bims-mascan 2021-02-21 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021‒02‒21
twenty-five papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.
Charting Metabolism Heterogeneity by Nanostructure Imaging Mass Spectrometry: From Biological Systems to Subcellular Functions.
Metabolic Codependencies in the Tumor Microenvironment.
Metabolic compensation activates pro-survival mTORC1 signaling upon 3-phosphoglycerate dehydrogenase inhibition in osteosarcoma.
A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics.
Whole-body insulin resistance and energy expenditure indices, serum lipids, and skeletal muscle metabolome in a state of lipoprotein lipase overexpression.
Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting.
Selenium-dependent metabolic reprogramming during inflammation and resolution.
Metabolic support of tumour-infiltrating regulatory T cells by lactic acid.
Tandem MS-Based Metabolite Profiling of 19,20-Epoxycytochalasin C Reveals the Importance of a Hydroxy Group at the C7 Position for Biological Activity.
Creatine-mediated crosstalk between adipocytes and cancer cells regulates obesity-driven breast cancer.
Minimizing ion competition boosts volatile metabolome coverage by secondary electrospray ionization orbitrap mass spectrometry.
Derivatization with 2-hydrazino-1-methylpyridine enhances sensitivity of analysis of 5α-dihydrotestosterone in human plasma by liquid chromatography tandem mass spectrometry.
Overview of Lipidomic Analysis of Triglyceride Molecular Species in Biological Lipid Extracts.
Deep learning the collisional cross sections of the peptide universe from a million experimental values.
Selective killing of cancer cells harboring mutant RAS by concomitant inhibition of NADPH oxidase and glutathione biosynthesis.
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.
Regulation and metabolic functions of mTORC1 and mTORC2.
Determination of ketone bodies in biological samples via rapid UPLC-MS/MS.
Metabolomics: small molecules that matter more.
Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells.
Accurate quantification of lipid species affected by isobaric overlap in Fourier-Transform mass spectrometry.
Extraction and quantitative determination of bile acids in feces.
Selective glutamine metabolism inhibition in tumor cells improves antitumor T lymphocyte activity in triple-negative breast cancer.
Lipid metabolism and cancer.

Lipids Health Dis. 2021 Feb 17. 20(1): 15

Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.

Lishann M Ingram, Morgan C Finnerty, Maryam Mansoura, Chau-Wen Chou, Brian S Cummings.

  BACKGROUND: The association of circulating lipids with clinical outcomes of drug-resistant castration-resistant prostate cancer (DR-CRPC) is not fully understood. While it is known that increases in select lipids correlate to decreased survival, neither the mechanisms mediating these alterations nor the correlation of resistance to drug treatments is well characterized.METHODS: This gap-in-knowledge was addressed using in vitro models of non-cancerous, hormone-sensitive, CRPC and drug-resistant cell lines combined with quantitative LC-ESI-Orbitrap-MS (LC-ESI-MS/MS) lipidomic analysis and subsequent analysis such as Metaboanalyst and Lipid Pathway Enrichment Analysis (LIPEA).
RESULTS: Several lipid regulatory pathways were identified that are associated with Docetaxel resistance in prostate cancer (PCa). These included those controlling glycerophospholipid metabolism, sphingolipid signaling and ferroptosis. In total, 7460 features were identified as being dysregulated between the cell lines studied, and 21 lipid species were significantly altered in drug-resistant cell lines as compared to nonresistant cell lines. Docetaxel resistance cells (PC3-Rx and DU145-DR) had higher levels of phosphatidylcholine (PC), oxidized lipid species, phosphatidylethanolamine (PE), and sphingomyelin (SM) as compared to parent control cells (PC-3 and DU-145). Alterations were also identified in the levels of phosphatidic acid (PA) and diacylglyceride (DAG), whose levels are regulated by Lipin (LPIN), a phosphatidic acid phosphatase that converts PA to DAG. Data derived from cBioPortal demonstrated a population of PCa patients expressing mutations aligning with amplification of LPIN1, LPIN2 and LPIN3 genes. Lipin amplification in these genes correlated to decreased survival in these patients. Lipin-1 mRNA expression also showed a similar trend in PCa patient data. Lipin-1, but not Lipin-2 or - 3, was detected in several prostate cancer cells, and was increased in 22RV1 and PC-3 cell lines. The increased expression of Lipin-1 in these cells correlated with the level of PA.
CONCLUSION: These data identify lipids whose levels may correlate to Docetaxel sensitivity and progression of PCa. The data also suggest a correlation between the expression of Lipin-1 in cells and patients with regards to prostate cancer cell aggressiveness and patient survivability. Ultimately, these data may be useful for identifying markers of lethal and/or metastatic prostate cancer.

Keywords:  Drug resistance; Lipid metabolism; Lipid species; Lipidomics; Lipids; Mass spectrometry; Metastasis; Prostate; Prostate Cancer

DOI:  https://doi.org/10.1186/s12944-021-01437-5
J Am Soc Mass Spectrom. 2020 Dec 02. 31(12): 2392-2400

Charting Metabolism Heterogeneity by Nanostructure Imaging Mass Spectrometry: From Biological Systems to Subcellular Functions.

Amelia Palermo.

  The study of metabolism heterogeneity is essential to understand the role of metabolites in supporting and regulating biological functions. To this end, several mass spectrometry imaging (MSI) approaches have been proposed for the detection of small molecule metabolites. However, high noise from the ionization matrix and low metabolome coverage hinder their applicability for untargeted metabolomics studies across space. In this context, nanostructure imaging (/initiator) mass spectrometry (NIMS) and NIMS with fluorinated gold nanoparticles (f-AuNPs) are attractive strategies for comprehensive MSI of metabolites in biological systems, which can provide heterogeneous metabolome coverage, ultrahigh sensitivity, and high lateral resolution. In particular, NIMS with f-AuNPs permits the simultaneous detection of polar metabolites and lipids in a single and cohesive analytical session, thus allowing the systems-level interpretation of metabolic changes. In this Perspective article, we discuss the use of NIMS and f-AuNPs in the exploration of metabolism heterogeneity and provide a critical outlook on future applications of this technology for revealing the metabolic architecture that supports biological functions in health and disease, from whole organisms to tissues, single cells, and subcellular compartments.

Keywords:  Nanostructure imaging mass spectrometry; metabolism heterogeneity; metabolomics; single cell approaches; subcellular metabolism; systems biology

DOI:  https://doi.org/10.1021/jasms.0c00204
Cancer Discov. 2021 Jan 27. pii: candisc.1211.2020. [Epub ahead of print]

Metabolic Codependencies in the Tumor Microenvironment.

Prasenjit Dey, Alec C Kimmelman, Ronald A DePinho.

Metabolic reprogramming enables cancer cell growth, proliferation, and survival. This reprogramming is driven by the combined actions of oncogenic alterations in cancer cells and host cell factors acting on cancer cells in the tumor microenvironment. Cancer cell intrinsic mechanisms activate signal transduction components that either directly enhance metabolic enzyme activity or upregulate transcription factors that in turn increase expression of metabolic regulators. Extrinsic signaling mechanisms involve host-derived factors that further promote and amplify metabolic reprogramming in cancer cells. This review describes intrinsic and extrinsic mechanisms driving cancer metabolism in the tumor microenvironment and how such mechanisms may be targeted therapeutically.

DOI: https://doi.org/10.1158/2159-8290.CD-20-1211
Cell Rep. 2021 Jan 26. pii: S2211-1247(20)31667-3. [Epub ahead of print]34(4): 108678

Metabolic compensation activates pro-survival mTORC1 signaling upon 3-phosphoglycerate dehydrogenase inhibition in osteosarcoma.

Richa Rathore, Katharine E Caldwell, Charles Schutt, Caitlyn B Brashears, Bethany C Prudner, William R Ehrhardt, Cheuk Hong Leung, Heather Lin, Najat C Daw, Hannah C Beird, Abigail Giles, Wei-Lien Wang, Alexander J Lazar, John S A Chrisinger, J Andrew Livingston, Brian A Van Tine.

  Osteosarcoma is the most common pediatric and adult primary malignant bone cancer. Curative regimens target the folate pathway, downstream of serine metabolism, with high-dose methotrexate. Here, the rate-limiting enzyme in the biosynthesis of serine from glucose, 3-phosphoglycerate dehydrogenase (PHGDH), is examined, and an inverse correlation between PHGDH expression and relapse-free and overall survival in osteosarcoma patients is found. PHGDH inhibition in osteosarcoma cell lines attenuated cellular proliferation without causing cell death, prompting a robust metabolic analysis to characterize pro-survival compensation. Using metabolomic and lipidomic profiling, cellular response to PHGDH inhibition is identified as accumulation of unsaturated lipids, branched chain amino acids, and methionine cycle intermediates, leading to activation of pro-survival mammalian target of rapamycin complex 1 (mTORC1) signaling. Increased mTORC1 activation sensitizes cells to mTORC1 pathway inhibition, resulting in significant, synergistic cell death in vitro and in vivo. Identifying a therapeutic combination for PHGDH-high cancers offers preclinical justification for a dual metabolism-based combination therapy for osteosarcoma.

Keywords:  GATOR; PHGDH; SAMTOR; lipid metabolism; mTORC1; methotrexate; one-carbon metabolism; osteosarcoma; perhexiline; serine biosynthesis

DOI:  https://doi.org/10.1016/j.celrep.2020.108678
Mol Cell Proteomics. 2018 Nov;pii: S1535-9476(20)32029-6. [Epub ahead of print]17(11): 2284-2296

A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics.

Nicolai Bache, Philipp E Geyer, Dorte B Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V Treit, Sophia Doll, Igor Paron, Johannes B Müller, Florian Meier, Jesper V Olsen, Ole Vorm, Matthias Mann.

  To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop. An auxiliary gradient creates an offset, ensuring the re-focusing of the peptides before the separation on the analytical column by a single high-pressure pump. This simplified design enables robust operation over thousands of sample injections. Furthermore, the steps between injections are performed in parallel, reducing overhead time to a few minutes and allowing analysis of more than 200 samples per day. From fractionated HeLa cell lysates, deep proteomes covering more than 130,000 sequence unique peptides and close to 10,000 proteins were rapidly acquired. Using this data as a library, we demonstrate quantitation of 5200 proteins in only 21 min. Thus, the new system - termed Evosep One - analyzes samples in an extremely robust and high throughput manner, without sacrificing in depth proteomics coverage.

Keywords:  Automation; Clinical proteomics; HPLC; High Throughput Screening; Mass Spectrometry; Pre-formed gradient; Robustness; StageTip

DOI:  https://doi.org/10.1074/mcp.TIR118.000853
Metabolomics. 2021 Feb 16. 17(3): 26

Whole-body insulin resistance and energy expenditure indices, serum lipids, and skeletal muscle metabolome in a state of lipoprotein lipase overexpression.

Yuichiro Nishida, Kazutoshi Nishijima, Yosuke Yamada, Hiroaki Tanaka, Akiko Matsumoto, Jianglin Fan, Yoichi Uda, Hajime Tomatsu, Hiroyuki Yamamoto, Kenjiro Kami, Shuji Kitajima, Keitaro Tanaka.

  INTRODUCTION: Overexpression of lipoprotein lipase (LPL) protects against high-fat-diet (HFD)-induced obesity and insulin resistance in transgenic rabbits; however, the molecular mechanisms remain unclear. Skeletal muscle is a major organ responsible for insulin-stimulated glucose uptake and energy expenditure.OBJECTIVES: The main purpose of the current study was to examine the effects of the overexpression of LPL on the skeletal muscle metabolomic profiles to test our hypothesis that the mitochondrial oxidative metabolism would be activated in the skeletal muscle of LPL transgenic rabbits and that the higher mitochondrial oxidative metabolism activity would confer better phenotypic metabolic outcomes.
METHODS: Under a HFD, insulin resistance index was measured using the intravenous glucose tolerance test, and total energy expenditure (TEE) was measured by doubly-labeled water in control and LPL transgenic rabbits (n = 12, each group). Serum lipids, such as triglycerides and free fatty acid, were also measured. The skeletal muscle metabolite profile was analyzed using capillary electrophoresis time-of flight mass spectrometry in the two groups (n = 9, each group). A metabolite set enrichment analysis (MSEA) with muscle metabolites and a false discovery rate q < 0.2 was performed to identify significantly different metabolic pathways between the 2 groups.
RESULTS: The triglycerides and free fatty acid levels and insulin resistance index were lower, whereas the TEE was higher in the LPL transgenic rabbits than in the control rabbits. Among 165 metabolites detected, the levels of 37 muscle metabolites were significantly different between the 2 groups after false discovery rate correction (q < 0.2). The MSEA revealed that the TCA cycle and proteinogenic amino acid metabolism pathways were significantly different between the 2 groups (P < 0.05). In the MSEA, all four selected metabolites for the TCA cycle (2-oxoglutaric acid, citric acid, malic acid, fumaric acid), as well as eight selected metabolites for proteinogenic amino acid metabolism (asparagine, proline, methionine, phenylalanine, histidine, arginine, leucine, isoleucine) were consistently increased in the transgenic rabbits compared with control rabbits, suggesting that these two metabolic pathways were activated in the transgenic rabbits. Some of the selected metabolites, such as citric acid and methionine, were significantly associated with serum lipids and insulin resistance (P < 0.05).
CONCLUSION: The current results suggest that the overexpression of LPL may lead to increased activities of TCA cycle and proteinogenic amino acid metabolism pathways in the skeletal muscle, and these enhancements may play an important role in the biological mechanisms underlying the anti-obesity/anti-diabetes features of LPL overexpression.

Keywords:  Diabetes; Insulin resistance; Metabolism; Metabolomics; Obesity; Skeletal muscle

DOI:  https://doi.org/10.1007/s11306-021-01777-4
Anal Chem. 2021 Feb 17.

Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting.

Yangyang Bian, Florian P Bayer, Yun-Chien Chang, Chen Meng, Stefanie Hoefer, Nan Deng, Runsheng Zheng, Oleksandr Boychenko, Bernhard Kuster.

Microflow liquid chromatography tandem mass spectrometry (μLC-MS/MS) is becoming a viable alternative to nanoflow LC-MS/MS for the analysis of proteomes. We have recently demonstrated the potential of such a system operating with a 1 mm i.d. × 150 mm column and at a flow rate of 50 μL/min for high-throughput applications. On the basis of the analysis of ∼38 000 samples measured on two instruments over the past two years, we now show that the approach is extremely robust. Up to 1500 analyses were performed within one month, and >14 000 samples could be analyzed on a single column without loss of chromatographic performance. Samples included proteomes of cell lines, tissues, and human body fluids, which were analyzed with or without prior peptide fractionation or stable isotope labeling. We show that the μLC-MS/MS system is capable of measuring 2600 proteins from undepleted human plasma and ∼5000 proteins from crude human urine in 1 day, demonstrating its potential for in-depth as well as high-throughput clinical application.

DOI: https://doi.org/10.1021/acs.analchem.1c00257
J Biol Chem. 2021 Feb 10. pii: S0021-9258(21)00182-4. [Epub ahead of print] 100410

Selenium-dependent metabolic reprogramming during inflammation and resolution.

Arvind M Korwar, Ayaan Hossain, Tai-Jung Lee, Ashley E Shay, Venkatesha Basrur, Kevin Conlon, Philip B Smith, Bradley A Carlson, Howard M Salis, Andrew D Patterson, K Sandeep Prabhu.

  Trace element selenium (Se) is incorporated as the 21st amino acid, selenocysteine (Sec), into selenoproteins through tRNA[Ser]Sec. Selenoproteins act as gatekeepers of redox homeostasis and modulate immune function to effect anti-inflammation and resolution. However, mechanistic underpinnings involving metabolic reprogramming during inflammation and resolution remain poorly understood. Bacterial endotoxin lipopolysaccharide (LPS) activation of murine bone marrow-derived macrophages (BMDMs) cultured in the presence or absence of Se (as selenite) was used to examine temporal changes in the proteome and metabolome by multiplexed tandem mass tag-quantitative proteomics, metabolomics, and machine-learning approaches. Kinetic deltagram and clustering analysis indicated addition of Se led to extensive reprogramming of cellular metabolism upon stimulation with LPS enhancing PPP, TCA cycle, and OXPHOS, to aid in the phenotypic transition towards alternatively activated macrophages, synonymous with resolution of inflammation. Remodeling of metabolic pathways and consequent metabolic adaptation towards pro-resolving phenotypes began with Se treatment at 0 h and became most prominent around 8 h post LPS stimulation that included succinate dehydrogenase complex (Sdh), pyruvate kinase (Pkm), and Sedoheptulokinase (Shpk). Se-dependent modulation of these pathways predisposed BMDMs to preferentially increase OXPHOS to efficiently regulate inflammation and its timely resolution. Use of macrophages lacking selenoproteins, indicated that all three metabolic nodes were sensitive to selenoproteome expression. Furthermore, inhibition of Sdh with dimethylmalonate affected the pro-resolving effects of Se by increasing the resolution interval in a murine peritonitis model. In summary, our studies provide novel insights into the role of cellular Se via metabolic reprograming to facilitate anti-inflammation and pro-resolution.

Keywords:  macrophages; peritonitis; proteomics; redox; succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.jbc.2021.100410
Nature. 2021 Feb 15.

Metabolic support of tumour-infiltrating regulatory T cells by lactic acid.

McLane J Watson, Paolo D A Vignali, Steven J Mullett, Abigail E Overacre-Delgoffe, Ronal M Peralta, Stephanie Grebinoski, Ashley V Menk, Natalie L Rittenhouse, Kristin DePeaux, Ryan D Whetstone, Dario A A Vignali, Timothy W Hand, Amanda C Poholek, Brett M Morrison, Jeffrey D Rothstein, Stacy G Wendell, Greg M Delgoffe.

Regulatory T (Treg) cells, although vital for immune homeostasis, also represent a major barrier to anti-cancer immunity, as the tumour microenvironment (TME) promotes the recruitment, differentiation and activity of these cells1,2. Tumour cells show deregulated metabolism, leading to a metabolite-depleted, hypoxic and acidic TME3, which places infiltrating effector T cells in competition with the tumour for metabolites and impairs their function4-6. At the same time, Treg cells maintain a strong suppression of effector T cells within the TME7,8. As previous studies suggested that Treg cells possess a distinct metabolic profile from effector T cells9-11, we hypothesized that the altered metabolic landscape of the TME and increased activity of intratumoral Treg cells are linked. Here we show that Treg cells display broad heterogeneity in their metabolism of glucose within normal and transformed tissues, and can engage an alternative metabolic pathway to maintain suppressive function and proliferation. Glucose uptake correlates with poorer suppressive function and long-term instability, and high-glucose conditions impair the function and stability of Treg cells in vitro. Treg cells instead upregulate pathways involved in the metabolism of the glycolytic by-product lactic acid. Treg cells withstand high-lactate conditions, and treatment with lactate prevents the destabilizing effects of high-glucose conditions, generating intermediates necessary for proliferation. Deletion of MCT1-a lactate transporter-in Treg cells reveals that lactate uptake is dispensable for the function of peripheral Treg cells but required intratumorally, resulting in slowed tumour growth and an increased response to immunotherapy. Thus, Treg cells are metabolically flexible: they can use 'alternative' metabolites in the TME to maintain their suppressive identity. Further, our results suggest that tumours avoid destruction by not only depriving effector T cells of nutrients, but also metabolically supporting regulatory populations.

DOI: https://doi.org/10.1038/s41586-020-03045-2
ACS Omega. 2021 Feb 09. 6(5): 3717-3726

Tandem MS-Based Metabolite Profiling of 19,20-Epoxycytochalasin C Reveals the Importance of a Hydroxy Group at the C7 Position for Biological Activity.

Manoj Kushwaha, Arem Qayum, Shreyans K Jain, Jasvinder Singh, Amit Kumar Srivastava, Shubham Srivastava, Nisha Sharma, Vidushi Abrol, Ruchi Malik, Shashank K Singh, Ram A Vishwakarma, Sundeep Jaglan.

Seven cytochalasins, 19,20-epoxycytochalasin N, cytochalasin P1, deacetyl 19,20-epoxycytochalasin C, 19,20-epoxycytochalasin D, 19,20-epoxycytochalasin C, cytochalasin D, and cytochalasin C, were isolated from a fungal (Rosellinia sanctae-cruciana) crude extract. A cytotoxicity assay (sulforhodamine B) was performed on a series of cancer cell lines: HT-29, A-549, PC-3, HCT-116, SW-620, and MCF-7. Simultaneously, the liquid chromatography-mass spectrometry (LC-MS)/MS profile of 19,20-epoxycytochalasin C-treated cell lines revealed that 19,20-epoxycytochalasin C (m/z 524.25) oxidized to a metabolite of m/z 522.25 Da (-2 Da (-2H) from 19,20-epoxycytochalasin C). Further chemical oxidation of 19,20-epoxycytochalasin C using the Dess-Martin reagent produced an identical metabolite. It has been noticed that the parent molecule (19,20-epoxycytochalasin C) showed an IC50 of 650 nM (on HT-29), whereas for the oxidized metabolite (m/z 522.24) of 19,20-epoxycytochalasin C, the IC50 was >10 μM. It is clear that the parent molecule had 16 times higher cytotoxic potential as compared to the oxidized metabolite. The spectroscopic investigation indicated that the oxidation of the hydroxyl (-OH) group occurred at the C7 position in 19,20-epoxycyctochalsin C and led to the inactivation of 19,20-epoxycytochalasin C. Further, cell cycle analysis and histopathological evidence support the findings, and CDK2 could be a possible target of 19,20-epoxycyctochalasin C.

DOI: https://doi.org/10.1021/acsomega.0c05307
Cell Metab. 2021 Feb 10. pii: S1550-4131(21)00056-5. [Epub ahead of print]

Creatine-mediated crosstalk between adipocytes and cancer cells regulates obesity-driven breast cancer.

Olivia A Maguire, Sarah E Ackerman, Sarah K Szwed, Aarthi V Maganti, François Marchildon, Xiaojing Huang, Daniel J Kramer, Adriana Rosas-Villegas, Rebecca G Gelfer, Lauren E Turner, Victor Ceballos, Asal Hejazi, Bozena Samborska, Janane F Rahbani, Christien B Dykstra, Matthew G Annis, Ji-Dung Luo, Thomas S Carroll, Caroline S Jiang, Andrew J Dannenberg, Peter M Siegel, Sarah A Tersey, Raghavendra G Mirmira, Lawrence Kazak, Paul Cohen.

  Obesity is a major risk factor for adverse outcomes in breast cancer; however, the underlying molecular mechanisms have not been elucidated. To investigate the role of crosstalk between mammary adipocytes and neoplastic cells in the tumor microenvironment (TME), we performed transcriptomic analysis of cancer cells and adjacent adipose tissue in a murine model of obesity-accelerated breast cancer and identified glycine amidinotransferase (Gatm) in adipocytes and Acsbg1 in cancer cells as required for obesity-driven tumor progression. Gatm is the rate-limiting enzyme in creatine biosynthesis, and deletion in adipocytes attenuated obesity-driven tumor growth. Similarly, genetic inhibition of creatine import into cancer cells reduced tumor growth in obesity. In parallel, breast cancer cells in obese animals upregulated the fatty acyl-CoA synthetase Acsbg1 to promote creatine-dependent tumor progression. These findings reveal key nodes in the crosstalk between adipocytes and cancer cells in the TME necessary for obesity-driven breast cancer progression.

Keywords:  Acsbg1; Gatm; breast cancer; creatine; hypoxia; obesity

DOI:  https://doi.org/10.1016/j.cmet.2021.01.018
Anal Chim Acta. 2021 Mar 15. pii: S0003-2670(21)00029-5. [Epub ahead of print]1150 338209

Minimizing ion competition boosts volatile metabolome coverage by secondary electrospray ionization orbitrap mass spectrometry.

Jiayi Lan, Jérôme Kaeslin, Giorgia Greter, Renato Zenobi.

  Secondary electrospray ionization high-resolution mass spectrometry (SESI-HRMS) is an emerging technique for the detection of volatile metabolites. However, sensitivity and reproducibility of SESI-HRMS have limited its applications in untargeted metabolomics profiling. Ion suppression in the SESI source has been considered to be the main cause. Here, we show that besides ion suppression, ion competition in the C-trap of Orbitrap instruments is another important factor that influences sensitivity and reproducibility of SESI-MS. Instead of acquiring the full mass-to-charge ratio (m/z) range, acquisition of consecutive m/z windows to minimize the ion competition effect allows the detection of more features. m/z window ranges are optimized to fill the C-trap either with an equal number of features or an equal cumulative intensity per window. Considering a balance between maximizing scanning speed and minimizing ion competition, splitting the m/z = 50-500 range into 4 windows is selected for measuring human breath and bacterial culture samples on SESI-Orbitrap MS, corresponding to a duty cycle of 2.3 s at a resolution of 140'000. In a small cohort of human subjects, the proposed splitting into 4 windows allows three times more features to be detected compared to the classical full m/z range method.

Keywords:  Ion competition; Ion suppression; Metabolomics; Secondary electrospray; Volatile metabolites

DOI:  https://doi.org/10.1016/j.aca.2021.338209
J Chromatogr A. 2021 Jan 23. pii: S0021-9673(21)00057-1. [Epub ahead of print]1640 461933

Derivatization with 2-hydrazino-1-methylpyridine enhances sensitivity of analysis of 5α-dihydrotestosterone in human plasma by liquid chromatography tandem mass spectrometry.

Abdullah Mm Faqehi, Scott G Denham, Gregorio Naredo, Diego F Cobice, Shazia Khan, Joanna P Simpson, Ghazali Sabil, Rita Upreti, Fraser Gibb, Natalie Zm Homer, Ruth Andrew.

  Liquid Chromatography tandem mass spectrometry (LC-MS/MS) is the gold-standard approach for androgen analysis in biological fluids, superseding immunoassays in selectivity, particularly at low concentrations. While LC-MS/MS is established for analysis of testosterone and androstenedione, 5α-dihydrotestosterone (DHT) presents greater analytical challenges. DHT circulates at low nanomolar concentrations in men and lower in women, ionizing inefficiently and suffering from isobaric interference from other androgens. Even using current LC-MS/MS technology, large plasma volumes (>0.5 mL) are required for detection, undesirable clinically and unsuitable for animals. This study investigated derivatization approaches using hydrazine-based reagents to enhance ionization efficiency and sensitivity of analysis of DHT by LC-MS/MS. Derivatization of DHT using 2-hydrazino-1-methylpyridine (HMP) and 2-hydrazino-4-(trifluoromethyl)-pyrimidine (HTP) were compared. A method was validated using an UHPLC interfaced by electrospray with a triple quadruple mass spectrometer , analyzing human plasma (male and post-menopausal women) following solid-phase extraction. HMP derivatives were selected for validation affording greater sensitivity than those formed with HTP. HMP derivatives were detected by selected reaction monitoring (DHT-HMP m/z 396→108; testosterone-HMP m/z 394→108; androstenedione-HMP m/z 392→108). Chromatographic separation of androgen derivatives was optimized, carefully separating isobaric interferents and acceptable outputs for precision and trueness achieved following injection of 0.4 pg on column (approximately 34 pmol/L). HMP derivatives of all androgens tested could be detected in low plasma volumes: male (100 µL) and post-menopausal female (200 µL), and derivatives were stable over 30 days at -20°C. In conclusion, HMP derivatization, in conjunction with LC-MS/MS, is suitable for quantitative analysis of DHT, testosterone and androstenedione in low plasma volumes, offering advantages in sensitivity over current methodologies.

Keywords:  5α-Dihydrotestosterone; Androstenedione; Derivatization; Liquid chromatography mass spectrometry; Testosterone

DOI:  https://doi.org/10.1016/j.chroma.2021.461933
J Agric Food Chem. 2021 Feb 19.

Overview of Lipidomic Analysis of Triglyceride Molecular Species in Biological Lipid Extracts.

Xianlin Han, Hongping Ye.

  Triglyceride (TG) is a class of neutral lipids, which functions as an energy storage depot and is important for cellular growth, metabolism, and function. The composition and content of TG molecular species are crucial factors for nutritional aspects in food chemistry and are directly associated with several diseases, including atherosclerosis, diabetes, obesity, stroke, etc. As a result of the complexities of aliphatic moieties and their different connections/locations to the glycerol backbone in TG molecules, accurate identification of individual TG molecular species and quantitative assessment of TG composition and content are particularly challenging, even at the current stage of lipidomics development. Herein, methods developed for analysis of TG species, such as liquid chromatography-mass spectrometry with a variety of columns and different mass spectrometric techniques, shotgun lipidomics approaches, and ion-mobility-based analysis, are reviewed. Moreover, the potential limitations of the methods are discussed. It is our sincere hope that the overviews and discussions can provide some insights for researchers to select an appropriate approach for TG analysis and can serve as the basis for those who would like to establish a methodology for TG analysis or develop a new method when novel tools become available. Biologically accurate analysis of TG species with an enabling method should lead us toward improving the nutritional quality, revealing the effects of TG on diseases, and uncovering the underlying biochemical mechanisms related to these diseases.

Keywords:  lipidomics; mass spectrometry; metabolic syndrome; regioisomers; shotgun lipidomics; triglycerides

DOI:  https://doi.org/10.1021/acs.jafc.0c07175
Nat Commun. 2021 Feb 19. 12(1): 1185

Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Florian Meier, Niklas D Köhler, Andreas-David Brunner, Jean-Marc H Wanka, Eugenia Voytik, Maximilian T Strauss, Fabian J Theis, Matthias Mann.

The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF). The scale and precision (CV < 1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools peptides validate the model within a 1.4% median relative error (R > 0.99). Hydrophobicity, proportion of prolines and position of histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information.

DOI: https://doi.org/10.1038/s41467-021-21352-8
Cell Death Dis. 2021 Feb 16. 12(2): 189

Selective killing of cancer cells harboring mutant RAS by concomitant inhibition of NADPH oxidase and glutathione biosynthesis.

Muyun Liu, Dan Wang, Yongde Luo, Lianghao Hu, Yawei Bi, Juntao Ji, Haojie Huang, Guoqiang Wang, Liang Zhu, Jianjia Ma, Eunice Kim, Catherine K Luo, James L Abbruzzese, Xiaokun Li, Vincent W Yang, Zhaoshen Li, Weiqin Lu.

Oncogenic RAS is a critical driver for the initiation and progression of several types of cancers. However, effective therapeutic strategies by targeting RAS, in particular RASG12D and RASG12V, and associated downstream pathways have been so far unsuccessful. Treatment of oncogenic RAS-ravaged cancer patients remains a currently unmet clinical need. Consistent with a major role in cancer metabolism, oncogenic RAS activation elevates both reactive oxygen species (ROS)-generating NADPH oxidase (NOX) activity and ROS-scavenging glutathione biosynthesis. At a certain threshold, the heightened oxidative stress and antioxidant capability achieve a higher level of redox balance, on which cancer cells depend to gain a selective advantage on survival and proliferation. However, this prominent metabolic feature may irrevocably render cancer cells vulnerable to concurrent inhibition of both NOX activity and glutathione biosynthesis, which may be exploited as a novel therapeutic strategy. In this report, we test this hypothesis by treating the HRASG12V-transformed ovarian epithelial cells, mutant KRAS-harboring pancreatic and colon cancer cells of mouse and human origins, as well as cancer xenografts, with diphenyleneiodonium (DPI) and buthionine sulfoximine (BSO) combination, which inhibit NOX activity and glutathione biosynthesis, respectively. Our results demonstrate that concomitant targeting of NOX and glutathione biosynthesis induces a highly potent lethality to cancer cells harboring oncogenic RAS. Therefore, our studies provide a novel strategy against RAS-bearing cancers that warrants further mechanistic and translational investigation.

DOI: https://doi.org/10.1038/s41419-021-03473-6
Sci Adv. 2021 Feb;pii: eabf0717. [Epub ahead of print]7(8):

The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.

Florian A Schober, David Moore, Ilian Atanassov, Marco F Moedas, Paula Clemente, Ákos Végvári, Najla El Fissi, Roberta Filograna, Anna-Lena Bucher, Yvonne Hinze, Matthew The, Erik Hedman, Ekaterina Chernogubova, Arjana Begzati, Rolf Wibom, Mohit Jain, Roland Nilsson, Lukas Käll, Anna Wedell, Christoph Freyer, Anna Wredenberg.

Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.

DOI: https://doi.org/10.1126/sciadv.abf0717
Physiol Rev. 2021 Feb 18.

Regulation and metabolic functions of mTORC1 and mTORC2.

Angelia Szwed, Eugene Kim, Estela Jacinto.

  Cells metabolize nutrients for biosynthetic and bioenergetic needs to fuel growth and proliferation. The uptake of nutrients from the environment and their intracellular metabolism is a highly controlled process that involves crosstalk between growth signaling and metabolic pathways. Despite constant fluctuations in nutrient availability and environmental signals, normal cells restore metabolic homeostasis to maintain cellular functions and prevent disease. A central signaling molecule that integrates growth with metabolism is the mechanistic target of rapamycin (mTOR). mTOR is a protein kinase that responds to levels of nutrients and growth signals. mTOR forms two protein complexes, mTORC1, which is sensitive to rapamycin and mTORC2, which is not directly inhibited by this drug. Rapamycin has facilitated the discovery of the various functions of mTORC1 in metabolism. Genetic models that disrupt either mTORC1 or mTORC2 have expanded our knowledge on their cellular, tissue as well as systemic functions in metabolism. Nevertheless, our knowledge on the regulation and functions of mTORC2, particularly in metabolism, has lagged behind. Since mTOR is an important target for cancer, aging and other metabolism-related pathologies, understanding the distinct and overlapping regulation and functions of the two mTOR complexes is vital for the development of more effective therapeutic strategies. This review will discuss the key discoveries and recent findings on the regulation and metabolic functions of the mTOR complexes. We highlight findings from cancer models, but also discuss other examples of the mTOR-mediated metabolic reprogramming occurring in stem and immune cells, type 2 diabetes/obesity, neurodegenerative disorders and aging.

Keywords:  cancer metabolism; mTOR; mTORC; metabolic reprogramming; metabolism

DOI:  https://doi.org/10.1152/physrev.00026.2020
Talanta. 2021 Apr 01. pii: S0039-9140(20)31339-4. [Epub ahead of print]225 122048

Determination of ketone bodies in biological samples via rapid UPLC-MS/MS.

Patrycja Puchalska, Alisa B Nelson, David B Stagg, Peter A Crawford.

  Efforts to enhance wellness and ameliorate disease via nutritional, chronobiological, and pharmacological interventions have markedly intensified interest in ketone body metabolism. The two ketone body redox partners, acetoacetate (AcAc) and D-β-hydroxybutyrate (D-βOHB) serve distinct metabolic and signaling roles in biological systems. A highly efficient, specific, and reliable approach to simultaneously quantify AcAc and D-βOHB in biological specimens is lacking, due to challenges of separating the structural isomers and enantiomers of βOHB, and to the chemical instability of AcAc. Here we present a single UPLC-MS/MS method that simultaneously quantifies both AcAc and βOHB using independent stable isotope internal standards for both ketones. This method incorporates one sample preparation step requiring only 7 min of analysis per sample. The output is linear over three orders of magnitude, shows very low limits of detection and quantification, is highly specific, and shows favorable recovery yields from mammalian serum and tissue samples. Tandem MS discriminates D-βOHB from structural isomers 2- or 4-hydroxybutyrate as well as 3-hydroxyisobutyrate (3-HIB). Finally, a simple derivatization distinguishes D- and L-enantiomers of βOHB, 3-HIB, and 2-OHB, using the same rapid chromatographic platform. Together, this simple, efficient, reproducible, scalable, and all-encompassing method will support basic and clinical research laboratories interrogating ketone metabolism and redox biochemistry.

Keywords:  Acetoacetate instability; Acetoacetate internal standard; D-beta-hydroxybutyrate structural and stereo-isomers; Quantification of ketone bodies; UPLC-MS/MS

DOI:  https://doi.org/10.1016/j.talanta.2020.122048
Mol Omics. 2021 Feb 18.

Metabolomics: small molecules that matter more.

Balasubramanian Chellammal Muthubharathi, Thirumugam Gowripriya, Krishnaswamy Balamurugan.

Metabolomics, an analytical study with high-throughput profiling, helps to understand interactions within a biological system. Small molecules, called metabolites or metabolomes with the size of <1500 Da, depict the status of a biological system in a different manner. Currently, we are in need to globally analyze the metabolome and the pathways involved in healthy, as well as diseased conditions, for possible therapeutic applications. Metabolome analysis has revealed high-abundance molecules during different conditions such as diet, environmental stress, microbiota, and disease and treatment states. As a result, it is hard to understand the complete and stable network of metabolites of a biological system. This review helps readers know the available techniques to study metabolomics in addition to other major omics such as genomics, transcriptomics, and proteomics. This review also discusses the metabolomics in various pathological conditions and the importance of metabolomics in therapeutic applications.

DOI: https://doi.org/10.1039/d0mo00176g
BMC Cancer. 2021 Feb 17. 21(1): 174

Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells.

Jing Guo, Kiyotoshi Satoh, Sho Tabata, Masaru Mori, Masaru Tomita, Tomoyoshi Soga.

  BACKGROUND: Cisplatin (CDDP) significantly prolongs survival in various cancers, but many patients also develop resistance that results in treatment failure. Thus, this study aimed to elucidate the underlying mechanisms by which ovarian cancer cells acquire CDDP resistance.METHODS: We evaluated the metabolic profiles in CDDP-sensitive ovarian cancer A2780 cells and CDDP-resistant A2780cis cells using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). We further examined the expression of glutamine metabolism enzymes using real-time PCR and Western blot analyses. Cell viability was accessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay.
RESULTS: The results showed that levels of glutamine, glutamate, and glutathione (GSH), a key drug resistance mediator synthesized from glutamate, were significantly elevated in A2780cis cells than those in A2780 cells. Furthermore, glutamine starvation decreased the GSH levels and CDDP resistance in A2780cis cells. Interestingly, the expression of glutamine synthetase (GS/GLUL), which synthesizes glutamine from glutamate and thereby negatively regulates GSH production, was almost completely suppressed in resistant A2780cis cells. In addition, treatment of A2780cis cells with 5-aza-2'-deoxycytidine, a DNA-demethylating agent, restored GS expression and reduced CDDP resistance. In contrast, GS knockdown in CDDP-sensitive A2780 cells induced CDDP resistance.
CONCLUSIONS: The results indicate that upregulation of GSH synthesis from glutamine via DNA methylation-mediated silencing of GS causes CDDP resistance in A2780cis cells. Therefore, glutamine metabolism could be a novel therapeutic target against CDDP resistance.

Keywords:  CE-TOFMS; Cisplatin resistance; Glutamine synthetase; Metabolome; Ovarian cancer

DOI:  https://doi.org/10.1186/s12885-021-07879-5
J Lipid Res. 2021 Feb 15. pii: S0022-2275(21)00030-4. [Epub ahead of print] 100050

Accurate quantification of lipid species affected by isobaric overlap in Fourier-Transform mass spectrometry.

Marcus Höring, Christer S Ejsing, Sabrina Krautbauer, Verena M Ertl, Ralph Burkhardt, Gerhard Liebisch.

  Lipidomics data require consideration of ions with near-identical masses, which comprises amongst others the Type-II isotopic overlap. This overlap occurs in series of lipid species differing only by number of double bonds (DB) mainly due to the natural abundance of 13C-atoms. High-resolution mass spectrometry, such as Fourier-Transform mass spectrometry (FTMS), is capable of resolving Type-II overlap depending on mass resolving power. In this work, we evaluated FTMS quantification accuracy of lipid species affected by Type-II overlap. Spike experiments with lipid species pairs of various lipid classes were analyzed by flow-injection-analysis (FIA)-FTMS. Accuracy of quantification was evaluated without and with Type-II correction (using relative isotope abundance) as well as utilizing the first isotopic peak (M+1). Isobaric peaks, which were sufficiently resolved, were most accurate without Type-II correction. In cases of partially resolved peaks, we observed peak interference causing distortions in mass and intensity, which is a well described phenomenon in FTMS. Concentrations of respective species were more accurate when calculated from M+1. Moreover, some minor species, affected by considerable Type-II overlap, could only be quantified by M+1. Unexpectedly, even completely unresolved peaks were substantially overcorrected by Type-II correction due to peak interference. The described method was validated including intra and inter-day precisions for human serum and fibroblast samples. Taken together, our results show that accurate quantification of lipid species by FTMS requires resolution-depended data analysis.

Keywords:  Data processing; Fourier-Transform mass spectrometry; Isotope correction; Lipidomics; Lipids; Mass spectrometry; Peak interference; Phospholipids; Sphingolipids; Triglycerides

DOI:  https://doi.org/10.1016/j.jlr.2021.100050
Anal Chim Acta. 2021 Mar 15. pii: S0003-2670(21)00050-7. [Epub ahead of print]1150 338224

Extraction and quantitative determination of bile acids in feces.

Armaghan Shafaei, Joanna Rees, Claus T Christophersen, Amanda Devine, David Broadhurst, Mary C Boyce.

  With rapid advances in gut microbiome research, fecal bile acids are increasingly being monitored as potential biomarkers of diet related disease susceptibility. As such, rapid, robust and reliable methods for their analysis are of increasing importance. Herein is described a simple extraction method for the analysis of bile acids in feces suitable for subsequent quantification by liquid chromatography and tandem mass spectrometry. A C18 column separated the analytes with excellent peak shape and retention time repeatability maintained across 800 injections. The intra-day and inter-day precision and accuracy was greater than 80%. Recoveries ranged from 83.58 to 122.41%. The limit of detection and limit of quantification were in the range 2.5-15 nM, respectively. The optimized method involved extracting bile acids from wet feces with minimal clean up. A second aliquot of fecal material was dried and weighed to correct for water content. Extracting from dried feces showed reduced recovery that could be corrected for by spiking the feces with deuterated standards prior to drying. Storage of the extracts and standards in a refrigerated autosampler prior to analysis on the LC-MS is necessary. Multiple freeze-thaws of both extracts and standards lead to poor recoveries for some bile acids. The method was successfully applied to 100 human fecal samples.

Keywords:  Bile acids; Extraction; Fecal; LC-MS/MS; Stability

DOI:  https://doi.org/10.1016/j.aca.2021.338224
J Clin Invest. 2021 Feb 15. pii: 140100. [Epub ahead of print]131(4):

Selective glutamine metabolism inhibition in tumor cells improves antitumor T lymphocyte activity in triple-negative breast cancer.

Deanna N Edwards, Verra M Ngwa, Ariel L Raybuck, Shan Wang, Yoonha Hwang, Laura C Kim, Sung Hoon Cho, Yeeun Paik, Qingfei Wang, Siyuan Zhang, H Charles Manning, Jeffrey C Rathmell, Rebecca S Cook, Mark R Boothby, Jin Chen.

  Rapidly proliferating tumor and immune cells need metabolic programs that support energy and biomass production. The amino acid glutamine is consumed by effector T cells and glutamine-addicted triple-negative breast cancer (TNBC) cells, suggesting that a metabolic competition for glutamine may exist within the tumor microenvironment, potentially serving as a therapeutic intervention strategy. Here, we report that there is an inverse correlation between glutamine metabolic genes and markers of T cell-mediated cytotoxicity in human basal-like breast cancer (BLBC) patient data sets, with increased glutamine metabolism and decreased T cell cytotoxicity associated with poor survival. We found that tumor cell-specific loss of glutaminase (GLS), a key enzyme for glutamine metabolism, improved antitumor T cell activation in both a spontaneous mouse TNBC model and orthotopic grafts. The glutamine transporter inhibitor V-9302 selectively blocked glutamine uptake by TNBC cells but not CD8+ T cells, driving synthesis of glutathione, a major cellular antioxidant, to improve CD8+ T cell effector function. We propose a "glutamine steal" scenario, in which cancer cells deprive tumor-infiltrating lymphocytes of needed glutamine, thus impairing antitumor immune responses. Therefore, tumor-selective targeting of glutamine metabolism may be a promising therapeutic strategy in TNBC.

Keywords:  Amino acid metabolism; Breast cancer; Cancer immunotherapy; Oncology

DOI:  https://doi.org/10.1172/JCI140100
J Exp Med. 2021 Jan 04. pii: e20201606. [Epub ahead of print]218(1):

Lipid metabolism and cancer.

Xueli Bian, Rui Liu, Ying Meng, Dongming Xing, Daqian Xu, Zhimin Lu.

Dysregulation in lipid metabolism is among the most prominent metabolic alterations in cancer. Cancer cells harness lipid metabolism to obtain energy, components for biological membranes, and signaling molecules needed for proliferation, survival, invasion, metastasis, and response to the tumor microenvironment impact and cancer therapy. Here, we summarize and discuss current knowledge about the advances made in understanding the regulation of lipid metabolism in cancer cells and introduce different approaches that have been clinically used to disrupt lipid metabolism in cancer therapy.

DOI: https://doi.org/10.1084/jem.20201606