1
|
Giaimo BD, Friedrich T, Ferrante F, Bartkuhn M, Borggrefe T. Comprehensive genomic features indicative for Notch responsiveness. Nucleic Acids Res 2024:gkae292. [PMID: 38647081 DOI: 10.1093/nar/gkae292] [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: 12/14/2023] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription factor RBPJ is the central component in Notch signal transduction and directly forms a coactivator complex together with the Notch intracellular domain (NICD). While RBPJ protein levels remain constant in most tissues, dynamic expression of Notch target genes varies depending on the given cell-type and the Notch activity state. To elucidate dynamic RBPJ binding genome-wide, we investigated RBPJ occupancy by ChIP-Seq. Surprisingly, only a small set of the total RBPJ sites show a dynamic binding behavior in response to Notch signaling. Compared to static RBPJ sites, dynamic sites differ in regard to their chromatin state, binding strength and enhancer positioning. Dynamic RBPJ sites are predominantly located distal to transcriptional start sites (TSSs), while most static sites are found in promoter-proximal regions. Importantly, gene responsiveness is preferentially associated with dynamic RBPJ binding sites and this static and dynamic binding behavior is repeatedly observed across different cell types and species. Based on the above findings we used a machine-learning algorithm to predict Notch responsiveness with high confidence in different cellular contexts. Our results strongly support the notion that the combination of binding strength and enhancer positioning are indicative of Notch responsiveness.
Collapse
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany
- Institute for Lung Health, Aulweg 132, 35392 Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
2
|
Taylor J, Uhl L, Moll I, Hasan SS, Wiedmann L, Morgenstern J, Giaimo BD, Friedrich T, Alsina-Sanchis E, De Angelis Rigotti F, Mülfarth R, Kaltenbach S, Schenk D, Nickel F, Fleming T, Sprinzak D, Mogler C, Korff T, Billeter AT, Müller-Stich BP, Berriel Diaz M, Borggrefe T, Herzig S, Rohm M, Rodriguez-Vita J, Fischer A. Endothelial Notch1 signaling in white adipose tissue promotes cancer cachexia. Nat Cancer 2023; 4:1544-1560. [PMID: 37749321 PMCID: PMC10663158 DOI: 10.1038/s43018-023-00622-y] [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] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/20/2023] [Indexed: 09/27/2023]
Abstract
Cachexia is a major cause of morbidity and mortality in individuals with cancer and is characterized by weight loss due to adipose and muscle tissue wasting. Hallmarks of white adipose tissue (WAT) remodeling, which often precedes weight loss, are impaired lipid storage, inflammation and eventually fibrosis. Tissue wasting occurs in response to tumor-secreted factors. Considering that the continuous endothelium in WAT is the first line of contact with circulating factors, we postulated whether the endothelium itself may orchestrate tissue remodeling. Here, we show using human and mouse cancer models that during precachexia, tumors overactivate Notch1 signaling in distant WAT endothelium. Sustained endothelial Notch1 signaling induces a WAT wasting phenotype in male mice through excessive retinoic acid production. Pharmacological blockade of retinoic acid signaling was sufficient to inhibit WAT wasting in a mouse cancer cachexia model. This demonstrates that cancer manipulates the endothelium at distant sites to mediate WAT wasting by altering angiocrine signals.
Collapse
Affiliation(s)
- Jacqueline Taylor
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leonie Uhl
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Iris Moll
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sana Safatul Hasan
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Lena Wiedmann
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Morgenstern
- Department of Internal Medicine Endocrinology and Clinical Chemistry, University of Heidelberg, Heidelberg, Germany
| | | | - Tobias Friedrich
- Institute of Biochemistry, University of Giessen, Giessen, Germany
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Giessen, Germany
| | - Elisenda Alsina-Sanchis
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Francesca De Angelis Rigotti
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Tumor-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Ronja Mülfarth
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sarah Kaltenbach
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Darius Schenk
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Nickel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Department of Internal Medicine Endocrinology and Clinical Chemistry, University of Heidelberg, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Carolin Mogler
- Institute of Pathology, Technical University of Munich School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas Korff
- Institute of Physiology and Pathophysiology, Department of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Adrian T Billeter
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Beat P Müller-Stich
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Mauricio Berriel Diaz
- Institute for Diabetes and Cancer, Helmholtz Center Munich, German Center for Diabetes Research (DZD), Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Unit, Department of Inner Medicine I, Heidelberg University Hospital, Heidelberg, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Stephan Herzig
- Institute for Diabetes and Cancer, Helmholtz Center Munich, German Center for Diabetes Research (DZD), Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Unit, Department of Inner Medicine I, Heidelberg University Hospital, Heidelberg, Germany
- Chair Molecular Metabolic Control, Technical University of Munich, Munich, Germany
| | - Maria Rohm
- Institute for Diabetes and Cancer, Helmholtz Center Munich, German Center for Diabetes Research (DZD), Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Unit, Department of Inner Medicine I, Heidelberg University Hospital, Heidelberg, Germany
| | - Juan Rodriguez-Vita
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Tumor-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain.
| | - Andreas Fischer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
- German Center for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany.
| |
Collapse
|
3
|
Hall D, Giaimo BD, Park SS, Hemmer W, Friedrich T, Ferrante F, Bartkuhn M, Yuan Z, Oswald F, Borggrefe T, Rual JF, Kovall R. The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3. Nucleic Acids Res 2022; 50:13083-13099. [PMID: 36477367 PMCID: PMC9825171 DOI: 10.1093/nar/gkac1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The Notch pathway transmits signals between neighboring cells to elicit downstream transcriptional programs. Notch is a major regulator of cell fate specification, proliferation, and apoptosis, such that aberrant signaling leads to a pleiotropy of human diseases, including developmental disorders and cancers. The pathway signals through the transcription factor CSL (RBPJ in mammals), which forms an activation complex with the intracellular domain of the Notch receptor and the coactivator Mastermind. CSL can also function as a transcriptional repressor by forming complexes with one of several different corepressor proteins, such as FHL1 or SHARP in mammals and Hairless in Drosophila. Recently, we identified L3MBTL3 as a bona fide RBPJ-binding corepressor that recruits the repressive lysine demethylase LSD1/KDM1A to Notch target genes. Here, we define the RBPJ-interacting domain of L3MBTL3 and report the 2.06 Å crystal structure of the RBPJ-L3MBTL3-DNA complex. The structure reveals that L3MBTL3 interacts with RBPJ via an unusual binding motif compared to other RBPJ binding partners, which we comprehensively analyze with a series of structure-based mutants. We also show that these disruptive mutations affect RBPJ and L3MBTL3 function in cells, providing further insights into Notch mediated transcriptional regulation.
Collapse
Affiliation(s)
- Daniel Hall
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | | | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Wiebke Hemmer
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, University of Giessen, 35392 Giessen, Germany
| | - Zhenyu Yuan
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rhett A Kovall
- To whom correspondence should be addressed. Tel: +1 513 558 4631;
| |
Collapse
|
4
|
Alsina-Sanchis E, Mülfarth R, Moll I, Böhn S, Wiedmann L, Jordana-Urriza L, Ziegelbauer T, Zimmer E, Taylor J, De Angelis Rigotti F, Stögbauer A, Giaimo BD, Cerwenka A, Borggrefe T, Fischer A, Rodriguez-Vita J. Endothelial RBPJ Is Essential for the Education of Tumor-Associated Macrophages. Cancer Res 2022; 82:4414-4428. [PMID: 36200806 DOI: 10.1158/0008-5472.can-22-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 01/24/2023]
Abstract
Epithelial ovarian cancer (EOC) is one of the most lethal gynecologic cancers worldwide. EOC cells educate tumor-associated macrophages (TAM) through CD44-mediated cholesterol depletion to generate an immunosuppressive tumor microenvironment (TME). In addition, tumor cells frequently activate Notch1 receptors on endothelial cells (EC) to facilitate metastasis. However, further work is required to establish whether the endothelium also influences the education of recruited monocytes. Here, we report that canonical Notch signaling through RBPJ in ECs is an important player in the education of TAMs and EOC progression. Deletion of Rbpj in the endothelium of adult mice reduced infiltration of monocyte-derived macrophages into the TME of EOC and prevented the acquisition of a typical TAM gene signature; this was associated with stronger cytotoxic activity of T cells and decreased tumor burden. Mechanistically, CXCL2 was identified as a novel Notch/RBPJ target gene that regulated the expression of CD44 on monocytes and subsequent cholesterol depletion of TAMs. Bioinformatic analysis of ovarian cancer patient data showed that increased CXCL2 expression is accompanied by higher expression of CD44 and TAM education. Together, these findings indicate that EOC cells induce the tumor endothelium to secrete CXCL2 to establish an immunosuppressive microenvironment. SIGNIFICANCE Endothelial Notch signaling favors immunosuppression by increasing CXCL2 secretion to stimulate CD44 expression in macrophages, facilitating their education by tumor cells.
Collapse
Affiliation(s)
- Elisenda Alsina-Sanchis
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ronja Mülfarth
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Iris Moll
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sarah Böhn
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Wiedmann
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Lorea Jordana-Urriza
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tara Ziegelbauer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eleni Zimmer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jacqueline Taylor
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesca De Angelis Rigotti
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Tumour-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Adrian Stögbauer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Adelheid Cerwenka
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany Tissue
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Andreas Fischer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Juan Rodriguez-Vita
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Tumour-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| |
Collapse
|
5
|
Giaimo BD, Borggrefe T. Enhancer-promoter communication: unraveling enhancer strength and positioning within a given topologically associating domain (TAD). Signal Transduct Target Ther 2022; 7:281. [PMID: 35961952 PMCID: PMC9374741 DOI: 10.1038/s41392-022-01114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
| | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
| |
Collapse
|
6
|
Friedrich T, Ferrante F, Pioger L, Nist A, Stiewe T, Andrau JC, Bartkuhn M, Giaimo BD, Borggrefe T. Notch-dependent and -independent functions of transcription factor RBPJ. Nucleic Acids Res 2022; 50:7925-7937. [PMID: 35848919 PMCID: PMC9371899 DOI: 10.1093/nar/gkac601] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/27/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
Signal transduction pathways often involve transcription factors that promote activation of defined target gene sets. The transcription factor RBPJ is the central player in Notch signaling and either forms an activator complex with the Notch intracellular domain (NICD) or a repressor complex with corepressors like KYOT2/FHL1. The balance between these two antagonizing RBPJ-complexes depends on the activation state of the Notch receptor regulated by cell-to-cell interaction, ligand binding and proteolytic cleavage events. Here, we depleted RBPJ in mature T-cells lacking active Notch signaling and performed RNA-Seq, ChIP-Seq and ATAC-seq analyses. RBPJ depletion leads to upregulation of many Notch target genes. Ectopic expression of NICD1 activates several Notch target genes and enhances RBPJ occupancy. Based on gene expression changes and RBPJ occupancy we define four different clusters, either RBPJ- and/or Notch-regulated genes. Importantly, we identify early (Hes1 and Hey1) and late Notch-responsive genes (IL2ra). Similarly, to RBPJ depletion, interfering with transcriptional repression by squelching with cofactor KYOT2/FHL1, leads to upregulation of Notch target genes. Taken together, RBPJ is not only an essential part of the Notch co-activator complex but also functions as a repressor in a Notch-independent manner.
Collapse
Affiliation(s)
- Tobias Friedrich
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany.,Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Léo Pioger
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, 34293 cedex 5, Montpellier, France
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, 34293 cedex 5, Montpellier, France
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany.,Institute for Lung Health, Aulweg 132, 35392 Giessen, Germany
| | - Benedetto Daniele Giaimo
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
7
|
Ferrante F, Giaimo BD, Friedrich T, Sugino T, Mertens D, Kugler S, Gahr BM, Just S, Pan L, Bartkuhn M, Potente M, Oswald F, Borggrefe T. Hydroxylation of the NOTCH1 intracellular domain regulates Notch signaling dynamics. Cell Death Dis 2022; 13:600. [PMID: 35821235 PMCID: PMC9276811 DOI: 10.1038/s41419-022-05052-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 01/21/2023]
Abstract
Notch signaling plays a pivotal role in the development and, when dysregulated, it contributes to tumorigenesis. The amplitude and duration of the Notch response depend on the posttranslational modifications (PTMs) of the activated NOTCH receptor - the NOTCH intracellular domain (NICD). In normoxic conditions, the hydroxylase FIH (factor inhibiting HIF) catalyzes the hydroxylation of two asparagine residues of the NICD. Here, we investigate how Notch-dependent gene transcription is regulated by hypoxia in progenitor T cells. We show that the majority of Notch target genes are downregulated upon hypoxia. Using a hydroxyl-specific NOTCH1 antibody we demonstrate that FIH-mediated NICD1 hydroxylation is reduced upon hypoxia or treatment with the hydroxylase inhibitor dimethyloxalylglycine (DMOG). We find that a hydroxylation-resistant NICD1 mutant is functionally impaired and more ubiquitinated. Interestingly, we also observe that the NICD1-deubiquitinating enzyme USP10 is downregulated upon hypoxia. Moreover, the interaction between the hydroxylation-defective NICD1 mutant and USP10 is significantly reduced compared to the NICD1 wild-type counterpart. Together, our data suggest that FIH hydroxylates NICD1 in normoxic conditions, leading to the recruitment of USP10 and subsequent NICD1 deubiquitination and stabilization. In hypoxia, this regulatory loop is disrupted, causing a dampened Notch response.
Collapse
Affiliation(s)
- Francesca Ferrante
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Benedetto Daniele Giaimo
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tobias Friedrich
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany ,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany
| | - Toshiya Sugino
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Daniel Mertens
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Bridging Group Mechanisms of Leukemogenesis, B061, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Kugler
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Bernd Martin Gahr
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steffen Just
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Leiling Pan
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany ,Institute for Lung Health (ILH), Aulweg 132, 35392 Giessen, Germany
| | - Michael Potente
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany ,grid.484013.a0000 0004 6879 971XBerlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Franz Oswald
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Tilman Borggrefe
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
8
|
Robert-Finestra T, Tan BF, Mira-Bontenbal H, Timmers E, Gontan C, Merzouk S, Giaimo BD, Dossin F, van IJcken WFJ, Martens JWM, Borggrefe T, Heard E, Gribnau J. SPEN is required for Xist upregulation during initiation of X chromosome inactivation. Nat Commun 2021; 12:7000. [PMID: 34853312 PMCID: PMC8636516 DOI: 10.1038/s41467-021-27294-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
At initiation of X chromosome inactivation (XCI), Xist is monoallelically upregulated from the future inactive X (Xi) chromosome, overcoming repression by its antisense transcript Tsix. Xist recruits various chromatin remodelers, amongst them SPEN, which are involved in silencing of X-linked genes in cis and establishment of the Xi. Here, we show that SPEN plays an important role in initiation of XCI. Spen null female mouse embryonic stem cells (ESCs) are defective in Xist upregulation upon differentiation. We find that Xist-mediated SPEN recruitment to the Xi chromosome happens very early in XCI, and that SPEN-mediated silencing of the Tsix promoter is required for Xist upregulation. Accordingly, failed Xist upregulation in Spen-/- ESCs can be rescued by concomitant removal of Tsix. These findings indicate that SPEN is not only required for the establishment of the Xi, but is also crucial in initiation of the XCI process.
Collapse
Affiliation(s)
- Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | - Beatrice F Tan
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | - Erika Timmers
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | - Sarra Merzouk
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands
| | | | - François Dossin
- European Molecular Biology Laboratory, Director's Research, 69117, Heidelberg, Germany
| | - Wilfred F J van IJcken
- Center for Biomics, Erasmus University Medical Center, 3015CN, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN, Rotterdam, The Netherlands
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, 35392, Giessen, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Research, 69117, Heidelberg, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Oncode Institute, 3015GD, Rotterdam, The Netherlands.
| |
Collapse
|
9
|
Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
Collapse
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| |
Collapse
|
10
|
Borggrefe T, Daniele Giaimo B. Correction to: Enhancers and Promoters. Methods Mol Biol 2021; 2351:C1. [PMID: 35157265 DOI: 10.1007/978-1-0716-1597-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Gießen, Hessen, Germany
| | | |
Collapse
|
11
|
Ferrante F, Giaimo BD, Bartkuhn M, Zimmermann T, Close V, Mertens D, Nist A, Stiewe T, Meier-Soelch J, Kracht M, Just S, Klöble P, Oswald F, Borggrefe T. HDAC3 functions as a positive regulator in Notch signal transduction. Nucleic Acids Res 2020; 48:3496-3512. [PMID: 32107550 PMCID: PMC7144913 DOI: 10.1093/nar/gkaa088] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 04/30/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022] Open
Abstract
Aberrant Notch signaling plays a pivotal role in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL). Amplitude and duration of the Notch response is controlled by ubiquitin-dependent proteasomal degradation of the Notch1 intracellular domain (NICD1), a hallmark of the leukemogenic process. Here, we show that HDAC3 controls NICD1 acetylation levels directly affecting NICD1 protein stability. Either genetic loss-of-function of HDAC3 or nanomolar concentrations of HDAC inhibitor apicidin lead to downregulation of Notch target genes accompanied by a local reduction of histone acetylation. Importantly, an HDAC3-insensitive NICD1 mutant is more stable but biologically less active. Collectively, these data show a new HDAC3- and acetylation-dependent mechanism that may be exploited to treat Notch1-dependent leukemias.
Collapse
Affiliation(s)
- Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | | | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Viola Close
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany.,Cooperation Unit "Mechanisms of Leukemogenesis'' (B061), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg Germany
| | - Daniel Mertens
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany.,Cooperation Unit "Mechanisms of Leukemogenesis'' (B061), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, University of Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, University of Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Steffen Just
- University Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Patricia Klöble
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
12
|
Yuan Z, VanderWielen BD, Giaimo BD, Pan L, Collins CE, Turkiewicz A, Hein K, Oswald F, Borggrefe T, Kovall RA. Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site. Cell Rep 2020; 26:845-854.e6. [PMID: 30673607 PMCID: PMC6352735 DOI: 10.1016/j.celrep.2018.12.097] [Citation(s) in RCA: 31] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/05/2018] [Accepted: 12/21/2018] [Indexed: 11/28/2022] Open
Abstract
Notch is a conserved signaling pathway that is essential for metazoan development and homeostasis; dysregulated signaling underlies the pathophysiology of numerous human diseases. Receptor-ligand interactions result in gene expression changes, which are regulated by the transcription factor RBPJ. RBPJ forms a complex with the intracellular domain of the Notch receptor and the coactivator Mastermind to activate transcription, but it can also function as a repressor by interacting with corepressor proteins. Here, we determine the structure of RBPJ bound to the corepressor SHARP and DNA, revealing its mode of binding to RBPJ. We tested structure-based mutants in biophysical and biochemical-cellular as-says to characterize the role of RBPJ as a repressor, clearly demonstrating that RBPJ mutants deficient for SHARP binding are incapable of repressing transcription of genes responsive to Notch signaling in cells. Altogether, our structure-function studies provide significant insights into the repressor function of RBPJ. Yuan et al. determine the X-ray structure of the corepressor SHARP bound to RBPJ, the nuclear effector of the Notch pathway. The structure-function analysis provides insights into corepressor binding to RBPJ and how RBPJ functions as a repressor of transcription of Notch target genes.
Collapse
Affiliation(s)
- Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bradley D VanderWielen
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Leiling Pan
- Department of Internal Medicine I, Center for Internal Medicine, University Medical Center Ulm, 89081 Ulm, Germany
| | - Courtney E Collins
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Franz Oswald
- Department of Internal Medicine I, Center for Internal Medicine, University Medical Center Ulm, 89081 Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
13
|
Agrawal M, Schwarz P, Giaimo BD, Bedzhov I, Corbacioglu A, Weber D, Gaidzik VI, Jahn N, Rücker FG, Schroeder T, Kindler T, Wattad M, Götze K, Lübbert M, Salwender H, Ringhoffer M, Lange E, Koller E, Thol F, Heuser M, Ganser A, Bullinger L, Paschka P, Döhner H, Geiger H, Borggrefe T, Döhner K, Oswald F. Functional and clinical characterization of the alternatively spliced isoform AML1-ETO9a in adult patients with translocation t(8;21)(q22;q22.1) acute myeloid leukemia (AML). Leukemia 2019; 34:630-634. [PMID: 31462736 PMCID: PMC7214266 DOI: 10.1038/s41375-019-0551-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 12/04/2022]
Affiliation(s)
- Mridul Agrawal
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Peggy Schwarz
- Klinik für Innere Medizin I, Universitätsklinikum Ulm, Ulm, Germany
| | | | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | | | - Daniela Weber
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Verena I Gaidzik
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Nikolaus Jahn
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Frank G Rücker
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Thomas Schroeder
- Klinik für Hämatologie, Onkologie und Klinische Immunologie, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Thomas Kindler
- III. Medizinische Klinik und Poliklinik, Universitätsmedizin Mainz, Mainz, Germany
| | - Mohammed Wattad
- Klinik für Hämatologie, Internistische Onkologie und Stammzellentransplantation, Evangelisches Krankenhaus Essen-Werden, Essen, Germany
| | - Katharina Götze
- III. Medizinische Klinik, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Michael Lübbert
- Klinik für Innere Medizin I, Universitätsklinikum Freiburg, Freiburg, Germany
| | - Hans Salwender
- II. Medizinische Abteilung, Asklepios Klinik Altona, Hamburg, Germany
| | - Mark Ringhoffer
- Medizinische Klinik III, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | - Elisabeth Lange
- Klinik für Hämatologie, Onkologie und Palliativmedizin, Evangelisches Krankenhaus Hamm, Hamm, Germany
| | - Elisabeth Koller
- Medizinische Abteilung, Hanusch-Krankenhaus der WGKK, Wien, Austria
| | - Felicitas Thol
- Klinik für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Hannover, Germany
| | - Michael Heuser
- Klinik für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Hannover, Germany
| | - Arnold Ganser
- Klinik für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Hannover, Germany
| | - Lars Bullinger
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Campus Virchow-Klinikum, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Paschka
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Hartmut Döhner
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany
| | - Hartmut Geiger
- Institut für Molekulare Medizin, Universität Ulm, Ulm, Germany.,Division of Experimental Hematology and Cancer Biology, CCHMC, Cincinnati, OH, USA
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Konstanze Döhner
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Germany.
| | - Franz Oswald
- Klinik für Innere Medizin I, Universitätsklinikum Ulm, Ulm, Germany
| |
Collapse
|
14
|
Giaimo BD, Ferrante F, Vallejo DM, Hein K, Gutierrez-Perez I, Nist A, Stiewe T, Mittler G, Herold S, Zimmermann T, Bartkuhn M, Schwarz P, Oswald F, Dominguez M, Borggrefe T. Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response. Nucleic Acids Res 2019; 46:8197-8215. [PMID: 29986055 PMCID: PMC6144792 DOI: 10.1093/nar/gky551] [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: 11/10/2016] [Accepted: 06/28/2018] [Indexed: 02/04/2023] Open
Abstract
A fundamental as yet incompletely understood feature of Notch signal transduction is a transcriptional shift from repression to activation that depends on chromatin regulation mediated by transcription factor RBP-J and associated cofactors. Incorporation of histone variants alter the functional properties of chromatin and are implicated in the regulation of gene expression. Here, we show that depletion of histone variant H2A.Z leads to upregulation of canonical Notch target genes and that the H2A.Z-chaperone TRRAP/p400/Tip60 complex physically associates with RBP-J at Notch-dependent enhancers. When targeted to RBP-J-bound enhancers, the acetyltransferase Tip60 acetylates H2A.Z and upregulates Notch target gene expression. Importantly, the Drosophila homologs of Tip60, p400 and H2A.Z modulate Notch signaling response and growth in vivo. Together, our data reveal that loading and acetylation of H2A.Z are required to assure tight control of canonical Notch activation.
Collapse
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albertstrasse 19A, 79104 Freiburg, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Diana M Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Irene Gutierrez-Perez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Universities Giessen & Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Peggy Schwarz
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
15
|
Diéguez-Hurtado R, Kato K, Giaimo BD, Nieminen-Kelhä M, Arf H, Ferrante F, Bartkuhn M, Zimmermann T, Bixel MG, Eilken HM, Adams S, Borggrefe T, Vajkoczy P, Adams RH. Loss of the transcription factor RBPJ induces disease-promoting properties in brain pericytes. Nat Commun 2019; 10:2817. [PMID: 31249304 PMCID: PMC6597568 DOI: 10.1038/s41467-019-10643-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
Sufficient vascular supply is indispensable for brain development and function, whereas dysfunctional blood vessels are associated with human diseases such as vascular malformations, stroke or neurodegeneration. Pericytes are capillary-associated mesenchymal cells that limit vascular permeability and protect the brain by preserving blood-brain barrier integrity. Loss of pericytes has been linked to neurodegenerative changes in genetically modified mice. Here, we report that postnatal inactivation of the Rbpj gene, encoding the transcription factor RBPJ, leads to alteration of cell identity markers in brain pericytes, increases local TGFβ signalling, and triggers profound changes in endothelial behaviour. These changes, which are not mimicked by pericyte ablation, imperil vascular stability and induce the acquisition of pathological landmarks associated with cerebral cavernous malformations. In adult mice, loss of Rbpj results in bigger stroke lesions upon ischemic insult. We propose that brain pericytes can acquire deleterious properties that actively enhance vascular lesion formation and promote pathogenic processes. Pericytes are perivascular cells essential for blood-brain barrier maintenance. Here Diéguez-Hurtado et al. show that depletion of the transcription factor RBPJ in pericytes affects their molecular identity and disturbs endothelial cell behaviour, inducing the formation of vascular lesions in the brain.
Collapse
Affiliation(s)
- Rodrigo Diéguez-Hurtado
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.,Faculty of Medicine, University of Münster, 48149, Münster, Germany
| | - Katsuhiro Kato
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | | | - Melina Nieminen-Kelhä
- Department of Neurosurgery, Charité-Universitätsmedizin, Charitéplatz 1, Berlin, 10117, Germany.,Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Hendrik Arf
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - M Gabriele Bixel
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Hanna M Eilken
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.,Bayer AG, Aprather Weg 18a, 42113, Wuppertal, Germany
| | - Susanne Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité-Universitätsmedizin, Charitéplatz 1, Berlin, 10117, Germany. .,Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Ralf H Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany. .,Faculty of Medicine, University of Münster, 48149, Münster, Germany.
| |
Collapse
|
16
|
Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [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] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
Collapse
Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
| |
Collapse
|
17
|
Giaimo BD, Borggrefe T. Introduction to Molecular Mechanisms in Notch Signal Transduction and Disease Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:3-30. [DOI: 10.1007/978-3-319-89512-3_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
18
|
Zakrzewicz D, Didiasova M, Krüger M, Giaimo BD, Borggrefe T, Mieth M, Hocke AC, Zakrzewicz A, Schaefer L, Preissner KT, Wygrecka M. Protein arginine methyltransferase 5 mediates enolase-1 cell surface trafficking in human lung adenocarcinoma cells. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1816-1827. [PMID: 29501774 DOI: 10.1016/j.bbadis.2018.02.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/12/2018] [Accepted: 02/27/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Enolase-1-dependent cell surface proteolysis plays an important role in cell invasion. Although enolase-1 (Eno-1), a glycolytic enzyme, has been found on the surface of various cells, the mechanism responsible for its exteriorization remains elusive. Here, we investigated the involvement of post-translational modifications (PTMs) of Eno-1 in its lipopolysaccharide (LPS)-triggered trafficking to the cell surface. RESULTS We found that stimulation of human lung adenocarcinoma cells with LPS triggered the monomethylation of arginine 50 (R50me) within Eno-1. The Eno-1R50me was confirmed by its interaction with the tudor domain (TD) from TD-containing 3 (TDRD3) protein recognizing methylarginines. Substitution of R50 with lysine (R50K) reduced Eno-1 association with epithelial caveolar domains, thereby diminishing its exteriorization. Similar effects were observed when pharmacological inhibitors of arginine methyltransferases were applied. Protein arginine methyltransferase 5 (PRMT5) was identified to be responsible for Eno-1 methylation. Overexpression of PRMT5 and caveolin-1 enhanced levels of membrane-bound extracellular Eno-1 and, conversely, pharmacological inhibition of PRMT5 attenuated Eno-1 cell-surface localization. Importantly, Eno-1R50me was essential for cancer cell motility since the replacement of Eno-1 R50 by lysine or the suppression of PRMT 5 activity diminished Eno-1-triggered cell invasion. CONCLUSIONS LPS-triggered Eno-1R50me enhances Eno-1 cell surface levels and thus potentiates the invasive properties of cancer cells. Strategies to target Eno-1R50me may offer novel therapeutic approaches to attenuate tumor metastasis in cancer patients.
Collapse
Affiliation(s)
- Dariusz Zakrzewicz
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany.
| | - Miroslava Didiasova
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Marcus Krüger
- Center for Molecular Medicine, University of Cologne, Germany
| | - Benedetto Daniele Giaimo
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tilman Borggrefe
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Maren Mieth
- Department of Internal Medicine, Infectious Diseases and Pulmonary Medicine, Charité-University Medicine Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Andreas C Hocke
- Department of Internal Medicine, Infectious Diseases and Pulmonary Medicine, Charité-University Medicine Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Anna Zakrzewicz
- Laboratory of Experimental Surgery, Department of General and Thoracic Surgery, Justus Liebig University Giessen, Feulgenstrasse 10-12, 35385 Giessen, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Klaus T Preissner
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Malgorzata Wygrecka
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany; Member of the German Center for Lung Research, Giessen, Germany
| |
Collapse
|
19
|
Thiel VN, Giaimo BD, Schwarz P, Soller K, Vas V, Bartkuhn M, Blätte TJ, Döhner K, Bullinger L, Borggrefe T, Geiger H, Oswald F. Heterodimerization of AML1/ETO with CBFβ is required for leukemogenesis but not for myeloproliferation. Leukemia 2017; 31:2491-2502. [PMID: 28360416 PMCID: PMC5668496 DOI: 10.1038/leu.2017.105] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 02/18/2017] [Accepted: 03/13/2017] [Indexed: 02/07/2023]
Abstract
The AML1/Runx1 transcription factor and its heterodimerization partner CBFβ are essential regulators of myeloid differentiation. The chromosomal translocation t(8;21), fusing the DNA binding domain of AML1 to the corepressor eight-twenty-one (ETO), is frequently associated with acute myeloid leukemia and generates the AML1/ETO (AE) fusion protein. AE represses target genes usually activated by AML1 and also affects the endogenous repressive function of ETO at Notch target genes. In order to analyze the contribution of CBFβ in AE-mediated leukemogenesis and deregulation of Notch target genes, we introduced two point mutations in a leukemia-initiating version of AE in mice, called AE9a, that disrupt the AML1/CBFβ interaction (AE9aNT). We report that the AE9a/CBFβ interaction is not required for the AE9a-mediated aberrant expression of AML1 target genes, while upregulation/derepression of Notch target genes does require the interaction with CBFβ. Using retroviral transduction to express AE9a in murine adult bone marrow-derived hematopoietic progenitors, we observed that both AE9a and AE9aNT lead to increased myeloproliferation in vivo. However, both development of leukemia and long-term replating capacity are only observed with AE9a but not with AE9aNT. Thus, deregulation of both AML1 and Notch target genes is required for the development of AE9a-driven leukemia.
Collapse
Affiliation(s)
- V N Thiel
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, University of Ulm, Ulm, Germany
| | - B D Giaimo
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - P Schwarz
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, University of Ulm, Ulm, Germany
| | - K Soller
- Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - V Vas
- Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - M Bartkuhn
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - T J Blätte
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - K Döhner
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - L Bullinger
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - T Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - H Geiger
- Institute of Molecular Medicine, University of Ulm, Ulm, Germany
- Division of Experimental Hematology and Cancer Biology, CCHMC, Cincinnati, OH, USA
| | - F Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, University of Ulm, Ulm, Germany
| |
Collapse
|
20
|
Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, Govindarajoo B, Zhang Y, Sun Y, Dou Y, Basrur V, Elenitoba-Johnson KS, Nesvizhskii AI, Ceron J, Lee CY, Borggrefe T, Kovall RA, Rual JF. RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO J 2017; 36:3232-3249. [PMID: 29030483 PMCID: PMC5666606 DOI: 10.15252/embj.201796525] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [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: 01/13/2017] [Revised: 08/31/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022] Open
Abstract
Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. Upon ligand binding, the Notch intracellular domain (NOTCH ICD) translocates into the nucleus and forms a complex with the transcription factor RBPJ (also known as CBF1 or CSL) to activate expression of Notch target genes. In the absence of a Notch signal, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 (also known as MBT1) as a novel RBPJ interactor. L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and the histone demethylase KDM1A (also known as LSD1) to the enhancers of Notch target genes, leading to H3K4me2 demethylation and to transcriptional repression. Importantly, in vivo analyses of the homologs of RBPJ and L3MBTL3 in Drosophila melanogaster and Caenorhabditis elegans demonstrate that the functional link between RBPJ and L3MBTL3 is evolutionarily conserved, thus identifying L3MBTL3 as a universal modulator of Notch signaling in metazoans.
Collapse
Affiliation(s)
- Tao Xu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel Hall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diana M Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kazuya Hori
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - Honglai Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eléna Milon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kimberly Ha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rork Kuick
- Center for Cancer Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Brandon Govindarajoo
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Sun
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Julian Ceron
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| |
Collapse
|
21
|
Pitulescu ME, Schmidt I, Giaimo BD, Antoine T, Berkenfeld F, Ferrante F, Park H, Ehling M, Biljes D, Rocha SF, Langen UH, Stehling M, Nagasawa T, Ferrara N, Borggrefe T, Adams RH. Dll4 and Notch signalling couples sprouting angiogenesis and artery formation. Nat Cell Biol 2017; 19:915-927. [DOI: 10.1038/ncb3555] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/15/2017] [Indexed: 02/07/2023]
|
22
|
Abstract
Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational modifications (PTMs) of histone tails, the exchange of canonical histones with histone variants, and nucleosome eviction. Such regulation requires the binding of signal-sensitive transcription factors (TFs) that recruit chromatin-modifying enzymes at regulatory elements defined as enhancers. Understanding how signaling cascades regulate enhancer activity requires a comprehensive analysis of the binding of TFs, chromatin modifying enzymes, and the occupancy of specific histone marks and histone variants. Chromatin immunoprecipitation (ChIP) assays utilize highly specific antibodies to immunoprecipitate specific protein/DNA complexes. The subsequent analysis of the purified DNA allows for the identification the region occupied by the protein recognized by the antibody. This work describes a protocol to efficiently perform ChIP of histone proteins in a mature mouse T-cell line. The presented protocol allows for the performance of ChIP assays in a reasonable timeframe and with high reproducibility.
Collapse
|
23
|
Abstract
RBPJ is the central transcription factor that controls the Notch-dependent transcriptional response by coordinating repressing histone H3K27 deacetylation and activating histone H3K4 methylation. Here, we discuss the molecular mechanisms how RBPJ interacts with opposing NCoR/HDAC-corepressing or KMT2D/UTX-coactivating complexes and how this is controlled by phosphorylation of chromatin modifiers.
Collapse
Affiliation(s)
| | - Franz Oswald
- b Department of Internal Medicine I , Center for Internal Medicine, University Medical Center Ulm , Ulm , Germany
| | - Tilman Borggrefe
- a Institute of Biochemistry, Justus Liebig University , Giessen , Germany
| |
Collapse
|
24
|
Oswald F, Rodriguez P, Giaimo BD, Antonello ZA, Mira L, Mittler G, Thiel VN, Collins KJ, Tabaja N, Cizelsky W, Rothe M, Kühl SJ, Kühl M, Ferrante F, Hein K, Kovall RA, Dominguez M, Borggrefe T. A phospho-dependent mechanism involving NCoR and KMT2D controls a permissive chromatin state at Notch target genes. Nucleic Acids Res 2016; 44:4703-20. [PMID: 26912830 PMCID: PMC4889922 DOI: 10.1093/nar/gkw105] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/11/2016] [Indexed: 01/24/2023] Open
Abstract
The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3 lysine-4 (H3K4) demethylases are key chromatin modifiers that establish the repressive chromatin state at Notch target genes. However, the counteracting histone methyltransferase required for the active chromatin state remained elusive. Here, we show that the RBP-J interacting factor SHARP is not only able to interact with the NCoR corepressor complex, but also with the H3K4 methyltransferase KMT2D coactivator complex. KMT2D and NCoR compete for the C-terminal SPOC-domain of SHARP. We reveal that the SPOC-domain exclusively binds to phosphorylated NCoR. The balance between NCoR and KMT2D binding is shifted upon mutating the phosphorylation sites of NCoR or upon inhibition of the NCoR kinase CK2β. Furthermore, we show that the homologs of SHARP and KMT2D in Drosophila also physically interact and control Notch-mediated functions in vivo. Together, our findings reveal how signaling can fine-tune a committed chromatin state by phosphorylation of a pivotal chromatin-modifier.
Collapse
Affiliation(s)
- Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Patrick Rodriguez
- Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland
| | - Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany Spemann Graduate School of Biology and Medicine (SGBM), Faculty of Biology, Albert Ludwigs University Freiburg, Germany
| | - Zeus A Antonello
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernández, Campus de Sant Joan, Alicante, Spain
| | - Laura Mira
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernández, Campus de Sant Joan, Alicante, Spain
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Verena N Thiel
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Kelly J Collins
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Nassif Tabaja
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Wiebke Cizelsky
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany International Graduate School in Molecular Medicine Ulm (IGradU), Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Melanie Rothe
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany International Graduate School in Molecular Medicine Ulm (IGradU), Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Susanne J Kühl
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michael Kühl
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernández, Campus de Sant Joan, Alicante, Spain
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| |
Collapse
|
25
|
Borggrefe T, Lauth M, Zwijsen A, Huylebroeck D, Oswald F, Giaimo BD. The Notch intracellular domain integrates signals from Wnt, Hedgehog, TGFβ/BMP and hypoxia pathways. Biochim Biophys Acta 2015; 1863:303-13. [PMID: 26592459 DOI: 10.1016/j.bbamcr.2015.11.020] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 01/12/2023]
Abstract
Notch signaling is a highly conserved signal transduction pathway that regulates stem cell maintenance and differentiation in several organ systems. Upon activation, the Notch receptor is proteolytically processed, its intracellular domain (NICD) translocates into the nucleus and activates expression of target genes. Output, strength and duration of the signal are tightly regulated by post-translational modifications. Here we review the intracellular post-translational regulation of Notch that fine-tunes the outcome of the Notch response. We also describe how crosstalk with other conserved signaling pathways like the Wnt, Hedgehog, hypoxia and TGFβ/BMP pathways can affect Notch signaling output. This regulation can happen by regulation of ligand, receptor or transcription factor expression, regulation of protein stability of intracellular key components, usage of the same cofactors or coregulation of the same key target genes. Since carcinogenesis is often dependent on at least two of these pathways, a better understanding of their molecular crosstalk is pivotal.
Collapse
Affiliation(s)
| | - Matthias Lauth
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Germany
| | - An Zwijsen
- VIB Center for the Biology of Disease and Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Franz Oswald
- University Medical Center Ulm, Department of Internal Medicine I, Ulm, Germany
| | | |
Collapse
|