bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2023–01–22
28 papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh
  1. Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics.
  2. Lipidomics Analysis with Triple Quadrupole Mass Spectrometry.
  3. Analysis of Lipid Contents in Human Trabecular Meshwork Cells by Multiple Reaction Monitoring (MRM) Profiling Lipidomics.
  4. Accurate Analysis of Lipid Building Blocks Using the Tool LipidOne.
  5. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps.
  6. High-Resolution Liquid Chromatography-Mass Spectrometry for Lipidomics.
  7. Acetyl-CoA metabolism in cancer.
  8. Quantification of Endocannabinoids from Biological Samples Using Liquid Chromatography-Tandem Mass Spectrometry.
  9. Rapid Analysis of Plasmalogen Individual Species by High-Resolution Mass Spectrometry.
  10. Protocol and Methods Applicable to Retinal Vascular Diseases.
  11. Characterization of Gangliosides from Mouse Optic Nerve Samples Using Mass Spectrometry.
  12. Downloading and Analysis of Metabolomic and Lipidomic Data from Metabolomics Workbench Using MetaboAnalyst 5.0.
  13. Isolation of Mitochondrial Lipids and Mass Spectrometric Analysis.
  14. Mass Spectrometry Approaches for Detection and Determination of Prostaglandins from Biological Samples.
  15. Analysis of Cholesterol Lipids Using Gas Chromatography Mass Spectrometry.
  16. Untargeted Analysis of Lipids Containing Very Long Chain Fatty Acids in Retina and Retinal Tight Junctions.
  17. Frontiers in mass spectrometry-based clinical proteomics for cancer diagnosis and treatment.
  18. Recent advances in kinase signaling network profiling by mass spectrometry.
  19. Metabolic Adjustments following Glutaminase Inhibition by CB-839 in Glioblastoma Cell Lines.
  20. Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles.
  21. Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry.
  22. Analysis and Annotation of Phospholipids by Mass Spectrometry-Based Metabolomics.
  23. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease.
  24. Metabolic deuterium oxide (D2O) labeling in quantitative omics studies: A tutorial review.
  25. Fundamental Role of Pentose Phosphate Pathway within the Endoplasmic Reticulum in Glutamine Addiction of Triple-Negative Breast Cancer Cells.
  26. Analyses and Localization of Phosphatidylcholine and Phosphatidylserine in Murine Ocular Tissue Using Imaging Mass Spectrometry.
  27. Lipid Extraction and Sample Preservation Techniques for Stable Isotope Analysis and Ecological Assays.
  28. Comprehensive lipidome of human plasma using minimal sample manipulation by liquid chromatography coupled with mass spectrometry.
  1. Methods Mol Biol. 2023 ;2625 89-102
    Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics.
    Mads Møller Foged, Kenji Maeda, Mesut Bilgin.
      The emerging field of lipidomics presents the systems biology approach to identify and quantify the full lipid repertoire of cells, tissues, and organisms. The importance of the lipidome is demonstrated by a number of biological studies on dysregulation of lipid metabolism in human diseases such as cancer, diabetes, and neurodegenerative diseases. Exploring changes and regulations in the huge networks of lipids and their metabolic pathways requires a lipidomics methodology: advanced mass spectrometry that resolves the complexity of the lipidome. Here, we report a comprehensive protocol of quantitative shotgun lipidomics that enables identification and quantification of hundreds of molecular lipid species, covering a wide range of lipid classes, extracted from cultured mammalian cells.
    Keywords:  Lipid extraction; Lipidome profiling; Lipidomics; Mammalian cells; Mass spectrometry; Quantification; Shotgun lipidomics; Systems biology
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_8
  2. Methods Mol Biol. 2023 ;2625 103-106
    Lipidomics Analysis with Triple Quadrupole Mass Spectrometry.
    Meher A Saleem, Anna Mueller, Sanjoy K Bhattacharya.
      Lipids serve an essential role in multiple cellular functions including signaling, metabolism, energy storage, and membrane constitution. Lipidomics, the study of lipids using analytical chemistry, allows for the study of disease states and cellular metabolism. Shotgun lipidomics is a technique that involves direct-infusion electrospray ionization (ESI) and analysis with a triple quadrupole mass spectrometer. Triple quadrupole mass spectrometry is ideally suited for lipidomics analysis because it allows for class-specific identification of lipids. Individual lipid class can be identified by the adjustment of three parameters-collision energy, ion mode, and scan type. This chapter describes the use of a triple quadrupole mass spectrometer, the TSQ Quantum Access MAX, to perform lipidomics analysis with high sensitivity, accuracy, and precision.
    Keywords:  Lipidomics; Lipids; Mass spectrometry; Shotgun lipidomics; Triple quadrupole mass spectrometry
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_9
  3. Methods Mol Biol. 2023 ;2625 291-298
    Analysis of Lipid Contents in Human Trabecular Meshwork Cells by Multiple Reaction Monitoring (MRM) Profiling Lipidomics.
    Ting Wang, Padmanabhan Paranji Pattabiraman.
      Lipids are among the major constituents of cells and play many important cellular functions. Lipid levels in the trabecular meshwork (TM) aqueous humor outflow pathway play an important role in the maintenance of aqueous humor drainage and intraocular pressure (IOP) homeostasis. Therefore, it is important to characterize the changes in the lipid contents in the aqueous humor outflow pathway tissues to better understand their functional significance in the maintenance of IOP. The multiple reaction monitoring (MRM)-based profiling aids in the analysis of the metabolome as a collection of functional groups and is utilized as an exploratory metabolomics and lipidomics approach. The MRM-based profiling utilizes tandem mass spectrometry experiments carried out on a commercial triple quadrupole mass spectrometer with three aligned quadrupole mass filters (Q1, Q2, and Q3). This screening methodology can be utilized for targeted lipidomics screening. This chapter focuses on the methodology for isolation and culturing of the TM cells, lipid extraction, and the MRM-based lipidomics approach with data analysis.
    Keywords:  Human trabecular meshwork cell culture; Human trabecular meshwork dissection; Lipid content analysis; Lipid extraction; Multiple reaction monitoring (MRM) profiling lipidomics
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_24
  4. Methods Mol Biol. 2023 ;2625 323-336
    Accurate Analysis of Lipid Building Blocks Using the Tool LipidOne.
    Roberto Maria Pellegrino, Matteo Giulietti, Husam B R Alabed, Anna Aurora Taddei, Sandra Buratta, Lorena Urbanelli, Francesco Piva, Carla Emiliani.
      LC/MS-based analysis techniques combined with specialized lipid platforms allow the qualitative and quantitative determination of thousands of lipid molecules. Each individual molecule can be considered as an assembly of smaller parts, often called building blocks that are the result of a myriad of biochemical synthesis and transformation processes. LipidOne is a new lipidomic tool that automatically highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and between experimental groups. Thanks to LipidOne, the discovered differences among lipid building blocks can be easily linked to the activity of specific enzymes.
    Keywords:  Lipid building blocks; Lipid chains; Lipidomics
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_27
  5. Cancers (Basel). 2023 Jan 16. pii: 555. [Epub ahead of print]15(2):
    Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps.
    Paula Carrillo-Rodriguez, Frode Selheim, Maria Hernandez-Valladares.
      The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
    Keywords:  bioinformatics; data analysis; data-dependent acquisition (DDA); data-independent acquisition (DIA); mass spectrometry; proteomics; sample preparation; workflows
    DOI:  https://doi.org/10.3390/cancers15020555
  6. Methods Mol Biol. 2023 ;2625 57-63
    High-Resolution Liquid Chromatography-Mass Spectrometry for Lipidomics.
    Faith Christine Harvey, Vanessa Collao, Sanjoy K Bhattacharya.
      Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is a powerful tool for identification and classification of lipids. Ultra-high performance liquid chromatography (UHPLC) allows for robust separations of complex mixtures, while high-resolution mass spectrometry (HRMS) identifies compounds with efficiency and accuracy (Zullig T and Kofeler HC, Mass Spectrom Rev 40:162-176, 2021). The high specificity and sensitivity of mass spectrometry makes it the method of choice when analyzing lipids (Kofeler HC, J Lipid Res 62:100138, 2021). Untargeted mass spectrometry identifies all lipids within a sample and is useful for identification and further discovery. This chapter describes the use of a Q Exactive mass spectrometer to perform an untargeted LC-MS/MS lipidomics analysis.
    Keywords:  Lipidomics; Mass spectrometry; Ultra-high performance liquid chromatography
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_4
  7. Nat Rev Cancer. 2023 Jan 19.
    Acetyl-CoA metabolism in cancer.
    David A Guertin, Kathryn E Wellen.
      Few metabolites can claim a more central and versatile role in cell metabolism than acetyl coenzyme A (acetyl-CoA). Acetyl-CoA is produced during nutrient catabolism to fuel the tricarboxylic acid cycle and is the essential building block for fatty acid and isoprenoid biosynthesis. It also functions as a signalling metabolite as the substrate for lysine acetylation reactions, enabling the modulation of protein functions in response to acetyl-CoA availability. Recent years have seen exciting advances in our understanding of acetyl-CoA metabolism in normal physiology and in cancer, buoyed by new mouse models, in vivo stable-isotope tracing approaches and improved methods for measuring acetyl-CoA, including in specific subcellular compartments. Efforts to target acetyl-CoA metabolic enzymes are also advancing, with one therapeutic agent targeting acetyl-CoA synthesis receiving approval from the US Food and Drug Administration. In this Review, we give an overview of the regulation and cancer relevance of major metabolic pathways in which acetyl-CoA participates. We further discuss recent advances in understanding acetyl-CoA metabolism in normal tissues and tumours and the potential for targeting these pathways therapeutically. We conclude with a commentary on emerging nodes of acetyl-CoA metabolism that may impact cancer biology.
    DOI:  https://doi.org/10.1038/s41568-022-00543-5
  8. Methods Mol Biol. 2023 ;2625 115-127
    Quantification of Endocannabinoids from Biological Samples Using Liquid Chromatography-Tandem Mass Spectrometry.
    Zhiying Wang, Chenglin Mo, Lynda Bonewald, Marco Brotto.
      Endocannabinoids (eCBs) are a family of lipid molecules with important regulatory function in the brain and immune system. The two well-studied eCBs are arachidonic acid derivatives, N-arachidonoylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG). Currently one of the most important methods for quantitative analysis of eCBs and related lipids from biological matrices is liquid chromatographic separation coupled with tandem mass spectroscopy (LC-MS/MS) owing to its high sensitivity and selectivity, as well as no derivatization procedures needed. Here we describe pretreatment procedures using solid-phase extraction for tissue sampling and an in vivo brain microdialysis approach prior to LC-MS/MS analysis, followed by detailed steps of LC-MS/MS analytic method to demonstrate the potential and application of this method in quantification of eCBs and congeners from various biological matrices.
    Keywords:  Brain; Endocannabinoids (eCBs); LC-MS/MS; Microdialysis; Serum; Skeletal muscle; Solid-phase extraction
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_11
  9. Methods Mol Biol. 2023 ;2625 259-267
    Rapid Analysis of Plasmalogen Individual Species by High-Resolution Mass Spectrometry.
    Glenda Vasku, Niyazi Acar, Olivier Berdeaux.
      Analysis and quantification of ether-lipid phospholipid species-also known as plasmalogens-is a crucial step in the study of the biological functions played by these lipids. Application of analytical separation methods and high-resolution mass spectrometry has gained much attention in this regard, while resolution issues and time-consuming sequences interfered with these advances. Herein, we describe a simple and rapid method for the analysis of plasmalogen (Pl) species by HILIC-HRMS. This method is able to identify and quantify relative levels of ethanolamine-plasmalogens (PlsEtn) and choline-plasmalogens (PlsCho) in biological matrices such as whole blood, plasma, erythrocytes, and also retina. Moreover, we provide a detailed and modified lipid extraction method that is applicable to almost all biological matrices.
    Keywords:  Annotation; Hydrophilic interaction liquid chromatography (HILIC); Lipid extraction; Mass spectrometry (MS); Plasmalogens (Pls)
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_22
  10. Methods Mol Biol. 2023 ;2625 71-78
    Protocol and Methods Applicable to Retinal Vascular Diseases.
    Saurabh Kumar, Manjunath B Joshi, Inderjeet Kaur.
      Lipidomics is a branch of omics biology that enables the characterization and determination of different lipid classes. Mass spectrometry is a widely used tool to identify and obtain qualitative and quantitative measurements of the range of lipid species in various cell/tissue types. Human retina is highly rich in different classes of lipids that are liable to undergo modification such as oxidation, isomerization, peroxidation, and hydroxylation due to continuous metabolic activity in response to light photons. Alterations in lipid metabolism are associated with retinal diseases such as age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity. However, a clear understanding on the type of lipids/alterations involved in these diseases is not established yet. The unavailability of suitable biological retinal tissue need for this research has prompted us to explore vitreous humor and tear film for studying lipidomic alterations in different ocular diseases. Subjecting the lipid extract to tandem mass spectrometry further gives qualitative and quantitative lipidome of the diseased tissue. While the mass spectrometry approaches for lipid profiling have been adequately described, the present chapter focusses on a simplified protocol for extracting sufficient lipids/metabolites from vitreous humor and tear samples obtained from patients and their subsequent mass spectrometry analysis.
    Keywords:  LC-MS/MS; Lipidome profiling; Retinal vascular diseases; Tear film; Vitreous humor
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_6
  11. Methods Mol Biol. 2023 ;2625 65-69
    Characterization of Gangliosides from Mouse Optic Nerve Samples Using Mass Spectrometry.
    Jennifer Arcuri, Sanjoy K Bhattacharya.
      This chapter focuses on identifying gangliosides in the optic nerve of the mouse using mass spectrometry techniques. The described protocol will also permit the characterization of the sample's lipidome. Two deuterium-labeled ganglioside standards and a general lipid class standard will be utilized for extraction efficiency and quantification. Using reversed-phase high-performance liquid chromatography (HPLC) coupled to a Q Exactive mass spectrometer, the samples will be analyzed. The method will consist of both an untargeted approach and a targeted approach with a ganglioside-specific inclusion list.
    Keywords:  Gangliosides; Lipidomics; Mass spectrometry; Optic nerve
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_5
  12. Methods Mol Biol. 2023 ;2625 313-321
    Downloading and Analysis of Metabolomic and Lipidomic Data from Metabolomics Workbench Using MetaboAnalyst 5.0.
    Ashley Howell, Charles Yaros.
      Advances in computational and data processing technology have enabled the development of many novel tools for analyzing metabolomic and lipidomic data. These advances involved the catalyst for the creation of publicly accessible complex web-based databases such as the Metabolomics Workbench. Open Source internet-based software packages such as MetaboAnalyst 5.0 enable researchers to perform a wide range of analyte identification and statistical analyses of their own and other researchers' data in order to identify biomarkers and classify compounds. In this paper, we set forth a protocol for obtaining experimental data of interest from a public data repository (Metabolomics Workbench), converting the data into a format suitable for submission to MetaboAnalyst 5.0, and then uploading the data to the MetaboAnalyst server for identification and statistical analysis.
    Keywords:  Lipidomics; MetaboAnalyst; Metabolomics; Metabolomics Workbench; Statistical analysis
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_26
  13. Methods Mol Biol. 2023 ;2625 1-6
    Isolation of Mitochondrial Lipids and Mass Spectrometric Analysis.
    Alexa M Jauregui, Zoé M Cubero Cortés, Sean D Meehan, Sanjoy K Bhattacharya.
      Mitochondria participate in many important metabolic processes in the body. The lipid profile of mitochondria is especially important in membrane regulation and pathway signaling. The isolation and study of these lipids can provide unparalleled information about the mechanisms behind these cellular processes. In this chapter, we describe a protocol to isolate mitochondrial lipids from homogenized murine optic nerves. The lipid extraction was performed using butanol-methanol (BUME) and subsequently analyzed using liquid chromatography-mass spectrometry. Further analysis of the raw data was conducted using LipidSearch™ and MetaboAnalyst 4.0.
    Keywords:  Lipidomics; Liquid chromatography; Mitochondrial lipids; Neurodegeneration; mass spectrometry
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_1
  14. Methods Mol Biol. 2023 ;2625 299-311
    Mass Spectrometry Approaches for Detection and Determination of Prostaglandins from Biological Samples.
    Zhiying Wang, Chenglin Mo, Kamal Awad, Lynda Bonewald, Marco Brotto.
      Accurate determination of prostaglandins (PGs) from biological samples is critical for understanding their biological functions and interactions during physiological and pathological processes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a highly sensitive, accurate, and high-throughput approach for simultaneous detection of ultra-trace PGs from a single biological sample. Here we describe LC-MS/MS techniques and related sample pretreatment methods including both off-line and on-line SPE for the determination of PGs in biological samples.
    Keywords:  LC–MS/MS; Prostaglandins; Restricted access media (RAM)-based on-line SPE-LC-MS/MS; Sample preparation; Solid phase extraction
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_25
  15. Methods Mol Biol. 2023 ;2625 141-148
    Analysis of Cholesterol Lipids Using Gas Chromatography Mass Spectrometry.
    Emily J Neag, Vanessa Collao, Sanjoy K Bhattacharya.
      An optimized Bligh and Dyer protocol and subsequent derivatization is described in this chapter for the extraction of free cholesterol and cholesterol esters from tissue samples. Quantification analysis of lipid species is then described utilizing gas chromatography-mass spectrometry, the ideal method for analysis of volatile organic compounds and extraction of sterols.
    Keywords:  Bligh and Dyer extraction; Cholesterol; Derivatization; Gas chromatography–mass spectrometry; Lipidomic; Optic tissue
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_13
  16. Methods Mol Biol. 2023 ;2625 269-290
    Untargeted Analysis of Lipids Containing Very Long Chain Fatty Acids in Retina and Retinal Tight Junctions.
    Julia V Busik, Hannah Decot, Anna B Lin, Todd A Lydic.
      Several recent studies suggest that C24-C38 very long chain fatty acids (VLCFA) play an important role in vision, and decreased levels of retina VLCFA have been associated with vision disorders including the onset and progression of diabetic retinopathy in animal models. Traditional methods for VLCFA analysis lack the sensitivity and specificity needed to enable detailed characterization of VLCFA incorporation into complex lipids in tissues and subcellular components. To assess whether decreased VLCFA in diabetic retina are directly implicated in diabetes-induced breakdown of the blood-retinal barrier, we demonstrated the utility of performing untargeted lipid analysis via Orbitrap high resolution/accurate mass MS and MS/MS-based shotgun lipidomics to identify structural lipids containing VLCFA substituents. This comprehensive and highly sensitive approach to untargeted lipid identification enabled us to characterize low-abundance sphingolipids containing very long chain fatty acids from isolated retinal tight junction complexes, as well as VLCFA-containing phospholipids in retinal tissues. To facilitate future biochemical and physiological studies of the roles of VLCFA in blood-retina barrier integrity and maintenance of vision, this chapter describes steps to isolate tight junction complexes from a cell culture model of the outer blood-retinal barrier and perform untargeted Orbitrap high resolution/accurate mass-based lipid analysis to identify VLCFA in tight junctions and retina tissue.
    Keywords:  Blood-retina barrier; Diabetic retinopathy; ELOVL4; High resolution/accurate mass spectrometry; Lipidomics; Retina; Tight junction; Very long chain fatty acids
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_23
  17. Cancer Sci. 2023 Jan 20.
    Frontiers in mass spectrometry-based clinical proteomics for cancer diagnosis and treatment.
    Yoshimi Haga, Yuriko Minegishi, Koji Ueda.
      Numerous omics studies, primarily genomics analyses, have been conducted to fully understand the molecular biological characteristics of cancer. In recent years, the depth of proteomic analysis, which comprehensively analyzes proteins and molecules that function directly in vivo, has increased dramatically. Proteomics using mass spectrometry (MS) is a promising technology to directly examine proteoforms, including post-translational modifications and variants originating from genomic aberrations. Recent advances in MS-based proteomics have enabled direct, in depth, and quantitative analysis of the expression levels of various cancer-related proteins, as well as their cancer specific proteoforms, and proteins that fluctuate with cancer initiation and progression in cell lines and tissue samples. Additionally, the integration of proteomic data with genomic, epigenomic, and transcriptomic data has formed the growing field of proteogenomics, which is already yielding new biological and diagnostic knowledge. Deep proteomic profiling provides clinically useful information in various aspects, including understanding the mechanisms of cancer development and progression and discovering targets for diagnosis and drug development. Furthermore, it is expected to make a significant contribution to the promotion of personalized medicine. In this review, recent advances and impacts in MS-based clinical proteomics are highlighted with a focus on oncology.
    Keywords:  Biomarker; cancer; glycoproteomics; mass spectrometry; proteogenomics
    DOI:  https://doi.org/10.1111/cas.15731
  18. Curr Opin Chem Biol. 2023 Jan 17. pii: S1367-5931(22)00145-4. [Epub ahead of print]73 102260
    Recent advances in kinase signaling network profiling by mass spectrometry.
    Giulia Franciosa, Marie Locard-Paulet, Lars J Jensen, Jesper V Olsen.
      Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.
    Keywords:  Kinase; Phosphoproteomics; Phosphorylation; Signaling
    DOI:  https://doi.org/10.1016/j.cbpa.2022.102260
  19. Cancers (Basel). 2023 Jan 15. pii: 531. [Epub ahead of print]15(2):
    Metabolic Adjustments following Glutaminase Inhibition by CB-839 in Glioblastoma Cell Lines.
    Juan De Los Santos-Jiménez, Tracy Rosales, Bookyung Ko, José A Campos-Sandoval, Francisco J Alonso, Javier Márquez, Ralph J DeBerardinis, José M Matés.
      Most tumor cells can use glutamine (Gln) for energy generation and biosynthetic purposes. Glutaminases (GAs) convert Gln into glutamate and ammonium. In humans, GAs are encoded by two genes: GLS and GLS2. In glioblastoma, GLS is commonly overexpressed and considered pro-oncogenic. We studied the metabolic effects of inhibiting GLS activity in T98G, LN229, and U87MG human glioblastoma cell lines by using the inhibitor CB-839. We performed metabolomics and isotope tracing experiments using U-13C-labeled Gln, as well as 15N-labeled Gln in the amide group, to determine the metabolic fates of Gln carbon and nitrogen atoms. In the presence of the inhibitor, the results showed an accumulation of Gln and lower levels of tricarboxylic acid cycle intermediates, and aspartate, along with a decreased oxidative labeling and diminished reductive carboxylation-related labeling of these metabolites. Additionally, CB-839 treatment caused decreased levels of metabolites from pyrimidine biosynthesis and an accumulation of intermediate metabolites in the de novo purine nucleotide biosynthesis pathway. The levels of some acetylated and methylated metabolites were significantly increased, including acetyl-carnitine, trimethyl-lysine, and 5-methylcytosine. In conclusion, we analyzed the metabolic landscape caused by the GLS inhibition of CB-839 in human glioma cells, which might lead to the future development of new combination therapies with CB-839.
    Keywords:  CB-839; aspartate; cancer; cancer metabolism; citrate; glioblastoma; glutaminase; glutamine; metabolic reprogramming; metabolomics
    DOI:  https://doi.org/10.3390/cancers15020531
  20. Adv Clin Chem. 2023 ;pii: S0065-2423(22)00071-3. [Epub ahead of print]112 119-153
    Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles.
    Xiaofeng Wu, Anton B Iliuk, W Andy Tao.
      We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.
    Keywords:  Extracellular vesicle; Liquid chromatography/mass spectrometry; Nucleic acid; Phosphoproteomics; Protein; Proteomics; Tissue/liquid biopsy
    DOI:  https://doi.org/10.1016/bs.acc.2022.09.003
  21. Anal Chim Acta. 2023 Feb 08. pii: S0003-2670(23)00016-8. [Epub ahead of print]1241 340795
    Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry.
    Zhuanghao Hou, Liujuan Zhan, Kaiming Cao, Moujun Luan, Xinchen Wang, Buchun Zhang, Likun Ma, Hao Yin, Zhicheng Liu, Yangzhong Liu, Guangming Huang.
      Direct observation of metabolites in living cells by mass spectrometry offers a bright future for biological studies but also suffers a severe challenge to untargeted peak assignment to tentative metabolite candidates. In this study, we developed a method combining stable isotope tracing and induced electrospray mass spectrometry for living-cells metabolite measurement and identification. By using 13C6-glucose and ammonium chloride-15N as the sole carbon and nitrogen sources for cell culture, Escherichia coli synthesized metabolites with 15N and 13C elements. Tracing the number of carbon and nitrogen atoms could offer a complementary dimension for candidate peak searching. As a result, the identification confidence of metabolites achieved a universal improvement based on carbon/nitrogen labelling and filtration.
    Keywords:  Induced electrospray mass spectrometry; Living cell measurement; Metabolite identification; Metabolite profiling; Peak assignment
    DOI:  https://doi.org/10.1016/j.aca.2023.340795
  22. Methods Mol Biol. 2023 ;2625 79-88
    Analysis and Annotation of Phospholipids by Mass Spectrometry-Based Metabolomics.
    Álvaro González-Domínguez, María Santos-Martín, Ana Sayago, Alfonso María Lechuga-Sancho, Ángeles Fernández-Recamales, Raúl González-Domínguez.
      Phospholipids are essential components of membrane lipid bilayers and serve as precursors of multiple signaling molecules, so alterations in their homeostasis are associated with the pathogenesis of numerous diseases. In this context, the application of mass spectrometry-based metabolomics has demonstrated great potential to comprehensively characterize the human phospholipidome. In this chapter, we describe an untargeted method for the determination of phospholipids and other related metabolites in a variety of biological matrices, including plasma/serum, erythrocytes, and tissues, based on the combination of high-throughput direct mass spectrometry fingerprinting and subsequent profiling by ultra-high-performance reversed-phase liquid chromatography coupled to mass spectrometry. Furthermore, we also review the characteristic fragmentation patterns of phospholipids with the aim of providing simple guidelines for their straightforward annotation.
    Keywords:  Annotation; Direct infusion; Liquid chromatography; Mass spectrometry; Metabolomics; Phospholipids
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_7
  23. Inflamm Bowel Dis. 2023 Jan 20. pii: izac281. [Epub ahead of print]
    Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease.
    NIDDK IBD Genetics Consortium, iGenoMed Consortium
       BACKGROUND: There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation.
    METHODS: We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients.
    RESULTS: We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location.
    CONCLUSIONS: Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.
    Keywords:  Crohn’s disease; comprehensive untargeted lipidomics; lipid biomarkers; subtype stratification
    DOI:  https://doi.org/10.1093/ibd/izac281
  24. Anal Chim Acta. 2023 Feb 15. pii: S0003-2670(22)01293-4. [Epub ahead of print]1242 340722
    Metabolic deuterium oxide (D2O) labeling in quantitative omics studies: A tutorial review.
    Jonghyun Kim, Seungwoo Seo, Tae-Young Kim.
      Mass spectrometry (MS) is an invaluable tool for sensitive detection and characterization of individual biomolecules in omics studies. MS combined with stable isotope labeling enables the accurate and precise determination of quantitative changes occurring in biological samples. Metabolic isotope labeling, wherein isotopes are introduced into biomolecules through biosynthetic metabolism, is one of the main labeling strategies. Among the precursors employed in metabolic isotope labeling, deuterium oxide (D2O) is cost-effective and easy to implement in any biological systems. This tutorial review aims to explain the basic principle of D2O labeling and its applications in omics research. D2O labeling incorporates D into stable C-H bonds in various biomolecules, including nucleotides, proteins, lipids, and carbohydrates. Typically, D2O labeling is performed at low enrichment of 1%-10% D2O, which causes subtle changes in the isotopic distribution of a biomolecule, instead of the complete separation between labeled and unlabeled samples in a mass spectrum. D2O labeling has been employed in various omics studies to determine the metabolic flux, turnover rate, and relative quantification. Moreover, the advantages and challenges of D2O labeling and its future prospects in quantitative omics are discussed. The economy, versatility, and convenience of D2O labeling will be beneficial for the long-term omics studies for higher organisms.
    Keywords:  Deuterium oxide; Metabolic labeling; Omics; Relative quantification; Turnover rate
    DOI:  https://doi.org/10.1016/j.aca.2022.340722
  25. Antioxidants (Basel). 2022 Dec 26. pii: 43. [Epub ahead of print]12(1):
    Fundamental Role of Pentose Phosphate Pathway within the Endoplasmic Reticulum in Glutamine Addiction of Triple-Negative Breast Cancer Cells.
    Cecilia Marini, Vanessa Cossu, Sonia Carta, Elisa Greotti, Daniela Gaglio, Nadia Bertola, Sabrina Chiesa, Silvia Bruno, Francesca Vitale, Marcella Bonanomi, Danilo Porro, Mattia Riondato, Anna Maria Orengo, Matteo Bauckneht, Silvia Morbelli, Silvia Ravera, Gianmario Sambuceti.
      Cancer utilization of large glutamine equivalents contributes to diverging glucose-6-P flux toward the pentose phosphate shunt (PPP) to feed the building blocks and the antioxidant responses of rapidly proliferating cells. In addition to the well-acknowledged cytosolic pathway, cancer cells also run a largely independent PPP, triggered by hexose-6P-dehydrogenase within the endoplasmic reticulum (ER), whose activity is mandatory for the integrity of ER-mitochondria networking. To verify whether this reticular metabolism is dependent on glutamine levels, we complemented the metabolomic characterization of intermediates of the glucose metabolism and tricarboxylic acid cycle with the estimation of proliferating activity, energy metabolism, redox damage, and mitochondrial function in two breast cancer cell lines. ER-PPP activity and its determinants were estimated by the ER accumulation of glucose analogs. Glutamine shortage decreased the proliferation rate despite increased ATP and NADH levels. It depleted NADPH reductive power and increased malondialdehyde content despite a marked increase in glucose-6P-dehydrogenase. This paradox was explained by the deceleration of ER-PPP favored by the decrease in hexose-6P-dehydrogenase expression coupled with the opposite response of its competitor enzyme glucose-6P-phosphatase. The decreased ER-PPP activity eventually hampered mitochondrial function and calcium exchanges. These data configure the ER-PPP as a powerful, unrecognized regulator of cancer cell metabolism and proliferation.
    Keywords:  18F-fluoro-deoxy-glucose; breast cancer; calcium flux; endoplasmic reticulum; endoplasmic reticulum–mitochondria network; glutamine metabolism; hexose-6-phosphate-dehydrogenase; pentose phosphate pathway; redox balance
    DOI:  https://doi.org/10.3390/antiox12010043
  26. Methods Mol Biol. 2023 ;2625 149-161
    Analyses and Localization of Phosphatidylcholine and Phosphatidylserine in Murine Ocular Tissue Using Imaging Mass Spectrometry.
    Varun Krishnan, Sean D Meehan, Colin Hayter, Sanjoy K Bhattacharya.
      Imaging mass spectrometry (IMS) allows for spatial visualization of proteins, lipids, and metabolite distributions in a tissue. Identifying these compounds through mass spectrometry, combined with mapping the compound distribution in the sample in a targeted or untargeted approach, renders IMS a powerful tool for lipidomics. IMS analysis for lipid species such as phosphatidylcholine and phosphatidylserine allows researchers to pinpoint areas of lipid deficiencies or accumulations associated with ocular disorders such as age-related macular degeneration and diabetic retinopathy. Here, we describe an end-to-end IMS approach from sample preparation to data analysis for phosphatidylcholine and phosphatidylserine analysis.
    Keywords:  AP/MALDI; High-resolution mass spectrometry; Imaging mass spectrometry; Lipid localization; Phosphatidylcholine; Phosphatidylserine
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_14
  27. Methods Mol Biol. 2023 ;2625 241-257
    Lipid Extraction and Sample Preservation Techniques for Stable Isotope Analysis and Ecological Assays.
    Kyle H Elliott, James D Roth, Kevin Crook, David Yurkowski.
      Lipid extraction is an important component of many ecological and ecotoxicological measurements. For instance, percent lipid is often used as a measure of body condition, under the assumption that those individuals with higher lipid reserves are healthier. Likewise, lipids are depleted in 13C compared with protein, and it is consequently a routine to remove lipids prior to measuring carbon isotopes in ecological studies so that variation in lipid content does not obscure variation in diet. We provide detailed methods for two different protocols for lipid extraction: Soxhlet apparatus and manual distillation. We also provide methods for polar and non-polar solvents. Neutral (non-polar) solvents remove some lipids but few non-lipid compounds whereas polar solvents remove not only most lipids but also many non-lipid compounds. We discuss each of the methods and provide guidelines for best practices. We recommend that for stable isotope analysis, researchers test for a relationship between the change in the carbon stable isotope ratio and the amount of lipid extracted to see if the degree of extraction has an impact on isotope ratios. Stable isotope analysis is widely used by ecologists, and we provide a detailed methodology that minimizes known biases.
    Keywords:  Diet reconstruction; Ecophysiology; Ecotoxicology; Lipid extraction; Neutral lipids; Polar lipids; Soxhlet apparatus; Stable isotope analysis
    DOI:  https://doi.org/10.1007/978-1-0716-2966-6_21
  28. Rapid Commun Mass Spectrom. 2023 Jan 18. e9472
    Comprehensive lipidome of human plasma using minimal sample manipulation by liquid chromatography coupled with mass spectrometry.
    Bebiana C Sousa, Zulema Gonzalez Klein, Diane Taylor, Greg West, Aveline Neo Huipeng, Michael J O Wakelam, Andrea F Lopez-Clavijo.
      The present work shows a comprehensive chromatographic methods and MS conditions that have been developed according to the chemical properties of each lipid subclass to detect low abundance molecular species. This manuscript shows that the developed methods can detect low and/or very low-abundant lipids like phosphatidic acid (PA) in the glycerophospholipids method, dhCer, dhSPB in the ceramides method, and LPA, LPI, LPG, SPBP in the lysolipids method. Abundant lipid subclasses in human plasma are chromatographically separated from low abundance lipids prior to detection, avoiding the need for derivatisation. Lipid subclasses from the de novo lipogenesis and sphingolipids pathways are presented in this work. Three chromatographic methods here were implemented using a tertiary pumping system to allow for the inclusion of a gradient for analyte separation using A and B pumps, while an isocratic wash elutes interfering compounds. The isocratic wash enabled elution of lipid subclasses not targeted within the method that would otherwise cause background signal in the subsequent sample injection and reduction in column lifetime. Four chromatographic methods coupled with mass spectrometry using targeted and untargeted approaches to separate high and low abundance lipid subclasses are described here. An optimised extraction method for lysolipids is also used in addition to Folch extraction in human plasma.
    DOI:  https://doi.org/10.1002/rcm.9472
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