bims-mascan 2021-07-25 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–07–25
eleven papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh

How the amino acid leucine activates the key cell-growth regulator mTOR.
Spatially resolved sampling for untargeted metabolomics: A new tool for salivomics.
tRNA Modifications as a Readout of S and Fe-S Metabolism.
Metabolic Drivers of Invasion in Glioblastoma.
Amino acid metabolism as a therapeutic target in cancer: a review.
Lipidomics reveals carnitine palmitoyltransferase 1C protects cancer cells from lipotoxicity and senescence.
Arginine Signaling and Cancer Metabolism.
Fatty acids and evolving roles of their proteins in neurological, cardiovascular disorders and cancers.
Lactate and glutamine support NADPH generation in cancer cells under glucose deprived conditions.
Single-cell analysis defines a pancreatic fibroblast lineage that supports anti-tumor immunity.
Bridging the Polar and Hydrophobic Metabolome in Single-Run Untargeted Liquid Chromatography-Mass Spectrometry Dried Blood Spot Metabolomics for Clinical Purposes.

Nature. 2021 Jul 21.

How the amino acid leucine activates the key cell-growth regulator mTOR.

Tibor Vellai.



Keywords:  Cancer; Cell biology; Metabolism

DOI:  https://doi.org/10.1038/d41586-021-01943-7
iScience. 2021 Jul 23. 24(7): 102768

Spatially resolved sampling for untargeted metabolomics: A new tool for salivomics.

Alessio Ciurli, Maximiliam Liebl, Rico J E Derks, Jacques J C Neefjes, Martin Giera.

  Saliva is a complex bodily fluid composed of metabolites secreted by major and minor glands, as well as by-products of host oral cells, oral bacteria, gingival crevicular fluid, and exogenous compounds. Major salivary glands include the paired parotid, submandibular, and sublingual glands. The secreted fluids of the salivary glands vary in composition, flow rate, site of release, and clearance suggesting that different types of saliva fulfill different functions and therefore can provide unique biological information. Consequently, for the comprehension of the functionality of the salivary components, spatially resolved investigations are warranted. To understand and comprehensively map the highly heterogeneous environment of the oral cavity, advanced spatial sampling techniques for metabolomics analysis are needed. Here, we present a systematic evaluation of collection devices for spatially resolved sampling aimed at untargeted metabolomics and propose a comprehensive and reproducible collection and analysis protocol for the spatially resolved analysis of the human oral metabolome.

Keywords:  Liquid chromatography and tandem mass spectrometry; Saliva; Salivomics; Spatially resolved sampling; Untargeted metabolomics

DOI:  https://doi.org/10.1016/j.isci.2021.102768
Methods Mol Biol. 2021 ;2353 137-154

tRNA Modifications as a Readout of S and Fe-S Metabolism.

Ashley M Edwards, Maame A Addo, Patricia C Dos Santos.

  Iron-Sulfur (Fe-S) clusters function as core prosthetic groups known to modulate the activity of metalloenzymes, act as trafficking vehicles for biological iron and sulfur, and participate in several intersecting metabolic pathways. The formation of these clusters is initiated by a class of enzymes called cysteine desulfurases, whose primary function is to shuttle sulfur from the amino acid L-cysteine to a variety of sulfur transfer proteins involved in Fe-S cluster synthesis as well as in the synthesis of other thiocofactors. Thus, sulfur and Fe-S cluster metabolism are connected through shared enzyme intermediates, and defects in their associated pathways cause a myriad of pleiotropic phenotypes, which are difficult to dissect. Post-transcriptionally modified transfer RNA (tRNA) represents a large class of analytes whose synthesis often requires the coordinated participation of sulfur transfer and Fe-S enzymes. Therefore, these molecules can be used as biologically relevant readouts for cellular Fe and S status. Methods employing LC-MS technology provide a valuable experimental tool to determine the relative levels of tRNA modification in biological samples and, consequently, to assess genetic, nutritional, and environmental factors modulating reactions dependent on Fe-S clusters. Herein, we describe a robust method for extracting RNA and analytically evaluating the degree of Fe-S-dependent and -independent tRNA modifications via an LC-MS platform.

Keywords:  Bacteria; Iron-sulfur cluster; LC-MS; RNA extraction; Sulfur metabolism; Thionucleosides; tRNA; tRNA modification

DOI:  https://doi.org/10.1007/978-1-0716-1605-5_8
Front Cell Dev Biol. 2021 ;9 683276

Metabolic Drivers of Invasion in Glioblastoma.

Joseph H Garcia, Saket Jain, Manish K Aghi.

  Glioblastoma is a primary malignant brain tumor with a median survival under 2 years. The poor prognosis glioblastoma caries is largely due to cellular invasion, which enables escape from resection, and drives inevitable recurrence. While most studies to date have focused on pathways that enhance the invasiveness of tumor cells in the brain microenvironment as the primary driving forces behind GBM's ability to invade adjacent tissues, more recent studies have identified a role for adaptations in cellular metabolism in GBM invasion. Metabolic reprogramming allows invasive cells to generate the energy necessary for colonizing surrounding brain tissue and adapt to new microenvironments with unique nutrient and oxygen availability. Historically, enhanced glycolysis, even in the presence of oxygen (the Warburg effect) has dominated glioblastoma research with respect to tumor metabolism. More recent global profiling experiments, however, have identified roles for lipid, amino acid, and nucleotide metabolism in tumor growth and invasion. A thorough understanding of the metabolic traits that define invasive GBM cells may provide novel therapeutic targets for this devastating disease. In this review, we focus on metabolic alterations that have been characterized in glioblastoma, the dynamic nature of tumor metabolism and how it is shaped by interaction with the brain microenvironment, and how metabolic reprogramming generates vulnerabilities that may be ripe for exploitation.

Keywords:  brain tumor; glioblastoma; invasion; metabolism; microenvironment

DOI:  https://doi.org/10.3389/fcell.2021.683276
Amino Acids. 2021 Jul 22.

Amino acid metabolism as a therapeutic target in cancer: a review.

Molly Endicott, Michael Jones, Jonathon Hull.

  Malignant cells often demonstrate a proliferative advantage when compared to non-malignant cells. However, the rapid growth and metabolism required for survival can also highlight vulnerabilities specific to these malignant cells. One such vulnerability exhibited by cancer is an increased demand for amino acids (AAs), which often results in a dependency on exogenous sources of AAs or requires upregulation of de novo synthesis. These metabolic alterations can be exploited by therapy, which aims to improve treatment outcome and decrease relapse and reoccurrence. One clinically utilised strategy targeting AA dependency is the use of asparaginase in the treatment of acute lymphoblastic leukaemia (ALL), which results in a depletion of exogenous asparagine and subsequent cancer cell death. Examples of other successful strategies include the exploitation of arginine deiminase and methioninase, nutrient restriction of methionine and the inhibition of glutaminase. In this review, we summarise these treatment strategies into three promising avenues: AA restriction, enzymatic depletion and inhibition of metabolism. This review provides an insight into the complexity of metabolism in cancer, whilst highlighting these three current research avenues that have support in both preclinical and clinical settings.

Keywords:  Amino acids; Asparaginase; Cancer; Metabolism; Oncology

DOI:  https://doi.org/10.1007/s00726-021-03052-1
J Pharm Anal. 2021 Jun;11(3): 340-350

Lipidomics reveals carnitine palmitoyltransferase 1C protects cancer cells from lipotoxicity and senescence.

Huizhen Zhang, Yongtao Wang, Lihuan Guan, Yixin Chen, Panpan Chen, Jiahong Sun, Frank J Gonzalez, Min Huang, Huichang Bi.

  Lipotoxicity, caused by intracellular lipid accumulation, accelerates the degenerative process of cellular senescence, which has implications in cancer development and therapy. Previously, carnitine palmitoyltransferase 1C (CPT1C), a mitochondrial enzyme that catalyzes carnitinylation of fatty acids, was found to be a critical regulator of cancer cell senescence. However, whether loss of CPT1C could induce senescence as a result of lipotoxicity remains unknown. An LC/MS-based lipidomic analysis of PANC-1, MDA-MB-231, HCT-116 and A549 cancer cells was conducted after siRNA depletion of CPT1C. Cellular lipotoxicity was further confirmed by lipotoxicity assays. Significant changes were found in the lipidome of CPT1C-depleted cells, including major alterations in fatty acid, diacylglycerol, triacylglycerol, oxidative lipids, cardiolipin, phosphatidylglycerol, phosphatidylcholine/phosphatidylethanolamine ratio and sphingomyelin. This was coincident with changes in expressions of mRNAs involved in lipogenesis. Histological and biochemical analyses revealed higher lipid accumulation and increased malondialdehyde and reactive oxygen species, signatures of lipid peroxidation and oxidative stress. Reduction of ATP synthesis, loss of mitochondrial transmembrane potential and down-regulation of expression of mitochondriogenesis gene mRNAs indicated mitochondrial dysfunction induced by lipotoxicity, which could further result in cellular senescence. Taken together, this study demonstrated CPT1C plays a critical role in the regulation of cancer cell lipotoxicity and cell senescence, suggesting that inhibition of CPT1C may serve as a new therapeutic strategy through induction of tumor lipotoxicity and senescence.

Keywords:  Anticancer target; Lipid accumulation; Lipid peroxidation; Lipidomics; Mitochondrial dysfunction; Oxidative stress

DOI:  https://doi.org/10.1016/j.jpha.2020.04.004
Cancers (Basel). 2021 Jul 15. pii: 3541. [Epub ahead of print]13(14):

Arginine Signaling and Cancer Metabolism.

Chia-Lin Chen, Sheng-Chieh Hsu, David K Ann, Yun Yen, Hsing-Jien Kung.

  Arginine is an amino acid critically involved in multiple cellular processes including the syntheses of nitric oxide and polyamines, and is a direct activator of mTOR, a nutrient-sensing kinase strongly implicated in carcinogenesis. Yet, it is also considered as a non- or semi-essential amino acid, due to normal cells' intrinsic ability to synthesize arginine from citrulline and aspartate via ASS1 (argininosuccinate synthase 1) and ASL (argininosuccinate lyase). As such, arginine can be used as a dietary supplement and its depletion as a therapeutic strategy. Strikingly, in over 70% of tumors, ASS1 transcription is suppressed, rendering the cells addicted to external arginine, forming the basis of arginine-deprivation therapy. In this review, we will discuss arginine as a signaling metabolite, arginine's role in cancer metabolism, arginine as an epigenetic regulator, arginine as an immunomodulator, and arginine as a therapeutic target. We will also provide a comprehensive summary of ADI (arginine deiminase)-based arginine-deprivation preclinical studies and an update of clinical trials for ADI and arginase. The different cell killing mechanisms associated with various cancer types will also be described.

Keywords:  ADI; arginase; arginine; arginine-deprivation therapy; cancer metabolism; epigenetics

DOI:  https://doi.org/10.3390/cancers13143541
Prog Lipid Res. 2021 Jul 19. pii: S0163-7827(21)00032-1. [Epub ahead of print] 101116

Fatty acids and evolving roles of their proteins in neurological, cardiovascular disorders and cancers.

Rahul Mallick, Sanjay Basak, Asim K Duttaroy.

The dysregulation of fat metabolism is involved in various disorders, including neurodegenerative, cardiovascular, and cancers. The uptake of long-chain fatty acids (LCFAs) with 14 or more carbons plays a pivotal role in cellular metabolic homeostasis. Therefore, the uptake and metabolism of LCFAs must constantly be in tune with the cellular, metabolic, and structural requirements of cells. Many metabolic diseases are thought to be driven by the abnormal flow of fatty acids either from the dietary origin and/or released from adipose stores. Cellular uptake and intracellular trafficking of fatty acids are facilitated ubiquitously with unique combinations of fatty acid transport proteins and cytoplasmic fatty acid-binding proteins in every tissue. Extensive data are emerging on the defective transporters and metabolism of LCFAs and their clinical implications. Uptake and metabolism of LCFAs are crucial for the brain's functional development and cardiovascular health and maintenance. In addition, data suggest fatty acid metabolic transporter can normalize activated inflammatory response by reprogramming lipid metabolism in cancers. Here we review the current understanding of how LCFAs and their proteins contribute to the pathophysiology of three crucial diseases and the mechanisms involved in the processes.

DOI: https://doi.org/10.1016/j.plipres.2021.101116
Redox Biol. 2021 Jul 11. pii: S2213-2317(21)00224-X. [Epub ahead of print]46 102065

Lactate and glutamine support NADPH generation in cancer cells under glucose deprived conditions.

Minfeng Ying, Duo You, Xiaobing Zhu, Limeng Cai, Siying Zeng, Xun Hu.

  Although glucose, through pentose phosphate pathway (PPP), is the main source to generate NADPH, solid tumors are often deprived of glucose, hence alternative metabolic pathways to maintain NADPH homeostasis in cancer cells are required. Here, we report that lactate and glutamine support NADPH production via isocitrate dehydrogenase 1 (IDH1) and malic enzyme 1 (ME1), respectively, under glucose-deprived conditions. Isotopic tracing demonstrates that lactate participates in the formation of isocitrate. Malate derived from glutamine in mitochondria shuttles to cytosol to produce NADPH. In cells cultured in the absence of glucose, knockout of IDH1 and ME1 decreases NADPH/NADP+ and GSH/GSSG, increases ROS level and facilitates cell necrosis. In 4T1 murine breast tumors, knockout of ME1 retards tumor growth in vivo, with combined ME1/IDH1 knockout more strongly suppressing tumor growth. Our findings reveal two alternative NADPH-producing pathways that cancer cells use to resist glucose starvation, reflecting the metabolic plasticity and flexibility of cancer cells adapting to nutrition stress.

Keywords:  Glucose deprivation; Glutamine; IDH1; Lactate; ME1; NADPH

DOI:  https://doi.org/10.1016/j.redox.2021.102065
Cancer Cell. 2021 Jul 14. pii: S1535-6108(21)00339-1. [Epub ahead of print]

Single-cell analysis defines a pancreatic fibroblast lineage that supports anti-tumor immunity.

Colin Hutton, Felix Heider, Adrian Blanco-Gomez, Antonia Banyard, Alexander Kononov, Xiaohong Zhang, Saadia Karim, Viola Paulus-Hock, Dale Watt, Nina Steele, Samantha Kemp, Elizabeth K J Hogg, Joanna Kelly, Rene-Filip Jackstadt, Filipa Lopes, Matteo Menotti, Luke Chisholm, Angela Lamarca, Juan Valle, Owen J Sansom, Caroline Springer, Angeliki Malliri, Richard Marais, Marina Pasca di Magliano, Santiago Zelenay, Jennifer P Morton, Claus Jørgensen.

  Fibroblasts display extensive transcriptional heterogeneity, yet functional annotation and characterization of their heterocellular relationships remains incomplete. Using mass cytometry, we chart the stromal composition of 18 murine tissues and 5 spontaneous tumor models, with an emphasis on mesenchymal phenotypes. This analysis reveals extensive stromal heterogeneity across tissues and tumors, and identifies coordinated relationships between mesenchymal and immune cell subsets in pancreatic ductal adenocarcinoma. Expression of CD105 demarks two stable and functionally distinct pancreatic fibroblast lineages, which are also identified in murine and human healthy tissues and tumors. Whereas CD105-positive pancreatic fibroblasts are permissive for tumor growth in vivo, CD105-negative fibroblasts are highly tumor suppressive. This restrictive effect is entirely dependent on functional adaptive immunity. Collectively, these results reveal two functionally distinct pancreatic fibroblast lineages and highlight the importance of mesenchymal and immune cell interactions in restricting tumor growth.

Keywords:  CAF; CD105; CyTOF; Eng; cancer-associated fibroblast lineages; mass cytometry; pancreatic cancer; tumor microenvironment; tumor-restrictive fibroblasts

DOI:  https://doi.org/10.1016/j.ccell.2021.06.017
J Proteome Res. 2021 Jul 23.

Bridging the Polar and Hydrophobic Metabolome in Single-Run Untargeted Liquid Chromatography-Mass Spectrometry Dried Blood Spot Metabolomics for Clinical Purposes.

Hanne Bendiksen Skogvold, Elise Mørk Sandås, Anja Østeby, Camilla Løkken, Helge Rootwelt, Per Ola Rønning, Steven Ray Wilson, Katja Benedikte Prestø Elgstøen.

  Dried blood spot (DBS) metabolite analysis is a central tool for the clinic, e.g., newborn screening. Instead of applying multiple analytical methods, a single liquid chromatography-mass spectrometry (LC-MS) method was developed for metabolites spanning from highly polar glucose to hydrophobic long-chain acylcarnitines. For liquid chromatography, a diphenyl column and a multi-linear solvent gradient operated at elevated flow rates allowed for an even-spread resolution of diverse metabolites. Injecting moderate volumes of DBS organic extracts directly, in contrast to evaporation and reconstitution, provided substantial increases in analyte recovery. Q Exactive MS settings were also tailored for sensitivity increases, and the method allowed for analyte retention time and peak area repeatabilities of 0.1-0.4 and 2-10%, respectively, for a wide polarity range of metabolites (log P -4.4 to 8.8). The method's performance was suited for both untargeted analysis and targeted approaches evaluated in clinically relevant experiments.

Keywords:  LC−MS; dried blood spots; inborn errors of metabolism; metabolomics

DOI:  https://doi.org/10.1021/acs.jproteome.1c00326