1
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Glaser KM, Egg M, Hobitz S, Mitterer M, Schain-Zota D, Schönberger K, Schuldes K, Cabezas-Wallscheid N, Lämmermann T, Rambold A, Buescher JM. Targeted Metabolomics on Rare Primary Cells. J Vis Exp 2024. [PMID: 38465941 DOI: 10.3791/65690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
Cellular function critically depends on metabolism, and the function of the underlying metabolic networks can be studied by measuring small molecule intermediates. However, obtaining accurate and reliable measurements of cellular metabolism, particularly in rare cell types like hematopoietic stem cells, has traditionally required pooling cells from multiple animals. A protocol now enables researchers to measure metabolites in rare cell types using only one mouse per sample while generating multiple replicates for more abundant cell types. This reduces the number of animals that are required for a given project. The protocol presented here involves several key differences over traditional metabolomics protocols, such as using 5 g/L NaCl as a sheath fluid, sorting directly into acetonitrile, and utilizing targeted quantification with rigorous use of internal standards, allowing for more accurate and comprehensive measurements of cellular metabolism. Despite the time required for the isolation of single cells, fluorescent staining, and sorting, the protocol can preserve differences among cell types and drug treatments to a large extent.
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Affiliation(s)
| | - Mirijam Egg
- Max Planck Institute of Immunobiology and Epigenetics
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2
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Villa M, Sanin DE, Apostolova P, Corrado M, Kabat AM, Cristinzio C, Regina A, Carrizo GE, Rana N, Stanczak MA, Baixauli F, Grzes KM, Cupovic J, Solagna F, Hackl A, Globig AM, Hässler F, Puleston DJ, Kelly B, Cabezas-Wallscheid N, Hasselblatt P, Bengsch B, Zeiser R, Sagar, Buescher JM, Pearce EJ, Pearce EL. Prostaglandin E 2 controls the metabolic adaptation of T cells to the intestinal microenvironment. Nat Commun 2024; 15:451. [PMID: 38200005 PMCID: PMC10781727 DOI: 10.1038/s41467-024-44689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Immune cells must adapt to different environments during the course of an immune response. Here we study the adaptation of CD8+ T cells to the intestinal microenvironment and how this process shapes the establishment of the CD8+ T cell pool. CD8+ T cells progressively remodel their transcriptome and surface phenotype as they enter the gut wall, and downregulate expression of mitochondrial genes. Human and mouse intestinal CD8+ T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We find that the intestinal microenvironment is rich in prostaglandin E2 (PGE2), which drives mitochondrial depolarization in CD8+ T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE2 sensing promotes CD8+ T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell pool. Thus, a PGE2-autophagy-glutathione axis defines the metabolic adaptation of CD8+ T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
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Affiliation(s)
- Matteo Villa
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Division of Rheumatology and Immunology, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria.
| | - David E Sanin
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petya Apostolova
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine I (Hematology and Oncology), University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Mauro Corrado
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Agnieszka M Kabat
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carmine Cristinzio
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Annamaria Regina
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Department of Life Sciences, University of Trieste, 34128, Trieste, Italy
| | - Gustavo E Carrizo
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Nisha Rana
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Michal A Stanczak
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Francesc Baixauli
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Katarzyna M Grzes
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Jovana Cupovic
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Francesca Solagna
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Alexandra Hackl
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Anna-Maria Globig
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Fabian Hässler
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Daniel J Puleston
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Beth Kelly
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | | | - Peter Hasselblatt
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Bertram Bengsch
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
| | - Robert Zeiser
- Department of Medicine I (Hematology and Oncology), University Medical Center Freiburg, 79106, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
| | - Sagar
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Edward J Pearce
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erika L Pearce
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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3
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Castoldi A, Sanin DE, van Teijlingen Bakker N, Aguiar CF, de Brito Monteiro L, Rana N, Grzes KM, Kabat AM, Curtis J, Cameron AM, Caputa G, Antônio de Souza T, Souto FO, Buescher JM, Edwards-Hicks J, Pearce EL, Pearce EJ, Saraiva Camara NO. Metabolic and functional remodeling of colonic macrophages in response to high-fat diet-induced obesity. iScience 2023; 26:107719. [PMID: 37674984 PMCID: PMC10477064 DOI: 10.1016/j.isci.2023.107719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
Little is known about the effects of high-fat diet (HFD)-induced obesity on resident colonic lamina propria (LP) macrophages (LPMs) function and metabolism. Here, we report that obesity and diabetes resulted in increased macrophage infiltration in the colon. These macrophages exhibited the residency phenotype CX3CR1hiMHCIIhi and were CD4-TIM4-. During HFD, resident colonic LPM exhibited a lipid metabolism gene expression signature that overlapped that used to define lipid-associated macrophages (LAMs). Via single-cell RNA sequencing, we identified a sub-cluster of macrophages, increased in HFD, that were responsible for the LAM signature. Compared to other macrophages in the colon, these cells were characterized by elevated glycolysis, phagocytosis, and efferocytosis signatures. CX3CR1hiMHCIIhi colonic resident LPMs had fewer lipid droplets (LDs) and decreased triacylglycerol (TG) content compared to equivalent cells in lean mice and exhibited increased phagocytic capacity, suggesting that HFD induces adaptive responses in LPMs to limit bacterial translocation.
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Affiliation(s)
- Angela Castoldi
- Department of Immunology, University of Sao Paulo, Sao Paulo, Brazil
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Institute Keizo Asami, Federal University of Pernambuco, Pernambuco, Brazil
| | - David E. Sanin
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nikki van Teijlingen Bakker
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Lauar de Brito Monteiro
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Nisha Rana
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Katarzyna M. Grzes
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Agnieszka M. Kabat
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan Curtis
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alanna M. Cameron
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - George Caputa
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Fabrício O. Souto
- Institute Keizo Asami, Federal University of Pernambuco, Pernambuco, Brazil
| | - Joerg M. Buescher
- Metabolomics Facility, Max Planck Institute of Epigenetics and Immunobiology, Freiburg im Breisgau, Germany
| | - Joy Edwards-Hicks
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Erika L. Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Edward J. Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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4
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Forde AJ, Kolter J, Zwicky P, Baasch S, Lohrmann F, Eckert M, Gres V, Lagies S, Gorka O, Rambold AS, Buescher JM, Kammerer B, Lachmann N, Prinz M, Groß O, Pearce EJ, Becher B, Henneke P. Metabolic rewiring tunes dermal macrophages in staphylococcal skin infection. Sci Immunol 2023; 8:eadg3517. [PMID: 37566679 DOI: 10.1126/sciimmunol.adg3517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
The skin needs to balance tolerance of colonizing microflora with rapid detection of potential pathogens. Flexible response mechanisms would seem most suitable to accommodate the dynamic challenges of effective antimicrobial defense and restoration of tissue homeostasis. Here, we dissected macrophage-intrinsic mechanisms and microenvironmental cues that tune macrophage signaling in localized skin infection with the colonizing and opportunistic pathogen Staphylococcus aureus. Early in skin infection, the cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) produced by γδ T cells and hypoxic conditions within the dermal microenvironment diverted macrophages away from a homeostatic M-CSF- and hypoxia-inducible factor 1α (HIF-1α)-dependent program. This allowed macrophages to be metabolically rewired for maximal inflammatory activity, which requires expression of Irg1 and generation of itaconate, but not HIF-1α. This multifactorial macrophage rewiring program was required for both the timely clearance of bacteria and for the provision of local immune memory. These findings indicate that immunometabolic conditioning allows dermal macrophages to cycle between antimicrobial activity and protection against secondary infections.
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Affiliation(s)
- Aaron James Forde
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Julia Kolter
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Pascale Zwicky
- Institute of Experimental Immunology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sebastian Baasch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Florens Lohrmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
| | - Marleen Eckert
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Vitka Gres
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Lagies
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
- 1 Core Competence Metabolomics, Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Gorka
- Institute of Neuropathology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Angelika S Rambold
- Department of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Joerg M Buescher
- Department of Immunometabolism, Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Bernd Kammerer
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
- 1 Core Competence Metabolomics, Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centre's BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Nico Lachmann
- Department of Pediatric Pneumology, Allergology and Neonatology and Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centre's BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- CIBSS-Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Olaf Groß
- Institute of Neuropathology, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centre's BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- CIBSS-Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Edward J Pearce
- Department of Immunometabolism, Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Philipp Henneke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
- CIBSS-Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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5
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Villa M, Sanin DE, Apostolova P, Corrado M, Kabat AM, Cristinzio C, Regina A, Carrizo GE, Rana N, Stanczak MA, Baixauli F, Grzes KM, Cupovic J, Solagna F, Hackl A, Globig AM, Hässler F, Puleston DJ, Kelly B, Cabezas-Wallscheid N, Hasselblatt P, Bengsch B, Zeiser R, Sagar, Buescher JM, Pearce EJ, Pearce EL. Prostaglandin E 2 controls the metabolic adaptation of T cells to the intestinal microenvironment. bioRxiv 2023:2023.03.13.532431. [PMID: 36993703 PMCID: PMC10054978 DOI: 10.1101/2023.03.13.532431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Immune cells must adapt to different environments during the course of an immune response. We studied the adaptation of CD8 + T cells to the intestinal microenvironment and how this process shapes their residency in the gut. CD8 + T cells progressively remodel their transcriptome and surface phenotype as they acquire gut residency, and downregulate expression of mitochondrial genes. Human and mouse gut-resident CD8 + T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We found that the intestinal microenvironment is rich in prostaglandin E 2 (PGE 2 ), which drives mitochondrial depolarization in CD8 + T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE 2 sensing promotes CD8 + T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell population. Thus, a PGE 2 -autophagy-glutathione axis defines the metabolic adaptation of CD8 + T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
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6
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Schönberger K, Mitterer M, Glaser K, Stecher M, Hobitz S, Schain-Zota D, Schuldes K, Lämmermann T, Rambold AS, Cabezas-Wallscheid N, Buescher JM. LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells. Anal Chem 2023; 95:4325-4334. [PMID: 36812587 PMCID: PMC9996616 DOI: 10.1021/acs.analchem.2c04396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Metabolism plays a fundamental role in regulating cellular functions and fate decisions. Liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomic approaches provide high-resolution insights into the metabolic state of a cell. However, the typical sample size is in the order of 105-107 cells and thus not compatible with rare cell populations, especially in the case of a prior flow cytometry-based purification step. Here, we present a comprehensively optimized protocol for targeted metabolomics on rare cell types, such as hematopoietic stem cells and mast cells. Only 5000 cells per sample are required to detect up to 80 metabolites above background. The use of regular-flow liquid chromatography allows for robust data acquisition, and the omission of drying or chemical derivatization avoids potential sources of error. Cell-type-specific differences are preserved while the addition of internal standards, generation of relevant background control samples, and targeted metabolite with quantifiers and qualifiers ensure high data quality. This protocol could help numerous studies to gain thorough insights into cellular metabolic profiles and simultaneously reduce the number of laboratory animals and the time-consuming and costly experiments associated with rare cell-type purification.
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Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Katharina Glaser
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Manuel Stecher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-MCB), 79108 Freiburg, Germany
| | - Sebastian Hobitz
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Dominik Schain-Zota
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Konrad Schuldes
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Angelika S Rambold
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | | | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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7
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Edwards-Hicks J, Apostolova P, Buescher JM, Maib H, Stanczak MA, Corrado M, Klein Geltink RI, Maccari ME, Villa M, Carrizo GE, Sanin DE, Baixauli F, Kelly B, Curtis JD, Haessler F, Patterson A, Field CS, Caputa G, Kyle RL, Soballa M, Cha M, Paul H, Martin J, Grzes KM, Flachsmann L, Mitterer M, Zhao L, Winkler F, Rafei-Shamsabadi DA, Meiss F, Bengsch B, Zeiser R, Puleston DJ, O'Sullivan D, Pearce EJ, Pearce EL. Phosphoinositide acyl chain saturation drives CD8 + effector T cell signaling and function. Nat Immunol 2023; 24:516-530. [PMID: 36732424 PMCID: PMC10908374 DOI: 10.1038/s41590-023-01419-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
How lipidome changes support CD8+ effector T (Teff) cell differentiation is not well understood. Here we show that, although naive T cells are rich in polyunsaturated phosphoinositides (PIPn with 3-4 double bonds), Teff cells have unique PIPn marked by saturated fatty acyl chains (0-2 double bonds). PIPn are precursors for second messengers. Polyunsaturated phosphatidylinositol bisphosphate (PIP2) exclusively supported signaling immediately upon T cell antigen receptor activation. In late Teff cells, activity of phospholipase C-γ1, the enzyme that cleaves PIP2 into downstream mediators, waned, and saturated PIPn became essential for sustained signaling. Saturated PIP was more rapidly converted to PIP2 with subsequent recruitment of phospholipase C-γ1, and loss of saturated PIPn impaired Teff cell fitness and function, even in cells with abundant polyunsaturated PIPn. Glucose was the substrate for de novo PIPn synthesis, and was rapidly utilized for saturated PIP2 generation. Thus, separate PIPn pools with distinct acyl chain compositions and metabolic dependencies drive important signaling events to initiate and then sustain effector function during CD8+ T cell differentiation.
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Affiliation(s)
- Joy Edwards-Hicks
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Petya Apostolova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Hannes Maib
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michal A Stanczak
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mauro Corrado
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Maria Elena Maccari
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matteo Villa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gustavo E Carrizo
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David E Sanin
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesc Baixauli
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Beth Kelly
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabian Haessler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Annette Patterson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cameron S Field
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - George Caputa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ryan L Kyle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Melanie Soballa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Minsun Cha
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harry Paul
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacob Martin
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katarzyna M Grzes
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lea Flachsmann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Liang Zhao
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Frances Winkler
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - David Ali Rafei-Shamsabadi
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Meiss
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Bengsch
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Robert Zeiser
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel J Puleston
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David O'Sullivan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Edward J Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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8
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Abstract
Metabolomics is a continuously dynamic field of research that is driven by demanding research questions and technological advances alike. In this review we highlight selected recent and ongoing developments in the area of mass spectrometry-based metabolomics. The field of view that can be seen through the metabolomics lens can be broadened by adoption of separation techniques such as hydrophilic interaction chromatography and ion mobility mass spectrometry (going broader). For a given biospecimen, deeper metabolomic analysis can be achieved by resolving smaller entities such as rare cell populations or even single cells using nano-LC and spatially resolved metabolomics or by extracting more useful information through improved metabolite identification in untargeted metabolomic experiments (going deeper). Integration of metabolomics with other (omics) data allows researchers to further advance in the understanding of the complex metabolic and regulatory networks in cells and model organisms (going further). Taken together, diverse fields of research from mechanistic studies to clinics to biotechnology applications profit from these technological developments.
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Affiliation(s)
- Sofia Moco
- Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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9
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Bondareva O, Rodríguez-Aguilera JR, Oliveira F, Liao L, Rose A, Gupta A, Singh K, Geier F, Schuster J, Boeckel JN, Buescher JM, Kohli S, Klöting N, Isermann B, Blüher M, Sheikh BN. Single-cell profiling of vascular endothelial cells reveals progressive organ-specific vulnerabilities during obesity. Nat Metab 2022; 4:1591-1610. [PMID: 36400935 PMCID: PMC9684070 DOI: 10.1038/s42255-022-00674-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022]
Abstract
Obesity promotes diverse pathologies, including atherosclerosis and dementia, which frequently involve vascular defects and endothelial cell (EC) dysfunction. Each organ has distinct EC subtypes, but whether ECs are differentially affected by obesity is unknown. Here we use single-cell RNA sequencing to analyze transcriptomes of ~375,000 ECs from seven organs in male mice at progressive stages of obesity to identify organ-specific vulnerabilities. We find that obesity deregulates gene expression networks, including lipid handling, metabolic pathways and AP1 transcription factor and inflammatory signaling, in an organ- and EC-subtype-specific manner. The transcriptomic aberrations worsen with sustained obesity and are only partially mitigated by dietary intervention and weight loss. For example, dietary intervention substantially attenuates dysregulation of liver, but not kidney, EC transcriptomes. Through integration with human genome-wide association study data, we further identify a subset of vascular disease risk genes that are induced by obesity. Our work catalogs the impact of obesity on the endothelium, constitutes a useful resource and reveals leads for investigation as potential therapeutic targets.
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Affiliation(s)
- Olga Bondareva
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Jesús Rafael Rodríguez-Aguilera
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Fabiana Oliveira
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Longsheng Liao
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Alina Rose
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Anubhuti Gupta
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Kunal Singh
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Florian Geier
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
| | - Jenny Schuster
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
| | - Jes-Niels Boeckel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, University of Leipzig, Leipzig, Germany
| | - Joerg M Buescher
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Shrey Kohli
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Nora Klöting
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig, Germany
| | - Bilal N Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, Leipzig, Germany.
- Medical Faculty, University of Leipzig, Leipzig, Germany.
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10
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Ho JNHG, Schmidt D, Lowinus T, Ryoo J, Dopfer EP, Gonzalo Núñez N, Costa-Pereira S, Toffalori C, Punta M, Fetsch V, Wertheimer T, Rittmann MC, Braun LM, Follo M, Briere C, Vinnakota JM, Langenbach M, Koppers F, Shoumariyeh K, Engel H, Rückert T, Märklin M, Holzmayer S, Illert AL, Magon F, Andrieux G, Duquesne S, Pfeifer D, Staniek J, Rizzi M, Miething C, Köhler N, Duyster J, Menssen HD, Boerries M, Buescher JM, Cabezas-Wallscheid N, Blazar BR, Apostolova P, Vago L, Pearce EL, Becher B, Zeiser R. Targeting MDM2 enhances antileukemia immunity after allogeneic transplantation via MHC-II and TRAIL-R1/2 upregulation. Blood 2022; 140:1167-1181. [PMID: 35853161 PMCID: PMC9461473 DOI: 10.1182/blood.2022016082] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with acute myeloid leukemia (AML) often achieve remission after allogeneic hematopoietic cell transplantation (allo-HCT) but subsequently die of relapse driven by leukemia cells resistant to elimination by allogeneic T cells based on decreased major histocompatibility complex II (MHC-II) expression and apoptosis resistance. Here we demonstrate that mouse-double-minute-2 (MDM2) inhibition can counteract immune evasion of AML. MDM2 inhibition induced MHC class I and II expression in murine and human AML cells. Using xenografts of human AML and syngeneic mouse models of leukemia, we show that MDM2 inhibition enhanced cytotoxicity against leukemia cells and improved survival. MDM2 inhibition also led to increases in tumor necrosis factor-related apoptosis-inducing ligand receptor-1 and -2 (TRAIL-R1/2) on leukemia cells and higher frequencies of CD8+CD27lowPD-1lowTIM-3low T cells, with features of cytotoxicity (perforin+CD107a+TRAIL+) and longevity (bcl-2+IL-7R+). CD8+ T cells isolated from leukemia-bearing MDM2 inhibitor-treated allo-HCT recipients exhibited higher glycolytic activity and enrichment for nucleotides and their precursors compared with vehicle control subjects. T cells isolated from MDM2 inhibitor-treated AML-bearing mice eradicated leukemia in secondary AML-bearing recipients. Mechanistically, the MDM2 inhibitor-mediated effects were p53-dependent because p53 knockdown abolished TRAIL-R1/2 and MHC-II upregulation, whereas p53 binding to TRAILR1/2 promotors increased upon MDM2 inhibition. The observations in the mouse models were complemented by data from human individuals. Patient-derived AML cells exhibited increased TRAIL-R1/2 and MHC-II expression on MDM2 inhibition. In summary, we identified a targetable vulnerability of AML cells to allogeneic T-cell-mediated cytotoxicity through the restoration of p53-dependent TRAIL-R1/2 and MHC-II production via MDM2 inhibition.
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Affiliation(s)
- Jenny N H G Ho
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dominik Schmidt
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Theresa Lowinus
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Jeongmin Ryoo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Elaine-Pashupati Dopfer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | | | - Sara Costa-Pereira
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Cristina Toffalori
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Viktor Fetsch
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tobias Wertheimer
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Marie-Claire Rittmann
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Lukas M Braun
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marie Follo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Christelle Briere
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Janaki Manoja Vinnakota
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marlene Langenbach
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Felicitas Koppers
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Helena Engel
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tamina Rückert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Samuel Holzmayer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Anna L Illert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Federica Magon
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Julian Staniek
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
| | - Cornelius Miething
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Justus Duyster
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | | | - Melanie Boerries
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joerg M Buescher
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bruce R Blazar
- Division of Blood & Marrow Transplant and Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, MN; and
| | - Petya Apostolova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Erika L Pearce
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Robert Zeiser
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
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11
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Schuster EM, Epple MW, Glaser KM, Mihlan M, Lucht K, Zimmermann JA, Bremser A, Polyzou A, Obier N, Cabezas-Wallscheid N, Trompouki E, Ballabio A, Vogel J, Buescher JM, Westermann AJ, Rambold AS. TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages. Nat Metab 2022; 4:856-866. [PMID: 35864246 PMCID: PMC9314259 DOI: 10.1038/s42255-022-00605-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/13/2022] [Indexed: 01/04/2023]
Abstract
Successful elimination of bacteria in phagocytes occurs in the phago-lysosomal system, but also depends on mitochondrial pathways. Yet, how these two organelle systems communicate is largely unknown. Here we identify the lysosomal biogenesis factor transcription factor EB (TFEB) as regulator for phago-lysosome-mitochondria crosstalk in macrophages. By combining cellular imaging and metabolic profiling, we find that TFEB activation, in response to bacterial stimuli, promotes the transcription of aconitate decarboxylase (Acod1, Irg1) and synthesis of its product itaconate, a mitochondrial metabolite with antimicrobial activity. Activation of the TFEB-Irg1-itaconate signalling axis reduces the survival of the intravacuolar pathogen Salmonella enterica serovar Typhimurium. TFEB-driven itaconate is subsequently transferred via the Irg1-Rab32-BLOC3 system into the Salmonella-containing vacuole, thereby exposing the pathogen to elevated itaconate levels. By activating itaconate production, TFEB selectively restricts proliferating Salmonella, a bacterial subpopulation that normally escapes macrophage control, which contrasts TFEB's role in autophagy-mediated pathogen degradation. Together, our data define a TFEB-driven metabolic pathway between phago-lysosomes and mitochondria that restrains Salmonella Typhimurium burden in macrophages in vitro and in vivo.
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Affiliation(s)
- Ev-Marie Schuster
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maximilian W Epple
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Katharina M Glaser
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Michael Mihlan
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Kerstin Lucht
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Julia A Zimmermann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Center of Chronic Immunodeficiency, Medical Center University of Freiburg, Freiburg, Germany
| | - Anna Bremser
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Aikaterini Polyzou
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nadine Obier
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nina Cabezas-Wallscheid
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Eirini Trompouki
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Medical Genetics Unit, Department of Medical and Translational Science and SSM School for Advanced Studies, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research (HZI), University of Würzburg, Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research (HZI), University of Würzburg, Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Angelika S Rambold
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Center of Chronic Immunodeficiency, Medical Center University of Freiburg, Freiburg, Germany.
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12
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Schönberger K, Mitterer M, Buescher JM, Cabezas-Wallscheid N. Targeted LC-MS/MS-based metabolomics and lipidomics on limited hematopoietic stem cell numbers. STAR Protoc 2022; 3:101408. [PMID: 35620073 PMCID: PMC9127697 DOI: 10.1016/j.xpro.2022.101408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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13
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Abstract
Preprocessing of liquid chromatography-mass spectrometry (LC-MS) raw data facilitates downstream statistical and biological data analyses. In the case of targeted LC-MS data, consistent recognition of chromatographic peaks is a main challenge, in particular, for low abundant signals. Fully automatic preprocessing is faster than manual peak review and does not depend on the individual operator. Here, we present the R package automRm for fully automatic preprocessing of LC-MS data recorded in MRM mode. Using machine learning (ML) for detection of chromatographic peaks and quality control of reported results enables the automatic recognition of complex patterns in raw data. In addition, this approach renders automRm generally applicable to a wide range of analytical methods including hydrophilic interaction liquid chromatography (HILIC), which is known for sample-to-sample variations in peak shape and retention time. We demonstrate the impact of the choice of training data set, of the applied ML algorithm, and of individual peak characteristics on automRm's ability to correctly report chromatographic peaks. Next, we show that automRm can replicate results obtained by manual peak review on published data. Moreover, automRm outperforms alternative software solutions regarding the variation in peak integration among replicate measurements and the number of correctly reported peaks when applied to a HILIC-MS data set. The R package is freely available from gitlab (https://gitlab.gwdg.de/joerg.buescher/automrm).
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Affiliation(s)
- Daniel Eilertz
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Michael Mitterer
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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14
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Schönberger K, Obier N, Romero-Mulero MC, Cauchy P, Mess J, Pavlovich PV, Zhang YW, Mitterer M, Rettkowski J, Lalioti ME, Jäcklein K, Curtis JD, Féret B, Sommerkamp P, Morganti C, Ito K, Ghyselinck NB, Trompouki E, Buescher JM, Pearce EL, Cabezas-Wallscheid N. Multilayer omics analysis reveals a non-classical retinoic acid signaling axis that regulates hematopoietic stem cell identity. Cell Stem Cell 2022; 29:131-148.e10. [PMID: 34706256 PMCID: PMC9093043 DOI: 10.1016/j.stem.2021.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/05/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
Hematopoietic stem cells (HSCs) rely on complex regulatory networks to preserve stemness. Due to the scarcity of HSCs, technical challenges have limited our insights into the interplay between metabolites, transcription, and the epigenome. In this study, we generated low-input metabolomics, transcriptomics, chromatin accessibility, and chromatin immunoprecipitation data, revealing distinct metabolic hubs that are enriched in HSCs and their downstream multipotent progenitors. Mechanistically, we uncover a non-classical retinoic acid (RA) signaling axis that regulates HSC function. We show that HSCs rely on Cyp26b1, an enzyme conventionally considered to limit RA effects in the cell. In contrast to the traditional view, we demonstrate that Cyp26b1 is indispensable for production of the active metabolite 4-oxo-RA. Further, RA receptor beta (Rarb) is required for complete transmission of 4-oxo-RA-mediated signaling to maintain stem cells. Our findings emphasize that a single metabolite controls stem cell fate by instructing epigenetic and transcriptional attributes.
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Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Julian Mess
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany
| | - Polina V Pavlovich
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Yu Wei Zhang
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jasmin Rettkowski
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria-Eleni Lalioti
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Karin Jäcklein
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Betty Féret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Pia Sommerkamp
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Norbert B Ghyselinck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany.
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15
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Mossad O, Nent E, Woltemate S, Folschweiller S, Buescher JM, Schnepf D, Erny D, Staeheli P, Bartos M, Szalay A, Stecher B, Vital M, Sauer JF, Lämmermann T, Prinz M, Blank T. Microbiota-dependent increase in δ-valerobetaine alters neuronal function and is responsible for age-related cognitive decline. Nat Aging 2021; 1:1127-1136. [PMID: 37117525 DOI: 10.1038/s43587-021-00141-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/25/2021] [Indexed: 04/30/2023]
Abstract
Understanding the physiological origins of age-related cognitive decline is of critical importance given the rising age of the world's population1. Previous work in animal models has established a strong link between cognitive performance and the microbiota2-5, and it is known that the microbiome undergoes profound remodeling in older adults6. Despite growing evidence for the association between age-related cognitive decline and changes in the gut microbiome, the mechanisms underlying such interactions between the brain and the gut are poorly understood. Here, using fecal microbiota transplantation (FMT), we demonstrate that age-related remodeling of the gut microbiota leads to decline in cognitive function in mice and that this impairment can be rescued by transplantation of microbiota from young animals. Moreover, using a metabolomic approach, we found elevated concentrations of δ-valerobetaine, a gut microbiota-derived metabolite, in the blood and brain of aged mice and older adults. We then demonstrated that δ-valerobetaine is deleterious to learning and memory processes in mice. At the neuronal level, we showed that δ-valerobetaine modulates inhibitory synaptic transmission and neuronal network activity. Finally, we identified specific bacterial taxa that significantly correlate with δ-valerobetaine levels in the brain. Based on our findings, we propose that δ-valerobetaine contributes to microbiota-driven brain aging and that the associated mechanisms represent a promising target for countering age-related cognitive decline.
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Affiliation(s)
- Omar Mossad
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Elisa Nent
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Shani Folschweiller
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Institute of Physiology I, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Daniel Schnepf
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Daniel Erny
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Staeheli
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marlene Bartos
- Institute of Physiology I, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Jonas F Sauer
- Institute of Physiology I, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Blank
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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16
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Puleston DJ, Baixauli F, Sanin DE, Edwards-Hicks J, Villa M, Kabat AM, Kamiński MM, Stanckzak M, Weiss HJ, Grzes KM, Piletic K, Field CS, Corrado M, Haessler F, Wang C, Musa Y, Schimmelpfennig L, Flachsmann L, Mittler G, Yosef N, Kuchroo VK, Buescher JM, Balabanov S, Pearce EJ, Green DR, Pearce EL. Polyamine metabolism is a central determinant of helper T cell lineage fidelity. Cell 2021; 184:4186-4202.e20. [PMID: 34216540 PMCID: PMC8358979 DOI: 10.1016/j.cell.2021.06.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/16/2021] [Accepted: 06/02/2021] [Indexed: 12/24/2022]
Abstract
Polyamine synthesis represents one of the most profound metabolic changes during T cell activation, but the biological implications of this are scarcely known. Here, we show that polyamine metabolism is a fundamental process governing the ability of CD4+ helper T cells (TH) to polarize into different functional fates. Deficiency in ornithine decarboxylase, a crucial enzyme for polyamine synthesis, results in a severe failure of CD4+ T cells to adopt correct subset specification, underscored by ectopic expression of multiple cytokines and lineage-defining transcription factors across TH cell subsets. Polyamines control TH differentiation by providing substrates for deoxyhypusine synthase, which synthesizes the amino acid hypusine, and mice in which T cells are deficient for hypusine develop severe intestinal inflammatory disease. Polyamine-hypusine deficiency caused widespread epigenetic remodeling driven by alterations in histone acetylation and a re-wired tricarboxylic acid (TCA) cycle. Thus, polyamine metabolism is critical for maintaining the epigenome to focus TH cell subset fidelity.
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Affiliation(s)
- Daniel J Puleston
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Francesc Baixauli
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David E Sanin
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joy Edwards-Hicks
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Matteo Villa
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Agnieszka M Kabat
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Marcin M Kamiński
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michal Stanckzak
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Hauke J Weiss
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Katarzyna M Grzes
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Klara Piletic
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Cameron S Field
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Mauro Corrado
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Fabian Haessler
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Chao Wang
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yaarub Musa
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Lea Flachsmann
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Stefan Balabanov
- Division of Haematology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Edward J Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA.
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17
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Kelly B, Carrizo GE, Edwards-Hicks J, Sanin DE, Stanczak MA, Priesnitz C, Flachsmann LJ, Curtis JD, Mittler G, Musa Y, Becker T, Buescher JM, Pearce EL. Sulfur sequestration promotes multicellularity during nutrient limitation. Nature 2021; 591:471-476. [PMID: 33627869 PMCID: PMC7969356 DOI: 10.1038/s41586-021-03270-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
The behaviour of Dictyostelium discoideum depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This biology makes D. discoideum an ideal model for investigating how fundamental metabolism commands cell differentiation and function. Here we show that reactive oxygen species-generated as a consequence of nutrient limitation-lead to the sequestration of cysteine in the antioxidant glutathione. This sequestration limits the use of the sulfur atom of cysteine in processes that contribute to mitochondrial metabolism and cellular proliferation, such as protein translation and the activity of enzymes that contain an iron-sulfur cluster. The regulated sequestration of sulfur maintains D. discoideum in a nonproliferating state that paves the way for multicellular development. This mechanism of signalling through reactive oxygen species highlights oxygen and sulfur as simple signalling molecules that dictate cell fate in an early eukaryote, with implications for responses to nutrient fluctuations in multicellular eukaryotes.
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Affiliation(s)
- Beth Kelly
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Gustavo E. Carrizo
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Joy Edwards-Hicks
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - David E. Sanin
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Michal A. Stanczak
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Chantal Priesnitz
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZMBZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lea J. Flachsmann
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Jonathan D. Curtis
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Gerhard Mittler
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Yaarub Musa
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Becker
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Joerg M. Buescher
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Erika L. Pearce
- grid.429509.30000 0004 0491 4256Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany ,grid.21107.350000 0001 2171 9311Present Address: The Bloomberg–Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD USA
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18
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Klein Geltink RI, Edwards-Hicks J, Apostolova P, O'Sullivan D, Sanin DE, Patterson AE, Puleston DJ, Ligthart NAM, Buescher JM, Grzes KM, Kabat AM, Stanczak M, Curtis JD, Hässler F, Uhl FM, Fabri M, Zeiser R, Pearce EJ, Pearce EL. Metabolic conditioning of CD8 + effector T cells for adoptive cell therapy. Nat Metab 2020; 2:703-716. [PMID: 32747793 PMCID: PMC10863625 DOI: 10.1038/s42255-020-0256-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 07/01/2020] [Indexed: 01/06/2023]
Abstract
CD8+ effector T (TE) cell proliferation and cytokine production depends on enhanced glucose metabolism. However, circulating T cells continuously adapt to glucose fluctuations caused by diet and inter-organ metabolite exchange. Here we show that transient glucose restriction (TGR) in activated CD8+ TE cells metabolically primes effector functions and enhances tumour clearance in mice. Tumour-specific TGR CD8+ TE cells co-cultured with tumour spheroids in replete conditions display enhanced effector molecule expression, and adoptive transfer of these cells in a murine lymphoma model leads to greater numbers of immunologically functional circulating donor cells and complete tumour clearance. Mechanistically, TE cells treated with TGR undergo metabolic remodelling that, after glucose re-exposure, supports enhanced glucose uptake, increased carbon allocation to the pentose phosphate pathway (PPP) and a cellular redox shift towards a more reduced state-all indicators of a more anabolic programme to support their enhanced functionality. Thus, metabolic conditioning could be used to promote efficiency of T-cell products for adoptive cellular therapy.
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Affiliation(s)
- Ramon I Klein Geltink
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Pathology and Laboratory Medicine, University of British Columbia / BC Children's Hospital Research Institute, Vancouver, British Colombia, Canada
| | - Joy Edwards-Hicks
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Petya Apostolova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - David O'Sullivan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - David E Sanin
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Daniel J Puleston
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nina A M Ligthart
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Katarzyna M Grzes
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Agnieszka M Kabat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Michal Stanczak
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fabian Hässler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Franziska M Uhl
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Mario Fabri
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Dermatology and Venereology, University of Cologne, Cologne, Germany
| | - Robert Zeiser
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Edward J Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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19
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Puleston DJ, Buck MD, Klein Geltink RI, Kyle RL, Caputa G, O'Sullivan D, Cameron AM, Castoldi A, Musa Y, Kabat AM, Zhang Y, Flachsmann LJ, Field CS, Patterson AE, Scherer S, Alfei F, Baixauli F, Austin SK, Kelly B, Matsushita M, Curtis JD, Grzes KM, Villa M, Corrado M, Sanin DE, Qiu J, Pällman N, Paz K, Maccari ME, Blazar BR, Mittler G, Buescher JM, Zehn D, Rospert S, Pearce EJ, Balabanov S, Pearce EL. Polyamines and eIF5A Hypusination Modulate Mitochondrial Respiration and Macrophage Activation. Cell Metab 2019; 30:352-363.e8. [PMID: 31130465 PMCID: PMC6688828 DOI: 10.1016/j.cmet.2019.05.003] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/05/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
How cells adapt metabolism to meet demands is an active area of interest across biology. Among a broad range of functions, the polyamine spermidine is needed to hypusinate the translation factor eukaryotic initiation factor 5A (eIF5A). We show here that hypusinated eIF5A (eIF5AH) promotes the efficient expression of a subset of mitochondrial proteins involved in the TCA cycle and oxidative phosphorylation (OXPHOS). Several of these proteins have mitochondrial targeting sequences (MTSs) that in part confer an increased dependency on eIF5AH. In macrophages, metabolic switching between OXPHOS and glycolysis supports divergent functional fates stimulated by activation signals. In these cells, hypusination of eIF5A appears to be dynamically regulated after activation. Using in vivo and in vitro models, we show that acute inhibition of this pathway blunts OXPHOS-dependent alternative activation, while leaving aerobic glycolysis-dependent classical activation intact. These results might have implications for therapeutically controlling macrophage activation by targeting the polyamine-eIF5A-hypusine axis.
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Affiliation(s)
- Daniel J Puleston
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany; The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Michael D Buck
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Ryan L Kyle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - George Caputa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - David O'Sullivan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Alanna M Cameron
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Angela Castoldi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Yaarub Musa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Agnieszka M Kabat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Ying Zhang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Lea J Flachsmann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Cameron S Field
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Annette E Patterson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Stefanie Scherer
- Department of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Francesca Alfei
- Department of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Francesc Baixauli
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - S Kyle Austin
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Beth Kelly
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Mai Matsushita
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Katarzyna M Grzes
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Matteo Villa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Mauro Corrado
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - David E Sanin
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Jing Qiu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Nora Pällman
- Division of Haematology, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Katelyn Paz
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Maria Elena Maccari
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Center for Pediatrics, and Faculty of Medicine, Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Dietmar Zehn
- Department of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Edward J Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany; Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Stefan Balabanov
- Division of Haematology, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.
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20
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Klein Geltink RI, O'Sullivan D, Corrado M, Bremser A, Buck MD, Buescher JM, Firat E, Zhu X, Niedermann G, Caputa G, Kelly B, Warthorst U, Rensing-Ehl A, Kyle RL, Vandersarren L, Curtis JD, Patterson AE, Lawless S, Grzes K, Qiu J, Sanin DE, Kretz O, Huber TB, Janssens S, Lambrecht BN, Rambold AS, Pearce EJ, Pearce EL. Mitochondrial Priming by CD28. Cell 2017; 171:385-397.e11. [PMID: 28919076 DOI: 10.1016/j.cell.2017.08.018] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/31/2017] [Accepted: 08/11/2017] [Indexed: 10/18/2022]
Abstract
T cell receptor (TCR) signaling without CD28 can elicit primary effector T cells, but memory T cells generated during this process are anergic, failing to respond to secondary antigen exposure. We show that, upon T cell activation, CD28 transiently promotes expression of carnitine palmitoyltransferase 1a (Cpt1a), an enzyme that facilitates mitochondrial fatty acid oxidation (FAO), before the first cell division, coinciding with mitochondrial elongation and enhanced spare respiratory capacity (SRC). microRNA-33 (miR33), a target of thioredoxin-interacting protein (TXNIP), attenuates Cpt1a expression in the absence of CD28, resulting in cells that thereafter are metabolically compromised during reactivation or periods of increased bioenergetic demand. Early CD28-dependent mitochondrial engagement is needed for T cells to remodel cristae, develop SRC, and rapidly produce cytokines upon restimulation-cardinal features of protective memory T cells. Our data show that initial CD28 signals during T cell activation prime mitochondria with latent metabolic capacity that is essential for future T cell responses.
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Affiliation(s)
- Ramon I Klein Geltink
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David O'Sullivan
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Mauro Corrado
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Anna Bremser
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, 79106 Freiburg, Germany; Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Michael D Buck
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Elke Firat
- Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Xuekai Zhu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), Shanghai Tech University, 201210 Shanghai, People's Republic of China
| | - Gabriele Niedermann
- Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - George Caputa
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Beth Kelly
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ursula Warthorst
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Anne Rensing-Ehl
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Ryan L Kyle
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Lana Vandersarren
- Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Internal Medicine, Ghent University, 9000 Ghent, Belgium
| | - Jonathan D Curtis
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Annette E Patterson
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Simon Lawless
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Katarzyna Grzes
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jing Qiu
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - David E Sanin
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Oliver Kretz
- Department of Neuroanatomy, University of Freiburg, 79104 Freiburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; BIOSS Center for Biological Signaling Studies and Center for Systems Biology (ZBSA), Albert-Ludwigs-University, 79104 Freiburg, Germany
| | - Sophie Janssens
- Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Internal Medicine, Ghent University, 9000 Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Internal Medicine, Ghent University, 9000 Ghent, Belgium
| | - Angelika S Rambold
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, 79106 Freiburg, Germany; Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Erika L Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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21
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Zambanini T, Hosseinpour Tehrani H, Geiser E, Merker D, Schleese S, Krabbe J, Buescher JM, Meurer G, Wierckx N, Blank LM. Efficient itaconic acid production from glycerol with Ustilago vetiveriae TZ1. Biotechnol Biofuels 2017; 10:131. [PMID: 28533815 PMCID: PMC5438567 DOI: 10.1186/s13068-017-0809-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/03/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND The family of Ustilaginaceae is known for their capability to naturally produce industrially valuable chemicals from different carbon sources. Recently, several Ustilaginaceae were reported to produce organic acids from glycerol, which is the main side stream in biodiesel production. RESULTS In this study, we present Ustilago vetiveriae as new production organism for itaconate synthesis from glycerol. In a screening of 126 Ustilaginaceae, this organism reached one of the highest titers for itaconate combined with a high-glycerol uptake rate. By adaptive laboratory evolution, the production characteristics of this strain could be improved. Further medium optimization with the best single colony, U. vetiveriae TZ1, in 24-deep well plates resulted in a maximal itaconate titer of 34.7 ± 2.5 g L-1 produced at a rate of 0.09 ± 0.01 g L-1 h-1 from 196 g L-1 glycerol. Simultaneously, this strain produced 46.2 ± 1.4 g L-1 malate at a rate of 0.12 ± 0.00 g L-1 h-1. Due to product inhibition, the itaconate titer in NaOH-titrated bioreactor cultivations was lower (24 g L-1). Notably, an acidic pH value of 5.5 resulted in decreased itaconate production, however, completely abolishing malate production. Overexpression of ria1 or mtt1, encoding a transcriptional regulator and mitochondrial transporter, respectively, from the itaconate cluster of U. maydis resulted in a 2.0-fold (ria1) and 1.5-fold (mtt1) higher itaconate titer in comparison to the wild-type strain, simultaneously reducing malate production by 75 and 41%, respectively. CONCLUSIONS The observed production properties of U. vetiveriae TZ1 make this strain a promising candidate for microbial itaconate production. The outcome of the overexpression experiments, which resulted in reduced malate production in favor of an increased itaconate titer, clearly strengthens its potential for industrial itaconate production from glycerol as major side stream of biodiesel production.
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Affiliation(s)
- Thiemo Zambanini
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Hamed Hosseinpour Tehrani
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Elena Geiser
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Dorothee Merker
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sarah Schleese
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Judith Krabbe
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | | | - Guido Meurer
- BRAIN AG, Darmstädter Straße 34, 64673 Zwingenberg, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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22
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Zambanini T, Hosseinpour Tehrani H, Geiser E, Sonntag CK, Buescher JM, Meurer G, Wierckx N, Blank LM. Metabolic engineering of Ustilago trichophora TZ1 for improved malic acid production. Metab Eng Commun 2017; 4:12-21. [PMID: 29142828 PMCID: PMC5678829 DOI: 10.1016/j.meteno.2017.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/22/2016] [Accepted: 01/16/2017] [Indexed: 12/30/2022] Open
Abstract
Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species. Here we investigate and adapt existing molecular tools from U. maydis for use in U. trichophora. Selection markers from U. maydis that confer carboxin, hygromycin, nourseothricin, and phleomycin resistance are applicable in U. trichophora. A plasmid was constructed containing the ip-locus of U. trichophora RK089, resulting in site-specific integration into the genome. Using this plasmid, overexpression of pyruvate carboxylase, two malate dehydrogenases (mdh1, mdh2), and two malate transporters (ssu1, ssu2) was possible in U. trichophora TZ1 under control of the strong Petef promoter. Overexpression of mdh1, mdh2, ssu1, and ssu2 increased the product (malate) to substrate (glycerol) yield by up to 54% in shake flasks reaching a titer of up to 120 g L−1. In bioreactor cultivations of U. trichophora TZ1 Petefssu2 and U. trichophora TZ1 Petefmdh2 a drastically lowered biomass formation and glycerol uptake rate resulted in 29% (Ssu1) and 38% (Mdh2) higher specific production rates and 38% (Ssu1) and 46% (Mdh2) increased yields compared to the reference strain U. trichophora TZ1. Investigation of the product spectrum resulted in an 87% closed carbon balance with 134 g L−1 malate and biomass (73 g L−1), succinate (20 g L−1), CO2 (17 g L−1), and α-ketoglutarate (8 g L−1) as main by-products. These results open up a wide range of possibilities for further optimization, especially combinatorial metabolic engineering to increase the flux from pyruvate to malic acid and to reduce by-product formation. Metabolic engineering tools established for U. trichophora Potentially carbon neutral process through CO2 co-metabolism Optimized malic acid production from glycerol by overexpression of rTCA cycle Specific production rate and yield increased up to 38% and 46%, respectively
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Affiliation(s)
- Thiemo Zambanini
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Hamed Hosseinpour Tehrani
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Elena Geiser
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Christiane K Sonntag
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Joerg M Buescher
- BRAIN AG, Darmstädter Straße 34-36, D-64673 Zwingenberg, Germany.,MPI Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Guido Meurer
- BRAIN AG, Darmstädter Straße 34-36, D-64673 Zwingenberg, Germany
| | - Nick Wierckx
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Lars M Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
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23
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Zambanini T, Kleineberg W, Sarikaya E, Buescher JM, Meurer G, Wierckx N, Blank LM. Enhanced malic acid production from glycerol with high-cell density Ustilago trichophora TZ1 cultivations. Biotechnol Biofuels 2016; 9:135. [PMID: 27375775 PMCID: PMC4930609 DOI: 10.1186/s13068-016-0553-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/23/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND In order to establish a cost-efficient biodiesel biorefinery, valorization of its main by-product, crude glycerol, is imperative. Recently, Ustilago trichophora TZ1 was found to efficiently produce malic acid from glycerol. By adaptive laboratory evolution and medium optimization, titer and rate could be improved significantly. RESULTS Here we report on the investigation of this strain in fed-batch bioreactors. With pH controlled at 6.5 (automatic NaOH addition), a titer of 142 ± 1 g L(-1) produced at an overall rate of 0.54 ± 0.00 g L(-1) h(-1) was reached by optimizing the initial concentrations of ammonium and glycerol. Combining the potential of bioreactors and CaCO3 as buffer system, we were able to increase the overall production rate to 0.74 ± 0.06 g L(-1) h(-1) with a maximum production rate of 1.94 ± 0.32 g L(-1) reaching a titer of 195 ± 15 g L(-1). The initial purification strategy resulted in 90 % pure calcium malate as solid component. Notably, the fermentation is not influenced by an increased temperature of up to 37 °C, which reduces the energy required for cooling. However, direct acid production is not favored as at a lowered pH value of pH 4.5 the malic acid titer decreased to only 9 ± 1 g L(-1). When using crude glycerol as substrate, only the product to substrate yield is decreased. The results are discussed in the context of valorizing glycerol with Ustilaginaceae. CONCLUSIONS Combining these results reveals the potential of U. trichophora TZ1 to become an industrially applicable production host for malic acid from biodiesel-derived glycerol, thus making the overall biodiesel production process economically and ecologically more feasible.
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Affiliation(s)
- Thiemo Zambanini
- />Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Wiebke Kleineberg
- />Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Eda Sarikaya
- />Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | | | | | - Nick Wierckx
- />Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Lars M. Blank
- />Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
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24
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Zambanini T, Sarikaya E, Kleineberg W, Buescher JM, Meurer G, Wierckx N, Blank LM. Efficient malic acid production from glycerol with Ustilago trichophora TZ1. Biotechnol Biofuels 2016; 9:67. [PMID: 26989444 PMCID: PMC4794837 DOI: 10.1186/s13068-016-0483-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/10/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND The large surplus of crude glycerol, as main low-value waste stream in biodiesel production, has led to the investigation of new possibilities for the production of value-added chemicals from this feedstock. New and efficient (bio-) catalysts are needed that are able to convert glycerol to versatile chemical building blocks. This would contribute to further develop away from a mainly petroleum based, to a sustainable, bio-based industry. One promising group of discussed building block chemicals are dicarbonic acids. RESULTS Here, we report the efficient synthesis of malate from glycerol using Ustilago trichophora RK089, which was identified in a screening of 74 Ustilaginaceae. For economically feasible production that can compete with existing processes, a high productivity is required. By adaptive laboratory evolution, the growth and production rate were increased by 2.5- and 6.6-fold, respectively. Further medium optimization increased the final titer, yield, and overall production rate to 196 g L(-1), 0.82 gmal ggly (-1), and 0.39 g L(-1) h(-1), respectively. CONCLUSIONS This titer is the highest reported for microbial malate production, making U. trichophora TZ1 a promising microbial production host for malate from crude glycerol, especially since it is not genetically engineered. Since this production process starts from an industrial waste stream as substrate and yields an interesting platform chemical, which can be used to replace petro-chemicals, it greatly contributes to a sustainable bio-economy.
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Affiliation(s)
- Thiemo Zambanini
- />Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Eda Sarikaya
- />Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Wiebke Kleineberg
- />Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | | | | | - Nick Wierckx
- />Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M. Blank
- />Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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25
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Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks ODK, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Vander Heiden MG, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt SM. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr Opin Biotechnol 2015; 34:189-201. [PMID: 25731751 PMCID: PMC4552607 DOI: 10.1016/j.copbio.2015.02.003] [Citation(s) in RCA: 433] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 12/12/2022]
Abstract
Measuring intracellular metabolism has increasingly led to important insights in biomedical research. (13)C tracer analysis, although less information-rich than quantitative (13)C flux analysis that requires computational data integration, has been established as a time-efficient method to unravel relative pathway activities, qualitative changes in pathway contributions, and nutrient contributions. Here, we review selected key issues in interpreting (13)C metabolite labeling patterns, with the goal of drawing accurate conclusions from steady state and dynamic stable isotopic tracer experiments.
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Affiliation(s)
- Joerg M Buescher
- Vesalius Research Center, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Laszlo G Boros
- Department of Pediatrics, UCLA School of Medicine, Los Angeles Biomedical Research Institute at the Harbor-UCLA Medical Center and Sidmap, LLC, Los Angeles, CA, USA
| | - Shawn C Burgess
- Advanced Imaging Research Center-Division of Metabolic Mechanisms of Disease and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Henri Brunengraber
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Olivier Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Bart Ghesquiere
- Vesalius Research Center, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Russell G Jones
- Goodman Cancer Research Centre, Department of Physiology, McGill University, Montreal, QC, Canada
| | | | - Richard G Kibbey
- Internal Medicine, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Alec C Kimmelman
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason W Locasale
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Craig Malloy
- Advanced Imaging Research Center-Division of Metabolic Mechanisms of Disease and Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuelle J Meuillet
- L'Institut des Technologies Avancées en Sciences du Vivant (ITAV), Toulouse Cedex 1, France; The University of Arizona Cancer Center, and Department of Nutritional Sciences, The University of Arizona, Tucson, AZ, USA
| | - Joshua Munger
- Department of Biochemistry, University of Rochester Medical Center, Rochester, NY, USA; Department of Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Markus Ralser
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK; Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, UK
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julie St-Pierre
- Goodman Cancer Research Centre, and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Daniel A Tennant
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sarah-Maria Fendt
- Vesalius Research Center, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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Abstract
MOTIVATION Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components. RESULT Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation. AVAILABILITY AND IMPLEMENTATION The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip.
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Affiliation(s)
- John T Sauls
- BRAIN Aktiengesellschaft, Microbial Production Technologies, Platform for Quantitative Biology and Sequencing, D-64673 Zwingenberg, Germany
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27
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Bar-Even A, Noor E, Flamholz A, Buescher JM, Milo R. Hydrophobicity and charge shape cellular metabolite concentrations. PLoS Comput Biol 2011; 7:e1002166. [PMID: 21998563 PMCID: PMC3188480 DOI: 10.1371/journal.pcbi.1002166] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 07/04/2011] [Indexed: 11/18/2022] Open
Abstract
What governs the concentrations of metabolites within living cells? Beyond specific metabolic and enzymatic considerations, are there global trends that affect their values? We hypothesize that the physico-chemical properties of metabolites considerably affect their in-vivo concentrations. The recently achieved experimental capability to measure the concentrations of many metabolites simultaneously has made the testing of this hypothesis possible. Here, we analyze such recently available data sets of metabolite concentrations within E. coli, S. cerevisiae, B. subtilis and human. Overall, these data sets encompass more than twenty conditions, each containing dozens (28-108) of simultaneously measured metabolites. We test for correlations with various physico-chemical properties and find that the number of charged atoms, non-polar surface area, lipophilicity and solubility consistently correlate with concentration. In most data sets, a change in one of these properties elicits a ~100 fold increase in metabolite concentrations. We find that the non-polar surface area and number of charged atoms account for almost half of the variation in concentrations in the most reliable and comprehensive data set. Analyzing specific groups of metabolites, such as amino-acids or phosphorylated nucleotides, reveals even a higher dependence of concentration on hydrophobicity. We suggest that these findings can be explained by evolutionary constraints imposed on metabolite concentrations and discuss possible selective pressures that can account for them. These include the reduction of solute leakage through the lipid membrane, avoidance of deleterious aggregates and reduction of non-specific hydrophobic binding. By highlighting the global constraints imposed on metabolic pathways, future research could shed light onto aspects of biochemical evolution and the chemical constraints that bound metabolic engineering efforts.
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Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Elad Noor
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Avi Flamholz
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Joerg M. Buescher
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ron Milo
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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28
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Kleijn RJ, Buescher JM, Le Chat L, Jules M, Aymerich S, Sauer U. Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis. J Biol Chem 2009; 285:1587-96. [PMID: 19917605 DOI: 10.1074/jbc.m109.061747] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Commonly glucose is considered to be the only preferred substrate in Bacillus subtilis whose presence represses utilization of other alternative substrates. Because recent data indicate that malate might be an exception, we quantify here the carbon source utilization hierarchy. Based on physiology and transcriptional data during co-utilization experiments with eight carbon substrates, we demonstrate that malate is a second preferred carbon source for B. subtilis, which is rapidly co-utilized with glucose and strongly represses the uptake of alternative substrates. From the different hierarchy and degree of catabolite repression exerted by glucose and malate, we conclude that both substrates might act through different molecular mechanisms. To obtain a quantitative and functional network view of how malate is (co)metabolized, we developed a novel approach to metabolic flux analysis that avoids error-prone, intuitive, and ad hoc decisions on (13)C rearrangements. In particular, we developed a rigorous approach for deriving reaction reversibilities by combining in vivo intracellular metabolite concentrations with a thermodynamic feasibility analysis. The thus-obtained analytical model of metabolism was then used for network-wide isotopologue balancing to estimate the intracellular fluxes. These (13)C-flux data revealed an extraordinarily high malate influx that is primarily catabolized via the gluconeogenic reactions and toward overflow metabolism. Furthermore, a considerable NADPH-producing malic enzyme flux is required to supply the biosynthetically required NADPH in the presence of malate. Co-utilization of glucose and malate resulted in a synergistic decrease of the respiratory tricarboxylic acid cycle flux.
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Affiliation(s)
- Roelco J Kleijn
- Institute of Molecular System Biology, ETH Zürich, CH-8093 Zürich, Switzerland
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29
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Buescher JM, Margaritis A. Microbial Biosynthesis of Polyglutamic Acid Biopolymer and Applications in the Biopharmaceutical, Biomedical and Food Industries. Crit Rev Biotechnol 2008; 27:1-19. [PMID: 17364686 DOI: 10.1080/07388550601166458] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This review article provides an updated critical literature review on the production and applications of Polyglutamic Acid (PGA). alpha-PGA is synthesized chemically, whereas gamma-PGA can be produced by a number of microbial species, most prominently various Bacilli. Great insight into the microbial formation of gamma-PGA has been gained thanks to the development of molecular biological techniques. Moreover, there is a great variety of applications for both isoforms of PGA, many of which have not been discovered until recently. These applications include: wastewater treatment, food products, drug delivery, medical adhesives, vaccines, PGA nanoparticles for on-site drug release in cancer chemotherapy, and tissue engineering.
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Affiliation(s)
- Joerg M Buescher
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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