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Karkossa I, Fürst S, Großkopf H, von Bergen M, Schubert K. Oxidation is an underappreciated post-translational modification in the regulation of immune responses associated with changes in phosphorylation. Front Immunol 2023; 14:1244431. [PMID: 37809076 PMCID: PMC10559879 DOI: 10.3389/fimmu.2023.1244431] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Although macrophages are known to be affected by their redox status, oxidation is not yet a well-recognized post-translational modification (PTM) in regulating macrophages and immune cells in general. While it has been described that the redox status of single cysteines in specific proteins is relevant for macrophage functions, global oxidation information is scarce. Hence, we globally assessed the impact of oxidation on macrophage activation using untargeted proteomics and PTM-omics. We exposed THP-1 macrophages to lipopolysaccharide (LPS) for 4 h and 24 h and applied a sequential iodoTMT labeling approach to get information on overall oxidation as well as reversible oxidation of cysteines. Thus, we identified 10452 oxidation sites, which were integratively analyzed with 5057 proteins and 7148 phosphorylation sites to investigate their co-occurance with other omics layers. Based on this integrative analysis, we found significant upregulation of several immune-related pathways, e.g. toll-like receptor 4 (TLR4) signaling, for which 19 proteins, 7 phosphorylation sites, and 39 oxidation sites were significantly affected, highlighting the relevance of oxidations in TLR4-induced macrophage activation. Co-regulation of oxidation and phosphorylation was observed, as evidenced by multiply modified proteins related to inflammatory pathways. Additionally, we observed time-dependent effects, with differences in the dynamics of oxidation sites compared to proteins and phosphorylation sites. Overall, this study highlights the importance of oxidation in regulating inflammatory processes and provides a method that can be readily applied to study the cellular redoxome globally.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sabine Fürst
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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Großkopf H, Vogel S, Müller CD, Köhling S, Dürig JN, Möller S, Schnabelrauch M, Rademann J, Hempel U, von Bergen M, Schubert K. Identification of intracellular glycosaminoglycan-interacting proteins by affinity purification mass spectrometry. Biol Chem 2021; 402:1427-1440. [PMID: 34472763 DOI: 10.1515/hsz-2021-0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/25/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) are essential functional components of the extracellular matrix (ECM). Artificial GAGs like sulfated hyaluronan (sHA) exhibit pro-osteogenic properties and boost healing processes. Hence, they are of high interest for supporting bone regeneration and wound healing. Although sulfated GAGs (sGAGs) appear intracellularly, the knowledge about intracellular effects and putative interaction partners is scarce. Here we used an affinity-purification mass spectrometry-based (AP-MS) approach to identify novel and particularly intracellular sGAG-interacting proteins in human bone marrow stromal cells (hBMSC). Overall, 477 proteins were found interacting with at least one of four distinct sGAGs. Enrichment analysis for protein localization showed that mainly intracellular and cell-associated interacting proteins were identified. The interaction of sGAG with α2-macroglobulin receptor-associated protein (LRPAP1), exportin-1 (XPO1), and serine protease HTRA1 (HTRA1) was confirmed in reverse assays. Consecutive pathway and cluster analysis led to the identification of biological processes, namely processes involving binding and processing of nucleic acids, LRP1-dependent endocytosis, and exosome formation. Respecting the preferentially intracellular localization of sGAG in vesicle-like structures, also the interaction data indicate sGAG-specific modulation of vesicle-based transport processes. By identifying many sGAG-specific interacting proteins, our data provide a resource for upcoming studies aimed at molecular mechanisms and understanding of sGAG cellular effects.
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Affiliation(s)
- Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
| | - Sarah Vogel
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Claudia Damaris Müller
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Sebastian Köhling
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Jan-Niklas Dürig
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Stephanie Möller
- Biomaterials Department, INNOVENT e.V. Technologieentwicklung Jena, Jena D-07745, Germany
| | - Matthias Schnabelrauch
- Biomaterials Department, INNOVENT e.V. Technologieentwicklung Jena, Jena D-07745, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Ute Hempel
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
- Institute of Biochemistry, Faculty of Life Sciences, Universität Leipzig, Leipzig D-04103, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
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Wang Z, Karkossa I, Großkopf H, Canzler S, Rolle-Kampczyk U, Hackermüller J, Bergen M, Schubert K. Quantitative proteomics reveal mechanistic insights into direct and indirect drug-induced thyroid toxicity in rats. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00550-6] [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: 10/20/2022]
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Großkopf H, Walter K, Karkossa I, von Bergen M, Schubert K. Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. Front Immunol 2021; 12:620270. [PMID: 33868237 PMCID: PMC8045971 DOI: 10.3389/fimmu.2021.620270] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Emerging studies revealed that the Aryl hydrocarbon receptor (AhR), a receptor sensing environmental contaminants, is executing an immunomodulatory function. However, it is an open question to which extent this is achieved by its role as a transcription factor or via non-genomic signaling. We utilized a multi-post-translational modification-omics approach to examine non-genomic AhR-signaling after activation with endogenous (FICZ) or exogenous (BaP) ligand in endotoxin-activated (LPS) monocyte-derived macrophages. While AhR activation affected abundances of few proteins, regulation of ubiquitination and phosphorylation were highly pronounced. Although the number and strength of effects depended on the applied AhR-ligand, both ligands increased ubiquitination of Rac1, which participates in PI3K/AKT-pathway-dependent macrophage activation, resulting in a pro-inflammatory phenotype. In contrast, co-treatment with ligand and LPS revealed a decreased AKT activity mediating an anti-inflammatory effect. Thus, our data show an immunomodulatory effect of AhR activation through a Rac1ubiquitination-dependent mechanism that attenuated AKT-signaling, resulting in a mitigated inflammatory response.
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Affiliation(s)
- Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Katharina Walter
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany.,Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Wang Z, Karkossa I, Großkopf H, Rolle-Kampczyk U, Hackermüller J, von Bergen M, Schubert K. Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP. Toxicology 2020; 448:152652. [PMID: 33278487 DOI: 10.1016/j.tox.2020.152652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/10/2020] [Revised: 11/19/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
The application of quantitative proteomics provides a new and promising tool for standardized toxicological research. However, choosing a suitable quantitative method still puzzles many researchers because the optimal method needs to be determined. In this study, we investigated the advantages and limitations of two of the most commonly used global quantitative proteomics methods, namely label-free quantitation (LFQ) and tandem mass tags (TMT). As a case study, we exposed hepatocytes (HepG2) to the environmental contaminant benzo[a]pyrene (BaP) using a concentration of 2 μM. Our results revealed that both methods yield a similar proteome coverage, in which for LFQ a wider range of fold changes was observed but with less significant p-values compared to TMT. We detected 37 and 47 significantly enriched pathways by LFQ and TMT, respectively, with 17 overlapping pathways. To define the minimally required effort in proteomics as a benchmark, we artificially reduced the LFQ, and TMT data sets stepwise and compared the pathway enrichment. Thereby, we found that fewer proteins are necessary for detecting significant enrichment of pathways in TMT compared to LFQ, which might be explained by the higher reproducibility of the TMT data that was observed. In summary, we showed that the TMT approach is the preferable one when investigating toxicological questions because it offers a high reproducibility and sufficient proteome coverage in a comparably short time.
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Affiliation(s)
- Zhipeng Wang
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jörg Hackermüller
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
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Großkopf H, Böhmer A, Tsikas D. Letter to the editor: “Role of the human erythrocyte in generation and storage of asymmetric dimethylarginine”. Am J Physiol Heart Circ Physiol 2012; 303:H751-2. [DOI: 10.1152/ajpheart.00449.2012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Henning Großkopf
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany
| | - Anke Böhmer
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany
| | - Dimitrios Tsikas
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany
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Böhmer A, Großkopf H, Jordan J, Tsikas D. Human hemoglobin does not contain asymmetric dimethylarginine (ADMA). Nitric Oxide 2012; 27:72-4. [PMID: 22504048 DOI: 10.1016/j.niox.2012.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 02/27/2012] [Accepted: 03/28/2012] [Indexed: 01/19/2023]
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