bims-mascan 2021-02-07 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–02–07
twenty-six papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

ELOVL5 is a critical and targetable fatty acid elongase in prostate cancer.
Lipid Metabolism in Oncology: Why It Matters, How to Research, and How to Treat.
Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance.
Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis.
Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification.
Evaluation of Fumaric Acid and Maleic Acid as Internal Standards for NMR Analysis of Protein Precipitated Plasma, Serum, and Whole Blood.
How does hepatic lipid accumulation lead to lipotoxicity in non-alcoholic fatty liver disease?
BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples.
Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures.
The Role of Pi, Glutamine and the Essential Amino Acids in Modulating the Metabolism in Diabetes and Cancer.
Lactate production is a prioritized feature of adipocyte metabolism.
Bioactive Lipids in MSCs Biology: State of the Art and Role in Inflammation.
Metabolomics study reveals the potential evidence of metabolic reprogramming towards the Warburg effect in precancerous lesions.
Phosphatidic acid drives mTORC1 lysosomal translocation in the absence of amino acids.
The cancer metabolic reprogramming and immune response.
LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring.
Mapping the Metabolic Networks of Tumor Cells and Cancer-Associated Fibroblasts.
Tumor Metabolic Reprogramming by Adipokines as a Critical Driver of Obesity-Associated Cancer Progression.
Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics.
SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.
Integrated Metabolomics and Lipidomics Analysis Reveal Remodeling of Lipid Metabolism and Amino Acid Metabolism in Glucagon Receptor-Deficient Zebrafish.
GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability.
Suppressing post-collection lysophosphatidic acid (LPA) metabolism improves the precision of plasma LPA quantification.
Quantitative Proteomic Analysis of the Senescence-Associated Secretory Phenotype by Data-Independent Acquisition.
1-Methylnicotinamide is an immune regulatory metabolite in human ovarian cancer.
The Effects of SGLT2 Inhibitors on Lipid Metabolism.

Cancer Res. 2021 Feb 05. pii: canres.2511.2020. [Epub ahead of print]

ELOVL5 is a critical and targetable fatty acid elongase in prostate cancer.

Margaret M Centenera, Julia S Scott, Jelle Machiels, Zeyad D Nassar, Deanna C Miller, Irene Zininos, Jonas Dehairs, Ingrid J G Burvenich, Giorgia Zadra, Paolo Chetta, Clyde Bango, Emma Evergren, Natalie K Ryan, Joanna L Gillis, Chui Yan Mah, Terence Tieu, Adrienne R Hanson, Ryan Carelli, Katarzyna Bloch, Vasilios Panagopoulos, Etienne Waelkens, Rita Derua, Elizabeth D Williams, Andreas Evdokioou, Anna Cifuentes-Rius, Nicolas H Voelcker, Ian G Mills, Wayne D Tilley, Andrew M Scott, Massimo Loda, Luke A Selth, Johannes V Swinnen, Lisa M Butler.

The androgen receptor (AR) is the key oncogenic driver of prostate cancer, and despite implementation of novel AR targeting therapies, outcomes for metastatic disease remain dismal. There is an urgent need to better understand androgen-regulated cellular processes to more effectively target the AR-dependence of prostate cancer cells through new therapeutic vulnerabilities. Transcriptomic studies have consistently identified lipid metabolism as a hallmark of enhanced AR signaling in prostate cancer, yet the relationship between AR and the lipidome remain undefined. Using mass spectrometry-based lipidomics, this study reveals increased fatty acyl chain length in phospholipids from prostate cancer cells and patient-derived explants as one of the most striking androgen-regulated changes to lipid metabolism. Potent and direct AR-mediated induction of ELOVL fatty acid elongase 5 (ELOVL5), an enzyme that catalyzes fatty acid elongation, was demonstrated in prostate cancer cells, xenografts, and clinical tumors. Assessment of mRNA and protein in large-scale datasets revealed ELOVL5 as the predominant ELOVL expressed and upregulated in prostate cancer compared to non-malignant prostate. ELOVL5 depletion markedly altered mitochondrial morphology and function, leading to excess generation of reactive oxygen species and resulting in suppression of prostate cancer cell proliferation, 3D growth, and in vivo tumor growth and metastasis. Supplementation with the monounsaturated fatty acid cis-vaccenic acid, a direct product of ELOVL5 elongation, reversed the oxidative stress and associated cell proliferation and migration effects of ELOVL5 knockdown. Collectively, these results identify lipid elongation as a pro-tumorigenic metabolic pathway in prostate cancer that is androgen-regulated, critical for metastasis, and targetable via ELOVL5.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-2511
Cancers (Basel). 2021 Jan 26. pii: 474. [Epub ahead of print]13(3):

Lipid Metabolism in Oncology: Why It Matters, How to Research, and How to Treat.

Yuki Matsushita, Hayato Nakagawa, Kazuhiko Koike.

  Lipids in our body, which are mainly composed of fatty acids, triacylglycerides, sphingolipids, phospholipids, and cholesterol, play important roles at the cellular level. In addition to being energy sources and structural components of biological membranes, several types of lipids serve as signaling molecules or secondary messengers. Metabolic reprogramming has been recognized as a hallmark of cancer, but changes in lipid metabolism in cancer have received less attention compared to glucose or glutamine metabolism. However, recent innovations in mass spectrometry- and chromatography-based lipidomics technologies have increased our understanding of the role of lipids in cancer. Changes in lipid metabolism, so-called "lipid metabolic reprogramming", can affect cellular functions including the cell cycle, proliferation, growth, and differentiation, leading to carcinogenesis. Moreover, interactions between cancer cells and adjacent immune cells through altered lipid metabolism are known to support tumor growth and progression. Characterization of cancer-specific lipid metabolism can be used to identify novel metabolic targets for cancer treatment, and indeed, several clinical trials are currently underway. Thus, we discuss the latest findings on the roles of lipid metabolism in cancer biology and introduce current advances in lipidomics technologies, focusing on their applications in cancer research.

Keywords:  cholesterol metabolism; fatty acid metabolism; lipid droplet metabolism; lipidomics; mass spectrometry; metabolic reprogramming; phospholipid metabolism; tumor microenvironment

DOI:  https://doi.org/10.3390/cancers13030474
Mol Cell Proteomics. 2019 Jun;pii: S1535-9476(20)31823-5. [Epub ahead of print]18(6): 1242-1254

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance.

Roland Bruderer, Jan Muntel, Sebastian Müller, Oliver M Bernhardt, Tejas Gandhi, Ornella Cominetti, Charlotte Macron, Jérôme Carayol, Oliver Rinner, Arne Astrup, Wim H M Saris, Jörg Hager, Armand Valsesia, Loïc Dayon, Lukas Reiter.

  Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%. The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA. In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.

Keywords:  Absolute quantification; Clinical proteomics; Label-free quantification; Plasma or serum analysis; SWATH-MS; data-independent acquisition; high throughput; single shot; stable isotope standards

DOI:  https://doi.org/10.1074/mcp.RA118.001288
J Biol Chem. 2020 Jan 03. pii: S0021-9258(17)49553-6. [Epub ahead of print]295(1): 111-124

Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis.

Maria V Liberti, Annamarie E Allen, Vijyendra Ramesh, Ziwei Dai, Katherine R Singleton, Zufeng Guo, Jun O Liu, Kris C Wood, Jason W Locasale.

  Aerobic glycolysis or the Warburg effect (WE) is characterized by increased glucose uptake and incomplete oxidation to lactate. Although the WE is ubiquitous, its biological role remains controversial, and whether glucose metabolism is functionally different during fully oxidative glycolysis or during the WE is unknown. To investigate this question, here we evolved resistance to koningic acid (KA), a natural product that specifically inhibits glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-controlling glycolytic enzyme, during the WE. We found that KA-resistant cells lose the WE but continue to conduct glycolysis and surprisingly remain dependent on glucose as a carbon source and also on central carbon metabolism. Consequently, this altered state of glycolysis led to differential metabolic activity and requirements, including emergent activities in and dependences on fatty acid metabolism. These findings reveal that aerobic glycolysis is a process functionally distinct from conventional glucose metabolism and leads to distinct metabolic requirements and biological functions.

Keywords:  Warburg effect; cancer; glucose metabolism; glyceraldehyde-3-phosphate dehydrogenase GAPDH; glycolysis; mass spectrometry (MS); metabolic regulation; metabolic reprogramming; metabolomics; oxidative metabolism

DOI:  https://doi.org/10.1074/jbc.RA119.010903
J Proteome Res. 2021 Feb 02.

Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification.

Prasad Phapale, Andrew Palmer, Rose Muthoni Gathungu, Dipali Kale, Britta Brügger, Theodore Alexandrov.

  Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics studies require high-quality spectral libraries for reliable metabolite identification. We have constructed EMBL-MCF (European Molecular Biology Laboratory-Metabolomics Core Facility), an open LC-MS/MS spectral library that currently contains over 1600 fragmentation spectra from 435 authentic standards of endogenous metabolites and lipids. The unique features of the library include the presence of chromatographic profiles acquired with different LC-MS methods and coverage of different adduct ions. The library covers many biologically important metabolites with some unique metabolites and lipids as compared with other public libraries. The EMBL-MCF spectral library is created and shared using an in-house-developed web application at https://curatr.mcf.embl.de/. The library is freely available online and also integrated with other mass spectral repositories.

Keywords:  LC-MS/MS; Orbitrap; fragmentation spectra; high-resolution mass spectrometry; liquid chromatography; mass spectral library

DOI:  https://doi.org/10.1021/acs.jproteome.0c00930
Anal Chem. 2021 Feb 04.

Evaluation of Fumaric Acid and Maleic Acid as Internal Standards for NMR Analysis of Protein Precipitated Plasma, Serum, and Whole Blood.

G A Nagana Gowda, Natalie N Hong, Daniel Raftery.

Significant advances have been made in unknown metabolite identification and expansion of the number of quantifiable metabolites in human plasma, serum, and whole blood using NMR spectroscopy. However, reliable quantitation of metabolites is still a challenge. A major bottleneck is the lack of a suitable internal standard that does not interact with the complex blood sample matrix and also does not overlap with metabolite peaks apart from exhibiting other favorable characteristics. With the goal of addressing this challenge, a comprehensive investigation of fumaric and maleic acids as potential internal standards was made along with a comparison with the conventional standards, TSP (trimethylsilylpropionic acid) and DSS (trimethylsilylpropanesulfonic acid). Both fumaric acid and maleic acid exhibited a surprisingly high performance with a quantitation error <1%, while the TSP and DSS caused an average error of up to 35% in plasma, serum, and whole blood. Further, the results indicate that while fumaric acid is a robust standard for all three biospecimens, maleic acid is suitable for only plasma and serum. Maleic acid is not suited for the analysis of whole blood due to its overlap with coenzyme peaks. These findings provide new opportunities for improved and accurate quantitation of metabolites in human plasma, serum, and whole blood using NMR spectroscopy. Moreover, the use of protein precipitation prior to NMR analysis mirrors the sample preparation commonly used for mass spectrometry based metabolomics, such that these findings further strengthen efforts to combine and compare NMR and MS based metabolite data of human plasma, serum, and whole blood for metabolomics based research.

DOI: https://doi.org/10.1021/acs.analchem.0c04766
Hepatol Int. 2021 Feb 06.

How does hepatic lipid accumulation lead to lipotoxicity in non-alcoholic fatty liver disease?

Yana Geng, Klaas Nico Faber, Vincent E de Meijer, Hans Blokzijl, Han Moshage.

   BACKGROUND: Non-alcoholic fatty liver disease (NAFLD), characterized as excess lipid accumulation in the liver which is not due to alcohol use, has emerged as one of the major health problems around the world. The dysregulated lipid metabolism creates a lipotoxic environment which promotes the development of NAFLD, especially the progression from simple steatosis (NAFL) to non-alcoholic steatohepatitis (NASH).
PURPOSEAND AIM: This review focuses on the mechanisms of lipid accumulation in the liver, with an emphasis on the metabolic fate of free fatty acids (FFAs) in NAFLD and presents an update on the relevant cellular processes/mechanisms that are involved in lipotoxicity. The changes in the levels of various lipid species that result from the imbalance between lipolysis/lipid uptake/lipogenesis and lipid oxidation/secretion can cause organellar dysfunction, e.g. ER stress, mitochondrial dysfunction, lysosomal dysfunction, JNK activation, secretion of extracellular vesicles (EVs) and aggravate (or be exacerbated by) hypoxia which ultimately lead to cell death. The aim of this review is to provide an overview of how abnormal lipid metabolism leads to lipotoxicity and the cellular mechanisms of lipotoxicity in the context of NAFLD.

Keywords:  Cell death; ER stress; Free fatty acids; JNK; Lipid metabolism; Lipotoxicity; MAFLD; Mitochondrial dysfunction; NAFLD; NASH

DOI:  https://doi.org/10.1007/s12072-020-10121-2
Anal Chem. 2021 Feb 03.

BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples.

Barbora Salovska, Wenxue Li, Yi Di, Yansheng Liu.

The data-independent acquisition (DIA) performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (DIA-MS) combined with the isotopic labeling approach holds a particular promise for increasing the multiplexity of DIA-MS analysis, which could assist the relative protein quantification and the proteome-wide turnover profiling. However, the wide MS1 isolation windows employed in conventional DIA methods lead to a limited efficiency in identifying and quantifying isotope-labeled peptide pairs through peptide fragment ions. Here, we optimized a high-selectivity DIA-MS named BoxCarmax that supports the analysis of complex samples, such as those generated from Stable isotope labeling by amino acids in cell culture (SILAC) and pulse SILAC (pSILAC) experiments. BoxCarmax enables multiplexed acquisition at both MS1 and MS2 levels, through the integration of BoxCar and MSX features, as well as a gas-phase separation strategy. We found BoxCarmax significantly improved the quantitative accuracy in SILAC and pSILAC samples by mitigating the ratio suppression of isotope-peptide pairs. We further applied BoxCarmax to measure protein degradation regulation during serum starvation stress in cultured cells, revealing valuable biological insights. Our study offered an alternative and accurate approach for the MS analysis of protein turnover and complex samples.

DOI: https://doi.org/10.1021/acs.analchem.0c04293
J Lipid Res. 2020 Dec;pii: S0022-2275(20)60017-7. [Epub ahead of print]61(12): 1539-1555

Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures.

Gerhard Liebisch, Eoin Fahy, Junken Aoki, Edward A Dennis, Thierry Durand, Christer S Ejsing, Maria Fedorova, Ivo Feussner, William J Griffiths, Harald Köfeler, Alfred H Merrill, Robert C Murphy, Valerie B O'Donnell, Olga Oskolkova, Shankar Subramaniam, Michael J O Wakelam, Friedrich Spener.

  A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation.

Keywords:  fatty acyls; glycerolipids; glycerophospholipids; lipidomics; mass spectrometry; sphingolipids; sterols

DOI:  https://doi.org/10.1194/jlr.S120001025
J Diabetes Metab Disord. 2020 Dec;19(2): 1731-1775

The Role of Pi, Glutamine and the Essential Amino Acids in Modulating the Metabolism in Diabetes and Cancer.

Lakshmipathi Vadlakonda, Meera Indracanti, Suresh K Kalangi, B Meher Gayatri, Navya G Naidu, Aramati B M Reddy.

   Purpose: Re-examine the current metabolic models.
Methods: Review of literature and gene networks.
Results: Insulin activates Pi uptake, glutamine metabolism to stabilise lipid membranes. Tissue turnover maintains the metabolic health. Current model of intermediary metabolism (IM) suggests glucose is the source of energy, and anaplerotic entry of fatty acids and amino acids into mitochondria increases the oxidative capacity of the TCA cycle to produce the energy (ATP). The reduced cofactors, NADH and FADH2, have different roles in regulating the oxidation of nutrients, membrane potentials and biosynthesis. Trans-hydrogenation of NADH to NADPH activates the biosynthesis. FADH2 sustains the membrane potential during the cell transformations. Glycolytic enzymes assume the non-canonical moonlighting functions, enter the nucleus to remodel the genetic programmes to affect the tissue turnover for efficient use of nutrients. Glycosylation of the CD98 (4F2HC) stabilises the nutrient transporters and regulates the entry of cysteine, glutamine and BCAA into the cells. A reciprocal relationship between the leucine and glutamine entry into cells regulates the cholesterol and fatty acid synthesis and homeostasis in cells. Insulin promotes the Pi transport from the blood to tissues, activates the mitochondrial respiratory activity, and glutamine metabolism, which activates the synthesis of cholesterol and the de novo fatty acids for reorganising and stabilising the lipid membranes for nutrient transport and signal transduction in response to fluctuations in the microenvironmental cues. Fatty acids provide the lipid metabolites, activate the second messengers and protein kinases. Insulin resistance suppresses the lipid raft formation and the mitotic slippage activates the fibrosis and slow death pathways.

Keywords:  CD98; Fatty acids; Glutamine; Leucine; Mitochondrial pyruvate carrier proteins (MPC1&2); Tissue turnover; mTORC1

DOI:  https://doi.org/10.1007/s40200-020-00566-5
J Biol Chem. 2020 Jan 03. pii: S0021-9258(17)49551-2. [Epub ahead of print]295(1): 83-98

Lactate production is a prioritized feature of adipocyte metabolism.

James R Krycer, Lake-Ee Quek, Deanne Francis, Daniel J Fazakerley, Sarah D Elkington, Alexis Diaz-Vegas, Kristen C Cooke, Fiona C Weiss, Xiaowen Duan, Sergey Kurdyukov, Ping-Xin Zhou, Uttam K Tambar, Akiyoshi Hirayama, Satsuki Ikeda, Yushi Kamei, Tomoyoshi Soga, Gregory J Cooney, David E James.

  Adipose tissue is essential for whole-body glucose homeostasis, with a primary role in lipid storage. It has been previously observed that lactate production is also an important metabolic feature of adipocytes, but its relationship to adipose and whole-body glucose disposal remains unclear. Therefore, using a combination of metabolic labeling techniques, here we closely examined lactate production of cultured and primary mammalian adipocytes. Insulin treatment increased glucose uptake and conversion to lactate, with the latter responding more to insulin than did other metabolic fates of glucose. However, lactate production did not just serve as a mechanism to dispose of excess glucose, because we also observed that lactate production in adipocytes did not solely depend on glucose availability and even occurred independently of glucose metabolism. This suggests that lactate production is prioritized in adipocytes. Furthermore, knocking down lactate dehydrogenase specifically in the fat body of Drosophila flies lowered circulating lactate and improved whole-body glucose disposal. These results emphasize that lactate production is an additional metabolic role of adipose tissue beyond lipid storage and release.

Keywords:  Drosophila; adipocyte; cell metabolism; fat tissue; glucose disposal; insulin; insulin resistance; lactate; metabolic regulation; whole-body glucose homeostasis

DOI:  https://doi.org/10.1074/jbc.RA119.011178
Int J Mol Sci. 2021 Feb 02. pii: 1481. [Epub ahead of print]22(3):

Bioactive Lipids in MSCs Biology: State of the Art and Role in Inflammation.

Sara Casati, Chiara Giannasi, Stefania Niada, Roberta F Bergamaschi, Marica Orioli, Anna T Brini.

  Lipidomics is a lipid-targeted metabolomics approach that aims to the comprehensive analysis of lipids in biological systems in order to highlight the specific functions of lipid species in health and disease. Lipids play pivotal roles as they are major structural components of the cellular membranes and energy storage molecules but also, as most recently shown, they act as functional and regulatory components of intra- and intercellular signaling. Herein, emphasis is given to the recently highlighted roles of specific bioactive lipids species, as polyunsaturated fatty acids (PUFA)-derived mediators (generally known as eicosanoids), endocannabinoids (eCBs), and lysophospholipids (LPLs), and their involvement in the mesenchymal stem cells (MSCs)-related inflammatory scenario. Indeed, MSCs are a heterogenous population of multipotent cells that have attracted much attention for their potential in regulating inflammation, immunomodulatory capabilities, and reparative roles. The lipidomics of the inflammatory disease osteoarthritis (OA) and the influence of MSCs-derived lipids have also been addressed.

Keywords:  bioactive lipids; inflammation; lipidomics; mesenchymal stem cells; osteoarthritis

DOI:  https://doi.org/10.3390/ijms22031481
J Cancer. 2021 ;12(5): 1563-1574

Metabolomics study reveals the potential evidence of metabolic reprogramming towards the Warburg effect in precancerous lesions.

Xun Chen, Chen Yi, Man-Jun Yang, Xueqi Sun, Xubin Liu, Hanyu Ma, Yiming Li, Hongyu Li, Chao Wang, Yi He, Guanhui Chen, Shangwu Chen, Li Yu, Dongsheng Yu.

  Background: Most tumors have an enhanced glycolysis flux, even when oxygen is available, called the aerobic glycolysis or the Warburg effect. Metabolic reprogramming promotes cancer progression, and is even related to the tumorigenesis. However, it is not clear whether the observed metabolic changes act as a driver or a bystander in cancer development. Methods: In this study, the metabolic characteristics of oral precancerous cells and cervical precancerous lesions were analyzed by metabolomics, and the expression of glycolytic enzymes in cervical precancerous lesions was evaluated by RT-PCR and Western blot analysis. Results: In total, 115 and 23 metabolites with reliable signals were identified in oral cells and cervical tissues, respectively. Based on the metabolome, oral precancerous cell DOK could be clearly separated from normal human oral epithelial cells (HOEC) and oral cancer cells. Four critical differential metabolites (pyruvate, glutamine, methionine and lysine) were identified between DOK and HOEC. Metabolic profiles could clearly distinguish cervical precancerous lesions from normal cervical epithelium and cervical cancer. Compared with normal cervical epithelium, the glucose consumption and lactate production increased in cervical precancerous lesions. The expression of glycolytic enzymes LDHA, HK II and PKM2 showed an increased tendency in cervical precancerous lesions compared with normal cervical epithelium. Conclusions: Our findings suggest that cell metabolism may be reprogrammed at the early stage of tumorigenesis, implying the contribution of metabolic reprogramming to the development of tumor.

Keywords:  glycolytic enzymes; metabolic reprogramming; metabolomics; precancerous lesions; the Warburg-like effect

DOI:  https://doi.org/10.7150/jca.54252
J Biol Chem. 2020 Jan 03. pii: S0021-9258(17)49565-2. [Epub ahead of print]295(1): 263-274

Phosphatidic acid drives mTORC1 lysosomal translocation in the absence of amino acids.

Maria A Frias, Suman Mukhopadhyay, Elyssa Lehman, Aleksandra Walasek, Matthew Utter, Deepak Menon, David A Foster.

  Mammalian target of rapamycin complex 1 (mTORC1) promotes cell growth and proliferation in response to nutrients and growth factors. Amino acids induce lysosomal translocation of mTORC1 via the Rag GTPases. Growth factors activate Ras homolog enriched in brain (Rheb), which in turn activates mTORC1 at the lysosome. Amino acids and growth factors also induce the phospholipase D (PLD)-phosphatidic acid (PA) pathway, required for mTORC1 signaling through mechanisms that are not fully understood. Here, using human and murine cell lines, along with immunofluorescence, confocal microscopy, endocytosis, PLD activity, and cell viability assays, we show that exogenously supplied PA vesicles deliver mTORC1 to the lysosome in the absence of amino acids, Rag GTPases, growth factors, and Rheb. Of note, pharmacological or genetic inhibition of endogenous PLD prevented mTORC1 lysosomal translocation. We observed that precancerous cells with constitutive Rheb activation through loss of tuberous sclerosis complex subunit 2 (TSC2) exploit the PLD-PA pathway and thereby sustain mTORC1 activation at the lysosome in the absence of amino acids. Our findings indicate that sequential inputs from amino acids and growth factors trigger PA production required for mTORC1 translocation and activation at the lysosome.

Keywords:  amino acid; cancer biology; cancer therapy; growth factor; lysosome; mTOR complex (mTORC); phosphatidic acid; phospholipase D; phospholipid vesicle

DOI:  https://doi.org/10.1074/jbc.RA119.010892
Mol Cancer. 2021 Feb 05. 20(1): 28

The cancer metabolic reprogramming and immune response.

Longzheng Xia, Linda Oyang, Jinguan Lin, Shiming Tan, Yaqian Han, Nayiyuan Wu, Pin Yi, Lu Tang, Qing Pan, Shan Rao, Jiaxin Liang, Yanyan Tang, Min Su, Xia Luo, Yiqing Yang, Yingrui Shi, Hui Wang, Yujuan Zhou, Qianjin Liao.

  The overlapping metabolic reprogramming of cancer and immune cells is a putative determinant of the antitumor immune response in cancer. Increased evidence suggests that cancer metabolism not only plays a crucial role in cancer signaling for sustaining tumorigenesis and survival, but also has wider implications in the regulation of antitumor immune response through both the release of metabolites and affecting the expression of immune molecules, such as lactate, PGE2, arginine, etc. Actually, this energetic interplay between tumor and immune cells leads to metabolic competition in the tumor ecosystem, limiting nutrient availability and leading to microenvironmental acidosis, which hinders immune cell function. More interestingly, metabolic reprogramming is also indispensable in the process of maintaining self and body homeostasis by various types of immune cells. At present, more and more studies pointed out that immune cell would undergo metabolic reprogramming during the process of proliferation, differentiation, and execution of effector functions, which is essential to the immune response. Herein, we discuss how metabolic reprogramming of cancer cells and immune cells regulate antitumor immune response and the possible approaches to targeting metabolic pathways in the context of anticancer immunotherapy. We also describe hypothetical combination treatments between immunotherapy and metabolic intervening that could be used to better unleash the potential of anticancer therapies.

Keywords:  Immune checkpoint…; Immunity; Metabolic reprogramming; Oxysterols; TIL; TME

DOI:  https://doi.org/10.1186/s12943-021-01316-8
Anal Chem. 2021 Feb 03.

LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring.

Liang Gao, Shanshan Ji, Bo Burla, Markus R Wenk, Federico Torta, Amaury Cazenave-Gassiot.

Lipidomics is developing as an important area in biomedical and clinical research. Reliable quantification of lipid species is required for clinical translation of lipidomic studies. Hydrophilic interaction chromatography (HILIC), normal-phase liquid chromatography (NPLC), and supercritical fluid chromatography (SFC) are commonly used techniques in lipidomics and provide class-based separation of lipids. While co-elution of lipid species and their internal standards is an advantage for accurate quantification, it leads to isotopic overlap between species of the same lipid class. In shotgun lipidomics, isotopic correction is typically done based on elemental formulas of precursor ions. In multiple reaction monitoring (MRM) analyses, however, this approach should not be used, as the overall contribution of heavy isotopes to the MRM transitions' intensities depends on their location in the molecule with respect to the fragmentation pattern. We present an algorithm, provided in the R programming language, for isotopic correction in class-based separation using MRM, extracting relevant structural information from MRM transitions to apply adequate isotopic correction factors. Using standards, we show that our algorithm accurately estimates the isotopic contribution of isotopologues to MRM transitions' measured intensities. Using human plasma as an example, we demonstrate the necessity of adequate isotopic correction for accurate quantitation of lipids measured by MRM with class-based chromatographic separation. We show that over a third of the measured phosphatidylcholine species had their intensity corrected by more than 10%. This isotopic correction algorithm and R-implemented application enable a more accurate quantification of lipids in class-based separation-MRM, a prerequisite for successful translation of lipidomic applications.

DOI: https://doi.org/10.1021/acs.analchem.0c04565
Cells. 2021 Feb 02. pii: 304. [Epub ahead of print]10(2):

Mapping the Metabolic Networks of Tumor Cells and Cancer-Associated Fibroblasts.

Jessica Karta, Ysaline Bossicard, Konstantinos Kotzamanis, Helmut Dolznig, Elisabeth Letellier.

  Metabolism is considered to be the core of all cellular activity. Thus, extensive studies of metabolic processes are ongoing in various fields of biology, including cancer research. Cancer cells are known to adapt their metabolism to sustain high proliferation rates and survive in unfavorable environments with low oxygen and nutrient concentrations. Hence, targeting cancer cell metabolism is a promising therapeutic strategy in cancer research. However, cancers consist not only of genetically altered tumor cells but are interwoven with endothelial cells, immune cells and fibroblasts, which together with the extracellular matrix (ECM) constitute the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs), which are linked to poor prognosis in different cancer types, are one important component of the TME. CAFs play a significant role in reprogramming the metabolic landscape of tumor cells, but how, and in what manner, this interaction takes place remains rather unclear. This review aims to highlight the metabolic landscape of tumor cells and CAFs, including their recently identified subtypes, in different tumor types. In addition, we discuss various in vitro and in vivo metabolic techniques as well as different in silico computational tools that can be used to identify and characterize CAF-tumor cell interactions. Finally, we provide our view on how mapping the complex metabolic networks of stromal-tumor metabolism will help in finding novel metabolic targets for cancer treatment.

Keywords:  CAF-tumor cross-talk; cancer; cancer-associated fibroblasts (CAFs); in silico modeling; metabolomics’ measurement techniques; personalized metabolic drugs; tumor metabolism

DOI:  https://doi.org/10.3390/cells10020304
Int J Mol Sci. 2021 Feb 01. pii: 1444. [Epub ahead of print]22(3):

Tumor Metabolic Reprogramming by Adipokines as a Critical Driver of Obesity-Associated Cancer Progression.

Duc-Vinh Pham, Pil-Hoon Park.

  Adiposity is associated with an increased risk of various types of carcinoma. One of the plausible mechanisms underlying the tumor-promoting role of obesity is an aberrant secretion of adipokines, a group of hormones secreted from adipose tissue, which have exhibited both oncogenic and tumor-suppressing properties in an adipokine type- and context-dependent manner. Increasing evidence has indicated that these adipose tissue-derived hormones differentially modulate cancer cell-specific metabolism. Some adipokines, such as leptin, resistin, and visfatin, which are overproduced in obesity and widely implicated in different stages of cancer, promote cellular glucose and lipid metabolism. Conversely, adiponectin, an adipokine possessing potent anti-tumor activities, is linked to a more favorable metabolic phenotype. Adipokines may also play a pivotal role under the reciprocal regulation of metabolic rewiring of cancer cells in tumor microenvironment. Given the fact that metabolic reprogramming is one of the major hallmarks of cancer, understanding the modulatory effects of adipokines on alterations in cancer cell metabolism would provide insight into the crosstalk between obesity, adipokines, and tumorigenesis. In this review, we summarize recent insights into putative roles of adipokines as mediators of cellular metabolic rewiring in obesity-associated tumors, which plays a crucial role in determining the fate of tumor cells.

Keywords:  adipokine; cancer metabolism; metabolic reprogramming; obesity

DOI:  https://doi.org/10.3390/ijms22031444
Mass Spectrom Rev. 2021 Feb 01.

Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics.

Giuseppe Paglia, Andrew J Smith, Giuseppe Astarita.

  Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.

Keywords:  CCS; DTIM-MS; FAIM-MS; IM-MS; MS imaging; MSI; TIM-MS; TWIM-MS; cIM-MS; collision cross-section; lipids; metabolites; spatial lipidomics; spatial metabolomics

DOI:  https://doi.org/10.1002/mas.21686
J Proteome Res. 2021 Feb 02.

SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.

Vidur Kailash, Luis Mendoza, Robert L Moritz, Michael R Hoopmann.

  The efficiency of shotgun proteomic analysis is dependent on the reproducibility of the peptide cleavage process during sample preparation. To generate rapid and useful metrics for peptide cleavage efficiency, as in enzymatic or chemical cleavage, SPACEPro was developed to evaluate efficiency and reproducibility of protein cleavage in peptide samples following data-dependent analysis by mass spectrometry. SPACEPro analyzes samples at the peptide-spectrum match (PSM), peptide, and protein levels to provide a comprehensive representation of the overall sample processing to peptides. All output is provided in human-readable text and JSON files that can be further processed to assess the cleavage efficiency on proteins within the sample. SPACEPro provides a snapshot of the protein cleavage efficiency through very minimal effort so that the user is informed of the quality of the sample processing efficiency and can accordingly develop protocols to improve the initial sample preparation for subsequent analyses.

Keywords:  bottom-up mass spectrometry; chemical cleavage; cleavage efficiency; data-dependent analysis; endopeptidase; endoprotease; enzymatic digestion; missed cleavage; nonspecific cleavage; shotgun mass spectrometry; trypsin

DOI:  https://doi.org/10.1021/acs.jproteome.0c00928
Front Cell Dev Biol. 2020 ;8 605979

Integrated Metabolomics and Lipidomics Analysis Reveal Remodeling of Lipid Metabolism and Amino Acid Metabolism in Glucagon Receptor-Deficient Zebrafish.

Xuanxuan Bai, Jianxin Jia, Qi Kang, Yadong Fu, You Zhou, Yingbin Zhong, Chao Zhang, Mingyu Li.

  The glucagon receptor (GCGR) is activated by glucagon and is essential for glucose, amino acid, and lipid metabolism of animals. GCGR blockade has been demonstrated to induce hypoglycemia, hyperaminoacidemia, hyperglucagonemia, decreased adiposity, hepatosteatosis, and pancreatic α cells hyperplasia in organisms. However, the mechanism of how GCGR regulates these physiological functions is not yet very clear. In our previous study, we revealed that GCGR regulated metabolic network at transcriptional level by RNA-seq using GCGR mutant zebrafish (gcgr -/-). Here, we further performed whole-organism metabolomics and lipidomics profiling on wild-type and gcgr -/- zebrafish to study the changes of metabolites. We found 107 significantly different metabolites from metabolomics analysis and 87 significantly different lipids from lipidomics analysis. Chemical substance classification and pathway analysis integrated with transcriptomics data both revealed that amino acid metabolism and lipid metabolism were remodeled in gcgr-deficient zebrafish. Similar to other studies, our study showed that gcgr -/- zebrafish exhibited decreased ureagenesis and impaired cholesterol metabolism. More interestingly, we found that the glycerophospholipid metabolism was disrupted, the arachidonic acid metabolism was up-regulated, and the tryptophan metabolism pathway was down-regulated in gcgr -/- zebrafish. Based on the omics data, we further validated our findings by revealing that gcgr -/- zebrafish exhibited dampened melatonin diel rhythmicity and increased locomotor activity. These global omics data provide us a better understanding about the role of GCGR in regulating metabolic network and new insight into GCGR physiological functions.

Keywords:  glucagon; glucagon receptor; lipidomics; metabolomics; zebrafish

DOI:  https://doi.org/10.3389/fcell.2020.605979
Int J Mol Sci. 2021 Feb 02. pii: 1470. [Epub ahead of print]22(3):

GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability.

Ewelina Weglarz-Tomczak, Demi J Rijlaarsdam, Jakub M Tomczak, Stanley Brul.

  Cancer cell metabolism is dependent on cell-intrinsic factors, such as genetics, and cell-extrinsic factors, such nutrient availability. In this context, understanding how these two aspects interact and how diet influences cellular metabolism is important for developing personalized treatment. In order to achieve this goal, genome-scale metabolic models (GEMs) are used; however, genetics and nutrient availability are rarely considered together. Here, we propose integrated metabolic profiling, a framework that allows enriching GEMs with metabolic gene expression data and information about nutrients. First, the RNA-seq is converted into Reaction Activity Score (RAS) to further scale reaction bounds. Second, nutrient availability is converted to Maximal Uptake Rate (MUR) to modify exchange reactions in a GEM. We applied our framework to the human osteosarcoma cell line (U2OS). Osteosarcoma is a common and primary malignant form of bone cancer with poor prognosis, and, as indicated in our study, a glutamine-dependent type of cancer.

Keywords:  genome-scale metabolic models; metabolism; nutrients; osteosarcoma; transcription

DOI:  https://doi.org/10.3390/ijms22031470
J Lipid Res. 2021 Jan 29. pii: S0022-2275(21)00009-2. [Epub ahead of print] 100029

Suppressing post-collection lysophosphatidic acid (LPA) metabolism improves the precision of plasma LPA quantification.

Kuniyuki Kano, Hirotaka Matsumoto, Nozomu Kono, Makoto Kurano, Yutaka Yatomi, Junken Aoki.

  Lysophosphatidic acid (LPA) is a potent signaling lipid, and state-dependent alterations in LPA make it a promising diagnostic marker for various diseases. However, plasma LPA concentrations vary widely among reports, even under normal conditions. These variations can be attributed, at least in part, to the artificial metabolism of LPA after blood collection, thus complicating the use of plasma LPA as a clinical biomarker. Previous studies focused on suppressing LPA production by the LPA-producing enzyme autotaxin (ATX) but did not take the artificial LPA degradation into account. Here, we aimed to develop an optimized plasma preparation method that reflects the concentration of LPA in the circulating blood by finding conditions to suppress both the production and degradation of LPA after blood collection. The main features of the devised method were suppression of LPA production and degradation after blood collection by keeping whole blood samples at low temperature and followed by adding an ATX inhibitor to plasma samples. Using this devised method, the LPA level did not change for 30 minutes after blood collection, and mouse plasma LPA concentrations showed minimal variation across individual animals, as determined by LC-MS/MS. Additionally, human and mouse LPA levels were found to be much lower than those previously reported, ranging from 40 to 50 nM. Finally, the increased accuracy made it possible to detect circadian rhythms in the levels of certain LPA species in mouse plasma. These results demonstrate the usefulness of the devised plasma preparation method to determine accurate plasma LPA concentrations.

Keywords:  LC-MS; Lysophosphatidic acid; autotaxin; biomarker; clinical specimen; metabolism; plasma

DOI:  https://doi.org/10.1016/j.jlr.2021.100029
Curr Protoc. 2021 Feb;1(2): e32

Quantitative Proteomic Analysis of the Senescence-Associated Secretory Phenotype by Data-Independent Acquisition.

Francesco Neri, Nathan Basisty, Pierre-Yves Desprez, Judith Campisi, Birgit Schilling.

  Cellular senescence is a complex stress response that induces an essentially permanent cell cycle arrest and a complex secretory phenotype termed the senescence-associated secretory phenotype (SASP), which drives numerous aging pathologies. Characterization of the SASP can provide insights into aging and disease mechanisms, aging biomarker candidates, and targets for counteracting the deleterious effects of senescent cells. Here we describe a mass spectrometry (MS)-compatible protocol to (1) generate senescent cells using different stimuli, (2) collect conditioned medium containing proteins secreted by senescent cells (i.e., SASP), and (3) prepare the SASP for quantitative proteomic analysis using data-independent acquisition (DIA) MS. © 2021 The Authors. Basic Protocol 1: Generating ionizing radiation-induced senescent and control cells Alternate Protocol 1: Generating doxorubicin-induced senescent and control cells Alternate Protocol 2: Generating oncogenic RAS-induced senescent and control cells Alternate Protocol 3: Generating mitochondrial dysfunction-induced senescent and control cells Alternate Protocol 4: Generating atazanavir/ritonavir-induced senescent and control cells Support Protocol: A multiple-assay approach to confirm the phenotype of senescent cells Basic Protocol 2: Generating conditioned medium from senescent cells cultured in low serum and quiescent control cells Alternate Protocol 5: Generating conditioned medium from senescent cells cultured in complete medium and quiescent control cells Basic Protocol 3: Quantitative proteomic analysis of the SASP.

Keywords:  aging; data-independent acquisition; mass spectrometry; quantitative proteomic analysis; secretome; senescence

DOI:  https://doi.org/10.1002/cpz1.32
Sci Adv. 2021 Jan;pii: eabe1174. [Epub ahead of print]7(4):

1-Methylnicotinamide is an immune regulatory metabolite in human ovarian cancer.

Marisa K Kilgour, Sarah MacPherson, Lauren G Zacharias, Abigail E Ellis, Ryan D Sheldon, Elaine Y Liu, Sarah Keyes, Brenna Pauly, Gillian Carleton, Bertrand Allard, Julian Smazynski, Kelsey S Williams, Peter H Watson, John Stagg, Brad H Nelson, Ralph J DeBerardinis, Russell G Jones, Phineas T Hamilton, Julian J Lum.

Immune regulatory metabolites are key features of the tumor microenvironment (TME), yet with a few exceptions, their identities remain largely unknown. Here, we profiled tumor and T cells from tumor and ascites of patients with high-grade serous carcinoma (HGSC) to uncover the metabolomes of these distinct TME compartments. Cells within the ascites and tumor had pervasive metabolite differences, with a notable enrichment in 1-methylnicotinamide (MNA) in T cells infiltrating the tumor compared with ascites. Despite the elevated levels of MNA in T cells, the expression of nicotinamide N-methyltransferase, the enzyme that catalyzes the transfer of a methyl group from S-adenosylmethionine to nicotinamide, was restricted to fibroblasts and tumor cells. Functionally, MNA induces T cells to secrete the tumor-promoting cytokine tumor necrosis factor alpha. Thus, TME-derived MNA contributes to the immune modulation of T cells and represents a potential immunotherapy target to treat human cancer.

DOI: https://doi.org/10.1126/sciadv.abe1174
Metabolites. 2021 Feb 01. pii: 87. [Epub ahead of print]11(2):

The Effects of SGLT2 Inhibitors on Lipid Metabolism.

Zsolt Szekeres, Kalman Toth, Eszter Szabados.

  Sodium glucose co-transporter 2 (SGLT2) inhibitors are effective antihyperglycemic agents by inhibiting glucose reabsorption in the proximal tubule of the kidney. Besides improving glycemic control in patients with type 2 diabetes, they also have additional favorable effects, such as lowering body weight and body fat. Several clinical studies have demonstrated their positive effect in reducing cardiovascular morbidity and mortality. Furthermore, the use of SGLT2 inhibitors were associated with fewer adverse renal outcomes comparing to other diabetic agents, substantiating their renoprotective effect in diabetic patients. SGLT2 inhibitors have also remarkable effect on lipid metabolism acting at different cellular levels. By decreasing the lipid accumulation, visceral and subcutaneous fat, they do not only decrease the body weight but also change body composition. They also regulate key molecules in lipid synthesis and transportation, and they affect the oxidation of fatty acids. Notably, they shift substrate utilization from carbohydrates to lipids and ketone bodies. In this review we intended to summarize the role of SGLT2 inhibitors in lipid metabolism especially on lipoprotein levels, lipid regulation, fat storage and substrate utilization.

Keywords:  SGLT2 inhibitors; lipid metabolism; type 2 diabetes mellitus

DOI:  https://doi.org/10.3390/metabo11020087