bims-mascan 2024-03-10 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2024–03–10
twenty papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

A comprehensive UHPLC-MS/MS method for metabolomics profiling of signaling lipids: Markers of oxidative stress, immunity and inflammation.
Profiling of Oxylipins as Markers of Oxidative Stress in Biological Samples.
Metabolism-regulated ferroptosis in cancer progression and therapy.
Computational tools and algorithms for ion mobility spectrometry-mass spectrometry.
Regulation of urea cycle by reversible high-stoichiometry lysine succinylation.
Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS.
Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry.
An Integrated Hepatocyte Stability Assay for Simultaneous Metabolic Stability Assessment and Metabolite Profiling.
The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes.
Preparation of thiol-free amino acid plasma matrix for quantification of thiol amino acids and their oxidized forms in human plasma by UPLC-MS/MS.
Growth Signaling Networks Orchestrate Cancer Metabolic Networks.
Accurate redox state indication by in situ derivatization with n-ethylmaleimide - Profiling of transsulfuration and glutathione pathway metabolites by UPLC-MS/MS.
Targeted ultra performance liquid chromatography tandem mass spectrometry procedures for the diagnosis of inborn errors of metabolism: validation through ERNDIM external quality assessment schemes.
The potential of aryl hydrocarbon receptor as receptors for metabolic changes in tumors.
Mitochondrial ATP generation is more proteome efficient than glycolysis.
An ultra-sensitive and high-throughput trapping-micro-LC-MS method for quantification of circulating vitamin D metabolites and application in multiple sclerosis patients.
Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases.
Untargeted metabolomics reveals potential plasma biomarkers for diagnosis of primary aldosteronism using liquid chromatography-mass spectrometry.
Lipid droplets and cellular lipid flux.
Inhibition of mitochondrial folate metabolism drives differentiation through mTORC1 mediated purine sensing.

Anal Chim Acta. 2024 Apr 08. pii: S0003-2670(24)00149-1. [Epub ahead of print]1297 342348

A comprehensive UHPLC-MS/MS method for metabolomics profiling of signaling lipids: Markers of oxidative stress, immunity and inflammation.

Wei Yang, Johannes C Schoeman, Xinyu Di, Lieke Lamont, Amy C Harms, Thomas Hankemeier.

  Signaling lipids (SLs) play a crucial role in various signaling pathways, featuring diverse lipid backbone structures. Emerging evidence showing the biological significance and biomedical values of SLs has strongly spurred the advancement of analytical approaches aimed at profiling SLs. Nevertheless, the dramatic differences in endogenous abundances across lipid classes as well as multiple isomers within the same lipid class makes the development of a generic analytical method challenging. A better analytical method that combines comprehensive coverage and high sensitivity is needed to enable us to gain a deeper understanding of the biochemistry of these molecules in health and disease. In this study, we developed a fast and comprehensive targeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for profiling SLs. The platform enables analyses of 260 metabolites covering oxylipins (isoprostanes, prostaglandins and other oxidized lipids), free fatty acids, lysophospholipids, sphingoid bases (C16, C18), platelet activating factors (C16, C18), endocannabinoids and bile acids. Various validation parameters including linearity, limit of detection, limit of quantification, extraction recovery, matrix effect, intra-day and inter-day precision were used to characterize this method. Metabolite quantitation was successfully achieved in both NIST Standard Reference Material for human plasma (NIST SRM 1950) and pooled human plasma, with 109 and 144 metabolites quantitated. The quantitation results in NIST SRM 1950 plasma demonstrated good correlations with certified or previously reported values in published literature. This study introduced quantitative data for 37 SLs for the first time. Metabolite concentrations measured in NIST SRM 1950 will serve as essential reference data for facilitating interlaboratory comparisons. The methodology established here will be the cornerstone for in-depth profiling of signaling lipids across diverse biological samples and contexts.

Keywords:  Bile acids; Endocannabinoids; Inflammation; Lysophospholipids; Oxylipins; SRM 1950

DOI:  https://doi.org/10.1016/j.aca.2024.342348
Curr Protoc. 2024 Mar;4(3): e992

Profiling of Oxylipins as Markers of Oxidative Stress in Biological Samples.

Liping Yang, Jaewoo Choi, Claudia S Maier, Jan F Stevens.

  Oxylipins are oxidized metabolites of polyunsaturated fatty acids (PUFAs). They represent a class of risk markers and/or therapeutic targets for diseases associated with inflammation, including cardiovascular disease and brain disorders. Because the biological activities of free PUFAs and oxylipins depend on their chemical structures and concentrations, monitoring PUFAs and oxylipin levels in biological systems is critical for understanding their roles in health and disease. Traditionally, accurate quantification of free PUFAs and oxylipins in biological samples was performed separately, as PUFAs are often 1000-fold more abundant than the derived oxidized fatty acids (oxylipins). This article describes a liquid chromatography multiple reaction monitoring tandem mass spectrometry method for the quantitative analysis of five free PUFAs and 88 oxylipins in various biological fluids, including plasma, platelet supernatants, and tissues. The same approach can also be used in conjunction with an alkaline hydrolysis step to quantify total oxylipins in fish oils. We observed that in some samples, linoleic acid levels in plasma and eicosapentaenoic acid and arachidonic acid levels in brain tissue were above the upper limit of quantification. To address this issue, we developed a data analysis method to obtain PUFA and oxylipin concentrations in these samples without additional sample preparation, thus significantly saving time and labor. © 2024 Wiley Periodicals LLC. Basic Protocol: Quantification of polyunsaturated fatty acids (PUFAs) and oxylipins using liquid chromatography multiple reaction monitoring tandem mass spectrometry Support Protocol 1: Preparation of internal standard mixed working solution Support Protocol 2: Preparation of standard mixed stock solution Support Protocol 3: Preparation of standard mixed working solution Alternate Protocol 1: Extraction and quantitation of free PUFAs and oxylipins from mouse brain tissue Alternate Protocol 2: Extraction and quantitation of total PUFAs and oxylipins from fish oil.

Keywords:  eicosanoids; multiple reaction monitoring mass spectrometry; oxylipins; polyunsaturated fatty acids; protectins; resolvins

DOI:  https://doi.org/10.1002/cpz1.992
Cell Death Dis. 2024 Mar 08. 15(3): 196

Metabolism-regulated ferroptosis in cancer progression and therapy.

Lvlan Ye, Xiangqiong Wen, Jiale Qin, Xiang Zhang, Youpeng Wang, Ziyang Wang, Ti Zhou, Yuqin Di, Weiling He.

Cancer metabolism mainly includes carbohydrate, amino acid and lipid metabolism, each of which can be reprogrammed. These processes interact with each other to adapt to the complicated microenvironment. Ferroptosis is a regulated cell death induced by iron-dependent lipid peroxidation, which is morphologically different from apoptosis, necrosis, necroptosis, pyroptosis, autophagy-dependent cell death and cuprotosis. Cancer metabolism plays opposite roles in ferroptosis. On the one hand, carbohydrate metabolism can produce NADPH to maintain GPX4 and FSP1 function, and amino acid metabolism can provide substrates for synthesizing GPX4; on the other hand, lipid metabolism might synthesize PUFAs to trigger ferroptosis. The mechanisms through which cancer metabolism affects ferroptosis have been investigated extensively for a long time; however, some mechanisms have not yet been elucidated. In this review, we summarize the interaction between cancer metabolism and ferroptosis. Importantly, we were most concerned with how these targets can be utilized in cancer therapy.

DOI: https://doi.org/10.1038/s41419-024-06584-y
Proteomics. 2024 Mar 04. e2200436

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry.

Dylan H Ross, Harsh Bhotika, Xueyun Zheng, Richard D Smith, Kristin E Burnum-Johnson, Aivett Bilbao.

  Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

Keywords:  algorithm; collision-cross section; computational tool; data processing; ion mobility spectrometry-mass spectrometry; lipidomics; metabolomics; proteomics; software

DOI:  https://doi.org/10.1002/pmic.202200436
Nat Metab. 2024 Mar 06.

Regulation of urea cycle by reversible high-stoichiometry lysine succinylation.

Ran Zhang, Jingqi Fang, Xueshu Xie, Chris Carrico, Jesse G Meyer, Lei Wei, Joanna Bons, Jacob Rose, Rebeccah Riley, Ryan Kwok, Prasanna Vadhana Ashok Kumaar, Yini Zhang, Wenjuan He, Yuya Nishida, Xiaojing Liu, Jason W Locasale, Birgit Schilling, Eric Verdin.

The post-translational modification lysine succinylation is implicated in the regulation of various metabolic pathways. However, its biological relevance remains uncertain due to methodological difficulties in determining high-impact succinylation sites. Here, using stable isotope labelling and data-independent acquisition mass spectrometry, we quantified lysine succinylation stoichiometries in mouse livers. Despite the low overall stoichiometry of lysine succinylation, several high-stoichiometry sites were identified, especially upon deletion of the desuccinylase SIRT5. In particular, multiple high-stoichiometry lysine sites identified in argininosuccinate synthase (ASS1), a key enzyme in the urea cycle, are regulated by SIRT5. Mutation of the high-stoichiometry lysine in ASS1 to succinyl-mimetic glutamic acid significantly decreased its enzymatic activity. Metabolomics profiling confirms that SIRT5 deficiency decreases urea cycle activity in liver. Importantly, SIRT5 deficiency compromises ammonia tolerance, which can be reversed by the overexpression of wild-type, but not succinyl-mimetic, ASS1. Therefore, lysine succinylation is functionally important in ammonia metabolism.

DOI: https://doi.org/10.1038/s42255-024-01005-y
J Proteome Res. 2024 Mar 06.

Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS.

Soroush Torkamannejad, Ge Chang, Fabusuyi A Aroge, Bingyun Sun.

  Targeted mass spectrometry (MS)-based absolute quantitative analysis has been increasingly used in biomarker discovery. The ability to accurately measure the masses by MS enabled the use of isotope-incorporated surrogates having virtually identical physiochemical properties with the target analytes as calibrators. Such a unique capacity allowed for accurate in-sample calibration. Current in-sample calibration uses multiple isotopologues or structural analogues for both the surrogate and the internal standard. Here, we simplified this common practice by using endogenous light peptides as the internal standards and used a mathematical deduction of "heavy matching light, HML" to directly quantify an endogenous analyte. This method provides all necessary assay performance parameters in the authentic matrix, including the lower limit of quantitation (LLOQ) and intercept of the calibration curve, by using only a single isotopologue of the analyte. This method can be applied to the quantitation of proteins, peptides, and small molecules. Using this method, we quantified the efficiency of heart tissue digestion and recovery using sodium deoxycholate as a detergent and two spiked exogenous proteins as mimics of heart proteins. The results demonstrated the robustness of the assay.

Keywords:  absolute protein quantification; digestion and recovery efficiency; in-sample calibration; membrane proteins; parallel reaction monitoring (PRM); stable isotope dilution; surrogate analyte method; surrogate matrix method; targeted mass spectrometry

DOI:  https://doi.org/10.1021/acs.jproteome.3c00848
J Am Soc Mass Spectrom. 2024 Mar 05.

Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry.

Hoi-Ting Wu, Brielle L Van Orman, Ryan R Julian.

  Isomerized amino acid residues have been identified in many peptides extracted from tissues or excretions of humans and animals. These isomerized residues can play key roles by affecting biological activity or by exerting an influence on the process of aging. Isomerization occurs spontaneously and does not result in a mass shift. Thus, identifying and localizing isomerized residues in biological samples is challenging. Herein, we introduce a fast and efficient method using tandem mass spectrometry (MS) to locate isomerized residues in peptides. Although MS2 spectra are useful for identifying peptides that contain an isomerized residue, they cannot reliably localize isomerization sites. We show that this limitation can be overcome by utilizing MS3 experiments to further evaluate each fragment ion from the MS2 stage. Comparison at the MS3 level, utilizing statistical analyses, reveals which MS2 fragments differ between samples and, therefore, must contain the isomerized sites. The approach is similar to previous work relying on ion mobility to discriminate MS2 product ions by collision cross-section. The MS3 approach can be implemented using either ion-trap or beam-type collisional activation and is compatible with the quantification of isomer mixtures when coupled to a calibration curve. The method can also be implemented in combination with liquid chromatography in a targeted approach. Enabling the identification and localization of isomerized residues in peptides with an MS-only methodology will expand accessibility to this important information.

Keywords:  Epimer; Fragmentation; Isoleucine; Isomer; Leucine; isoAsp

DOI:  https://doi.org/10.1021/jasms.3c00373
Drug Metab Dispos. 2024 Mar 04. pii: DMD-AR-2023-001618. [Epub ahead of print]

An Integrated Hepatocyte Stability Assay for Simultaneous Metabolic Stability Assessment and Metabolite Profiling.

Christian Leung, Joyce Liu, Katherine Cunico, Kevin Johnson, Zhengyin Yan, Jingwei Cai.

  The determination of metabolic stability is critical for drug discovery programs, allowing for the optimization of chemical entities and compound prioritization. As such, it is common to perform high-volume in vitro metabolic stability experiments early in the lead optimization process to understand metabolic liabilities. Additional metabolite identification experiments are subsequently performed for a more comprehensive understanding of the metabolic clearance routes to aid medicinal chemists in the structural design of compounds. Collectively, these experiments require extensive sample preparation and a substantial amount of time and resources. To overcome the challenges, a high-throughput integrated assay for simultaneous hepatocyte metabolic stability assessment and metabolite profiling was developed. This assay platform consists of four parts: 1) an automated liquid-handling system for sample preparation and incubation; 2) a liquid chromatography and high-resolution mass spectrometry-based system to simultaneously monitor the parent compound depletion and metabolite formation; 3) an automated data analysis and report system for hepatic clearance assessment; and 4) a streamlined auto-batch processing for software-based metabolite profiling. The assay platform was evaluated using eight control compounds with various metabolic rates and biotransformation routes in hepatocytes across three species. Multiple sample preparation and data analysis steps were evaluated and validated for accuracy, repeatability, and metabolite coverage. The combined utility of an automated liquid-handling instrument, a high-resolution mass spectrometer, and multiple streamlined data processing software improves the process of these highly demanding screening assays, and allows for simultaneous determination of metabolic stability and metabolite profiles for more efficient lead optimization during early drug discovery. Significance Statement Metabolic stability assessment and metabolite profiling are pivotal in drug discovery to fully comprehend metabolic liabilities for chemical entity optimization and lead selection. The process of these assays can be repetitive, time-consuming, and resource demanding. Here, we developed an integrated hepatocyte stability assay that combines automation, HRMS and batch-processing softwares, to improve and combine the workflow of these assays. The integrated approach allows simultaneous metabolic stability assessment and metabolite profiling, significantly accelerating screening and lead optimization in a resource-effective manner.

Keywords:  High performance liquid chromatography (HPLC); Mass spectrometry (MS); drug clearance; hepatocytes; high throughput screening; metabolite identification

DOI:  https://doi.org/10.1124/dmd.123.001618
Microbiome. 2024 Mar 07. 12(1): 46

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes.

Thibaut Dumas, Roxana Martinez Pinna, Clément Lozano, Sonja Radau, Olivier Pible, Lucia Grenga, Jean Armengaud.

   BACKGROUND: By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems.
RESULTS: Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria.
CONCLUSIONS: Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.

Keywords:  Functional analysis; Microbiome; Proteotyping; Tandem mass spectrometry; Taxonomy

DOI:  https://doi.org/10.1186/s40168-024-01766-4
J Chromatogr A. 2024 Feb 27. pii: S0021-9673(24)00149-3. [Epub ahead of print]1720 464776

Preparation of thiol-free amino acid plasma matrix for quantification of thiol amino acids and their oxidized forms in human plasma by UPLC-MS/MS.

Ting Tao, Yuyu Cao, Liping Zhang, Dayi Xu, Kaiyuan Pang, Yanli Li, Xiaobao Wei, Zengxian Sun.

  Thiol amino acids, with great physiological significance, are unstable, and have small molecular weights, as well as very low endogenous concentrations. Therefore, to quantitatively and directly analyze them using liquid chromatography-tandem mass spectrometry is difficult. To overcome these problems, we aimed to prepare a thiol-free amino acid plasm matrix as blank sample to reduce the background for the first time. Using compounds with maleimide group that react with classical thiols to generate water-insoluble products. Reducing agents Tris(2-carboxyethyl)phosphine (TCEP) was applied to cooperate with bismaleimide (DM) for elimination of thiol amino acids from plasma 10 min at room temperature and pH 7. Further, the residual TCEP from plasma were removed using an anion exchange resin within 10 min. Methodological validation analysis revealed good performance in linearity, precision, extraction recovery (≥ 82 %), and stability (except oxidized glutathione). This quantitative analysis was successfully applied to blood samples of 9 people in good health. This study provides a foundation for the development of accurate and rigorous quantitative analysis methods targeting thiol amino acids in different body fluids or tissues. Moreover, it paves the way toward realizing several clinical applications.

Keywords:  Thiol amino acids; Thiol-free amino acid plasma; UPLC- MS/MS

DOI:  https://doi.org/10.1016/j.chroma.2024.464776
Cold Spring Harb Perspect Med. 2024 Mar 04. pii: a041543. [Epub ahead of print]

Growth Signaling Networks Orchestrate Cancer Metabolic Networks.

Brendan D Manning, Christian C Dibble.

Normal cells grow and divide only when instructed to by signaling pathways stimulated by exogenous growth factors. A nearly ubiquitous feature of cancer cells is their capacity to grow independent of such signals, in an uncontrolled, cell-intrinsic manner. This property arises due to the frequent oncogenic activation of core growth factor signaling pathway components, including receptor tyrosine kinases, PI3K-AKT, RAS-RAF, mTORC1, and MYC, leading to the aberrant propagation of pro-growth signals independent of exogenous growth factors. The growth of both normal and cancer cells requires the acquisition of nutrients and their anabolic conversion to the primary macromolecules underlying biomass production (protein, nucleic acids, and lipids). The core growth factor signaling pathways exert tight regulation of these metabolic processes and the oncogenic activation of these pathways drive the key metabolic properties of cancer cells and tumors. Here, we review the molecular mechanisms through which these growth signaling pathways control and coordinate cancer metabolism.

DOI: https://doi.org/10.1101/cshperspect.a041543
J Chromatogr B Analyt Technol Biomed Life Sci. 2024 Feb 27. pii: S1570-0232(24)00070-9. [Epub ahead of print]1236 124062

Accurate redox state indication by in situ derivatization with n-ethylmaleimide - Profiling of transsulfuration and glutathione pathway metabolites by UPLC-MS/MS.

Mathias Langner, Dennis Fröbel, Jana Helm, Triantafyllos Chavakis, Mirko Peitzsch, Nicole Bechmann.

   BACKGROUND: Reduced and oxidized glutathione play an important role for the intracellular detoxification of reactive oxygen species. The iron-dependent formation of such reactive oxygen species in conjunction with the inhibition of the redox-balancing enzyme glutathione peroxidase 4 underlie an imbalance in the cellular redox state, thereby resulting in a non-apoptotic form of cell death, defined as ferroptosis, which is relevant in several pathologies.
METHODS: Here we present a rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based method providing the accurate quantification of 12 glutathione pathway metabolites after in situ derivatization with N-Ethylmaleimide (NEM). The method was validated regards linearity, recovery and accuracy as well as precision. The assay includes glutathione and its oxidized form glutathione disulfide. Furthermore, the related precursors cysteine, cystine, glutamic acid, γ-glutamylcysteine and cysteinylglycine, biomarkers of protein crosslinking such as cystathionine and lanthionine, as well as metabolites of the transsulfuration pathway, methionine, homocysteine and serine are simultaneously determined.
RESULTS: Twelve glutathione pathway metabolites were simultaneously analyzed in four different human cell line extracts within a total LC run time of 5.5 min. Interday coefficients of variation (1.7 % to 12.0 %), the mean observed accuracy (100.0 % ± 5.2 %), linear quantification ranges over three orders of magnitude for all analytes and sufficient metabolite stability after NEM-derivatization demonstrate method reliability. Immediate derivatization with NEM at cell harvesting prevents autooxidation of glutathione, ensures accurate results for the GSH/GSSG redox ratio and thereby allows interpretation of cellular redox state.
CONCLUSION: The described UPLC-MS/MS method provides a sensitive and selective tool for a fast and simultaneous analysis of glutathione pathway metabolites, its direct precursors and related compounds. Assay performance characteristics demonstrate the suitability of the method for applications in different cell cultures. Therefore, by providing glutathione related functional metabolic readouts, the method enables investigations in mechanisms of ferroptosis and alterations in oxidative stress levels in several pathophysiologies.

Keywords:  Ferroptosis; Glutathione; LC-MS/MS; NEM; Oxidative stress

DOI:  https://doi.org/10.1016/j.jchromb.2024.124062
Clin Chem Lab Med. 2024 Mar 11.

Targeted ultra performance liquid chromatography tandem mass spectrometry procedures for the diagnosis of inborn errors of metabolism: validation through ERNDIM external quality assessment schemes.

Clara Oliva, Angela Arias, Pedro Ruiz-Sala, Judit Garcia-Villoria, Rachel Carling, Jörgen Bierau, George J G Ruijter, Mercedes Casado, Aida Ormazabal, Rafael Artuch.

   OBJECTIVES: Early diagnosis of inborn errors of metabolism (IEM) is crucial to ensure early detection of conditions which are treatable. This study reports on targeted metabolomic procedures for the diagnosis of IEM of amino acids, acylcarnitines, creatine/guanidinoacetate, purines/pyrimidines and oligosaccharides, and describes its validation through external quality assessment schemes (EQA).
METHODS: Analysis was performed on a Waters ACQUITY UPLC H-class system coupled to a Waters Xevo triple-quadrupole (TQD) mass spectrometer, operating in both positive and negative electrospray ionization mode. Chromatographic separation was performed on a CORTECS C18 column (2.1 × 150, 1.6 µm). Data were collected by multiple reaction monitoring.
RESULTS: The internal and EQA results were generally adequate, with a few exceptions. We calculated the relative measurement error (RME) and only a few metabolites displayed a RME higher than 30 % (asparagine and some acylcarnitine species). For oligosaccharides, semi-quantitative analysis of an educational panel clearly identified the 8 different diseases included.
CONCLUSIONS: Overall, we have validated our analytical system through an external quality control assessment. This validation will contribute to harmonization between laboratories, thus improving identification and management of patients with IEM.

Keywords:  UPLC; external quality assessment; inborn errors of metabolism; tandem mass spectrometry; targeted metabolomics

DOI:  https://doi.org/10.1515/cclm-2023-1291
Front Oncol. 2024 ;14 1328606

The potential of aryl hydrocarbon receptor as receptors for metabolic changes in tumors.

Zhiying Wang, Yuanqi Zhang, Zhihong Liao, Mingzhang Huang, Xiaorong Shui.

  Cancer cells can alter their metabolism to meet energy and molecular requirements due to unfavorable environments with oxygen and nutritional deficiencies. Therefore, metabolic reprogramming is common in a tumor microenvironment (TME). Aryl hydrocarbon receptor (AhR) is a ligand-activated nuclear transcription factor, which can be activated by many exogenous and endogenous ligands. Multiple AhR ligands can be produced by both TME and tumor cells. By attaching to various ligands, AhR regulates cancer metabolic reprogramming by dysregulating various metabolic pathways, including glycolysis, lipid metabolism, and nucleotide metabolism. These regulated pathways greatly contribute to cancer cell growth, metastasis, and evading cancer therapies; however, the underlying mechanisms remain unclear. Herein, we review the relationship between TME and metabolism and describe the important role of AhR in cancer regulation. We also focus on recent findings to discuss the idea that AhR acts as a receptor for metabolic changes in tumors, which may provide new perspectives on the direction of AhR research in tumor metabolic reprogramming and future therapeutic interventions.

Keywords:  aryl hydrocarbon receptor; cancer; metabolic reprogramming; metabolism; tumor microenvironment

DOI:  https://doi.org/10.3389/fonc.2024.1328606
Nat Chem Biol. 2024 Mar 06.

Mitochondrial ATP generation is more proteome efficient than glycolysis.

Yihui Shen, Hoang V Dinh, Edward R Cruz, Zihong Chen, Caroline R Bartman, Tianxia Xiao, Catherine M Call, Rolf-Peter Ryseck, Jimmy Pratas, Daniel Weilandt, Heide Baron, Arjuna Subramanian, Zia Fatma, Zong-Yen Wu, Sudharsan Dwaraknath, John I Hendry, Vinh G Tran, Lifeng Yang, Yasuo Yoshikuni, Huimin Zhao, Costas D Maranas, Martin Wühr, Joshua D Rabinowitz.

Metabolic efficiency profoundly influences organismal fitness. Nonphotosynthetic organisms, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. Although respiration is more energy efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (that is, faster). Through quantitative flux analysis and proteomics, we find, however, that mitochondrial respiration is actually more proteome efficient than aerobic glycolysis. This is shown across yeast strains, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which promotes hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth but outgrow respiratory cells during oxygen limitation. We accordingly propose that aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

DOI: https://doi.org/10.1038/s41589-024-01571-y
Sci Rep. 2024 03 06. 14(1): 5545

An ultra-sensitive and high-throughput trapping-micro-LC-MS method for quantification of circulating vitamin D metabolites and application in multiple sclerosis patients.

Flora Qu, Ming Zhang, Bianca Weinstock-Guttman, Robert Zivadinov, Jun Qu, Xiaoyu Zhu, Murali Ramanathan.

Quantitative analysis of the biologically-active metabolites of vitamin D (VitD), which are crucial in regulating various physiological and pathological processes, is important for clinical investigations. Liquid chromatography-tandem mass spectrometry (LC-MS) has been widely used for this purpose but existing LC-MS methods face challenges in achieving highly sensitive and accurate quantification of low-abundance VitD metabolites while maintaining high throughput and robustness. Here we developed a novel pipeline that combines a trapping-micro-LC-(T-µLC) with narrow-window-isolation selected-reaction monitoring MS(NWI-SRM) for ultra-sensitive, robust and high-throughput quantification of VitD metabolites in serum samples after derivatization. The selective-trapping and delivery approach efficiently removes matrix components, enabling high-capacity sample loading and enhancing sensitivity, throughput, and robustness. The NWI-SRM further improves the sensitivity by providing high selectivity. The lower limits of quantification (LOQs) achieved were markedly lower than any existing LC-MS methods: 1.0 pg/mL for 1,25(OH)2D3, 5.0 pg/mL for 24,25(OH)2D3, 30 pg/mL for both 25(OH)D2 and 25(OH)D3, all within a 9-min cycle. The method is applied to quantify VitD metabolites from 218 patients with multiple sclerosis. This study revealed negative correlations(r=- 0.44 to - 0.51) between the levels of 25(OH)D2 and all the three D3 metabolites in multiple sclerosis patients.

DOI: https://doi.org/10.1038/s41598-024-55939-0
Metabolomics. 2024 Mar 08. 20(2): 37

Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases.

Sutanu Sarkar, Deotima Roy, Bhaskar Chatterjee, Rajgourab Ghosh.

   BACKGROUND: Lipids play key roles in numerous biological processes, including energy storage, cell membrane structure, signaling, immune responses, and homeostasis, making lipidomics a vital branch of metabolomics that analyzes and characterizes a wide range of lipid classes. Addressing the complex etiology, age-related risk, progression, inflammation, and research overlap in conditions like Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and Cancer poses significant challenges in the quest for effective therapeutic targets, improved diagnostic markers, and advanced treatments. Mass spectrometry is an indispensable tool in clinical lipidomics, delivering quantitative and structural lipid data, and its integration with technologies like Liquid Chromatography (LC), Magnetic Resonance Imaging (MRI), and few emerging Matrix-Assisted Laser Desorption Ionization- Imaging Mass Spectrometry (MALDI-IMS) along with its incorporation into Tissue Microarray (TMA) represents current advances. These innovations enhance lipidomics assessment, bolster accuracy, and offer insights into lipid subcellular localization, dynamics, and functional roles in disease contexts.
AIM OF THE REVIEW: The review article summarizes recent advancements in lipidomic methodologies from 2019 to 2023 for diagnosing major neurodegenerative diseases, Alzheimer's and Parkinson's, serious non-communicable cardiovascular diseases and cancer, emphasizing the role of lipid level variations, and highlighting the potential of lipidomics data integration with genomics and proteomics to improve disease understanding and innovative prognostic, diagnostic and therapeutic strategies.
KEY SCIENTIFIC CONCEPTS OF REVIEW: Clinical lipidomic studies are a promising approach to track and analyze lipid profiles, revealing their crucial roles in various diseases. This lipid-focused research provides insights into disease mechanisms, biomarker identification, and potential therapeutic targets, advancing our understanding and management of conditions such as Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and specific cancers.

Keywords:  Alzheimer’s; Cancer; Cardiovascular; Lipidomics; Mass-Spectrometry; Parkinson’s

DOI:  https://doi.org/10.1007/s11306-024-02100-7
Biomed Chromatogr. 2024 Mar 05. e5855

Untargeted metabolomics reveals potential plasma biomarkers for diagnosis of primary aldosteronism using liquid chromatography-mass spectrometry.

Jing-Jing Song, Jun Cai, Wen-Jun Ma, Ying Lou, Jin Bian, Beibei Zhao, Xuhui She, Xiao-Ning Liu.

  Metabolite profiling has the potential to comprehensively bridge phenotypes and complex heterogeneous physiological and pathological states. We performed a metabolomics study using parallel liquid chromatography-mass spectrometry (LC-MS) combined with multivariate data analysis to screen for biomarkers of primary aldosteronism (PA) from a cohort of 111 PA patients and 218 primary hypertension (PH) patients. Hydrophilic interaction chromatography and reversed-phase liquid chromatography separations were employed to obtain a global plasma metabolome of endogenous metabolites. The satisfactory classification between PA and PH patients was obtained using the MVDA model. A total of 35 differential metabolites were screened out and identified. A diagnostic biomarker panel was established using the least absolute shrinkage and selection operator (LASSO) binary logistic regression model and receiver operating characteristic analysis. Joint analysis with clinical indicators, including plasma supine aldosterone level, plasma orthostatic aldosterone level, body mass index, and blood potassium, revealed that the combination of metabolite biomarker panel and plasma supine aldosterone has the best clinical diagnostic efficacy.

Keywords:  LC-MS; diagnostic biomarker; metabolomics; plasma; primary aldosteronism

DOI:  https://doi.org/10.1002/bmc.5855
Nat Cell Biol. 2024 Mar 07.

Lipid droplets and cellular lipid flux.

Alyssa J Mathiowetz, James A Olzmann.

Lipid droplets are dynamic organelles that store neutral lipids, serve the metabolic needs of cells, and sequester lipids to prevent lipotoxicity and membrane damage. Here we review the current understanding of the mechanisms of lipid droplet biogenesis and turnover, the transfer of lipids and metabolites at membrane contact sites, and the role of lipid droplets in regulating fatty acid flux in lipotoxicity and cell death.

DOI: https://doi.org/10.1038/s41556-024-01364-4
Nat Commun. 2024 Mar 02. 15(1): 1931

Inhibition of mitochondrial folate metabolism drives differentiation through mTORC1 mediated purine sensing.

Martha M Zarou, Kevin M Rattigan, Daniele Sarnello, Engy Shokry, Amy Dawson, Angela Ianniciello, Karen Dunn, Mhairi Copland, David Sumpton, Alexei Vazquez, G Vignir Helgason.

Supporting cell proliferation through nucleotide biosynthesis is an essential requirement for cancer cells. Hence, inhibition of folate-mediated one carbon (1C) metabolism, which is required for nucleotide synthesis, has been successfully exploited in anti-cancer therapy. Here, we reveal that mitochondrial folate metabolism is upregulated in patient-derived leukaemic stem cells (LSCs). We demonstrate that inhibition of mitochondrial 1C metabolism through impairment of de novo purine synthesis has a cytostatic effect on chronic myeloid leukaemia (CML) cells. Consequently, changes in purine nucleotide levels lead to activation of AMPK signalling and suppression of mTORC1 activity. Notably, suppression of mitochondrial 1C metabolism increases expression of erythroid differentiation markers. Moreover, we find that increased differentiation occurs independently of AMPK signalling and can be reversed through reconstitution of purine levels and reactivation of mTORC1. Of clinical relevance, we identify that combination of 1C metabolism inhibition with imatinib, a frontline treatment for CML patients, decreases the number of therapy-resistant CML LSCs in a patient-derived xenograft model. Our results highlight a role for folate metabolism and purine sensing in stem cell fate decisions and leukaemogenesis.

DOI: https://doi.org/10.1038/s41467-024-46114-0