shift between oxidative phosphorylation and glycolysis is mainly regulated by the AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR) pathways. Chondrocyte metabolic changes are likely to be a feature of different OA phenotypes. Determining the role of chondrocyte metabolism in OA has revealed key features of disease pathogenesis. Future research should place greater emphasis on immunometabolism and altered metabolic pathways as a means to understand the pathophysiology of age-related OA. This knowledge will advance the development of new drugs against therapeutic targets of metabolic significance.

Keywords:  Osteoarthritis (OA); cartilage; chondrocyte; glycolysis; hypoxia; metabolic dysfunction; metabolism; oxidative phosphorylation; therapeutic

DOI:  https://doi.org/10.1016/j.arr.2020.101249
Cell Metab. 2020 Dec 17. pii: S1550-4131(20)30660-4. [Epub ahead of print]

High Fructose Drives the Serine Synthesis Pathway in Acute Myeloid Leukemic Cells.

Sangmoo Jeong, Angela Maria Savino, Rachel Chirayil, Ersilia Barin, Yuanming Cheng, Sun-Mi Park, Alexandra Schurer, Edouard Mullarky, Lewis C Cantley, Michael G Kharas, Kayvan R Keshari.

  A significant increase in dietary fructose consumption has been implicated as a potential driver of cancer. Metabolic adaptation of cancer cells to utilize fructose confers advantages for their malignant growth, but compelling therapeutic targets have not been identified. Here, we show that fructose metabolism of leukemic cells can be inhibited by targeting the de novo serine synthesis pathway (SSP). Leukemic cells, unlike their normal counterparts, become significantly dependent on the SSP in fructose-rich conditions as compared to glucose-rich conditions. This metabolic program is mediated by the ratio of redox cofactors, NAD+/NADH, and the increased SSP flux is beneficial for generating alpha-ketoglutarate from glutamine, which allows leukemic cells to proliferate even in the absence of glucose. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, dramatically reduces leukemia engraftment in mice in the presence of high fructose, confirming the essential role of the SSP in the metabolic plasticity of leukemic cells.

Keywords:  in vivo isotope tracing; metabolic flux; redox; serine synthesis pathway

DOI:  https://doi.org/10.1016/j.cmet.2020.12.005
Metabolites. 2020 Dec 23. pii: E3. [Epub ahead of print]11(1):

Liquid Chromatography-High-Resolution Mass Spectrometry-Based In Vitro Toxicometabolomics of the Synthetic Cathinones 4-MPD and 4-MEAP in Pooled Human Liver Microsomes.

Sascha K Manier, Florian Schwermer, Lea Wagmann, Niels Eckstein, Markus R Meyer.

  Synthetic cathinones belong to the most often seized new psychoactive substances on an international level. This study investigated the toxicometabolomics, particularly the in vitro metabolism of 2-(methylamino)-1-(4-methylphenyl)-1-pentanone (4-MPD) and 2-(ethylamino)-1-(4-methylphenyl)-1-pentanone (4-MEAP) in pooled human liver microsomes (pHLM) using untargeted metabolomics techniques. Incubations were performed with the substrates in concentrations ranging from 0, 12.5, and 25 µM. Analysis was done by means of high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS/MS) in full scan only and the obtained data was evaluated using XCMS Online and MetaboAnalyst. Significant features were putatively identified using a separate parallel reaction monitoring method. Statistical analysis was performed using Kruskal-Wallis test for prefiltering significant features and subsequent hierarchical clustering, as well as principal component analysis (PCA). Hierarchical clustering or PCA showed a distinct clustering of all concentrations with most of the features z-scores rising with the concentration of the investigated substances. Identification of significant features left many of them unidentified but revealed metabolites of both 4-MPD and 4-MEAP. Both substances formed carboxylic acids, were hydroxylated at the alkyl chain, and formed metabolites after combined hydroxylation and reduction of the cathinone oxo group. 4-MPD additionally formed a dihydroxy metabolite and a hydroxylamine. 4-MEAP was additionally found reduced at the cathinone oxo group, N-dealkylated, and formed an oxo metabolite. These findings are the first to describe the metabolic pathways of 4-MPD and to extend our knowledge about the metabolism of 4-MEAP. Findings, particularly the MS data of the metabolites, are essential for setting up metabolite-based toxicological (urine) screening procedures.

Keywords:  4-MEAP; 4-MPD; HPLC-HRMS/MS; metabolism; untargeted metabolomics

DOI:  https://doi.org/10.3390/metabo11010003
Adv Med Sci. 2020 Dec 24. pii: S1896-1126(20)30045-6. [Epub ahead of print]66(1): 46-51

Identification of novel diagnostic biomarkers in endometrial cancer using targeted metabolomic profiling.

Nejc Kozar, Kristi Kruusmaa, Andraž Dovnik, Marko Bitenc, Rosa Argamasilla, Antonio Adsuar, Nandu Goswami, Iztok Takač, Darja Arko.

   PURPOSE: Endometrial cancer (EC) is the most common gynecological malignancy with high disease burden especially in advanced stages of the disease. Our study investigated the metabolomic profile of EC patient's serum with the aim of identifying novel diagnostic biomarkers that could be used especially in early disease detection.
MATERIAL AND METHODS: Using targeted metabolomic serum profiling based on HPLC-TQ/MS, women with EC (n = 15) and controls (n = 21) were examined for 232 endogenous metabolites.
RESULTS: Top performing biomarkers included ceramides, acylcarnitines and 1-methyl adenosine. Top 4 biomarkers combined achieved 94% sensitivity with 75% specificity with AUC 92.5% (CI 90.5-94.5%). Individual markers also provided significant predictive values: C16-ceramide achieved sensitivity 73%, specificity 81%, AUC 0.83, C22-ceramide sensitivity 67%, specificity 81%, AUC 0.77, hydroxyhexadecenoylcarnitine sensitivity 60%, specificity 96%, AUC 0.76 and 1-methyladenosine sensitivity 67%, specificity 81%, AUC 0.75. The individual markers, however, did not reach the high sensitivity and specificity of the 4-biomarker combination.
CONCLUSIONS: Using mass spectrometry targeted metabolomic profiling, ceramides, acylcarnitines and 1-methyladenosine were identified as potential diagnostic biomarkers for EC. Additionally, these identified metabolites may provide additional insight into cancer cell metabolism.

Keywords:  1-Methyladenosine; Acylcarnitines; Ceramides; Endometrial cancer; Metabolomics

DOI:  https://doi.org/10.1016/j.advms.2020.12.001
Front Mol Biosci. 2020 ;7 604492

Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview.

Philip H Lindhorst, Amanda B Hummon.

  Proteomics, the study of the complete protein composition of a sample, is an important field for cancer research. Changes in the proteome can serve as a biomarker of cancer or lead to the development of a targeted therapy. This minireview will focus on mass spectrometry-based proteomics studies applied specifically to colorectal cancer, particularly the variety of cancer model systems used, including tumor samples, two-dimensional (2D) and three-dimensional (3D) cell cultures such as spheroids and organoids. A thorough discussion of the application of these systems will accompany the review of the literature, as each provides distinct advantages and disadvantages for colorectal cancer research. Finally, we provide conclusions and future perspectives for the application of these model systems to cancer research as a whole.

Keywords:  biomarkers; cell culture; colorectal cancer; mass spectrometry; organoids; proteomics; tumors

DOI:  https://doi.org/10.3389/fmolb.2020.604492
Metabolites. 2020 Dec 25. pii: E8. [Epub ahead of print]11(1):

Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism.

Michiel Bongaerts, Ramon Bonte, Serwet Demirdas, Edwin H Jacobs, Esmee Oussoren, Ans T van der Ploeg, Margreet A E M Wagenmakers, Robert M W Hofstra, Henk J Blom, Marcel J T Reinders, George J G Ruijter.

  Untargeted metabolomics is an emerging technology in the laboratory diagnosis of inborn errors of metabolism (IEM). Analysis of a large number of reference samples is crucial for correcting variations in metabolite concentrations that result from factors, such as diet, age, and gender in order to judge whether metabolite levels are abnormal. However, a large number of reference samples requires the use of out-of-batch samples, which is hampered by the semi-quantitative nature of untargeted metabolomics data, i.e., technical variations between batches. Methods to merge and accurately normalize data from multiple batches are urgently needed. Based on six metrics, we compared the existing normalization methods on their ability to reduce the batch effects from nine independently processed batches. Many of those showed marginal performances, which motivated us to develop Metchalizer, a normalization method that uses 10 stable isotope-labeled internal standards and a mixed effect model. In addition, we propose a regression model with age and sex as covariates fitted on reference samples that were obtained from all nine batches. Metchalizer applied on log-transformed data showed the most promising performance on batch effect removal, as well as in the detection of 195 known biomarkers across 49 IEM patient samples and performed at least similar to an approach utilizing 15 within-batch reference samples. Furthermore, our regression model indicates that 6.5-37% of the considered features showed significant age-dependent variations. Our comprehensive comparison of normalization methods showed that our Log-Metchalizer approach enables the use out-of-batch reference samples to establish clinically-relevant reference values for metabolite concentrations. These findings open the possibilities to use large scale out-of-batch reference samples in a clinical setting, increasing the throughput and detection accuracy.

Keywords:  batch effects; inborn errors of metabolism; internal standards; normalization; untargeted metabolomics

DOI:  https://doi.org/10.3390/metabo11010008
Int J Mol Sci. 2020 Dec 28. pii: E198. [Epub ahead of print]22(1):

Coenzyme Q Depletion Reshapes MCF-7 Cells Metabolism.

Wenping Wang, Irene Liparulo, Nicola Rizzardi, Paola Bolignano, Natalia Calonghi, Christian Bergamini, Romana Fato.

  Mitochondrial dysfunction plays a significant role in the metabolic flexibility of cancer cells. This study aimed to investigate the metabolic alterations due to Coenzyme Q depletion in MCF-7 cells.
METHOD: The Coenzyme Q depletion was induced by competitively inhibiting with 4-nitrobenzoate the coq2 enzyme, which catalyzes one of the final reactions in the biosynthetic pathway of CoQ. The bioenergetic and metabolic characteristics of control and coenzyme Q depleted cells were investigated using polarographic and spectroscopic assays. The effect of CoQ depletion on cell growth was analyzed in different metabolic conditions.
RESULTS: we showed that cancer cells could cope from energetic and oxidative stress due to mitochondrial dysfunction by reshaping their metabolism. In CoQ depleted cells, the glycolysis was upregulated together with increased glucose consumption, overexpression of GLUT1 and GLUT3, as well as activation of pyruvate kinase (PK). Moreover, the lactate secretion rate was reduced, suggesting that the pyruvate flux was redirected, toward anabolic pathways. Finally, we found a different expression pattern in enzymes involved in glutamine metabolism, and TCA cycle in CoQ depleted cells in comparison to controls.
CONCLUSION: This work elucidated the metabolic alterations in CoQ-depleted cells and provided an insightful understanding of cancer metabolism targeting.

Keywords:  bioenergetics; cancer metabolism targeting; coenzyme Q; glutamine metabolism; glycolysis; metabolic reprogramming; mitochondrial dysfunction; spheroids

DOI:  https://doi.org/10.3390/ijms22010198
STAR Protoc. 2021 Mar 19. 2(1): 100235

Profiling of mouse macrophage lipidome using direct infusion shotgun mass spectrometry.

Wei-Yuan Hsieh, Kevin J Williams, Baolong Su, Steven J Bensinger.

  Immune cells, such as macrophages, reprogram their lipid metabolism in response to the activation of pattern recognition receptors (e.g., TLRs, NLRs) and cytokine receptors (e.g., interferons, interleukins). Profiling these changes can be achieved with shotgun mass spectrometry. This protocol provides step-by-step instructions on the generation and stimulation of bone marrow-derived macrophages (BMDMs), sample collection, and lipid extraction for profiling the macrophage lipidome. For complete details on the use and execution of this protocol, please refer to Hsieh et al. (2020).

Keywords:  Cell culture; High Throughput Screening; Immunology; Mass Spectrometry; Metabolism; Model Organisms

DOI:  https://doi.org/10.1016/j.xpro.2020.100235
J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Nov 30. pii: S1570-0232(20)31344-1. [Epub ahead of print]1162 122468

A preliminary study procedure for detection of polyamines in plasma samples as a potential diagnostic tool in prostate cancer.

Donatella Coradduzza, Emanuela Azara, Serenella Medici, Caterina Arru, Tatiana Solinas, Massimo Madonia, Angelo Zinellu, Ciriaco Carru.

   BACKGROUND: Many scientific contributions recognize polyamines as important biomarkers for the diagnosis and treatment of cancer. Several authors have suggested the use of LC/MS instruments as an elective method for their measurement, providing good detection limits and specificity; however, many of these procedures suffer from long chromatographic run times, high detection limits and lengthy and expensive sample pre-treatment steps.
METHODS: UHPLC coupled with high-resolution Orbitrap mass spectrometry (UHPLC/Orbitrap) was set up for the identification and separation ofpolyamines, together with some of their metabolites and catabolites, in the plasma of healthy and prostate cancer human patients. Thirteen metabolites were measured in deproteinized plasma samples through a new analytical approach known as the parallel reaction monitoring (PRM) for targeted quantitative analysis.
RESULTS: The calibration curves were linear and R2 ranged from 0.9913 to 0.9995 for all analytes. LOQ values are between 0.382 and 25 ng mL-1 and LOD values are between 0.109 and 7.421 ng mL-1. The method shows an accuracy and precision for intra-day and inter-day < 15% RSD and R.E.% for all the QC samples. The matrix effect calculated at different concentration levels did not exceed 15%.
CONCLUSIONS: The method developed provides rapid, easy and robust identification and measurement of a wide range of polyamines, and some of their metabolites that can be evaluated as biomarkers to predict the clinical features of prostate cancer patients, avoiding invasive diagnostic procedures.

Keywords:  Biomarkers; Orbitrap mass spectrometer; PRM mode; Plasma polyamines; Prostate cancer; UHPLC

DOI:  https://doi.org/10.1016/j.jchromb.2020.122468
Metabolites. 2020 Dec 18. pii: E514. [Epub ahead of print]10(12):

Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma.

Tom van der Laan, Isabelle Boom, Joshua Maliepaard, Anne-Charlotte Dubbelman, Amy C Harms, Thomas Hankemeier.

  A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91-113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Keywords:  MSALL; SWATH; chromatography; data-independent acquisition; mass spectrometry; metabolomics

DOI:  https://doi.org/10.3390/metabo10120514
Front Oncol. 2020 ;10 599915

How Autophagy Shapes the Tumor Microenvironment in Ovarian Cancer.

Alessandra Ferraresi, Carlo Girone, Andrea Esposito, Chiara Vidoni, Letizia Vallino, Eleonora Secomandi, Danny N Dhanasekaran, Ciro Isidoro.

  Ovarian cancer (OC) is characterized by a high mortality rate due to the late diagnosis and the elevated metastatic potential. Autophagy, a lysosomal-driven catabolic process, contributes to the macromolecular turnover, cell homeostasis, and survival, and as such, it represents a pathway targetable for anti-cancer therapies. It is now recognized that the vascularization and the cellular composition of the tumor microenvironment influence the development and progression of OC by controlling the availability of nutrients, oxygen, growth factors, and inflammatory and immune-regulatory soluble factors that ultimately impinge on autophagy regulation in cancer cells. An increasing body of evidence indicates that OC carcinogenesis is associated, at least in the early stages, to insufficient autophagy. On the other hand, when the tumor is already established, autophagy activation provides a survival advantage to the cancer cells that face metabolic stress and protects from the macromolecules and organelles damages induced by chemo- and radiotherapy. Additionally, upregulation of autophagy may lead cancer cells to a non-proliferative dormant state that protects the cells from toxic injuries while preserving their stem-like properties. Further to complicate the picture, autophagy is deregulated also in stromal cells. Thus, changes in the tumor microenvironment reflect on the metabolic crosstalk between cancer and stromal cells impacting on their autophagy levels and, consequently, on cancer progression. Here, we present a brief overview of the role of autophagy in OC hallmarks, including tumor dormancy, chemoresistance, metastasis, and cell metabolism, with an emphasis on the bidirectional metabolic crosstalk between cancer cells and stromal cells in shaping the OC microenvironment.

Keywords:  autophagy; cancer; cancer associated fibroblasts; cell metabolism; chemoresistance; cytokines; dormancy; inflammatory stroma

DOI:  https://doi.org/10.3389/fonc.2020.599915
Free Radic Biol Med. 2020 Dec 25. pii: S0891-5849(20)31674-9. [Epub ahead of print]163 220-233

ER stress-induced adipocytes secrete-aldo-keto reductase 1B7-containing exosomes that cause nonalcoholic steatohepatitis in mice.

Huihui Gu, Kun Yang, Zhentong Shen, Kai Jia, Ping Liu, Miao Pan, Chao Sun.

  Nonalcoholic steatohepatitis (NASH) is an increasingly prevalent liver disease linked to obesity and associated complications. Endoplasmic reticulum (ER) stress provokes dysfunction in lipid metabolism, which often leads to a progression of obesity-induced hepatic steatosis to NASH. However, the underlying mechanisms in which ER stress in adipose tissue induces hepatic pathology remain elusive. Here, we used male C57BL/6J mice to develop an animal model of NASH induced by a high fat (HFD) diet and methionine- and choline-deficient (MCD) diets. Using a gene-silencing approach with a recombinant lentiviral vector and extensive LC-MS/MS-based proteomics and lipidomics, we demonstrate that the ER stress-induced adipocyte-secreted exosome (ATEx) orchestrates lipid dynamics in the liver. We also noted that ATEx causes hepatic steatosis, inflammation, and fibrosis that lead to NASH through initial accumulation of glycerol and triglycerides in hepatocytes. We also determined that aldo-keto-reductase 1B7 (Akr1b7), a key mediator in liver lipid metabolism, is involved in ATEx-mediated NASH induction. Of note, Akr1b7 deficiency in ER stress-induced ATEx strongly protected the murine liver against HFD and MCD-induced NASH. Our results indicated that ER stress-induced, adipocyte-secreted ATEx triggers NASH by delivering exosomal AKR1B7 to, and elevating glycerol level, in hepatocytes. These findings suggest potential therapeutic strategie that target ATEx to prevent or manage obesity-induced NASH.

Keywords:  Aldo-keto reductase 1B7(Akr1b7); Endoplasmic reticulum stress; Exosomes; Fatty liver; Inflammation; Lipidomics; Metabolic disorder; Nonalcoholic steatohepatitis(NASH); Obesity; Proteomics

DOI:  https://doi.org/10.1016/j.freeradbiomed.2020.12.011
Front Pharmacol. 2020 ;11 595498

Eicosanoids in Cancer: New Roles in Immunoregulation.

Amber M Johnson, Emily K Kleczko, Raphael A Nemenoff.

  Eicosanoids represent a family of active biolipids derived from arachidonic acid primarily through the action of cytosolic phospholipase A2-α. Three major downstream pathways have been defined: the cyclooxygenase (COX) pathway which produces prostaglandins and thromboxanes; the 5-lipoxygenase pathway (5-LO), which produces leukotrienes, lipoxins and hydroxyeicosatetraenoic acids, and the cytochrome P450 pathway which produces epoxygenated fatty acids. In general, these lipid mediators are released and act in an autocrine or paracrine fashion through binding to cell surface receptors. The pattern of eicosanoid production is cell specific, and is determined by cell-specific expression of downstream synthases. Increased eicosanoid production is associated with inflammation and a panel of specific inhibitors have been developed designated non-steroidal anti-inflammatory drugs. In cancer, eicosanoids are produced both by tumor cells as well as cells of the tumor microenvironment. Earlier studies demonstrated that prostaglandin E2, produced through the action of COX-2, promoted cancer cell proliferation and metastasis in multiple cancers. This resulted in the development of COX-2 inhibitors as potential therapeutic agents. However, cardiac toxicities associated with these agents limited their use as therapeutic agents. The advent of immunotherapy, especially the use of immune checkpoint inhibitors has revolutionized cancer treatment in multiple malignancies. However, the majority of patients do not respond to these agents as monotherapy, leading to intense investigation of other pathways mediating immunosuppression in order to develop rational combination therapies. Recent data have indicated that PGE2 has immunosuppressive activity, leading to renewed interest in targeting this pathway. However, little is known regarding the role of other eicosanoids in modulating the tumor microenvironment, and regulating anti-tumor immunity. This article reviews the role of eicosanoids in cancer, with a focus on their role in modulating the tumor microenvironment. While the role of PGE2 will be discussed, data implicating other eicosanoids, especially products produced through the lipoxygenase and cytochrome P450 pathway will be examined. The existence of small molecular inhibitors and activators of eicosanoid pathways such as specific receptor blockers make them attractive candidates for therapeutic trials, especially in combination with novel immunotherapies such as immune checkpoint inhibitors.

Keywords:  T cells; Tumor microenvironment; cancer; eicosanoids; immunosuppression

DOI:  https://doi.org/10.3389/fphar.2020.595498
Nat Rev Mol Cell Biol. 2020 Dec 22.

NAD+ metabolism and its roles in cellular processes during ageing.

Anthony J Covarrubias, Rosalba Perrone, Alessia Grozio, Eric Verdin.

Nicotinamide adenine dinucleotide (NAD+) is a coenzyme for redox reactions, making it central to energy metabolism. NAD+ is also an essential cofactor for non-redox NAD+-dependent enzymes, including sirtuins, CD38 and poly(ADP-ribose) polymerases. NAD+ can directly and indirectly influence many key cellular functions, including metabolic pathways, DNA repair, chromatin remodelling, cellular senescence and immune cell function. These cellular processes and functions are critical for maintaining tissue and metabolic homeostasis and for healthy ageing. Remarkably, ageing is accompanied by a gradual decline in tissue and cellular NAD+ levels in multiple model organisms, including rodents and humans. This decline in NAD+ levels is linked causally to numerous ageing-associated diseases, including cognitive decline, cancer, metabolic disease, sarcopenia and frailty. Many of these ageing-associated diseases can be slowed down and even reversed by restoring NAD+ levels. Therefore, targeting NAD+ metabolism has emerged as a potential therapeutic approach to ameliorate ageing-related disease, and extend the human healthspan and lifespan. However, much remains to be learnt about how NAD+ influences human health and ageing biology. This includes a deeper understanding of the molecular mechanisms that regulate NAD+ levels, how to effectively restore NAD+ levels during ageing, whether doing so is safe and whether NAD+ repletion will have beneficial effects in ageing humans.

DOI: https://doi.org/10.1038/s41580-020-00313-x
Mol Metab. 2020 Dec 22. pii: S2212-8778(20)30224-6. [Epub ahead of print] 101150

Hepatic synthesis of triacylglycerols containing medium-chain fatty acids is dominated by diacylglycerol acyltransferase 1 and efficiently inhibited by etomoxir.

Klaus Wunderling, Christina Leopold, Isabell Jamitzky, Mohamed Yaghmour, Fabian Zink, Dagmar Kratky, Christoph Thiele.

OBJECTIVE: Medium-chain fatty acids (MCFAs) play an increasing role in human nutrition. In the liver, one fraction is used for synthesis of MCFA-containing triacylglycerol (MCFA-TG), the rest is used for oxidative energy production or ketogenesis. We investigated which enzymes catalyze the synthesis of MCFA-TG and how inhibition of MCFA-TG synthesis or fatty acid (FA) oxidation influences the metabolic fate of the MCFAs.
METHODS: Fatty acid metabolism was followed by time-resolved tracing of alkyne-labeled FAs in freshly isolated mouse hepatocytes. Quantitative data were obtained by mass spectrometry of several hundred labeled lipid species. Wildtype hepatocytes as well as cells from diacylglycerol acyltransferase (DGAT)1-/- mice were treated with inhibitors against DGAT1, DGAT2, or FA β-oxidation.
RESULTS: Inhibition or deletion of DGAT1 resulted in a reduction of MCFA-TG synthesis by 70%, while long-chain (LC)FA-TG synthesis was reduced by 20%. In contrast, DGAT2 inhibition increased MCFA-TG formation by 50%, while LCFA-TG synthesis was reduced by 5-25%. Inhibition of β-oxidation by the specific inhibitor teglicar strongly increased MCFA-TG synthesis. In contrast, the widely used β-oxidation inhibitor etomoxir blocked MCFA-TG synthesis, phenocopying DGAT1 inhibition.
CONCLUSIONS: DGAT1 is the major enzyme for hepatic MCFA-TG synthesis. Its loss can only partially be compensated by DGAT2. Specific inhibition of β-oxidation gives rise to a compensatory increase in MCFA-TG synthesis, whereas etomoxir blocks both β-oxidation and MCFA-TG synthesis, indicating a strong off-target effect on DGAT1.

DOI: https://doi.org/10.1016/j.molmet.2020.101150
Talanta. 2021 Mar 01. pii: S0039-9140(20)31159-0. [Epub ahead of print]224 121868

Simultaneous determination of methionine cycle metabolites, urea cycle intermediates and polyamines in serum, urine and intestinal tissue by using UHPLC-MS/MS.

Xiuli Su, Xiaona Li, Haojiang Wang, Zongwei Cai.

  Metabolites of methionine cycle, urea cycle and polyamine metabolism play important roles in regulating the metabolic processes and the development of diseases. It is rewarding and interesting to monitor the levels of the above metabolites in biological matrices to investigate pathological mechanisms. However, their quantitation is still unsatisfactory due to the poor retention behavior of the analytes on the traditional reversed-phase column. And never a single analytical method simultaneously quantify these three classes of metabolites. Besides, the concentrations of some metabolites are too low to be detected in the biological samples. In this study, we developed a UHPLC-ESI-MS/MS method to simultaneously determine the levels of 14 metabolites, including 4 methionine metabolism metabolites (methionine, homocysteine, S-adenosylmethionine and S-adenosylhomocysteine), 3 urea cycle intermediates (arginine, citrulline and ornithine) and 7 polyamines (putrescine, spermidine, spermine, N1-acetylputrescine, N1-acetylspermidine, N1-acetylspermine and N1,N12-diacetylspermine). The chromatographic separation was performed on the BEH amide column within 14 min using water and acetonitrile (both with 0.1% formic acid) as the mobile phases. The results of method validation showed good selectivity, linearity (r2 > 0.99), recovery (93.1%-112.1%), inter-day and intra-day precision (RSD < 13.6% and RSD < 11.0%, respectively), stability (RSD < 15.1%) and matrix effect (76.0%-113.2%). The method is simple, quick and sensitive without derivatization processes and the use of ion-pairing reagents. This approach was successfully applied in urine, serum and tissue matrices, as well as in identifying potential biomarkers for hyperthyroidism and hypothyroidism. The method is promising to provide more information on pathophysiological mechanisms in metabolomics study.

Keywords:  Biological matrices; Methionine cycle metabolites; Polyamines; Thyroid disorder; UHPLC-MS/MS; Urea cycle intermediates

DOI:  https://doi.org/10.1016/j.talanta.2020.121868