bims-mascan 2021-08-22 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021‒08‒22
twenty-nine papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

Lipidomics in Biomarker Research.
Untargeted UHPLC-ESI-QTOF-MS/MS analysis with targeted feature extraction at precursor and fragment level for profiling of the platelet lipidome with ex vivo thrombin-activation.
Tumour fatty acid metabolism in the context of therapy resistance and obesity.
The Crucial Roles of Intermediate Metabolites in Cancer.
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data.
Metabolic Alterations in Preneoplastic Development Revealed by Untargeted Metabolomic Analysis.
Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review.
Artificial intelligence for proteomics and biomarker discovery.
Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat.
Bottom-Up Community Proteome Analysis of Saliva Samples and Tongue Swabs by Data-Dependent Acquisition Nano LC-MS/MS Mass Spectrometry.
Mammalian lipids: structure, synthesis and function.
High-Resolution Native Mass Spectrometry.
Very long-chain acyl-CoA synthetase 3 mediates onco-sphingolipid metabolism in malignant glioma.
Metabolic convergence on lipogenesis in RAS, BCR-ABL, and MYC-driven lymphoid malignancies.
Metabolic decisions in development and disease-a Keystone Symposia report.
Lipoprotein lipase hydrolysis products induce pro-inflammatory cytokine expression in triple-negative breast cancer cells.
Quantitative analysis of m6A RNA modification by LC-MS.
Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples.
Feeding mice a diet high in oxidized linoleic acid metabolites does not alter liver oxylipin concentrations.
Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation - Serial Fragmentation (PASEF) in Proteomics.
Editorial: Metabolomics in the Study of Unconventional Biological Matrices.
Comprehensive lipidomics reveals phenotypic differences in hepatic lipid turnover in ALD and NAFLD during alcohol intoxication.
Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting.
CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification.
Improving data quality in liquid chromatography-mass spectrometry metabolomics of human urine.
[Arachidonic acid metabolism in liver glucose and lipid homeostasis].
Autophagy is a major metabolic regulator involved in cancer therapy resistance.
Off-the-shelf proximity biotinylation for interaction proteomics.
Dietary fructose improves intestinal cell survival and nutrient absorption.

Handb Exp Pharmacol. 2021 Aug 19.

Lipidomics in Biomarker Research.

Th Hornemann.

  Lipids are natural substances found in all living organisms and involved in many biological functions. Imbalances in the lipid metabolism are linked to various diseases such as obesity, diabetes, or cardiovascular disease. Lipids comprise thousands of chemically distinct species making them a challenge to analyze because of their great structural diversity.Thanks to the technological improvements in the fields of chromatography, high-resolution mass spectrometry, and bioinformatics over the last years, it is now possible to perform global lipidomics analyses, allowing the concomitant detection, identification, and relative quantification of hundreds of lipid species. This review shall provide an insight into a general lipidomics workflow and its application in metabolic biomarker research.

Keywords:  Biomarkers; Data analysis; Dyslipidemia; LC/MS; Lipids; Metabolic disease; Metabolites

DOI:  https://doi.org/10.1007/164_2021_517
J Pharm Biomed Anal. 2021 Aug 04. pii: S0731-7085(21)00412-X. [Epub ahead of print]205 114301

Untargeted UHPLC-ESI-QTOF-MS/MS analysis with targeted feature extraction at precursor and fragment level for profiling of the platelet lipidome with ex vivo thrombin-activation.

Malgorzata Cebo, Carlos Calderón Castro, Jörg Schlotterbeck, Meinrad Gawaz, Madhumita Chatterjee, Michael Lämmerhofer.

  Lipids play a major role in platelet signaling and activation. In this study, we analyzed the platelet lipidome in an untargeted manner by reversed-phase UHPLC for lipid species separation coupled to high-resolution QTOF-MS/MS in data-independent acquisition (DIA) mode with sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) for compound detection. Lipid identification and peak picking was supported by the characteristic regular elution pattern of lipids differing in carbon and double bond numbers. It was primarily based on post-acquisition targeted feature extraction from the SWATH data. Multiple extracted ion chromatograms (EICs) from SWATH data of diagnostic ions on MS1 and MS2 level from both positive and negative ion mode allowed to distinguish between poorly resolved isomeric lipids based on their distinct fragment ions, which were used for relative quantification at a molecular lipid species level. It supports assay specificity for relative lipid quantitation via multiple quantifiably ions unlike to data-dependent acquisition methods which rely on precursor ions only. This approach was used to analyze human platelet samples. 457 lipids were annotated. Concentrations of lipids were estimated by stable isotope-labelled lipid class-specific internal standards as surrogate calibrants. Heatmaps of lipid concentrations in dependence on carbon and double bond numbers for the distinct lipid classes revealed a snapshot of the platelet lipidome in the resting state with lipid species distributions within classes supporting some functional interpretations. As expected, activation of the platelets by thrombin has led to significant alterations in the platelet lipidome as proven by univariate (volcano plot) and multivariate (PLS-DA) statistics. Several lipids were significantly up-regulated (lysophosphatidylinositols, oxylipins such as thromboxane B2 (TXB2), hydroxyheptadecatrienoic acid (HHT), hydroxyeicosatetraenoic acid (HETE), hydroxyoctadecadienoic acid (HODE), sphingoid-bases, (very) long chain saturated fatty acids) or down-regulated (lysophosphatidylethanolamines, polyunsaturated fatty acids, phosphatidylinositols). Several of them are well known as biomarkers of platelet activation while others may provide some further insights into pathways of platelet activation and platelet metabolism.

Keywords:  Biomarker; Lipid identification; Lipidomics; Platelet activation; Platelet lipidome; Sequential window acquisition of all theoretical fragment ion mass spectra

DOI:  https://doi.org/10.1016/j.jpba.2021.114301
Nat Rev Cancer. 2021 Aug 20.

Tumour fatty acid metabolism in the context of therapy resistance and obesity.

Andrew J Hoy, Shilpa R Nagarajan, Lisa M Butler.

Fatty acid metabolism is known to support tumorigenesis and disease progression as well as treatment resistance through enhanced lipid synthesis, storage and catabolism. More recently, the role of membrane fatty acid composition, for example, ratios of saturated, monounsaturated and polyunsaturated fatty acids, in promoting cell survival while limiting lipotoxicity and ferroptosis has been increasingly appreciated. Alongside these insights, it has become clear that tumour cells exhibit plasticity with respect to fatty acid metabolism, responding to extratumoural and systemic metabolic signals, such as obesity and cancer therapeutics, to promote the development of aggressive, treatment-resistant disease. Here, we describe cellular fatty acid metabolic changes that are connected to therapy resistance and contextualize obesity-associated changes in host fatty acid metabolism that likely influence the local tumour microenvironment to further modify cancer cell behaviour while simultaneously creating potential new vulnerabilities.

DOI: https://doi.org/10.1038/s41568-021-00388-4
Cancer Manag Res. 2021 ;13 6291-6307

The Crucial Roles of Intermediate Metabolites in Cancer.

Sisi Huang, Zhiqin Wang, Liang Zhao.

  Metabolic alteration, one of the hallmarks of cancer cells, is important for cancer initiation and development. To support their rapid growth, cancer cells alter their metabolism so as to obtain the necessary energy and building blocks for biosynthetic pathways, as well as to adjust their redox balance. Once thought to be merely byproducts of metabolic pathways, intermediate metabolites are now known to mediate epigenetic modifications and protein post-transcriptional modifications (PTM), as well as connect cellular metabolism with signal transduction. Consequently, they can affect a myriad of processes, including proliferation, apoptosis, and immunity. In this review, we summarize multiple representative metabolites involved in glycolysis, the pentose phosphate pathway (PPP), the tricarboxylic acid (TCA) cycle, lipid synthesis, ketogenesis, methionine metabolism, glutamine metabolism, and tryptophan metabolism, focusing on their roles in chromatin and protein modifications and as signal-transducing messengers.

Keywords:  epigenetic modification; extra-metabolic functions; oncometabolites; post-transcriptional modifications; signaling transduction

DOI:  https://doi.org/10.2147/CMAR.S321433
Nat Commun. 2021 08 17. 12(1): 4992

A hierarchical approach to removal of unwanted variation for large-scale metabolomics data.

Taiyun Kim, Owen Tang, Stephen T Vernon, Katharine A Kott, Yen Chin Koay, John Park, David E James, Stuart M Grieve, Terence P Speed, Pengyi Yang, Gemma A Figtree, John F O'Sullivan, Jean Yee Hwa Yang.

Liquid chromatography-mass spectrometry-based metabolomics studies are increasingly applied to large population cohorts, which run for several weeks or even years in data acquisition. This inevitably introduces unwanted intra- and inter-batch variations over time that can overshadow true biological signals and thus hinder potential biological discoveries. To date, normalisation approaches have struggled to mitigate the variability introduced by technical factors whilst preserving biological variance, especially for protracted acquisitions. Here, we propose a study design framework with an arrangement for embedding biological sample replicates to quantify variance within and between batches and a workflow that uses these replicates to remove unwanted variation in a hierarchical manner (hRUV). We use this design to produce a dataset of more than 1000 human plasma samples run over an extended period of time. We demonstrate significant improvement of hRUV over existing methods in preserving biological signals whilst removing unwanted variation for large scale metabolomics studies. Our tools not only provide a strategy for large scale data normalisation, but also provides guidance on the design strategy for large omics studies.

DOI: https://doi.org/10.1038/s41467-021-25210-5
Front Cell Dev Biol. 2021 ;9 684036

Metabolic Alterations in Preneoplastic Development Revealed by Untargeted Metabolomic Analysis.

Henna Myllymäki, Jeanette Astorga Johansson, Estefania Grados Porro, Abigail Elliot, Tessa Moses, Yi Feng.

  Metabolic rewiring is a critical hallmark of tumorigenesis and is essential for the development of cancer. Although many key features of metabolic alteration that are crucial for tumor cell survival, proliferation and progression have been identified, these are obtained from studies with established tumors and cancer cell lines. However, information on the essential metabolic changes that occur during pre-neoplastic cell (PNC) development that enables its progression to full blown tumor is still lacking. Here, we present an untargeted metabolomics analysis of human oncogene HRASG12V induced PNC development, using a transgenic inducible zebrafish larval skin development model. By comparison with normal sibling controls, we identified six metabolic pathways that are significantly altered during PNC development in the skin. Amongst these altered pathways are pyrimidine, purine and amino acid metabolism that are common to the cancer metabolic changes that support rapid cell proliferation and growth. Our data also suggest alterations in post transcriptional modification of RNAs that might play a role in PNC development. Our study provides a proof of principle work flow for identifying metabolic alterations during PNC development driven by an oncogenic mutation. In the future, this approach could be combined with transcriptomic or proteomic approaches to establish the detailed interaction between signaling networks and cellular metabolic pathways that occur at the onset of tumor progression.

Keywords:  HRAS; cancer metabolism; metabolome; preneoplastic; untargeted metabolomics; zebrafish

DOI:  https://doi.org/10.3389/fcell.2021.684036
Food Sci Biotechnol. 2021 Jul;30(7): 881-890

Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review.

Min Kyung Park, Young-Suk Kim.

  Metabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.

Keywords:  Fermentation; Mass spectrometry; Metabolic pathway; Metabolomics; Volatile metabolites

DOI:  https://doi.org/10.1007/s10068-021-00917-9
Cell Syst. 2021 Aug 18. pii: S2405-4712(21)00250-7. [Epub ahead of print]12(8): 759-770

Artificial intelligence for proteomics and biomarker discovery.

Matthias Mann, Chanchal Kumar, Wen-Feng Zeng, Maximilian T Strauss.

  There is an avalanche of biomedical data generation and a parallel expansion in computational capabilities to analyze and make sense of these data. Starting with genome sequencing and widely employed deep sequencing technologies, these trends have now taken hold in all omics disciplines and increasingly call for multi-omics integration as well as data interpretation by artificial intelligence technologies. Here, we focus on mass spectrometry (MS)-based proteomics and describe how machine learning and, in particular, deep learning now predicts experimental peptide measurements from amino acid sequences alone. This will dramatically improve the quality and reliability of analytical workflows because experimental results should agree with predictions in a multi-dimensional data landscape. Machine learning has also become central to biomarker discovery from proteomics data, which now starts to outperform existing best-in-class assays. Finally, we discuss model transparency and explainability and data privacy that are required to deploy MS-based biomarkers in clinical settings.

Keywords:  FAIR principles; bioinformatics; data integration; data privacy; mass spectrometry; open source; plasma proteomics; transparent science

DOI:  https://doi.org/10.1016/j.cels.2021.06.006
Dev Cell. 2021 Aug 12. pii: S1534-5807(21)00601-8. [Epub ahead of print]

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat.

Anete Romanauska, Alwin Köhler.

  The cell nucleus is surrounded by a double membrane. The lipid packing and viscosity of membranes is critical for their function and is tightly controlled by lipid saturation. Circuits regulating the lipid saturation of the outer nuclear membrane (ONM) and contiguous endoplasmic reticulum (ER) are known. However, how lipid saturation is controlled in the inner nuclear membrane (INM) has remained enigmatic. Using INM biosensors and targeted genetic manipulations, we show that increased lipid unsaturation causes a reprogramming of lipid storage metabolism across the nuclear envelope (NE). Cells induce lipid droplet (LD) formation specifically from the distant ONM/ER, whereas LD formation at the INM is suppressed. In doing so, unsaturated fatty acids are shifted away from the INM. We identify the transcription circuits that topologically reprogram LD synthesis and identify seipin and phosphatidic acid as critical effectors. Our study suggests a detoxification mechanism protecting the INM from excess lipid unsaturation.

Keywords:  Mga2/Ole1; endoplasmic reticulum; inner nuclear membrane; lipid biosensors; lipid droplets; lipid metabolism; nuclear envelope; phosphatidic acid; seipin; unsaturated fatty acids

DOI:  https://doi.org/10.1016/j.devcel.2021.07.018
Methods Mol Biol. 2021 ;2327 221-238

Bottom-Up Community Proteome Analysis of Saliva Samples and Tongue Swabs by Data-Dependent Acquisition Nano LC-MS/MS Mass Spectrometry.

Alexander Rabe, Manuela Gesell Salazar, Uwe Völker.

  Analysis using mass spectrometry enables the characterization of metaproteomes in their native environments and overcomes the limitation of proteomics of pure cultures. Metaproteomics is a promising approach to link functions of currently actively expressed genes to the phylogenetic composition of the microbiome in their habitat. In this chapter, we describe the preparation of saliva samples and tongue swabs for nLC-MS/MS measurements and their bioinformatic analysis based on the Trans-Proteomic Pipeline and Prophane to study the oral microbiome .

Keywords:  Human oral microbiome; Metaproteomics; Saliva; Tongue; nLC-MS/MS

DOI:  https://doi.org/10.1007/978-1-0716-1518-8_13
Essays Biochem. 2021 Aug 20. pii: EBC20200067. [Epub ahead of print]

Mammalian lipids: structure, synthesis and function.

Shamshad Cockcroft.

  Lipids are essential constituents of cellular membranes. Once regarded merely as structural components, lipids have taken centre stage with the discovery of their roles in cell signalling and in the generation of bioactive metabolites. Lipids regulate many physiological functions of cells and alterations in membrane lipid metabolism are associated with major diseases including cancer, Type II diabetes, cardiovascular disease and immune disorders. Understanding lipid diversity, their synthesis and metabolism to generate signalling molecules will provide insight into the fundamental function of the cell. This review summarises the biosynthesis of the lipids of the mammalian cell; phospholipids, sphingolipids and cholesterol and how lipid diversity is achieved. The fatty acids (FAs) are the main building blocks of lipids and contribute to the diversity. Lipid synthesis is intimately connected to their transport within cells; the contribution by proteins that transport lipids, lipid transport proteins will be described. Cellular lipids are metabolised by phospholipases, lipid kinases and phosphatases to make new bioactive metabolites. These transient bioactive metabolites allow cells to respond to the external environment to maintain cellular health. The function of individual metabolites is also highlighted. Bioactive metabolites can be second messengers, or released to the external medium to regulate other cells. Alternatively, bioactive lipids also provide a platform for reversible recruitment of proteins to membranes using their lipid-binding domains. The wide range of physiological processes in which a specific involvement of lipids has been identified explains the need for lipid diversity present in mammalian cells.

Keywords:  Cholesterol; Signalling; phosphatidylinositol; phospholipases; sphingolipids

DOI:  https://doi.org/10.1042/EBC20200067
Chem Rev. 2021 Aug 20.

High-Resolution Native Mass Spectrometry.

Sem Tamara, Maurits A den Boer, Albert J R Heck.

Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of-among others-biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.

DOI: https://doi.org/10.1021/acs.chemrev.1c00212
Med Res Arch. 2021 May;pii: 2433. [Epub ahead of print]9(5):

Very long-chain acyl-CoA synthetase 3 mediates onco-sphingolipid metabolism in malignant glioma.

Elizabeth A Kolar, Xiaohai Shi, Emily M Clay, Ann B Moser, Bachchu Lal, Raja Sekhar Nirujogi, Akhilesh Pandey, Veera Venkata Ratnam Bandaru, John Laterra, Zhengtong Pei, Paul A Watkins.

  Gliomas are the largest category of primary malignant brain tumors in adults, and glioblastomas account for nearly half of malignant gliomas. Glioblastomas are notoriously aggressive and drug-resistant, with a very poor 5 year survival rate of about 5%. New approaches to treatment are thus urgently needed. We previously identified an enzyme of fatty acid metabolism, very long-chain acyl-CoA synthetase 3 (ACSVL3), as a potential therapeutic target in glioblastoma. Using the glioblastoma cell line U87MG, we created a cell line with genomic deletion of ACSVL3 (U87-KO) and investigated potential mechanisms to explain how this enzyme supports the malignant properties of glioblastoma cells. Compared to U87MG cells, U87-KO cells grew slower and assumed a more normal morphology. They produced fewer, and far smaller, subcutaneous xenografts in nude mice. Acyl-CoA synthetases, including ACSVL3, convert fatty acids to their acyl-CoA derivatives, allowing participation in diverse downstream lipid pathways. We examined the effect of ACSVL3 depletion on several such pathways. Fatty acid degradation for energy production was not affected in U87-KO cells. Fatty acid synthesis, and incorporation of de novo synthesized fatty acids into membrane phospholipids needed for rapid tumor cell growth, was not significantly affected by lack of ACSVL3. In contrast, U87-KO cells exhibited evidence of altered sphingolipid metabolism. Levels of ceramides containing 18-22 carbon fatty acids were significantly lower in U87-KO cells. This paralleled the fatty acid substrate specificity profile of ACSVL3. The rate of incorporation of stearate, an 18-carbon saturated fatty acid, into ceramides was reduced in U87-KO cells, and proteomics revealed lower abundance of ceramide synthesis pathway enzymes. Sphingolipids, including gangliosides, are functional constituents of lipid rafts, membrane microdomains thought to be organizing centers for receptor-mediated signaling. Both raft morphology and ganglioside composition were altered by deficiency of ACSVL3. Finally, levels of sphingosine-1-phosphate, a sphingolipid signaling molecule, were reduced in U87-KO cells. We conclude that ACSVL3 supports the malignant behavior of U87MG cells, at least in part, by altering cellular sphingolipid metabolism.

Keywords:  GBM; Glioma; U87MG cells; sphingolipid metabolism; very long-chain acyl-CoA synthetase 3

DOI:  https://doi.org/10.18103/mra.v9i5.2433
Cancer Metab. 2021 Aug 16. 9(1): 31

Metabolic convergence on lipogenesis in RAS, BCR-ABL, and MYC-driven lymphoid malignancies.

Daniel F Liefwalker, Meital Ryan, Zhichao Wang, Khyatiben V Pathak, Seema Plaisier, Vidhi Shah, Bobby Babra, Gabrielle S Dewson, Ian K Lai, Adriane R Mosley, Patrick T Fueger, Stephanie C Casey, Lei Jiang, Patrick Pirrotte, Srividya Swaminathan, Rosalie C Sears.

  BACKGROUND: Metabolic reprogramming is a central feature in many cancer subtypes and a hallmark of cancer. Many therapeutic strategies attempt to exploit this feature, often having unintended side effects on normal metabolic programs and limited efficacy due to integrative nature of metabolic substrate sourcing. Although the initiating oncogenic lesion may vary, tumor cells in lymphoid malignancies often share similar environments and potentially similar metabolic profiles. We examined cells from mouse models of MYC-, RAS-, and BCR-ABL-driven lymphoid malignancies and find a convergence on de novo lipogenesis. We explore the potential role of MYC in mediating lipogenesis by 13C glucose tracing and untargeted metabolic profiling. Inhibition of lipogenesis leads to cell death both in vitro and in vivo and does not induce cell death of normal splenocytes.METHODS: We analyzed RNA-seq data sets for common metabolic convergence in lymphoma and leukemia. Using in vitro cell lines derived in from conditional MYC, RAS, and BCR-ABL transgenic murine models and oncogene-driven human cell lines, we determined gene regulation, metabolic profiles, and sensitivity to inhibition of lipogenesis in lymphoid malignancies. We utilize preclinical murine models and transgenic primary model of T-ALL to determine the effect of lipogenesis blockade across BCR-ABL-, RAS-, and c-MYC-driven lymphoid malignancies. Statistical significance was calculated using unpaired t-tests and one-way ANOVA.
RESULTS: This study illustrates that de novo lipid biogenesis is a shared feature of several lymphoma subtypes. Using cell lines derived from conditional MYC, RAS, and BCR-ABL transgenic murine models, we demonstrate shared responses to inhibition of lipogenesis by the acetyl-coA carboxylase inhibitor 5-(tetradecloxy)-2-furic acid (TOFA), and other lipogenesis inhibitors. We performed metabolic tracing studies to confirm the influence of c-MYC and TOFA on lipogenesis. We identify specific cell death responses to TOFA in vitro and in vivo and demonstrate delayed engraftment and progression in vivo in transplanted lymphoma cell lines. We also observe delayed progression of T-ALL in a primary transgenic mouse model upon TOFA administration. In a panel of human cell lines, we demonstrate sensitivity to TOFA treatment as a metabolic liability due to the general convergence on de novo lipogenesis in lymphoid malignancies driven by MYC, RAS, or BCR-ABL. Importantly, cell death was not significantly observed in non-malignant cells in vivo.
CONCLUSIONS: These studies suggest that de novo lipogenesis may be a common survival strategy for many lymphoid malignancies and may be a clinically exploitable metabolic liability.
TRIAL REGISTRATION: This study does not include any clinical interventions on human subjects.

Keywords:  ACACA; BCR-ABL; Cancer metabolism; De novo lipogenesis; FASN; Fatty acid synthesis; Lipogenesis; Lymphoma; Oncogene addiction; RAS; T-ALL; c-MYC

DOI:  https://doi.org/10.1186/s40170-021-00263-8
Ann N Y Acad Sci. 2021 Aug 19.

Metabolic decisions in development and disease-a Keystone Symposia report.

Jennifer Cable, Olivier Pourquié, Kathryn E Wellen, Lydia W S Finley, Alexander Aulehla, Alex P Gould, Aurelio Teleman, William B Tu, Wendy Sarah Garrett, Irene Miguel-Aliaga, Norbert Perrimon, Lora V Hooper, A J Marian Walhout, Wei Wei, Theodore Alexandrov, Ayelet Erez, Markus Ralser, Joshua D Rabinowitz, Anupama Hemalatha, Paula Gutiérrez-Pérez, Navdeep S Chandel, Jared Rutter, Jason W Locasale, Juan C Landoni, Heather Christofk.

  There is an increasing appreciation for the role of metabolism in cell signaling and cell decision making. Precise metabolic control is essential in development, as evident by the disorders caused by mutations in metabolic enzymes. The metabolic profile of cells is often cell-type specific, changing as cells differentiate or during tumorigenesis. Recent evidence has shown that changes in metabolism are not merely a consequence of changes in cell state but that metabolites can serve to promote and/or inhibit these changes. Metabolites can link metabolic pathways with cell signaling pathways via several mechanisms, for example, by serving as substrates for protein post-translational modifications, by affecting enzyme activity via allosteric mechanisms, or by altering epigenetic markers. Unraveling the complex interactions governing metabolism, gene expression, and protein activity that ultimately govern a cell's fate will require new tools and interactions across disciplines. On March 24 and 25, 2021, experts in cell metabolism, developmental biology, and human disease met virtually for the Keystone eSymposium, "Metabolic Decisions in Development and Disease." The discussions explored how metabolites impact cellular and developmental decisions in a diverse range of model systems used to investigate normal development, developmental disorders, dietary effects, and cancer-mediated changes in metabolism.

Keywords:  cell signaling; development; inborn errors of metabolism; metabolism; metabolome; stem cell differentiation

DOI:  https://doi.org/10.1111/nyas.14678
BMC Res Notes. 2021 Aug 17. 14(1): 315

Lipoprotein lipase hydrolysis products induce pro-inflammatory cytokine expression in triple-negative breast cancer cells.

Alexandria J Tobin, Nicholas P Noel, Sherri L Christian, Robert J Brown.

  OBJECTIVES: Breast cancer cell growth and proliferation requires lipids for energy production, cell membrane synthesis, or as signaling molecules. Lipids can be delivered to cells by lipoprotein lipase (LPL), an extracellular lipase that hydrolyzes triacylglycerols and phospholipids from lipoproteins, that is expressed by adipose tissue and some breast cancer cell lines. Studies have shown that lipoprotein hydrolysis products induce pro-inflammatory cytokine secretion by endothelial cells. Thus, our objective was to determine if hydrolysis products generated by LPL from total lipoproteins can also promote pro-inflammatory cytokine secretion from breast cancer cells.RESULTS: Using cytokine arrays, we found that MDA-MB-231 cells increased secretion of seven cytokines in response to treatment with lipoprotein hydrolysis products. In contrast, MCF-7 cells showed decreased secretion of two cytokines. Expanding the analysis to additional cell lines by ELISA, we found increased secretion of TNF-α and IL-6 by MDA-MB-468 cells, and increased secretion of IL-4 by MDA-MB-468 and SKBR3 cells. The changes to cytokine secretion profiles of the breast cancer cell types examined, including the non-cancerous MCF-10a breast cells, were independent of increased cell metabolic activity. These results provide information on how lipoprotein hydrolysis products within the tumor microenvironment might affect breast cancer cell viability and progression.

Keywords:  Antibody arrays; Breast cancer; Cytokines; Lipoprotein lipase; Lipoproteins; Metabolic activity

DOI:  https://doi.org/10.1186/s13104-021-05728-z
STAR Protoc. 2021 Sep 17. 2(3): 100724

Quantitative analysis of m6A RNA modification by LC-MS.

Lavina Mathur, Sunhee Jung, Cholsoon Jang, Gina Lee.

  N 6-adenosine methylation (m6A) of messenger RNA (mRNA) plays key regulatory roles in gene expression. Accurate measurement of m6A levels is thus critical to understand its dynamic changes in various biological settings. Here, we provide a protocol to quantitate the levels of adenosine and m6A in cellular mRNAs. Using nuclease and phosphatase, we digest mRNA into nucleosides, which are subsequently quantified using liquid chromatography mass spectrometry. For complete details on the use and execution of this protocol, please refer to Cho et al. (2021).

Keywords:  cell biology; cell culture; chemistry; mass spectrometry; metabolism; molecular biology

DOI:  https://doi.org/10.1016/j.xpro.2021.100724
Mol Cell Proteomics. 2021 Aug 12. pii: S1535-9476(21)00105-5. [Epub ahead of print] 100133

Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples.

Susan Klaeger, Annie Apffel, Karl R Clauser, Siranush Sarkizova, Giacomo Oliveira, Suzanna Rachimi, Phuong M Le, Anna Tarren, Vipheaviny Chea, Jennifer G Abelin, David A Braun, Patrick A Ott, Hasmik Keshishian, Nir Hacohen, Derin B Keskin, Catherine J Wu, Steven A Carr.

Mass spectrometry is the most effective method to directly identify peptides presented on HLA molecules. However, current standard approaches often use 500 million or more cells as input to achieve high coverage of the immunopeptidome and therefore these methods are not compatible with the often limited amounts of tissue available from clinical tumor samples. Here, we evaluated microscaled basic reversed-phase fractionation to separate HLA peptide samples off-line followed by ion mobility coupled to LC-MS/MS for analysis. The combination of these two separation methods enabled identification of 20% to 50% more peptides compared to samples analyzed without either prior fractionation or use of ion mobility alone. We demonstrate coverage of HLA immunopeptidomes with up to 8,107 distinct peptides starting with as few as 100 million cells. The increased sensitivity obtained using our methods can provide data useful to improve HLA binding prediction algorithms as well as to enable detection of clinically relevant epitopes such as neoantigens.

DOI: https://doi.org/10.1016/j.mcpro.2021.100133
Prostaglandins Leukot Essent Fatty Acids. 2021 Jun 24. pii: S0952-3278(21)00079-X. [Epub ahead of print]172 102316

Feeding mice a diet high in oxidized linoleic acid metabolites does not alter liver oxylipin concentrations.

Nuanyi Liang, Marie Hennebelle, Susanne Gaul, Casey D Johnson, Zhichao Zhang, Irina A Kirpich, Craig J McClain, Ariel E Feldstein, Christopher E Ramsden, Ameer Y Taha.

  The oxidation of dietary linoleic acid (LA) produces oxidized LA metabolites (OXLAMs) known to regulate multiple signaling pathways in vivo. Recently, we reported that feeding OXLAMs to mice resulted in liver inflammation and apoptosis. However, it is not known whether this is due to a direct effect of OXLAMs accumulating in the liver, or to their degradation into bioactive shorter chain molecules (e.g. aldehydes) that can provoke inflammation and related cascades. To address this question, mice were fed a low or high LA diet low in OXLAMs, or a low LA diet supplemented with OXLAMs from heated corn oil (high OXLAM diet). Unesterified oxidized fatty acids (i.e. oxylipins), including OXLAMs, were measured in liver after 8 weeks of dietary intervention using ultra-high pressure liquid chromatography coupled to tandem mass-spectrometry. The high OXLAM diet did not alter liver oxylipin concentrations compared to the low LA diet low in OXLAMs. Significant increases in several omega-6 derived oxylipins and reductions in omega-3 derived oxylipins were observed in the high LA dietary group compared to the low LA group. Our findings suggest that dietary OXLAMs do not accumulate in liver, and likely exert pro-inflammatory and pro-apoptotic effects via downstream secondary metabolites.

Keywords:  Free oxylipins; Linoleic acid; Lipid mediators; Liver; Oxidized fatty acids; UPLC-MS/MS

DOI:  https://doi.org/10.1016/j.plefa.2021.102316
Mol Cell Proteomics. 2021 Aug 17. pii: S1535-9476(21)00110-9. [Epub ahead of print] 100138

Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation - Serial Fragmentation (PASEF) in Proteomics.

Florian Meier, Melvin A Park, Matthias Mann.

Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique which separates gas phase ions by their size and shape and which can be hybridized with conventional liquid chromatography and mass spectrometry. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to time-of-flight mass analysis. In particular, the parallel accumulation - serial fragmentation (PASEF) operation mode offers unique advantages in terms of sequencing speed and sensitivity. Its defining feature is that it synchronizes the release of ions from the TIMS device with the downstream selection of precursors for fragmentation in a TIMS - quadrupole - time-of-flight (timsTOF) configuration. As ions are compressed into narrow ion mobility peaks, the number of peptide fragment ion spectra obtained in data-dependent or targeted analyses can be increased by an order of magnitude without compromising sensitivity. Taking advantage of the correlation between ion mobility and mass, the PASEF principle also multiplies the efficiency of data-independent acquisition. This makes the technology well suited for rapid proteome profiling, an increasingly important attribute in clinical proteomics, as well as for ultra-sensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section (CCS) values at the scale of more than a million data points, and the development of neural networks capable of predicting them based only on peptide sequences. Peptide CCS values can differ for isobaric sequences or positional isomers of post-translational modifications. This additional information may be leveraged in real-time to direct data acquisition or in post-processing to increase confidence in peptide identifications. These developments make timsTOF-PASEF a powerful and expandable platform for proteomics and beyond.

DOI: https://doi.org/10.1016/j.mcpro.2021.100138
Front Chem. 2021 ;9 736661

Editorial: Metabolomics in the Study of Unconventional Biological Matrices.

Elena Sánchez-López, Tommaso Lomonaco, Masahiro Sugimoto, Yunping Qiu, Beatrice Campanella.



Keywords:  biomarkers; mass spectrometry; metabolomics; sample preparation; unconventional matrices

DOI:  https://doi.org/10.3389/fchem.2021.736661
JHEP Rep. 2021 Oct;3(5): 100325

Comprehensive lipidomics reveals phenotypic differences in hepatic lipid turnover in ALD and NAFLD during alcohol intoxication.

Mads Israelsen, Min Kim, Tommi Suvitaival, Bjørn Stæhr Madsen, Camilla Dalby Hansen, Nikolaj Torp, Kajetan Trost, Maja Thiele, Torben Hansen, Cristina Legido-Quigley, Aleksander Krag, .

  Background & Aims: In experimental models, alcohol induces acute changes in lipid metabolism that cause hepatocyte lipoapoptosis and inflammation. Here we study human hepatic lipid turnover during controlled alcohol intoxication.Methods: We studied 39 participants with 3 distinct hepatic phenotypes: alcohol-related liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), and healthy controls. Alcohol was administrated via nasogastric tube over 30 min. Hepatic and systemic venous blood was sampled simultaneously at 3 time points: baseline, 60, and 180 min after alcohol intervention. Liver biopsies were sampled 240 min after alcohol intervention. We used ultra-high performance liquid chromatography mass spectrometry to measure levels of more than 250 lipid species from the blood and liver samples.
Results: After alcohol intervention, the levels of blood free fatty acid (FFA) and lysophosphatidylcholine (LPC) decreased, while triglyceride (TG) increased. FFA was the only lipid class to decrease in NAFLD after alcohol intervention, whereas LPC and FFA decreased and TG increased after intervention in ALD and healthy controls. Fatty acid chain uptake preference in FFAs and LPCs were oleic acid, linoleic acid, arachidonic acid, and docosahexaenoic acid. Hepatic venous blood FFA and LPC levels were lower when compared with systemic venous blood levels throughout the intervention. After alcohol intoxication, liver lipidome in ALD was similar to that in NAFLD.
Conclusions: Alcohol intoxication induces rapid changes in circulating lipids including hepatic turnaround from FFA and LPC, potentially leading to lipoapoptosis and steatohepatitis. TG clearance was suppressed in NAFLD, possibly explaining why alcohol and NAFLD are synergistic risk factors for disease progression. These effects may be central to the pathogenesis of ALD.
Clinical Trials Registration: The study is registered at Clinicaltrials.gov (NCT03018990).
Lay summary: We report that alcohol induces hepatic extraction of free unsaturated fatty acids and lysophosphatidylcholines, hepatotoxic lipids which have not been previously associated with alcohol-induced liver injury. We also found that individuals with non-alcoholic fatty liver disease have reduced lipid turnover during alcohol intoxication when compared with people with alcohol-related fatty liver disease. This may explain why alcohol is particularly more harmful in people with non-alcoholic fatty liver and why elevated BMI and alcohol have a synergistic effect on the risk of liver-related death.

Keywords:  ALD, alcohol-related liver disease; ALT, alanine aminotransferase; AST, asparagine aminotransferase; Alcohol; CTL, healthy control; Cer, ceramide; DG, diglyceride; Ethanol; FFA, free fatty acid; Fatty acids; GGT, gamma-glutamyl transferase; HOMA-IR, Homeostatic Model Assessment of Insulin Resistance; Heavy drinking; HexCer, hexosylceramide; LPC, lysophosphatidylcholine; LPE, lysophosphatidylethanolamine; LacCer, lactosylceramides; Lipidomics; Liver disease; Lysophosphatidylcholines; NAFLD, non-alcoholic fatty liver disease; P-glucose, plasma glucose; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; PLA2, phospholipase A2; QC, quality control; SHexCer, sulfatides hexosylceramide; SM, sphingomyelin; TE, transient elastography; TG, triglyceride; Triglycerides

DOI:  https://doi.org/10.1016/j.jhepr.2021.100325
Nat Commun. 2021 08 16. 12(1): 4961

Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting.

Wei Liu, Lei Xie, Yao-Hui He, Zhi-Yong Wu, Lu-Xin Liu, Xue-Feng Bai, Dan-Xia Deng, Xiu-E Xu, Lian-Di Liao, Wan Lin, Jing-Hua Heng, Xin Xu, Liu Peng, Qing-Feng Huang, Cheng-Yu Li, Zhi-Da Zhang, Wei Wang, Guo-Rui Zhang, Xiang Gao, Shao-Hong Wang, Chun-Quan Li, Li-Yan Xu, Wen Liu, En-Min Li.

Esophageal cancer (EC) is a type of aggressive cancer without clinically relevant molecular subtypes, hindering the development of effective strategies for treatment. To define molecular subtypes of EC, we perform mass spectrometry-based proteomic and phosphoproteomics profiling of EC tumors and adjacent non-tumor tissues, revealing a catalog of proteins and phosphosites that are dysregulated in ECs. The EC cohort is stratified into two molecular subtypes-S1 and S2-based on proteomic analysis, with the S2 subtype characterized by the upregulation of spliceosomal and ribosomal proteins, and being more aggressive. Moreover, we identify a subtype signature composed of ELOA and SCAF4, and construct a subtype diagnostic and prognostic model. Potential drugs are predicted for treating patients of S2 subtype, and three candidate drugs are validated to inhibit EC. Taken together, our proteomic analysis define molecular subtypes of EC, thus providing a potential therapeutic outlook for improving disease outcomes in patients with EC.

DOI: https://doi.org/10.1038/s41467-021-25202-5
Anal Chem. 2021 Aug 17.

CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification.

Fei Wang, Jaanus Liigand, Siyang Tian, David Arndt, Russell Greiner, David S Wishart.

In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries, we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID's ability to predict ESI-MS/MS spectra from compounds by (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations, and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a web server and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid.

DOI: https://doi.org/10.1021/acs.analchem.1c01465
J Chromatogr A. 2021 Aug 08. pii: S0021-9673(21)00581-1. [Epub ahead of print]1654 462457

Improving data quality in liquid chromatography-mass spectrometry metabolomics of human urine.

Rosilene Cristina Rossetto Burgos, Adriana Nori de Macedo, Pedro Luis Rocha da Cruz, Hélio Tedesco-Silva Júnior, Karina Helena Morais Cardozo, Valdemir Melechco Carvalho, Marina Franco Maggi Tavares.

  Signal variation is a common drawback in untargeted metabolomics using liquid chromatography-mass spectrometry (LC-MS), mainly due to the complexity of biological matrices and reduced sample preparation, which results in the accumulation of sample components in the column and the ion source. Here we propose a simple, easy to implement approach to improve data quality in untargeted metabolomics by LC-MS. This approach involves the use of a divert valve to direct the column effluent to waste at the beginning of the chromatographic run and during column cleanup and equilibration, in combination with longer column cleanups in between injections. Our approach was tested using urine samples collected from patients after renal transplantation. Analytical responses were contrasted before and after introducing these modifications by analyzing a batch of untargeted metabolomics data. A significant improvement in peak area repeatability was observed for the quality controls, with relative standard deviations (RSDs) for several metabolites decreasing from ∼60% to ∼10% when our approach was introduced. Similarly, RSDs of peak areas for internal standards improved from ∼40% to ∼10%. Furthermore, calibrant solutions were more consistent after introducing these modifications when comparing peak areas of solutions injected at the beginning and the end of each analytical sequence. Therefore, we recommend the use of a divert valve and extended column cleanup as a powerful strategy to improve data quality in untargeted metabolomics, especially for very complex types of samples where minimum sample preparation is required, such as in this untargeted metabolomics study with urine from renal transplanted patients.

Keywords:  Column cleanup; Divert valve; Liquid chromatography; Quality control; Untargeted metabolomics

DOI:  https://doi.org/10.1016/j.chroma.2021.462457
Sheng Li Xue Bao. 2021 Aug 25. 73(4): 657-664

[Arachidonic acid metabolism in liver glucose and lipid homeostasis].

Sha Li, Wen Su, Xiao-Yan Zhang, You-Fei Guan.

Arachidonic acid (AA) is an ω-6 polyunsaturated fatty acid, which mainly exists in the cell membrane in the form of phospholipid. Three major enzymatic pathways including the cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 monooxygenase (CYP450) pathways are involved in AA metabolism leading to the generation of a variety of lipid mediators such as prostaglandins, leukotrienes, hydroxyeicosatetraenoic acids (HETEs) and epoxyeicoastrienoic acids (EETs). These bioactive AA metabolites play an important role in the regulation of many physiological processes including the maintenance of liver glucose and lipid homeostasis. As the central metabolic organ, the liver is essential in metabolism of carbohydrates, lipids and proteins, and its dysfunction is associated with the pathogenesis of many metabolic diseases such as type 2 diabetes mellitus, dyslipidemia and nonalcoholic fatty liver disease (NAFLD). This article aims to provide an overview of the enzymatic pathways of AA and discuss the role of AA-derived lipid mediators in the regulation of hepatic glucose and lipid metabolism and their associations with the pathogenesis of major metabolic disorders.
Cell Rep. 2021 Aug 17. pii: S2211-1247(21)00959-1. [Epub ahead of print]36(7): 109528

Autophagy is a major metabolic regulator involved in cancer therapy resistance.

Laura Poillet-Perez, Jean-Emmanuel Sarry, Carine Joffre.

  Autophagy sustains cellular homeostasis and metabolism in numerous diseases. By regulating cancer metabolism, both tumor and microenvironmental autophagy promote tumor growth. However, autophagy can support cancer progression through other biological functions such as immune response regulation or cytokine/growth factor secretion. Moreover, autophagy is induced in numerous tumor types as a resistance mechanism following therapy, highlighting autophagy inhibition as a promising target for anti-cancer therapy. Thus, better understanding the mechanisms involved in tumor growth and resistance regulation through autophagy, which are not fully understood, will provide insights into patient treatment.

Keywords:  Poillet-Perez et al. review how both tumor and microenvironmental autophagy promote tumor growth by regulating cancer metabolism and the immune response. Moreover; autophagy is induced as a cell death or resistance mechanism following therapy. Better understanding the role of autophagy and the mechanisms involved will provide insights into patient treatment

DOI:  https://doi.org/10.1016/j.celrep.2021.109528
Nat Commun. 2021 08 18. 12(1): 5015

Off-the-shelf proximity biotinylation for interaction proteomics.

Irene Santos-Barriopedro, Guido van Mierlo, Michiel Vermeulen.

Proximity biotinylation workflows typically require CRISPR-based genetic manipulation of target cells. To overcome this bottleneck, we fused the TurboID proximity biotinylation enzyme to Protein A. Upon target cell permeabilization, the ProtA-Turbo enzyme can be targeted to proteins or post-translational modifications of interest using bait-specific antibodies. Addition of biotin then triggers bait-proximal protein biotinylation. Biotinylated proteins can subsequently be enriched from crude lysates and identified by mass spectrometry. We demonstrate this workflow by targeting Emerin, H3K9me3 and BRG1. Amongst the main findings, our experiments reveal that the essential protein FLYWCH1 interacts with a subset of H3K9me3-marked (peri)centromeres in human cells. The ProtA-Turbo enzyme represents an off-the-shelf proximity biotinylation enzyme that facilitates proximity biotinylation experiments in primary cells and can be used to understand how proteins cooperate in vivo and how this contributes to cellular homeostasis and disease.

DOI: https://doi.org/10.1038/s41467-021-25338-4
Nature. 2021 Aug 18.

Dietary fructose improves intestinal cell survival and nutrient absorption.

Samuel R Taylor, Shakti Ramsamooj, Roger J Liang, Alyna Katti, Rita Pozovskiy, Neil Vasan, Seo-Kyoung Hwang, Navid Nahiyaan, Nancy J Francoeur, Emma M Schatoff, Jared L Johnson, Manish A Shah, Andrew J Dannenberg, Robert P Sebra, Lukas E Dow, Lewis C Cantley, Kyu Y Rhee, Marcus D Goncalves.

Fructose consumption is linked to the rising incidence of obesity and cancer, which are two of the leading causes of morbidity and mortality globally1,2. Dietary fructose metabolism begins at the epithelium of the small intestine, where fructose is transported by glucose transporter type 5 (GLUT5; encoded by SLC2A5) and phosphorylated by ketohexokinase to form fructose 1-phosphate, which accumulates to high levels in the cell3,4. Although this pathway has been implicated in obesity and tumour promotion, the exact mechanism that drives these pathologies in the intestine remains unclear. Here we show that dietary fructose improves the survival of intestinal cells and increases intestinal villus length in several mouse models. The increase in villus length expands the surface area of the gut and increases nutrient absorption and adiposity in mice that are fed a high-fat diet. In hypoxic intestinal cells, fructose 1-phosphate inhibits the M2 isoform of pyruvate kinase to promote cell survival5-7. Genetic ablation of ketohexokinase or stimulation of pyruvate kinase prevents villus elongation and abolishes the nutrient absorption and tumour growth that are induced by feeding mice with high-fructose corn syrup. The ability of fructose to promote cell survival through an allosteric metabolite thus provides additional insights into the excess adiposity generated by a Western diet, and a compelling explanation for the promotion of tumour growth by high-fructose corn syrup.

DOI: https://doi.org/10.1038/s41586-021-03827-2