1
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Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Lipidome Unsaturation Affects the Morphology and Proteome of the Drosophila Eye. J Proteome Res 2024; 23:1188-1199. [PMID: 38484338 PMCID: PMC11002927 DOI: 10.1021/acs.jproteome.3c00570] [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: 09/28/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/26/2024]
Abstract
Organisms respond to dietary and environmental challenges by altering the molecular composition of their glycerolipids and glycerophospholipids (GPLs), which may favorably adjust the physicochemical properties of lipid membranes. However, how lipidome changes affect the membrane proteome and, eventually, the physiology of specific organs is an open question. We addressed this issue in Drosophila melanogaster, which is not able to synthesize sterols and polyunsaturated fatty acids but can acquire them from food. We developed a series of semisynthetic foods to manipulate the length and unsaturation of fatty acid moieties in GPLs and singled out proteins whose abundance is specifically affected by membrane lipid unsaturation in the Drosophila eye. Unexpectedly, we identified a group of proteins that have muscle-related functions and increased their abundances under unsaturated eye lipidome conditions. In contrast, the abundance of two stress response proteins, Turandot A and Smg5, is decreased by lipid unsaturation. Our findings could guide the genetic dissection of homeostatic mechanisms that maintain visual function when the eye is exposed to environmental and dietary challenges.
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Affiliation(s)
- Mukesh Kumar
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Canan Has
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Khanh Lam-Kamath
- Department
of Biology, University of Massachusetts
Boston, Integrated Sciences Complex, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Sophie Ayciriex
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Deepshe Dewett
- Department
of Biology, University of Massachusetts
Boston, Integrated Sciences Complex, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Mhamed Bashir
- Department
of Biology, University of Massachusetts
Boston, Integrated Sciences Complex, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Clara Poupault
- Department
of Biology, University of Massachusetts
Boston, Integrated Sciences Complex, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Kai Schuhmann
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Henrik Thomas
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Oskar Knittelfelder
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Bharath Kumar Raghuraman
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Robert Ahrends
- Department
of Analytical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Jens Rister
- Department
of Biology, University of Massachusetts
Boston, Integrated Sciences Complex, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Andrej Shevchenko
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
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2
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Jumel T, Shevchenko A. Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics. J Proteome Res 2024; 23:684-691. [PMID: 38243904 PMCID: PMC10845134 DOI: 10.1021/acs.jproteome.3c00531] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
We present an instrument-independent benchmark procedure and software (LFQ_bout) for the validation and comparative evaluation of the performance of LC-MS/MS and data processing workflows in bottom-up proteomics. The procedure enables a back-to-back comparison of common and emerging workflows, e.g., diaPASEF or ScanningSWATH, and evaluates the impact of arbitrary and inadequately documented settings or black-box data processing algorithms. It enhances the overall performance and quantification accuracy by recognizing and reporting common quantification errors.
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Affiliation(s)
- Tobias Jumel
- Max Planck Institute of
Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of
Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
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3
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Schmeisser K, Kaptan D, Raghuraman BK, Shevchenko A, Rodenfels J, Penkov S, Kurzchalia TV. Mobilization of cholesterol induces the transition from quiescence to growth in Caenorhabditis elegans through steroid hormone and mTOR signaling. Commun Biol 2024; 7:121. [PMID: 38267699 PMCID: PMC10808130 DOI: 10.1038/s42003-024-05804-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Recovery from the quiescent developmental stage called dauer is an essential process in C. elegans and provides an excellent model to understand how metabolic transitions contribute to developmental plasticity. Here we show that cholesterol bound to the small secreted proteins SCL-12 or SCL-13 is sequestered in the gut lumen during the dauer state. Upon recovery from dauer, bound cholesterol undergoes endocytosis into lysosomes of intestinal cells, where SCL-12 and SCL-13 are degraded and cholesterol is released. Free cholesterol activates mTORC1 and is used for the production of dafachronic acids. This leads to promotion of protein synthesis and growth, and a metabolic switch at the transcriptional level. Thus, mobilization of sequestered cholesterol stores is the key event for transition from quiescence to growth, and cholesterol is the major signaling molecule in this process.
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Affiliation(s)
- Kathrin Schmeisser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Damla Kaptan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jonathan Rodenfels
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Physics of Life (PoL), Technical University Dresden, Dresden, Germany
| | - Sider Penkov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Faculty of Medicine, Technical University Dresden, Dresden, Germany
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4
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Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. Proteomics 2023:e2300330. [PMID: 37963819 DOI: 10.1002/pmic.202300330] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Drosophila melanogaster is a popular model organism to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies, aging, light-induced damage, or dietary deficiencies. Large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which led to the discovery of key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins, including the absolute (molar) quantities of 43 proteins in the eye of adult male Drosophila reared on standard laboratory food. This work provides a generic and expandable resource for further genetic, pharmacological, and dietary studies.
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Affiliation(s)
- Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Khanh Lam-Kamath
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Sophie Ayciriex
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Deepshe Dewett
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Mhamed Bashir
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Clara Poupault
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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5
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Abstract
Photoreceptor cells generate neuronal signals in response to capturing light. This process, called phototransduction, takes place in a highly specialized outer segment organelle. There are significant discrepancies in the reported amounts of many proteins supporting this process, particularly those of low abundance, which limits our understanding of their molecular organization and function. In this study, we used quantitative mass spectrometry to simultaneously determine the abundances of 20 key structural and functional proteins residing in mouse rod outer segments. We computed the absolute number of molecules of each protein residing within an individual outer segment and the molar ratio among all 20 proteins. The molar ratios of proteins comprising three well-characterized constitutive complexes in outer segments differed from the established subunit stoichiometries of these complexes by less than 7%, highlighting the exceptional precision of our quantification. Overall, this study resolves multiple existing discrepancies regarding the outer segment abundances of these proteins, thereby advancing our understanding of how the phototransduction pathway functions as a single, well-coordinated molecular ensemble.
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Affiliation(s)
- Nikolai P. Skiba
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Tylor R. Lewis
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - William J. Spencer
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Carson M. Castillo
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany 01307
| | - Vadim Y. Arshavsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
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6
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Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Lipidome unsaturation affects the morphology and proteome of the Drosophila eye. bioRxiv 2023:2023.05.07.539765. [PMID: 37214967 PMCID: PMC10197557 DOI: 10.1101/2023.05.07.539765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
While the proteome of an organism is largely determined by the genome, the lipidome is shaped by a poorly understood interplay of environmental factors and metabolic processes. To gain insights into the underlying mechanisms, we analyzed the impacts of dietary lipid manipulations on the ocular proteome of Drosophila melanogaster . We manipulated the lipidome with synthetic food media that differed in the supplementation of an equal amount of saturated or polyunsaturated triacylglycerols. This allowed us to generate flies whose eyes had a highly contrasting length and unsaturation of glycerophospholipids, the major lipid class of biological membranes, while the abundance of other membrane lipid classes remained unchanged. By bioinformatically comparing the resulting ocular proteomic trends and contrasting them with the impacts of vitamin A deficiency, we identified ocular proteins whose abundances are differentially affected by lipid saturation and unsaturation. For instance, we unexpectedly identified a group of proteins that have muscle-related functions and increase their abundances in the eye upon lipidome unsaturation but are unaffected by lipidome saturation. Moreover, we identified two differentially lipid-responsive proteins involved in stress responses, Turandot A and Smg5, whose abundances decrease with lipid unsaturation. Lastly, we discovered that the ocular lipid class composition is robust to dietary changes and propose that this may be a general homeostatic feature of the organization of eukaryotic tissues, while the length and unsaturation of fatty acid moieties is more variable to compensate environmental challenges. We anticipate that these insights into the molecular responses of the Drosophila eye proteome to specific lipid manipulations will guide the genetic dissection of the mechanisms that maintain visual function when the eye is exposed to dietary challenges.
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7
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Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. bioRxiv 2023:2023.03.04.531088. [PMID: 36945598 PMCID: PMC10028839 DOI: 10.1101/2023.03.04.531088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The Drosophila melanogaster eye is a popular model to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies. For instance, the Drosophila eye has been used to investigate the impacts of ageing and environmental stresses such as light-induced damage or dietary deficiencies. Moreover, large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which includes key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins he adult Drosophila melanogaster eye and provide a generic and expandable resource for further genetic, pharmacological, and dietary studies.
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8
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Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods 2023; 20:193-204. [PMID: 36543939 PMCID: PMC10263382 DOI: 10.1038/s41592-022-01710-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 05/24/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022]
Abstract
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
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Affiliation(s)
- Zhixu Ni
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Michele Wölk
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Lucila Aimo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Jorge Alvarez-Jarreta
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Robert Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Geremy C Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealthe-University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Dominik Kopczyinki
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Slenter
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Kutmon
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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9
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Skiba NP, Lewis TR, Spencer WJ, Castillo CM, Shevchenko A, Arshavsky VY. Absolute quantification of photoreceptor outer segment proteins. bioRxiv 2023:2023.01.19.524794. [PMID: 36711880 PMCID: PMC9882265 DOI: 10.1101/2023.01.19.524794] [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: 01/22/2023]
Abstract
Photoreceptor cells generate neuronal signals in response to capturing light. This process, called phototransduction, takes place in a highly specialized outer segment organelle. There are significant discrepancies in the reported amounts of many proteins supporting this process, particularly those of low abundance, which limits our understanding of their molecular organization and function. In this study, we used quantitative mass spectrometry to simultaneously measure the outer segment content of twenty key structural and functional proteins. We determined the molar ratio amongst all twenty proteins as well as the number of molecules of each protein residing within an outer segment. To assess the precision of this quantification, we took advantage of the fact that seven of these proteins exist within three constitutive complexes of well-established subunit stoichiometries. Remarkably, our measurements differed from these stoichiometries by less than 7%, highlighting the exceptional precision of our quantification. This allowed us to resolve the existing discrepancies regarding the outer segment abundances of these proteins, thereby advancing our understanding of how the phototransduction pathway functions as a single, well-coordinated molecular ensemble.
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10
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Trautenberg LC, Brankatschk M, Shevchenko A, Wigby S, Reinhardt K. Ecological lipidology. eLife 2022; 11:79288. [PMID: 36069772 PMCID: PMC9451535 DOI: 10.7554/elife.79288] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary lipids (DLs), particularly sterols and fatty acids, are precursors for endogenous lipids that, unusually for macronutrients, shape cellular and organismal function long after ingestion. These functions – cell membrane structure, intracellular signalling, and hormonal activity – vary with the identity of DLs, and scale up to influence health, survival, and reproductive fitness, thereby affecting evolutionary change. Our Ecological Lipidology approach integrates biochemical mechanisms and molecular cell biology into evolution and nutritional ecology. It exposes our need to understand environmental impacts on lipidomes, the lipid specificity of cell functions, and predicts the evolution of lipid-based diet choices. Broad interdisciplinary implications of Ecological Lipidology include food web alterations, species responses to environmental change, as well as sex differences and lifestyle impacts on human nutrition, and opportunities for DL-based therapies.
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Affiliation(s)
| | - Marko Brankatschk
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stuart Wigby
- Applied Zoology, Technische Universität Dresden, Dresden, Germany.,Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Klaus Reinhardt
- Applied Zoology, Technische Universität Dresden, Dresden, Germany
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11
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab 2022; 4:1086-1088. [PMID: 35934691 DOI: 10.1038/s42255-022-00628-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - John A Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Maria Fedorova
- Center for Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | | | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Todd W Mitchell
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Dominik Schwudke
- Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Candice Z Ulmer
- Office of Public Health Science, Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Robert Ahrends
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
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12
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Rudolph M, Wang Y, Simolka T, Huc-Claustre E, Dai L, Grotenbreg G, Besra GS, Shevchenko A, Shevchenko A, Zeissig S. Sortase A-Cleavable CD1d Identifies Sphingomyelins as Major Class of CD1d-Associated Lipids. Front Immunol 2022; 13:897873. [PMID: 35874748 PMCID: PMC9301999 DOI: 10.3389/fimmu.2022.897873] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
CD1d is an atypical MHC class I molecule which binds endogenous and exogenous lipids and can activate natural killer T (NKT) cells through the presentation of lipid antigens. CD1d surveys different cellular compartments including the secretory and the endolysosomal pathway and broadly binds lipids through its two hydrophobic pockets. Purification of the transmembrane protein CD1d for the analysis of bound lipids is technically challenging as the use of detergents releases CD1d-bound lipids. To address these challenges, we have developed a novel approach based on Sortase A-dependent enzymatic release of CD1d at the cell surface of live mammalian cells, which allows for single step release and affinity tagging of CD1d for shotgun lipidomics. Using this system, we demonstrate that CD1d carrying the Sortase A recognition motif shows unimpaired subcellular trafficking through the secretory and endolysosomal pathway and is able to load lipids in these compartments and present them to NKT cells. Comprehensive shotgun lipidomics demonstrated that the spectrum and abundance of CD1d-associated lipids is not representative of the total cellular lipidome but rather characterized by preferential binding to long chain sphingolipids and glycerophospholipids. As such, sphingomyelin species recently identified as critical negative regulators of NKT cell activation, represented the vast majority of endogenous CD1d-associated lipids. Moreover, we observed that inhibition of endolysosomal trafficking of CD1d surprisingly did not affect the spectrum of CD1d-bound lipids, suggesting that the majority of endogenous CD1d-associated lipids load onto CD1d in the secretory rather than the endolysosomal pathway. In conclusion, we present a novel system for the analysis of CD1d-bound lipids in mammalian cells and provide new insight into the spectrum of CD1d-associated lipids, with important functional implications for NKT cell activation.
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Affiliation(s)
- Maren Rudolph
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Yuting Wang
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Theresa Simolka
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Emilie Huc-Claustre
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Lingyun Dai
- Department of Geriatrics, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People’s Hospital), Shenzhen, China
| | | | | | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
- *Correspondence: Sebastian Zeissig,
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13
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Seth A, Landau M, Shevchenko A, Traikov S, Schultz A, Elsabbagh S, Schultz JE. Distinct glycerophospholipids potentiate Gsα-activated adenylyl cyclase activity. Cell Signal 2022; 97:110396. [PMID: 35787445 DOI: 10.1016/j.cellsig.2022.110396] [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: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]
Abstract
Nine mammalian adenylyl cyclases (AC) are pseudoheterodimers with two hexahelical membrane domains, which are isoform-specifically conserved. Previously we proposed that these membrane domains are orphan receptors (https://doi.org/10.7554/eLife.13098; https://doi.org/10.1016/j.cellsig.2020.109538). Lipids extracted from fetal bovine serum at pH 1 inhibited several mAC activities. Guided by a lipidomic analysis we tested glycerophospholipids as potential ligands. Contrary to expectations we surprisingly discovered that 1-stearoyl-2-docosahexaenoyl-phosphatidic acid (SDPA) potentiated Gsα-activated activity of human AC isoform 3 seven-fold. The specificity of fatty acyl esters at glycerol positions 1 and 2 was rather stringent. 1-Stearoyl-2-docosahexaenoyl-phosphatidylserine and 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine significantly potentiated several Gsα-activated mAC isoforms to different extents. SDPA appears not interact with forskolin activation of AC isoform 3. SDPA enhanced Gsα-activated AC activities in membranes from mouse brain cortex. The action of SDPA was reversible. Unexpectedly, SDPA did not affect cAMP generation in HEK293 cells stimulated by isoproterenol, PGE2 and adenosine, virtually excluding a role as an extracellular ligand and, instead, suggesting an intracellular role. In summary, we discovered a new dimension of intracellular AC regulation by chemically defined glycerophospholipids.
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Affiliation(s)
- Anubha Seth
- Max-Planck-Institut für Biologie, Tübingen, Germany
| | - Marius Landau
- Pharmazeutisches Institut der Universität Tübingen, Tübingen, Germany
| | - Andrej Shevchenko
- Max-Planck-Institut für molekulare Zellbiologie und Genetik, Dresden, Germany
| | - Sofia Traikov
- Max-Planck-Institut für molekulare Zellbiologie und Genetik, Dresden, Germany
| | - Anita Schultz
- Pharmazeutisches Institut der Universität Tübingen, Tübingen, Germany
| | - Sherif Elsabbagh
- Pharmazeutisches Institut der Universität Tübingen, Tübingen, Germany
| | - Joachim E Schultz
- Pharmazeutisches Institut der Universität Tübingen, Tübingen, Germany.
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14
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Patsenker E, Thangapandi VR, Knittelfelder O, Palladini A, Hefti M, Beil-Wagner J, Rogler G, Buch T, Shevchenko A, Hampe J, Stickel F. The Pnpla3 Variant I148M Reveals Protective Effects Towards Hepatocellular Carcinoma in Mice via Restoration of Omega-3 Polyunsaturated Fats. J Nutr Biochem 2022; 108:109081. [PMID: 35691594 DOI: 10.1016/j.jnutbio.2022.109081] [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: 06/02/2021] [Revised: 02/02/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022]
Abstract
Alcohol consumption and high caloric diet are leading causes of progressive fatty liver disease. Genetic variant rs738409 in patatin-like phospholipase domain-containing protein 3 (PNPLA3 rs738409 C>G) has been repeatedly described as one of the major risk loci for alcoholic liver cirrhosis (ALC) and hepatocellular carcinoma (HCC) in humans, however, the mechanism behind this association is incompletely understood. We generated mice carrying the rs738409 variant (PNPLA3 I148M) in order to detect genotype-phenotype relationships in mice upon chow and alcohol-high fat/high sugar diet (EtOH/WD). We could clearly demonstrate that the presence of rs738409 per se is sufficient to induce spontaneous development of steatosis after one year in mice on a chow diet, whereas in the setting of unhealthy diet feeding, PNPLA3 I148M did not affect hepatic inflammation or fibrosis, but induced a striking lipid remodelling, microvesicular steatosis and protected from HCC formation. Using shot gun lipidomics, we detected a striking restoration of reduced long chain-polyunsaturated fatty acids (LC-PUFA)-containing TGs, docosapentaenoic acid (C22:5 n3) and omega-3-derived eicosanoids (5-HEPE, 20-HEPE, 19,20-EDP, 21-HDHA) in PNPLA3 I148M mice upon EtOH/WD. At the molecular level, PNPLA3 I148M modulated enzymes for fatty acid and TG transport and metabolism. These findings suggest (dietary) lipids as an important and independent driver of hepatic tumorigenesis. Genetic variant in PNPLA3 exerted protective effects in mice, conflicting with findings in humans. Species-related differences in physiology and metabolism should be taken into account when modelling unhealthy human lifestyle, as genetic mouse models may not always allow for translation of insight gained in humans.
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Affiliation(s)
- Eleonora Patsenker
- Department of Gastroenterology and Hepatology, University of Zurich, 8091 Zurich, Switzerland.
| | - Veera Raghavan Thangapandi
- Department of Gastroenterology and Hepatology, Universitätsklinikum Dresden, 01304 Dresden, Germany; Center for Regenerative Therapies, TU Dresden, 01307 Dresden, Germany
| | - Oskar Knittelfelder
- Max Plank Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Michaela Hefti
- Department of Gastroenterology and Hepatology, University of Zurich, 8091 Zurich, Switzerland
| | - Jane Beil-Wagner
- Institute of Laboratory Animal Science, University of Zurich, 8952 Schlieren, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University of Zurich, 8091 Zurich, Switzerland
| | - Thorsten Buch
- Institute of Laboratory Animal Science, University of Zurich, 8952 Schlieren, Switzerland
| | - Andrej Shevchenko
- Max Plank Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jochen Hampe
- Department of Gastroenterology and Hepatology, Universitätsklinikum Dresden, 01304 Dresden, Germany; Center for Regenerative Therapies, TU Dresden, 01307 Dresden, Germany
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University of Zurich, 8091 Zurich, Switzerland
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15
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Skeffington AW, Gentzel M, Ohara A, Milentyev A, Heintze C, Böttcher L, Görlich S, Shevchenko A, Poulsen N, Kröger N. Shedding light on silica biomineralization by comparative analysis of the silica-associated proteomes from three diatom species. Plant J 2022; 110:1700-1716. [PMID: 35403318 DOI: 10.1111/tpj.15765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/17/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species-specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis of the extracts identified 92 proteins that we name 'soluble silicome proteins' (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In-depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.
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Affiliation(s)
- Alastair W Skeffington
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Marc Gentzel
- Center for Cellular and Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Andre Ohara
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Alexander Milentyev
- Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Christoph Heintze
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Lorenz Böttcher
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Stefan Görlich
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Nils Kröger
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, TU Dresden, 01062, Dresden, Germany
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16
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Ott F, Körner C, Werner K, Gericke M, Liebscher I, Lobsien D, Radrezza S, Shevchenko A, Hofmann U, Kratzsch J, Gebhardt R, Berg T, Matz-Soja M. Hepatic Hedgehog Signaling Participates in the Crosstalk between Liver and Adipose Tissue in Mice by Regulating FGF21. Cells 2022; 11:cells11101680. [PMID: 35626717 PMCID: PMC9139566 DOI: 10.3390/cells11101680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
The Hedgehog signaling pathway regulates many processes during embryogenesis and the homeostasis of adult organs. Recent data suggest that central metabolic processes and signaling cascades in the liver are controlled by the Hedgehog pathway and that changes in hepatic Hedgehog activity also affect peripheral tissues, such as the reproductive organs in females. Here, we show that hepatocyte-specific deletion of the Hedgehog pathway is associated with the dramatic expansion of adipose tissue in mice, the overall phenotype of which does not correspond to the classical outcome of insulin resistance-associated diabetes type 2 obesity. Rather, we show that alterations in the Hedgehog signaling pathway in the liver lead to a metabolic phenotype that is resembling metabolically healthy obesity. Mechanistically, we identified an indirect influence on the hepatic secretion of the fibroblast growth factor 21, which is regulated by a series of signaling cascades that are directly transcriptionally linked to the activity of the Hedgehog transcription factor GLI1. The results of this study impressively show that the metabolic balance of the entire organism is maintained via the activity of morphogenic signaling pathways, such as the Hedgehog cascade. Obviously, several pathways are orchestrated to facilitate liver metabolic status to peripheral organs, such as adipose tissue.
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Affiliation(s)
- Fritzi Ott
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
- Division of Hepatology, Clinic and Polyclinic for Oncology, Gastroenterology, Hepatology, Infectious Diseases, and Pneumology, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Christiane Körner
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
- Division of Hepatology, Clinic and Polyclinic for Oncology, Gastroenterology, Hepatology, Infectious Diseases, and Pneumology, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Kim Werner
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
| | - Martin Gericke
- Institute for Anatomy, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany;
| | - Ines Liebscher
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
| | - Donald Lobsien
- Institute for Diagnostic and Interventional Radiology and Neuroradiology, Helios Clinic Erfurt, 99089 Erfurt, Germany;
- Institute for Neuroradiology, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Silvia Radrezza
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (S.R.); (A.S.)
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (S.R.); (A.S.)
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany;
| | - Jürgen Kratzsch
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany;
| | - Rolf Gebhardt
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
| | - Thomas Berg
- Division of Hepatology, Clinic and Polyclinic for Oncology, Gastroenterology, Hepatology, Infectious Diseases, and Pneumology, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Madlen Matz-Soja
- Rudolf-Schönheimer Institute for Biochemistry, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany; (F.O.); (C.K.); (K.W.); (I.L.); (R.G.)
- Division of Hepatology, Clinic and Polyclinic for Oncology, Gastroenterology, Hepatology, Infectious Diseases, and Pneumology, University Hospital Leipzig, 04103 Leipzig, Germany;
- Correspondence:
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17
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Rzagalinski I, Bogdanova A, Raghuraman BK, Geertsma ER, Hersemann L, Ziemssen T, Shevchenko A. FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards. J Proteome Res 2022; 21:1408-1417. [PMID: 35561006 PMCID: PMC9171895 DOI: 10.1021/acs.jproteome.2c00014] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Absolute (molar)
quantification of clinically relevant proteins
determines their reference values in liquid and solid biopsies. The
FastCAT (for Fast-track QconCAT) method employs multiple short (<50
kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated
quantotypic (Q)-peptides representing the quantified proteins. Each
CP also comprises scrambled sequences of reference (R)-peptides that
relate its abundance to a single protein standard (bovine serum albumin,
BSA). FastCAT not only alleviates the need to purify CP or use sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but
also improves the accuracy, precision, and dynamic range of the absolute
quantification by grouping Q-peptides according to the expected abundance
of the target proteins. We benchmarked FastCAT against the reference
method of MS Western and tested it in the direct molar quantification
of neurological markers in human cerebrospinal fluid at the low ng/mL
level.
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Affiliation(s)
- Ignacy Rzagalinski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Department of Neurology, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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18
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Shevchenko O, Sharapchenko S, Gichkun O, Velikiy D, Mozheiko N, Makarova L, Koloskova N, Shevchenko A. W276 Diagnostic value of microrna-27, microrna-101 and st2 for heart transplant acute rejection. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Raghuraman BK, Bogdanova A, Moon H, Rzagalinski I, Geertsma ER, Hersemann L, Shevchenko A. Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS). J Proteome Res 2021; 21:132-141. [PMID: 34807614 PMCID: PMC8749952 DOI: 10.1021/acs.jproteome.1c00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Indexed: 12/25/2022]
Abstract
![]()
By reporting the
molar abundance of proteins, absolute quantification
determines their stoichiometry in complexes, pathways, or networks.
Typically, absolute quantification relies either on protein-specific
isotopically labeled peptide standards or on a semiempirical calibration
against the average abundance of peptides chosen from arbitrarily
selected proteins. In contrast, a generic protein standard FUGIS (fully
unlabeled generic internal standard) requires no isotopic labeling,
chemical synthesis, or external calibration and is applicable to quantifying
proteins of any organismal origin. The median intensity of the peptide
peaks produced by the tryptic digestion of FUGIS is used as a single-point
calibrant to determine the molar abundance of any codigested protein.
Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed
other methods of untargeted proteome-wide absolute quantification.
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Affiliation(s)
- Bharath Kumar Raghuraman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ignacy Rzagalinski
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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20
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Girard V, Jollivet F, Knittelfelder O, Celle M, Arsac JN, Chatelain G, Van den Brink DM, Baron T, Shevchenko A, Kühnlein RP, Davoust N, Mollereau B. Abnormal accumulation of lipid droplets in neurons induces the conversion of alpha-Synuclein to proteolytic resistant forms in a Drosophila model of Parkinson's disease. PLoS Genet 2021; 17:e1009921. [PMID: 34788284 PMCID: PMC8635402 DOI: 10.1371/journal.pgen.1009921] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 12/01/2021] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by alpha-synuclein (αSyn) aggregation and associated with abnormalities in lipid metabolism. The accumulation of lipids in cytoplasmic organelles called lipid droplets (LDs) was observed in cellular models of PD. To investigate the pathophysiological consequences of interactions between αSyn and proteins that regulate the homeostasis of LDs, we used a transgenic Drosophila model of PD, in which human αSyn is specifically expressed in photoreceptor neurons. We first found that overexpression of the LD-coating proteins Perilipin 1 or 2 (dPlin1/2), which limit the access of lipases to LDs, markedly increased triacylglyclerol (TG) loaded LDs in neurons. However, dPlin-induced-LDs in neurons are independent of lipid anabolic (diacylglycerol acyltransferase 1/midway, fatty acid transport protein/dFatp) and catabolic (brummer TG lipase) enzymes, indicating that alternative mechanisms regulate neuronal LD homeostasis. Interestingly, the accumulation of LDs induced by various LD proteins (dPlin1, dPlin2, CG7900 or KlarsichtLD-BD) was synergistically amplified by the co-expression of αSyn, which localized to LDs in both Drosophila photoreceptor neurons and in human neuroblastoma cells. Finally, the accumulation of LDs increased the resistance of αSyn to proteolytic digestion, a characteristic of αSyn aggregation in human neurons. We propose that αSyn cooperates with LD proteins to inhibit lipolysis and that binding of αSyn to LDs contributes to the pathogenic misfolding and aggregation of αSyn in neurons. Parkinson’s disease (PD) is a neurodegenerative disease characterized by the neurotoxic aggregation of the alpha-synuclein (αSyn) protein. Cellular models of the disease are also associated with an abnormal fat storage in the form of lipid droplets (LDs). However, in which cells, neuron or glial cells, LDs accumulate in the organism remains unknown. To understand the relationship between αSyn and the accumulation of LDs, we used a Drosophila (fruit fly) model of PD. We found that, in the presence of a protein that coats LDs, perilipin, LDs accumulate in photoreceptor neurons of the fly. Interestingly, the accumulation of LDs induced by perilipin or other LD-coating proteins was enhanced in the presence of αSyn. Using human neuronal cell lines and the fly, we could show that LD-coating and αSyn proteins localize at the surface of LDs. Finally, we observed that the process of αSyn aggregation was enhanced in the presence of LDs by using a biochemical approach. We thus propose that the association of αSyn with LDs could contribute to αSyn aggregation and progression of the pathology.
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Affiliation(s)
- Victor Girard
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
| | - Florence Jollivet
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
| | - Oskar Knittelfelder
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marion Celle
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
| | - Jean-Noel Arsac
- Neurodegenerative Disease Unit; French Agency for Food, Environmental and Occupational Health & Safety Laboratory (Anses) of Lyon, University of Lyon, Lyon, France
| | - Gilles Chatelain
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
| | - Daan M. Van den Brink
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
- Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Thierry Baron
- Neurodegenerative Disease Unit; French Agency for Food, Environmental and Occupational Health & Safety Laboratory (Anses) of Lyon, University of Lyon, Lyon, France
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ronald P. Kühnlein
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Nathalie Davoust
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
- * E-mail: (ND); (BM)
| | - Bertrand Mollereau
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, University of Lyon, Lyon, France
- * E-mail: (ND); (BM)
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21
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Ecker J, Benedetti E, Kindt ASD, Höring M, Perl M, Machmüller AC, Sichler A, Plagge J, Wang Y, Zeissig S, Shevchenko A, Burkhardt R, Krumsiek J, Liebisch G, Janssen KP. The Colorectal Cancer Lipidome: Identification of a Robust Tumor-Specific Lipid Species Signature. Gastroenterology 2021; 161:910-923.e19. [PMID: 34000281 DOI: 10.1053/j.gastro.2021.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/12/2021] [Accepted: 05/06/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Lipidomic changes were causally linked to metabolic diseases, but the scenario for colorectal cancer (CRC) is less clear. We investigated the CRC lipidome for putative tumor-specific alterations through analysis of 3 independent retrospective patient cohorts from 2 clinical centers, to derive a clinically useful signature. DESIGN Quantitative comprehensive lipidomic analysis was performed using direct infusion electrospray ionization coupled with tandem mass spectrometry (ESI-MS/MS) and high-resolution mass spectrometry (HR-MS) on matched nondiseased mucosa and tumor tissue in a discovery cohort (n = 106). Results were validated in 2 independent cohorts (n = 28, and n = 20), associated with genomic and clinical data, and lipidomic data from a genetic mouse tumor model (Apc1638N). RESULTS Significant differences were found between tumor and normal tissue for glycero-, glycerophospho-, and sphingolipids in the discovery cohort. Comparison to the validation collectives unveiled that glycerophospholipids showed high interpatient variation and were strongly affected by preanalytical conditions, whereas glycero- and sphingolipids appeared more robust. Signatures of sphingomyelin and triacylglycerol (TG) species significantly differentiated cancerous from nondiseased tissue in both validation studies. Moreover, lipogenic enzymes were significantly up-regulated in CRC, and FASN gene expression was prognostically detrimental. The TG profile was significantly associated with postoperative disease-free survival and lymphovascular invasion, and was essentially conserved in murine digestive cancer, but not associated with microsatellite status, KRAS or BRAF mutations, or T-cell infiltration. CONCLUSION Analysis of the CRC lipidome revealed a robust TG-species signature with prognostic potential. A better understanding of the cancer-associated glycerolipid and sphingolipid metabolism may lead to novel therapeutic strategies.
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Affiliation(s)
- Josef Ecker
- ZIEL-Institute for Food & Health, Research Group Lipid Metabolism, Technical University of Munich, Freising, Germany.
| | - Elisa Benedetti
- Institute of Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Alida S D Kindt
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands; Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Markus Perl
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Andrea Christel Machmüller
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna Sichler
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Johannes Plagge
- ZIEL-Institute for Food & Health, Research Group Lipid Metabolism, Technical University of Munich, Freising, Germany
| | - Yuting Wang
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany; Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sebastian Zeissig
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany; Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Jan Krumsiek
- Institute of Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany.
| | - Klaus-Peter Janssen
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany.
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22
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Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. Nonalcoholic fatty liver disease stratification by liver lipidomics. J Lipid Res 2021; 62:100104. [PMID: 34384788 PMCID: PMC8488246 DOI: 10.1016/j.jlr.2021.100104] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including nonsteatotic patients with normal or excessive weight, patients diagnosed with NAFL (nonalcoholic fatty liver) or NASH (nonalcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and triacylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of nonsteatotic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.
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Affiliation(s)
- Olga Vvedenskaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Tim Daniel Rose
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Yuting Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany; Department of Membrane Biochemistry and Lipid Research, University Hospital Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Witigo von Schoenfels
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Christian-Albrechts-University Kiel, Kiel, Germany; Christian Albrechts University in Kiel Center of Clinical Anatomy Kiel, Schleswig-Holstein, Germany
| | - Justus Gross
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Josch Konstantin Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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23
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Thangapandi VR, Knittelfelder O, Brosch M, Patsenker E, Vvedenskaya O, Buch S, Hinz S, Hendricks A, Nati M, Herrmann A, Rekhade DR, Berg T, Matz-Soja M, Huse K, Klipp E, Pauling JK, Wodke JA, Miranda Ackerman J, Bonin MV, Aigner E, Datz C, von Schönfels W, Nehring S, Zeissig S, Röcken C, Dahl A, Chavakis T, Stickel F, Shevchenko A, Schafmayer C, Hampe J, Subramanian P. Loss of hepatic Mboat7 leads to liver fibrosis. Gut 2021; 70:940-950. [PMID: 32591434 PMCID: PMC8040158 DOI: 10.1136/gutjnl-2020-320853] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 02/07/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The rs641738C>T variant located near the membrane-bound O-acyltransferase domain containing 7 (MBOAT7) locus is associated with fibrosis in liver diseases, including non-alcoholic fatty liver disease (NAFLD), alcohol-related liver disease, hepatitis B and C. We aim to understand the mechanism by which the rs641738C>T variant contributes to pathogenesis of NAFLD. DESIGN Mice with hepatocyte-specific deletion of MBOAT7 (Mboat7Δhep) were generated and livers were characterised by histology, flow cytometry, qPCR, RNA sequencing and lipidomics. We analysed the association of rs641738C>T genotype with liver inflammation and fibrosis in 846 NAFLD patients and obtained genotype-specific liver lipidomes from 280 human biopsies. RESULTS Allelic imbalance analysis of heterozygous human liver samples pointed to lower expression of the MBOAT7 transcript on the rs641738C>T haplotype. Mboat7Δhep mice showed spontaneous steatosis characterised by increased hepatic cholesterol ester content after 10 weeks. After 6 weeks on a high fat, methionine-low, choline-deficient diet, mice developed increased hepatic fibrosis as measured by picrosirius staining (p<0.05), hydroxyproline content (p<0.05) and transcriptomics, while the inflammatory cell populations and inflammatory mediators were minimally affected. In a human biopsied NAFLD cohort, MBOAT7 rs641738C>T was associated with fibrosis (p=0.004) independent of the presence of histological inflammation. Liver lipidomes of Mboat7Δhep mice and human rs641738TT carriers with fibrosis showed increased total lysophosphatidylinositol levels. The altered lysophosphatidylinositol and phosphatidylinositol subspecies in MBOAT7Δhep livers and human rs641738TT carriers were similar. CONCLUSION Mboat7 deficiency in mice and human points to an inflammation-independent pathway of liver fibrosis that may be mediated by lipid signalling and a potentially targetable treatment option in NAFLD.
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Affiliation(s)
- Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Oskar Knittelfelder
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Eleonora Patsenker
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Olga Vvedenskaya
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Hinz
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Marina Nati
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
| | - Alexander Herrmann
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Devavrat Ravindra Rekhade
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Berg
- Division of Hepatology, Department of Oncology, Gastroenterology, Hepatology Pulmonology, and Infectious Diseases, University Hospital Leipzig, Leipzig, Sachsen, Germany
| | - Madlen Matz-Soja
- Division of Hepatology, Department of Oncology, Gastroenterology, Hepatology Pulmonology, and Infectious Diseases, University Hospital Leipzig, Leipzig, Sachsen, Germany
- Rudolf Schönheimer- Institute of Biochemistry, University of Leipzig Faculty of Medicine, Leipzig, Germany
| | - Klaus Huse
- Leibniz Institute for Age Research Fritz-Lipmann Institute, Jena, Thüringen, Germany
| | - Edda Klipp
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Josch K Pauling
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Bayern, Germany
| | - Judith Ah Wodke
- Department of Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Malte von Bonin
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- German Cancer Consortium, Heidelberg, Baden-Württemberg, Germany
| | - Elmar Aigner
- Department of Medicine, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private University of Salzburg, Obendorf, Austria
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Sophie Nehring
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Andreas Dahl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Triantafyllos Chavakis
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Sachsen, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplantation Surgery, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Pallavi Subramanian
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Sachsen, Germany
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24
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Bespalaya Y, Przhiboro A, Aksenova O, Berezina N, Gofarov M, Kondakov A, Kurashov E, Litvinchuk L, Sokolova S, Spitsyn V, Shevchenko A, Tsiplenkina I, Travina O, Tomilova A. Preliminary study of the benthic fauna in lakes of the Novaya Zemlya Archipelago and Vaigach Island (the Russian Arctic). Polar Biol 2021. [DOI: 10.1007/s00300-021-02817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Heier C, Knittelfelder O, Hofbauer HF, Mende W, Pörnbacher I, Schiller L, Schoiswohl G, Xie H, Grönke S, Shevchenko A, Kühnlein RP. Hormone-sensitive lipase couples intergenerational sterol metabolism to reproductive success. eLife 2021; 10:63252. [PMID: 33538247 PMCID: PMC7880688 DOI: 10.7554/elife.63252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 09/28/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Triacylglycerol (TG) and steryl ester (SE) lipid storage is a universal strategy to maintain organismal energy and membrane homeostasis. Cycles of building and mobilizing storage fat are fundamental in (re)distributing lipid substrates between tissues or to progress ontogenetic transitions. In this study, we show that Hormone-sensitive lipase (Hsl) specifically controls SE mobilization to initiate intergenerational sterol transfer in Drosophila melanogaster. Tissue-autonomous Hsl functions in the maternal fat body and germline coordinately prevent adult SE overstorage and maximize sterol allocation to embryos. While Hsl-deficiency is largely dispensable for normal development on sterol-rich diets, animals depend on adipocyte Hsl for optimal fecundity when dietary sterol becomes limiting. Notably, accumulation of SE but not of TG is a characteristic of Hsl-deficient cells across phyla including murine white adipocytes. In summary, we identified Hsl as an ancestral regulator of SE degradation, which improves intergenerational sterol transfer and reproductive success in flies.
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Affiliation(s)
- Christoph Heier
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Harald F Hofbauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Wolfgang Mende
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Ingrid Pörnbacher
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Laura Schiller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gabriele Schoiswohl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Hao Xie
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Sebastian Grönke
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ronald P Kühnlein
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Field of Excellence BioHealth - University of Graz, Graz, Austria.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Fu T, Knittelfelder O, Geffard O, Clément Y, Testet E, Elie N, Touboul D, Abbaci K, Shevchenko A, Lemoine J, Chaumot A, Salvador A, Degli-Esposti D, Ayciriex S. Shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in Gammarus fossarum lipid composition. iScience 2021; 24:102115. [PMID: 33615205 PMCID: PMC7881238 DOI: 10.1016/j.isci.2021.102115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/11/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 01/14/2023] Open
Abstract
Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the lipidome of these species is thus an essential step toward understanding the mechanism of toxicity induced by pollutants. Both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum were extensively examined herein. The baseline lipidome of gammarids of different sex and reproductive stages was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. A diverse and dynamic lipid composition in G. fossarum was uncovered, which deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies. Baseline lipidome profiling of G. fossarum of different sex and reproductive stages Spatial localization of lipids in gammarid tissue by mass spectrometry imaging SIMS imaging guided discovery of sulfate-based lipids in hepatopancreas epithelium Disclosure of a dynamic lipid composition in maturing female oocytes
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Affiliation(s)
- Tingting Fu
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625 Villeurbanne, France
| | - Yohann Clément
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Eric Testet
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Nicolas Elie
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Khedidja Abbaci
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625 Villeurbanne, France
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Jerome Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625 Villeurbanne, France
| | - Arnaud Salvador
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | | | - Sophie Ayciriex
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
- Corresponding author
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Nyman M, Kaivola M, Shevchenko A. All-optical modulation and detection using a gain medium in a pulse shaper. Opt Express 2020; 28:35869-35883. [PMID: 33379694 DOI: 10.1364/oe.408472] [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] [Received: 08/26/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
We demonstrate all-optical modulation and ultrafast detection using an on-resonance optical gain medium, combined with spectral splitting in a Fourier transform pulse shaper. Multiple spectral channels of one optical beam can be independently modulated in time by another beam, allowing high-rate modulation and multiplexing without requiring ultrafast response from the gain medium. For detection of sub-picosecond signals we demonstrate a method of ultrafast signal detection (temporal imaging with no spatial resolution) that utilizes the spatio-temporal tilt of an optical pulse in a pulse shaper. The proposed methods can find applications in optical information technology and ultrafast imaging.
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Hebbar S, Schuhmann K, Shevchenko A, Knust E. Hydroxylated sphingolipid biosynthesis regulates photoreceptor apical domain morphogenesis. J Cell Biol 2020; 219:211460. [PMID: 33048164 PMCID: PMC7557679 DOI: 10.1083/jcb.201911100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 08/07/2020] [Accepted: 09/08/2020] [Indexed: 01/04/2023] Open
Abstract
Apical domains of epithelial cells often undergo dramatic changes during morphogenesis to form specialized structures, such as microvilli. Here, we addressed the role of lipids during morphogenesis of the rhabdomere, the microvilli-based photosensitive organelle of Drosophila photoreceptor cells. Shotgun lipidomics analysis performed on mutant alleles of the polarity regulator crumbs, exhibiting varying rhabdomeric growth defects, revealed a correlation between increased abundance of hydroxylated sphingolipids and abnormal rhabdomeric growth. This could be attributed to an up-regulation of fatty acid hydroxylase transcription. Indeed, direct genetic perturbation of the hydroxylated sphingolipid metabolism modulated rhabdomere growth in a crumbs mutant background. One of the pathways targeted by sphingolipid metabolism turned out to be the secretory route of newly synthesized Rhodopsin, a major rhabdomeric protein. In particular, altered biosynthesis of hydroxylated sphingolipids impaired apical trafficking via Rab11, and thus apical membrane growth. The intersection of lipid metabolic pathways with apical domain growth provides a new facet to our understanding of apical growth during morphogenesis.
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Kaptan D, Penkov S, Zhang X, Gade VR, Raghuraman BK, Galli R, Sampaio JL, Haase R, Koch E, Shevchenko A, Zaburdaev V, Kurzchalia TV. Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation. Aging Cell 2020; 19:e13214. [PMID: 32898317 PMCID: PMC7576309 DOI: 10.1111/acel.13214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/02/2020] [Revised: 07/01/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
The dauer larva of Caenorhabditis elegans, destined to survive long periods of food scarcity and harsh environment, does not feed and has a very limited exchange of matter with the exterior. It was assumed that the survival time is determined by internal energy stores. Here, we show that ethanol can provide a potentially unlimited energy source for dauers by inducing a controlled metabolic shift that allows it to be metabolized into carbohydrates, amino acids, and lipids. Dauer larvae provided with ethanol survive much longer and have greater desiccation tolerance. On the cellular level, ethanol prevents the deterioration of mitochondria caused by energy depletion. By modeling the metabolism of dauers of wild‐type and mutant strains with and without ethanol, we suggest that the mitochondrial health and survival of an organism provided with an unlimited source of carbon depends on the balance between energy production and toxic product(s) of lipid metabolism.
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Affiliation(s)
- Damla Kaptan
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Sider Penkov
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden Dresden Germany
- Institute for Clinical Chemistry and Laboratory Medicine University Clinic and Medical FacultyTU Dresden Dresden Germany
| | - Xingyu Zhang
- Max Planck Institute for the Physics of Complex Systems Dresden Germany
- Friedrich‐Alexander‐University Erlangen‐Nuremberg Erlangen Germany
- Max‐Planck‐Zentrum für Physik und Medizin Erlangen Germany
| | - Vamshidhar R. Gade
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | | | - Roberta Galli
- Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring Faculty of Medicine Carl Gustav Carus TU Dresden Dresden Germany
| | - Júlio L. Sampaio
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Robert Haase
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Edmund Koch
- Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring Faculty of Medicine Carl Gustav Carus TU Dresden Dresden Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems Dresden Germany
- Friedrich‐Alexander‐University Erlangen‐Nuremberg Erlangen Germany
- Max‐Planck‐Zentrum für Physik und Medizin Erlangen Germany
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Trautenberg LC, Knittelfelder O, Hofmann C, Shevchenko A, Brankatschk M, Prince E. How to use the development of individual Drosophila larvae as a metabolic sensor. J Insect Physiol 2020; 126:104095. [PMID: 32783958 DOI: 10.1016/j.jinsphys.2020.104095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Metabolic research is a challenge because of the variety of data within experimental series and the difficulty of replicating results among scientific groups. The fruit fly, Drosophila melanogaster, is a cost-effective and reliable pioneer model to screen dietary variables for metabolic research. One of the main reasons for problems in this field are differences in food recipes, diet-associated microbial environments and the pharmacokinetic behavior of nutrients across the gut-blood barrier. To prevent such experimental shortcomings, a common strategy is to pool scores of subjects into one sample to create an average statement. However, this approach lacks information about the biological spread and may provoke misleading interpretations. We propose to use the developmental rate of individual Drosophila larvae as a metabolic sensor. To do so, we introduce here a 96-well plate-based assay, which allows screening for multiple variables including food quality, microbial load, and genetic differences. We demonstrate that on a diet that is rich in calories, pupation is sensitive to the variation of dietary lipid compounds and that genotypes considered as wild-types/controls produce different developmental profiles. Our platform is suited for later automation and represents a potent high-throughput screening tool for the pharmacology and food industry. If used systematically, our assay could become a powerful reference tool to compare the quality of used dietary configurations with published benchmark recipes.
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Affiliation(s)
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Carla Hofmann
- Biotechnology Center (BIOTEC) of the Technische Universitat Dresden (TUD), Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Marko Brankatschk
- Biotechnology Center (BIOTEC) of the Technische Universitat Dresden (TUD), Dresden, Germany.
| | - Elodie Prince
- Biotechnology Center (BIOTEC) of the Technische Universitat Dresden (TUD), Dresden, Germany.
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Raghuraman BK, Hebbar S, Kumar M, Moon H, Henry I, Knust E, Shevchenko A. Absolute Quantification of Proteins in the Eye of Drosophila melanogaster. Proteomics 2020; 20:e1900049. [PMID: 32663363 DOI: 10.1002/pmic.201900049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/24/2020] [Revised: 05/29/2020] [Indexed: 01/26/2023]
Abstract
Absolute (molar) quantification of proteins determines their molar ratios in complexes, networks, and metabolic pathways. MS Western workflow is employed to determine molar abundances of proteins potentially critical for morphogenesis and phototransduction (PT) in eyes of Drosophila melanogaster using a single chimeric 264 kDa protein standard that covers, in total, 197 peptides from 43 proteins. The majority of proteins are independently quantified with two to four proteotypic peptides with the coefficient of variation of less than 15%, better than 1000-fold dynamic range and sub-femtomole sensitivity. Here, the molar abundance of proteins of the PT machinery and of the rhabdomere, the photosensitive organelle, is determined in eyes of wild-type flies as well as in crumbs (crb) mutant eyes, which exhibit perturbed rhabdomere morphogenesis.
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Affiliation(s)
- Bharath Kumar Raghuraman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Sarita Hebbar
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany.,Centre for Systems Biology Dresden, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Ian Henry
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany.,Centre for Systems Biology Dresden, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Elisabeth Knust
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, 01307, Germany
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32
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Knittelfelder O, Prince E, Sales S, Fritzsche E, Wöhner T, Brankatschk M, Shevchenko A. Sterols as dietary markers for Drosophila melanogaster. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158683. [DOI: 10.1016/j.bbalip.2020.158683] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 11/16/2022]
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Finkelstein S, Gospe SM, Schuhmann K, Shevchenko A, Arshavsky VY, Lobanova ES. Phosphoinositide Profile of the Mouse Retina. Cells 2020; 9:cells9061417. [PMID: 32517352 PMCID: PMC7349851 DOI: 10.3390/cells9061417] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/24/2022] Open
Abstract
Phosphoinositides are known to play multiple roles in eukaryotic cells. Although dysregulation of phosphoinositide metabolism in the retina has been reported to cause visual dysfunction in animal models and human patients, our understanding of the phosphoinositide composition of the retina is limited. Here, we report a characterization of the phosphoinositide profile of the mouse retina and an analysis of the subcellular localization of major phosphorylated phosphoinositide forms in light-sensitive photoreceptor neurons. Using chromatography of deacylated phosphatidylinositol headgroups, we established PI(4,5)P2 and PI(4)P as two major phosphorylated phosphoinositides in the retina. Using high-resolution mass spectrometry, we revealed 18:0/20:4 and 16:0/20:4 as major fatty-acyl chains of retinal phosphoinositides. Finally, analysis of fluorescent phosphoinositide sensors in rod photoreceptors demonstrated distinct subcellular distribution patterns of major phosphoinositides. The PI(4,5)P2 reporter was enriched in the inner segments and synapses, but was barely detected in the light-sensitive outer segments. The PI(4)P reporter was mostly found in the outer and inner segments and the areas around nuclei, but to a lesser degree in the synaptic region. These findings provide support for future mechanistic studies defining the biological significance of major mono- (PI(4)P) and bisphosphate (PI(4,5)P2) phosphatidylinositols in photoreceptor biology and retinal health.
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Affiliation(s)
- Stella Finkelstein
- Department of Ophthalmology, Duke University, Durham, NC 27710, USA; (S.F.); (S.M.G.III); (V.Y.A.)
| | - Sidney M. Gospe
- Department of Ophthalmology, Duke University, Durham, NC 27710, USA; (S.F.); (S.M.G.III); (V.Y.A.)
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (K.S.); (A.S.)
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (K.S.); (A.S.)
| | - Vadim Y. Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC 27710, USA; (S.F.); (S.M.G.III); (V.Y.A.)
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Ekaterina S. Lobanova
- Department of Ophthalmology, University of Florida, Gainesville, FL 32610, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
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Omelchenko V, Letyagina E, Kurochkina Y, Akimova A, Shevchenko A, Korolev M. AB0017 CONSTANT GENETIC MARKER IL1B T-31С IS ASSOCIATED WITH ANAMNESIS OF BIOLOGICAL DRUGS TREATMENT IN RHEUMATOID ARTHRITIS. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.2404] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Rheumatoid arthritis (RA) is chronic progressive joint disease with erosions formation. Timely and effectiveness treatment is important due to quickly structural damage and progressive losing of active motion. Synthetic DMARDs didn’t have a sufficient effect. Using biological drugs seemed like a panacea, but according to investigations at least 30-40% RA-patients lost treatment efficiency. Biological drugs act through immune cascade, that’s why mutation in regulatory region of cytokine genes may partly determine treatment failure.Objectives:The objective of our study was to analyze the frequency ofIL1 T-31Csingle nucleotide polymorphism in patient with rheumatoid arthritis and its association with biological drugs prescribing.Methods:One hundred two Caucasian RA-patients (age – 56 yrs [45; 61]; DAS28 4.7 [3.8; 5.9]) were enrolled in our study. All of them had American College of Rheumatology (ACR)-defined RA (1987 classification criteria) and gave written inform consent. Single nucleotide polymorphismsIL1B T-31C(rs1143627),IL4 C-590T(rs2243250), IL10 C-592A (rs1800872),IL10 A-1082G(rs1800896) were determined by restriction fragment length polymorphism. Descriptive statistics, Chi-squared test were used for data analysis. Results are presented as median and 25th/75th percentiles (Me [25th percentile; 75th percentile]).Results:The most of SNPs analyzed had corresponded to the Hardy Weinberg equilibrium (HWE). The only exception was IL1B T-31C – the frequencies were differed statistically significant from HWE (p=0,03). Forty seven (46.1%) patients were treatment with biological drugs. Homozygotes IL1b -31CС were founded more frequently beside patients with biological treatment compare with other group (13 from 47 (27,7%) vs. 6 from 52 (11.5%), p=0,042). Other SNPs didn’t demonstrate any associations.Conclusion:Single nucleotide polymorphismIL1B T-31C(rs1143627) may be used for prognosis of basic anti-inflammatory therapy inefficiency and the needing for prescribing biological therapy.Disclosure of Interests:None declared
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Penkov S, Raghuraman BK, Erkut C, Oertel J, Galli R, Ackerman EJM, Vorkel D, Verbavatz JM, Koch E, Fahmy K, Shevchenko A, Kurzchalia TV. A metabolic switch regulates the transition between growth and diapause in C. elegans. BMC Biol 2020; 18:31. [PMID: 32188449 PMCID: PMC7081555 DOI: 10.1186/s12915-020-0760-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Metabolic activity alternates between high and low states during different stages of an organism's life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental conditions, as a model to study the global metabolic changes and underlying molecular mechanisms associated with growth to quiescence transition. RESULTS Here, we show that the metabolic switch involves the concerted activity of several regulatory pathways. Whereas the steroid hormone receptor DAF-12 controls dauer morphogenesis, the insulin pathway maintains low energy expenditure through DAF-16/FoxO, which also requires AAK-2/AMPKα. DAF-12 and AAK-2 separately promote a shift in the molar ratios between competing enzymes at two key branch points within the central carbon metabolic pathway diverting carbon atoms from the TCA cycle and directing them to gluconeogenesis. When both AAK-2 and DAF-12 are suppressed, the TCA cycle is active and the developmental arrest is bypassed. CONCLUSIONS The metabolic status of each developmental stage is defined by stoichiometric ratios within the constellation of metabolic enzymes driving metabolic flux and controls the transition between growth and quiescence.
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Affiliation(s)
- Sider Penkov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. .,Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany. .,Institute for Clinical Chemistry and Laboratory Medicine, University Clinic and Medical Faculty, TU Dresden, Dresden, Germany.
| | | | - Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Present address: German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Oertel
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Roberta Galli
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | | | - Daniela Vorkel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Institut Jacques Monod, Université de Paris/CNRS, Paris, France
| | - Edmund Koch
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Wang Y, Hinz S, Uckermann O, Hönscheid P, von Schönfels W, Burmeister G, Hendricks A, Ackerman JM, Baretton GB, Hampe J, Brosch M, Schafmayer C, Shevchenko A, Zeissig S. Shotgun lipidomics-based characterization of the landscape of lipid metabolism in colorectal cancer. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158579. [DOI: 10.1016/j.bbalip.2019.158579] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 11/20/2019] [Indexed: 01/18/2023]
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Shevchenko A, Kydin S, Svitlychnyy O, Korotun O, Zahumenna Y. [CONSTITUTIONAL BASES OF ENSURING THE HUMAN RIGHT TO HEALTH: COMPARATIVE LEGAL ASPECT]. Georgian Med News 2020:140-146. [PMID: 32383718] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The objective of the article is to identify common and distinctive features of the constitutional provision of human right to health in Ukraine, the Czech Republic and the Republic of Poland on the basis of a comparative and legal study. The main task is to summarize the experience of the Czech Republic and the Republic of Poland, and taking it into account - to determine the directions of improving the constitutional legislation of Ukraine in this area. It has been established that the constitutional provision of human right to health in Ukraine is contained both in the Basic Law and in a number of constitutional and legal acts, and the conducted analysis of the relevant norms confirms the imperfection of the concepts and terms' definitions that should reflect the said right. The author has defined that the problems in the health care sector in Ukraine are: lack of a sustainable Concept of building a new national health care system, the slow pace of medical reform started only in 2017, and refusal from the Soviet centralized system of public health management. It has been found out that the Constitutions of Ukraine, the Republic of Poland and the Czech Republic have common features regarding the formulation of constitutional principles of ensuring human rights to health. At the same time, it has been found out that the experience of organizing the health care system in the Republic of Poland and the Czech Republic requires amendments to the constitutional and legal acts of Ukraine, which would aim at a clearer formulation of the definitions of the basic concepts and terms determining human right to health, the formation of decentralized health care system that would be in line with the basic principles of the EU policy in the health care sector.
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Affiliation(s)
- A Shevchenko
- 1University of the State Fiscal Service of Ukraine, Irpin, Ukraine
| | - S Kydin
- 1University of the State Fiscal Service of Ukraine, Irpin, Ukraine
| | - O Svitlychnyy
- 2National University of Life and Environmental Sciences of Ukraine
| | - O Korotun
- 3Naukovo-Doslidnyy Instytut Publichnoho Prava, Ukraine
| | - Yu Zahumenna
- 4Kharkiv National University of Internal Affairs, Ukraine
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Bedard M, Shrestha D, Priestman DA, Wang Y, Schneider F, Matute JD, Iyer SS, Gileadi U, Prota G, Kandasamy M, Veerapen N, Besra G, Fritzsche M, Zeissig S, Shevchenko A, Christianson JC, Platt FM, Eggeling C, Blumberg RS, Salio M, Cerundolo V. Sterile activation of invariant natural killer T cells by ER-stressed antigen-presenting cells. Proc Natl Acad Sci U S A 2019; 116:23671-23681. [PMID: 31690657 PMCID: PMC6876220 DOI: 10.1073/pnas.1910097116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Invariant NKT (iNKT) cells have the unique ability to shape immunity during antitumor immune responses and other forms of sterile and nonsterile inflammation. Recent studies have highlighted a variety of classes of endogenous and pathogen-derived lipid antigens that can trigger iNKT cell activation under sterile and nonsterile conditions. However, the context and mechanisms that drive the presentation of self-lipid antigens in sterile inflammation remain unclear. Here we report that endoplasmic reticulum (ER)-stressed myeloid cells, via signaling events modulated by the protein kinase RNA-like ER kinase (PERK) pathway, increase CD1d-mediated presentation of immunogenic endogenous lipid species, which results in enhanced iNKT cell activation both in vitro and in vivo. In addition, we demonstrate that actin cytoskeletal reorganization during ER stress results in an altered distribution of CD1d on the cell surface, which contributes to enhanced iNKT cell activation. These results define a previously unidentified mechanism that controls iNKT cell activation during sterile inflammation.
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Affiliation(s)
- Melissa Bedard
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Dilip Shrestha
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - David A Priestman
- Department of Pharmacology, University of Oxford, OX1 3QT Oxford, United Kingdom
| | - Yuting Wang
- Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Falk Schneider
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Juan D Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
- Division of Neonatology, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Shankar S Iyer
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
| | - Uzi Gileadi
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Gennaro Prota
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Matheswaran Kandasamy
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Natacha Veerapen
- School of Biosciences, University of Birmingham, B15 2TT Egdbaston, United Kingdom
| | - Gurdyal Besra
- School of Biosciences, University of Birmingham, B15 2TT Egdbaston, United Kingdom
| | - Marco Fritzsche
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, OX3 7LF Oxford, United Kingdom
| | - Sebastian Zeissig
- Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
- Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - John C Christianson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, OX3 7LD Oxford, United Kingdom
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, OX1 3QT Oxford, United Kingdom
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics and Biophysics, 07743 Jena, Germany
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technologies e.V., 07745 Jena, Germany
| | - Richard S Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
| | - Mariolina Salio
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom;
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Vvedenskaya O, Wang Y, Ackerman JM, Knittelfelder O, Shevchenko A. Analytical challenges in human plasma lipidomics: A winding path towards the truth. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Shevchenko A, Gautier S, Shevchenko O, Kachanova J, Kwan V. P6313RAAS inhibition improves event-free survival in cardiac transplant recipients: results of the prospective cohort study. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz746.0910] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Despite known achievements, long-term survival of heart transplant (HT) recipients still needs to be improved. The Renin-Angiotensin-Aldosterone System (RAAS) hyper-activation could be the result of heart denervation and immune suppressive therapy in these patients. Angiotensin-converting enzyme inhibitors (ACEI) and angiotensin receptor blockers (ARB) have been shown to be beneficial in patients with hypertension, heart failure (HF) and diabetic nephropathy.
Purpose
The study was aimed to assess the effects of ACEI and ARB on the prognosis and cardiac transplant remodelling in HT recipients.
Methods
Four hundred ninety-six critical HF patients had cardiac transplant surgery between January 2012 and December 2016 in Shumakov National Research Centre of Transplantology, and Artificial Organs (Moscow, Russian Federation) which accounted to 57.9% of all heart transplantations (HTx) performed in the country during that period. All patients >18 years old who survived 30 days after the operation without known contraindications for ACEI or ARB were sequentially included in the study. A non-randomised controlled trial study design was used. Study endpoints included death from any cause and re-transplantation due to the irreversible cardiac transplant failure.
Results
385 HT recipients (mean age 46.3±2.3 years, 51 females and 334 males) enrolled in the study. Thirty days after the HTx, a RAAS inhibitor was assigned to 141 recipients. Patients receiving ACEI or ARB had significantly better event-free survival than the control group (log-rank p=0.045) during the follow-up for 1856.5±68.3 days. Unadjusted analysis revealed other factors related to the risk of death or irreversible HT failure: recipient age <37 years old, donor age>44 years old, aortic cross-clamping time >117 min, peri-operational ECMO>3 days of duration, acute renal failure requiring dialysis during first 30 days after the operation, right atrium size, mitral regurgitation 2+, tricuspid regurgitation 1+, donor's heart posterior wall thickness (PWT) >12mm, and left ventricle (LV) end-diastolic dimension (EDD). When adjusted to the RAAS inhibitors use, only the donor's age and early renal failure remained significant. LV EDD did not change over time in both groups, whereas LV PWT in the control group significantly increased from 12.3±0.3 to 13.5±0.5 mm (p<0.05).
Conclusions
Heart transplant recipients who received RAAS inhibitors had better survival and less LV hypertrophy progression that could reflect the beneficial effects of ACEI and ARB after heart transplantation.
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Affiliation(s)
- A Shevchenko
- Russian State Medical University, Cardiology CME cathedra, Moscow, Russian Federation
| | - S Gautier
- Institute of Transplantology and Artificial Organs, Moscow, Russian Federation
| | - O Shevchenko
- Russian State Medical University, Cardiology CME cathedra, Moscow, Russian Federation
| | - J Kachanova
- Institute of Transplantology and Artificial Organs, Moscow, Russian Federation
| | - V Kwan
- Institute of Transplantology and Artificial Organs, Moscow, Russian Federation
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Schuhmann K, Moon H, Thomas H, Ackerman JM, Groessl M, Wagner N, Kellmann M, Henry I, Nadler A, Shevchenko A. Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics. Anal Chem 2019; 91:12085-12093. [PMID: 31441640 PMCID: PMC6751524 DOI: 10.1021/acs.analchem.9b03270] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/23/2019] [Indexed: 01/01/2023]
Abstract
Quantitative bottom-up shotgun lipidomics relies on molecular species-specific "signature" fragments consistently detectable in tandem mass spectra of analytes and standards. Molecular species of glycerophospholipids are typically quantified using carboxylate fragments of their fatty acid moieties produced by higher-energy collisional dissociation of their molecular anions. However, employing standards whose fatty acids moieties are similar, yet not identical, to the target lipids could severely compromise their quantification. We developed a generic and portable fragmentation model implemented in the open-source LipidXte software that harmonizes the abundances of carboxylate anion fragments originating from fatty acid moieties having different sn-1/2 positions at the glycerol backbone, length of the hydrocarbon chain, and number and location of double bonds. The postacquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.
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Affiliation(s)
- Kai Schuhmann
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - HongKee Moon
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Henrik Thomas
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Jacobo Miranda Ackerman
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Michael Groessl
- Department
of Nephrology and Hypertension, Inselspital,
Bern University Hospital, Freiburgstr. 15, 3010 Bern, Switzerland
- Department
for BioMedical Research, University of Bern, Murtenstr. 35, 3010 Bern, Switzerland
| | - Nicolai Wagner
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Markus Kellmann
- Thermo
Fisher Scientific, Hanna-Kunath-Str.
11, 28199 Bremen, Germany
| | - Ian Henry
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - André Nadler
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
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Bonzón-Kulichenko E, Moltó E, Pintado C, Fernández A, Arribas C, Schwudke D, Gallardo N, Shevchenko A, Andrés A. Changes in Visceral Adipose Tissue Plasma Membrane Lipid Composition in Old Rats Are Associated With Adipocyte Hypertrophy With Aging. J Gerontol A Biol Sci Med Sci 2019; 73:1139-1146. [PMID: 29668887 DOI: 10.1093/gerona/gly081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/13/2017] [Accepted: 04/13/2018] [Indexed: 12/17/2022] Open
Abstract
Increased adiposity, through adipocyte hypertrophy, and/or hyperplasia, characterizes aging and obesity. Both are leptin-resistant states, associated with disturbed lipid metabolism, reduced insulin sensitivity and inflammation. Nevertheless, fat tissue dysfunction appears earlier in obesity than in normal aging. In contrast, lipodystrophy is accompanied by diabetes, and improving the fat cell capacity to expand rescues the diabetic phenotype. Fat tissue dysfunction is extensively studied in the diet-induced obesity, but remains relatively neglected in the aging-associated obesity. In the Wistar rat, as occurs in humans, early or middle aging is accompanied by an increase in adiposity. Using this experimental model, we describe the molecular mechanisms contributing to the white adipose tissue (WAT) hypertrophy. WAT from middle-old age rats is characterized by decreased basal lipogenesis and lipolysis, increased esterification, as demonstrated by the higher TAG and cholesterol content in visceral WAT, and the maintenance of total ceramide levels within normal values. In addition, we describe alterations in the adipose tissue plasma membrane lipid composition, as increased total ether-phosphatidylcholine, sphingomyelin, and free cholesterol levels that favor an enlarged fat cell size with aging. All these metabolic changes may be regarded as a survival advantage that prevents the aged rats from becoming overtly diabetic.
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Affiliation(s)
- Elena Bonzón-Kulichenko
- Área de Bioquímica, Facultad de Ciencias y Tecnologías Químicas, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Eduardo Moltó
- Área de Bioquímica, Facultad de Ciencias Medioambientales y Bioquímica, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Cristina Pintado
- Área de Bioquímica, Facultad de Ciencias Medioambientales y Bioquímica, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Alejandro Fernández
- Área de Bioquímica, Facultad de Ciencias y Tecnologías Químicas, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Carmen Arribas
- Área de Bioquímica, Facultad de Ciencias Medioambientales y Bioquímica, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Germany
| | - Nilda Gallardo
- Área de Bioquímica, Facultad de Ciencias y Tecnologías Químicas, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Antonio Andrés
- Área de Bioquímica, Facultad de Ciencias y Tecnologías Químicas, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
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Gross AS, Zimmermann A, Pendl T, Schroeder S, Schoenlechner H, Knittelfelder O, Lamplmayr L, Santiso A, Aufschnaiter A, Waltenstorfer D, Ortonobes Lara S, Stryeck S, Kast C, Ruckenstuhl C, Hofer SJ, Michelitsch B, Woelflingseder M, Müller R, Carmona-Gutierrez D, Madl T, Büttner S, Fröhlich KU, Shevchenko A, Eisenberg T. Acetyl-CoA carboxylase 1-dependent lipogenesis promotes autophagy downstream of AMPK. J Biol Chem 2019; 294:12020-12039. [PMID: 31209110 PMCID: PMC6690696 DOI: 10.1074/jbc.ra118.007020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 12/05/2018] [Revised: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
Autophagy, a membrane-dependent catabolic process, ensures survival of aging cells and depends on the cellular energetic status. Acetyl-CoA carboxylase 1 (Acc1) connects central energy metabolism to lipid biosynthesis and is rate-limiting for the de novo synthesis of lipids. However, it is unclear how de novo lipogenesis and its metabolic consequences affect autophagic activity. Here, we show that in aging yeast, autophagy levels highly depend on the activity of Acc1. Constitutively active Acc1 (acc1S/A) or a deletion of the Acc1 negative regulator, Snf1 (yeast AMPK), shows elevated autophagy levels, which can be reversed by the Acc1 inhibitor soraphen A. Vice versa, pharmacological inhibition of Acc1 drastically reduces cell survival and results in the accumulation of Atg8-positive structures at the vacuolar membrane, suggesting late defects in the autophagic cascade. As expected, acc1S/A cells exhibit a reduction in acetate/acetyl-CoA availability along with elevated cellular lipid content. However, concomitant administration of acetate fails to fully revert the increase in autophagy exerted by acc1S/A. Instead, administration of oleate, while mimicking constitutively active Acc1 in WT cells, alleviates the vacuolar fusion defects induced by Acc1 inhibition. Our results argue for a largely lipid-dependent process of autophagy regulation downstream of Acc1. We present a versatile genetic model to investigate the complex relationship between acetate metabolism, lipid homeostasis, and autophagy and propose Acc1-dependent lipogenesis as a fundamental metabolic path downstream of Snf1 to maintain autophagy and survival during cellular aging.
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Affiliation(s)
- Angelina S Gross
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; Central Lab Gracia, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Sabrina Schroeder
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Hannes Schoenlechner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Laura Lamplmayr
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Ana Santiso
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Andreas Aufschnaiter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 114 19 Stockholm, Sweden
| | - Daniel Waltenstorfer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Sandra Ortonobes Lara
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Sarah Stryeck
- Gottfried Schatz Research Center for Cell Signaling, Metabolism, and Aging, Institute of Molecular Biology and Biochemistry, Medical University of Graz, 8036 Graz, Austria
| | - Christina Kast
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Christoph Ruckenstuhl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Birgit Michelitsch
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; Division of Plastic, Aesthetic, and Reconstructive Surgery, Department of Surgery, Medical University of Graz, 8036 Graz, Austria
| | | | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbrücken, Germany
| | | | - Tobias Madl
- BioTechMed-Graz, 8010 Graz, Austria; Gottfried Schatz Research Center for Cell Signaling, Metabolism, and Aging, Institute of Molecular Biology and Biochemistry, Medical University of Graz, 8036 Graz, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 114 19 Stockholm, Sweden
| | - Kai-Uwe Fröhlich
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; Central Lab Gracia, NAWI Graz, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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Marbach-Breitrück E, Matz-Soja M, Abraham U, Schmidt-Heck W, Sales S, Rennert C, Kern M, Aleithe S, Spormann L, Thiel C, Gerlini R, Arnold K, Klöting N, Guthke R, Rozman D, Teperino R, Shevchenko A, Kramer A, Gebhardt R. Tick-tock hedgehog-mutual crosstalk with liver circadian clock promotes liver steatosis. J Hepatol 2019; 70:1192-1202. [PMID: 30711403 DOI: 10.1016/j.jhep.2019.01.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 01/16/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS The mammalian circadian clock controls various aspects of liver metabolism and integrates nutritional signals. Recently, we described Hedgehog (Hh) signaling as a novel regulator of liver lipid metabolism. Herein, we investigated crosstalk between hepatic Hh signaling and circadian rhythm. METHODS Diurnal rhythms of Hh signaling were investigated in liver and hepatocytes from mice with ablation of Smoothened (SAC-KO) and crossbreeds with PER2::LUC reporter mice. By using genome-wide screening, qPCR, immunostaining, ELISA and RNAi experiments in vitro we identified relevant transcriptional regulatory steps. Shotgun lipidomics and metabolic cages were used for analysis of metabolic alterations and behavior. RESULTS Hh signaling showed diurnal oscillations in liver and hepatocytes in vitro. Correspondingly, the level of Indian Hh, oscillated in serum. Depletion of the clock gene Bmal1 in hepatocytes resulted in significant alterations in the expression of Hh genes. Conversely, SAC-KO mice showed altered expression of clock genes, confirmed by RNAi against Gli1 and Gli3. Genome-wide screening revealed that SAC-KO hepatocytes showed time-dependent alterations in various genes, particularly those associated with lipid metabolism. The clock/hedgehog module further plays a role in rhythmicity of steatosis, and in the response of the liver to a high-fat diet or to differently timed starvation. CONCLUSIONS For the first time, Hh signaling in hepatocytes was found to be time-of-day dependent and to feed back on the circadian clock. Our findings suggest an integrative role of Hh signaling, mediated mainly by GLI factors, in maintaining homeostasis of hepatic lipid metabolism by balancing the circadian clock. LAY SUMMARY The results of our investigation show for the first time that the Hh signaling in hepatocytes is time-of-day dependent, leading to differences not only in transcript levels but also in the amount of Hh ligands in peripheral blood. Conversely, Hh signaling is able to feed back to the circadian clock.
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Affiliation(s)
- Eugenia Marbach-Breitrück
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Madlen Matz-Soja
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
| | - Ute Abraham
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christiane Rennert
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Matthias Kern
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Susanne Aleithe
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Clinic and Polyclinic of Neurology, Faculty of Medicine, Leipzig University, Germany
| | - Luise Spormann
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Carlo Thiel
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics (IEG), HDC, Neuherberg, Germany
| | - Katrin Arnold
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Nora Klöting
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Damjana Rozman
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Raffaele Teperino
- Institute of Experimental Genetics (IEG), HDC, Neuherberg, Germany; DZD, German Center for Diabetes Research, Neuherberg, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Rolf Gebhardt
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
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Thommen A, Werner S, Frank O, Philipp J, Knittelfelder O, Quek Y, Fahmy K, Shevchenko A, Friedrich BM, Jülicher F, Rink JC. Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians. eLife 2019; 8:e38187. [PMID: 30608231 PMCID: PMC6320072 DOI: 10.7554/elife.38187] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Kleiber's law, or the 3/4 -power law scaling of the metabolic rate with body mass, is considered one of the few quantitative laws in biology, yet its physiological basis remains unknown. Here, we report Kleiber's law scaling in the planarian Schmidtea mediterranea. Its reversible and life history-independent changes in adult body mass over 3 orders of magnitude reveal that Kleiber's law does not emerge from the size-dependent decrease in cellular metabolic rate, but from a size-dependent increase in mass per cell. Through a combination of experiment and theoretical analysis of the organismal energy balance, we further show that the mass allometry is caused by body size dependent energy storage. Our results reveal the physiological origins of Kleiber's law in planarians and have general implications for understanding a fundamental scaling law in biology.
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Affiliation(s)
- Albert Thommen
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Steffen Werner
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- FOM Institute AMOLFAmsterdamThe Netherlands
| | - Olga Frank
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jenny Philipp
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | | | - Yihui Quek
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Massachusetts Institute of TechnologyCambridgeUnited States
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Benjamin M Friedrich
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Center for Advancing Electronics DresdenTechnische Universität DresdenDresdenGermany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
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46
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Shevchenko A, Stepanets O, Sokolenko A, Bilyk O. Hydrodynamic and energy parameters of gas-liquid media. ХНТ 2018. [DOI: 10.15673/fst.v12i3.1047] [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: 11/22/2022]
Abstract
The paper presents the results of studies related to determining the interconnections between hydrodynamic and energy parameters of gas-liquid media. The whole scope of information about them taken together allows evaluating the prospects of searching for new technologies and their improvement. In the studies, phenomenological generalizations of theories that comply with Archimedes’, Henry’s, Pascal’s laws and the superposition principle have been used to determine the driving and resistance factors when circulation circuits of media appear.
It is shown that the energy potential of the latter results from the dissolution of the gas phase and the synthesis of the dispersed gas phase during self-organized or forced processes. These two causes are interrelated, but their manifestations are different. The presence of a dispersed gas phase, regardless of the form it appears in, a priori means the presence of a driving factor in the creation of circulation circuits, whereas the presence of a dissolved gas phase is only the root cause of the formation of the dispersed gas phase. In anaerobic processes, gas phase is represented by carbon dioxide, and in aerobic, by air or nitrogen from the composition of air and CO2. The total driving potential of circulation circuits is determined by the gas-holding capacity that, in turn, depends on the intensity of the synthesis of the dispersed gas phase, on the geometry of the media volumes, and on the physical properties of the phases. The gradient by the level of saturation of the liquid phase by the gas phase is determined basing on their physical and chemical properties and by the hydrostatic pressures of the liquid phase. The boundary saturation depends on the gas phase pressure in the supraliquid volume and the hydrostatic pressure. It is shown that a factor that intensifies mass-exchange processes is the relative rate of emergence of the bubbles in the gas phase. Calculation formulae are developed to estimate the gas-holding capacity and driving factors in the form of Archimedes’ buoyant forces. It is pointed out how important circulation circuits are in creating desaturation and saturation zones of media in order to improve the living conditions for microorganisms.
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47
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res 2018; 59:2001-2017. [PMID: 30115755 PMCID: PMC6168311 DOI: 10.1194/jlr.s087163] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [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] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/11/2018] [Indexed: 12/19/2022] Open
Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
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Affiliation(s)
- Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Masanori Arita
- National Institute of Genetics, Shizuoka, Japan and RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Anne K Bendt
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies and Department of Medicine-Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Michelle K Lin
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matej Orešič
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland and School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Oswald Quehenberger
- Departments of Pharmacology and Medicine, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Federico Torta
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | | | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
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48
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Brankatschk M, Gutmann T, Knittelfelder O, Palladini A, Prince E, Grzybek M, Brankatschk B, Shevchenko A, Coskun Ü, Eaton S. A Temperature-Dependent Switch in Feeding Preference Improves Drosophila Development and Survival in the Cold. Dev Cell 2018; 47:257-259. [DOI: 10.1016/j.devcel.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Rennert C, Vlaic S, Marbach-Breitrück E, Thiel C, Sales S, Shevchenko A, Gebhardt R, Matz-Soja M. The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism - A Systems Biology Analysis Using Self-Organizing Maps. Front Physiol 2018; 9:1180. [PMID: 30271348 PMCID: PMC6146234 DOI: 10.3389/fphys.2018.01180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 03/29/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022] Open
Abstract
Organisms adapt their metabolism and draw on reserves as a consequence of food deprivation. The central role of the liver in starvation response is to coordinate a sufficient energy supply for the entire organism, which has frequently been investigated. However, knowledge of how circadian rhythms impact on and alter this response is scarce. Therefore, we investigated the influence of different timings of starvation on global hepatic gene expression. Mice (n = 3 each) were challenged with 24-h food deprivation started in the morning or evening, coupled with refeeding for different lengths and compared with ad libitum fed control groups. Alterations in hepatocyte gene expression were quantified using microarrays and confirmed or complemented with qPCR, especially for lowly detectable transcription factors. Analysis was performed using self-organizing maps (SOMs), which bases on clustering genes with similar expression profiles. This provides an intuitive overview of expression trends and allows easier global comparisons between complex conditions. Transcriptome analysis revealed a strong circadian-driven response to fasting based on the diurnal expression of transcription factors (e.g., Ppara, Pparg). Starvation initiated in the morning produced known metabolic adaptations in the liver; e.g., switching from glucose storage to consumption and gluconeogenesis. However, starvation initiated in the evening produced a different expression signature that was controlled by yet unknown regulatory mechanisms. For example, the expression of genes involved in gluconeogenesis decreased and fatty acid and cholesterol synthesis genes were induced. The differential regulation after morning and evening starvation were also reflected at the lipidome level. The accumulation of hepatocellular storage lipids (triacylglycerides, cholesteryl esters) was significantly higher after the initiation of starvation in the morning compared to the evening. Concerning refeeding, the gene expression pattern after a 12 h refeeding period largely resembled that of the corresponding starvation state but approached the ad libitum control state after refeeding for 21 h. Some components of these regulatory circuits are discussed. Collectively, these data illustrate a highly time-dependent starvation response in the liver and suggest that a circadian influence cannot be neglected when starvation is the focus of research or medicine, e.g., in the case of treating victims of sudden starvation events.
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Affiliation(s)
- Christiane Rennert
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Sebastian Vlaic
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Eugenia Marbach-Breitrück
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.,Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carlo Thiel
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Rolf Gebhardt
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Madlen Matz-Soja
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
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50
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Brankatschk M, Gutmann T, Knittelfelder O, Palladini A, Prince E, Grzybek M, Brankatschk B, Shevchenko A, Coskun Ü, Eaton S. A Temperature-Dependent Switch in Feeding Preference Improves Drosophila Development and Survival in the Cold. Dev Cell 2018; 46:781-793.e4. [DOI: 10.1016/j.devcel.2018.05.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 03/17/2018] [Accepted: 08/27/2018] [Indexed: 01/01/2023]
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