1
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Villar J, Cros A, De Juan A, Alaoui L, Bonte PE, Lau CM, Tiniakou I, Reizis B, Segura E. ETV3 and ETV6 enable monocyte differentiation into dendritic cells by repressing macrophage fate commitment. Nat Immunol 2023; 24:84-95. [PMID: 36543959 PMCID: PMC9810530 DOI: 10.1038/s41590-022-01374-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
In inflamed tissues, monocytes differentiate into macrophages (mo-Macs) or dendritic cells (mo-DCs). In chronic nonresolving inflammation, mo-DCs are major drivers of pathogenic events. Manipulating monocyte differentiation would therefore be an attractive therapeutic strategy. However, how the balance of mo-DC versus mo-Mac fate commitment is regulated is not clear. In the present study, we show that the transcriptional repressors ETV3 and ETV6 control human monocyte differentiation into mo-DCs. ETV3 and ETV6 inhibit interferon (IFN)-stimulated genes; however, their action on monocyte differentiation is independent of IFN signaling. Instead, we find that ETV3 and ETV6 directly repress mo-Mac development by controlling MAFB expression. Mice deficient for Etv6 in monocytes have spontaneous expression of IFN-stimulated genes, confirming that Etv6 regulates IFN responses in vivo. Furthermore, these mice have impaired mo-DC differentiation during inflammation and reduced pathology in an experimental autoimmune encephalomyelitis model. These findings provide information about the molecular control of monocyte fate decision and identify ETV6 as a therapeutic target to redirect monocyte differentiation in inflammatory disorders.
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Affiliation(s)
- Javiera Villar
- Institut Curie, PSL Research University, INSERM, U932,, Paris, France
| | - Adeline Cros
- Institut Curie, PSL Research University, INSERM, U932,, Paris, France
| | - Alba De Juan
- Institut Curie, PSL Research University, INSERM, U932,, Paris, France
| | - Lamine Alaoui
- Institut Curie, PSL Research University, INSERM, U932,, Paris, France
| | | | - Colleen M Lau
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Elodie Segura
- Institut Curie, PSL Research University, INSERM, U932,, Paris, France.
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2
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Role of Histone Deacetylases in Monocyte Function in Health and Chronic Inflammatory Diseases. Rev Physiol Biochem Pharmacol 2021; 180:1-47. [PMID: 33974124 DOI: 10.1007/112_2021_59] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Histone deacetylases (HDACs) are a family of 18 members that participate in the epigenetic regulation of gene expression. In addition to histones, some HDACs also deacetylate transcription factors and specific cytoplasmic proteins.Monocytes, as part of the innate immune system, maintain tissue homeostasis and help fight infections and cancer. In these cells, HDACs are involved in multiple processes including proliferation, migration, differentiation, inflammatory response, infections, and tumorigenesis. Here, a systematic description of the role that most HDACs play in these functions is reviewed. Specifically, some HDACs induce a pro-inflammatory response and play major roles in host defense. Conversely, other HDACs reprogram monocytes and macrophages towards an immunosuppressive phenotype. The right balance between both types helps monocytes to respond correctly to the different physiological/pathological stimuli. However, aberrant expressions or activities of specific HDACs are associated with autoimmune diseases along with other chronic inflammatory diseases, infections, or cancer.This paper critically reviews the interesting and extensive knowledge regarding the role of some HDACs in these pathologies. It also shows that as yet, very little progress has been made toward the goal of finding effective HDAC-targeted therapies. However, given their obvious potential, we conclude that it is worth the effort to develop monocyte-specific drugs that selectively target HDAC subtypes with the aim of finding effective treatments for diseases in which our innate immune system is involved.
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3
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Cardon T, Ozcan B, Aboulouard S, Kobeissy F, Duhamel M, Rodet F, Fournier I, Salzet M. Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. ACS OMEGA 2020; 5:27774-27782. [PMID: 33163760 PMCID: PMC7643081 DOI: 10.1021/acsomega.0c02530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Our previous investigation on macrophages has allowed us to show that the inhibition of the enzyme proprotein convertase (PC1/3) controls the activation of macrophages. We demonstrated that PC1/3 knockdown (KD) in macrophages exhibits an increased secretion of proinflammatory and antitumoral factors. In this biological context, we assessed the presence of histone modifications and the presence and contribution of a "ghost proteome" in these macrophages. We identified a set of alternative proteins (AltProts) that have a key role in the regulation of various signaling pathways. In this study, to further investigate the underlying mechanisms involved in the resistance of PC1/3-KD macrophages to anti-inflammatory stimuli, we have conducted a proteomic system biology study to assess the epigenome variation, focusing on histone modifications. Results from our study have indicated the presence of significant variations in histone modifications along with the identification of 28 AltProts, which can be correlated with antitumoral resistance under IL-10 stimulation. These findings highlight a key role of altered epigenome histone modifications in driving resistance and indicate that like the reference proteins, AltProts can have a major impact in the field of epigenetics and regulation of gene expression, as shown in our results.
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Affiliation(s)
- Tristan Cardon
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Bilgehan Ozcan
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Soulaimane Aboulouard
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Firas Kobeissy
- Department
of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Marie Duhamel
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Franck Rodet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Isabelle Fournier
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
| | - Michel Salzet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
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4
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Pinton G, Ferraro A, Balma M, Moro L. Specific low-frequency electromagnetic fields induce expression of active KDM6B associated with functional changes in U937 cells. Electromagn Biol Med 2020; 39:139-153. [PMID: 32151171 DOI: 10.1080/15368378.2020.1737807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this study, we investigated the effects of specific low-frequency electromagnetic field sequences on U937 cells, an in vitro model of human monocyte/macrophage differentiation. U937 cells were exposed to electromagnetic stimulation by means of the SynthéXer system using two similar sequences, XR-BC31 and XR-BC31/F. Each sequence was a time series of 29 wave segments, equal to a total duration of 77 min. Here, we report that exposure (4 d, once a day) of U937 cells to the XR-BC31 setting, but not to the XR-BC31/F, resulted in increased expression of the histone demethylase KDM6B along with a global reduction in histone H3 lysine 27 tri-methylation (H3K27me3). Furthermore, exposure to the XR-BC31 sequence induced differentiation of U937 cells towards a macrophage-like phenotype displaying a KDM6B dependent increase in expression and secretion of the anti-inflammatory interleukins (ILs), IL-10 and IL-4. Importantly, all the observed changes were highly dependent on the nature of the sequence. Our results open a new way of interpretation for the effects of low-frequency electromagnetic fields observed in vivo. Indeed, it is conceivable that a specific low-frequency electromagnetic fields treatment may cause the reprogramming of H3K27me3 and cell differentiation.
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Affiliation(s)
- Giulia Pinton
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Angelo Ferraro
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | | | - Laura Moro
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
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5
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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: 0.4] [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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6
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Ribechini E, Eckert I, Beilhack A, Du Plessis N, Walzl G, Schleicher U, Ritter U, Lutz MB. Heat-killed Mycobacterium tuberculosis prime-boost vaccination induces myeloid-derived suppressor cells with spleen dendritic cell-killing capability. JCI Insight 2019; 5:128664. [PMID: 31162143 DOI: 10.1172/jci.insight.128664] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis patients and mice infected with live Mycobacterium tuberculosis (Mtb) accumulate high numbers of myeloid-derived suppressor cells (MDSCs). Here, we hypothesized that also dead Mtb vaccines may induce MDSCs that could impair the efficacy of vaccination. We found that repeated injections of Mtb vaccines (heat-killed Mtb in Incomplete Freund's Adjuvant, like Montanide) but not single or control vaccines without Mtb strongly expanded CD11b+ myeloid cells in the spleen, that suppressed T cell proliferation and killing ex vivo. Dead Mtb vaccination induced the generation of CD11b+ Ly-6Chigh CD115+ iNOS/Nos2+ monocytic MDSCs (M-MDSCs) upon application of inflammatory or microbial activation signals. In vivo these M-MDSCs positioned strategically in the spleen by infiltrating the splenic bridging channels and white pulp areas. Notably, within 6 to 24 hours in a Nos2-dependent fashion they produced NO to rapidly kill conventional and plasmacytoid dendritic cells (cDCs, pDCs) while, surprisingly, sparing T cells in vivo. Thus, we demonstrate that Mtb vaccine induced M-MDSCs to not directly suppress T cell in vivo but, instead, M-MDSCs directly target DC subpopulations thereby indirectly suppressing effector T cell responses. Collectively, we demonstrate that Mtb booster vaccines induce M-MDSCs in the spleen that can be activated to kill DCs cautioning to thoroughly investigate MDSC formation in individuals after Mtb vaccination in clinical trials.
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Affiliation(s)
- Eliana Ribechini
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Ina Eckert
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Andreas Beilhack
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Nelita Du Plessis
- South African Medical Research Council, Centre for Tuberculosis Research, Department of Science and Technology - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- South African Medical Research Council, Centre for Tuberculosis Research, Department of Science and Technology - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ulrike Schleicher
- Microbiology Institute, Clinical Microbiology, Immunology and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Uwe Ritter
- RCI Regensburg Center for Interventional Immunology, Institute of Immunology, University Medical Center Regensburg, University of Regensburg, Regensburg, Germany
| | - Manfred B Lutz
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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7
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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Lutz MB, Strobl H, Schuler G, Romani N. GM-CSF Monocyte-Derived Cells and Langerhans Cells As Part of the Dendritic Cell Family. Front Immunol 2017; 8:1388. [PMID: 29109731 PMCID: PMC5660299 DOI: 10.3389/fimmu.2017.01388] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022] Open
Abstract
Dendritic cells (DCs) and macrophages (Mph) share many characteristics as components of the innate immune system. The criteria to classify the multitude of subsets within the mononuclear phagocyte system are currently phenotype, ontogeny, transcription patterns, epigenetic adaptations, and function. More recently, ontogenetic, transcriptional, and proteomic research approaches uncovered major developmental differences between Flt3L-dependent conventional DCs as compared with Mphs and monocyte-derived DCs (MoDCs), the latter mainly generated in vitro from murine bone marrow-derived DCs (BM-DCs) or human CD14+ peripheral blood monocytes. Conversely, in vitro GM-CSF-dependent monocyte-derived Mphs largely resemble MoDCs whereas tissue-resident Mphs show a common embryonic origin from yolk sac and fetal liver with Langerhans cells (LCs). The novel ontogenetic findings opened discussions on the terminology of DCs versus Mphs. Here, we bring forward arguments to facilitate definitions of BM-DCs, MoDCs, and LCs. We propose a group model of terminology for all DC subsets that attempts to encompass both ontogeny and function.
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Affiliation(s)
- Manfred B Lutz
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Herbert Strobl
- Institute of Pathophysiology and Immunology, Medical University of Graz, Graz, Austria
| | - Gerold Schuler
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Nikolaus Romani
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
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9
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Acute Strenuous Exercise Induces an Imbalance on Histone H4 Acetylation/Histone Deacetylase 2 and Increases the Proinflammatory Profile of PBMC of Obese Individuals. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1530230. [PMID: 29142617 PMCID: PMC5671743 DOI: 10.1155/2017/1530230] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/07/2017] [Accepted: 09/10/2017] [Indexed: 02/08/2023]
Abstract
This study evaluated the response of global histone H4 acetylation (H4ac), histone deacetylase 2 (HDAC2) activity, as well as the production of proinflammatory cytokines and monocyte phenotypes of lean and obese males after exercise. Ten lean and ten obese sedentary men were submitted to one session of strenuous exercise, and peripheral blood mononuclear cells (PBMC) were stimulated in vitro with lipopolysaccharide (LPS). Global H4ac levels, HDAC2 activity in PBMC, and IL-6, IL-8, and TNF-α production were analyzed. Monocyte phenotype was determined in accordance with the expression of CD14 and CD16. At rest, obese individuals presented higher frequency of proinflammatory CD14+CD16+ monocytes. LPS induced a significant augment in global H4ac and in the production of IL-6, IL-8, and TNF-α mainly in obese individuals. After exercise, the increased production of IL-8 and TNF-α and peripheral frequency of CD14+CD16+ were observed in both groups. In addition, exercise also induced a significant hyperacetylation of histone H4 and decreased HDAC2 activity in both nonstimulated and LPS-stimulated PBMC of obese individuals. Our data indicate that the obesity impacts on H4ac levels and that strenuous exercise leads to an enhanced chronic low-grade inflammation profile in obesity via an imbalance on H4ac/HDAC2.
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10
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Zhang K, Xu P, Sowers JL, Machuca DF, Mirfattah B, Herring J, Tang H, Chen Y, Tian B, Brasier AR, Sowers LC. Proteome Analysis of Hypoxic Glioblastoma Cells Reveals Sequential Metabolic Adaptation of One-Carbon Metabolic Pathways. Mol Cell Proteomics 2017; 16:1906-1921. [PMID: 28874504 DOI: 10.1074/mcp.ra117.000154] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 02/04/2023] Open
Abstract
Rapidly proliferating tumors are exposed to a hypoxic microenvironment because of their density, high metabolic consumption, and interruptions in blood flow because of immature angiogenesis. Cellular responses to hypoxia promote highly malignant and metastatic behavior, as well as a chemotherapy-resistant state. To better understand the complex relationships between hypoxic adaptations and cancer progression, we studied the dynamic proteome responses of glioblastoma cells exposed to hypoxia via an innovative approach: quantification of newly synthesized proteins using heavy stable-isotope arginine labeling combined with accurate assessment of cell replication by quantification of the light/heavy arginine ratio of peptides in histone H4. We found that hypoxia affects cancer cells in multiple intertwined ways: inflammation, typically with over-expressed glucose transporter (GLUT1), DUSP4/MKP2, and RelA proteins; a metabolic adaptation with overexpression of all glycolytic pathway enzymes for pyruvate/lactate synthesis; and the EMT (epithelial-mesenchymal transition) and cancer stem cell (CSC) renewal with characteristic morphological changes and mesenchymal/CSC protein expression profiles. For the first time, we identified the vitamin B12 transporter protein TCN2, which is essential for one-carbon metabolism, as being significantly downregulated. Further, we found, by knockdown and overexpression experiments, that TCN2 plays an important role in controlling cancer cell transformation toward the highly aggressive mesenchymal/CSC stage; low expression of TCN2 has an effect similar to hypoxia, whereas high expression of TCN2 can reverse it. We conclude that hypoxia induces sequential metabolic responses of one-carbon metabolism in tumor cells. Our mass spectrometry data are available via ProteomeXchange with identifiers PXD005487 (TMT-labeling) and PXD007280 (label-free).
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Affiliation(s)
- Kangling Zhang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555; .,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Pei Xu
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - James L Sowers
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Daniel F Machuca
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Barsam Mirfattah
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Jason Herring
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Hui Tang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Yan Chen
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Bing Tian
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Allan R Brasier
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Lawrence C Sowers
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555.,§Institute for Translational Sciences, UTMB, Galveston, Texas, 77555
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11
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Short JD, Tavakoli S, Nguyen HN, Carrera A, Farnen C, Cox LA, Asmis R. Dyslipidemic Diet-Induced Monocyte "Priming" and Dysfunction in Non-Human Primates Is Triggered by Elevated Plasma Cholesterol and Accompanied by Altered Histone Acetylation. Front Immunol 2017; 8:958. [PMID: 28878765 PMCID: PMC5572238 DOI: 10.3389/fimmu.2017.00958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Monocytes and the recruitment of monocyte-derived macrophages into sites of inflammation play a key role in atherogenesis and other chronic inflammatory diseases linked to cardiometabolic syndrome and obesity. Previous studies from our group have shown that metabolic stress promotes monocyte priming, i.e., enhanced adhesion and accelerated chemotaxis of monocytes in response to chemokines, both in vitro and in dyslipidemic LDLR-/- mice. We also showed that metabolic stress-induced monocyte dysfunction is, at least to a large extent caused by the S-glutathionylation, inactivation, and subsequent degradation of mitogen-activated protein kinase phosphatase 1. Here, we analyzed the effects of a Western-style, dyslipidemic diet (DD), which was composed of high levels of saturated fat, cholesterol, and simple sugars, on monocyte (dys)function in non-human primates (NHPs). We found that similar to mice, a DD enhances monocyte chemotaxis in NHP within 4 weeks, occurring concordantly with the onset of hypercholesterolemia but prior to changes in triglycerides, blood glucose, monocytosis, or changes in monocyte subset composition. In addition, we identified transitory decreases in the acetylation of histone H3 at the lysine residues 18 and 23 in metabolically primed monocytes, and we found that monocyte priming was correlated with the acetylation of histone H3 at lysine 27 after an 8-week DD regimen. Our data show that metabolic stress promotes monocyte priming and hyper-chemotactic responses in NHP. The histone modifications accompanying monocyte priming in primates suggest a reprogramming of the epigenetic landscape, which may lead to dysregulated responses and functionalities in macrophages derived from primed monocytes that are recruited to sites of inflammation.
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Affiliation(s)
- John D Short
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Sina Tavakoli
- Department of Radiology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Huynh Nga Nguyen
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ana Carrera
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Chelbee Farnen
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, United States.,Southwest National Primate Research Center, San Antonio, TX, United States
| | - Reto Asmis
- Department of Radiology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Clinical Laboratory Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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12
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Jia SJ, Gao KQ, Zhao M. Epigenetic regulation in monocyte/macrophage: A key player during atherosclerosis. Cardiovasc Ther 2017; 35. [PMID: 28371472 DOI: 10.1111/1755-5922.12262] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/23/2017] [Accepted: 03/26/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Su-Jie Jia
- Hunan Key Laboratory of Medical Epigenomics; The Second Xiangya Hospital, Central South University; Changsha China
- Department of Pharmaceutics; The Third Xiangya Hospital, Central South University; Changsha China
| | - Ke-Qin Gao
- Department of Pharmaceutics; The Third Xiangya Hospital, Central South University; Changsha China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics; The Second Xiangya Hospital, Central South University; Changsha China
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13
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Nicholas DA, Zhang K, Hung C, Glasgow S, Aruni AW, Unternaehrer J, Payne KJ, Langridge WHR, De Leon M. Palmitic acid is a toll-like receptor 4 ligand that induces human dendritic cell secretion of IL-1β. PLoS One 2017; 12:e0176793. [PMID: 28463985 PMCID: PMC5413048 DOI: 10.1371/journal.pone.0176793] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/17/2017] [Indexed: 01/22/2023] Open
Abstract
Palmitic acid (PA) and other saturated fatty acids are known to stimulate pro-inflammatory responses in human immune cells via Toll-like receptor 4 (TLR4). However, the molecular mechanism responsible for fatty acid stimulation of TLR4 remains unknown. Here, we demonstrate that PA functions as a ligand for TLR4 on human monocyte derived dendritic cells (MoDCs). Hydrophobicity protein modeling indicated PA can associate with the hydrophobic binding pocket of TLR4 adaptor protein MD-2. Isothermal titration calorimetry quantified heat absorption that occurred during PA titration into TLR4/MD2, indicating that PA binds to TLR4/MD2. Treatment of human MoDCs with PA resulted in endocytosis of TLR4, further supporting the function of PA as a TLR4 agonist. In addition, PA stimulated DC maturation and activation based on the upregulation of DC costimulatory factors CD86 and CD83. Further experiments showed that PA induced TLR4 dependent secretion of the pro-inflammatory cytokine IL-1β. Lastly, our experimental data show that PA stimulation of NF-κB canonical pathway activation is regulated by TLR4 signaling and that reactive oxygen species may be important in upregulating this pro-inflammatory response. Our experiments demonstrate for the first time that PA activation of TLR4 occurs in response to direct molecular interactions between PA and MD-2. In summary, our findings suggest a likely molecular mechanism for PA induction of pro-inflammatory immune responses in human dendritic cells expressing TLR4.
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Affiliation(s)
- Dequina A. Nicholas
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Christopher Hung
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Shane Glasgow
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Aruni Wilson Aruni
- Department of Basic Sciences, Division of Microbiology and Molecular Genetics, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Juli Unternaehrer
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Kimberly J. Payne
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Department of Anatomy and Physiology, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - William H. R. Langridge
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School Medicine, Loma Linda, California, United States of America
| | - Marino De Leon
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- Department of Basic Sciences, Division of Physiology, Loma Linda University School Medicine, Loma Linda, California, United States of America
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14
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Chen YC, Chao TY, Leung SY, Chen CJ, Wu CC, Fang WF, Wang YH, Chang HC, Wang TY, Lin YY, Zheng YX, Lin MC, Hsiao CC. Histone H3K14 hypoacetylation and H3K27 hypermethylation along with HDAC1 up-regulation and KDM6B down-regulation are associated with active pulmonary tuberculosis disease. Am J Transl Res 2017; 9:1943-1955. [PMID: 28469799 PMCID: PMC5411942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/26/2016] [Indexed: 06/07/2023]
Abstract
The aim of this study is to determine the roles of global histone acetylation (Ac)/methylation (me), their modifying enzymes, and gene-specific histone enrichment in active pulmonary tuberculosis (TB) disease. Global histone H3K27me3, H3K27me2, H3K9me3, H3K9Ac, and H3K14Ac expressions, and their modifying enzyme expressions, including KDM1A, KDM6B, EZH2, HDAC1, and HDAC2, were assessed in blood leukocytes from 81 patients with active pulmonary TB disease and 44 matched healthy subjects (HS). TLR2, TNF-α, IFN-γ, and IL12B-specific histone enrichment of peripheral blood mononuclear cells was measured by chromatin immunoprecipitation method. We found that Global H3K14Ac was decreased and H3K27me2 was increased in TB patients as compared with that in HS. TB patients with low H3K14Ac had lower one-year survival. Global H3K27me3 was increased in TB patients with high bacterial burden, or systemic symptoms as compared with that in those without the attribute or HS. HDAC1 gene/protein expressions were increased in TB patients as compared with that in HS, whereas KDM6B gene/protein expressions were decreased. Global H3K27me2, HDAC1 and KDM6B protein expressions were all reversed to normal after 6-month anti-TB treatment. TNF-α/IL12B promoter-specific H3K14Ac and TNF-α/IL12B/IFN-γ promoter-specific H3K27me2 enrichment were all decreased in 10 TB patients as compared with that in 10 HS. Among them, IL12B-specific H3K27me2 enrichment was reversed to normal after treatment, while the other 4 remained depressed. In conclusions, H3K14 hypoacetylation and H3K27 hypermethylation play a role in the development of active pulmonary TB disease or its clinical phenotypes, probably through up-regulation of HDAC1 and down-regulation of KDM6B, respectively.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial HospitalTaiwan
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Sum-Yee Leung
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Chung-Jen Chen
- Division of Rheumatology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Wen-Feng Fang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Yi-Hsi Wang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Huang-Chih Chang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Yong-Yong Lin
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Yi-Xin Zheng
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung, Taiwan
| | - Chang-Chun Hsiao
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial HospitalTaiwan
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15
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López-García I, Gerő D, Szczesny B, Szoleczky P, Olah G, Módis K, Zhang K, Gao J, Wu P, Sowers LC, DeWitt D, Prough DS, Szabo C. Development of a stretch-induced neurotrauma model for medium-throughput screening in vitro: identification of rifampicin as a neuroprotectant. Br J Pharmacol 2016; 175:284-300. [PMID: 27723079 DOI: 10.1111/bph.13642] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND PURPOSE We hypothesized that an in vitro, stretch-based model of neural injury may be useful to identify compounds that decrease the cellular damage in neurotrauma. EXPERIMENTAL APPROACH We screened three neural cell lines (B35, RN33B and SH-SY5Y) subjected to two differentiation methods and selected all-trans-retinoic acid-differentiated B35 rat neuroblastoma cells subjected to rapid stretch injury, coupled with a subthreshold concentration of H2 O2 , for the screen. The model induced marked alterations in gene expression and proteomic signature of the cells and culminated in delayed cell death (LDH release) and mitochondrial dysfunction [reduced 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) conversion]. Follow-up studies utilized human stem cell-derived neurons subjected to rapid stretch injury. KEY RESULTS From screening of a composite library of 3500 drugs, five drugs (when applied in a post-treatment regimen relative to stretch injury) improved both LDH and MTT responses. The effects of rifampicin were investigated in further detail. Rifampicin reduced cell necrosis and apoptosis and improved cellular bioenergetics. In a second model (stretch injury in human stem cell-derived neurons), rifampicin pretreatment attenuated LDH release, protected against the loss of neurite length and maintained neuron-specific class III β-tubulin immunoreactivity. CONCLUSIONS AND IMPLICATIONS We conclude that the current model is suitable for medium-throughput screening to identify compounds with neuroprotective potential. Rifampicin, when applied either in pre- or post-treatment, improves the viability of neurons subjected to stretch injury and protects against neurite loss. Rifampicin may be a candidate for repurposing for the therapy of traumatic brain injury. LINKED ARTICLES This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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Affiliation(s)
- Isabel López-García
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Domokos Gerő
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bartosz Szczesny
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Petra Szoleczky
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gabor Olah
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Katalin Módis
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kangling Zhang
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jungling Gao
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Wu
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lawrence C Sowers
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Doug DeWitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Donald S Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
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16
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Cole J, Morris P, Dickman MJ, Dockrell DH. The therapeutic potential of epigenetic manipulation during infectious diseases. Pharmacol Ther 2016; 167:85-99. [PMID: 27519803 PMCID: PMC5109899 DOI: 10.1016/j.pharmthera.2016.07.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/20/2016] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications are increasingly recognized as playing an important role in the pathogenesis of infectious diseases. They represent a critical mechanism regulating transcriptional profiles in the immune system that contributes to the cell-type and stimulus specificity of the transcriptional response. Recent data highlight how epigenetic changes impact macrophage functional responses and polarization, influencing the innate immune system through macrophage tolerance and training. In this review we will explore how post-translational modifications of histone tails influence immune function to specific infectious diseases. We will describe how these may influence outcome, highlighting examples derived from responses to acute bacterial pathogens, models of sepsis, maintenance of viral latency and HIV infection. We will discuss how emerging classes of pharmacological agents, developed for use in oncology and other settings, have been applied to models of infectious diseases and their potential to modulate key aspects of the immune response to bacterial infection and HIV therapy.
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Affiliation(s)
- Joby Cole
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK; Chemical and Biologic Engineering, University of Sheffield, UK
| | - Paul Morris
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK
| | - Mark J Dickman
- Chemical and Biologic Engineering, University of Sheffield, UK
| | - David H Dockrell
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK.
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17
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Measurement of Histone Methylation Dynamics by One-Carbon Metabolic Isotope Labeling and High-energy Collisional Dissociation Methylation Signature Ion Detection. Sci Rep 2016; 6:31537. [PMID: 27530234 PMCID: PMC4987619 DOI: 10.1038/srep31537] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/21/2016] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence suggests that cellular metabolites and nutrition levels control epigenetic modifications, including histone methylation. However, it is not currently possible to measure the metabolic control of histone methylation. Here we report a novel detection method to monitor methyl transfer from serine to histones through the one-carbon metabolic pathway, using stable-isotope labeling and detection of lysine methylation signature ions generated in high-energy-dissociation (HCD) tandem mass spectrometry. This method is a long-needed tool to study the metabolic control of histone methylation.
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18
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Sowers JL, Mirfattah B, Xu P, Tang H, Park IY, Walker C, Wu P, Laezza F, Sowers LC, Zhang K. Quantification of histone modifications by parallel-reaction monitoring: a method validation. Anal Chem 2016; 87:10006-14. [PMID: 26356480 DOI: 10.1021/acs.analchem.5b02615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal epigenetic reprogramming is one of the major causes leading to irregular gene expression and regulatory pathway perturbations, in the cells, resulting in unhealthy cell development or diseases. Accurate measurements of these changes of epigenetic modifications, especially the complex histone modifications, are very important, and the methods for these measurements are not trivial. By following our previous introduction of PRM to targeting histone modifications (Tang, H.; Fang, H.; Yin, E.; Brasier, A. R.; Sowers, L. C.; Zhang, K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal. Chem. 2014, 86 (11), 5526-34), herein we validated this method by varying the protein/trypsin ratios via serial dilutions. Our data demonstrated that PRM with SILAC histones as the internal standards allowed reproducible measurements of histone H3/H4 acetylation and methylation in the samples whose histone contents differ at least one-order of magnitude. The method was further validated by histones isolated from histone H3 K36 trimethyltransferase SETD2 knockout mouse embryonic fibroblasts (MEF) cells. Furthermore, histone acetylation and methylation in human neural stem cells (hNSC) treated with ascorbic acid phosphate (AAP) were measured by this method, revealing that H3 K36 trimethylation was significantly down-regulated by 6 days of treatment with vitamin C.
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Affiliation(s)
| | | | | | | | - In Young Park
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
| | - Cheryl Walker
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
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19
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Stützer A, Liokatis S, Kiesel A, Schwarzer D, Sprangers R, Söding J, Selenko P, Fischle W. Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails. Mol Cell 2016; 61:247-59. [PMID: 26778125 DOI: 10.1016/j.molcel.2015.12.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/23/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
Abstract
Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function.
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Affiliation(s)
- Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stamatios Liokatis
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany
| | - Anja Kiesel
- Research Group of Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Department of Chemical Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Johannes Söding
- Research Group of Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Philipp Selenko
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany.
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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20
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Zhang Y, Bottinelli D, Lisacek F, Luban J, Strambio-De-Castillia C, Varesio E, Hopfgartner G. Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies. Anal Biochem 2015; 484:40-50. [PMID: 25983236 PMCID: PMC4732721 DOI: 10.1016/j.ab.2015.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 12/11/2022]
Abstract
Dendritic cells (DCs) are specialized leukocytes that orchestrate the adaptive immune response. Mass spectrometry (MS)-based proteomic study of these cells presents technical challenges, especially when the DCs are human in origin due to the paucity of available biological material. Here, to maximize MS coverage of the global human DC proteome, different cell disruption methods, lysis conditions, protein precipitation, and protein pellet solubilization and denaturation methods were compared. Mechanical disruption of DC cell pellets under cryogenic conditions, coupled with the use of RIPA (radioimmunoprecipitation assay) buffer, was shown to be the method of choice based on total protein extraction and on the solubilization and identification of nuclear proteins. Precipitation by acetone was found to be more efficient than that by 10% trichloroacetic acid (TCA)/acetone, allowing in excess of 28% more protein identifications. Although being an effective strategy to eliminate the detergent residue, the acetone wash step caused a loss of protein identifications. However, this potential drawback was overcome by adding 1% sodium deoxycholate into the dissolution buffer, which enhanced both solubility of the precipitated proteins and digestion efficiency. This in turn resulted in 6 to 11% more distinct peptides and 14 to 19% more total proteins identified than using 0.5M triethylammonium bicarbonate alone, with the greatest increase (34%) for hydrophobic proteins.
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Affiliation(s)
- Ying Zhang
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Dario Bottinelli
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva 4, Switzerland; Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Emmanuel Varesio
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
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21
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Tarasova NK, Ytterberg AJ, Lundberg K, Zhang XM, Harris RA, Zubarev RA. Proteomics Reveals a Role for Attachment in Monocyte Differentiation into Efficient Proinflammatory Macrophages. J Proteome Res 2015. [PMID: 26216291 DOI: 10.1021/acs.jproteome.5b00659] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Monocytes are blood-borne cells of the innate immune system. They can be differentiated and activated into proinflammatory macrophages that might be employed in tumor immune therapy. Monocyte exposure to lipopolysaccharide (LPS) is a standard method to induce a proinflammatory macrophage state, with the resultant population comprising both adherent and nonadherent cells. In the current study, we aimed to identify the differences in proteomes of these monocyte subpopulations, which addresses a more general question about the role of attachment in monocyte differentiation. Label-free proteomics of a model of human monocytes (THP-1 cell line) revealed that the cells remaining in suspension upon LPS treatment were activated by cytokines and primed for rapid responsiveness to pathogens. In terms of proteome change, the adhesion process was orthogonal to activation. Adherent cells exhibited signs of differentiation and enhanced innate immune responsivity, being closer to macrophages. These findings indicate that adherent, LPS-treated cells would be more appropriate for use in tumor therapeutic applications.
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Affiliation(s)
| | | | - Karin Lundberg
- Centre for Molecular Medicine, Karolinska Hospital , SE 17176 Stockholm, Sweden
| | - Xing-Mei Zhang
- Centre for Molecular Medicine, Karolinska Hospital , SE 17176 Stockholm, Sweden
| | - Robert A Harris
- Centre for Molecular Medicine, Karolinska Hospital , SE 17176 Stockholm, Sweden
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