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Magalhães DM, Stewart NA, Mampay M, Rolle SO, Hall CM, Moeendarbary E, Flint MS, Sebastião AM, Valente CA, Dymond MK, Sheridan GK. The sphingosine 1-phosphate analogue, FTY720, modulates the lipidomic signature of the mouse hippocampus. J Neurochem 2024; 168:1113-1142. [PMID: 38339785 DOI: 10.1111/jnc.16073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The small-molecule drug, FTY720 (fingolimod), is a synthetic sphingosine 1-phosphate (S1P) analogue currently used to treat relapsing-remitting multiple sclerosis in both adults and children. FTY720 can cross the blood-brain barrier (BBB) and, over time, accumulate in lipid-rich areas of the central nervous system (CNS) by incorporating into phospholipid membranes. FTY720 has been shown to enhance cell membrane fluidity, which can modulate the functions of glial cells and neuronal populations involved in regulating behaviour. Moreover, direct modulation of S1P receptor-mediated lipid signalling by FTY720 can impact homeostatic CNS physiology, including neurotransmitter release probability, the biophysical properties of synaptic membranes, ion channel and transmembrane receptor kinetics, and synaptic plasticity mechanisms. The aim of this study was to investigate how chronic FTY720 treatment alters the lipid composition of CNS tissue in adolescent mice at a key stage of brain maturation. We focused on the hippocampus, a brain region known to be important for learning, memory, and the processing of sensory and emotional stimuli. Using mass spectrometry-based lipidomics, we discovered that FTY720 increases the fatty acid chain length of hydroxy-phosphatidylcholine (PCOH) lipids in the mouse hippocampus. It also decreases PCOH monounsaturated fatty acids (MUFAs) and increases PCOH polyunsaturated fatty acids (PUFAs). A total of 99 lipid species were up-regulated in the mouse hippocampus following 3 weeks of oral FTY720 exposure, whereas only 3 lipid species were down-regulated. FTY720 also modulated anxiety-like behaviours in young mice but did not affect spatial learning or memory formation. Our study presents a comprehensive overview of the lipid classes and lipid species that are altered in the hippocampus following chronic FTY720 exposure and provides novel insight into cellular and molecular mechanisms that may underlie the therapeutic or adverse effects of FTY720 in the central nervous system.
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Affiliation(s)
- Daniela M Magalhães
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Lisboa, Portugal
- School of Applied Sciences, University of Brighton, Brighton, UK
| | | | - Myrthe Mampay
- School of Applied Sciences, University of Brighton, Brighton, UK
| | - Sara O Rolle
- Green Templeton College, University of Oxford, Oxford, UK
| | - Chloe M Hall
- School of Applied Sciences, University of Brighton, Brighton, UK
- Department of Mechanical Engineering, University College London, London, UK
| | - Emad Moeendarbary
- Department of Mechanical Engineering, University College London, London, UK
- 199 Biotechnologies Ltd, London, UK
| | - Melanie S Flint
- School of Applied Sciences, University of Brighton, Brighton, UK
| | - Ana M Sebastião
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Lisboa, Portugal
| | - Cláudia A Valente
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Lisboa, Portugal
| | - Marcus K Dymond
- School of Applied Sciences, University of Brighton, Brighton, UK
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2
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Anderson BJ, Brademan DR, He Y, Overmyer KA, Coon JJ. LipiDex 2 Integrates MS n Tree-Based Fragmentation Methods and Quality Control Modules to Improve Discovery Lipidomics. Anal Chem 2024; 96:6715-6723. [PMID: 38640432 DOI: 10.1021/acs.analchem.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
As lipidomics experiments increase in scale and complexity, data processing tools must support workflows for new liquid chromatography-mass spectrometry (LC-MS) methods while simultaneously supporting quality controls to maximize the confidence in lipid identifications. LipiDex 2 improves lipidomics data processing algorithms from LipiDex 1 and introduces new tools for spectral matching and peak annotation functions, with improvements in speed and user-friendliness. In silico spectral library generation now supports tandem mass spectral (MSn) tree-based fragmentation methods, and the LipiDex 2 workflow fully integrates the fragmentation logic into the data processing steps to enable lipid identification at the appropriate level of structural resolution. Finally, LipiDex 2 features new modules for automated quality control checks that also allow users to visualize data quality in a data dashboard user interface.
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Affiliation(s)
- Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Dain R Brademan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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3
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Xu R, Liu H, Yuan F, Kim S, Kirpich I, McClain CJ, Zhang X. Lipid Wizard: Analysis Software for Comprehensive Two-Dimensional Liquid Chromatography-Mass Spectrometry-Based Lipid Profiling. Anal Chem 2024; 96:5375-5383. [PMID: 38523323 DOI: 10.1021/acs.analchem.3c04419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Lipids play a significant role in life activities and participate in the biological system through different pathways. Although comprehensive two-dimensional liquid chromatography-mass spectrometry (2DLC-MS) has been developed to profile lipid abundance changes, lipid identification and quantification from 2DLC-MS data remain a challenge. We created Lipid Wizard, open-source software for lipid assignment and isotopic peak stripping of the 2DLC-MS data. Lipid Wizard takes the peak list deconvoluted from the 2DLC-MS data as input and assigns each isotopic peak to the lipids recorded in the LIPID MAPS database by precursor ion m/z matching. The matched lipids are then filtered by the first-dimension retention time (1D RT), followed by the second-dimension retention time (2D RT), where the 2D RT of each lipid is predicted using an equivalent carbon number (ECN) model. The remaining assigned lipids are used for isotopic peak stripping via an iterative linear regression. The performance of Lipid Wizard was tested using a set of lipid standards and then applied to study the lipid changes in the livers of mice (fat-1) fed with alcohol.
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Affiliation(s)
- Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Huan Liu
- Department of Computer Science and Engineering, University of Louisville, Louisville, Kentucky 40292, United States
| | - Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Seongho Kim
- Department of Oncology, Wayne State University, Detroit, Michigan 48201, United States
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, United States
| | - Irina Kirpich
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky 40292, United States
| | - Craig J McClain
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky 40206, United States
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
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4
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Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y. Constitutive activation mechanism of a class C GPCR. Nat Struct Mol Biol 2024; 31:678-687. [PMID: 38332368 DOI: 10.1038/s41594-024-01224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Class C G-protein-coupled receptors (GPCRs) are activated through binding of agonists to the large extracellular domain (ECD) followed by rearrangement of the transmembrane domains (TMDs). GPR156, a class C orphan GPCR, is unique because it lacks an ECD and exhibits constitutive activity. Impaired GPR156-Gi signaling contributes to loss of hearing. Here we present the cryo-electron microscopy structures of human GPR156 in the Go-free and Go-coupled states. We found that an endogenous phospholipid molecule is located within each TMD of the GPR156 dimer. Asymmetric binding of Gα to the phospholipid-bound GPR156 dimer restructures the first and second intracellular loops and the carboxy-terminal part of the elongated transmembrane 7 (TM7) without altering dimer conformation. Our findings reveal that GPR156 is a transducer for phospholipid signaling. Constant binding of abundant phospholipid molecules and the G-protein-induced reshaping of the cytoplasmic face provide a basis for the constitutive activation of GPR156.
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Affiliation(s)
- Jinwoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Junhyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jieun Jeong
- Department of Applied Chemistry, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea
| | - Jordy Homing Lam
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Kuglae Kim
- Department of Pharmacy, Yonsei University, Incheon, Republic of Korea
| | - Joo-Youn Lee
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jaekyung Hyun
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea.
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea.
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Medical Science and Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
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5
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Kraus F, He Y, Swarup S, Overmyer KA, Jiang Y, Brenner J, Capitanio C, Bieber A, Jen A, Nightingale NM, Anderson BJ, Lee C, Paulo JA, Smith IR, Plitzko JM, Schulman BA, Wilfling F, Coon JJ, Wade Harper J. Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586828. [PMID: 38585873 PMCID: PMC10996675 DOI: 10.1101/2024.03.26.586828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneously quantify HeLa cell proteomes and lipidomes from more than two dozen LSD mutants, revealing diverse molecular phenotypes. Defects in delivery of ferritin and its autophagic receptor NCOA4 to lysosomes (ferritinophagy) were pronounced in NPC2-/- cells, which correlated with increased lyso-phosphatidylcholine species and multi-lamellar membrane structures visualized by cryo-electron-tomography. Ferritinophagy defects correlated with loss of mitochondrial cristae, MICOS-complex components, and electron transport chain complexes rich in iron-sulfur cluster proteins. Strikingly, mitochondrial defects were alleviated when iron was provided through the transferrin system. This resource reveals how defects in lysosomal function can impact mitochondrial homeostasis in trans and highlights nMOST as a discovery tool for illuminating molecular phenotypes across LSDs.
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Affiliation(s)
- Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- equal contribution
| | - Yuchen He
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- equal contribution
| | - Sharan Swarup
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- equal contribution
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yizhi Jiang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Johann Brenner
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Nightingale
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chan Lee
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ian R Smith
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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6
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Moreno-Torres M, Quintás G, Martínez-Sena T, Jover R, Castell JV. Exploring Individual Variability in Drug-Induced Liver Injury (DILI) Responses through Metabolomic Analysis. Int J Mol Sci 2024; 25:3003. [PMID: 38474249 DOI: 10.3390/ijms25053003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Drug-induced liver injury (DILI) is a serious adverse hepatic event presenting diagnostic and prognostic challenges. The clinical categorization of DILI into hepatocellular, cholestatic, or mixed phenotype is based on serum alanine aminotransferase (ALT) and alkaline phosphatase (ALP) values; however, this classification may not capture the full spectrum of DILI subtypes. With this aim, we explored the utility of assessing changes in the plasma metabolomic profiles of 79 DILI patients assessed by the RUCAM (Roussel Uclaf Causality Assessment Method) score to better characterize this condition and compare results obtained with the standard clinical characterization. Through the identification of various metabolites in the plasma (including free and conjugated bile acids and glycerophospholipids), and the integration of this information into predictive models, we were able to evaluate the extent of the hepatocellular or cholestatic phenotype and to assign a numeric value with the contribution of each specific DILI sub-phenotype into the patient's general condition. Additionally, our results showed that metabolomic analysis enabled the monitoring of DILI variability responses to the same drug, the transitions between sub-phenotypes during disease progression, and identified a spectrum of residual DILI metabolic features, which can be overlooked using standard clinical diagnosis during patient follow-up.
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Affiliation(s)
- Marta Moreno-Torres
- Unidad Mixta de Hepatología Experimental, Instituto de Investigación Sanitaria del Hospital La Fe (IIS La Fe), 46026 Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Guillermo Quintás
- Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Metabolomics and Bioanalysis, Leitat Technological Center (LEITAT,) 46026 Valencia, Spain
| | - Teresa Martínez-Sena
- Unidad Mixta de Hepatología Experimental, Instituto de Investigación Sanitaria del Hospital La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Ramiro Jover
- Unidad Mixta de Hepatología Experimental, Instituto de Investigación Sanitaria del Hospital La Fe (IIS La Fe), 46026 Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José V Castell
- Unidad Mixta de Hepatología Experimental, Instituto de Investigación Sanitaria del Hospital La Fe (IIS La Fe), 46026 Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
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7
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Rivera Vazquez J, Trujillo E, Williams J, She F, Getahun F, Callaghan MM, Coon JJ, Amador-Noguez D. Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:14. [PMID: 38281959 PMCID: PMC10823705 DOI: 10.1186/s13068-023-02450-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism's vulnerability to isobutanol toxicity, adversely affecting its growth and productivity. The limited understanding of the physiological impacts of isobutanol on Z. mobilis constrains our ability to overcome these production barriers. RESULTS We utilized a systems-level approach comprising LC-MS/MS-based lipidomics, metabolomics, and shotgun proteomics, to investigate how exposure to ethanol and isobutanol impact the lipid membrane composition and overall physiology of Z. mobilis. Our analysis revealed significant and distinct alterations in membrane phospholipid and fatty acid composition resulting from ethanol and isobutanol exposure. Notably, ethanol exposure increased membrane cyclopropane fatty acid content and expression of cyclopropane fatty acid (CFA) synthase. Surprisingly, isobutanol decreased cyclopropane fatty acid content despite robust upregulation of CFA synthase. Overexpression of the native Z. mobilis' CFA synthase increased cyclopropane fatty acid content in all phospholipid classes and was associated with a significant improvement in growth rates in the presence of added ethanol and isobutanol. Heterologous expression of CFA synthase from Clostridium acetobutylicum resulted in a near complete replacement of unsaturated fatty acids with cyclopropane fatty acids, affecting all lipid classes. However, this did not translate to improved growth rates under isobutanol exposure. Correlating with its greater susceptibility to isobutanol, Z. mobilis exhibited more pronounced alterations in its proteome, metabolome, and overall cell morphology-including cell swelling and formation of intracellular protein aggregates -when exposed to isobutanol compared to ethanol. Isobutanol triggered a broad stress response marked by the upregulation of heat shock proteins, efflux transporters, DNA repair systems, and the downregulation of cell motility proteins. Isobutanol also elicited widespread dysregulation of Z. mobilis' primary metabolism evidenced by increased levels of nucleotide degradation intermediates and the depletion of biosynthetic and glycolytic intermediates. CONCLUSIONS This study provides a comprehensive, systems-level evaluation of the impact of ethanol and isobutanol exposure on the lipid membrane composition and overall physiology of Z. mobilis. These findings will guide engineering of Z. mobilis towards the creation of isobutanol-tolerant strains that can serve as robust platforms for the industrial production of isobutanol from lignocellulosic sugars.
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Affiliation(s)
- Julio Rivera Vazquez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Edna Trujillo
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Genome Center of Wisconsin, Madison, WI, USA
| | - Jonathan Williams
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Fukang She
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Fitsum Getahun
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Melanie M Callaghan
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Morgridge Institute for Research, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Gao AW, Alam GE, Zhu Y, Li W, Katsyuba E, Sulc J, Li TY, Li X, Overmyer KA, Lalou A, Mouchiroud L, Sleiman MB, Cornaglia M, Morel JD, Houtkooper RH, Coon JJ, Auwerx J. High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575638. [PMID: 38293129 PMCID: PMC10827074 DOI: 10.1101/2024.01.15.575638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Lifespan is influenced by complex interactions between genetic and environmental factors. Studying those factors in model organisms of a single genetic background limits their translational value for humans. Here, we mapped lifespan determinants in 85 genetically diverse C. elegans recombinant intercross advanced inbred lines (RIAILs). We assessed molecular profiles - transcriptome, proteome, and lipidome - and life-history traits, including lifespan, development, growth dynamics, and reproduction. RIAILs exhibited large variations in lifespan, which positively correlated with developmental time. Among the top candidates obtained from multi-omics data integration and QTL mapping, we validated known and novel longevity modulators, including rict-1, gfm-1 and mltn-1. We translated their relevance to humans using UK Biobank data and showed that variants in RICTOR and GFM1 are associated with an elevated risk of age-related heart disease, dementia, diabetes, kidney, and liver diseases. We organized our dataset as a resource (https://lisp-lms.shinyapps.io/RIAILs/) that allows interactive explorations for new longevity targets.
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Weisha Li
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Elena Katsyuba
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jonathan Sulc
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Terytty Y. Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Present address: State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Metabolic Remodeling and Health, Laboratory of Longevity and Metabolic Adaptations, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Amelia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Mouchiroud
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Cornaglia
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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9
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Li X, Zang Q, Zhu Y, Tu X, Liu J, Li T, Zhu S, Wang L, Abliz Z, Zhang R. Database-Driven Spatially Resolved Lipidomics Highlights Heterogeneous Metabolic Alterations in Type 2 Diabetic Mice. Anal Chem 2023; 95:18691-18696. [PMID: 38088904 DOI: 10.1021/acs.analchem.3c03765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Spatially resolved lipidomics is pivotal for detecting and interpreting lipidomes within spatial contexts using the mass spectrometry imaging (MSI) technique. However, comprehensive and efficient lipid identification in MSI remains challenging. Herein, we introduce a high-coverage, database-driven approach combined with air-flow-assisted desorption electrospray ionization (AFADESI)-MSI to generate spatial lipid profiles across whole-body mice. Using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), we identified 2868 unique lipids in the serum and various organs of mice. Subsequently, we systematically evaluated the distinct ionization properties of the lipids between LC-MS and MSI and created a detailed MSI database containing 14 123 ions. This method enabled the visualization of aberrant fatty acid and phospholipid metabolism across organs in a diabetic mouse model. As a powerful extension incorporated into the MSIannotator tool, our strategy facilitates the rapid and accurate annotation of lipids, providing new research avenues for probing spatially resolved heterogeneous metabolic changes in response to diseases.
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Affiliation(s)
- Xinzhu Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ying Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xinyi Tu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jialin Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ting Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiyu Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lingzhi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
- Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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10
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Liao R, Babatunde A, Qiu S, Harikumar H, Coon JJ, Overmyer KA, Hannun YA, Luberto C, Bresnick EH. A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process. Nat Commun 2023; 14:7262. [PMID: 37945603 PMCID: PMC10636182 DOI: 10.1038/s41467-023-42978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Transcriptional mechanisms controlling developmental processes establish and maintain proteomic networks, which can govern the levels of intracellular small molecules. Although dynamic changes in bioactive small molecules can link transcription factor and genome activity with cell state transitions, many mechanistic questions are unresolved. Using quantitative lipidomics and multiomics, we discover that the hematopoietic transcription factor GATA1 establishes ceramide homeostasis during erythroid differentiation by regulating genes encoding sphingolipid metabolic enzymes. Inhibiting a GATA1-induced sphingolipid biosynthetic enzyme, delta(4)-desaturase, or disrupting ceramide homeostasis with cell-permeable dihydroceramide or ceramide is detrimental to erythroid, but not myeloid, progenitor activity. Coupled with genetic editing-based rewiring of the regulatory circuitry, we demonstrate that ceramide homeostasis commissions vital stem cell factor and erythropoietin signaling by opposing an inhibitory protein phosphatase 2A-dependent, dual-component mechanism. Integrating bioactive lipids as essential components of GATA factor mechanisms to control cell state transitions has implications for diverse cell and tissue types.
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Affiliation(s)
- Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Abiola Babatunde
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Stephanie Qiu
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Hamsini Harikumar
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, National Center for Quantitative Biology of Complex Systems, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, National Center for Quantitative Biology of Complex Systems, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Book University, Stony Brook, NY, USA
- Northport Veterans Affairs Medical Center, Northport, NY, USA
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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11
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Chang JK, Teo G, Pewzner-Jung Y, Cuthbertson DJ, Futerman AH, Wenk MR, Choi H, Torta F. Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci Rep 2023; 13:19281. [PMID: 37935746 PMCID: PMC10630469 DOI: 10.1038/s41598-023-46312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Untargeted lipidomics has been increasingly adopted for hypothesis generation in a biological context or discovery of disease biomarkers. Most of the current liquid chromatography mass spectrometry (LC-MS) based untargeted methodologies utilize a data dependent acquisition (DDA) approach in pooled samples for identification and MS-only acquisition for semi-quantification in individual samples. In this study, we present for the first time an untargeted lipidomic workflow that makes use of the newly implemented Quadrupole Resolved All-Ions (Q-RAI) acquisition function on the Agilent 6546 quadrupole time-of-flight (Q-TOF) mass spectrometer to acquire MS2 spectra in data independent acquisition (DIA) mode. This is followed by data processing and analysis on MetaboKit, a software enabling DDA-based spectral library construction and extraction of MS1 and MS2 peak areas, for reproducible identification and quantification of lipids in DIA analysis. This workflow was tested on lipid extracts from human plasma and showed quantification at MS1 and MS2 levels comparable to multiple reaction monitoring (MRM) targeted analysis of the same samples. Analysis of serum from Ceramide Synthase 2 (CerS2) null mice using the Q-RAI DIA workflow identified 88 lipid species significantly different between CerS2 null and wild type mice, including well-characterized changes previously associated with this phenotype. Our results show the Q-RAI DIA as a reliable option to perform simultaneous identification and reproducible relative quantification of lipids in exploratory biological studies.
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Affiliation(s)
- Jing Kai Chang
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hyungwon Choi
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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12
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Anderson BJ, Curtis AM, Jen A, Thomson JA, Clegg DO, Jiang P, Coon JJ, Overmyer KA, Toh H. Plasma metabolomics supports non-fasted sampling for metabolic profiling across a spectrum of glucose tolerance in the Nile rat model for type 2 diabetes. Lab Anim (NY) 2023; 52:269-277. [PMID: 37857753 PMCID: PMC10611569 DOI: 10.1038/s41684-023-01268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/12/2023] [Indexed: 10/21/2023]
Abstract
Type 2 diabetes is a challenge in modern healthcare, and animal models are necessary to identify underlying mechanisms. The Nile rat (Arvicanthis niloticus) develops diet-induced diabetes rapidly on a conventional rodent chow diet without genetic or chemical manipulation. Unlike common laboratory models, the outbred Nile rat model is diurnal and has a wide range of overt diabetes onset and diabetes progression patterns in both sexes, better mimicking the heterogeneous diabetic phenotype in humans. While fasted blood glucose has historically been used to monitor diabetic progression, postprandial blood glucose is more sensitive to the initial stages of diabetes. However, there is a long-held assumption that ad libitum feeding in rodent models leads to increased variance, thus masking diabetes-related metabolic changes in the plasma. Here we compared repeatability within triplicates of non-fasted or fasted plasma samples and assessed metabolic changes relevant to glucose tolerance in fasted and non-fasted plasma of 8-10-week-old male Nile rats. We used liquid chromatography-mass spectrometry lipidomics and polar metabolomics to measure relative metabolite abundances in the plasma samples. We found that, compared to fasted metabolites, non-fasted plasma metabolites are not only more strongly associated with glucose tolerance on the basis of unsupervised clustering and elastic net regression model, but also have a lower replicate variance. Between the two sampling groups, we detected 66 non-fasted metabolites and 32 fasted metabolites that were associated with glucose tolerance using a combined approach with multivariable elastic net and individual metabolite linear models. Further, to test if metabolite replicate variance is affected by age and sex, we measured non-fasted replicate variance in a cohort of mature 30-week-old male and female Nile rats. Our results support using non-fasted plasma metabolomics to study glucose tolerance in Nile rats across the progression of diabetes.
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Affiliation(s)
- Benton J Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Curtis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - James A Thomson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Dennis O Clegg
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Peng Jiang
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA.
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13
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Kajtazi A, Russo G, Wicht K, Eghbali H, Lynen F. Facilitating structural elucidation of small environmental solutes in RPLC-HRMS by retention index prediction. CHEMOSPHERE 2023; 337:139361. [PMID: 37392796 DOI: 10.1016/j.chemosphere.2023.139361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Implementing effective environmental management strategies requires a comprehensive understanding of the chemical composition of environmental pollutants, particularly in complex mixtures. Utilizing innovative analytical techniques, such as high-resolution mass spectrometry and predictive retention index models, can provide valuable insights into the molecular structures of environmental contaminants. Liquid Chromatography-High-Resolution Mass Spectrometry is a powerful tool for the identification of isomeric structures in complex samples. However, there are some limitations that can prevent accurate isomeric structure identification, particularly in cases where the isomers have similar mass and fragmentation patterns. Liquid chromatographic retention, determined by the size, shape, and polarity of the analyte and its interactions with the stationary phase, contains valuable 3D structural information that is vastly underutilized. Therefore, a predictive retention index model is developed which is transferrable to LC-HRMS systems and can assist in the structural elucidation of unknowns. The approach is currently restricted to carbon, hydrogen, and oxygen-based molecules <500 g mol-1. The methodology facilitates the acceptance of accurate structural formulas and the exclusion of erroneous hypothetical structural representations by leveraging retention time estimations, thereby providing a permissible tolerance range for a given elemental composition and experimental retention time. This approach serves as a proof of concept for the development of a Quantitative Structure-Retention Relationship model using a generic gradient LC approach. The use of a widely used reversed-phase (U)HPLC column and a relatively large set of training (101) and test compounds (14) demonstrates the feasibility and potential applicability of this approach for predicting the retention behaviour of compounds in complex mixtures. By providing a standard operating procedure, this approach can be easily replicated and applied to various analytical challenges, further supporting its potential for broader implementation.
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Affiliation(s)
- Ardiana Kajtazi
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium
| | - Giacomo Russo
- School of Applied Sciences, Sighthill Campus, Edinburgh Napier University, 9 Sighthill Ct, EH11 4BN, Edinburgh, United Kingdom
| | - Kristina Wicht
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium
| | - Hamed Eghbali
- Packaging and Specialty Plastics R&D, Dow Benelux B.V., Terneuzen, 4530 AA, the Netherlands
| | - Frédéric Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium.
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14
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Fernandez-Fuente G, Overmyer KA, Lawton AJ, Kasza I, Shapiro SL, Gallego-Muñoz P, Coon JJ, Denu JM, Alexander CM, Puglielli L. The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse. Commun Biol 2023; 6:926. [PMID: 37689798 PMCID: PMC10492862 DOI: 10.1038/s42003-023-05311-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
Cytosolic citrate is imported from the mitochondria by SLC25A1, and from the extracellular milieu by SLC13A5. In the cytosol, citrate is used by ACLY to generate acetyl-CoA, which can then be exported to the endoplasmic reticulum (ER) by SLC33A1. Here, we report the generation of mice with systemic overexpression (sTg) of SLC25A1 or SLC13A5. Both animals displayed increased cytosolic levels of citrate and acetyl-CoA; however, SLC13A5 sTg mice developed a progeria-like phenotype with premature death, while SLC25A1 sTg mice did not. Analysis of the metabolic profile revealed widespread differences. Furthermore, SLC13A5 sTg mice displayed increased engagement of the ER acetylation machinery through SLC33A1, while SLC25A1 sTg mice did not. In conclusion, our findings point to different biological responses to SLC13A5- or SLC25A1-mediated import of citrate and suggest that the directionality of the citrate/acetyl-CoA pathway can transduce different signals.
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Affiliation(s)
- Gonzalo Fernandez-Fuente
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Alexis J Lawton
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Ildiko Kasza
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha L Shapiro
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Gallego-Muñoz
- Department of Cell Biology, Genetics, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, Valladolid, Spain
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Caroline M Alexander
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, USA.
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA.
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15
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Zhu Y, Jen A, Overmyer KA, Gao AW, Shishkova E, Auwerx J, Coon JJ. Mass Spectrometry-Based Multi-omics Integration with a Single Set of C. elegans Samples. Anal Chem 2023; 95:10930-10938. [PMID: 37432911 PMCID: PMC10863427 DOI: 10.1021/acs.analchem.3c00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Mass spectrometry-based large-scale multi-omics research has proven to be powerful in answering biological questions; nonetheless, it faces many challenges from sample preparation to downstream data integration. To efficiently extract biomolecules of different physicochemical properties, preparation of various sample type needs specific tailoring, especially of difficult ones, such as Caenorhabditis elegans. In this study, we sought to develop a multi-omics sample preparation method starting with a single set ofC. elegans samples to save time, minimize variability, expand biomolecule coverage, and promote multi-omics integration. We investigated tissue disruption methods to effectively release biomolecules and optimized extraction strategies to achieve broader and more reproducible biomolecule coverage in proteomics, lipidomics, and metabolomics workflows. In our assessment, we also considered speediness and usability of the approaches. The developed method was validated through a study of 16C. elegans samples designed to shine light on mitochondrial unfolded protein response (UPRmt), induced by three unique stressors─knocking down electron transfer chain element cco-1, mitochondrial ribosome protein S5 mrps-5, and antibiotic treatment Doxycycline. Our findings suggested that the method achieved great coverage of proteome, lipidome, and metabolome with high reproducibility and validated that all stressors triggered UPRmt in C. elegans, although generating unique molecular signatures. Innate immune response was activated, and triglycerides were decreased under all three stressor conditions. Additionally, Doxycycline treatment elicited more distinct proteomic, lipidomic, and metabolomic response than the other two treatments. This method has been successfully used to process Saccharomyces cerevisiae (data not shown) and can likely be applied to other organisms for multi-omics research.
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Affiliation(s)
- Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Katherine A Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Arwen W Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
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16
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Wagner ER, Nightingale NM, Jen A, Overmyer KA, McGee M, Coon JJ, Gasch AP. PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae. PLoS Genet 2023; 19:e1010593. [PMID: 37410771 DOI: 10.1371/journal.pgen.1010593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how pathways are integrated to produce systemic changes in a cell, especially in dynamic conditions. We previously showed that deletion of Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth and metabolism in Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing for robust fermentation in the absence of division. This provides an opportunity to understand how PKA signaling normally coordinates these processes. Here, we integrated transcriptomic, lipidomic, and phospho-proteomic responses upon a glucose to xylose shift across a series of strains with different genetic mutations promoting either coupled or decoupled xylose-dependent growth and metabolism. Together, results suggested that defects in lipid homeostasis limit growth in the bcy1Δ strain despite robust metabolism. To further understand this mechanism, we performed adaptive laboratory evolutions to re-evolve coupled growth and metabolism in the bcy1Δ parental strain. The evolved strain harbored mutations in PKA subunit TPK1 and lipid regulator OPI1, among other genes, and evolved changes in lipid profiles and gene expression. Deletion of the evolved opi1 gene partially reverted the strain's phenotype to the bcy1Δ parent, with reduced growth and robust xylose fermentation. We suggest several models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.
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Affiliation(s)
- Ellen R Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicole M Nightingale
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Annie Jen
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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17
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Brademan DR, Overmyer KA, He Y, Barshop WD, Canterbury JD, Bills BJ, Anderson BJ, Hutchins PD, Sharma S, Zabrouskov V, McAlister GC, Coon JJ. Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching. Anal Chem 2023; 95:7813-7821. [PMID: 37172325 PMCID: PMC10840458 DOI: 10.1021/acs.analchem.2c04633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In mass spectrometry-based lipidomics, complex lipid mixtures undergo chromatographic separation, are ionized, and are detected using tandem MS (MSn) to simultaneously quantify and structurally characterize eluting species. The reported structural granularity of these identified lipids is strongly reliant on the analytical techniques leveraged in a study. For example, lipid identifications from traditional collisionally activated data-dependent acquisition experiments are often reported at either species level or molecular species level. Structural resolution of reported lipid identifications is routinely enhanced by integrating both positive and negative mode analyses, requiring two separate runs or polarity switching during a single analysis. MS3+ can further elucidate lipid structure, but the lengthened MS duty cycle can negatively impact analysis depth. Recently, functionality has been introduced on several Orbitrap Tribrid mass spectrometry platforms to identify eluting molecular species on-the-fly. These real-time identifications can be leveraged to trigger downstream MSn to improve structural characterization with lessened impacts on analysis depth. Here, we describe a novel lipidomics real-time library search (RTLS) approach, which utilizes the lipid class of real-time identifications to trigger class-targeted MSn and to improve the structural characterization of phosphotidylcholines, phosphotidylethanolamines, phosphotidylinositols, phosphotidylglycerols, phosphotidylserine, and sphingomyelins in the positive ion mode. Our class-based RTLS method demonstrates improved selectivity compared to the current methodology of triggering MSn in the presence of characteristic ions or neutral losses.
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Affiliation(s)
- Dain R. Brademan
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Katherine A. Overmyer
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | | | | | | | - Benton J. Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | | | - Seema Sharma
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | - Joshua J. Coon
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
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18
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Yan Q, Jacobson TB, Ye Z, Cortés-Pena YR, Bhagwat SS, Hubbard S, Cordell WT, Oleniczak RE, Gambacorta FV, Vazquez JR, Shusta EV, Amador-Noguez D, Guest JS, Pfleger BF. Evaluation of 1,2-diacyl-3-acetyl triacylglycerol production in Yarrowia lipolytica. Metab Eng 2023; 76:18-28. [PMID: 36626963 DOI: 10.1016/j.ymben.2023.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/14/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Plants produce many high-value oleochemical molecules. While oil-crop agriculture is performed at industrial scales, suitable land is not available to meet global oleochemical demand. Worse, establishing new oil-crop farms often comes with the environmental cost of tropical deforestation. The field of metabolic engineering offers tools to transplant oleochemical metabolism into tractable hosts while simultaneously providing access to molecules produced by non-agricultural plants. Here, we evaluate strategies for rewiring metabolism in the oleaginous yeast Yarrowia lipolytica to synthesize a foreign lipid, 3-acetyl-1,2-diacyl-sn-glycerol (acTAG). Oils made up of acTAG have a reduced viscosity and melting point relative to traditional triacylglycerol oils making them attractive as low-grade diesels, lubricants, and emulsifiers. This manuscript describes a metabolic engineering study that established acTAG production at g/L scale, exploration of the impact of lipid bodies on acTAG titer, and a techno-economic analysis that establishes the performance benchmarks required for microbial acTAG production to be economically feasible.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zhou Ye
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yoel R Cortés-Pena
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarang S Bhagwat
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, IL, 61801, USA
| | - Susan Hubbard
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rebecca E Oleniczak
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Francesca V Gambacorta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Julio Rivera Vazquez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; Department of Neurological Surgery, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA
| | - Jeremy S Guest
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, IL, 61801, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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19
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Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut. Nat Microbiol 2023; 8:424-440. [PMID: 36759753 PMCID: PMC9981464 DOI: 10.1038/s41564-023-01326-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.
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20
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Ten-Doménech I, Cascant-Vilaplana MM, Navarro-Esteve V, Felderer B, Moreno-Giménez A, Rienda I, Gormaz M, Moreno-Torres M, Pérez-Guaita D, Quintás G, Kuligowski J. Metabolomic Diversity of Human Milk Cells over the Course of Lactation-A Preliminary Study. Nutrients 2023; 15:nu15051100. [PMID: 36904100 PMCID: PMC10005050 DOI: 10.3390/nu15051100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Human milk (HM) is a complex biofluid containing a wide cell variety including epithelial cells and leukocytes. However, the cellular compositions and their phenotypic properties over the course of lactation are poorly understood. The aim of this preliminary study was to characterize the cellular metabolome of HM over the course of lactation. Cells were isolated via centrifugation and the cellular fraction was characterized via cytomorphology and immunocytochemical staining. Cell metabolites were extracted and analyzed using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-QqTOF-MS) in the positive and negative electrospray ionization modes. Immunocytochemical analysis revealed a high variability of the number of detected cells with relative median abundances of 98% of glandular epithelial cells, 1% of leukocytes, and 1% of keratinocytes. Significant correlations between the milk postnatal age with percentage of epithelial cells and leukocytes, and with total cell count were observed. Results from the Hierarchical Cluster Analysis of immunocytochemical profiles were very similar to those observed in the analysis of the metabolomic profiles. In addition, metabolic pathway analysis showed alterations in seven metabolic pathways correlating with postnatal age. This work paves the way for future investigations on changes in the metabolomic fraction of the cellular compartment of HM.
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Affiliation(s)
- Isabel Ten-Doménech
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Mari Merce Cascant-Vilaplana
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Víctor Navarro-Esteve
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Birgit Felderer
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
- Master Program Biotechnical Processes, Austrian Biotech University of Applied Sciences, Konrad Lorenz-Strasse 10, 3430 Tulln, Austria
| | - Alba Moreno-Giménez
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Iván Rienda
- Servicio de Anatomía Patológica, University & Polytechnic Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - María Gormaz
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
- Division of Neonatology, University & Polytechnic Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Marta Moreno-Torres
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, C/Blasco Ibáñez 15, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - David Pérez-Guaita
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Guillermo Quintás
- Health and Biomedicine, Leitat Technological Center, Carrer de la Innovació, 2, 08225 Terrassa, Spain
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026 Valencia, Spain
- Correspondence: ; Tel.: +34-96-1246661
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21
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Gertner DS, Violi JP, Bishop DP, Padula MP. Lipid Spectrum Generator: A Simple Script for the Generation of Accurate In Silico Lipid Fragmentation Spectra. Anal Chem 2023; 95:2909-2916. [PMID: 36692449 DOI: 10.1021/acs.analchem.2c04518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Due to the complexity of lipids in nature, the use of in silico generated spectral libraries to identify lipid species from mass spectral data has become an integral part of many lipidomic workflows. However, many in silico libraries are either limited in usability or their capacity to represent lipid species. Here, we introduce Lipid Spectrum Generator, an open-source in silico spectral library generator specifically designed to aid in the identification of lipids in liquid chromatography-tandem mass spectrometry analysis.
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Affiliation(s)
- David S Gertner
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Jake P Violi
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - David P Bishop
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Matthew P Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
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22
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Muehlbauer LK, Jen A, Zhu Y, He Y, Shishkova E, Overmyer KA, Coon JJ. Rapid Multi-Omics Sample Preparation for Mass Spectrometry. Anal Chem 2023; 95:659-667. [PMID: 36594155 PMCID: PMC10026941 DOI: 10.1021/acs.analchem.2c02042] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multi-omics analysis is a powerful and increasingly utilized approach to gain insight into complex biological systems. One major hindrance with multi-omics, however, is the lengthy and wasteful sample preparation process. Preparing samples for mass spectrometry (MS)-based multi-omics involves extraction of metabolites and lipids with organic solvents, precipitation of proteins, and overnight digestion of proteins. These existing workflows are disparate and laborious. Here, we present a simple, efficient, and unified approach to prepare lipids, metabolites, and proteins for MS analysis. Our approach, termed the Bead-enabled Accelerated Monophasic Multi-omics (BAMM) method, combines an n-butanol-based monophasic extraction with unmodified magnetic beads and accelerated protein digestion. We demonstrate that the BAMM method affords comparable depth, quantitative reproducibility, and recovery of biomolecules as state-of-the-art multi-omics methods (e.g., Matyash extraction and overnight protein digestion). However, the BAMM method only requires about 3 h to perform, which saves 11 steps and 19 h on average compared to published multi-omics methods. Furthermore, we validate the BAMM method for multiple sample types and formats (biofluid, culture plate, and pellet) and show that in all cases, it produces high biomolecular coverage and data quality.
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Affiliation(s)
- Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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23
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Data for "Oxidative stress is inhibited by plant-based supplements: a quantitative lipidomic analysis of antioxidant activity and lipid compositional change". Data Brief 2023; 46:108879. [PMID: 36660444 PMCID: PMC9842857 DOI: 10.1016/j.dib.2022.108879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Raw data obtained by ultra-high pressure liquid chromatography-mass spectrometry, and processed lipid compositional data are presented alongside detailed methodology. Data were obtained as bovine liver lipid extract oxidizes, initiated by 2,2'-Azobis(2-amidinopropane) dihydrochloride, at 0, 6 and 24 h post initiation. Lipid oxidation data in the presence and absence of some supplements with antioxidant properties was obtained. The supplements used were grape seed extract, pine bark extract, milk thistle extract, hawthorn extract and turmeric extract.
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24
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Guan XL, Loh JYX, Lizwan M, Chan SCM, Kwan JMC, Lim TP, Koh TH, Hsu LY, Lee BTK. LipidA-IDER to Explore the Global Lipid A Repertoire of Drug-Resistant Gram-Negative Bacteria. Anal Chem 2023; 95:602-611. [PMID: 36599414 PMCID: PMC9850412 DOI: 10.1021/acs.analchem.1c03566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
With the global emergence of drug-resistant bacteria causing difficult-to-treat infections, there is an urgent need for a tool to facilitate studies on key virulence and antimicrobial resistant factors. Mass spectrometry (MS) has contributed substantially to the elucidation of the structure-function relationships of lipid A, the endotoxic component of lipopolysaccharide which also serves as an important protective barrier against antimicrobials. Here, we present LipidA-IDER, an automated structure annotation tool for system-level scale identification of lipid A from high-resolution tandem mass spectrometry (MS2) data. LipidA-IDER was validated against previously reported structures of lipid A in the reference bacteria, Escherichia coli and Pseudomonas aeruginosa. Using MS2 data of variable quality, we demonstrated LipidA-IDER annotated lipid A with a performance of 71.2% specificity and 70.9% sensitivity, offering greater accuracy than existing lipidomics software. The organism-independent workflow was further applied to a panel of six bacterial species: E. coli and Gram-negative members of ESKAPE pathogens. A comprehensive atlas comprising 188 distinct lipid A species, including remodeling intermediates, was generated and can be integrated with software including MS-DIAL and Metabokit for identification and semiquantitation. Systematic comparison of a pair of polymyxin-sensitive and polymyxin-resistant Acinetobacter baumannii isolated from a human patient unraveled multiple key lipid A structural features of polymyxin resistance within a single analysis. Probing the lipid A landscape of bacteria using LipidA-IDER thus holds immense potential for advancing our understanding of the vast diversity and structural complexity of a key lipid virulence and antimicrobial-resistant factor. LipidA-IDER is freely available at https://github.com/Systems-Biology-Of-Lipid-Metabolism-Lab/LipidA-IDER.
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Affiliation(s)
- Xue Li Guan
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore,. Tel: +65 6592 3957
| | - Johnathan Yi-Xiong Loh
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore
| | - Marco Lizwan
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore
| | - Sharon Cui Mun Chan
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore
| | - Jeric Mun Chung Kwan
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore
| | - Tze Peng Lim
- Department
of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore
| | - Tse Hsien Koh
- Department
of Microbiology, Singapore General Hospital, Singapore 169608, Singapore
| | - Li-Yang Hsu
- Saw Swee
Hock School of Public Health, National University
of Singapore, Singapore 117549, Singapore
| | - Bernett Teck Kwong Lee
- Lee
Kong Chian School of Medicine, Nanyang Technological
University, Singapore 636921, Singapore,Centre
for Biomedical Informatics, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore,Singapore
Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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25
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Ramos-Garcia V, Ten-Doménech I, Albiach-Delgado A, Gómez-Ferrer M, Sepúlveda P, Parra-Llorca A, Campos-Berga L, Moreno-Giménez A, Quintás G, Kuligowski J. Isolation and Lipidomic Screening of Human Milk Extracellular Vesicles. Methods Mol Biol 2023; 2571:177-188. [PMID: 36152162 DOI: 10.1007/978-1-0716-2699-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Extracellular vesicles (EVs) are secreted by cells and can be found in biological fluids (e.g., blood, saliva, urine, cerebrospinal fluid, and milk). EV isolation needs to be optimized carefully depending on the type of biofluid and tissue. Human milk (HM) is known to be a rich source of EVs, and they are thought to be partially responsible for the benefits associated with breastfeeding. Here, a workflow for the isolation and lipidomic analysis of HM-EVs is described. The procedure encompasses initial steps such as sample collection and storage, a detailed description for HM-EV isolation by multistage ultracentrifugation, metabolite extraction, and analysis by liquid chromatography coupled to mass spectrometry, as well as data analysis and curation.
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Affiliation(s)
| | | | | | - Marta Gómez-Ferrer
- Regenerative Medicine and Heart Transplantation Unit, Health Research Institute La Fe, Valencia, Spain
| | - Pilar Sepúlveda
- Regenerative Medicine and Heart Transplantation Unit, Health Research Institute La Fe, Valencia, Spain
| | - Anna Parra-Llorca
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain
| | - Laura Campos-Berga
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain
| | | | - Guillermo Quintás
- Health and Biomedicine, Leitat Technological Center, Terrassa, Spain
- Analytical Unit, Health Research Institute La Fe, Valencia, Spain
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.
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26
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Kotnala A, Anderson DMG, Messinger JD, Curcio CA, Schey KL. Untargeted Lipidomic Profiling of Aged Human Retina With and Without Age-Related Macular Degeneration (AMD). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:37-42. [PMID: 37440011 DOI: 10.1007/978-3-031-27681-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The molecular characterization of extracellular deposits is crucial to understanding the clinical progression of AMD. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is a powerful analytical discovery tool capable of identifying lipids in an untargeted manner. NanoLC-MS/MS is an analytical tool capable of identifying lipids with high sensitivity and minimum sample usage. Hence, the purpose of this study was to compare retina lipid identification from RPE-choroid samples using high flow LC-MS/MS and nanoLC-MS/MS. Manually dissected paraformaldehyde-fixed human donor tissues sections were used for LC-MS/MS and nanoLC-MS/MS analysis. Lipids were extracted with MeOH/MTBE/CHCl3 (MMC) and were analyzed by LC-MS/MS and nanoLC-MS/MS using negative and positive ionization modes. Untargeted lipidomics using LC-MS/MS identified 215 lipids from 4 lipid classes and 15 subclasses. We observed a 78% increase in lipid identifications using nanoLC-MS/MS with lipid numbers totaling 384. The nanoLC-MS/MS method is expected to provide extensive lipid identifications from small retina samples, e.g., from drusen and drusenoid deposits in aged and AMD eyes, and could help elucidate how lipids are involved in extracellular deposit formation in AMD.
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Affiliation(s)
- Ankita Kotnala
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Jeffrey D Messinger
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Christine A Curcio
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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27
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Bormotov DS, Shamraeva MA, Kuzin AA, Shamarina EV, Eliferov VA, Silkin SV, Zhdanova EV, Pekov SI, Popov IA. Ambient ms profiling of meningiomas: intraoperative oncometabolite-based monitoring. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The primary method of initial treatment of meningiomas is radical neurosurgical intervention. Various methods of intraoperative diagnostics currently in development aim to improve resection efficiency; we focus on methods based on molecular profiling using ambient ionization mass spectrometry. Such methods have been proven effective on various tumors, but the specifics of the molecular structure and the mechanical properties of meningiomas raise the question of applicability of protocols developed for other conditions for this particular task. The study aimed to compare the potential clinical use of three methods of ambient ionization in meningioma sample analysis: spray from tissue, inline cartridge extraction, and touch spherical sampler probe spray. To this end, lipid and metabolic profiles of meningioma tissues removed in the course of planned neurosurgical intervention have been analyzed. It is shown that in clinical practice, the lipid components of the molecular profile are best analyzed using the inline cartridge extraction method, distinguished by its ease of implementation and highest informational value. Analysis of oncometabolites with low molecular mass is optimally performed with the touch spherical sampler probe spray method, which scores high in both sensitivity and mass-spectrometric complex productivity.
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Affiliation(s)
- DS Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - MA Shamraeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - AA Kuzin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - EV Shamarina
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - VA Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - SV Silkin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - EV Zhdanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - SI Pekov
- Skoltech, Moscow, Russia; Siberian State Medical University, Tomsk, Russia
| | - IA Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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28
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Yao X, Wang Y, Wang Z, Fan X, Wu D, Huang J, Mueller A, Gao S, Hu M, Robinson CV, Yu Y, Gao S, Yan N. Structures of the R-type human Ca v2.3 channel reveal conformational crosstalk of the intracellular segments. Nat Commun 2022; 13:7358. [PMID: 36446785 PMCID: PMC9708679 DOI: 10.1038/s41467-022-35026-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
The R-type voltage-gated Ca2+ (Cav) channels Cav2.3, widely expressed in neuronal and neuroendocrine cells, represent potential drug targets for pain, seizures, epilepsy, and Parkinson's disease. Despite their physiological importance, there have lacked selective small-molecule inhibitors targeting these channels. High-resolution structures may aid rational drug design. Here, we report the cryo-EM structure of human Cav2.3 in complex with α2δ-1 and β3 subunits at an overall resolution of 3.1 Å. The structure is nearly identical to that of Cav2.2, with VSDII in the down state and the other three VSDs up. A phosphatidylinositol 4,5-bisphosphate (PIP2) molecule binds to the interface of VSDII and the tightly closed pore domain. We also determined the cryo-EM structure of a Cav2.3 mutant in which a Cav2-unique cytosolic helix in repeat II (designated the CH2II helix) is deleted. This mutant, named ΔCH2, still reserves a down VSDII, but PIP2 is invisible and the juxtamembrane region on the cytosolic side is barely discernible. Our structural and electrophysiological characterizations of the wild type and ΔCH2 Cav2.3 show that the CH2II helix stabilizes the inactivated conformation of the channel by tightening the cytosolic juxtamembrane segments, while CH2II helix is not necessary for locking the down state of VSDII.
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Affiliation(s)
- Xia Yao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Yan Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Zhifei Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Xiao Fan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Di Wu
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Jian Huang
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Alexander Mueller
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Sarah Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Miaohui Hu
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Carol V. Robinson
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Yong Yu
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Shuai Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA ,grid.49470.3e0000 0001 2331 6153Present Address: Department of Radiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Nieng Yan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
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29
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Manicki M, Aydin H, Abriata LA, Overmyer KA, Guerra RM, Coon JJ, Dal Peraro M, Frost A, Pagliarini DJ. Structure and functionality of a multimeric human COQ7:COQ9 complex. Mol Cell 2022; 82:4307-4323.e10. [PMID: 36306796 PMCID: PMC10058641 DOI: 10.1016/j.molcel.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/01/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.
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Affiliation(s)
- Mateusz Manicki
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Halil Aydin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53506, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub and Altos Labs Bay Area Institute of Science, San Francisco, CA, USA.
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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30
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Multi-omics HeCaToS dataset of repeated dose toxicity for cardiotoxic & hepatotoxic compounds. Sci Data 2022; 9:699. [PMCID: PMC9663581 DOI: 10.1038/s41597-022-01825-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractThe data currently described was generated within the EU/FP7 HeCaToS project (Hepatic and Cardiac Toxicity Systems modeling). The project aimed to develop an in silico prediction system to contribute to drug safety assessment for humans. For this purpose, multi-omics data of repeated dose toxicity were obtained for 10 hepatotoxic and 10 cardiotoxic compounds. Most data were gained from in vitro experiments in which 3D microtissues (either hepatic or cardiac) were exposed to a therapeutic (physiologically relevant concentrations calculated through PBPK-modeling) or a toxic dosing profile (IC20 after 7 days). Exposures lasted for 14 days and samples were obtained at 7 time points (therapeutic doses: 2-8-24-72-168-240-336 h; toxic doses 0-2-8-24-72-168-240 h). Transcriptomics (RNA sequencing & microRNA sequencing), proteomics (LC-MS), epigenomics (MeDIP sequencing) and metabolomics (LC-MS & NMR) data were obtained from these samples. Furthermore, functional endpoints (ATP content, Caspase3/7 and O2 consumption) were measured in exposed microtissues. Additionally, multi-omics data from human biopsies from patients are available. This data is now being released to the scientific community through the BioStudies data repository (https://www.ebi.ac.uk/biostudies/).
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31
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Schmidpeter PAM, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat Struct Mol Biol 2022; 29:1092-1100. [PMID: 36352139 PMCID: PMC10022520 DOI: 10.1038/s41594-022-00851-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/25/2022] [Indexed: 11/11/2022]
Abstract
Lipids play important roles in regulating membrane protein function, but the molecular mechanisms used are elusive. Here we investigated how anionic lipids modulate SthK, a bacterial pacemaker channel homolog, and HCN2, whose activity contributes to pacemaking in the heart and brain. Using SthK allowed the reconstitution of purified channels in controlled lipid compositions for functional and structural assays that are not available for the eukaryotic channels. We identified anionic lipids bound tightly to SthK and their exact binding locations and determined that they potentiate channel activity. Cryo-EM structures in the most potentiating lipids revealed an open state and identified a nonannular lipid bound with its headgroup near an intersubunit salt bridge that clamps the intracellular channel gate shut. Breaking this conserved salt bridge abolished lipid modulation in SthK and eukaryotic HCN2 channels, indicating that anionic membrane lipids facilitate channel opening by destabilizing these interactions. Our findings underline the importance of state-dependent protein-lipid interactions.
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Affiliation(s)
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
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32
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Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics. Nat Commun 2022; 13:6112. [PMID: 36245040 PMCID: PMC9573879 DOI: 10.1038/s41467-022-33881-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Degradation and recycling of plasma membrane proteins occurs via the endolysosomal system, wherein endosomes bud into the cytosol from the plasma membrane and subsequently mature into degradative lysosomal compartments. While methods have been developed for rapid selective capture of lysosomes (Lyso-IP), analogous methods for isolation of early endosome intermediates are lacking. Here, we develop an approach for rapid isolation of early/sorting endosomes through affinity capture of the early endosome-associated protein EEA1 (Endo-IP) and provide proteomic and lipidomic snapshots of EEA1-positive endosomes in action. We identify recycling, regulatory and membrane fusion complexes, as well as candidate cargo, providing a proteomic landscape of early/sorting endosomes. To demonstrate the utility of the method, we combined Endo- and Lyso-IP with multiplexed targeted proteomics to provide a spatial digital snapshot of amyloid precursor protein (APP) processing by β and γ-Secretases, which produce amyloidogenic Aβ species, and quantify small molecule modulation of Secretase action on endosomes. We anticipate that the Endo-IP approach will facilitate systematic interrogation of processes that are coordinated on EEA1-positive endosomes.
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33
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Jora M, Corcoran D, Parungao GG, Lobue PA, Oliveira LFL, Stan G, Addepalli B, Limbach PA. Higher-Energy Collisional Dissociation Mass Spectral Networks for the Rapid, Semi-automated Characterization of Known and Unknown Ribonucleoside Modifications. Anal Chem 2022; 94:13958-13967. [PMID: 36174068 DOI: 10.1021/acs.analchem.2c03172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Higher-energy collisional dissociation (HCD) of modified ribonucleosides generates characteristic and highly reproducible nucleoside-specific tandem mass spectra (MS/MS). Here, we demonstrate the capability of HCD spectra in combination with spectral matching for the semi-automated characterization of ribonucleosides. This process involved the generation of an HCD spectral library and the establishment of a mass spectral network for rapid detection with high sensitivity and specificity in a retention time-independent fashion. Systematic spectral matching analysis of the MS/MS spectra of tRNA hydrolysates from different organisms has helped us to uncover evidence for the existence of novel ribonucleoside modifications such as s2Cm and OHyW-14. Such an untargeted label-free approach has the potential to be integrated with other methods, including those that use isotope labeling, to simplify the characterization of unknown modified ribonucleosides. These findings suggest the compilation of a universal spectral network, for the characterization of known and unknown ribonucleosides, could accelerate discoveries in the epitranscriptome.
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Affiliation(s)
- Manasses Jora
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Daniel Corcoran
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Gwenn G Parungao
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Peter A Lobue
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Luiz F L Oliveira
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
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34
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Blevins MS, Shields SWJ, Cui W, Fallatah W, Moser AB, Braverman NE, Brodbelt JS. Structural Characterization and Quantitation of Ether-Linked Glycerophospholipids in Peroxisome Biogenesis Disorder Tissue by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2022; 94:12621-12629. [PMID: 36070546 PMCID: PMC9631334 DOI: 10.1021/acs.analchem.2c01274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biological impact of ether glycerophospholipids (GP) in peroxisomal disorders and other diseases makes them significant targets as biomarkers for diagnostic assays or deciphering pathology of the disorders. Ether lipids include both plasmanyl and plasmenyl lipids, which each contain an ether or a vinyl ether bond at the sn-1 linkage position, respectively. This linkage, in contrast to traditional diacyl GPs, precludes their detailed characterization by mass spectrometry via traditional collisional-based MS/MS techniques. Additionally, the isomeric nature of plasmanyl and plasmenyl pairs of ether lipids introduces a further level of complexity that impedes analysis of these species. Here, we utilize 213 nm ultraviolet photodissociation mass spectrometry (UVPD-MS) for detailed characterization of phosphatidylethanolamine (PE) and phosphatidylcholine (PC) plasmenyl and plasmanyl lipids in mouse brain tissue. 213 nm UVPD-MS enables the successful differentiation of these four ether lipid subtypes for the first time. We couple this UVPD-MS methodology to reversed-phase liquid chromatography (RPLC) for characterization and relative quantitation of ether lipids from normal and diseased (Pex7 deficiency modeling the peroxisome biogenesis disorder, RCDP) mouse brain tissue, highlighting the ability to pinpoint specific structural features of ether lipids that are important for monitoring aberrant lipid metabolism in peroxisomal disorders.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Wedad Fallatah
- Department of Medical Genetics, King Abdul-Aziz University, Jeddah, 21423, Saudi Arabia
| | - Ann B Moser
- Kennedy Krieger Institute, Baltimore, Maryland 21205, United States
- School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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35
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Ten-Doménech I, Ramos-Garcia V, Moreno-Torres M, Parra-Llorca A, Gormaz M, Vento M, Kuligowski J, Quintás G. The effect of Holder pasteurization on the lipid and metabolite composition of human milk. Food Chem 2022; 384:132581. [DOI: 10.1016/j.foodchem.2022.132581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/04/2022]
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36
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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37
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Rensvold JW, Shishkova E, Sverchkov Y, Miller IJ, Cetinkaya A, Pyle A, Manicki M, Brademan DR, Alanay Y, Raiman J, Jochem A, Hutchins PD, Peters SR, Linke V, Overmyer KA, Salome AZ, Hebert AS, Vincent CE, Kwiecien NW, Rush MJP, Westphall MS, Craven M, Akarsu NA, Taylor RW, Coon JJ, Pagliarini DJ. Defining mitochondrial protein functions through deep multiomic profiling. Nature 2022; 606:382-388. [PMID: 35614220 PMCID: PMC9310563 DOI: 10.1038/s41586-022-04765-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/14/2022] [Indexed: 11/08/2022]
Abstract
Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles1 and have linked their dysfunction to more than 150 distinct disorders2,3. Still, hundreds of mitochondrial proteins lack clear functions4, and the underlying genetic basis for approximately 40% of mitochondrial disorders remains unresolved5. Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PIGY upstream open reading frame (PYURF) is an S-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established RAB5IF as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.
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Affiliation(s)
- Jarred W Rensvold
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yuriy Sverchkov
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian J Miller
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Arda Cetinkaya
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mateusz Manicki
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Dain R Brademan
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yasemin Alanay
- Department of Pediatrics, Pediatric Genetics Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Department of Pediatrics, Pediatric Genetics Unit, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Julian Raiman
- Department of Clinical Inherited Metabolic Disorders, Birmingham Women's and Children's Hospital NHS Trust, Birmingham, UK
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean R Peters
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Vanessa Linke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander S Hebert
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Catherine E Vincent
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew J P Rush
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael S Westphall
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Craven
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Nurten A Akarsu
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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38
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Chen Y, Li EM, Xu LY. Guide to Metabolomics Analysis: A Bioinformatics Workflow. Metabolites 2022; 12:357. [PMID: 35448542 PMCID: PMC9032224 DOI: 10.3390/metabo12040357] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Metabolomics is an emerging field that quantifies numerous metabolites systematically. The key purpose of metabolomics is to identify the metabolites corresponding to each biological phenotype, and then provide an analysis of the mechanisms involved. Although metabolomics is important to understand the involved biological phenomena, the approach's ability to obtain an exhaustive description of the processes is limited. Thus, an analysis-integrated metabolomics, transcriptomics, proteomics, and other omics approach is recommended. Such integration of different omics data requires specialized statistical and bioinformatics software. This review focuses on the steps involved in metabolomics research and summarizes several main tools for metabolomics analyses. We also outline the most abnormal metabolic pathways in several cancers and diseases, and discuss the importance of multi-omics integration algorithms. Overall, our goal is to summarize the current metabolomics analysis workflow and its main analysis software to provide useful insights for researchers to establish a preferable pipeline of metabolomics or multi-omics analysis.
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Affiliation(s)
- Yang Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041,
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Capturing a rhodopsin receptor signalling cascade across a native membrane. Nature 2022; 604:384-390. [PMID: 35388214 PMCID: PMC9007743 DOI: 10.1038/s41586-022-04547-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/14/2022] [Indexed: 11/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are cell-surface receptors that respond to various stimuli to induce signalling pathways across cell membranes. Recent progress has yielded atomic structures of key intermediates1,2 and roles for lipids in signalling3,4. However, capturing signalling events of a wild-type receptor in real time, across a native membrane to its downstream effectors, has remained elusive. Here we probe the archetypal class A GPCR, rhodopsin, directly from fragments of native disc membranes using mass spectrometry. We monitor real-time photoconversion of dark-adapted rhodopsin to opsin, delineating retinal isomerization and hydrolysis steps, and further showing that the reaction is significantly slower in its native membrane than in detergent micelles. Considering the lipids ejected with rhodopsin, we demonstrate that opsin can be regenerated in membranes through photoisomerized retinal–lipid conjugates, and we provide evidence for increased association of rhodopsin with unsaturated long-chain phosphatidylcholine during signalling. Capturing the secondary steps of the signalling cascade, we monitor light activation of transducin (Gt) through loss of GDP to generate an intermediate apo-trimeric G protein, and observe Gαt•GTP subunits interacting with PDE6 to hydrolyse cyclic GMP. We also show how rhodopsin-targeting compounds either stimulate or dampen signalling through rhodopsin–opsin and transducin signalling pathways. Our results not only reveal the effect of native lipids on rhodopsin signalling and regeneration but also enable us to propose a paradigm for GPCR drug discovery in native membrane environments. The rhodopsin signalling cascade, initiated by light, is captured using mass spectrometry of a native membrane.
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40
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Blomme A, Peter C, Mui E, Rodriguez Blanco G, An N, Mason LM, Jamieson LE, McGregor GH, Lilla S, Ntala C, Patel R, Thiry M, Kung SHY, Leclercq M, Ford CA, Rushworth LK, McGarry DJ, Mason S, Repiscak P, Nixon C, Salji MJ, Markert E, MacKay GM, Kamphorst JJ, Graham D, Faulds K, Fazli L, Gleave ME, Avezov E, Edwards J, Yin H, Sumpton D, Blyth K, Close P, Murphy DJ, Zanivan S, Leung HY. THEM6-mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer. EMBO Mol Med 2022; 14:e14764. [PMID: 35014179 PMCID: PMC8899912 DOI: 10.15252/emmm.202114764] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/21/2022] Open
Abstract
Despite the clinical benefit of androgen-deprivation therapy (ADT), the majority of patients with advanced prostate cancer (PCa) ultimately develop lethal castration-resistant prostate cancer (CRPC). In this study, we identified thioesterase superfamily member 6 (THEM6) as a marker of ADT resistance in PCa. THEM6 deletion reduces in vivo tumour growth and restores castration sensitivity in orthograft models of CRPC. Mechanistically, we show that the ER membrane-associated protein THEM6 regulates intracellular levels of ether lipids and is essential to trigger the induction of the ER stress response (UPR). Consequently, THEM6 loss in CRPC cells significantly alters ER function, reducing de novo sterol biosynthesis and preventing lipid-mediated activation of ATF4. Finally, we demonstrate that high THEM6 expression is associated with poor survival and correlates with high levels of UPR activation in PCa patients. Altogether, our results highlight THEM6 as a novel driver of therapy resistance in PCa as well as a promising target for the treatment of CRPC.
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Affiliation(s)
| | | | - Ernest Mui
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | | | - Ning An
- Laboratory of Cancer SignalingGIGA‐InstituteUniversity of LiègeLiègeBelgium
| | | | - Lauren E Jamieson
- Centre for Molecular NanometrologyDepartment of Pure and Applied ChemistryTechnology and Innovation CentreUniversity of StrathclydeGlasgowUK
| | - Grace H McGregor
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | | | - Chara Ntala
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | | | - Marc Thiry
- GIGA‐NeurosciencesUnit of Cell and Tissue BiologyUniversity of LiègeLiègeBelgium
| | - Sonia H Y Kung
- Department of Urologic SciencesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
- Vancouver Prostate CentreVancouverBCCanada
| | - Marine Leclercq
- Laboratory of Cancer SignalingGIGA‐InstituteUniversity of LiègeLiègeBelgium
| | | | - Linda K Rushworth
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | | | - Susan Mason
- CRUK Beatson InstituteGarscube EstateGlasgowUK
| | | | - Colin Nixon
- CRUK Beatson InstituteGarscube EstateGlasgowUK
| | - Mark J Salji
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Elke Markert
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | | | - Jurre J Kamphorst
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Duncan Graham
- Centre for Molecular NanometrologyDepartment of Pure and Applied ChemistryTechnology and Innovation CentreUniversity of StrathclydeGlasgowUK
| | - Karen Faulds
- Centre for Molecular NanometrologyDepartment of Pure and Applied ChemistryTechnology and Innovation CentreUniversity of StrathclydeGlasgowUK
| | - Ladan Fazli
- Department of Urologic SciencesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
- Vancouver Prostate CentreVancouverBCCanada
| | - Martin E Gleave
- Department of Urologic SciencesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
- Vancouver Prostate CentreVancouverBCCanada
| | - Edward Avezov
- UK Dementia Research Institute at University of CambridgeDepartment of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Joanne Edwards
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Huabing Yin
- School of EngineeringUniversity of GlasgowGlasgowUK
| | | | - Karen Blyth
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Pierre Close
- Laboratory of Cancer SignalingGIGA‐InstituteUniversity of LiègeLiègeBelgium
| | - Daniel J Murphy
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Sara Zanivan
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
| | - Hing Y Leung
- CRUK Beatson InstituteGarscube EstateGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGarscube EstateGlasgowUK
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41
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He Y, Brademan DR, Hutchins PD, Overmyer KA, Coon JJ. Maximizing MS/MS Acquisition for Lipidomics Using Capillary Separation and Orbitrap Tribrid Mass Spectrometer. Anal Chem 2022; 94:3394-3399. [PMID: 35138847 PMCID: PMC8950118 DOI: 10.1021/acs.analchem.1c05552] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is a typical strategy for lipidomics analysis. Although capillary LC-MS is a common analytical technique for proteomics analysis, its application to lipidomics has been limited. In this study, we aim at improving lipid identifications achieved in a single LC-MS analysis by a 3-fold approach: capillary LC and nanoelectrospray for enhanced ionization, ion trap for higher sensitivity tandem MS, and parallelization of mass analyzers for increased speed of acquisition on an Orbitrap hybrid system. By applying the methods to a complex lipid mixture of human plasma, we identified and performed relative quantification on over 1500 lipids within a 60 min capillary LC-MS analysis.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | | | | | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA,Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA,Morgridge Institute for Research, Madison, WI 53715, USA,Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA,Correspondence: J.J.C. ()
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42
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Patil DN, Singh S, Laboute T, Strutzenberg TS, Qiu X, Wu D, Novick SJ, Robinson CV, Griffin PR, Hunt JF, Izard T, Singh AK, Martemyanov KA. Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex. Science 2022; 375:86-91. [PMID: 34793198 PMCID: PMC8926151 DOI: 10.1126/science.abl4732] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GPR158 is an orphan G protein–coupled receptor (GPCR) highly expressed in the brain, where it controls synapse formation and function. GPR158 has also been implicated in depression, carcinogenesis, and cognition. However, the structural organization and signaling mechanisms of GPR158 are largely unknown. We used single-particle cryo–electron microscopy (cryo-EM) to determine the structures of human GPR158 alone and bound to an RGS signaling complex. The structures reveal a homodimeric organization stabilized by a pair of phospholipids and the presence of an extracellular Cache domain, an unusual ligand-binding domain in GPCRs. We further demonstrate the structural basis of GPR158 coupling to RGS7-Gβ5. Together, these results provide insights into the unusual biology of orphan receptors and the formation of GPCR-RGS complexes.
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Affiliation(s)
- Dipak N. Patil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Shikha Singh
- Department of Biological Sciences, Columbia University New York, NY 10027
| | - Thibaut Laboute
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Xingyu Qiu
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Di Wu
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Scott J. Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,The Kavli Institute for Nanoscience Discovery, Oxford, OX1 3QU, UK
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - John F. Hunt
- Department of Biological Sciences, Columbia University New York, NY 10027
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Appu K. Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India,Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India,Co-corresponding authors: Dr. Kirill A. Martemyanov, ; Dr. Appu K. Singh,
| | - Kirill A. Martemyanov
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA,Co-corresponding authors: Dr. Kirill A. Martemyanov, ; Dr. Appu K. Singh,
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43
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Abstract
Helicobacter pylori colonization of the stomach is a strong risk factor for the development of stomach cancer and peptic ulcer disease. In this study, we tested the hypothesis that H. pylori infection triggers alterations in gastric lipid composition. Mongolian gerbils were experimentally infected with H. pylori for 3 months. Conventional histologic staining revealed mucosal inflammation in stomachs from the H. pylori-infected animals but not in stomachs from uninfected control animals. Atrophic gastritis (a premalignant condition characterized by loss of corpus-specific parietal and chief cells), gastric mucosal hyperplasia, dysplasia, and/or gastric cancer were detected in stomachs from several infected animals. We then used imaging mass spectrometry to analyze the relative abundance and spatial distribution of gastric lipids. We detected ions corresponding to 36 distinct lipids that were differentially abundant when comparing gastric tissues from H. pylori-infected animals with tissues from uninfected animals. Liquid chromatography-tandem mass spectrometry analysis of lipid extracts from homogenized gastric tissues provided additional supportive evidence for the identification of several differentially abundant lipids. Sixteen of the differentially abundant lipids were localized mainly to the gastric corpus in stomachs from uninfected animals and were markedly reduced in abundance in stomachs from H. pylori-infected animals with severe disease (atrophic gastritis and dysplasia or gastric cancer). These findings indicate that H. pylori infection can lead to alterations in gastric lipid composition and constitute a new approach for identifying biomarkers of gastric atrophy and premalignant changes. IMPORTANCE H. pylori colonization of the stomach triggers a cascade of gastric alterations that can potentially culminate in stomach cancer. The molecular alterations that occur in gastric tissue prior to development of stomach cancer are not well understood. We demonstrate here that H. pylori-induced premalignant changes in the stomach are accompanied by extensive alterations in gastric lipid composition. These alterations are predicted to have important functional consequences relevant to H. pylori-host interactions and the pathogenesis of gastric cancer.
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44
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Kotnala A, Anderson DM, Patterson NH, Cantrell LS, Messinger JD, Curcio CA, Schey KL. Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4798. [PMID: 34881479 PMCID: PMC8711642 DOI: 10.1002/jms.4798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/09/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Imaging mass spectrometry (IMS) allows the location and abundance of lipids to be mapped across tissue sections of human retina. For reproducible and accurate information, sample preparation methods need to be optimized. Paraformaldehyde fixation of a delicate multilayer structure like human retina facilitates the preservation of tissue morphology by forming methylene bridge crosslinks between formaldehyde and amine/thiols in biomolecules; however, retina sections analyzed by IMS are typically fresh-frozen. To determine if clinically significant inferences could be reliably based on fixed tissue, we evaluated the effect of fixation on analyte detection, spatial localization, and introduction of artifactual signals. Hence, we assessed the molecular identity of lipids generated by matrix-assisted laser desorption ionization (MALDI-IMS) and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) for fixed and fresh-frozen retina tissues in positive and negative ion modes. Based on MALDI-IMS analysis, more lipid signals were observed in fixed compared with fresh-frozen retina. More potassium adducts were observed in fresh-frozen tissues than fixed as the fixation process caused displacement of potassium adducts to protonated and sodiated species in ion positive ion mode. LC-MS/MS analysis revealed an overall decrease in lipid signals due to fixation that reduced glycerophospholipids and glycerolipids and conserved most sphingolipids and cholesteryl esters. The high quality and reproducible information from untargeted lipidomics analysis of fixed retina informs on all major lipid classes, similar to fresh-frozen retina, and serves as a steppingstone towards understanding of lipid alterations in retinal diseases.
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Affiliation(s)
- Ankita Kotnala
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - David M.G. Anderson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Nathan Heath Patterson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Lee S. Cantrell
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jeffrey D. Messinger
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Kevin L. Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
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45
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Moreno-Torres M, García-Llorens G, Moro E, Méndez R, Quintás G, Castell JV. Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey. Sci Rep 2021; 11:22119. [PMID: 34764412 PMCID: PMC8586040 DOI: 10.1038/s41598-021-01652-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/21/2021] [Indexed: 01/03/2023] Open
Abstract
REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) is a global strategy and regulation policy of the EU that aims to improve the protection of human health and the environment through the better and earlier identification of the intrinsic properties of chemical substances. It entered into force on 1st June 2007 (EC 1907/2006). REACH and EU policies plead for the use of robust high-throughput "omic" techniques for the in vitro investigation of the toxicity of chemicals that can provide an estimation of their hazards as well as information regarding the underlying mechanisms of toxicity. In agreement with the 3R's principles, cultured cells are nowadays widely used for this purpose, where metabolomics can provide a real-time picture of the metabolic effects caused by exposure of cells to xenobiotics, enabling the estimations about their toxicological hazards. High quality and robust metabolomics data sets are essential for precise and accurate hazard predictions. Currently, the acquisition of consistent and representative metabolomic data is hampered by experimental drawbacks that hinder reproducibility and difficult robust hazard interpretation. Using the differentiated human liver HepG2 cells as model system, and incubating with hepatotoxic (acetaminophen and valproic acid) and non-hepatotoxic compounds (citric acid), we evaluated in-depth the impact of several key experimental factors (namely, cell passage, processing day and storage time, and compound treatment) and instrumental factors (batch effect) on the outcome of an UPLC-MS metabolomic analysis data set. Results showed that processing day and storage time had a significant impact on the retrieved cell's metabolome, while the effect of cell passage was minor. Meta-analysis of results from pathway analysis showed that batch effect corrections and quality control (QC) measures are critical to enable consistent and meaningful estimations of the effects caused by compounds on cells. The quantitative analysis of the changes in metabolic pathways upon bioactive compound treatment remained consistent despite the concurrent causes of metabolomic data variation. Thus, upon appropriate data retrieval and correction and by an innovative metabolic pathway analysis, the metabolic alteration predictions remained conclusive despite the acknowledged sources of variability.
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Affiliation(s)
- Marta Moreno-Torres
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Guillem García-Llorens
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain
| | - Erika Moro
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Rebeca Méndez
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Guillermo Quintás
- Health and Biomedicine, LEITAT Technological Center, Barcelona, Spain.
- Unidad Analítica, Health Research Institute Hospital La Fe, Avda Fernando Abril Martorell 106, 46026, Valencia, Spain.
| | - José Vicente Castell
- Unidad de Hepatología Experimental y Trasplante Hepático, Health Research Institute Hospital La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain
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Ly R, Ly N, Sasaki K, Suzuki M, Kami K, Ohashi Y, Britz-McKibbin P. Nontargeted Serum Lipid Profiling of Nonalcoholic Steatohepatitis by Multisegment Injection-Nonaqueous Capillary Electrophoresis-Mass Spectrometry: A Multiplexed Separation Platform for Resolving Ionic Lipids. J Proteome Res 2021; 21:768-777. [PMID: 34676758 DOI: 10.1021/acs.jproteome.1c00682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New methods are needed for global lipid profiling due to the complex chemical structures and diverse physicochemical properties of lipids. Herein we introduce a robust data workflow to unambiguously select lipid features from serum ether extracts by multisegment injection-nonaqueous capillary electrophoresis-mass spectrometry (MSI-NACE-MS). An iterative three-stage screening strategy is developed for nontargeted lipid analyses when using multiplexed electrophoretic separations coupled to an Orbitrap mass analyzer under negative ion mode. This approach enables the credentialing of 270 serum lipid features annotated based on their accurate mass and relative migration time, including 128 ionic lipids reliably measured (median CV ≈ 13%) in most serum samples (>75%) from nonalcoholic steatohepatitis (NASH) patients (n = 85). A mobility map is introduced to classify charged lipid classes over a wide polarity range with selectivity complementary to chromatographic separations, including lysophosphatidic acids, phosphatidylcholines, phosphatidylinositols, phosphatidylethanolamines, and nonesterified fatty acids (NEFAs). Serum lipidome profiles were also used to differentiate high- from low-risk NASH patients using a k-means clustering algorithm, where elevated circulating NEFAs (e.g., palmitic acid) were associated with increased glucose intolerance, more severe liver fibrosis, and greater disease burden. MSI-NACE-MS greatly expands the metabolome coverage of conventional aqueous-based CE-MS protocols and is a promising platform for large-scale lipidomic studies.
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Affiliation(s)
- Ritchie Ly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Nicholas Ly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Kazunori Sasaki
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Makoto Suzuki
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Kenjiro Kami
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Yoshiaki Ohashi
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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47
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The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. Metabolites 2021; 11:metabo11110713. [PMID: 34822371 PMCID: PMC8624948 DOI: 10.3390/metabo11110713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022] Open
Abstract
Lipidomics is a newly emerged discipline involving the identification and quantification of thousands of lipids. As a part of the omics field, lipidomics has shown rapid growth both in the number of studies and in the size of lipidome datasets, thus, requiring specific and efficient data analysis approaches. This paper aims to provide guidelines for analyzing and interpreting lipidome data obtained using untargeted methods that rely on liquid chromatography coupled with mass spectrometry (LC-MS) to detect and measure the intensities of lipid compounds. We present a state-of-the-art untargeted LC-MS workflow for lipidomics, from study design to annotation of lipid features, focusing on practical, rather than theoretical, approaches for data analysis, and we outline possible applications of untargeted lipidomics for biological studies. We provide a detailed R notebook designed specifically for untargeted lipidome LC-MS data analysis, which is based on xcms software.
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McGranaghan P, Kirwan JA, Garcia-Rivera MA, Pieske B, Edelmann F, Blaschke F, Appunni S, Saxena A, Rubens M, Veledar E, Trippel TD. Lipid Metabolite Biomarkers in Cardiovascular Disease: Discovery and Biomechanism Translation from Human Studies. Metabolites 2021; 11:metabo11090621. [PMID: 34564437 PMCID: PMC8470800 DOI: 10.3390/metabo11090621] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Lipids represent a valuable target for metabolomic studies since altered lipid metabolism is known to drive the pathological changes in cardiovascular disease (CVD). Metabolomic technologies give us the ability to measure thousands of metabolites providing us with a metabolic fingerprint of individual patients. Metabolomic studies in humans have supported previous findings into the pathomechanisms of CVD, namely atherosclerosis, apoptosis, inflammation, oxidative stress, and insulin resistance. The most widely studied classes of lipid metabolite biomarkers in CVD are phospholipids, sphingolipids/ceramides, glycolipids, cholesterol esters, fatty acids, and acylcarnitines. Technological advancements have enabled novel strategies to discover individual biomarkers or panels that may aid in the diagnosis and prognosis of CVD, with sphingolipids/ceramides as the most promising class of biomarkers thus far. In this review, application of metabolomic profiling for biomarker discovery to aid in the diagnosis and prognosis of CVD as well as metabolic abnormalities in CVD will be discussed with particular emphasis on lipid metabolites.
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Affiliation(s)
- Peter McGranaghan
- Department of Internal Medicine and Cardiology, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany; (P.M.); (B.P.); (F.E.); (F.B.)
- Baptist Health South Florida, Miami, FL 33143, USA; (A.S.); (M.R.); (E.V.)
| | - Jennifer A. Kirwan
- Metabolomics Platform, Berlin Institute of Health at Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; (J.A.K.); (M.A.G.-R.)
- Max Delbrück Center for Molecular Research, 13125 Berlin, Germany
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5RD, UK
| | - Mariel A. Garcia-Rivera
- Metabolomics Platform, Berlin Institute of Health at Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; (J.A.K.); (M.A.G.-R.)
- Max Delbrück Center for Molecular Research, 13125 Berlin, Germany
| | - Burkert Pieske
- Department of Internal Medicine and Cardiology, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany; (P.M.); (B.P.); (F.E.); (F.B.)
- DZHK (German Centre for Cardiovascular Research), 13353 Berlin, Germany
- Berlin Institute of Health, 13353 Berlin, Germany
- German Heart Center Berlin, Department of Cardiology, 13353 Berlin, Germany
| | - Frank Edelmann
- Department of Internal Medicine and Cardiology, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany; (P.M.); (B.P.); (F.E.); (F.B.)
- DZHK (German Centre for Cardiovascular Research), 13353 Berlin, Germany
- German Heart Center Berlin, Department of Cardiology, 13353 Berlin, Germany
| | - Florian Blaschke
- Department of Internal Medicine and Cardiology, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany; (P.M.); (B.P.); (F.E.); (F.B.)
- DZHK (German Centre for Cardiovascular Research), 13353 Berlin, Germany
| | - Sandeep Appunni
- Department of Biochemistry, Government Medical College, Kozhikode, Kerala 673008, India;
| | - Anshul Saxena
- Baptist Health South Florida, Miami, FL 33143, USA; (A.S.); (M.R.); (E.V.)
| | - Muni Rubens
- Baptist Health South Florida, Miami, FL 33143, USA; (A.S.); (M.R.); (E.V.)
| | - Emir Veledar
- Baptist Health South Florida, Miami, FL 33143, USA; (A.S.); (M.R.); (E.V.)
- Department of Biostatistics, Florida International University, Miami, FL 33199, USA
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tobias Daniel Trippel
- Department of Internal Medicine and Cardiology, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany; (P.M.); (B.P.); (F.E.); (F.B.)
- DZHK (German Centre for Cardiovascular Research), 13353 Berlin, Germany
- Correspondence: ; Tel.: +49-30-450-553765
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Pekov SI, Sorokin AA, Kuzin AA, Bocharov KV, Bormotov DS, Shivalin AS, Shurkhay VA, Potapov AA, Nikolaev EN, Popov IA. Analysis of Phosphatidylcholines Alterations in Human Glioblastomas Ex Vivo. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2021. [DOI: 10.1134/s1990750821030070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Reply to "Quality control requirements for the correct annotation of lipidomics data". Nat Commun 2021; 12:4772. [PMID: 34362889 PMCID: PMC8346504 DOI: 10.1038/s41467-021-24985-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/15/2021] [Indexed: 11/18/2022] Open
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