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Gémes N, Balog JÁ, Neuperger P, Schlegl E, Barta I, Fillinger J, Antus B, Zvara Á, Hegedűs Z, Czimmerer Z, Manczinger M, Balogh GM, Tóvári J, Puskás LG, Szebeni GJ. Single-cell immunophenotyping revealed the association of CD4+ central and CD4+ effector memory T cells linking exacerbating chronic obstructive pulmonary disease and NSCLC. Front Immunol 2023; 14:1297577. [PMID: 38187374 PMCID: PMC10770259 DOI: 10.3389/fimmu.2023.1297577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Tobacco smoking generates airway inflammation in chronic obstructive pulmonary disease (COPD), and its involvement in the development of lung cancer is still among the leading causes of early death. Therefore, we aimed to have a better understanding of the disbalance in immunoregulation in chronic inflammatory conditions in smoker subjects with stable COPD (stCOPD), exacerbating COPD (exCOPD), or non-small cell lung cancer (NSCLC). Methods Smoker controls without chronic illness were recruited as controls. Through extensive mapping of single cells, surface receptor quantification was achieved by single-cell mass cytometry (CyTOF) with 29 antibodies. The CyTOF characterized 14 main immune subsets such as CD4+, CD8+, CD4+/CD8+, CD4-/CD8-, and γ/δ T cells and other subsets such as CD4+ or CD8+ NKT cells, NK cells, B cells, plasmablasts, monocytes, CD11cdim, mDCs, and pDCs. The CD4+ central memory (CM) T cells (CD4+/CD45RA-/CD45RO+/CD197+) and CD4+ effector memory (EM) T cells (CD4+/CD45RA-/CD45RO+/CD197-) were FACS-sorted for RNA-Seq analysis. Plasma samples were assayed by Luminex MAGPIX® for the quantitative measurement of 17 soluble immuno-oncology mediators (BTLA, CD28, CD80, CD27, CD40, CD86, CTLA-4, GITR, GITRL, HVEM, ICOS, LAG-3, PD-1, PD-L1, PD-L2, TIM-3, TLR-2) in the four studied groups. Results Our focus was on T-cell-dependent differences in COPD and NSCLC, where peripheral CD4+ central memory and CD4+ effector memory cells showed a significant reduction in exCOPD and CD4+ CM showed elevation in NSCLC. The transcriptome analysis delineated a perfect correlation of differentially expressed genes between exacerbating COPD and NSCLC-derived peripheral CD4+ CM or CD4+ EM cells. The measurement of 17 immuno-oncology soluble mediators revealed a disease-associated phenotype in the peripheral blood of stCOPD, exCOPD, and NSCLC patients. Discussion The applied single-cell mass cytometry, the whole transcriptome profiling of peripheral CD4+ memory cells, and the quantification of 17 plasma mediators provided complex data that may contribute to the understanding of the disbalance in immune homeostasis generated or sustained by tobacco smoking in COPD and NSCLC.
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Affiliation(s)
- Nikolett Gémes
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
- PhD School in Biology, University of Szeged, Szeged, Hungary
| | - József Á. Balog
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Patrícia Neuperger
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
- PhD School in Biology, University of Szeged, Szeged, Hungary
| | | | - Imre Barta
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - János Fillinger
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Balázs Antus
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Ágnes Zvara
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Zoltán Hegedűs
- Laboratory of Bioinformatics, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Zsolt Czimmerer
- Macrophage Polarization Group, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Gergő Mihály Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | | | - László G. Puskás
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
- Avicor Ltd., Szeged, Hungary
- Avidin Ltd., Szeged, Hungary
| | - Gábor J. Szebeni
- Laboratory of Functional Genomics, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- CS-Smartlab Devices Ltd., Kozármisleny, Hungary
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Czimmerer Z, Patsalos A, Hoeksema MA. Editorial: Transcriptional regulation of macrophage function. Front Immunol 2023; 14:1321064. [PMID: 38022640 PMCID: PMC10653439 DOI: 10.3389/fimmu.2023.1321064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
- Zsolt Czimmerer
- Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Andreas Patsalos
- Department of Medicine, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Marten A. Hoeksema
- Department of Medical Biochemistry, Amsterdam Immunity and Infection: Inflammatory Diseases, Amsterdam Cardiovascular Sciences: Atherosclerosis & Ischemic Syndrome, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
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Czimmerer Z, Nagy L. Epigenomic regulation of macrophage polarization: Where do the nuclear receptors belong? Immunol Rev 2023; 317:152-165. [PMID: 37074820 PMCID: PMC10524119 DOI: 10.1111/imr.13209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/20/2023]
Abstract
Our laboratory has a long-standing research interest in understanding how lipid-activated transcription factors, nuclear hormone receptors, contribute to dendritic cell and macrophage gene expression regulation, subtype specification, and responses to a changing extra and intracellular milieu. This journey in the last more than two decades took us from identifying target genes for various RXR heterodimers to systematically mapping nuclear receptor-mediated pathways in dendritic cells to identifying hierarchies of transcription factors in alternative polarization in macrophages to broaden the role of nuclear receptors beyond strictly ligand-regulated gene expression. We detail here the milestones of the road traveled and draw conclusions regarding the unexpectedly broad role of nuclear hormone receptors as epigenomic components of dendritic cell and macrophage gene regulation as we are getting ready for the next challenges.
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Affiliation(s)
- Zsolt Czimmerer
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Laszlo Nagy
- Departments Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, and Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St Petersburg, FL, United States
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Domokos A, Varga Z, Jambrovics K, Caballero-Sánchez N, Szabo E, Nagy G, Scholtz B, Halasz L, Varadi E, Bene KP, Mazlo A, Bacsi A, Jeney V, Szebeni GJ, Nagy L, Czimmerer Z. The transcriptional control of the VEGFA-VEGFR1 (FLT1) axis in alternatively polarized murine and human macrophages. Front Immunol 2023; 14:1168635. [PMID: 37215144 PMCID: PMC10192733 DOI: 10.3389/fimmu.2023.1168635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction Macrophages significantly contribute to the regulation of vessel formation under physiological and pathological conditions. Although the angiogenesis-regulating role of alternatively polarized macrophages is quite controversial, a growing number of evidence shows that they can participate in the later phases of angiogenesis, including vessel sprouting and remodeling or regression. However, the epigenetic and transcriptional regulatory mechanisms controlling this angiogenesis-modulating program are not fully understood. Results Here we show that IL-4 can coordinately regulate the VEGFA-VEGFR1 (FLT1) axis via simultaneously inhibiting the proangiogenic Vegfa and inducing the antiangiogenic Flt1 expression in murine bone marrow-derived macrophages, which leads to the attenuated proangiogenic activity of alternatively polarized macrophages. The IL-4-activated STAT6 and IL-4-STAT6 signaling pathway-induced EGR2 transcription factors play a direct role in the transcriptional regulation of the Vegfa-Flt1 axis. We demonstrated that this phenomenon is not restricted to the murine bone marrow-derived macrophages, but can also be observed in different murine tissue-resident macrophages ex vivo and parasites-elicited macrophages in vivo with minor cell type-specific differences. Furthermore, IL-4 exposure can modulate the hypoxic response of genes in both murine and human macrophages leading to a blunted Vegfa/VEGFA and synergistically induced Flt1/FLT1 expression. Discussion Our findings establish that the IL-4-activated epigenetic and transcriptional program can determine angiogenesis-regulating properties in alternatively polarized macrophages under normoxic and hypoxic conditions.
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Affiliation(s)
- Apolka Domokos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Karoly Jambrovics
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Noemí Caballero-Sánchez
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Eniko Szabo
- Laboratory of Functional Genomics, Biological Research Centre Eotvos Lorand Research Network, Szeged, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beata Scholtz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Eszter Varadi
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Krisztian P. Bene
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anett Mazlo
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Viktoria Jeney
- MTA-DE Lendület Vascular Pathophysiology Research Group, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gabor J. Szebeni
- Laboratory of Functional Genomics, Biological Research Centre Eotvos Lorand Research Network, Szeged, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
- Department of Immunology, Albert Szent-Györgyi Medical School, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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Jambrovics K, Botó P, Pap A, Sarang Z, Kolostyák Z, Czimmerer Z, Szatmari I, Fésüs L, Uray IP, Balajthy Z. Transglutaminase 2 associated with PI3K and PTEN in a membrane-bound signalosome platform blunts cell death. Cell Death Dis 2023; 14:217. [PMID: 36977701 PMCID: PMC10050012 DOI: 10.1038/s41419-023-05748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
Atypically expressed transglutaminase 2 (TG2) has been identified as a poor prognostic factor in a variety of cancers. In this study, we evaluated the contribution of TG2 to the prolonged cell survival of differentiated acute promyelocytic leukaemia (APL) cells in response to the standard treatment with combined retinoic acid (ATRA) and arsenic trioxide (ATO). We report that one advantage of ATRA + ATO treatment compared to ATRA alone diminishes the amount of activated and non-activated CD11b/CD18 and CD11c/CD18 cell surface integrin receptors. These changes suppress ATRA-induced TG2 docking on the cytosolic part of CD18 β2-integrin subunits and reduce cell survival. In addition, TG2 overexpresses and hyperactivates the phosphatidylinositol-3-kinase (PI3K), phospho-AKT S473, and phospho-mTOR S2481 signalling axis. mTORC2 acts as a functional switch between cell survival and death by promoting the full activation of AKT. We show that TG2 presumably triggers the formation of a signalosome platform, hyperactivates downstream mTORC2-AKT signalling, which in turn phosphorylates and inhibits the activity of FOXO3, a key pro-apoptotic transcription factor. In contrast, the absence of TG2 restores basic phospho-mTOR S2481, phospho-AKT S473, PI3K, and PTEN expression and activity, thereby sensitising APL cells to ATO-induced cell death. We conclude, that atypically expressed TG2 may serve as a hub, facilitating signal transduction via signalosome formation by the CD18 subunit with both PI3K hyperactivation and PTEN inactivation through the PI3K-PTEN cycle in ATRA-treated APL cells.
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Affiliation(s)
- Károly Jambrovics
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Pál Botó
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Attila Pap
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Zsolt Sarang
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Zsuzsanna Kolostyák
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Genetics, Szeged, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - László Fésüs
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Iván P Uray
- Department of Clinical Oncology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Zoltán Balajthy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary.
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6
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Daniel B, Belk JA, Meier SL, Chen AY, Sandor K, Czimmerer Z, Varga Z, Bene K, Buquicchio FA, Qi Y, Kitano H, Wheeler JR, Foster DS, Januszyk M, Longaker MT, Chang HY, Satpathy AT. Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. Mol Cell 2023; 83:121-138.e7. [PMID: 36521490 PMCID: PMC9831293 DOI: 10.1016/j.molcel.2022.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Cell cycle (CC) facilitates cell division via robust, cyclical gene expression. Protective immunity requires the expansion of pathogen-responsive cell types, but whether CC confers unique gene expression programs that direct the subsequent immunological response remains unclear. Here, we demonstrate that single macrophages (MFs) adopt different plasticity states in CC, which leads to heterogeneous cytokine-induced polarization, priming, and repolarization programs. Specifically, MF plasticity to interferon gamma (IFNG) is substantially reduced during S-G2/M, whereas interleukin 4 (IL-4) induces S-G2/M-biased gene expression, mediated by CC-biased enhancers. Additionally, IL-4 polarization shifts the CC-phase distribution of MFs toward the G2/M phase, providing a subpopulation-specific mechanism for IL-4-induced, dampened IFNG responsiveness. Finally, we demonstrate CC-dependent MF responses in murine and human disease settings in vivo, including Th2-driven airway inflammation and pulmonary fibrosis, where MFs express an S-G2/M-biased tissue remodeling gene program. Therefore, MF inflammatory and regenerative responses are gated by CC in a cyclical, phase-dependent manner.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Stefanie L Meier
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Andy Y Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary; Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary
| | - Krisztian Bene
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary
| | - Frank A Buquicchio
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hugo Kitano
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Joshua R Wheeler
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Program in Immunology, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
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7
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Czimmerer Z, Halasz L, Daniel B, Varga Z, Bene K, Domokos A, Hoeksema M, Shen Z, Berger WK, Cseh T, Jambrovics K, Kolostyak Z, Fenyvesi F, Varadi J, Poliska S, Hajas G, Szatmari I, Glass CK, Bacsi A, Nagy L. The epigenetic state of IL-4-polarized macrophages enables inflammatory cistromic expansion and extended synergistic response to TLR ligands. Immunity 2022; 55:2006-2026.e6. [PMID: 36323312 PMCID: PMC9649892 DOI: 10.1016/j.immuni.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 07/11/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Prior exposure to microenvironmental signals could fundamentally change the response of macrophages to subsequent stimuli. It is believed that T helper-2 (Th2)-cell-type cytokine interleukin-4 (IL-4) and Toll-like receptor (TLR) ligand-activated transcriptional programs mutually antagonize each other, and no remarkable convergence has been identified between them. In contrast, here, we show that IL-4-polarized macrophages established a hyperinflammatory gene expression program upon lipopolysaccharide (LPS) exposure. This phenomenon, which we termed extended synergy, was supported by IL-4-directed epigenomic remodeling, LPS-activated NF-κB-p65 cistrome expansion, and increased enhancer activity. The EGR2 transcription factor contributed to the extended synergy in a macrophage-subtype-specific manner. Consequently, the previously alternatively polarized macrophages produced increased amounts of immune-modulatory factors both in vitro and in vivo in a murine Th2 cell-type airway inflammation model upon LPS exposure. Our findings establish that IL-4-induced epigenetic reprogramming is responsible for the development of inflammatory hyperresponsiveness to TLR activation and contributes to lung pathologies.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,These authors contributed equally
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,Present address: Stanford University School of Medicine, Department of Pathology, Stanford, CA, USA
| | - Bence Daniel
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,These authors contributed equally,Present address: Stanford University School of Medicine, Department of Pathology, Stanford, CA, USA
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztian Bene
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Apolka Domokos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Molecular Cell and Immunobiology Doctoral School, Faculty of Medicine, University of Debrecen 4032, Debrecen, Hungary
| | - Marten Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA,Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Wilhelm K. Berger
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Timea Cseh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Karoly Jambrovics
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Kolostyak
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Molecular Cell and Immunobiology Doctoral School, Faculty of Medicine, University of Debrecen 4032, Debrecen, Hungary
| | - Ferenc Fenyvesi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Judit Varadi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyorgy Hajas
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA,Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,Lead contact,Correspondence:
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8
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Ivanovics B, Gazsi G, Reining M, Berta I, Poliska S, Toth M, Domokos A, Nagy B, Staszny A, Cserhati M, Csosz E, Bacsi A, Csenki-Bakos Z, Acs A, Urbanyi B, Czimmerer Z. Embryonic exposure to low concentrations of aflatoxin B1 triggers global transcriptomic changes, defective yolk lipid mobilization, abnormal gastrointestinal tract development and inflammation in zebrafish. J Hazard Mater 2021; 416:125788. [PMID: 33838512 DOI: 10.1016/j.jhazmat.2021.125788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Aflatoxin B1-contaminated feeds and foods induce various health problems in domesticated animals and humans, including tumor development and hepatotoxicity. Aflatoxin B1 also has embryotoxic effects in different livestock species and humans. However, it is difficult to distinguish between the indirect, maternally-mediated toxic effects and the direct embryotoxicity of aflatoxin B1 in mammals. In the present study, we investigated the aflatoxin B1-induced direct embryotoxic effects in a zebrafish embryo model system combining toxicological, transcriptomic, immunological, and biochemical approaches. Embryonic exposure to aflatoxin B1 induced significant changes at the transcriptome level resulting in elevated expression of inflammatory gene network and repression of lipid metabolism and gastrointestinal tract development-related gene sets. According to the gene expression changes, massive neutrophil granulocyte influx, elevated nitric oxide production, and yolk lipid accumulation were observed in the abdominal region of aflatoxin B1-exposed larvae. In parallel, aflatoxin B1-induced defective gastrointestinal tract development and reduced L-arginine level were found in our model system. Our results revealed the complex direct embryotoxic effects of aflatoxin B1, including inhibited lipid utilization, defective intestinal development, and inflammation.
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Affiliation(s)
- Bence Ivanovics
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Gyongyi Gazsi
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Marta Reining
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Izabella Berta
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Marta Toth
- Department of Immunology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Apolka Domokos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; Molecular Cell and Immunobiology Doctoral School, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Bela Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Adam Staszny
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Matyas Cserhati
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Eva Csosz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zsolt Csenki-Bakos
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Andras Acs
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary
| | - Bela Urbanyi
- Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Godollo, Hungary.
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.
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9
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Kovács EG, Alatshan A, Budai MM, Czimmerer Z, Bíró E, Benkő S. Caffeine Has Different Immunomodulatory Effect on the Cytokine Expression and NLRP3 Inflammasome Function in Various Human Macrophage Subpopulations. Nutrients 2021; 13:2409. [PMID: 34371919 PMCID: PMC8308523 DOI: 10.3390/nu13072409] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022] Open
Abstract
Besides its well-known psychoactive effects, caffeine has a broad range of actions. It regulates several physiological mechanisms as well as modulates both native and adaptive immune responses by various ways. Although caffeine is assumed to be a negative regulator of inflammation, the effect on the secretion of pro- and anti-inflammatory cytokines is highly controversial. Macrophages are major mediators of inflammatory responses; however, the various subpopulations develop different effects ranging from the initiation to the resolution of inflammation. Here we report a comparative analysis of the effect of caffeine on two subpopulations of human monocyte-derived macrophages differentiated in the presence of macrophage colony-stimulating factor (M-CSF) or granulocyte-macrophage colony-stimulating factor (GM-CSF), resulting in M-MΦs and GM-MΦs, respectively. We showed that although TNF-α secretion was downregulated in both LPS-activated MΦ subtypes by caffeine, the secretion of IL-8, IL-6, and IL-1β as well as the expression of Nod-like receptors was enhanced in M-MΦs, while it did not change in GM-MΦs. We showed that caffeine (1) altered adenosine receptor expression, (2) changed Akt/AMPK/mTOR signaling pathways, and (3) inhibited STAT1/IL-10 signaling axis in M-MΦs. We hypothesized that these alterations play an important modulatory role in the upregulation of NLRP3 inflammasome-mediated IL-1β secretion in LPS-activated M-MΦs following caffeine treatment.
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Affiliation(s)
- Elek Gergő Kovács
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (E.G.K.); (A.A.); (M.M.B.); (E.B.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Ahmad Alatshan
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (E.G.K.); (A.A.); (M.M.B.); (E.B.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Marietta Margit Budai
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (E.G.K.); (A.A.); (M.M.B.); (E.B.)
- Departments of Immunology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Eduárd Bíró
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (E.G.K.); (A.A.); (M.M.B.); (E.B.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Szilvia Benkő
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (E.G.K.); (A.A.); (M.M.B.); (E.B.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
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10
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Daniel B, Czimmerer Z, Halasz L, Boto P, Kolostyak Z, Poliska S, Berger WK, Tzerpos P, Nagy G, Horvath A, Hajas G, Cseh T, Nagy A, Sauer S, Francois-Deleuze J, Szatmari I, Bacsi A, Nagy L. The transcription factor EGR2 is the molecular linchpin connecting STAT6 activation to the late, stable epigenomic program of alternative macrophage polarization. Genes Dev 2020; 34:1474-1492. [PMID: 33060136 PMCID: PMC7608752 DOI: 10.1101/gad.343038.120] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
In this study, Daniel et al. examined the mechanisms of macrophage polarization in general and alternative polarization in particular. Using unbiased epigenomic, molecular biology, and genetic GOF and LOF approaches, the authors show that the zinc finger transcription factor EGR2 acts as an essential and evolutionarily conserved broad-acting factor, linking transient polarization signals to stable epigenomic and transcriptional changes in macrophages. Macrophages polarize into functionally distinct subtypes while responding to microenvironmental cues. The identity of proximal transcription factors (TFs) downstream from the polarization signals are known, but their activity is typically transient, failing to explain the long-term, stable epigenomic programs developed. Here, we mapped the early and late epigenomic changes of interleukin-4 (IL-4)-induced alternative macrophage polarization. We identified the TF, early growth response 2 (EGR2), bridging the early transient and late stable gene expression program of polarization. EGR2 is a direct target of IL-4-activated STAT6, having broad action indispensable for 77% of the induced gene signature of alternative polarization, including its autoregulation and a robust, downstream TF cascade involving PPARG. Mechanistically, EGR2 binding results in chromatin opening and the recruitment of chromatin remodelers and RNA polymerase II. Egr2 induction is evolutionarily conserved during alternative polarization of mouse and human macrophages. In the context of tissue resident macrophages, Egr2 expression is most prominent in the lung of a variety of species. Thus, EGR2 is an example of an essential and evolutionarily conserved broad acting factor, linking transient polarization signals to stable epigenomic and transcriptional changes in macrophages.
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Affiliation(s)
- Bence Daniel
- Department of Medicine, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Laszlo Halasz
- Department of Medicine, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Pal Boto
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Zsuzsanna Kolostyak
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Wilhelm K Berger
- Department of Medicine, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Petros Tzerpos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - György Hajas
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Timea Cseh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Aniko Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.,CU Systems Medicine, University of Würzburg, Würzburg 97070, Germany.,Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany.,Berlin Institute of Health, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Jean Francois-Deleuze
- Centre National de Génotypage, Institut de Génomique, Commissariat à l'Énergie Atomique, Evry 91000, France
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Laszlo Nagy
- Department of Medicine, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, Florida 33701, USA.,Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
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11
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Alatshan A, Kovács GE, Aladdin A, Czimmerer Z, Tar K, Benkő S. All-Trans Retinoic Acid Enhances both the Signaling for Priming and the Glycolysis for Activation of NLRP3 Inflammasome in Human Macrophage. Cells 2020; 9:cells9071591. [PMID: 32630207 PMCID: PMC7407903 DOI: 10.3390/cells9071591] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023] Open
Abstract
All-trans retinoic acid (ATRA) is a derivative of vitamin A that has many important biological functions, including the modulation of immune responses. ATRA actions are mediated through the retinoic acid receptor that functions as a nuclear receptor, either regulating gene transcription in the nucleus or modulating signal transduction in the cytoplasm. NLRP3 inflammasome is a multiprotein complex that is activated by a huge variety of stimuli, including pathogen- or danger-related molecules. Activation of the inflammasome is required for the production of IL-1β, which drives the inflammatory responses of infectious or non-infectious sterile inflammation. Here, we showed that ATRA prolongs the expression of IL-6 and IL-1β following a 2-, 6-, 12-, and 24-h LPS (100ng/mL) activation in human monocyte-derived macrophages. We describe for the first time that ATRA modulates both priming and activation signals required for NLRP3 inflammasome function. ATRA alone induces NLRP3 expression, and enhances LPS-induced expression of NLRP3 and pro-IL-1β via the regulation of signal transduction pathways, like NF-κB, p38, and ERK. We show that ATRA alleviates the negative feedback loop effect of IL-10 anti-inflammatory cytokine on NLRP3 inflammasome function by inhibiting the Akt-mTOR-STAT3 signaling axis. We also provide evidence that ATRA enhances hexokinase 2 expression, and shifts the metabolism of LPS-activated macrophages toward glycolysis, leading to the activation of NLRP3 inflammasome.
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Affiliation(s)
- Ahmad Alatshan
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (A.A.); (G.E.K.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Gergő E. Kovács
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (A.A.); (G.E.K.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
| | - Azzam Aladdin
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.A.); (K.T.)
- Doctoral School of Molecular Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Krisztina Tar
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (A.A.); (K.T.)
| | - Szilvia Benkő
- Departments of Physiology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary; (A.A.); (G.E.K.)
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, H-4012 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-255-575
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12
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Czimmerer Z, Halasz L, Nagy L. Unorthodox Transcriptional Mechanisms of Lipid-Sensing Nuclear Receptors in Macrophages: Are We Opening a New Chapter? Front Endocrinol (Lausanne) 2020; 11:609099. [PMID: 33362723 PMCID: PMC7758493 DOI: 10.3389/fendo.2020.609099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022] Open
Abstract
Work over the past 30 years has shown that lipid-activated nuclear receptors form a bridge between metabolism and immunity integrating metabolic and inflammatory signaling in innate immune cells. Ligand-induced direct transcriptional activation and protein-protein interaction-based transrepression were identified as the most common mechanisms of liganded-nuclear receptor-mediated transcriptional regulation. However, the integration of different next-generation sequencing-based methodologies including chromatin immunoprecipitation followed by sequencing and global run-on sequencing allowed to investigate the DNA binding and ligand responsiveness of nuclear receptors at the whole-genome level. Surprisingly, these studies have raised the notion that a major portion of lipid-sensing nuclear receptor cistromes are not necessarily responsive to ligand activation. Although the biological role of the ligand insensitive portion of nuclear receptor cistromes is largely unknown, recent findings indicate that they may play roles in the organization of chromatin structure, in the regulation of transcriptional memory, and the epigenomic modification of responsiveness to other microenvironmental signals in macrophages. In this review, we will provide an overview and discuss recent advances of our understanding of lipid-activated nuclear receptor-mediated non-classical or unorthodox actions in macrophages.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
- *Correspondence: Laszlo Nagy,
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13
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Horvath A, Daniel B, Szeles L, Cuaranta-Monroy I, Czimmerer Z, Ozgyin L, Steiner L, Kiss M, Simandi Z, Poliska S, Giannakis N, Raineri E, Gut IG, Nagy B, Nagy L. Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals. Nucleic Acids Res 2019; 47:2778-2792. [PMID: 30799488 PMCID: PMC6451134 DOI: 10.1093/nar/gkz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
The concept of tissue-specific gene expression posits that lineage-determining transcription factors (LDTFs) determine the open chromatin profile of a cell via collaborative binding, providing molecular beacons to signal-dependent transcription factors (SDTFs). However, the guiding principles of LDTF binding, chromatin accessibility and enhancer activity have not yet been systematically evaluated. We sought to study these features of the macrophage genome by the combination of experimental (ChIP-seq, ATAC-seq and GRO-seq) and computational approaches. We show that Random Forest and Support Vector Regression machine learning methods can accurately predict chromatin accessibility using the binding patterns of the LDTF PU.1 and four other key TFs of macrophages (IRF8, JUNB, CEBPA and RUNX1). Any of these TFs alone were not sufficient to predict open chromatin, indicating that TF binding is widespread at closed or weakly opened chromatin regions. Analysis of the PU.1 cistrome revealed that two-thirds of PU.1 binding occurs at low accessible chromatin. We termed these sites labelled regulatory elements (LREs), which may represent a dormant state of a future enhancer and contribute to macrophage cellular plasticity. Collectively, our work demonstrates the existence of LREs occupied by various key TFs, regulating specific gene expression programs triggered by divergent macrophage polarizing stimuli.
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Affiliation(s)
- Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Bence Daniel
- Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
| | - Lajos Szeles
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lilla Ozgyin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Laszlo Steiner
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zoltan Simandi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Nikolas Giannakis
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Emanuele Raineri
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Benedek Nagy
- Department of Mathematics, Eastern Mediterranean University, Famagusta, North Cyprus, Mersin 10, Turkey
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
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14
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Daniel B, Nagy G, Horvath A, Czimmerer Z, Cuaranta-Monroy I, Poliska S, Hays TT, Sauer S, Francois-Deleuze J, Nagy L. The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages. Nucleic Acids Res 2019; 46:4425-4439. [PMID: 29506156 PMCID: PMC5961189 DOI: 10.1093/nar/gky157] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Retinoid X receptor (RXR) is an obligate heterodimeric partner of several nuclear receptors (NRs), and as such a central component of NR signaling regulating the immune and metabolic phenotype of macrophages. Importantly, the binding motifs of RXR heterodimers are enriched in the tissue-selective open chromatin regions of resident macrophages, suggesting roles in subtype specification. Recent genome-wide studies revealed that RXR binds to thousands of sites in the genome, but the mechanistic details how the cistrome is established and serves ligand-induced transcriptional activity remained elusive. Here we show that IL-4-mediated macrophage plasticity results in a greatly extended RXR cistrome via both direct and indirect actions of the transcription factor STAT6. Activation of STAT6 leads to chromatin remodeling and RXR recruitment to de novo enhancers. In addition, STAT6 triggers a secondary transcription factor wave, including PPARγ. PPARγ appears to be indispensable for the development of RXR-bound de novo enhancers, whose activities can be modulated by the ligands of the PPARγ:RXR heterodimer conferring ligand selective cellular responses. Collectively, these data reveal the mechanisms leading to the dynamic extension of the RXR cistrome and identify the lipid-sensing enhancer sets responsible for the appearance of ligand-preferred gene signatures in alternatively polarized macrophages.
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Affiliation(s)
- Bence Daniel
- Sanford-Burnham-Prebys Medical Discovery Institute, Orlando, FL, USA.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tristan T Hays
- Sanford-Burnham-Prebys Medical Discovery Institute, Orlando, FL, USA
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,CU Systems Medicine, University of Würzburg, Würzburg, Germany.,Max Delbrück Center for Molecular Medicine (BIMSB and BIH), Berlin, Germany
| | | | - Laszlo Nagy
- Sanford-Burnham-Prebys Medical Discovery Institute, Orlando, FL, USA.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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15
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Czimmerer Z, Daniel B, Horvath A, Rückerl D, Nagy G, Kiss M, Peloquin M, Budai MM, Cuaranta-Monroy I, Simandi Z, Steiner L, Nagy B, Poliska S, Banko C, Bacso Z, Schulman IG, Sauer S, Deleuze JF, Allen JE, Benko S, Nagy L. The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages. Immunity 2018; 48:75-90.e6. [PMID: 29343442 PMCID: PMC5772169 DOI: 10.1016/j.immuni.2017.12.010] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/09/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, but our understanding remains limited regarding the molecular determinants of repression. Here we show that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during in vitro and in vivo alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300, and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation, and chromatin accessibility. The repressor function of STAT6 is HDAC3 dependent on a subset of IL-4-repressed genes. In addition, STAT6-repressed enhancers show extensive overlap with the NF-κB p65 cistrome and exhibit decreased responsiveness to lipopolysaccharide after IL-4 stimulus on a subset of genes. As a consequence, macrophages exhibit diminished inflammasome activation, decreased IL-1β production, and pyroptosis. Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. IL-4-activated STAT6 acts as a transcriptional repressor in macrophages IL-4-STAT6-repressed enhancers associate with reduced LDTF and p300 binding Inflammatory responsiveness of the IL-4-repressed enhancers is attenuated IL-4 limits the LPS-induced inflammasome activation, IL-1β production, and pyroptosis
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bence Daniel
- Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Dominik Rückerl
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; MTA-DE "Lendület" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Matthew Peloquin
- Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Marietta M Budai
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltan Simandi
- Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA
| | - Laszlo Steiner
- UD-Genomed Medical Genomic Technologies Ltd., Debrecen, Hungary
| | - Bela Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilard Poliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Csaba Banko
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Bacso
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ira G Schulman
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany; CU Systems Medicine, University of Würzburg, Würzburg, Germany; Max Delbrück Center for Molecular Medicine (BIMSB and BIH), Berlin, Germany
| | | | - Judith E Allen
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Szilvia Benko
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA; MTA-DE "Lendület" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary.
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Czimmerer Z, Nagy ZS, Nagy G, Horvath A, Silye-Cseh T, Kriston A, Jonas D, Sauer S, Steiner L, Daniel B, Deleuze JF, Nagy L. Extensive and functional overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte derived differentiating macrophages. Mol Cell Endocrinol 2018; 471:63-74. [PMID: 28774779 DOI: 10.1016/j.mce.2017.07.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/07/2017] [Accepted: 07/28/2017] [Indexed: 11/18/2022]
Abstract
Macrophages are able to differentiate into classically polarized (M1) or alternatively polarized (M2) states upon encountering pro-inflammatory cytokines such as interferon (IFN) γ or anti-inflammatory cytokines such as interleukin (IL) -4/IL-13, respectively. Moreover, macrophages are known to regulate lipid metabolism via multiple members of the nuclear hormone receptor family, including the retinoid X receptors (RXR). It has been also documented that cytokines are able to modulate macrophage responses to lipid signals but the nature of these interactions and the underlying mechanisms of these processes especially at the level of the chromatinized genome are not well understood. Previous work from our laboratory suggested that STAT6 is a facilitator of nuclear receptor mediated transcriptional activity acting at the genome level. This prompted us to investigate genome-wide DNA binding events and the development of cistromes in human CD14+ monocyte-derived macrophages upon exposure to IL-4. We determined the impact of IL-4 on the PU.1, RXR and STAT6 cistromes within the active enhancer regions marked by H3K27-acetylation using chromatin immunoprecipitation followed by deep sequencing and integrated bioinformatics analyses. We found that about 2/3rd of the IL-4 induced STAT6 peaks co-localized with RXR peaks. These STAT6/RXR co-peaks differed at least in part from the non-overlapping RXR peaks regarding the most enriched de novo transcription factor binding motifs. Interestingly, RXR-binding was not regulated at the STAT6/RXR co-bound enhancers following IL-4 stimulation, but differential enhancer interactions were observed between the IL-4/STAT6 and RXR signaling pathways acting in a gene selective manner. Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna S Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Hungarian Academy of Sciences, "Lendület" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Hungarian Academy of Sciences, "Lendület" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary
| | - Timea Silye-Cseh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Agnes Kriston
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - David Jonas
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sascha Sauer
- Max Delbruck Center for Molecular Medicine (BISMB and BIH), Germany
| | - Laszlo Steiner
- UD-Genomed Medical Genomic Technologies Ltd., Debrecen, Hungary
| | - Bence Daniel
- Sanford-Burnham-Prebys Medical Discovery Institute, Orlando, FL, USA
| | - Jean-Francois Deleuze
- Centre National de Recherche en Genomique Humaine, Institute de Biologie Francois Jacob, CEA, Evry, France
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Hungarian Academy of Sciences, "Lendület" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary; Sanford-Burnham-Prebys Medical Discovery Institute, Orlando, FL, USA.
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Czimmerer Z, Horvath A, Daniel B, Nagy G, Cuaranta-Monroy I, Kiss M, Kolostyak Z, Poliska S, Steiner L, Giannakis N, Varga T, Nagy L. Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2018; 1861:14-28. [DOI: 10.1016/j.bbagrm.2017.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/23/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022]
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Fejes Z, Póliska S, Czimmerer Z, Káplár M, Penyige A, Gál Szabó G, Beke Debreceni I, Kunapuli SP, Kappelmayer J, Nagy B. Hyperglycaemia suppresses microRNA expression in platelets to increase P2RY12 and SELP levels in type 2 diabetes mellitus. Thromb Haemost 2016; 117:529-542. [PMID: 27975100 DOI: 10.1160/th16-04-0322] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 11/26/2016] [Indexed: 12/19/2022]
Abstract
Megakaryocyte (MK)-derived miRNAs have been detected in platelets. Here, we analysed the expression of platelet and circulating miR-223, miR-26b, miR-126 and miR-140 that might be altered with their target mRNAs in type 2 diabetes mellitus (DM2). MiRNAs were isolated from leukocyte-depleted platelets and plasma samples obtained from 28 obese DM2, 19 non-DM obese and 23 healthy individuals. The effect of hyperglycaemia on miRNAs was also evaluated in MKs using MEG-01 and K562 cells under hyperglycaemic conditions after 8 hours up to four weeks. Quantitation of mature miRNA, pre-miRNAs and target mRNA levels (P2RY12 and SELP) were measured by RT-qPCR. To prove the association of miR-26b and miR-140 with SELP (P-selectin) mRNA level, overexpression or inhibition of these miRNAs in MEG-01 MKs was performed using mimics or anti-miRNAs, respectively. The contribution of calpain substrate Dicer to modulation of miRNAs was studied by calpain inhibition. Platelet activation was evaluated via surface P-selectin by flow cytometry. Mature and pre-forms of investigated miRNAs were significantly reduced in DM2, and platelet P2RY12 and SELP mRNA levels were elevated by two-fold at increased platelet activation compared to controls. Significantly blunted miRNA expressions were observed by hyperglycaemia in MEG-01 and K562-MK cells versus baseline values, while the manipulation of miR-26b and miR-140 expression affected SELP mRNA level. Calpeptin pretreatment restored miRNA levels in hyperglycaemic MKs. Overall, miR-223, miR-26b, miR-126 and miR-140 are expressed at a lower level in platelets and MKs in DM2 causing upregulation of P2RY12 and SELP mRNAs that may contribute to adverse platelet function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Béla Nagy
- Béla Nagy Jr, MD, PhD, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98. H-4032, Debrecen, Hungary, Tel.: +36 52 340 006, Fax: +36 52 417 631, E-mail:
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Czimmerer Z, Varga T, Kiss M, Vázquez CO, Doan-Xuan QM, Rückerl D, Tattikota SG, Yan X, Nagy ZS, Daniel B, Poliska S, Horvath A, Nagy G, Varallyay E, Poy MN, Allen JE, Bacso Z, Abreu-Goodger C, Nagy L. The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p. Genome Med 2016; 8:63. [PMID: 27245778 PMCID: PMC4886428 DOI: 10.1186/s13073-016-0315-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 01/06/2023] Open
Abstract
Background IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which primarily occurs during inflammatory responses. The signaling pathways defining the genome-wide microRNA expression profile as well as the cellular functions controlled by microRNAs during alternative macrophage activation are largely unknown. Hence, in the current work we examined the regulation and function of IL-4-regulated microRNAs in human and mouse alternative macrophage activation. Methods We utilized microarray-based microRNA profiling to detect the dynamic expression changes during human monocyte–macrophage differentiation and IL-4-mediated alternative macrophage activation. The expression changes and upstream regulatory pathways of selected microRNAs were further investigated in human and mouse in vitro and in vivo models of alternative macrophage activation by integrating small RNA-seq, ChIP-seq, ChIP-quantitative PCR, and gene expression data. MicroRNA-controlled gene networks and corresponding functions were identified using a combination of transcriptomic, bioinformatic, and functional approaches. Results The IL-4-controlled microRNA expression pattern was identified in models of human and mouse alternative macrophage activation. IL-4-dependent induction of miR-342-3p and repression of miR-99b along with miR-125a-5p occurred in both human and murine macrophages in vitro. In addition, a similar expression pattern was observed in peritoneal macrophages of Brugia malayi nematode-implanted mice in vivo. By using IL4Rα- and STAT6-deficient macrophages, we were able to show that IL-4-dependent regulation of miR-342-3p, miR-99b, and miR-125a-5p is mediated by the IL-4Rα–STAT6 signaling pathway. The combination of gene expression studies and chromatin immunoprecipitation experiments demonstrated that both miR-342-3p and its host gene, EVL, are coregulated directly by STAT6. Finally, we found that miR-342-3p is capable of controlling macrophage survival through targeting an anti-apoptotic gene network including Bcl2l1. Conclusions Our findings identify a conserved IL-4/STAT6-regulated microRNA signature in alternatively activated human and mouse macrophages. Moreover, our study indicates that miR-342-3p likely plays a pro-apoptotic role in such cells, thereby providing a negative feedback arm to IL-4-dependent macrophage proliferation. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0315-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Tamas Varga
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Cesaré Ovando Vázquez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México
| | - Quang Minh Doan-Xuan
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, H-4012, Debrecen, Hungary
| | - Dominik Rückerl
- University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Sudhir Gopal Tattikota
- Max Delbrueck Center for Molecular Medicine, Robert Roessle Strasse 10, Berlin, 13125, Germany
| | - Xin Yan
- Max Delbrueck Center for Molecular Medicine, Robert Roessle Strasse 10, Berlin, 13125, Germany
| | - Zsuzsanna S Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Bence Daniel
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary.,Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL, 32827, USA
| | - Szilard Poliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - Eva Varallyay
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi A. út 4, H-2100, Gödöllő, Hungary
| | - Matthew N Poy
- Max Delbrueck Center for Molecular Medicine, Robert Roessle Strasse 10, Berlin, 13125, Germany
| | - Judith E Allen
- University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Zsolt Bacso
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, H-4012, Debrecen, Hungary
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical, Nagyerdei krt. 98, H-4032, Debrecen, Hungary. .,Sanford-Burnham-Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL, 32827, USA. .,MTA-DE "Lendület" Immunogenomics Research Group, University of Debrecen, Egyetem tér 1, H-4012, Debrecen, Hungary.
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Daniel B, Nagy G, Hah N, Horvath A, Czimmerer Z, Poliska S, Gyuris T, Keirsse J, Gysemans C, Van Ginderachter JA, Balint BL, Evans RM, Barta E, Nagy L. The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages. Genes Dev 2014; 28:1562-77. [PMID: 25030696 PMCID: PMC4102764 DOI: 10.1101/gad.242685.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here, Nagy and colleagues use genome-wide approaches to uncover the activity of RXR, an enigmatic member of the nuclear receptor superfamily. RXR signaling is predicted to have a major impact in macrophages, but neither the biological consequence nor the genomic basis of its ligand activation is known. Integrating RNA-seq, ChIP-seq, GRO-seq, and 3C-seq, the authors unravel the mechanism of RXR-induced transcriptional events in mouse bone marrow-derived macrophages. Importantly, this study uncovers a novel biological activity—angiogenesis—that is promoted by the receptor. RXR signaling is predicted to have a major impact in macrophages, but neither the biological consequence nor the genomic basis of its ligand activation is known. Comprehensive genome-wide studies were carried out to map liganded RXR-mediated transcriptional changes, active binding sites, and cistromic interactions in the context of the macrophage genome architecture. The macrophage RXR cistrome has 5200 genomic binding sites, which are not impacted by ligand. Active enhancers are characterized by PU.1 binding, an increase of enhancer RNA, and P300 recruitment. Using these features, 387 liganded RXR-bound enhancers were linked to 226 genes, which predominantly reside in CTCF/cohesin-limited functional domains. These findings were molecularly validated using chromosome conformation capture (3C) and 3C combined with sequencing (3C-seq), and we show that selected long-range enhancers communicate with promoters via stable or RXR-induced loops and that some of the enhancers interact with each other, forming an interchromosomal network. A set of angiogenic genes, including Vegfa, has liganded RXR-controlled enhancers and provides the macrophage with a novel inducible program.
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Affiliation(s)
- Bence Daniel
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Nasun Hah
- The Salk Institute for Biological Studies, San Diego, California 92037, USA
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Tibor Gyuris
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Jiri Keirsse
- Myeloid Cell Immunology Laboratory, Vlaams Instituut voor Biotechnologie (VIB), Brussels B-1050, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels B-1050, Belgium
| | - Conny Gysemans
- Laboratory of Clinical and Experimental Endocrinology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Laboratory, Vlaams Instituut voor Biotechnologie (VIB), Brussels B-1050, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels B-1050, Belgium
| | - Balint L Balint
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Ronald M Evans
- The Salk Institute for Biological Studies, San Diego, California 92037, USA
| | - Endre Barta
- MTA-DE Lendület Immunogenomics Research Group, University of Debrecen, Debrecen H-4032, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen H-4032, Hungary; MTA-DE Lendület Immunogenomics Research Group, University of Debrecen, Debrecen H-4032, Hungary
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Gyongyosi A, Docs O, Czimmerer Z, Orosz L, Horvath A, Török O, Mehes G, Nagy L, Balint BL. Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples. Methods Mol Biol 2014; 1182:105-19. [PMID: 25055905 DOI: 10.1007/978-1-4939-1062-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MicroRNAs are involved in the regulation of various pathophysiological processes such as immune regulation and cancer. Next-generation sequencing methods enable us to monitor their presence in various types of samples but we need flexible methods for validating datasets generated by high-throughput methods. Here we describe the detailed protocols to be used with our MiRNA Primer Design Tool assay design system. The presented methods allow the flexible design of the oligonucleotides needed for the RT-qPCR detection of any variant of small regulatory RNA molecules from virtually any species. This method can be used to measure miRNA levels from formalin-fixed, paraffin-embedded (FFPE) samples and various body fluids. As an example, we show the results of the hsa-miR-515-3p, hsa-miR-325, and hsa-miR-155 quantification using a specific UPL probe (Universal Probe Library) and a stem-loop RT-qPCR assay. The small nucleolar RNA RNU43 is used as endogenous control for normalization of the results. Urine from healthy pregnant women and FFPE samples from patients diagnosed with colorectal cancer and treated with antibody-based anti-EGFR monotherapy were used as samples.
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Affiliation(s)
- Adrienn Gyongyosi
- Department of Biochemistry and Molecular Biology, Center for Clinical Genomics and Personalized Medicine, University of Debrecen Medical and Health Science Center (UD MHSC), Nagyerdei krt. 98, Debrecen, Hungary
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Brignull LM, Czimmerer Z, Saidi H, Daniel B, Villela I, Bartlett NW, Johnston SL, Meira LB, Nagy L, Nohturfft A. Reprogramming of lysosomal gene expression by interleukin-4 and Stat6. BMC Genomics 2013; 14:853. [PMID: 24314139 PMCID: PMC3880092 DOI: 10.1186/1471-2164-14-853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/26/2013] [Indexed: 01/05/2023] Open
Abstract
Background Lysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illuminate the physiological contexts in which lysosomal genes are coordinately regulated and to identify transcription factors involved in this control. Results As transcription factors and their target genes are often co-regulated, we performed meta-analyses of array-based expression data to identify regulators whose mRNA profiles are highly correlated with those of a core set of lysosomal genes. Among the ~50 transcription factors that rank highest by this measure, 65% are involved in differentiation or development, and 22% have been implicated in interferon signaling. The most strongly correlated candidate was Stat6, a factor commonly activated by interleukin-4 (IL-4) or IL-13. Publicly available chromatin immunoprecipitation (ChIP) data from alternatively activated mouse macrophages show that lysosomal genes are overrepresented among Stat6-bound targets. Quantification of RNA from wild-type and Stat6-deficient cells indicates that Stat6 promotes the expression of over 100 lysosomal genes, including hydrolases, subunits of the vacuolar H+ ATPase and trafficking factors. While IL-4 inhibits and activates different sets of lysosomal genes, Stat6 mediates only the activating effects of IL-4, by promoting increased expression and by neutralizing undefined inhibitory signals induced by IL-4. Conclusions The current data establish Stat6 as a broadly acting regulator of lysosomal gene expression in mouse macrophages. Other regulators whose expression correlates with lysosomal genes suggest that lysosome function is frequently re-programmed during differentiation, development and interferon signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Axel Nohturfft
- Division of Biomedical Sciences, Molecular and Metabolic Signaling Centre, St, George's University of London, Cranmer Terrace, London SW17 0RE, UK.
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Kiss M, Czimmerer Z, Nagy L. The role of lipid-activated nuclear receptors in shaping macrophage and dendritic cell function: From physiology to pathology. J Allergy Clin Immunol 2013; 132:264-86. [PMID: 23905916 DOI: 10.1016/j.jaci.2013.05.044] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/16/2013] [Accepted: 05/30/2013] [Indexed: 02/06/2023]
Abstract
Nuclear receptors are ligand-activated transcription factors linking lipid signaling to the expression of the genome. There is increasing appreciation of the involvement of this receptor network in the metabolic programming of macrophages and dendritic cells (DCs), essential members of the innate immune system. In this review we focus on the role of retinoid X receptor, retinoic acid receptor, peroxisome proliferator-associated receptor γ, liver X receptor, and vitamin D receptor in shaping the immune and metabolic functions of macrophages and DCs. We also provide an overview of the contribution of macrophage- and DC-expressed nuclear receptors to various immunopathologic conditions, such as rheumatoid arthritis, inflammatory bowel disease, systemic lupus erythematosus, asthma, and some others. We suggest that systematic analyses of the roles of these receptors and their activating lipid ligands in immunopathologies combined with complementary and focused translational and clinical research will be crucial for the development of new therapies using the many molecules available to target nuclear receptors.
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Affiliation(s)
- Mate Kiss
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Medical and Health Science Center, Debrecen, Hungary
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Nagy ZS, Czimmerer Z, Szanto A, Nagy L. Pro-inflammatory cytokines negatively regulate PPARγ mediated gene expression in both human and murine macrophages via multiple mechanisms. Immunobiology 2013; 218:1336-44. [PMID: 23870825 DOI: 10.1016/j.imbio.2013.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/17/2013] [Accepted: 06/24/2013] [Indexed: 12/19/2022]
Abstract
PPARγ is a lipid activated transcription factor that connects lipid metabolism and immune function. It is known that anti-inflammatory cytokines, such as IL-4 that mediates the differentiation of alternatively activated macrophages, positively modulate PPARγ at three levels: by (1) increasing its expression (2), initiating a complex formation with STAT6 enhances its transcriptional activity and (3) increasing endogenous ligand production. On the other hand, PPARγ is known to inhibit inflammatory processes via transrepression. However, the impact of a pro-inflammatory cytokine milieu on PPARγ transcriptional activity in macrophages is less understood. We hypothesized that pro-inflammatory cytokines, such as IFNγ and TNFα negatively regulate PPARγ activity and sought to test this within human and murine macrophage models using both global and single target gene expression analysis. We found that IFNγ/TNFα inhibited PPARγ expression in human CD14+ monocytes derived macrophages and mouse bone marrow derived macrophages, but not in macrophages originating from CD34+ stem cells or Thp-1 monocytic cells. Irrespective of the model system, the ability of PPARγ to regulate gene expression was inhibited. Moreover, we demonstrated that in Thp-1 cells PPARγ in vitro DNA binding remained unchanged following IFNγ/TNFα pre-treatment. Taken together, our data suggest that pro-inflammatory conditions inhibit PPARγ activity at the gene expression level and propose two, mutually not exclusive models as mechanisms: (1) the level of PPARγ itself is down-regulated by the cytokines leading to loss of function, while (2) PPARγ itself remains associated with the DNA though unable to initiate gene expression. These findings support that inflammatory conditions skew the lipid sensing function of macrophages, further contributing to the vicious circle of metabolic disorders.
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Affiliation(s)
- Zsuzsanna S Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, H-4032 Debrecen, Nagyerdei krt 98, Hungary
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Nagy ZS, Czimmerer Z, Nagy L. Nuclear receptor mediated mechanisms of macrophage cholesterol metabolism. Mol Cell Endocrinol 2013; 368:85-98. [PMID: 22546548 DOI: 10.1016/j.mce.2012.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/05/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
Macrophages comprise a family of multi-faceted phagocytic effector cells that differentiate "in situ" from circulating monocytes to exert various functions including clearance of foreign pathogens as well as debris derived from host cells. Macrophages also possess the ability to engulf and metabolize lipids and this way connect lipid metabolism and inflammation. The molecular link between these processes is provided by certain members of the nuclear receptor family. For instance, peroxisome proliferator activated receptors (PPAR) and liver X receptors (LXR) are able to sense the dynamically changing lipid environment and translate it to gene expression changes in order to modulate the cellular phenotype. Atherosclerosis embodies both sides of this coin: it is a disease in which macrophages with altered cholesterol metabolism keep the arteries in a chronically inflamed state. A large body of publications has accumulated during the past few decades describing the role of nuclear receptors in the regulation of macrophage cholesterol homeostasis, their contribution to the formation of atherosclerotic plaques and their crosstalk with inflammatory pathways. This review will summarize the most recent findings from this field narrowly focusing on the contribution of various nuclear receptors to macrophage cholesterol metabolism.
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Affiliation(s)
- Zsuzsanna S Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, H-4032 Debrecen, Nagyerdei krt 98, Hungary.
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26
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Czimmerer Z, Hulvely J, Simandi Z, Varallyay E, Havelda Z, Szabo E, Varga A, Dezso B, Balogh M, Horvath A, Domokos B, Torok Z, Nagy L, Balint BL. A versatile method to design stem-loop primer-based quantitative PCR assays for detecting small regulatory RNA molecules. PLoS One 2013; 8:e55168. [PMID: 23383094 PMCID: PMC3561390 DOI: 10.1371/journal.pone.0055168] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/19/2012] [Indexed: 11/18/2022] Open
Abstract
Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. These novel findings aim for new detection methods for the individual short regulatory RNA-s in order to be able to confirm the primary data and characterize newly identified subtypes in different biological conditions. We have developed a flexible method to design RT-qPCR assays that are very sensitive and robust. The newly designed assays were tested extensively in samples from plant, mouse and even human formalin fixed paraffin embedded tissues. Moreover, we have shown that these assays are able to quantify endogenously generated shRNA molecules. The assay design method is freely available for anyone who wishes to use a robust and flexible system for the quantitative analysis of matured regulatory RNA-s.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
| | | | - Zoltan Simandi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
| | - Eva Varallyay
- Plant Developmental Biology Group, Agricultural Biotechnology Center, Gödöllő, Hungary
| | - Zoltan Havelda
- Plant Developmental Biology Group, Agricultural Biotechnology Center, Gödöllő, Hungary
| | - Erzsebet Szabo
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
| | | | - Balazs Dezso
- Institute of Pathology, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
| | - Maria Balogh
- Center for Clinical Genomics and Personalized Medicine, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
- Astrid Research Ltd, Debrecen, Hungary
| | | | - Zsolt Torok
- Astrid Research Ltd, Debrecen, Hungary
- Department of Computer Graphics and Image Processing, University of Debrecen Centre of Arts, Humanities and Sciences, Debrecen, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
- MTA-DE “Lendulet” Immunogenomics Research Group, University of Debrecen, Medical and Health Science Center, Debrecen, Hungary
| | - Balint L. Balint
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
- Center for Clinical Genomics and Personalized Medicine, Research Center for Molecular Medicine, University of Debrecen Medical and Health Science Center, Debrecen, Hungary
- UD-Genomed Ltd, Debrecen, Hungary
- * E-mail:
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Czimmerer Z, Varga T, Poliska S, Nemet I, Szanto A, Nagy L. Identification of novel markers of alternative activation and potential endogenous PPARγ ligand production mechanisms in human IL-4 stimulated differentiating macrophages. Immunobiology 2012; 217:1301-14. [PMID: 22954708 DOI: 10.1016/j.imbio.2012.08.270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/30/2012] [Accepted: 08/02/2012] [Indexed: 01/28/2023]
Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Life Science Building, Egyetem ter 1, Debrecen H-4012, Hungary
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Nagy Z, Czimmerer Z, Szanto A, Daniel B, Schwabe J, Nagy L. P057 Cytokine mediated regulation of PPARg activity in human macrophages. Cytokine 2012. [DOI: 10.1016/j.cyto.2012.06.141] [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: 10/28/2022]
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Miko E, Margitai Z, Czimmerer Z, Várkonyi I, Dezso B, Lányi A, Bacsó Z, Scholtz B. miR-126 inhibits proliferation of small cell lung cancer cells by targeting SLC7A5. FEBS Lett 2011; 585:1191-6. [PMID: 21439283 DOI: 10.1016/j.febslet.2011.03.039] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 11/19/2022]
Abstract
Despite intensive efforts to improve therapies, small cell lung cancer (SCLC) still has a dismal median survival of 18 months. Since miR-126 is under-expressed in the majority of SCLC tumors, we investigated the effect of miR-126 overexpression on the proliferation and cell cycle distribution of H69 cells. Our results demonstrate that miR-126 inhibits proliferation of H69 cells, by delaying the cells in the G1 phase. Short interfering RNA (siRNA) mediated suppression of SLC7A5, a predicted target of mir-126, has the same effect on H69 cells. We also show for the first time that SLC7A5 is a direct target of miR-126.
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Affiliation(s)
- Edit Miko
- Dept. of Biochemistry and Molecular Biology, Clinical Genomics Center, University of Debrecen Medical and Health Science Center, Hungary
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Miko E, Czimmerer Z, Csánky E, Boros G, Buslig J, Dezső B, Scholtz B. DIFFERENTIALLY EXPRESSED MicroRNAs IN SMALL CELL LUNG CANCER. Exp Lung Res 2009; 35:646-64. [DOI: 10.3109/01902140902822312] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Röszer T, Czimmerer Z, Szentmiklósi AJ, Bánfalvi G. Nitric oxide synthesis is blocked in the enteral nervous system during dormant periods of the snail Helix lucorum. Cell Tissue Res 2004; 316:255-62. [PMID: 15052467 DOI: 10.1007/s00441-004-0870-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2003] [Accepted: 02/08/2004] [Indexed: 11/25/2022]
Abstract
During dormancy of terrestrial snails, the whole neuromodulation of the nervous system is deeply modified. In this work we studied the adaptation of a previously described, putatively nitric oxide (NO) forming enteral network to the long-term resting periods of the snail Helix lucorum. The standard NADPH diaphorase (NADPHd) technique, which is an accepted method for histochemical NO synthase (NOS) detection, labeled the same enteric neurons of the midintestine in active or hibernated snails. Quantification of the NO-derived nitrite by the Griess reaction established that the nitrite formation is confined to the NADPHd-reactive network containing the midintestinal segment. In active snails, the nitrite formation could be enhanced by the NOS substrate L-arginine (10 microM-1 mM), but decreased by the known NOS inhibitors 1 mM N(omega)-nitro-L-arginine (NOARG) and 10 mM aminoguanidine (AG). Application of 1 mM L-arginine and 1 mM NOARG decreased the amplitude of the midintestinal muscle contractile activity, but did not affect the rectal motility. In dormancy, the nitrite formation was reduced in the NADPHd-reactive midintestinal network. Application of l-arginine could not provoke nitrite production and did not influence the midintestinal motility. Our findings indicate that NO is involved in the neural transmission to intestinal muscles of gastropods, but enteric release of NO is blocked during dormancy. The decreased NO synthesis is possibly due to an as yet undefined mechanism, by which the L-arginine/NO conversion ability of NOS could temporarily be inhibited in the long-term resting period of H. lucorum.
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Affiliation(s)
- Tamás Röszer
- Department of Animal Anatomy and Physiology, Faculty of Science, Debrecen University, PO Box 15, 4010 Debrecen, Hungary.
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Röszer T, Jenei Z, Gáll T, Nagy O, Czimmerer Z, Serfözö Z, Elekes K, Bánfalvi G. A Possible Stimulatory Effect of FMRFamide on Neural Nitric Oxide Production in the Central Nervous System of Helix lucorum L. Brain Behav Evol 2003; 63:23-33. [PMID: 14673196 DOI: 10.1159/000073757] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 08/01/2003] [Indexed: 11/19/2022]
Abstract
The anatomical and functional relationship between neurons expressing nitric oxide (NO) synthase and molluscan cardioexcitatory (FMRFamide)-like neuropeptides was studied in the central ganglia of Helix lucorum (Pulmonata, Gastropoda), applying NADPHdiaphorase (NADPHd) histochemistry to visualize NO synthase and immunocytochemistry to demonstrate FMRFamide (FMRFa) at the light microscopic level. The NO production of the ganglia was detected by the colorimetric Griess determination of nitrite, a breakdown product of NO. Effects of the NO synthase substrate amino acid L-arginine, the NO synthase inhibitor Nomega-nitro-L-arginine (NOARG), synthetic FMRFa and the FMRFa sensitive ion channel blocker amiloride hydrochloride on nitrite production were also tested. NADPHd reaction labeled nerve cells and fibers in the procerebra, mesocerebra and metacerebra within the cerebral ganglia, and cell clusters in the postcerebral ganglia. FMRFa immunolabeling could be observed within subpopulations of NADPHd positive cells and in pericellular varicose fibers surrounding NADPHd stained neurons. Nitrite production of the ganglia was stimulated by L-arginine (10- 20 mM) but was decreased by NOARG (1-2 mM). Synthetic FMRFa (0.830-3.340 mM) increased the nitrite production in a dose dependent manner, but was ineffective in the presence of NOARG. Amiloride hydrochloride (7.890 mM) reduced the FMRFa evoked nitrite production in all ganglia. This is the first description of an anatomical relationship between putative NO producing and FMRFa containing cells, suggesting a possible regulatory role of FMRFa in the NO mediated signaling in an invertebrate nervous system.
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Affiliation(s)
- Tamás Röszer
- Department of Animal Anatomy and Physiology, Faculty of Natural Sciences, Debrecen University, Debrecen, Hungary.
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