Metabolomics articles within Nature Communications

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  • Article
    | Open Access

    In the fly Drosophila melanogaster commensal bacteria and dietary essential amino acids control food choice behavior. Here, by using chemically defined diets and metabolomics, the authors show that Acetobacter pomorum (Ap) and Lactobacilli plantarum (Lp) engage in a mutualistic metabolic relationship to overcome detrimental diets, and identify Ap as the bacterium altering the host’s feeding decisions.

    • Sílvia F. Henriques
    • , Darshan B. Dhakan
    •  & Carlos Ribeiro

  • Article
    | Open Access

    The relationship between DNA damage response (DDR) and regulation of the tolerance to glucose restriction is currently unclear. Here the authors reveal that maintaining a physiological level of histones by Rad53-Spt21 is necessary for glucose tolerance via multiple parallel pathways, including derepression of subtelomeric genes and acetyl-coA regulation by histone acetylation.

    • Christopher Bruhn
    • , Arta Ajazi
    •  & Marco Foiani

  • Article
    | Open Access

    As macrophages switch to a proinflammatory gylcolytic state they start to generate triglyceride-rich lipid droplets, but what function these droplets have in this context is not clear. Here the authors show that this triglyceride synthesis is requisite for prostaglandin E2 production and subsequent inflammatory activation.

    • Angela Castoldi
    • , Lauar B. Monteiro
    •  & Edward J. Pearce

  • Article
    | Open Access

    Plasmodium falciparum chloroquine resistance transporter (PfCRT) mediates multidrug resistance, but its natural function remains unclear. Here, Shafik et al. show that PfCRT transports host-derived peptides of 4-11 residues but not other ions or metabolites, and that drug-resistance-conferring PfCRT mutants have reduced peptide transport.

    • Sarah H. Shafik
    • , Simon A. Cobbold
    •  & Rowena E. Martin

  • Article
    | Open Access

    Existing fluorescent protein-based sensor measurements are limited to 4 or fewer simultaneously recorded modalities due to spectral overlap. Here the authors introduce Multiplexed Optical Sensors in Arrayed Islands of Cells (MOSAIC), which enables parallel recording of tens of physiological parameters using dense arrays of cell islands, each expressing a different fluorescent sensor.

    • Christopher A. Werley
    • , Stefano Boccardo
    •  & Adam E. Cohen

  • Article
    | Open Access

    Zika virus (ZIKV) remodels intracellular membranes for replication, but the role of different lipid types for infection and disease is unclear. Here, the authors perform lipidomics, show perturbation of the lipid network during ZIKV infection and show that ceramides are important for ZIKV infection.

    • Hans C. Leier
    • , Jules B. Weinstein
    •  & Fikadu G. Tafesse

  • Article
    | Open Access

    Cellular metabolism is altered in many cancer types and the advent of metabolomics has allowed us to understand more about how this is dysregulated. Here, the authors report a method named CARVE to analyse the arterial supply and venous drainage of glioma patients during surgery and identify the metabolites that may be consumed and produced by the cancer.

    • Nanxiang Xiong
    • , Xiaofei Gao
    •  & Woo-ping Ge

  • Article
    | Open Access

    Calorimetrically measuring the heat of single cells is currently not possible due to the sensitivity of existing calorimeters. Here the authors present on-chip single cell calorimetry, with a sensitivity over ten-fold greater than the current gold-standard.

    • Sahngki Hong
    • , Edward Dechaumphai
    •  & Renkun Chen

  • Article
    | Open Access

    Age-associated metabolic changes include lipid accumulation. Here, the authors show that with replicative aging yeast accumulate lipid droplets which protect cells from cold stress and can be modulated through Biosynthesis of NAD+ 2 (BNA2).

    • Anthony O. Beas
    • , Patricia B. Gordon
    •  & Daniel E. Gottschling

  • Article
    | Open Access

    Study of human heart failure is limited by access to human tissue. Here, the authors apply multi-omic screening in human ischaemic and dilated myocardial tissue and matched controls to determine molecular changes common and unique to each aetiology and to reveal differences between male and female hearts.

    • Mengbo Li
    • , Benjamin L. Parker
    •  & John F. O’Sullivan

  • Article
    | Open Access

    Androgen receptor (AR) signalling regulates cellular metabolism in prostate cancer. Here, the authors perform a proteomics and metabolomics characterisation of prostate cancer cells adapted to long-term resistance to AR inhibition and show rewiring of glucose and lipid metabolism, and further identify a signature associated with resistance to AR inhibition.

    • Arnaud Blomme
    • , Catriona A. Ford
    •  & Hing Y. Leung

  • Article
    | Open Access

    Macrophages undergo a Warburg-like switch from oxidative phosphorylation to glycolysis in response to inflammatory stimulus. Here the authors show that fungal melanin can trigger this switch in human macrophages by sequestering calcium in the phagosome and enabling protection against Aspergillus fumigatus infection.

    • Samuel M. Gonçalves
    • , Cláudio Duarte-Oliveira
    •  & Agostinho Carvalho

  • Article
    | Open Access

    Gene rv3722c is essential for in vitro growth of Mycobacterium tuberculosis, but its function is unclear. Here, Jansen et al. show that Rv3722c is the primary aspartate aminotransferase of this pathogen, mediates nitrogen distribution, and is important for virulence during infection of macrophages and mice.

    • Robert S. Jansen
    • , Lungelo Mandyoli
    •  & Kyu Y. Rhee

  • Article
    | Open Access

    Prematurely born babies need extra oxygen to survive, but this can cause damage to the eyes and lead to infant blindness. Here the authors show that this hyperoxia changes the metabolism of Müller cells in the retina such that they use up, rather than produce, glutamine and secrete excess ammonium.

    • Charandeep Singh
    • , Vincent Tran
    •  & Jonathan E. Sears

  • Article
    | Open Access

    Sex and the APOE ε4 genotype are important risk factors for late-onset Alzheimer’s disease. In the current study, the authors investigate how sex and APOE ε4 genotype modify the association between Alzheimer’s disease biomarkers and metabolites in serum.

    • Matthias Arnold
    • , Kwangsik Nho
    •  & Gabi Kastenmüller

  • Article
    | Open Access

    Blood metabolite levels are under the influence of environmental and genetic factors. Here, Hagenbeek et al. perform heritability estimations for metabolite measures and determine the contribution of known metabolite loci to metabolite levels using data from 40 genome-wide association studies.

    • Fiona A. Hagenbeek
    • , René Pool
    •  & Dorret I. Boomsma

  • Article
    | Open Access

    Here, the authors provide an in-depth study of the metabolome in two large population-based prospective cohorts and identify 32 microbial traits associated with various metabolic biomarkers and specific lipoprotein subfractions, providing insights into the role of microbiota in influencing host lipid levels.

    • Dina Vojinovic
    • , Djawad Radjabzadeh
    •  & Cornelia M. van Duijn

  • Article
    | Open Access

    Graft versus host disease (GvHD) still hinders allogeneic hematopoietic stem cell transplantation. Here, the authors use metabolomics to analyze two cohorts of paired transplant recipients and donors, identifying significant differences in both host- and microbiota-derived metabolites.

    • David Michonneau
    • , Eleonora Latis
    •  & Gérard Socié

  • Article
    | Open Access

    Plasmodium growth is adapted to the reproductive cycle of mosquitoes, but underlying mechanisms are unclear. Here, Lampe et al. show that the blood-meal induced miR-276 balances the termination of the mosquito amino acid catabolism and egg development, providing nutrients for Plasmodium sporozoite development.

    • Lena Lampe
    • , Marius Jentzsch
    •  & Elena A. Levashina

  • Article
    | Open Access

    ERCC1 is involved in a number of DNA repair pathways including nucleotide excision repair. Here the authors showed that reduced transcription in Ercc1-deficient mouse livers and cells increases ATP levels, suppressing glycolysis and rerouting glucose into the pentose phosphate shunt that generates reductive stress.

    • Chiara Milanese
    • , Cíntia R. Bombardieri
    •  & Pier G. Mastroberardino

  • Article
    | Open Access

    Genome-wide association studies of metabolites have revealed hundreds of genetic associations using univariate analyses. Here, the authors use a multivariate approach to perform association analyses for 158 serum metabolites, followed by fine mapping and GxE interaction tests with statin use and age.

    • Apolline Gallois
    • , Joel Mefford
    •  & Hugues Aschard

  • Article
    | Open Access

    Down syndrome (DS) is caused by trisomy 21 (T21), but the underlying etiology of the related immune and neurological dysfunction is unclear. Here, the authors show that T21 activates the kynurenine pathway via increased interferon receptor copy number, which could contribute to DS pathophysiology.

    • Rani K. Powers
    • , Rachel Culp-Hill
    •  & Joaquin M. Espinosa

  • Article
    | Open Access

    Enhanced cholesterol biosynthesis is associated with cancer progression. Here the authors identify the nuclear receptor RORγ as a novel master regulator of cholesterol metabolism in triple negative breast cancer (TNBC) and find that RORγ small-molecule antagonists induce tumor regression in patient-derived xenografts and immunocompetent mouse models.

    • Demin Cai
    • , Junjian Wang
    •  & Hong-Wu Chen

  • Article
    | Open Access

    Here, the authors study the interplay between the microbiome and faecal and blood metabolome, and how the microbiome interacts in the dialogue between these metabolic compartments, identifying a key role for microbial functions and underscoring their relevance for microbiome therapeutic strategies.

    • Alessia Visconti
    • , Caroline I. Le Roy
    •  & Mario Falchi

  • Article
    | Open Access

    Interactions between metabolites and transcription factors are known to control gene expression but analyzing these events at genome-scale is challenging. Here, the authors integrate dynamic metabolome and transcriptome data from E.coli to predict regulatory metabolite-transcription factor interactions.

    • Martin Lempp
    • , Niklas Farke
    •  & Hannes Link

  • Article
    | Open Access

    Cancer cells rely on mitochondrial respiration to satisfy their metabolic demands. Here the authors show that the mitochondrial supercomplex assembly factor COX7RP is abundantly expressed in breast and endometrial cancer cells and promotes tumor growth and hypoxia tolerance partially by altering levels of the tricarboxylic acid cycle intermediates.

    • Kazuhiro Ikeda
    • , Kuniko Horie-Inoue
    •  & Satoshi Inoue

  • Article
    | Open Access

    The relationship between metabolomic and behavioral changes is not well understood. Here, the authors analyze metabolome changes in D. melanogaster heads and bodies during hunger and satiety, and develop the Flyscape tool to visualize the resulting metabolic networks and integrate them with other omics data.

    • Daniel Wilinski
    • , Jasmine Winzeler
    •  & Monica Dus

  • Perspective
    | Open Access

    Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.

    • Mark R. Viant
    • , Timothy M. D. Ebbels
    •  & Ralf J. M. Weber

  • Article
    | Open Access

    Cancer subtypes may have distinct metabolic vulnerabilities that can be exploited for therapeutic interventions. Here, the authors show that in lung cancer, genetic activation of distinct oncogenic receptor tyrosine kinases results in unique metabolic liabilities and, in particular, EGFR aberrant cancers rely on the serine biosynthetic pathway while FGFR aberrant cancers rely on glycolysis.

    • Nan Jin
    • , Aiwei Bi
    •  & Min Huang

  • Article
    | Open Access

    Diabetes is a major cause of kidney disease. Here Kikuchi et al. show that phenol sulfate, a gut microbiota-derived metabolite, is increased in diabetic kidney disease and contributes to the pathology by promoting kidney injury, suggesting phenyl sulfate could be used a marker and therapeutic target for the treatment of diabetic kidney disease.

    • Koichi Kikuchi
    • , Daisuke Saigusa
    •  & Takaaki Abe

  • Article
    | Open Access

    Untargeted metabolomics detects large numbers of metabolites but their annotation remains challenging. Here, the authors develop a metabolic reaction network-based recursive algorithm that expands metabolite annotation by taking advantage of the mass spectral similarity of reaction-paired neighbor metabolites.

    • Xiaotao Shen
    • , Ruohong Wang
    •  & Zheng-Jiang Zhu

  • Article
    | Open Access

    D-lactic acidosis typically occurs in the context of short bowel syndrome; excess D-lactate is produced by intestinal bacteria. Here, the authors identify two point mutations in the human lactate dehydrogenase D (LDHD) gene that cause enzymatic loss of function and are associated with elevated plasma D-lactate.

    • Glen R. Monroe
    • , Albertien M. van Eerde
    •  & Judith J. Jans

  • Article
    | Open Access

    Accurate monitoring of chronic kidney disease (CKD) progression is essential for efficient disease management. Here Chen et al. identify five serum metabolites in patients with stage 1–5 CKD whose levels associate with disease progression, and find that 5-methoxytryptophan and its regulatory enzyme TPH-1 exert anti-fibrotic effects in mouse models of kidney injury.

    • Dan-Qian Chen
    • , Gang Cao
    •  & Ying-Yong Zhao

  • Article
    | Open Access

    The first week of life impacts health for all of life, but the mechanisms are little-understood. Here the authors extract multi-omic data from small volumes of blood to study the dynamic molecular changes during the first week of life, revealing a robust developmental trajectory common to different populations.

    • Amy H. Lee
    • , Casey P. Shannon
    •  & Tobias R. Kollmann

  • Article
    | Open Access

    Host metabolic reprogramming plays a role in functional responses against pathogens. Here, the authors characterise malonylated proteins in macrophages and show that malonylation of the glycolytic enzyme GAPDH impacts cytokine production by modulating both its enzymatic activity and RNA-binding capacity.

    • Silvia Galván-Peña
    • , Richard G. Carroll
    •  & Luke A. O’Neill

  • Article
    | Open Access

    Glutamine metabolism is increased in proliferating cells under hypoxia potentially generating exceeding nitrogen. Here the authors show that under hypoxia a specific metabolic pathway is activated to push glutamine carbons and excess nitrogen via the reductive pathway to dihyroorotate which is then secreted by the cells and that such pathway is necessary for tumor growth.

    • Yuanyuan Wang
    • , Changsen Bai
    •  & Binghui Li

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