bims-mascan 2024-10-20 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2024‒10‒20
seventeen papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

Met4DX: A Unified and Versatile Data Processing Tool for Multidimensional Untargeted Metabolomics Data.
Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950.
EMBL-MCF 2.0: an LC-MS/MS method and corresponding library for high-confidence targeted and untargeted metabolomics using low-adsorption HILIC chromatography.
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.
A charge reversal approach for the sensitive quantification of dicarboxylic acids using Liquid chromatography-tandem mass spectrometry.
Parallel sample processing for mass spectrometry-based single cell proteomics.
Multiomics Studies on Metabolism Changes in Alcohol-Associated Liver Disease.
Phosphoproteomic Analysis of Signaling Pathways in Lymphomas.
An integrated strategy for in-depth profiling of N-acylethanolamines in biological samples by UHPLC-HRMS.
Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer.
LC-MS simultaneous profiling of acyl-CoA and acyl-carnitine in dynamic metabolic status.
Empirically establishing drug exposure records directly from untargeted metabolomics data.
Quantification of relevant metabolites in apoptotic bodies from HK-2 cells by targeted metabolomics based on liquid chromatography-tandem mass spectrometry.
Two-Dimensional Liquid Chromatography Tandem Mass Spectrometry Untangles the Deep Metabolome of Marine Dissolved Organic Matter.
Regulation of lipid and serine metabolism by the oncogene c-Myc.
Combined spatially resolved metabolomics and spatial transcriptomics reveal the mechanism of RACK1-mediated fatty acid synthesis.
Targeted and Untargeted Amine Metabolite Quantitation in Single Cells with Isobaric Multiplexing.

J Am Soc Mass Spectrom. 2024 Oct 14.

Met4DX: A Unified and Versatile Data Processing Tool for Multidimensional Untargeted Metabolomics Data.

Yandong Yin, Mingdu Luo, Zheng-Jiang Zhu.

  Liquid chromatography-mass spectrometry (LC-MS) is a powerful tool in untargeted metabolomics, enabling the high-sensitivity and high-specificity characterization of metabolites. The integration of ion mobility (IM) with LC-MS, known as LC-IM-MS, enhances the analytical depth, facilitating more comprehensive metabolite profiling. However, the complexity of data generated by these technologies presents significant challenges in data processing. Addressing these challenges, we developed Met4DX, a unified and versatile software tool for processing both 3D and 4D untargeted metabolomics data. Met4DX incorporates a new MS1-oriented peak detection approach coupled with our bottom-up assembly algorithm, enabling highly sensitive and comprehensive peak detection in untargeted metabolomics data. Additionally, Met4DX employs a uniform quantification strategy to enhance the precision of peak integration across different samples. The software provides a user-friendly interface that simplifies data processing with default parameter sets, consolidating peak detection, alignment, quantification, and other procedures into a single streamlined workflow. Together, Met4DX offers a comprehensive solution for multidimensional metabolomics data processing, transforming raw data from diverse MS instruments into a final feature table containing quantification and identification results. We postulate Met4DX facilitates metabolite discovery in biological samples by deciphering the complex untargeted metabolomics data. Met4DX is freely available on the Internet (https://met4dx.zhulab.cn/).

Keywords:  data processing; ion mobility-mass spectrometry; mass spectrometry; untargeted metabolomics

DOI:  https://doi.org/10.1021/jasms.4c00290
J Lipid Res. 2024 Oct 10. pii: S0022-2275(24)00176-7. [Epub ahead of print] 100671

Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950.

Sara Martínez, Miguel Fernández-García, Sara Londoño-Osorio, Coral Barbas, Ana Gradillas.

  Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/-)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database -consisting of 592 lipid entries- for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies.

Keywords:  NIST SRM 1950; adduct profile; glycerolipids; glycerophospholipids; human plasma lipidome; in-house database; lipid annotation; lipidomic profiling; sphingolipids

DOI:  https://doi.org/10.1016/j.jlr.2024.100671
Metabolomics. 2024 Oct 13. 20(6): 114

EMBL-MCF 2.0: an LC-MS/MS method and corresponding library for high-confidence targeted and untargeted metabolomics using low-adsorption HILIC chromatography.

Svitlana Dekina, Theodore Alexandrov, Bernhard Drotleff.

  INTRODUCTION: Over the past two decades, liquid chromatography-mass spectrometry (LC-MS)-based metabolomics has experienced significant growth, playing a crucial role in various scientific disciplines. However, despite these advance-ments, metabolite identification (MetID) remains a significant challenge. To address this, stringent MetID requirements were established, emphasizing the necessity of aligning experimental data with authentic reference standards using multiple criteria. Establishing dependable methods and corresponding libraries is crucial for instilling confidence in MetID and driving further progress in metabolomics.OBJECTIVE: The EMBL-MCF 2.0 LC-MS/MS method and public library was designed to facilitate both targeted and untargeted metabolomics with exclusive focus on endogenous, polar metabolites, which are known to be challenging to analyze due to their hydrophilic nature. By accompanying spectral data with robust retention times obtained from authentic standards and low-adsorption chromatography, high confidence MetID is achieved and accessible to the metabolomics community.
METHODS: The library is built on hydrophilic interaction liquid chromatography (HILIC) and state-of-the-art low adsorption LC hardware. Both high-resolution tandem mass spectra and manually optimized multiple reaction monitoring (MRM) transitions were acquired on an Orbitrap Exploris 240 and a QTRAP 6500+, respectively.
RESULTS: Implementation of biocompatible HILIC has facilitated the separation of isomeric metabolites with significant enhancements in both selectivity and sensitivity. The resulting library comprises a diverse collection of more than 250 biologically relevant metabolites. The methodology was successfully applied to investigate a variety of biological matrices, with exemplary findings showcased using murine plasma samples.
CONCLUSIONS: Our work has resulted in the development of the EMBL-MCF 2.0 library, a powerful resource for sensitive metabolomics analyses and high-confidence MetID. The library is freely accessible and available in the universal .msp file format under the CC-BY 4.0 license: mona.fiehnlab.ucdavis.edu https://mona.fiehnlab.ucdavis.edu/spectra/browse?query=exists(tags.text:%27EMBL-MCF_2.0_HRMS_Library%27) , EMBL-MCF 2.0 HRMS https://www.embl.org/groups/metabolomics/instrumentation-and-software/#MCF-library .

Keywords:  LC-MS/MS; Low-adsorption chromatography; Spectral library; Targeted metabolomics; Untargeted metabolomics

DOI:  https://doi.org/10.1007/s11306-024-02176-1
Brief Bioinform. 2024 Sep 23. pii: bbae498. [Epub ahead of print]25(6):

Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.

Quang-Huy Nguyen, Ha Nguyen, Edwin C Oh, Tin Nguyen.

  Metabolite profiling is a powerful approach for the clinical diagnosis of complex diseases, ranging from cardiometabolic diseases, cancer, and cognitive disorders to respiratory pathologies and conditions that involve dysregulated metabolism. Because of the importance of systems-level interpretation, many methods have been developed to identify biologically significant pathways using metabolomics data. In this review, we first describe a complete metabolomics workflow (sample preparation, data acquisition, pre-processing, downstream analysis, etc.). We then comprehensively review 24 approaches capable of performing functional analysis, including those that combine metabolomics data with other types of data to investigate the disease-relevant changes at multiple omics layers. We discuss their availability, implementation, capability for pre-processing and quality control, supported omics types, embedded databases, pathway analysis methodologies, and integration techniques. We also provide a rating and evaluation of each software, focusing on their key technique, software accessibility, documentation, and user-friendliness. Following our guideline, life scientists can easily choose a suitable method depending on method rating, available data, input format, and method category. More importantly, we highlight outstanding challenges and potential solutions that need to be addressed by future research. To further assist users in executing the reviewed methods, we provide wrappers of the software packages at https://github.com/tinnlab/metabolite-pathway-review-docker.

Keywords:  functional analysis; liquid chromatography; mass spectrometry; metabolic pathways; metabolomics

DOI:  https://doi.org/10.1093/bib/bbae498
J Chromatogr A. 2024 Oct 09. pii: S0021-9673(24)00800-8. [Epub ahead of print]1737 465426

A charge reversal approach for the sensitive quantification of dicarboxylic acids using Liquid chromatography-tandem mass spectrometry.

Joby Jose, Alfred N Fonteh.

  Dicarboxylic acids (DCAs) are essential for intermediate metabolism and are implicated in multiple processes associated with various diseases. Several DCAs contribute to energy metabolism, impact mitochondrial function, and play a crucial role in body function. However, the low abundance of some DCAs in various body fluids makes their quantification particularly challenging. Therefore, an extremely sensitive method is required to determine DCA level fluctuations in biological samples in different diseases. We developed and optimized an LC-MS/MS method to quantify DCAs. We achieved charge reversal of the compounds from negative to positive ionization through chemical derivatization with dimethylaminophenacyl bromide (DmPABr) targeting the carboxyl group (R-COOH) under mild basic conditions. Derivatization enhanced sensitivity, mass fragmentation, and chromatographic separation for LC-tandem mass spectrometric quantification. The method was analytically optimized and demonstrated excellent linearity for individual DCAs (R2>0.99), as well as an exceptionally lower limit of detection (LLOD<266 fg) and lower limit of quantification (LLOQ<805 fg) for all DCAs. Furthermore, most derivatized DCAs were stable at room temperature and after ten repeated freeze-thaw cycles. After DCA extraction and quantification detection, we found differences in their distribution in plasma and urine. The rank order for DCAs in plasma is C4>C6>C7>C9>C5>C8>C22, whereas in the urine sample, the order is C4>C7>C6>C9>C5>C8>C10. For longer chains (C > 16), their proportions were >10x higher in plasma than in urine. Our optimized method using LC-MS/MS enables the quantification of DCAs with excellent sensitivity. The method will help in future studies investigating dicarboxylic acids' crucial role in health and biomarker discovery studies using targeted metabolomics.

Keywords:  Analytical validation; Charge reversal; Dicarboxylic acids; Liquid chromatography-tandem mass spectrometry (LC-MS/MS); Multiple reaction monitoring (MRM)

DOI:  https://doi.org/10.1016/j.chroma.2024.465426
Anal Chim Acta. 2024 Nov 15. pii: S0003-2670(24)01042-0. [Epub ahead of print]1329 343241

Parallel sample processing for mass spectrometry-based single cell proteomics.

Jing Wang, Bo Xue, Olanrewaju Awoyemi, Herbi Yuliantoro, Lihini Tharanga Mendis, Amanda DeVor, Stephen J Valentine, Peng Li.

BACKGROUND: Single cell mass spectrometry (scMS) has shown great promise for label free proteomics analysis recently. To present single cell samples for proteomics analysis by MS is not a trivial task. Existing methods rely on robotic liquid handlers to scale up sample preparation throughput. The cost associated with specialized equipment hinders the broad adoption of these workflows, and the sequential sample processing nature limits the ultimate throughput.RESULTS: In this work, we report a parallel sample processing workflow that can simultaneously process 10 single cells without the need of robotic liquid handlers for scMS. This method utilized 3D printed microfluidic devices to form reagent arrays on a glass slide, and a magnetic beads-based streamlined sample processing workflow to present peptides for LC-MS detection. We optimized key operational parameters of the method and demonstrated the quantification consistency among 10 parallel processed samples. Finally, the utility of the method in differentiating cell lines and studying the proteome change induced by drug treatment were demonstrated.
SIGNIFICANCE: The present method allows parallel sample processing for single cells without the need of expensive liquid handlers, which has great potential to further improve throughput and decrease the barrier for single cell proteomics.

DOI: https://doi.org/10.1016/j.aca.2024.343241
J Proteome Res. 2024 Oct 17.

Multiomics Studies on Metabolism Changes in Alcohol-Associated Liver Disease.

Liqing He, Raobo Xu, Xipeng Ma, Xinmin Yin, Eugene Mueller, Wenke Feng, Michael Menze, Seongho Kim, Craig J McClain, Xiang Zhang.

  Metabolic dysfunction in the liver represents a predominant feature in the early stages of alcohol-associated liver disease (ALD). However, the mechanisms underlying this are only partially understood. To investigate the metabolic characteristics of the liver in ALD, we did a relative quantification of polar metabolites and lipids in the liver of mice with experimental ALD using untargeted metabolomics and untargeted lipidomics. A total of 99 polar metabolites had significant abundance alterations in the livers of alcohol-fed mice. Pathway analysis revealed that amino acid metabolism was the most affected by alcohol in the mouse liver. Metabolites involved in glycolysis and the TCA cycle were decreased, while glycerol 3-phosphate (G3P) and long-chain fatty acids were increased. Relative quantification of lipids unveiled an upregulation of multiple lipid classes, suggesting that alcohol consumption drives metabolism toward lipid synthesis. Results from enzyme expression and activity detection indicated that the decreased activity of mitochondrial glycerol 3-phosphate dehydrogenase contributed to the disordered metabolism.

Keywords:  alcohol-associated liver disease; lipidomics; metabolic dysfunction; metabolomics; mitochondrial glycerol 3-phosphate dehydrogenase

DOI:  https://doi.org/10.1021/acs.jproteome.4c00451
Methods Mol Biol. 2025 ;2865 283-294

Phosphoproteomic Analysis of Signaling Pathways in Lymphomas.

Björn Häupl, Anne Christine Wilke, Henning Urlaub, Thomas Oellerich.

  Cellular fate is regulated by intricate signal transduction mediated by posttranslational protein modifications like phosphorylation to transmit information. As other cancer types, lymphomas frequently show dysregulation of signaling pathways that contribute to malignant transformation and tumor progression. For example, in diffuse large B-cell lymphoma the B-cell antigen receptor was identified as an oncogenic driver mediating cellular growth and survival signals. Thus, the elucidation of these complex signaling networks is crucial to gain insight into the mechanisms underlying tumorigenesis and to identify target proteins for innovative therapeutic approaches.Here, we describe a mass spectrometry-based phosphoproteomic approach for the global analysis of intracellular signaling events and their dynamics. The workflow combines phosphopeptide enrichment and fractionation with liquid chromatography-coupled mass spectrometry for the amino acid site-specific identification and quantification of thousands of phosphorylation events. Such global signaling analyses have great potential for the elucidation of oncogenic pathomechanisms, diagnostic biomarkers, and drug targets.

Keywords:   Antigen receptors; Cellular signaling; Lymphoma; Mass spectrometry; Phosphoproteomics

DOI:  https://doi.org/10.1007/978-1-0716-4188-0_13
Anal Chim Acta. 2024 Nov 15. pii: S0003-2670(24)01063-8. [Epub ahead of print]1329 343262

An integrated strategy for in-depth profiling of N-acylethanolamines in biological samples by UHPLC-HRMS.

Jun-Yi Zhou, Yan-Qing Chen, Guang Hu, Haiyu Zhao, Jian-Bo Wan.

  BACKGROUND: N-acylethanolamines (NAEs) are a class of naturally occurring bioactive lipids that play crucial roles in various physiological processes, particularly exhibiting neuroprotective and anti-inflammatory properties. However, the comprehensive profiling of endogenous NAEs in complex biological matrices is challenging due to their low abundance, structural similarity and the limited availability of commercial standards. Here, we propose an integrated strategy for comprehensive profiling of NAEs that combines chemical derivatization and a three-dimensional (3D) prediction model based on quantitative structure-retention time relationship (QSRR) using liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS).RESULTS: After acetyl chloride (ACC) derivatization, the detection sensitivity of NAEs was significantly improved. We developed a QSRR prediction model to construct an in-house database for 141 NAEs, encompassing information on RT, MS1 (m/z), and MS/MS spectra. Propargylamine-labeled fatty acids were synthesized as RT calibrants across various analytical conditions to enhance the robustness of the RT prediction model. NAEs in biological samples were then in-depth profiled using parallel reaction monitoring (PRM) acquisition. This integrated strategy identified and annotated a total of 50 NAEs across serum, hippocampus and cortex tissues from a 5xFAD mouse model of Alzheimer's disease (AD). Notably, the levels of polyunsaturated NAEs, particularly NAE 20:5 and NAE 22:6, were significantly decreased in 5xFAD mice compared to WT mice, as confirmed by accurate quantitation using ACC-d0/d3 derivatization.
SIGNIFICANCE: Our integrated strategy exhibits great potential for the in-depth profiling of NAEs in complex biological samples, facilitating the elucidation of NAE functions in diverse physiological and pathological processes.

Keywords:  Alzheimer's disease; Chemical derivatization; N-acylethanolamides; Parallel reaction monitoring; UHPLC-HRMS

DOI:  https://doi.org/10.1016/j.aca.2024.343262
EMBO J. 2024 Oct 17.

Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer.

Kanu Wahi, Natasha Freidman, Qian Wang, Michelle Devadason, Lake-Ee Quek, Angel Pang, Larissa Lloyd, Mark Larance, Fabio Zanini, Kate Harvey, Sandra O'Toole, Yi Fang Guan, Jeff Holst.

  Triple-negative breast cancer (TNBC) metabolism and cell growth uniquely rely on glutamine uptake by the transporter ASCT2. Despite previous data reporting cell growth inhibition after ASCT2 knockdown, we here show that ASCT2 CRISPR knockout is tolerated by TNBC cell lines. Despite the loss of a glutamine transporter and low rate of glutamine uptake, intracellular glutamine steady-state levels were increased in ASCT2 knockout compared to control cells. Proteomics analysis revealed upregulation of macropinocytosis, reduction in glutamine efflux and increased glutamine synthesis in ASCT2 knockout cells. Deletion of ASCT2 in the TNBC cell line HCC1806 induced a strong increase in macropinocytosis across five ASCT2 knockout clones, compared to a modest increase in ASCT2 knockdown. In contrast, ASCT2 knockout impaired cell proliferation in the non-macropinocytic HCC1569 breast cancer cells. These data identify macropinocytosis as a critical secondary glutamine acquisition pathway in TNBC and a novel resistance mechanism to strategies targeting glutamine uptake alone. Despite this adaptation, TNBC cells continue to rely on glutamine metabolism for their growth, providing a rationale for targeting of more downstream glutamine metabolism components.

Keywords:  ASCT2; Glutamine Metabolism; Macropinocytosis; Metabolomics; Triple-Negative Breast Cancer

DOI:  https://doi.org/10.1038/s44318-024-00271-6
Anal Chim Acta. 2024 Nov 15. pii: S0003-2670(24)01036-5. [Epub ahead of print]1329 343235

LC-MS simultaneous profiling of acyl-CoA and acyl-carnitine in dynamic metabolic status.

Jiangang Zhang, Juan Lei, Xudong Liu, Nan Zhang, Lei Wu, Yongsheng Li.

DOI: https://doi.org/10.1016/j.aca.2024.343235
bioRxiv. 2024 Oct 10. pii: 2024.10.07.617109. [Epub ahead of print]

Empirically establishing drug exposure records directly from untargeted metabolomics data.

Haoqi Nina Zhao, Kine Eide Kvitne, Corinna Brungs, Siddharth Mohan, Vincent Charron-Lamoureux, Wout Bittremieux, Runbang Tang, Robin Schmid, Santosh Lamichhane, Yasin El Abiead, Mohammadsobhan S Andalibi, Helena Mannochio-Russo, Madison Ambre, Nicole E Avalon, MacKenzie Bryant, Andrés Mauricio Caraballo-Rodríguez, Martin Casas Maya, Loryn Chin, Ronald J Ellis, Donald Franklin, Sagan Girod, Paulo Wender P Gomes, Lauren Hansen, Robert Heaton, Jennifer E Iudicello, Alan K Jarmusch, Lora Khatib, Scott Letendre, Sarolt Magyari, Daniel McDonald, Ipsita Mohanty, Andrés Cumsille, David J Moore, Prajit Rajkumar, Dylan H Ross, Harshada Sapre, Mohammad Reza Zare Shahneh, Sydney P Thomas, Caitlin Tribelhorn, Helena M Tubb, Corinn Walker, Crystal X Wang, Shipei Xing, Jasmine Zemlin, Simone Zuffa, David S Wishart, Rima Kaddurah-Daouk, Mingxun Wang, Manuela Raffatellu, Karsten Zengler, Tomáš Pluskal, Libin Xu, Rob Knight, Shirley M Tsunoda, Pieter C Dorrestein.

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N -acyl lipid changes in a human immunodeficiency virus cohort. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.

DOI: https://doi.org/10.1101/2024.10.07.617109
Anal Chim Acta. 2024 Nov 15. pii: S0003-2670(24)00991-7. [Epub ahead of print]1329 343190

Quantification of relevant metabolites in apoptotic bodies from HK-2 cells by targeted metabolomics based on liquid chromatography-tandem mass spectrometry.

Samuel Bernardo-Bermejo, Ana B Fernández-Martínez, Francisco Javier Lucio-Cazaña, María Castro-Puyana, María Luisa Marina.

  BACKGROUND: Apoptotic bodies play an important role in the cellular communication as a consequence of the great variety of biomolecules they harbor. There is evidence that 1st generation apoptotic bodies from HK-2 cells induced by cisplatin or UV light trigger apoptosis in naïve HK-2 cells whereas 2nd generation apoptotic bodies activate cell proliferation showing an opposite effect. Thus, the development of new analytical strategies to quantify the changes in the involved metabolites is imperative to shed light on the biological mechanisms which trigger apoptosis and cell proliferation.RESULTS: A LC-(Q-Orbitrap)MS method has been developed to quantify the metabolites unequivocally identified in the apoptotic body fluid from HK-2 cells in our previous works based on untargeted metabolomics. Thus, two different columns and gradients were tested and the HILIC column was selected taking into account the retention times and chromatographic separation. Also, different normal collision energies were tested for each metabolite and the parallel reaction monitoring was chosen to carry out the quantitative analysis. Once the method was optimized, it was evaluated in terms of linearity, limits of detection and quantification, matrix effects, accuracy, and precision, for each metabolite. Limits of detection ranged from 0.02 to 1.4 ng mL-1. A total of 9 relevant metabolites proposed as potential biomarkers to reveal metabolic differences among apoptotic bodies from HK-2 cells were quantified and some insights about the biological relevance were discussed.
SIGNIFICANCE: The first targeted metabolomics methodology enabling the quantification of relevant metabolites in apoptotic bodies from HK-2 cells was developed using LC-(Q-Orbitrap)MS. Pyridoxine, kynurenine, and creatine concentrations were determined in apoptotic bodies from HK-2 cells treated with cisplatin and UV light. Phenylacetylglycine, hippuric acid, butyrylcarnitine, acetylcarnitine, carnitine, and phenylalanine were determined in 1st and 2nd generation apoptotic bodies from HK-2 cells treated with cisplatin. Concentrations determined were useful to establish their biological role in the metabolism.

Keywords:  Apoptotic bodies; HK-2 cells; Liquid chromatography; Q-orbitrap-mass spectrometry; Quantitative analysis; Targeted metabolomics

DOI:  https://doi.org/10.1016/j.aca.2024.343190
Environ Sci Technol. 2024 Oct 16.

Two-Dimensional Liquid Chromatography Tandem Mass Spectrometry Untangles the Deep Metabolome of Marine Dissolved Organic Matter.

Stilianos Papadopoulos Lambidis, Tilman Schramm, Karoline Steuer-Lodd, Shane Farrell, Paolo Stincone, Robin Schmid, Irina Koester, Ralph Torres, Thorsten Dittmar, Lihini Aluwihare, Carsten Simon, Daniel Petras.

  Dissolved organic matter (DOM) is an ultracomplex mixture that plays a central role in global biogeochemical cycles. Despite its importance, DOM remains poorly understood at the molecular level. Over the last decades, significant efforts have been made to decipher the chemical composition of DOM by high-resolution mass spectrometry (HR-MS) and liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). Yet, the complexity and high degree of nonresolved isomers still hamper the full structural analysis of DOM. To address this challenge, we developed an offline two-dimensional (2D) LC approach using two reversed-phase dimensions with orthogonal pH levels, followed by MS/MS data acquisition and molecular networking. 2D-LC-MS/MS reduced the complexity of DOM, enhancing the quality of MS/MS spectra and increasing spectral annotation rates. Applying our approach to analyze coastal-surface DOM from Southern California (USA) and open-ocean DOM from the central North Pacific (Hawaii), we annotated in total more than 600 structures via MS/MS spectrum matching, which was up to 90% more than that in iterative 1D LC-MS/MS analysis with the same total run time. Our data offer unprecedented insights into the molecular composition of marine DOM and highlight the potential of 2D-LC-MS/MS approaches to decipher the chemical composition of ultracomplex samples.

Keywords:  2D chromatography; 2D-LC-MS/MS; dissolved organic matter; environmental metabolomics; molecular networking; tandem mass spectrometry

DOI:  https://doi.org/10.1021/acs.est.4c07173
Int Rev Cell Mol Biol. 2024 ;pii: S1937-6448(24)00044-3. [Epub ahead of print]389 236-256

Regulation of lipid and serine metabolism by the oncogene c-Myc.

Subhajit Chatterjee, Prarthana Prashanth, Vipin Rawat, Sounak Ghosh Roy.

  Tumor formation is supported by metabolic reprogramming, characterized by increase nutrient uptake, glycolysis and glutaminolysis. The c-Myc proto-oncogene is a transcription factor, upregulated in most cancers and several reports showed the role of c-Myc in other metabolic pathways such as glucose, amino acid, and nucleotide metabolism. In this short report, we tried to summarize the existing takeaway points from studies conducted in different cancer types with respect to c-Myc and lipid and serine metabolism. Here, we report that c-Myc can activate both lipid and serine metabolism against the backdrop of tumor formation, and different therapies like aspirin and lomitapide target the links between c-Myc and metabolism to slow down tumor progression and invasion. We also report diverse upstream regulators that influence c-Myc in different cancers, and interestingly components of the lipid metabolism (like lipid phosphate phosphatase and leptin) and serine metabolism can also act upstream of c-Myc in certain occasions. Finally, we also summarize the existing knowledge on the involvement of epigenetic pathways and non-coding RNAs in regulating lipid and serine metabolism and c-Myc in tumor cells. Identification of non-coding factors and epigenetic mechanisms present a promising avenue of study that could empower researchers with novel anticancer treatment targeting c-Myc and lipid and serine metabolism pathways!

Keywords:  Acetyl CoA; Acyl CoA synthetase (ACSL); C-Myc; Cancer; Fatty acid oxidation; Fatty acid synthase (FASN); Fatty acid synthesis; Serine hydroxymethyl transferase (SHMT); Serine palmitoyl transferase (SPT); Serine proteases

DOI:  https://doi.org/10.1016/bs.ircmb.2024.03.005
Mol Oncol. 2024 Oct 18.

Combined spatially resolved metabolomics and spatial transcriptomics reveal the mechanism of RACK1-mediated fatty acid synthesis.

Lixiu Xu, Jinqiu Li, Junqi Ma, Ayshamgul Hasim.

  Lipid metabolism is altered in rapidly proliferating cancer cells, where fatty acids (FAs) are utilized in the synthesis of sphingolipids and glycerophospholipids to produce cell membranes and signaling molecules. Receptor for activated C-kinase 1 (RACK1; also known as small ribosomal subunit protein) is an intracellular scaffolding protein involved in signaling pathways. Whether such lipid metabolism is regulated by RACK1 is unknown. Here, integrated spatially resolved metabolomics and spatial transcriptomics revealed that accumulation of lipids in cervical cancer (CC) samples correlated with overexpression of RACK1, and RACK1 promoted lipid synthesis in CC cells. Chromatin immunoprecipitation verified binding of sterol regulatory element-binding protein 1 (SREBP1) to acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN) promoters. RACK1 enhanced de novo FA synthesis by upregulating expression of sterol regulatory element binding transcription factor 1 (SREBP1) and lipogenic genes FASN and ACC1. Co-immunoprecipitation and western blotting revealed that RACK1 interacted with protein kinase B (AKT) to activate the AKT/mammalian target of rapamycin (mTOR)/SREBP1 signaling pathway to promote FA synthesis. Cell proliferation and apoptosis experiments suggested that RACK1-regulated FA synthesis is key in the progression of CC. Thus, RACK1 enhanced lipid synthesis through the AKT/mTOR/SREBP1 signaling pathway to promote the growth of CC cells. RACK1 may become a therapeutic target for CC.

Keywords:  RACK1; cervical cancer; metabolic alterations; spatial transcriptomics; spatially resolved metabolomics

DOI:  https://doi.org/10.1002/1878-0261.13752
Chemistry. 2024 Oct 18. e202403278

Targeted and Untargeted Amine Metabolite Quantitation in Single Cells with Isobaric Multiplexing.

Juho Heininen, Parisa Movahedi, Tapio Kotiaho, Risto Kostiainen, Tapio Pahikkala, Jaakko Teppo.

  We developed a single cell amine analysis approach utilizing isobarically multiplexed samples of 6 individual cells along with analyte abundant carrier. This methodology was applied for absolute quantitation of amino acids and untargeted relative quantitation of amines in a total of 108 individual cells using nanoflow LC with high-resolution mass spectrometry. Together with individually determined cell sizes, this provides quantification of intracellular concentrations within individual cells. The targeted method was partially validated for 10 amino acids with limits of detection in low attomoles, linear calibration range covering analyte amounts typically from 30 amol to 120 fmol, and correlation coefficients (R) above 0.99. This was applied with cell sizes recorded during dispensing to determine millimolar intracellular amino acid concentrations. The untargeted approach yielded 249 features that were detected in at least 25% of the single cells, providing modest cell type separation on principal component analysis. Using Greedy forward selection with regularized least squares, a sub-selection of 100 features explaining most of the difference was determined. These features were annotated using MS2 from analyte standards and accurate mass with library search. The approach provides accessible, sensitive, and high-throughput method with the potential to be expanded also to other forms of ultrasensitive analysis.

Keywords:  Mass spectrometry; Metabolomics; Single Cell; absolute quantitation; liquid chromatography

DOI:  https://doi.org/10.1002/chem.202403278