bims-mascan 2021-09-26 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021‒09‒26
fifteen papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

SnapShot: Cancer metabolism.
AlphaTims: Indexing trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization.
Lipid metabolism in sickness and in health: Emerging regulators of lipotoxicity.
Multiplexed analysis of amino acids in mice brain microdialysis samples using isobaric labeling and liquid chromatography-high resolution tandem mass spectrometry.
Rapid analysis of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) isotopologues in stable isotope-resolved metabolomics (SIRM) using direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS).
Moonlighting functions of metabolic enzymes and metabolites in cancer.
A glutamine 'tug-of-war': targets to manipulate glutamine metabolism for cancer immunotherapy.
NAD+ flux is maintained in aged mice despite lower tissue concentrations.
Significance of glutathione peroxidase 4 and intracellular iron level in ovarian cancer cells-"utilization" of ferroptosis mechanism.
Glucose Metabolism and Glucose Transporters in Breast Cancer.
In-silico-library-based method enables rapid and comprehensive annotation of cardiolipins and cardiolipin oxidation products using high resolution tandem mass spectrometer.
Supply and demand: Cellular nutrient uptake and exchange in cancer.
Linkage-selective derivatization for glycosylation site- and glycoform-specific characterization of sialic acid isomers using mass spectrometry.
3D and 4D Tumorigenesis Model for the Quantitative Analysis of Cancer Cell Behavior and Screening for Anticancer Drugs.
Untargeted metabolomics in primary murine bone marrow stromal cells reveals distinct profile throughout osteoblast differentiation.

Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00501-3. [Epub ahead of print]81(18): 3878-3878.e1

SnapShot: Cancer metabolism.

Julia S Brunner, Lydia W S Finley.

Metabolic networks support cancer cell survival, proliferation, and malignant progression. Cancer cells take up large amounts of nutrients such as glucose and glutamine whose metabolism provides the energy, reducing equivalents, and biosynthetic precursors required to meet the biosynthetic demands of proliferation. Intermediates of glycolysis and the tricarboxylic acid (TCA) cycle provide critical building blocks for synthesis of non-essential amino acids, nucleotides, and fatty acids. To view this SnapShot, open or download the PDF.

DOI: https://doi.org/10.1016/j.molcel.2021.06.021
Mol Cell Proteomics. 2021 Sep 17. pii: S1535-9476(21)00121-3. [Epub ahead of print] 100149

AlphaTims: Indexing trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization.

Sander Willems, Eugenia Voytik, Patricia Skowronek, Maximilian T Strauss, Matthias Mann.

High resolution mass spectrometry-based proteomics generates large amounts of data, even in the standard liquid chromatography (LC) - tandem mass spectrometry configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich data sets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole time-of-flight platform (Q-TOF) as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS) and microseconds (TOF). In our open source AlphaTims package, data are indexed, accessed and visualized by a combination of tools of the scientific Python ecosystem. We interpret unprocessed data as a sparse 4D matrix and use just-in-time compilation to machine code with Numba, accelerating our computational procedures by several orders of magnitude while keeping to familiar indexing and slicing notations. For samples with more than six billion detector events, a modern laptop can load and index raw data in about a minute. Loading is even faster when AlphaTims has already saved indexed data in a HDF5 file, a portable scientific standard used in extremely large-scale data acquisition. Subsequently, data accession along any dimension and interactive visualization happen in milliseconds. We have found AlphaTims to be a key enabling tool to explore high dimensional LC-TIMS-QTOF data and have made it freely available as an open-source Python package with a stand-alone graphical user interface at https://github.com/MannLabs/alphatims or as part of the AlphaPept 'ecosystem'.

DOI: https://doi.org/10.1016/j.mcpro.2021.100149
Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00694-8. [Epub ahead of print]81(18): 3708-3730

Lipid metabolism in sickness and in health: Emerging regulators of lipotoxicity.

Haejin Yoon, Jillian L Shaw, Marcia C Haigis, Anna Greka.

  Lipids play crucial roles in signal transduction, contribute to the structural integrity of cellular membranes, and regulate energy metabolism. Questions remain as to which lipid species maintain metabolic homeostasis and which disrupt essential cellular functions, leading to metabolic disorders. Here, we discuss recent advances in understanding lipid metabolism with a focus on catabolism, synthesis, and signaling. Technical advances, including functional genomics, metabolomics, lipidomics, lipid-protein interaction maps, and advances in mass spectrometry, have uncovered new ways to prioritize molecular mechanisms mediating lipid function. By reviewing what is known about the distinct effects of specific lipid species in physiological pathways, we provide a framework for understanding newly identified targets regulating lipid homeostasis with implications for ameliorating metabolic diseases.

Keywords:  cancer; cellular metabolism; free fatty acids (FFAs); lipid metabolism; lipidomics; lipids; lipotoxicity; obesity; triacylglycerol accumulation

DOI:  https://doi.org/10.1016/j.molcel.2021.08.027
J Chromatogr A. 2021 Sep 07. pii: S0021-9673(21)00661-0. [Epub ahead of print]1656 462537

Multiplexed analysis of amino acids in mice brain microdialysis samples using isobaric labeling and liquid chromatography-high resolution tandem mass spectrometry.

Juho Heininen, Ulrika Julku, Timo Myöhänen, Tapio Kotiaho, Risto Kostiainen.

  We developed a new multiplexed reversed phase liquid chromatography-high resolution tandem mass spectrometric (LC-MS/MS) method. The method is based on isobaric labeling with a tandem mass tag (TMT10-plex) and stable isotope-labeled internal standards, and was used to analyze amino acids in mouse brain microdialysis samples. The TMT10-plex labeling of amino acids allowed analysis of ten samples in one LC-MS/MS run, significantly increasing the sample throughput. The method provides good chromatographic performance (peak half-width between 0.04-0.12 min), allowing separation of all TMT-labeled amino acids with acceptable resolution and high sensitivity (limits of detection typically around 10 nM). The use of stable isotope-labeled internal standards, together with TMT10-plex labeling, ensured good repeatability (relative standard deviation ≤ 12.1 %) and linearity (correlation coefficient > 0.994), indicating good quantitative performance of the multiplexed method. The method was applied to study the effect of d-amphetamine microdialysis perfusion on amino acid concentrations in the mouse brain. All amino acids were reliably detected and quantified, indicating that the method is sensitive enough to detect low concentrations of amino acids in brain microdialysis samples.

Keywords:  Amino acids; High resolution tandem mass spectrometry; Isobaric labeling; Isotope dilution; Metabolites; Multiplexing

DOI:  https://doi.org/10.1016/j.chroma.2021.462537
Anal Chim Acta. 2021 Oct 09. pii: S0003-2670(21)00699-1. [Epub ahead of print]1181 338873

Rapid analysis of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) isotopologues in stable isotope-resolved metabolomics (SIRM) using direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS).

JoonSeon Yang, Teresa W M Fan, Jason A Brandon, Andrew N Lane, Richard M Higashi.

  S-Adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are important metabolites in the one-carbon cycle that modulates cellular methylation required for proliferation and epigenetic regulation. Their concentrations, synthesis, and turnover are difficult to determine conveniently and reliably. We have developed such a method by coupling a simple and rapid purification scheme that efficiently captures both compounds, with high sensitivity, sample throughput direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS). This method is compatible with Stable Isotope-Resolved Metabolomic (SIRM) analysis of numerous other metabolites. The limits of detection for both SAM and SAH were <1 nM, and the linearity range was up to 1000 nM. The method was first illustrated for SAM/SAH analysis of mouse livers, and lung adenocarcinoma A549 cells. We then applied the method to track 13C1-CH3-Met incorporation into SAM and 13C6-glucose transformation into SAM and SAH via de novo synthesis. We further used the method to show the distinct effects on A549 and H1299 cells with treatment of anti-cancer methylseleninic acid (MSA), selenite, and selenomethionine, notably SAM depletion and increased SAM to SAH ratio by MSA, which implicates altered epigenetic regulation.

Keywords:  DI-nESI-UHR-FTMS; Methylseleninic acid; S-adenosylhomocysteine; S-adenosylmethionine; Selenite; Stable isotope-resolved metabolomics

DOI:  https://doi.org/10.1016/j.aca.2021.338873
Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00698-5. [Epub ahead of print]81(18): 3760-3774

Moonlighting functions of metabolic enzymes and metabolites in cancer.

Chaoyun Pan, Bo Li, M Celeste Simon.

The growing field of tumor metabolism has greatly expanded our knowledge of metabolic reprogramming in cancer. Apart from their established roles, various metabolic enzymes and metabolites harbor non-canonical ("moonlighting") functions to support malignant transformation. In this article, we intend to review the current understanding of moonlighting functions of metabolic enzymes and related metabolites broadly existing in cancer cells by dissecting each major metabolic pathway and its regulation of cellular behaviors. Understanding these non-canonical functions may broaden the horizon of the cancer metabolism field and uncover novel therapeutic vulnerabilities in cancer.

DOI: https://doi.org/10.1016/j.molcel.2021.08.031
Immunother Adv. 2021 Jan;1(1): ltab010

A glutamine 'tug-of-war': targets to manipulate glutamine metabolism for cancer immunotherapy.

Laura J Pallett, Sarah Dimeloe, Linda V Sinclair, Adam J Byrne, Anna Schurich.

  Within the tumour microenvironment (TME), there is a cellular 'tug-of-war' for glutamine, the most abundant amino acid in the body. This competition is most evident when considering the balance between a successful anti-tumour immune response and the uncontrolled growth of tumour cells that are addicted to glutamine. The differential effects of manipulating glutamine abundance in individual cell types is an area of intense research and debate. Here, we discuss some of the current strategies in development altering local glutamine availability focusing on inhibition of enzymes involved in the utilisation of glutamine and its uptake by cells in the TME. Further studies are urgently needed to complete our understanding of glutamine metabolism, to provide critical insights into the pathways that represent promising targets and for the development of novel therapeutic strategies for the treatment of advanced or drug resistant cancers.

Keywords:  T cells; cancer immunotherapy; glutamine

DOI:  https://doi.org/10.1093/immadv/ltab010
Cell Syst. 2021 Sep 16. pii: S2405-4712(21)00338-0. [Epub ahead of print]

NAD+ flux is maintained in aged mice despite lower tissue concentrations.

Melanie R McReynolds, Karthikeyani Chellappa, Eric Chiles, Connor Jankowski, Yihui Shen, Li Chen, Hélène C Descamps, Sarmistha Mukherjee, Yashaswini R Bhat, Siddharth R Lingala, Qingwei Chu, Paul Botolin, Faisal Hayat, Tomohito Doke, Katalin Susztak, Christoph A Thaiss, Wenyun Lu, Marie E Migaud, Xiaoyang Su, Joshua D Rabinowitz, Joseph A Baur.

  NAD+ is an essential coenzyme for all living cells. NAD+ concentrations decline with age, but whether this reflects impaired production or accelerated consumption remains unclear. We employed isotope tracing and mass spectrometry to probe age-related changes in NAD+ metabolism across tissues. In aged mice, we observed modest tissue NAD+ depletion (median decrease ∼30%). Circulating NAD+ precursors were not significantly changed, and isotope tracing showed the unimpaired synthesis of nicotinamide from tryptophan. In most tissues of aged mice, turnover of the smaller tissue NAD+ pool was modestly faster such that absolute NAD+ biosynthetic flux was maintained, consistent with more active NAD+-consuming enzymes. Calorie restriction partially mitigated age-associated NAD+ decline by decreasing consumption. Acute inflammatory stress induced by LPS decreased NAD+ by impairing synthesis in both young and aged mice. Thus, the decline in NAD+ with normal aging is relatively subtle and occurs despite maintained NAD+ production, likely due to increased consumption.

Keywords:  CD38; NAD; NADH; PARP; PARP1; SIRT1; aging; flux; mononucleotide; niacin; nicotinamide; redox; riboside; sirtuins

DOI:  https://doi.org/10.1016/j.cels.2021.09.001
Inflamm Res. 2021 Sep 19.

Significance of glutathione peroxidase 4 and intracellular iron level in ovarian cancer cells-"utilization" of ferroptosis mechanism.

Dingxi Li, Mengli Zhang, Hongtu Chao.

  OBJECTIVE AND DESIGN: Ovarian cancer is the major cause of death in gynecologic diseases worldwide. Ferroptosis, a nonapoptotic form of cell death, is featured by accumulation of iron-based lipid peroxidation. The elevated iron level and malondialdehyde (MDA) in ovarian cancer cells suggest more vulnerable to ferroptosis, nevertheless, ferroptosis is not observed in ovarian cancer cells. Glutathione peroxidase 4 (GPX4) is a critical regulator of ferroptosis.METHODS: We determined whether GPX4 knockdown could induce ferroptosis to prevent cell proliferation in ovarian cancer. Human ovarian cancer cells and normal human ovarian epithelial cell line IOSE-80 were cultured and administrated with deferoxamine (DFO) or ferric ammonium citrate (FAC). GPX4 knockdown was established for investigating the functions of GPX4 in ovarian cancer cells and in tumor xenograft mice.
RESULTS: A positively correlation was showed among the levels of GPX4, iron and cell proliferation. Chelation of intracellular iron by DFO disrupted intracellular iron level and was detrimental to ovarian cancer cell survival. FAC-induced elevation of intracellular iron inhibited proliferation, aggravated apoptosis, boosted inflammation and suppressed lipid peroxide reducibility in ovarian cancer cells. Knockdown of GPX4 had similar effects with FAC in ovarian cancer cells. Inhibition of GPX4 suppressed tumor growth, induced ferroptosis, accelerated cell apoptosis, reduced Fe3+ accumulation and suppressed lipid peroxide reducibility in tumor bearing mice.
CONCLUSION: We demonstrate the significance of GPX4 and intracellular iron level in ovarian cancer cells. Importantly, inhibition of GPX4 interferes with both intracellular iron homeostasis and lipid peroxide reducibility, inducing ferroptosis and exerting anti-cancer effect, which can be a potential effective strategy for ovarian cancer therapy.

Keywords:  Ferroptosis; Glutathione peroxidase 4; Iron; Malondialdehyde; Ovarian cancer

DOI:  https://doi.org/10.1007/s00011-021-01495-6
Front Cell Dev Biol. 2021 ;9 728759

Glucose Metabolism and Glucose Transporters in Breast Cancer.

Eunah Shin, Ja Seung Koo.

  Breast cancer is the most common malignancy in women worldwide and is associated with high mortality rates despite the continuously advancing treatment strategies. Glucose is essential for cancer cell metabolism owing to the Warburg effect. During the process of glucose metabolism, various glycolytic metabolites, such as serine and glycine metabolites, are produced and other metabolic pathways, such as the pentose phosphate pathway (PPP), are associated with the process. Glucose is transported into the cell by glucose transporters, such as GLUT. Breast cancer shows high expressions of glucose metabolism-related enzymes and GLUT, which are also related to breast cancer prognosis. Triple negative breast cancer (TNBC), which is a high-grade breast cancer, is especially dependent on glucose metabolism. Breast cancer also harbors various stromal cells such as cancer-associated fibroblasts and immune cells as tumor microenvironment, and there exists a metabolic interaction between these stromal cells and breast cancer cells as explained by the reverse Warburg effect. Breast cancer is heterogeneous, and, consequently, its metabolic status is also diverse, which is especially affected by the molecular subtype, progression stage, and metastatic site. In this review, we will focus on glucose metabolism and glucose transporters in breast cancer, and we will additionally discuss their potential applications as cancer imaging tracers and treatment targets.

Keywords:  breast cancer; glucose metabolism; glucose transporter; pentose phosphate pathway; serine/glycine pathway

DOI:  https://doi.org/10.3389/fcell.2021.728759
Anal Chim Acta. 2021 Oct 02. pii: S0003-2670(21)00705-4. [Epub ahead of print]1180 338879

In-silico-library-based method enables rapid and comprehensive annotation of cardiolipins and cardiolipin oxidation products using high resolution tandem mass spectrometer.

Yu He, Binghuan Yuan, Yao Lu, Xia Zhao, Cunsi Shen, Jianjian Ji, Lili Lin, Jianya Xu, Tong Xie, Jinjun Shan.

  Accumulated evidences suggest that cardiolipins (CLs) and cardiolipin oxidation products (oxCLs) are a class of essential molecules that play critical roles in many physiological functions. Diversity of four acyl chains leads to high structure complexity for cardiolipin species including CLs, monolysocardiolipins (MLCLs) and their oxCLs. The ability to rapidly identify CL species can be implemented by the match of mass spectrometry (MS)-based in-silico spectral database. In this study, after optimizing the chromatography conditions and MS detection, an in-silico library containing 377,754 simulated tandem mass spectra deducing from 31,578 CLs to 52,160 of MLCLs was successfully augmented based on LipidBlast templates. For the construction of the oxCLs' library, twenty-five fatty acyls oxidation products relating to nine oxidation types were permuted and combined. A total of 42,180 oxCL spectra were predicted based on the experimental measurements of oxCLs forming by artificially oxidation. Applying the in-silico database to murine mitochondria and cell samples enabled the sensitive and comprehensive annotation of 86 MLCLs, 307 CLs and 112 oxCLs with high annotation confidence. Compared to the conventional method, our proposed in-silico database provides a more comprehensive interpretation for CL species' characterization with high throughput and sensitivity in nontarget lipidomic study.

Keywords:  Cardiolipin; Cardiolipin oxidation products; In-silico database; Mass spectrometry

DOI:  https://doi.org/10.1016/j.aca.2021.338879
Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00693-6. [Epub ahead of print]81(18): 3731-3748

Supply and demand: Cellular nutrient uptake and exchange in cancer.

Vasileios Papalazarou, Oliver D K Maddocks.

  Nutrient supply and demand delineate cell behavior in health and disease. Mammalian cells have developed multiple strategies to secure the necessary nutrients that fuel their metabolic needs. This is more evident upon disruption of homeostasis in conditions such as cancer, when cells display high proliferation rates in energetically challenging conditions where nutritional sources may be scarce. Here, we summarize the main routes of nutrient acquisition that fuel mammalian cells and their implications in tumorigenesis. We argue that the molecular mechanisms of nutrient acquisition not only tip the balance between nutrient supply and demand but also determine cell behavior upon nutrient limitation and energetic stress and contribute to nutrient partitioning and metabolic coordination between different cell types in inflamed or tumorigenic environments.

Keywords:  SLC proteins; amino acid; cancer; nutrient scavenging; nutrient transport; nutrient transporters

DOI:  https://doi.org/10.1016/j.molcel.2021.08.026
Chem Commun (Camb). 2021 Sep 21. 57(75): 9590-9593

Linkage-selective derivatization for glycosylation site- and glycoform-specific characterization of sialic acid isomers using mass spectrometry.

Ye Peng, Bing Gu, Zhenyu Sun, Yueyue Li, Ying Zhang, Haojie Lu.

Here, we developed a linkage-selective derivatization approach for the differentiation and relative quantification of α-2,3- and α-2,6-linked sialic acids in a site- and glycoform-specific manner. Linkage-selective derivatization with isotope molecules discriminates the isomeric glycopeptides easily using MS and provided a tool for biomarker discovery using the quantitative analysis of isomeric glycopeptides.

DOI: https://doi.org/10.1039/d1cc04142h
Methods Mol Biol. 2022 ;2364 299-318

3D and 4D Tumorigenesis Model for the Quantitative Analysis of Cancer Cell Behavior and Screening for Anticancer Drugs.

Deborah Wessels, Daniel F Lusche, Edward Voss, David R Soll.

  Cancer cells from cell lines and tumor biopsy tissue undergo aggregation and aggregate coalescence when dispersed in a 3D Matrigel™ matrix. Coalescence is a dynamic process mediated by a subset of cells within the population of cancer cells. In contrast, non-tumorigenic cells from normal cell lines and normal tissues do not aggregate or coalesce, nor do they possess the motile cell types that orchestrate coalescence of cancer cells. Therefore, coalescence is a cancer cell-specific phenotype that may drive tumor growth in vivo, especially in cases of field cancerization. Here, we describe a simple 3D tumorigenesis model that takes advantage of the coalescence capabilities of cancer cells and uses this feature as the basis for a screen for treatments that inhibit tumorigenesis. The screen is especially useful in testing monoclonal antibodies that target cell-cell interactions, cell-matrix interactions, cell adhesion molecules, cell surface receptors, and general cell surface markers. The model can also be used for 2D imaging in a 96-well plate for rapid screening and is adaptable for 3D high-resolution assessment. In the latter case, we show how the 3D model can be optically sectioned with differential interference contrast (DIC) optics, then reconstructed in 4D and quantitatively analyzed by computer-assisted methods, or, alternatively, imaged with confocal microscopy for 4D quantitative analysis of cancer cell interactions with normal cells within the tumor microenvironment. We demonstrate reconstructions and quantitative analyses using the advanced image analysis software J3D-DIAS 4.2, in order to illustrate the types of detailed phenotypic characterizations that have proven useful. Other software packages may be able to perform similar types of analyses.

Keywords:  3D model; Cancer therapy drug screen; Cell migration; Coalescence; Monoclonal antibody; Tumorigenesis

DOI:  https://doi.org/10.1007/978-1-0716-1661-1_14
Metabolomics. 2021 Sep 18. 17(10): 86

Untargeted metabolomics in primary murine bone marrow stromal cells reveals distinct profile throughout osteoblast differentiation.

Biswapriya B Misra, Shobana Jayapalan, Alison K Richards, Ron C M Helderman, Elizabeth Rendina-Ruedy.

  INTRODUCTION: Skeletal homeostasis is an exquisitely regulated process most directly influenced by bone resorbing osteoclasts, bone forming osteoblasts, and the mechano-sensing osteocytes. These cells work together to constantly remodel bone as a mechanism to prevent from skeletal fragility. As such, when an individual experiences a disconnect in these tightly coupled processes, fracture incidence increases, such as during ageing, gonadal hormone deficiency, weightlessness, and diabetes. While therapeutic options have significantly aided in the treatment of low bone mineral density (BMD) or osteoporosis, limited options remain for anabolic or bone forming agents. Therefore, it is of interest to continue to understand how osteoblasts regulate their metabolism to support the energy expensive process of bone formation.OBJECTIVE: The current project sought to rigorously characterize the distinct metabolic processes and intracellular metabolite profiles in stromal cells throughout osteoblast differentiation using untargeted metabolomics.
METHODS: Primary, murine bone marrow stromal cells (BMSCs) were characterized throughout osteoblast differentiation using standard staining protocols, Seahorse XFe metabolic flux analyses, and untargeted metabolomics.
RESULTS: We demonstrate here that the metabolic footprint of stromal cells undergoing osteoblast differentiation are distinct, and while oxidative phosphorylation drives adenosine triphosphate (ATP) generation early in the differentiation process, mature osteoblasts depend on glycolysis. Importantly, the intracellular metabolite profile supports these findings while also suggesting additional pathways critical for proper osteoblast function.
CONCLUSION: These data are the first of their kind to characterize these metabolites in conjunction with the bioenergetic profile in primary, murine stromal cells throughout osteoblast differentiation and provide provocative targets for future investigation.

Keywords:  ATP; Bioenergetics; Bone; LC–MS/MS; Metabolism; Metabolomics

DOI:  https://doi.org/10.1007/s11306-021-01829-9