bims-mascan 2023-10-22 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2023–10–22
23 papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

Human Cerebrospinal Fluid Sample Preparation and Annotation for Integrated Lipidomics and Metabolomics Profiling Studies.
Non-Mass Spectrometric Targeted Single-Cell Metabolomics.
Evaluating Proteomics Imputation Methods with Improved Criteria.
Mass spectrometry-based analysis of gut microbial metabolites of aromatic amino acids.
Delineating a role for methionine metabolism in colorectal cancer.
Combined metabolomic and lipidomic analysis uncovers metabolic profile and biomarkers for papillary thyroid carcinoma.
An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.
An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity.
Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics.
Aspirin reprogrammes colorectal cancer cell metabolism and sensitises to glutaminase inhibition.
Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics.
Stable isotope tracing reveals disturbed cellular energy and glutamate metabolism in hippocampal slices of aged male mice.
Metabolic control of cancer metastasis: role of amino acids at secondary organ sites.
Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics.
LIPID MAPS: update to databases and tools for the lipidomics community.
Revolutions in Lipid Isomer Resolution: Application of Ultrahigh-Resolution Ion Mobility to Reveal Lipid Diversity.
Sample Preparation in Microbial Metabolomics: Advances and Challenges.
Advances in Mass Spectrometry-Metabolomics Based Approaches.
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.
A comprehensive overview of recent developments on the mechanisms and pathways of ferroptosis in cancer: the potential implications for therapeutic strategies in ovarian cancer.
Caveolin-1 and lipids: Association and their dualism in oncogenic regulation.
Analytical Strategy for Oxylipin Annotation by Combining Chemical Derivatization-Based Retention Index Algorithm and Feature Tandem Mass Spectrometric Fragmentation as a Biomarker Discovery Tool.
Study on the effect of calibration standards prepared with different matrix on the accuracy of bile acid quantification using LC-MS/MS.

Mol Neurobiol. 2023 Oct 16.

Human Cerebrospinal Fluid Sample Preparation and Annotation for Integrated Lipidomics and Metabolomics Profiling Studies.

Kourosh Hooshmand, Jin Xu, Anja Hviid Simonsen, Asger Wretlind, Andressa de Zawadzki, Karolina Sulek, Steen Gregers Hasselbalch, Cristina Legido-Quigley.

  Cerebrospinal fluid (CSF) is a metabolically diverse biofluid and a key specimen for exploring biochemical changes in neurodegenerative diseases. Detecting lipid species in CSF using mass spectrometry (MS)-based techniques remains challenging because lipids are highly complex in structure, and their concentrations span over a broad dynamic range. This work aimed to develop a robust lipidomics and metabolomics method based on commonly used two-phase extraction systems from human CSF samples. Prioritizing lipid detection, biphasic extraction methods, Folch, Bligh and Dyer (B&D), Matyash, and acidified Folch and B&D (aFolch and aB&D) were compared using 150 μL of human CSF samples for the simultaneous extraction of lipids and metabolites with a wide range of polarity. Multiple chromatographical separation approaches, including reversed-phase liquid chromatography (RPLC), hydrophilic interaction liquid chromatography (HILIC), and gas chromatography (GC), were utilized to characterize human CSF metabolome. The aB&D method was found as the most reproducible technique (RSD < 15%) for lipid extraction. The aB&D and B&D yielded the highest peak intensities for targeted lipid internal standards and displayed superior extracting power for major endogenous lipid classes. A total of 674 unique metabolites with a wide polarity range were annotated in CSF using, combining RPLC-MS/MS lipidomics (n = 219), HILIC-MS/MS (n = 304), and GC-quadrupole time of flight (QTOF) MS (n = 151). Overall, our findings show that the aB&D extraction method provided suitable lipid coverage, reproducibility, and extraction efficiency for global lipidomics profiling of human CSF samples. In combination with RPLC-MS/MS lipidomics, complementary screening approaches enabled a comprehensive metabolite signature that can be employed in an array of clinical studies.

Keywords:  Cerebrospinal fluid; Lipidomics; Lipids; Mass spectrometry; Metabolomics

DOI:  https://doi.org/10.1007/s12035-023-03666-4
Trends Analyt Chem. 2023 Nov;pii: 117300. [Epub ahead of print]168

Non-Mass Spectrometric Targeted Single-Cell Metabolomics.

Hanjun Cheng, Yin Tang, Zhonghan Li, Zhili Guo, James R Heath, Min Xue, Wei Wei.

  Metabolic assays serve as pivotal tools in biomedical research, offering keen insights into cellular physiological and pathological states. While mass spectrometry (MS)-based metabolomics remains the gold standard for comprehensive, multiplexed analyses of cellular metabolites, innovative technologies are now emerging for the targeted, quantitative scrutiny of metabolites and metabolic pathways at the single-cell level. In this review, we elucidate an array of these advanced methodologies, spanning synthetic and surface chemistry techniques, imaging-based methods, and electrochemical approaches. We summarize the rationale, design principles, and practical applications for each method, and underscore the synergistic benefits of integrating single-cell metabolomics (scMet) with other single-cell omics technologies. Concluding, we identify prevailing challenges in the targeted scMet arena and offer a forward-looking commentary on future avenues and opportunities in this rapidly evolving field.

Keywords:  Raman microscopy; Single-cell metabolism; fluorescent metabolic tracer; microfluidic chip; single-cell amperometry; surface chemistry

DOI:  https://doi.org/10.1016/j.trac.2023.117300
J Proteome Res. 2023 Oct 20.

Evaluating Proteomics Imputation Methods with Improved Criteria.

Lincoln Harris, William E Fondrie, Sewoong Oh, William S Noble.

  Quantitative measurements produced by tandem mass spectrometry proteomics experiments typically contain a large proportion of missing values. Missing values hinder reproducibility, reduce statistical power, and make it difficult to compare across samples or experiments. Although many methods exist for imputing missing values, in practice, the most commonly used methods are among the worst performing. Furthermore, previous benchmarking studies have focused on relatively simple measurements of error such as the mean-squared error between imputed and held-out values. Here we evaluate the performance of commonly used imputation methods using three practical, "downstream-centric" criteria. These criteria measure the ability to identify differentially expressed peptides, generate new quantitative peptides, and improve the peptide lower limit of quantification. Our evaluation comprises several experiment types and acquisition strategies, including data-dependent and data-independent acquisition. We find that imputation does not necessarily improve the ability to identify differentially expressed peptides but that it can identify new quantitative peptides and improve the peptide lower limit of quantification. We find that MissForest is generally the best performing method per our downstream-centric criteria. We also argue that existing imputation methods do not properly account for the variance of peptide quantifications and highlight the need for methods that do.

Keywords:  differential expression; imputation; lower limit of quantification; machine learning; proteomics; quantitative mass spectrometry; statistics

DOI:  https://doi.org/10.1021/acs.jproteome.3c00205
Comput Struct Biotechnol J. 2023 ;21 4777-4789

Mass spectrometry-based analysis of gut microbial metabolites of aromatic amino acids.

Narumol Jariyasopit, Sakda Khoomrung.

  Small molecules derived from gut microbiota have been increasingly investigated to better understand the functional roles of the human gut microbiome. Microbial metabolites of aromatic amino acids (AAA) have been linked to many diseases, such as metabolic disorders, chronic kidney diseases, inflammatory bowel disease, diabetes, and cancer. Important microbial AAA metabolites are often discovered via global metabolite profiling of biological specimens collected from humans or animal models. Subsequent metabolite identity confirmation and absolute quantification using targeted analysis enable comparisons across different studies, which can lead to the establishment of threshold concentrations of potential metabolite biomarkers. Owing to their excellent selectivity and sensitivity, hyphenated mass spectrometry (MS) techniques are often employed to identify and quantify AAA metabolites in various biological matrices. Here, we summarize the developments over the past five years in MS-based methodology for analyzing gut microbiota-derived AAA. Sample preparation, method validation, analytical performance, and statistical methods for correlation analysis are discussed, along with future perspectives.

Keywords:  Aromatic amino acid; Gut microbial metabolite; Mass spectrometry; Metabolomics; Quantitative analysis

DOI:  https://doi.org/10.1016/j.csbj.2023.09.032
Cancer Res. 2023 Oct 17.

Delineating a role for methionine metabolism in colorectal cancer.

Shiyu Liu, Jason W Locasale.

Advances in mass spectrometry allow for broader applications of metabolomics in research and clinical applications. In a recent issue of Nature Metabolism, Voorde and colleagues utilized metabolite profiling to investigate the metabolism of colorectal cancer (CRC) in mouse models, organoids and patients. This study underscores the utility of metabolomics in distinguishing CRC, offering potential for its use in precision medicine. It also revealed a pivotal role for adenosylhomocysteinase in the methionine cycle and highlighted its potential as a therapeutic target.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3169
Sci Rep. 2023 Oct 17. 13(1): 17666

Combined metabolomic and lipidomic analysis uncovers metabolic profile and biomarkers for papillary thyroid carcinoma.

Zipeng Wang, Yiqin Yang, Yurong Xing, Dandan Si, Suhua Wang, Jiashuo Lin, Cai Li, Ji Zhang, Detao Yin.

Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy with a rapidly increasing incidence. The pathogenesis of PTC is unclear, but metabolic and lipidomic reprogramming may play a role in tumor growth. We applied ultra-performance liquid chromatography-tandem mass spectrometry to perform widely targeted metabolomics and lipidomics on plasma samples from 94 patients with PTC and 100 healthy controls. We identified 113 differential metabolites and 236 differential lipids, mainly involved in branched-chain amino acid metabolism, glutamate and glutamine metabolism, tricarboxylic acid cycle, and lipid metabolism. We also screened three potential metabolite biomarkers: sebacic acid, L-glutamine, and indole-3-carboxaldehyde. These biomarkers showed excellent diagnostic performance for PTC in both discovery and validation cohorts, with areas under the receiver operating characteristic curves of 0.994 and 0.925, respectively. Our findings reveal distinct metabolic and lipidomic features of PTC and provide novel targets for diagnosis and treatment.

DOI: https://doi.org/10.1038/s41598-023-41176-4
J Am Soc Mass Spectrom. 2023 Oct 18.

An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.

Richard M Searfoss, Rashmi Karki, Zongtao Lin, Faith Robison, Benjamin A Garcia.

Histones are DNA binding proteins that allow for packaging of the DNA into the nucleus. They are abundantly present across the genome and thus serve as a major site of epigenetic regulation through the use of post-translational modifications (PTMs). Aberrations in histone expression and modifications have been implicated in a variety of human diseases and thus are a major focus of disease etiology studies. A well-established method for studying histones and PTMs is through the chemical derivatization of isolated histones followed by liquid chromatography and mass spectrometry analysis. Using such an approach has allowed for a swath of discoveries to be found, leading to novel therapeutics such as histone deacetylase (HDAC) inhibitors that have already been applied in the clinic. However, with the rapid improvement in instrumentation and data analysis pipelines, it remains important to temporally re-evaluate the established protocols to improve throughput and ensure data quality. Here, we optimized the histone derivatization procedure to increase sample throughput without compromising peptide quantification. An implemented spike-in standard peptide further serves as a quality control to evaluate the propionylation and digestion efficiencies as well as reproducibility in chromatographic retention and separation. Last, the application of various data-independent acquisition (DIA) strategies was explored to ensure low variation between runs. The output of this study is a newly optimized derivatization protocol and mass spectrometry method that maintains high identification and quantification of histone PTMs while increasing sample throughput.

DOI: https://doi.org/10.1021/jasms.3c00223
Mol Cell Proteomics. 2023 Oct 13. pii: S1535-9476(23)00176-7. [Epub ahead of print] 100665

An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity.

Claudia Ctortecka, David Hartlmayr, Anjali Seth, Sasha Mendjan, Guilhem Tourniaire, Namrata D Udeshi, Steven A Carr, Karl Mechtler.

Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lags. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation including multiplexed labeling up to 16-plex with high sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE®, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1,500 protein groups per TMT10-plex with reduced or eliminated need for a carrier proteome. We evaluated the effect of wider precursor isolation windows at single-cell input levels and found that using 2 Da isolation windows increased overall sensitivity without significantly impacting interference. Using the dedicated MS acquisition strategies detailed here, we identified on average close to 2,000 proteins per TMT10-plex across 170 multiplexed single cells that readily distinguished human cell types. Overall, our workflow combines highly efficient sample preparation, chromatographic and ion mobility-based filtering, rapid wide-window DDA analysis and intelligent data analysis for optimal multiplexed single-cell proteomics. This versatile and automated proteoCHIP-based sample preparation approach is sufficiently sensitive to drive biological applications of single-cell proteomics and can be readily adopted by proteomics laboratories.

DOI: https://doi.org/10.1016/j.mcpro.2023.100665
Anal Chem. 2023 Oct 16.

Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics.

Peilin Jiang, Wenjing Peng, Jingfu Zhao, Mona Goli, Yifan Huang, Yunxiang Li, Yehia Mechref.

The complexity and heterogeneity of protein glycosylation present an analytical challenge to the studies of characterization and quantitation. Various LC-MS-based quantitation strategies have emerged in recent decades. Metabolic stable isotope labeling has been developed to enhance the accurate LC/MS-based quantitation between different cell lines. Stable isotope labeling by amino acids in a cell culture (SILAC) is the most widely used metabolic labeling method in proteomic analysis. However, it can only label the peptide backbone and is thus limited in glycomic studies. Here, we present a metabolic isotope labeling strategy, named GlyProSILC (Glycan Protein Stable Isotope Labeling in Cell Culture), that can label both the glycan motif and peptide backbone from the same batch of cells. It was performed by feeding cells with a heavy medium containing amide-15N-glutamine, 13C6-arginine (Arg6), and 13C6-15N2-lysine (Lys8). No significant change of cell line metabolism after GlyProSILC labeling was observed based on transcriptomic, glycomic, and proteomic data. The labeling conditions, labeling efficiency, and quantitation accuracy were investigated. After quantitation correction, we simultaneously quantified 62 N-glycans, 574 proteins, and 344 glycopeptides using the same batch of mixed 231BR/231 cell lines. So far, GlyProSILC provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.

DOI: https://doi.org/10.1021/acs.analchem.3c00247
Cancer Metab. 2023 Oct 19. 11(1): 18

Aspirin reprogrammes colorectal cancer cell metabolism and sensitises to glutaminase inhibition.

Amy K Holt, Arafath K Najumudeen, Tracey J Collard, Hao Li, Laura M Millett, Ashley J Hoskin, Danny N Legge, Eleanor M H Mortensson, Dustin J Flanagan, Nicholas Jones, Madhu Kollareddy, Penny Timms, Matthew D Hitchings, James Cronin, Owen J Sansom, Ann C Williams, Emma E Vincent.

   BACKGROUND: To support proliferation and survival within a challenging microenvironment, cancer cells must reprogramme their metabolism. As such, targeting cancer cell metabolism is a promising therapeutic avenue. However, identifying tractable nodes of metabolic vulnerability in cancer cells is challenging due to their metabolic plasticity. Identification of effective treatment combinations to counter this is an active area of research. Aspirin has a well-established role in cancer prevention, particularly in colorectal cancer (CRC), although the mechanisms are not fully understood.
METHODS: We generated a model to investigate the impact of long-term (52 weeks) aspirin exposure on CRC cells, which has allowed us comprehensively characterise the metabolic impact of long-term aspirin exposure (2-4mM for 52 weeks) using proteomics, Seahorse Extracellular Flux Analysis and Stable Isotope Labelling (SIL). Using this information, we were able to identify nodes of metabolic vulnerability for further targeting, investigating the impact of combining aspirin with metabolic inhibitors in vitro and in vivo.
RESULTS: We show that aspirin regulates several enzymes and transporters of central carbon metabolism and results in a reduction in glutaminolysis and a concomitant increase in glucose metabolism, demonstrating reprogramming of nutrient utilisation. We show that aspirin causes likely compensatory changes that render the cells sensitive to the glutaminase 1 (GLS1) inhibitor-CB-839. Of note given the clinical interest, treatment with CB-839 alone had little effect on CRC cell growth or survival. However, in combination with aspirin, CB-839 inhibited CRC cell proliferation and induced apoptosis in vitro and, importantly, reduced crypt proliferation in Apcfl/fl mice in vivo.
CONCLUSIONS: Together, these results show that aspirin leads to significant metabolic reprogramming in colorectal cancer cells and raises the possibility that aspirin could significantly increase the efficacy of metabolic cancer therapies in CRC.

Keywords:  Aspirin; CB-839; Colorectal cancer; Glutaminase; Metabolic reprogramming; Metabolism

DOI:  https://doi.org/10.1186/s40170-023-00318-y
Adv Exp Med Biol. 2023 ;1439 225-248

Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics.

Paulo Wender P Gomes, Talita Carla de Tralia Medeiros, Naydja Moralles Maimone, Tiago F Leão, Luiz Alberto Beraldo de Moraes, Anelize Bauermeister.

  Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades, microbial derived compounds have gained increasing attention in different fields from pharmacognosy to industry and agriculture. Microbial metabolites in microbiomes present specific functions and can be associated with the maintenance of the natural ecosystems. These metabolites may exhibit a broad range of biological activities of great interest to human purposes. Samples from either microbial isolated cultures or microbiomes consist of complex mixtures of metabolites and their analysis are not a simple process. Mass spectrometry-based metabolomics encompass a set of analytical methods that have brought several improvements to the microbial natural products field. This analytical tool allows the comprehensively detection of metabolites, and therefore, the access of the chemical profile from those biological samples. These analyses generate thousands of mass spectra which is challenging to analyse. In this context, bioinformatic metabolomics tools have been successfully employed to accelerate and facilitate the investigation of specialized microbial metabolites. Herein, we describe metabolomics tools used to provide chemical information for the metabolites, and furthermore, we discuss how they can improve investigation of microbial cultures and interactions.

Keywords:  Bioinformatic; Metabolite annotation; Metabolomics

DOI:  https://doi.org/10.1007/978-3-031-41741-2_9
Neurochem Int. 2023 Oct 12. pii: S0197-0186(23)00154-7. [Epub ahead of print]171 105626

Stable isotope tracing reveals disturbed cellular energy and glutamate metabolism in hippocampal slices of aged male mice.

Laura Mikél McNair, Jens Velde Andersen, Helle Sønderby Waagepetersen.

  Neurons and astrocytes work in close metabolic collaboration, linking neurotransmission to brain energy and neurotransmitter metabolism. Dysregulated energy metabolism is a hallmark of the aging brain and may underlie the progressive age-dependent cognitive decline. However, astrocyte and neurotransmitter metabolism remains understudied in aging brain research. In particular, how aging affects metabolism of glutamate, being the primary excitatory neurotransmitter, is still poorly understood. Here we investigated critical aspects of cellular energy metabolism in the aging male mouse hippocampus using stable isotope tracing in vitro. Metabolism of [U-13C]glucose demonstrated an elevated glycolytic capacity of aged hippocampal slices, whereas oxidative [U-13C]glucose metabolism in the TCA cycle was significantly reduced with aging. In addition, metabolism of [1,2-13C]acetate, reflecting astrocyte energy metabolism, was likewise reduced in the hippocampal slices of old mice. In contrast, uptake and subsequent metabolism of [U-13C]glutamate was elevated, suggesting increased capacity for cellular glutamate handling with aging. Finally, metabolism of [15N]glutamate was maintained in the aged slices, demonstrating sustained glutamate nitrogen metabolism. Collectively, this study reveals fundamental alterations in cellular energy and neurotransmitter metabolism in the aging brain, which may contribute to age-related hippocampal deficits.

Keywords:  Astrocytes; Glutamate uptake; Glutamate-glutamine cycle; Isotope tracing

DOI:  https://doi.org/10.1016/j.neuint.2023.105626
Oncogene. 2023 Oct 18.

Metabolic control of cancer metastasis: role of amino acids at secondary organ sites.

Breelyn Karno, Deanna N Edwards, Jin Chen.

Most cancer-related deaths are caused by the metastases, which commonly develop at multiple organ sites including the brain, bone, and lungs. Despite longstanding observations that the spread of cancer is not random, our understanding of the mechanisms that underlie metastatic spread to specific organs remains limited. However, metabolism has recently emerged as an important contributor to metastasis. Amino acids are a significant nutrient source to cancer cells and their metabolism which can serve to fuel biosynthetic pathways capable of facilitating cell survival and tumor expansion while also defending against oxidative stress. Compared to the primary tumor, each of the common metastatic sites exhibit vastly different nutrient compositions and environmental stressors, necessitating the need of cancer cells to metabolically thrive in their new environment during colonization and outgrowth. This review seeks to summarize the current literature on amino acid metabolism pathways that support metastasis to common secondary sites, including impacts on immune responses. Understanding the role of amino acids in secondary organ sites may offer opportunities for therapeutic inhibition of cancer metastasis.

DOI: https://doi.org/10.1038/s41388-023-02868-3
ISME J. 2023 Oct 19.

Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics.

Monica Thukral, Andrew E Allen, Daniel Petras.

Advances in bioanalytical technologies are constantly expanding our insights into complex ecosystems. Here, we highlight strategies and applications that make use of non-targeted metabolomics methods in aquatic chemical ecology research and discuss opportunities and remaining challenges of mass spectrometry-based methods to broaden our understanding of environmental systems.

DOI: https://doi.org/10.1038/s41396-023-01532-8
Nucleic Acids Res. 2023 Oct 19. pii: gkad896. [Epub ahead of print]

LIPID MAPS: update to databases and tools for the lipidomics community.

Matthew J Conroy, Robert M Andrews, Simon Andrews, Lauren Cockayne, Edward A Dennis, Eoin Fahy, Caroline Gaud, William J Griffiths, Geoff Jukes, Maksim Kolchin, Karla Mendivelso, Andrea F Lopez-Clavijo, Caroline Ready, Shankar Subramaniam, Valerie B O'Donnell.

LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.

DOI: https://doi.org/10.1093/nar/gkad896
Anal Chem. 2023 Oct 17.

Revolutions in Lipid Isomer Resolution: Application of Ultrahigh-Resolution Ion Mobility to Reveal Lipid Diversity.

Berwyck L J Poad, Lachlan J Jekimovs, Reuben S E Young, Puttandon Wongsomboon, David L Marshall, Felicia K M Hansen, Therese Fulloon, Michael C Pfrunder, Tyren Dodgen, Mark Ritchie, Stephen C C Wong, Stephen J Blanksby.

Many families of lipid isomers remain unresolved by contemporary liquid chromatography-mass spectrometry approaches, leading to a significant underestimation of the structural diversity within the lipidome. While ion mobility coupled to mass spectrometry has provided an additional dimension of lipid isomer resolution, some isomers require a resolving power beyond the capabilities of conventional platforms. Here, we present the application of high-resolution traveling-wave ion mobility for the separation of lipid isomers that differ in (i) the location of a single carbon-carbon double bond, (ii) the stereochemistry of the double bond (cis or trans), or, for glycerolipids, (iii) the relative substitution of acyl chains on the glycerol backbone (sn-position). Collisional activation following mobility separation allowed identification of the carbon-carbon double-bond position and sn-position, enabling confident interpretation of variations in mobility peak abundance. To demonstrate the applicability of this method, double-bond and sn-position isomers of an abundant phosphatidylcholine composition were resolved in extracts from a prostate cancer cell line and identified by comparison to pure isomer reference standards, revealing the presence of up to six isomers. These findings suggest that ultrahigh-resolution ion mobility has broad potential for isomer-resolved lipidomics and is attractive to consider for future integration with other modes of ion activation, thereby bringing together advanced orthogonal separations and structure elucidation to provide a more complete picture of the lipidome.

DOI: https://doi.org/10.1021/acs.analchem.3c02658
Adv Exp Med Biol. 2023 ;1439 149-183

Sample Preparation in Microbial Metabolomics: Advances and Challenges.

Heiter V M Boness, Hanna C de Sá, Emile K P Dos Santos, Gisele A B Canuto.

  Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Keywords:  Cellular cultivation; Extracellular metabolome; Intracellular metabolome; Metabolic quenching; Metabolite extraction; Microbial metabolomics; Sample preparation

DOI:  https://doi.org/10.1007/978-3-031-41741-2_7
Adv Exp Med Biol. 2023 ;1439 101-122

Advances in Mass Spectrometry-Metabolomics Based Approaches.

Nerilson Marques Lima, Gabriel Franco Dos Santos, Gesiane da Silva Lima, Boniek Gontijo Vaz.

  Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.

Keywords:  Ambient ionization techniques; Dereplication; Mass spectrometry; Mass spectrometry imaging; Microbial metabolomics

DOI:  https://doi.org/10.1007/978-3-031-41741-2_5
Nat Biotechnol. 2023 Oct 18.

Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.

Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda-Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, Kyung E Rhee, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez-Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein.

DOI: https://doi.org/10.1038/s41587-023-02025-x
Cancer Drug Resist. 2023 ;6(3): 547-566

A comprehensive overview of recent developments on the mechanisms and pathways of ferroptosis in cancer: the potential implications for therapeutic strategies in ovarian cancer.

Hiroshi Kobayashi, Chiharu Yoshimoto, Sho Matsubara, Hiroshi Shigetomi, Shogo Imanaka.

  Cancer cells adapt to environmental changes and alter their metabolic pathways to promote survival and proliferation. Metabolic reprogramming not only allows tumor cells to maintain a reduction-oxidation balance by rewiring resources for survival, but also causes nutrient addiction or metabolic vulnerability. Ferroptosis is a form of regulated cell death characterized by the iron-dependent accumulation of lipid peroxides. Excess iron in ovarian cancer amplifies free oxidative radicals and drives the Fenton reaction, thereby inducing ferroptosis. However, ovarian cancer is characterized by ferroptosis resistance. Therefore, the induction of ferroptosis is an exciting new targeted therapy for ovarian cancer. In this review, potential metabolic pathways targeting ferroptosis were summarized to promote anticancer effects, and current knowledge and future perspectives on ferroptosis for ovarian cancer therapy were discussed. Two therapeutic strategies were highlighted in this review: directly inducing the ferroptosis pathway and targeting metabolic vulnerabilities that affect ferroptosis. The overexpression of SLC7A11, a cystine/glutamate antiporter SLC7A11 (also known as xCT), is involved in the suppression of ferroptosis. xCT inhibition by ferroptosis inducers (e.g., erastin) can promote cell death when carbon as an energy source of glucose, glutamine, or fatty acids is abundant. On the contrary, xCT regulation has been reported to be highly dependent on the metabolic vulnerability. Drugs that target intrinsic metabolic vulnerabilities (e.g., GLUT1 inhibitors, PDK4 inhibitors, or glutaminase inhibitors) predispose cancer cells to death, which is triggered by decreased nicotinamide adenine dinucleotide phosphate generation or increased reactive oxygen species accumulation. Therefore, therapeutic approaches that either directly inhibit the xCT pathway or target metabolic vulnerabilities may be effective in overcoming ferroptosis resistance. Real-time monitoring of changes in metabolic pathways may aid in selecting personalized treatment modalities. Despite the rapid development of ferroptosis-inducing agents, therapeutic strategies targeting metabolic vulnerability remain in their infancy. Thus, further studies must be conducted to comprehensively understand the precise mechanism linking metabolic rewiring with ferroptosis.

Keywords:  Ferroptosis; glutaminolysis; glycolysis; metabolic vulnerability; ovarian cancer; pentose phosphate pathway

DOI:  https://doi.org/10.20517/cdr.2023.49
Biochim Biophys Acta Rev Cancer. 2023 Oct 15. pii: S0304-419X(23)00151-8. [Epub ahead of print]1878(6): 189002

Caveolin-1 and lipids: Association and their dualism in oncogenic regulation.

Sramana Bhowmick, Tannishtha Biswas, Mehnaz Ahmed, Debarshi Roy, Susmita Mondal.

  Caveolin-1 (Cav-1) is a structural protein of caveolae that functions as a molecular organizer for different cellular functions including endocytosis and cellular signaling. Cancer cells take advantage of the physical position of Cav-1, as it can communicate with extracellular matrix, help to organize growth factor receptors, redistribute cholesterol and glycosphingolipids, and finally transduce signals within the cells for oncogenesis. Recent studies emphasize the exceeding involvement of Cav-1 with different lipid bodies and in altering the metabolism, especially lipid metabolism. However, the association of Cav-1 with different lipid bodies like lipid rafts, lipid droplets, cholesterols, sphingolipids, and fatty acids is remarkably dynamic. The lipid-Cav-1 alliance plays a dual role in carcinogenesis. Both cancer progression and regression are modified and affected by the type of lipid molecule's association with Cav-1. Accordingly, this Cav-1-lipid cooperation exemplifies a cancer-type-specific treatment strategy for a better prognosis of the disease. In this review, we first present Cav-1 as an oncogenic molecule and its communication via lipid raft. We discussed the involvement of Cav-1 with lipid droplets, Cholesterol, sphingolipids, gangliosides, and ceramides. Further, we describe the Cav-1-mediated altered Fatty acid metabolism in cancer and the strategic therapeutic approaches toward Cav-1 targeting.

Keywords:  Cancer; Caveolin-1; Ceramides; Cholesterol; Fatty acids; Lipid raft; Sphingolipids

DOI:  https://doi.org/10.1016/j.bbcan.2023.189002
Anal Chem. 2023 Oct 18.

Analytical Strategy for Oxylipin Annotation by Combining Chemical Derivatization-Based Retention Index Algorithm and Feature Tandem Mass Spectrometric Fragmentation as a Biomarker Discovery Tool.

Zongyuan Wu, Huaming Xiao, Di Rao, Jie Wang, Xin Lv, Dan Wang, Ping Yao, Fenghong Huang, Hong Chen, Fang Wei.

Accurate oxylipin annotation is crucial for advancing our understanding of physiological processes in health and disease and identifying biomarkers. However, a full view of oxylipins for early diagnosis needs further attention due to the lack of proper analytical methods, which may be attributed to the wide dynamic range, poor sensitivity, extreme molecular complexity, and limited commercially available standards of oxylipins. Here, we devised a novel method by combining a chemical derivatization (CD)-based retention index (RI) algorithm and feature tandem mass spectrometric fragmentation annotation (CD-RI-LC-MS/MS) for identification and quantification of oxylipins. To this end, N,N-diethyl-1,3-diaminopropane (DEPA) was used for fast labeling of oxylipin (within 0.5 min at room temperature) to improve separation resolution and detection sensitivity. The RI algorithm was established to calibrate the retention time variances and assist the identification of oxylipins during liquid chromatography-tandem mass spectrometry (LC-MS) analysis. MS/MS analysis of in total 58 DEPA derivatives of authentic oxylipin standards was subsequently employed to obtain the tandem mass spectrometric feature fragmentation rules for further structure elucidation of the unknown regio-isomers. Finally, a method based upon CD-RI-LC-MS/MS was established for profiling oxylipins from Standard Reference Material (SRM) 1950 human plasma and nonalcoholic fatty liver disease (NAFLD) mouse liver tissue samples. A total of 87 and 96 potential oxylipins including 12 and 14 unreported oxylipins were detected and identified from human plasma and mouse liver tissues, respectively. The results showed that compared to the control group, in the liver samples of the NAFLD mouse, the content levels of prostaglandin (PG) E2, PGF2a, 8-hydroxy-eicosatrienoic acid (8-HETrE), and the newly discovered 2-hydroxy-octadecatrienoic acid (2-HOTrE) were remarkably increased, while the oxidation product of n-3 PUFA (p < 0.05) and all hydroperoxy oxylipins significantly decreased. On balance, this method contributes to future studies on oxylipin screening and application in other biological samples for facilitating the understanding of oxylipin roles in metabolic regulation of numerous diseases.

DOI: https://doi.org/10.1021/acs.analchem.3c02789
J Pharm Biomed Anal. 2023 Oct 10. pii: S0731-7085(23)00554-X. [Epub ahead of print]237 115785

Study on the effect of calibration standards prepared with different matrix on the accuracy of bile acid quantification using LC-MS/MS.

Jinni Yang, Jiachun Lin, Anhui Wang, Xue Yang, Yali Wang, Yuting Zhang, Haijuan Dong, Yuan Tian, Zunjian Zhang, Min Wang, Rui Song.

  The transition from relative to absolute quantification of metabolites is the future development trend of mass spectrometry-based metabolomics research, which could fundamentally solve the problem of comparability of data between different laboratories. However, absolute quantification of endogenous molecules is largely hampered by the lack of analyte-free matrix, leading to uncertainty and inconsistency in the preparation of calibration standards. Bile acids (BAs) are an important class of biomarkers that play a key role in disease progression. In this paper, the quantitative accuracy of calibration curves prepared in neat solvent (NSCCs), charcoal stripped matrix (SMCCs) and authentic matrix (AMCCs) were validated using quality control samples (QCs) prepared in authentic matrix. Results suggested that AMCCs could largely minimize the confidence interval (C.I.) and the deviation in accuracy compared with NSCCs and SMCCs when measured concentration is higher than 20% of the background level. In addition, experimental data demonstrated that two-step calibration strategy proposed here is a promising and reliable alternative strategy to quantify endogenous BAs in biological sample.

Keywords:  Accuracy; Authentic matrix; Bile acids; Calibration standards; Surrogate matrix

DOI:  https://doi.org/10.1016/j.jpba.2023.115785