101
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Mann M. The Origins of Organellar Mapping by Protein Correlation Profiling. Proteomics 2020; 20:e1900330. [PMID: 32744740 DOI: 10.1002/pmic.201900330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/27/2020] [Indexed: 11/09/2022]
Abstract
Cells have a rich inner structure that is commonly explored by microscopy. Classical biochemical methods that break apart the cells and fractionate them along a gradient have now gotten a new lease on life through modern methods of mass spectrometry-based proteomics. Their common principle is to comprehensively measure all the proteins in each of the fractions. The resulting quantitative profile then associates thousands of proteins to their cellular homes. Here, the author recounts how protein correlation profiling, the first such technique, was conceived and how it was applied to answer intricate cell biological questions.
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Affiliation(s)
- Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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102
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C57BL/6J substrain differences in response to high-fat diet intervention. Sci Rep 2020; 10:14052. [PMID: 32820201 PMCID: PMC7441320 DOI: 10.1038/s41598-020-70765-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
C57BL/6J-related mouse strains are widely used animal models for diet-induced obesity (DIO). Multiple vendors breed C57BL/6J-related substrains which may introduce genetic drift and environmental confounders such as microbiome differences. To address potential vendor/substrain specific effects, we compared DIO of C57BL/6J-related substrains from three different vendors: C57BL/6J (Charles Rivers), C57BL/6JBomTac (Taconic Bioscience) and C57BL/6JRj (Janvier). After local acclimatization, DIO was induced by either a high-fat diet (HFD, 60% energy from fat) or western diet (WD, 42% energy from fat supplemented with fructose in the drinking water). All three groups on HFD gained a similar amount of total body weight, yet the relative amount of fat percentage and mass of inguinal- and epididymal white adipose tissue (iWAT and eWAT) was lower in C57BL/6JBomTac compared to the two other C57BL/6J-releated substrains. In contrast to HFD, the three groups on WD responded differently in terms of body weight gain, where C57BL/6J was particularly prone to WD. This was associated with a relative higher amount of eWAT, iWAT, and liver triglycerides. Although the HFD and WD had significant impact on the microbiota, we did not observe any major differences between the three groups of mice. Together, these data demonstrate significant differences in HFD- and WD-induced adiposity in C57BL/6J-related substrains, which should be considered in the design of animal DIO studies.
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103
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Bohnert M. Tether Me, Tether Me Not—Dynamic Organelle Contact Sites in Metabolic Rewiring. Dev Cell 2020; 54:212-225. [DOI: 10.1016/j.devcel.2020.06.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 02/04/2023]
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104
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Borner GHH. Organellar Maps Through Proteomic Profiling - A Conceptual Guide. Mol Cell Proteomics 2020; 19:1076-1087. [PMID: 32345598 PMCID: PMC7338086 DOI: 10.1074/mcp.r120.001971] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/27/2020] [Indexed: 11/29/2022] Open
Abstract
Protein subcellular localization is an essential and highly regulated determinant of protein function. Major advances in mass spectrometry and imaging have allowed the development of powerful spatial proteomics approaches for determining protein localization at the whole cell scale. Here, a brief overview of current methods is presented, followed by a detailed discussion of organellar mapping through proteomic profiling. This relatively simple yet flexible approach is rapidly gaining popularity, because of its ability to capture the localizations of thousands of proteins in a single experiment. It can be used to generate high-resolution cell maps, and as a tool for monitoring protein localization dynamics. This review highlights the strengths and limitations of the approach and provides guidance to designing and interpreting profiling experiments.
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Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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105
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Crook OM, Smith T, Elzek M, Lilley KS. Moving Profiling Spatial Proteomics Beyond Discrete Classification. Proteomics 2020; 20:e1900392. [PMID: 32558233 DOI: 10.1002/pmic.201900392] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/18/2020] [Indexed: 12/12/2022]
Abstract
The spatial subcellular proteome is a dynamic environment; one that can be perturbed by molecular cues and regulated by post-translational modifications. Compartmentalization of this environment and management of these biomolecular dynamics allows for an array of ancillary protein functions. Profiling spatial proteomics has proved to be a powerful technique in identifying the primary subcellular localization of proteins. The approach has also been refashioned to study multi-localization and localization dynamics. Here, the analytical approaches that have been applied to spatial proteomics thus far are critiqued, and challenges particularly associated with multi-localization and dynamic relocalization is identified. To meet some of the current limitations in analytical processing, it is suggested that Bayesian modeling has clear benefits over the methods applied to date and should be favored whenever possible. Careful consideration of the limitations and challenges, and development of robust statistical frameworks, will ensure that profiling spatial proteomics remains a valuable technique as its utility is expanded.
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Affiliation(s)
- Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mohamed Elzek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
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106
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Hepatic lipid droplet homeostasis and fatty liver disease. Semin Cell Dev Biol 2020; 108:72-81. [PMID: 32444289 DOI: 10.1016/j.semcdb.2020.04.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/17/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
In cells, lipids are stored in lipid droplets, dynamic organelles that adapt their size, abundance, lipid and protein composition and organelle interactions to metabolic changes. Lipid droplet accumulation in the liver is the hallmark of non-alcoholic fatty liver disease (NAFLD). Due to the prevalence of obesity, the strongest risk factor for steatosis, NAFLD and its associated complications are currently affecting more than 1 billion people worldwide. Here, we review how triglyceride and phospholipid homeostasis are regulated in hepatocytes and how imbalances between lipid storage, degradation and lipoprotein secretion lead to NAFLD. We discuss how organelle interactions are altered in NAFLD and provide insights how NAFLD progression is associated with changes in hepatocellular signaling and organ-crosstalk. Finally, we highlight unsolved questions in hepatic LD and lipoprotein biology and give an outlook on therapeutic options counteracting hepatic lipid accumulation.
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107
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Mejhert N, Kuruvilla L, Gabriel KR, Elliott SD, Guie MA, Wang H, Lai ZW, Lane EA, Christiano R, Danial NN, Farese RV, Walther TC. Partitioning of MLX-Family Transcription Factors to Lipid Droplets Regulates Metabolic Gene Expression. Mol Cell 2020; 77:1251-1264.e9. [PMID: 32023484 PMCID: PMC7397554 DOI: 10.1016/j.molcel.2020.01.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/05/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Lipid droplets (LDs) store lipids for energy and are central to cellular lipid homeostasis. The mechanisms coordinating lipid storage in LDs with cellular metabolism are unclear but relevant to obesity-related diseases. Here we utilized genome-wide screening to identify genes that modulate lipid storage in macrophages, a cell type involved in metabolic diseases. Among ∼550 identified screen hits is MLX, a basic helix-loop-helix leucine-zipper transcription factor that regulates metabolic processes. We show that MLX and glucose-sensing family members MLXIP/MondoA and MLXIPL/ChREBP bind LDs via C-terminal amphipathic helices. When LDs accumulate in cells, these transcription factors bind to LDs, reducing their availability for transcriptional activity and attenuating the response to glucose. Conversely, the absence of LDs results in hyperactivation of MLX target genes. Our findings uncover a paradigm for a lipid storage response in which binding of MLX transcription factors to LD surfaces adjusts the expression of metabolic genes to lipid storage levels.
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Affiliation(s)
- Niklas Mejhert
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Leena Kuruvilla
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Katlyn R Gabriel
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Shane D Elliott
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Marie-Aude Guie
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Huajin Wang
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Zon Weng Lai
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth A Lane
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Romain Christiano
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nika N Danial
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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108
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Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020; 19:1718-1730. [PMID: 32134668 DOI: 10.1021/acs.jproteome.9b00862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic range compared to TMT-MS3, MS1, and DIA, which were similar. Using a protein clustering approach to evaluate data quality by assignment of reference proteins to their correct compartments, all methods performed well, with isobaric labeling approaches providing the highest quality localization. Finally, TMT-MS2 gave the lowest percentage of missing quantifiable data when analyzing orthogonal fractionation methods containing overlapping proteomes. In summary, despite inaccuracies resulting from ratio compression, data obtained by TMT-MS2 assigned protein localization as well as other methods but achieved the highest proteome coverage with the lowest proportion of missing values.
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Affiliation(s)
- Abla Tannous
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Marielle Boonen
- URPhyM-Intracellular Trafficking Biology, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Colin J Germain
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Michel Jadot
- URPhyM-Physiological Chemistry, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
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109
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Lundberg E, Borner GHH. Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 2020; 20:285-302. [PMID: 30659282 DOI: 10.1038/s41580-018-0094-y] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein subcellular localization is tightly controlled and intimately linked to protein function in health and disease. Capturing the spatial proteome - that is, the localizations of proteins and their dynamics at the subcellular level - is therefore essential for a complete understanding of cell biology. Owing to substantial advances in microscopy, mass spectrometry and machine learning applications for data analysis, the field is now mature for proteome-wide investigations of spatial cellular regulation. Studies of the human proteome have begun to reveal a complex architecture, including single-cell variations, dynamic protein translocations, changing interaction networks and proteins localizing to multiple compartments. Furthermore, several studies have successfully harnessed the power of comparative spatial proteomics as a discovery tool to unravel disease mechanisms. We are at the beginning of an era in which spatial proteomics finally integrates with cell biology and medical research, thereby paving the way for unbiased systems-level insights into cellular processes. Here, we discuss current methods for spatial proteomics using imaging or mass spectrometry and specifically highlight global comparative applications. The aim of this Review is to survey the state of the field and also to encourage more cell biologists to apply spatial proteomics approaches.
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Affiliation(s)
- Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Genetics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Georg H H Borner
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany.
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110
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Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. The functional landscape of the human phosphoproteome. Nat Biotechnol 2020; 38:365-373. [PMID: 31819260 PMCID: PMC7100915 DOI: 10.1038/s41587-019-0344-3] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually curated 112 datasets of phospho-enriched proteins, generated from 104 different human cell types or tissues. We re-analyzed the 6,801 proteomics experiments that passed our quality control criteria, creating a reference phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, we used machine learning to identify 59 features indicative of proteomic, structural, regulatory or evolutionary relevance and integrate them into a single functional score. Our approach identifies regulatory phosphosites across different molecular mechanisms, processes and diseases, and reveals genetic susceptibilities at a genomic scale. Several regulatory phosphosites were experimentally validated, including identifying a role in neuronal differentiation for phosphosites in SMARCC2, a member of the SWI/SNF chromatin-remodeling complex.
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Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maja Gehre
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Margaret Soucheray
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Askar A Kleefeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anthony Hill
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luz Garcia-Alonso
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frank Stein
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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111
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Abstract
The rising incidence of alcohol-related liver disease (ALD) demands making urgent progress in understanding the fundamental molecular basis of alcohol-related hepatocellular damage. One of the key early events accompanying chronic alcohol usage is the accumulation of lipid droplets (LDs) in the hepatocellular cytoplasm. LDs are far from inert sites of neutral lipid storage; rather, they represent key organelles that play vital roles in the metabolic state of the cell. In this review, we will examine the biology of these structures and outline recent efforts being made to understand the effects of alcohol exposure on the biogenesis, catabolism, and motility of LDs and how their dynamic nature is perturbed in the context of ALD.
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Affiliation(s)
- Ryan J. Schulze
- Department of Biochemistry and Molecular Biology and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA,Corresponding author. Department of Biochemistry and Molecular Biology and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. (R.J. Schulze)
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, KS, USA
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112
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van Pijkeren A, Bischoff R, Kwiatkowski M. Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture. Analyst 2019; 144:6812-6833. [PMID: 31650141 DOI: 10.1039/c9an01258c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.
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Affiliation(s)
- Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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113
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Knebel B, Fahlbusch P, Dille M, Wahlers N, Hartwig S, Jacob S, Kettel U, Schiller M, Herebian D, Koellmer C, Lehr S, Müller-Wieland D, Kotzka J. Fatty Liver Due to Increased de novo Lipogenesis: Alterations in the Hepatic Peroxisomal Proteome. Front Cell Dev Biol 2019; 7:248. [PMID: 31709254 PMCID: PMC6823594 DOI: 10.3389/fcell.2019.00248] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
In non-alcoholic fatty liver disease (NAFLD) caused by ectopic lipid accumulation, lipotoxicity is a crucial molecular risk factor. Mechanisms to eliminate lipid overflow can prevent the liver from functional complications. This may involve increased secretion of lipids or metabolic adaptation to ß-oxidation in lipid-degrading organelles such as mitochondria and peroxisomes. In addition to dietary factors, increased plasma fatty acid levels may be due to increased triglyceride synthesis, lipolysis, as well as de novo lipid synthesis (DNL) in the liver. In the present study, we investigated the impact of fatty liver caused by elevated DNL, in a transgenic mouse model with liver-specific overexpression of human sterol regulatory element-binding protein-1c (alb-SREBP-1c), on hepatic gene expression, on plasma lipids and especially on the proteome of peroxisomes by omics analyses, and we interpreted the results with knowledge-based analyses. In summary, the increased hepatic DNL is accompanied by marginal gene expression changes but massive changes in peroxisomal proteome. Furthermore, plasma phosphatidylcholine (PC) as well as lysoPC species were altered. Based on these observations, it can be speculated that the plasticity of organelles and their functionality may be directly affected by lipid overflow.
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Affiliation(s)
- Birgit Knebel
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Pia Fahlbusch
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Matthias Dille
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Natalie Wahlers
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Sonja Hartwig
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Sylvia Jacob
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Ulrike Kettel
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Martina Schiller
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Diran Herebian
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Children’s Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Cornelia Koellmer
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Stefan Lehr
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Dirk Müller-Wieland
- Department of Internal Medicine I, Clinical Research Centre, University Hospital Aachen, Aachen, Germany
| | - Jorg Kotzka
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
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114
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Seitz S, Kwon Y, Hartleben G, Jülg J, Sekar R, Krahmer N, Najafi B, Loft A, Gancheva S, Stemmer K, Feuchtinger A, Hrabe de Angelis M, Müller TD, Mann M, Blüher M, Roden M, Berriel Diaz M, Behrends C, Gilleron J, Herzig S, Zeigerer A. Hepatic Rab24 controls blood glucose homeostasis via improving mitochondrial plasticity. Nat Metab 2019; 1:1009-1026. [PMID: 32694843 DOI: 10.1038/s42255-019-0124-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/10/2019] [Indexed: 12/18/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) represents a key feature of obesity-related type 2 diabetes with increasing prevalence worldwide. To our knowledge, no treatment options are available to date, paving the way for more severe liver damage, including cirrhosis and hepatocellular carcinoma. Here, we show an unexpected function for an intracellular trafficking regulator, the small Rab GTPase Rab24, in mitochondrial fission and activation, which has an immediate impact on hepatic and systemic energy homeostasis. RAB24 is highly upregulated in the livers of obese patients with NAFLD and positively correlates with increased body fat in humans. Liver-selective inhibition of Rab24 increases autophagic flux and mitochondrial connectivity, leading to a strong improvement in hepatic steatosis and a reduction in serum glucose and cholesterol levels in obese mice. Our study highlights a potential therapeutic application of trafficking regulators, such as RAB24, for NAFLD and establishes a conceptual functional connection between intracellular transport and systemic metabolic dysfunction.
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Affiliation(s)
- Susanne Seitz
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Yun Kwon
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Götz Hartleben
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Jülg
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-University München, Munich, Germany
| | - Revathi Sekar
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalie Krahmer
- German Center for Diabetes Research, Neuherberg, Germany
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
| | - Bahar Najafi
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Anne Loft
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Sofiya Gancheva
- German Center for Diabetes Research, Neuherberg, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - Kerstin Stemmer
- German Center for Diabetes Research, Neuherberg, Germany
- Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Center Munich, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Center for Diabetes Research, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Timo D Müller
- German Center for Diabetes Research, Neuherberg, Germany
- Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Eberhard Karls University Hospitals and Clinics, Tübingen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- NF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Roden
- German Center for Diabetes Research, Neuherberg, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - Mauricio Berriel Diaz
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Ludwig-Maximilians-University München, Munich, Germany
| | - Jerome Gilleron
- Université Côte d'Azur, Institut National de la Santé et de la Recherche Médicale UMR1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Nice, France
| | - Stephan Herzig
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Chair Molecular Metabolic Control, Technical University Munich, Munich, Germany
| | - Anja Zeigerer
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany.
- German Center for Diabetes Research, Neuherberg, Germany.
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany.
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115
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Vitrinel B, Koh HWL, Mujgan Kar F, Maity S, Rendleman J, Choi H, Vogel C. Exploiting Interdata Relationships in Next-generation Proteomics Analysis. Mol Cell Proteomics 2019; 18:S5-S14. [PMID: 31126983 PMCID: PMC6692783 DOI: 10.1074/mcp.mr118.001246] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/01/2019] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry based proteomics and other technologies have matured to enable routine quantitative, system-wide analysis of concentrations, modifications, and interactions of proteins, mRNAs, and other molecules. These studies have allowed us to move toward a new field concerned with mining information from the combination of these orthogonal data sets, perhaps called "integromics." We highlight examples of recent studies and tools that aim at relating proteomic information to mRNAs, genetic associations, and changes in small molecules and lipids. We argue that productive data integration differs from parallel acquisition and interpretation and should move toward quantitative modeling of the relationships between the data. These relationships might be expressed by temporal information retrieved from time series experiments, rate equations to model synthesis and degradation, or networks of causal, evolutionary, physical, and other interactions. We outline steps and considerations toward such integromic studies to exploit the synergy between data sets.
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Affiliation(s)
- Burcu Vitrinel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Hiromi W L Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Funda Mujgan Kar
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.
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116
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Dittmann A, Kennedy NJ, Soltero NL, Morshed N, Mana MD, Yilmaz ÖH, Davis RJ, White FM. High-fat diet in a mouse insulin-resistant model induces widespread rewiring of the phosphotyrosine signaling network. Mol Syst Biol 2019; 15:e8849. [PMID: 31464373 PMCID: PMC6674232 DOI: 10.15252/msb.20198849] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Obesity-associated type 2 diabetes and accompanying diseases have developed into a leading human health risk across industrialized and developing countries. The complex molecular underpinnings of how lipid overload and lipid metabolites lead to the deregulation of metabolic processes are incompletely understood. We assessed hepatic post-translational alterations in response to treatment of cells with saturated and unsaturated free fatty acids and the consumption of a high-fat diet by mice. These data revealed widespread tyrosine phosphorylation changes affecting a large number of enzymes involved in metabolic processes as well as canonical receptor-mediated signal transduction networks. Targeting two of the most prominently affected molecular features in our data, SRC-family kinase activity and elevated reactive oxygen species, significantly abrogated the effects of saturated fat exposure in vitro and high-fat diet in vivo. In summary, we present a comprehensive view of diet-induced alterations of tyrosine signaling networks, including proteins involved in fundamental metabolic pathways.
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MESH Headings
- Animals
- Cell Line, Tumor
- Diabetes Mellitus, Type 2/etiology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diet, High-Fat/adverse effects
- Disease Models, Animal
- Fatty Acids/pharmacology
- Hepatocytes/drug effects
- Hepatocytes/metabolism
- Hepatocytes/pathology
- Liver/drug effects
- Liver/metabolism
- Liver/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Obesity/etiology
- Obesity/genetics
- Obesity/metabolism
- Obesity/pathology
- Phosphorylation/drug effects
- Phosphotyrosine/metabolism
- Protein Kinase Inhibitors/pharmacology
- Protein Processing, Post-Translational
- Proteomics/methods
- Rats
- Reactive Oxygen Species/agonists
- Reactive Oxygen Species/metabolism
- Signal Transduction
- src-Family Kinases/genetics
- src-Family Kinases/metabolism
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Affiliation(s)
- Antje Dittmann
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Norman J Kennedy
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMAUSA
| | - Nina L Soltero
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Nader Morshed
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Miyeko D Mana
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of Harvard and MITCambridgeMAUSA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of Harvard and MITCambridgeMAUSA
- Department of PathologyMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Roger J Davis
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMAUSA
- Howard Hughes Medical InstituteWorcesterMAUSA
| | - Forest M White
- The David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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117
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Abstract
Lipid droplets (LDs), important organelles for energy storage and involved in the development of metabolic disorders, are extremely dynamic and interact with many other cellular compartments to orchestrate lipid metabolism. Little is known about how these organelle contacts are changed according to cellular needs and functions under different metabolic and pathological conditions and which proteins regulate this. Here, we summarize recent exciting discoveries about the reorganization of organelle contacts in steatotic liver, including the identification of novel LD contact site proteins in cell lines and in animals. We also discuss state of the art proteomics workflows that enable the characterization of LD-organelle contacts and tethering proteins and give an outlook how this can inform obesity research.
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Affiliation(s)
- Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich-Neuherberg, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Denmark
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118
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Schulze RJ, Schott MB, Casey CA, Tuma PL, McNiven MA. The cell biology of the hepatocyte: A membrane trafficking machine. J Cell Biol 2019; 218:2096-2112. [PMID: 31201265 PMCID: PMC6605791 DOI: 10.1083/jcb.201903090] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022] Open
Abstract
The liver performs numerous vital functions, including the detoxification of blood before access to the brain while simultaneously secreting and internalizing scores of proteins and lipids to maintain appropriate blood chemistry. Furthermore, the liver also synthesizes and secretes bile to enable the digestion of food. These diverse attributes are all performed by hepatocytes, the parenchymal cells of the liver. As predicted, these cells possess a remarkably well-developed and complex membrane trafficking machinery that is dedicated to moving specific cargos to their correct cellular locations. Importantly, while most epithelial cells secrete nascent proteins directionally toward a single lumen, the hepatocyte secretes both proteins and bile concomitantly at its basolateral and apical domains, respectively. In this Beyond the Cell review, we will detail these central features of the hepatocyte and highlight how membrane transport processes play a key role in healthy liver function and how they are affected by disease.
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Affiliation(s)
- Ryan J Schulze
- Division of Gastroenterology and Hepatology, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Micah B Schott
- Division of Gastroenterology and Hepatology, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Carol A Casey
- Research Service, Department of Veterans Affairs, Nebraska-Western Iowa Health Care System, Omaha, NE
- Departments of Internal Medicine and Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE
| | | | - Mark A McNiven
- Division of Gastroenterology and Hepatology, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
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119
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Thiam AR, Dugail I. Lipid droplet-membrane contact sites - from protein binding to function. J Cell Sci 2019; 132:132/12/jcs230169. [PMID: 31209063 DOI: 10.1242/jcs.230169] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the general context of an increasing prevalence of obesity-associated diseases, which follows changing paradigms in food consumption and worldwide use of industry-transformed foodstuffs, much attention has been given to the consequences of excessive fattening on health. Highly related to this clinical problem, studies at the cellular and molecular level are focused on the fundamental mechanism of lipid handling in dedicated lipid droplet (LD) organelles. This Review briefly summarizes how views on LD functions have evolved from those of a specialized intracellular compartment dedicated to lipid storage to exerting a more generalized role in the stress response. We focus on the current understanding of how proteins bind to LDs and determine their function, and on the new paradigms that have emerged from the discoveries of the multiple contact sites formed by LDs. We argue that elucidating the important roles of LD tethering to other cellular organelles allows for a better understanding of LD diversity and dynamics.
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Affiliation(s)
- Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, 75005 Paris, France
| | - Isabelle Dugail
- U1269 INSERM/Sorbonne Université, Nutriomics, Faculté de Médecine Pitié-Salpêtrière, 75013 Paris, France
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120
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Yang L, Yang C, Thomes PG, Kharbanda KK, Casey CA, McNiven MA, Donohue TM. Lipophagy and Alcohol-Induced Fatty Liver. Front Pharmacol 2019; 10:495. [PMID: 31143122 PMCID: PMC6521574 DOI: 10.3389/fphar.2019.00495] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022] Open
Abstract
This review describes the influence of ethanol consumption on hepatic lipophagy, a selective form of autophagy during which fat-storing organelles known as lipid droplets (LDs) are degraded in lysosomes. During classical autophagy, also known as macroautophagy, all forms of macromolecules and organelles are sequestered in autophagosomes, which, with their cargo, fuse with lysosomes, forming autolysosomes in which the cargo is degraded. It is well established that excessive drinking accelerates intrahepatic lipid biosynthesis, enhances uptake of fatty acids by the liver from the plasma and impairs hepatic secretion of lipoproteins. All the latter contribute to alcohol-induced fatty liver (steatosis). Here, our principal focus is on lipid catabolism, specifically the impact of excessive ethanol consumption on lipophagy, which significantly influences the pathogenesis alcohol-induced steatosis. We review findings, which demonstrate that chronic ethanol consumption retards lipophagy, thereby exacerbating steatosis. This is important for two reasons: (1) Unlike adipose tissue, the liver is considered a fat-burning, not a fat-storing organ. Thus, under normal conditions, lipophagy in hepatocytes actively prevents lipid droplet accumulation, thereby maintaining lipostasis; (2) Chronic alcohol consumption subverts this fat-burning function by slowing lipophagy while accelerating lipogenesis, both contributing to fatty liver. Steatosis was formerly regarded as a benign consequence of heavy drinking. It is now recognized as the "first hit" in the spectrum of alcohol-induced pathologies that, with continued drinking, progresses to more advanced liver disease, liver failure, and/or liver cancer. Complete lipid droplet breakdown requires that LDs be digested to release their high-energy cargo, consisting principally of cholesteryl esters and triacylglycerols (triglycerides). These subsequently undergo lipolysis, yielding free fatty acids that are oxidized in mitochondria to generate energy. Our review will describe recent findings on the role of lipophagy in LD catabolism, how continuous heavy alcohol consumption affects this process, and the putative mechanism(s) by which this occurs.
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Affiliation(s)
- Li Yang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changqing Yang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Paul G. Thomes
- Research Service, Department of Veterans Affairs, Nebraska-Western Iowa Health Care System, Omaha, NE, United States
- Departments of Internal Medicine and of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kusum K. Kharbanda
- Research Service, Department of Veterans Affairs, Nebraska-Western Iowa Health Care System, Omaha, NE, United States
- Departments of Internal Medicine and of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Carol A. Casey
- Research Service, Department of Veterans Affairs, Nebraska-Western Iowa Health Care System, Omaha, NE, United States
- Departments of Internal Medicine and of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Mark A. McNiven
- Division of Gastroenterology and Hepatology, Department of Biochemistry and Molecular Biology, Center for Basic Research in Digestive Diseases, Mayo Clinic, Rochester, MN, United States
| | - Terrence M. Donohue
- Research Service, Department of Veterans Affairs, Nebraska-Western Iowa Health Care System, Omaha, NE, United States
- Departments of Internal Medicine and of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
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121
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Preuss C, Jelenik T, Bódis K, Müssig K, Burkart V, Szendroedi J, Roden M, Markgraf DF. A New Targeted Lipidomics Approach Reveals Lipid Droplets in Liver, Muscle and Heart as a Repository for Diacylglycerol and Ceramide Species in Non-Alcoholic Fatty Liver. Cells 2019; 8:cells8030277. [PMID: 30909521 PMCID: PMC6468791 DOI: 10.3390/cells8030277] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity is frequently associated with excessive accumulation of lipids in ectopic tissue and presents a major risk factor for type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD). Diacylglycerols (DAGs) and ceramides (CERs) were identified as key players in lipid-induced insulin resistance, typical for such diseases. Recent results suggest that the subcellular distribution of these lipids affects their lipotoxic properties. However, the subcellular dynamics of these lipids and the role of lipid droplets (LDs) as a potential storage site is not understood. Here, we developed a liquid chromatography triple quadrupole mass spectrometry (LC-MS/MS)-method for the rapid and simultaneous quantification of DAG and CER species in tissue sample fractions. The assay is characterized by excellent recovery of analytes, limit of quantification, accuracy and precision. We established a fractionation protocol that allows the separation of subcellular tissue fractions. This method was subsequently tested to measure the concentration of DAGs and CERs in subcellular fractions of human muscle and several mouse tissues. In a mouse model of NAFLD, application of this method revealed a prominent role for LDs as repository for lipotoxic DAG and CER species. In conclusion, the new method proved as a valuable tool to analyse the subcellular dynamics of lipotoxins, related to the pathogenesis of insulin resistance, T2D and NAFLD.
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Affiliation(s)
- Christina Preuss
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
| | - Tomas Jelenik
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
| | - Kálmán Bódis
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
| | - Karsten Müssig
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, D-40225, Düsseldorf, Germany.
| | - Volker Burkart
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
| | - Julia Szendroedi
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, D-40225, Düsseldorf, Germany.
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, D-40225, Düsseldorf, Germany.
| | - Daniel F Markgraf
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), München, D-85764 Neuherberg, Germany.
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122
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Needham EJ, Parker BL, Burykin T, James DE, Humphrey SJ. Illuminating the dark phosphoproteome. Sci Signal 2019; 12:12/565/eaau8645. [PMID: 30670635 DOI: 10.1126/scisignal.aau8645] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein phosphorylation is a major regulator of protein function and biological outcomes. This was first recognized through functional biochemical experiments, and in the past decade, major technological advances in mass spectrometry have enabled the study of protein phosphorylation on a global scale. This rapidly growing field of phosphoproteomics has revealed that more than 100,000 distinct phosphorylation events occur in human cells, which likely affect the function of every protein. Phosphoproteomics has improved the understanding of the function of even the most well-characterized protein kinases by revealing new downstream substrates and biology. However, current biochemical and bioinformatic approaches have only identified kinases for less than 5% of the phosphoproteome, and functional assignments of phosphosites are almost negligible. Notably, our understanding of the relationship between kinases and their substrates follows a power law distribution, with almost 90% of phosphorylation sites currently assigned to the top 20% of kinases. In addition, more than 150 kinases do not have a single known substrate. Despite a small group of kinases dominating biomedical research, the number of substrates assigned to a kinase does not correlate with disease relevance as determined by pathogenic human mutation prevalence and mouse model phenotypes. Improving our understanding of the substrates targeted by all kinases and functionally annotating the phosphoproteome will be broadly beneficial. Advances in phosphoproteomics technologies, combined with functional screening approaches, should make it feasible to illuminate the connectivity and functionality of the entire phosphoproteome, providing enormous opportunities for discovering new biology, therapeutic targets, and possibly diagnostics.
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Affiliation(s)
- Elise J Needham
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Timur Burykin
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
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123
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Liang N, Jakobsson T, Fan R, Treuter E. The Nuclear Receptor-Co-repressor Complex in Control of Liver Metabolism and Disease. Front Endocrinol (Lausanne) 2019; 10:411. [PMID: 31293521 PMCID: PMC6606711 DOI: 10.3389/fendo.2019.00411] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/07/2019] [Indexed: 12/21/2022] Open
Abstract
Hepatocytes are the major cell-type in the liver responsible for the coordination of metabolism in response to multiple signaling inputs. Coordination occurs primarily at the level of gene expression via transcriptional networks composed of transcription factors, in particular nuclear receptors (NRs), and associated co-regulators, including chromatin-modifying complexes. Disturbance of these networks by genetic, environmental or nutritional factors can lead to metabolic dysregulation and has been linked to the progression of non-alcoholic fatty liver disease (NAFLD) toward steatohepatitis and even liver cancer. Since there are currently no approved therapies, major efforts are dedicated to identify the critical factors that can be employed for drug development. Amongst the identified factors with clinical significance are currently lipid-sensing NRs including PPARs, LXRs, and FXR. However, major obstacles of NR-targeting are the undesired side effects associated with the genome-wide NR activities in multiple cell-types. Thus, of particular interest are co-regulators that determine NR activities, context-selectivity, and associated chromatin states. Current research on the role of co-regulators in hepatocytes is still premature due to the large number of candidates, the limited number of available mouse models, and the technical challenges in studying their chromatin occupancy. As a result, how NR-co-regulator networks in hepatocytes are coordinated by extracellular signals, and how NR-pathway selectivity is achieved, remains currently poorly understood. We will here review a notable exception, namely a fundamental transcriptional co-repressor complex that during the past decade has become the probably most-studied and best-understood physiological relevant co-regulator in hepatocytes. This multiprotein complex contains the core subunits HDAC3, NCOR, SMRT, TBL1, TBLR1, and GPS2 and is referred to as the "NR-co-repressor complex." We will particularly discuss recent advances in characterizing hepatocyte-specific loss-of-function mouse models and in applying genome-wide sequencing approaches including ChIP-seq. Both have been instrumental to uncover the role of each of the subunits under physiological conditions and in disease models, but they also revealed insights into the NR target range and genomic mechanisms of action of the co-repressor complex. We will integrate a discussion of translational aspects about the role of the complex in NAFLD pathways and in particular about the hypothesis that patient-specific alterations of specific subunits may determine NAFLD susceptibility and the therapeutic outcomes of NR-directed treatments.
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Affiliation(s)
- Ning Liang
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Tomas Jakobsson
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Rongrong Fan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Eckardt Treuter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- *Correspondence: Eckardt Treuter
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Li Z, Olzmann JA. A Proteomic Map to Navigate Subcellular Reorganization in Fatty Liver Disease. Dev Cell 2018; 47:139-141. [PMID: 30352174 DOI: 10.1016/j.devcel.2018.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a tour de force in this issue of Developmental Cell, Krahmer et al. leverage proteomic platforms to reveal subcellular proteome dynamics during development of nonalcoholic fatty liver disease. Their findings uncover a remarkable degree of subcellular reorganization, alterations in protein localization, and remodeling of organelle contact sites.
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Affiliation(s)
- Zhipeng Li
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
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125
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Itzhak DN, Schessner JP, Borner GHH. Dynamic Organellar Maps for Spatial Proteomics. ACTA ACUST UNITED AC 2018; 83:e81. [PMID: 30489039 DOI: 10.1002/cpcb.81] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Eukaryotic cells are highly compartmentalized and protein subcellular localization critically influences protein function. Identification of the subcellular localizations of proteins and their translocation events upon perturbation has mostly been confined to targeted studies or laborious microscopy-based methods. Here we describe a systematic mass spectrometry-based method for spatial proteomics. The approach uses simple fractionation profiling and has two applications: Firstly it can be used to infer subcellular protein localization on a proteome-wide scale, resulting in a protein map of the cell. Secondly, the method permits identification of changes in protein localization, by comparing maps made under different conditions, as a tool for unbiased systems cell biology. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julia P Schessner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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