1
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DeCotiis-Mauro J, Han SM, Mello H, Goyeneche C, Marchesini-Tovar G, Jin L, Bellofatto V, Lukac DM. The cellular Notch1 protein promotes KSHV reactivation in an Rta-dependent manner. J Virol 2024; 98:e0078824. [PMID: 38975769 PMCID: PMC11334469 DOI: 10.1128/jvi.00788-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
The cellular Notch signal transduction pathway is intimately associated with infections by Kaposi's sarcoma-associated herpesvirus (KSHV) and other gamma-herpesviruses. RBP-Jk, the cellular DNA binding component of the canonical Notch pathway, is the key Notch downstream effector protein in virus-infected and uninfected animal cells. Reactivation of KSHV from latency requires the viral lytic switch protein, Rta, to form complexes with RBP-Jk on numerous sites within the viral DNA. Constitutive Notch activity is essential for KSHV pathophysiology in models of Kaposi's sarcoma (KS) and Primary Effusion Lymphoma (PEL), and we demonstrate that Notch1 is also constitutively active in infected Vero cells. Although the KSHV genome contains >100 RBP-Jk DNA motifs, we show that none of the four isoforms of activated Notch can productively reactivate the virus from latency in a highly quantitative trans-complementing reporter virus system. Nevertheless, Notch contributed positively to reactivation because broad inhibition of Notch1-4 with gamma-secretase inhibitor (GSI) or expression of dominant negative mastermind-like1 (dnMAML1) coactivators severely reduced production of infectious KSHV from Vero cells. Reduction of KSHV production is associated with gene-specific reduction of viral transcription in both Vero and PEL cells. Specific inhibition of Notch1 by siRNA partially reduces the production of infectious KSHV, and NICD1 forms promoter-specific complexes with viral DNA during reactivation. We conclude that constitutive Notch activity is required for the robust production of infectious KSHV, and our results implicate activated Notch1 as a pro-viral member of a MAML1/RBP-Jk/DNA complex during viral reactivation. IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) manipulates the host cell oncogenic Notch signaling pathway for viral reactivation from latency and cell pathogenesis. KSHV reactivation requires that the viral protein Rta functionally interacts with RBP-Jk, the DNA-binding component of the Notch pathway, and with promoter DNA to drive transcription of productive cycle genes. We show that the Notch pathway is constitutively active during KSHV reactivation and is essential for robust production of infectious virus progeny. Inhibiting Notch during reactivation reduces the expression of specific viral genes yet does not affect the growth of the host cells. Although Notch cannot reactivate KSHV alone, the requisite expression of Rta reveals a previously unappreciated role for Notch in reactivation. We propose that activated Notch cooperates with Rta in a promoter-specific manner that is partially programmed by Rta's ability to redistribute RBP-Jk DNA binding to the virus during reactivation.
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Affiliation(s)
- Jennifer DeCotiis-Mauro
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Sun M. Han
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Helena Mello
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Corey Goyeneche
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Giuseppina Marchesini-Tovar
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Lianhua Jin
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Vivian Bellofatto
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - David M. Lukac
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
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2
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Foran G, Hallam RD, Megaly M, Turgambayeva A, Antfolk D, Li Y, Luca VC, Necakov A. Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.17.533124. [PMID: 39131356 PMCID: PMC11312450 DOI: 10.1101/2023.03.17.533124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The Notch receptor is a pleiotropic signaling protein that translates intercellular ligand interactions into changes in gene expression via the nuclear localization of the Notch intracellular Domain (NICD). Using a combination of immunohistochemistry, RNA in situ, Optogenetics and super-resolution live imaging of transcription in human cells, we show that the N1ICD can form condensates that positively facilitate Notch target gene expression. We determined that N1ICD undergoes Phase Separation Coupled Percolation (PSCP) into transcriptional condensates, which recruit, enrich, and encapsulate a broad set of core transcriptional proteins. We show that the capacity for condensation is due to the intrinsically disordered transcriptional activation domain of the N1ICD. In addition, the formation of such transcriptional condensates acts to promote Notch-mediated super enhancer-looping and concomitant activation of the MYC protooncogene expression. Overall, we introduce a novel mechanism of Notch1 activity in which discrete changes in nuclear N1ICD abundance are translated into the assembly of transcriptional condensates that facilitate gene expression by enriching essential transcriptional machineries at target genomic loci.
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Affiliation(s)
- Gregory Foran
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Ryan Douglas Hallam
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Marvel Megaly
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Anel Turgambayeva
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Daniel Antfolk
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Yifeng Li
- Department of Computer Science, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Vincent C. Luca
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Aleksandar Necakov
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
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3
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Cao R, Gozlan O, Airich A, Tveriakhina L, Zhou H, Jiang H, Cole PA, Aster JC, Klein T, Sprinzak D, Blacklow SC. Structural requirements for activity of Mind bomb1 in Notch signaling. Structure 2024:S0969-2126(24)00274-0. [PMID: 39121852 DOI: 10.1016/j.str.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2∼Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region (ccRING3) drive MIB1 dimerization and that MIB1 ubiquitin transfer activity relies solely on ccRING3. We report X-ray crystal structures of a UbcH5B-ccRING3 complex and the ANK domain. Directly tethering the MIB1 N-terminal region to ccRING3 forms a minimal MIB1 protein sufficient to induce a Notch response in receiver cells and rescue mib knockout phenotypes in flies. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.
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Affiliation(s)
- Ruili Cao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Oren Gozlan
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alina Airich
- Institute of Genetics, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Lena Tveriakhina
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hanjie Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Philip A Cole
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - David Sprinzak
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
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4
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Tveriakhina L, Scanavachi G, Egan ED, Da Cunha Correia RB, Martin AP, Rogers JM, Yodh JS, Aster JC, Kirchhausen T, Blacklow SC. Temporal dynamics and stoichiometry in human Notch signaling from Notch synaptic complex formation to nuclear entry of the Notch intracellular domain. Dev Cell 2024; 59:1425-1438.e8. [PMID: 38574735 DOI: 10.1016/j.devcel.2024.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Mammalian Notch signaling occurs when the binding of Delta or Jagged to Notch stimulates the proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to control target gene expression. To determine the temporal dynamics of events associated with Notch signaling under native conditions, we fluorescently tagged Notch and Delta at their endogenous genomic loci and visualized them upon pairing of receiver (Notch) and sender (Delta) cells as a function of time after cell contact. At contact sites, Notch and Delta immediately accumulated at 1:1 stoichiometry in synapses, which resolved by 15-20 min after contact. Synapse formation preceded the entrance of the Notch extracellular domain into the sender cell and accumulation of NICD in the nucleus of the receiver cell, which approached a maximum after ∼45 min and was prevented by chemical and genetic inhibitors of signaling. These findings directly link Notch-Delta synapse dynamics to NICD production with spatiotemporal precision.
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Affiliation(s)
- Lena Tveriakhina
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gustavo Scanavachi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Emily D Egan
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo Bango Da Cunha Correia
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alexandre P Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Julia M Rogers
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy S Yodh
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
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5
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Giaimo BD, Friedrich T, Ferrante F, Bartkuhn M, Borggrefe T. Comprehensive genomic features indicative for Notch responsiveness. Nucleic Acids Res 2024; 52:5179-5194. [PMID: 38647081 PMCID: PMC11109962 DOI: 10.1093/nar/gkae292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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.
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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
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6
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Cao R, Gozlan O, Tveriakhina L, Zhou H, Jiang H, Cole PA, Aster JC, Sprinzak D, Blacklow SC. Structural Requirements for Activity of Mind bomb1 in Notch Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582834. [PMID: 38464278 PMCID: PMC10925295 DOI: 10.1101/2024.03.01.582834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2~Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region of MIB1 (ccRING3) drives MIB1 dimerization and that ubiquitin transfer activity of MIB1 relies solely on RING3. We report x-ray crystal structures of a UbcH5B-ccRING3 complex as a fusion protein and of the ANK region. Directly tethering the N-terminal region to ccRING3 forms a minimal MIB1 protein, which is sufficient to induce a Notch response in receiver cells. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.
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Affiliation(s)
- Ruili Cao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Oren Gozlan
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lena Tveriakhina
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hanjie Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Philip A Cole
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - David Sprinzak
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Lead contact
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7
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Gazdik TR, Crow JJ, Lawton T, Munroe CJ, Theriault H, Wood TM, Albig AR. Notch intracellular domains form transcriptionally active heterodimeric complexes on sequence-paired sites. Sci Rep 2024; 14:218. [PMID: 38168761 PMCID: PMC10761890 DOI: 10.1038/s41598-023-50763-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Notch signaling is universally conserved in metazoans where it is important for a wide variety of both normal and abnormal physiology. All four mammalian Notch receptors are activated by a conserved mechanism that releases Notch intracellular domains (NICDs) from the plasma membrane to translocate to the nucleus. Once there, NICDs interact through highly conserved ankyrin domains to form head-to-head homodimers on Notch sensitive promoters and stimulate transcription. Due to the highly conserved nature of these Notch ankyrin domains in all four mammalian Notch proteins, we hypothesized that NICDs may also engage in heterodimerization. Our results reveal the presence of two NICD dimerization states that can both engage in homo and heterodimerization. Using a Co-IP approach, we show that all NICD's can form non-transcriptionally active dimers and that the N4ICD appears to perform this function better than the other NICDs. Using a combination of ChIP analysis and transcriptional reporter assays, we also demonstrate the formation of transcriptionally active heterodimers that form on DNA. In particular, we demonstrate heterodimerization between the N2ICD and N4ICD and show that this heterodimer pair appears to exhibit differential activity on various Notch sensitive promoters. These results illustrate a new diversification of Notch signaling mechanisms which will help us better understand basic Notch function.
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Affiliation(s)
- Tana R Gazdik
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Jacob J Crow
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Tyler Lawton
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Chloe J Munroe
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Hannah Theriault
- Department of Chemistry, Boise State University, Boise, ID, 83725, USA
| | - Travis M Wood
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Allan R Albig
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA.
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA.
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8
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Tveriakhina L, Scanavachi G, Egan ED, Correia RBDC, Martin AP, Rogers JM, Yodh JS, Aster JC, Kirchhausen T, Blacklow SC. Temporal Dynamics and Stoichiometry in Notch Signaling - from Notch Synaptic Complex Formation to NICD Nuclear Entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559780. [PMID: 37808809 PMCID: PMC10557745 DOI: 10.1101/2023.09.27.559780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Mammalian Notch signaling occurs when binding of Delta or Jagged to Notch stimulates proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to regulate target gene expression. To determine the temporal dynamics of events associated with Notch signaling under native conditions, we fluorescently tagged Notch and Delta at their endogenous genomic loci and visualized them upon pairing of receiver (Notch) and sender (Delta) cells as a function of time after cell contact. At contact sites, Notch and Delta immediately accumulated at 1:1 stoichiometry in synapses, which resolved by 15-20 min after contact. Synapse formation preceded entrance of the Notch extracellular domain into the sender cell and accumulation of NICD in the nucleus of the receiver cell, which approached a maximum after ∼45 min and was prevented by chemical and genetic inhibitors of signaling. These findings directly link Notch-Delta synapse dynamics to NICD production with unprecedented spatiotemporal precision.
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9
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Gazdik TR, Crow JJ, Lawton T, Munroe CJ, Theriault H, Wood TM, Albig AR. Notch Intracellular Domains form Transcriptionally Active Heterodimeric Complexes on Sequence-paired Sites. RESEARCH SQUARE 2023:rs.3.rs-3147210. [PMID: 37546896 PMCID: PMC10402268 DOI: 10.21203/rs.3.rs-3147210/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Notch signaling is universally conserved in metazoans where it is important for a wide variety of both normal and abnormal physiology. All four mammalian Notch receptors are activated by a conserved mechanism that releases Notch intracellular domains (NICDs) from the plasma membrane to translocate to the nucleus. Once there, NICDs interact through highly conserved ankyrin domains to form head-to-head homodimers on Notch sensitive promoters and stimulate transcription. Due to the highly conserved nature of these Notch ankyrin domains in all four mammalian Notch proteins, we hypothesized that NICDs may also engage in heterodimerization. Our results reveal the presence of two NICD dimerization states that can both engage in homo and heterodimerization. Using a Co-IP approach, we show that all NICD's can form non-transcriptionally active dimers and that the N4ICD appears to perform this function better than the other NICDs. Using a combination of ChIP analysis and transcriptional reporter assays, we also demonstrate the formation of transcriptionally active heterodimers that form on DNA. In particular, we demonstrate heterodimerization between the N2ICD and N4ICD and show that this heterodimer pair appears to exhibit differential activity on various Notch sensitive promoters. These results illustrate a new diversification of Notch signaling mechanisms which will help us better understand basic Notch function.
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10
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Abstract
Notch signaling is a highly conserved signaling pathway that coordinates cellular differentiation during the development and homeostasis in numerous organs and tissues across metazoans. Activation of Notch signaling relies on direct contact between neighboring cells and mechanical pulling of the Notch receptors by the Notch ligands. Notch signaling is commonly used in developmental processes to coordinate the differentiation into distinct cell fates of neighboring cells. In this Development at a Glance article, we describe the current understanding of the Notch pathway activation and the different regulatory levels that control the pathway. We then describe several developmental processes where Notch is crucial for coordinating differentiation. These examples include processes that are largely based on lateral inhibition mechanisms giving rise to alternating patterns (e.g. SOP selection, hair cell in the inner ear and neural stem cell maintenance), as well as processes where Notch activity is oscillatory (e.g. somitogenesis and neurogenesis in mammals).
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Affiliation(s)
- Oren Gozlan
- School of Neurobiology, Biochemistry, and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry, and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Leng F, Zhang W, Ramirez RN, Leon J, Zhong Y, Hou L, Yuki K, van der Veeken J, Rudensky AY, Benoist C, Hur S. The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis. Immunity 2022; 55:1354-1369.e8. [PMID: 35926508 PMCID: PMC9907729 DOI: 10.1016/j.immuni.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/03/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022]
Abstract
FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.
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Affiliation(s)
- Fangwei Leng
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxiang Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo N Ramirez
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yi Zhong
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifei Hou
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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12
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EBNA2-EBF1 complexes promote MYC expression and metabolic processes driving S-phase progression of Epstein-Barr virus-infected B cells. Proc Natl Acad Sci U S A 2022; 119:e2200512119. [PMID: 35857872 PMCID: PMC9335265 DOI: 10.1073/pnas.2200512119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Epstein-Barr virus (EBV) is a human tumor virus which preferentially infects resting human B cells. Upon infection in vitro, EBV activates and immortalizes these cells. The viral latent protein EBV nuclear antigen 2 (EBNA2) is essential for B cell activation and immortalization; it targets and binds the cellular and ubiquitously expressed DNA-binding protein CBF1, thereby transactivating a plethora of viral and cellular genes. In addition, EBNA2 uses its N-terminal dimerization (END) domain to bind early B cell factor 1 (EBF1), a pioneer transcription factor specifying the B cell lineage. We found that EBNA2 exploits EBF1 to support key metabolic processes and to foster cell cycle progression of infected B cells in their first cell cycles upon activation. The α1-helix within the END domain was found to promote EBF1 binding. EBV mutants lacking the α1-helix in EBNA2 can infect and activate B cells efficiently, but activated cells fail to complete the early S phase of their initial cell cycle. Expression of MYC, target genes of MYC and E2F, as well as multiple metabolic processes linked to cell cycle progression are impaired in EBVΔα1-infected B cells. Our findings indicate that EBF1 controls B cell activation via EBNA2 and, thus, has a critical role in regulating the cell cycle of EBV-infected B cells. This is a function of EBF1 going beyond its well-known contribution to B cell lineage specification.
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13
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Early-onset oral cancer as a clinical entity: aetiology and pathogenesis. Int J Oral Maxillofac Surg 2022; 51:1497-1509. [PMID: 35487818 DOI: 10.1016/j.ijom.2022.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/24/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most important medical and socio-economic problems in many of the developed countries worldwide, due to the high mortality. The incidence of OSCC among individuals under 45 years of age is growing every year; however, the aetiological factors and pathogenetic mechanisms are poorly understood. This review summarizes the available information regarding clinicopathological features, extrinsic and intrinsic aetiological factors, and the molecular and immune landscape of early-onset OSCC. This cancer shows high recurrence rates and is not associated with the aetiological factors specific to adult-onset OSCC. Young adults with OSCC are not infected with human papillomavirus and rarely consume alcohol or tobacco, but more frequently use smokeless tobacco. Data from single studies indicate the hereditary nature of early-onset OSCC: the KIR2DL1+-HLA-C2+ genotype and MMP-1 2 G allele are frequently detected in young patients. Early-onset OSCC shows specific genetic, epigenetic, transcriptomic, and proteomic changes. The tumour microenvironment in early-onset OSCC is tolerogenic rather than immunogenic. All of the data suggest that OSCC in young patients is a separate clinical entity with a specific aetiology and pathogenesis. Further studies are needed to reveal the causes and molecular targets of early-onset OSCC for the development of preventive and therapeutic strategies.
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14
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Lynch TR, Xue M, Czerniak CW, Lee C, Kimble J. Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal. Development 2022; 149:274985. [PMID: 35394007 PMCID: PMC9058496 DOI: 10.1242/dev.200332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/16/2022] [Indexed: 11/20/2022]
Abstract
A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. Reporter constructs, cell culture assays and computational modeling have made major contributions to answering this question, but analysis of elements in their natural context is an important complement. Here, we mutate Notch-dependent LAG-1 binding sites (LBSs) in the endogenous Caenorhabditis elegans sygl-1 gene, which encodes a key stem cell regulator, and analyze the consequences on sygl-1 expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of one LBS in a three-element cluster approximately halved both expression and stem cell pool size, whereas mutation of two LBSs essentially abolished them. Heterozygous LBS mutant clusters provided intermediate values. Our results lead to two major conclusions. First, both LBS number and configuration impact cluster activity: LBSs act additively in trans and synergistically in cis. Second, the SYGL-1 gradient promotes self-renewal above its functional threshold and triggers differentiation below the threshold. Our approach of coupling CRISPR/Cas9 LBS mutations with effects on both molecular and biological readouts establishes a powerful model for in vivo analyses of DNA cis-regulatory elements. Summary: Notch-dependent DNA cis-regulatory elements work together in their developmental context in C. elegans to shape a transcriptional gradient, control stem cell pool size, and govern differentiation onset.
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Affiliation(s)
- Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
| | - Mingyu Xue
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Cazza W. Czerniak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Joint Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
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15
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Kuang Y, Pyo A, Eafergan N, Cain B, Gutzwiller LM, Axelrod O, Gagliani EK, Weirauch MT, Kopan R, Kovall RA, Sprinzak D, Gebelein B. Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor. PLoS Genet 2021; 17:e1009039. [PMID: 34559800 PMCID: PMC8494340 DOI: 10.1371/journal.pgen.1009039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
Notch signaling controls many developmental processes by regulating gene expression. Notch-dependent enhancers recruit activation complexes consisting of the Notch intracellular domain, the Cbf/Su(H)/Lag1 (CSL) transcription factor (TF), and the Mastermind co-factor via two types of DNA sites: monomeric CSL sites and cooperative dimer sites called Su(H) paired sites (SPS). Intriguingly, the CSL TF can also bind co-repressors to negatively regulate transcription via these same sites. Here, we tested how synthetic enhancers with monomeric CSL sites versus dimeric SPSs bind Drosophila Su(H) complexes in vitro and mediate transcriptional outcomes in vivo. Our findings reveal that while the Su(H)/Hairless co-repressor complex similarly binds SPS and CSL sites in an additive manner, the Notch activation complex binds SPSs, but not CSL sites, in a cooperative manner. Moreover, transgenic reporters with SPSs mediate stronger, more consistent transcription and are more resistant to increased Hairless co-repressor expression compared to reporters with the same number of CSL sites. These findings support a model in which SPS containing enhancers preferentially recruit cooperative Notch activation complexes over Hairless repression complexes to ensure consistent target gene activation. Cell signaling provides a basic means of communication during development. Many signaling pathways, including the Notch pathway, convert extracellular signals into changes in gene expression via transcription factors that bind specific DNA sequences. Importantly, the Notch pathway transcription factor can either form activating complexes upon Notch activation to stimulate gene expression or repression complexes with co-repressors to inhibit gene expression. Prior studies showed that the Notch activation complex binds DNA as either an independent complex on monomer binding sites or as two cooperative complexes (dimer) on paired binding sites. In this study, we used synthetic biology to examine how these two types of DNA sites impact the binding of Notch activation versus repression complexes and the output of Notch target gene expression. Our studies reveal that unlike the Notch activation complex, the repression complex does not cooperatively bind dimer sites. Moreover, our findings support the model that the enhanced stability of the Notch activation complex on dimer sites makes target genes with dimer sites less sensitive to the repression complex than target genes with only monomer sites. Thus, our studies reveal how target genes with different binding sites differ in sensitivity to the ratio of Notch activation to repression complexes.
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Affiliation(s)
- Yi Kuang
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Anna Pyo
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Natanel Eafergan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Lisa M. Gutzwiller
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Ofri Axelrod
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Ellen K. Gagliani
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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16
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Sotomska M, Liefke R, Ferrante F, Schwederski H, Oswald F, Borggrefe T. SUMOylated non-canonical polycomb PRC1.6 complex as a prerequisite for recruitment of transcription factor RBPJ. Epigenetics Chromatin 2021; 14:38. [PMID: 34332624 PMCID: PMC8325870 DOI: 10.1186/s13072-021-00412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Notch signaling controls cell fate decisions in many contexts during development and adult stem cell homeostasis and, when dysregulated, leads to carcinogenesis. The central transcription factor RBPJ assembles the Notch coactivator complex in the presence of Notch signaling, and represses Notch target gene expression in its absence. RESULTS We identified L3MBTL2 and additional members of the non-canonical polycomb repressive PRC1.6 complex in DNA-bound RBPJ associated complexes and demonstrate that L3MBTL2 directly interacts with RBPJ. Depletion of RBPJ does not affect occupancy of PRC1.6 components at Notch target genes. Conversely, absence of L3MBTL2 reduces RBPJ occupancy at enhancers of Notch target genes. Since L3MBTL2 and additional members of the PRC1.6 are known to be SUMOylated, we investigated whether RBPJ uses SUMO-moieties as contact points. Indeed, we found that RBPJ binds to SUMO2/3 and that this interaction depends on a defined SUMO-interaction motif. Furthermore, we show that pharmacological inhibition of SUMOylation reduces RBPJ occupancy at Notch target genes. CONCLUSIONS We propose that the PRC1.6 complex and its conjugated SUMO-modifications provide a favorable environment for binding of RBPJ to Notch target genes.
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Affiliation(s)
- Małgorzata Sotomska
- Institute of Biochemistry, Justus-Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein Strasse 2, 35043, Marburg, Germany.,Department of Hematology, Oncology and Immunology, University Hospital Marburg and Philipps University of Marburg, Baldingerstrasse, 35043, Marburg, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, Justus-Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Heiko Schwederski
- Center for Internal Medicine, Department of Internal Medicine 1, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine 1, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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17
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Dong Y, Guo H, Wang D, Tu R, Qing G, Liu H. Genome-Wide Analysis Identifies Rag1 and Rag2 as Novel Notch1 Transcriptional Targets in Thymocytes. Front Cell Dev Biol 2021; 9:703338. [PMID: 34322489 PMCID: PMC8311795 DOI: 10.3389/fcell.2021.703338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/15/2021] [Indexed: 12/04/2022] Open
Abstract
Recombination activating genes 1 (Rag1) and Rag2 are expressed in immature lymphocytes and essential for generating the vast repertoire of antigen receptors. Yet, the mechanisms governing the transcription of Rag1 and Rag2 remain to be fully determined, particularly in thymocytes. Combining cDNA microarray and ChIP-seq analysis, we identify Rag1 and Rag2 as novel Notch1 transcriptional targets in acute T-cell lymphoblastic leukemia (T-ALL) cells. We further demonstrate that Notch1 transcriptional complexes directly bind the Rag1 and Rag2 locus in not only T-ALL but also primary double negative (DN) T-cell progenitors. Specifically, dimeric Notch1 transcriptional complexes activate Rag1 and Rag2 through a novel cis-element bearing a sequence-paired site (SPS). In T-ALL and DN cells, dimerization-defective Notch1 causes compromised Rag1 and Rag2 expression; conversely, dimerization-competent Notch1 achieves optimal upregulation of both. Collectively, these results reveal Notch1 dimerization-mediated transcription as one of the mechanisms for activating Rag1 and Rag2 expression in both primary and transformed thymocytes. Our data suggest a new role of Notch1 dimerization in compelling efficient TCRβ rearrangements in DN progenitors during T-cell development.
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Affiliation(s)
- Yang Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Hao Guo
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Donghai Wang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Rongfu Tu
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Guoliang Qing
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Hudan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
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18
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Frankenreiter L, Gahr BM, Schmid H, Zimmermann M, Deichsel S, Hoffmeister P, Turkiewicz A, Borggrefe T, Oswald F, Nagel AC. Phospho-Site Mutations in Transcription Factor Suppressor of Hairless Impact Notch Signaling Activity During Hematopoiesis in Drosophila. Front Cell Dev Biol 2021; 9:658820. [PMID: 33937259 PMCID: PMC8079769 DOI: 10.3389/fcell.2021.658820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The highly conserved Notch signaling pathway controls a multitude of developmental processes including hematopoiesis. Here, we provide evidence for a novel mechanism of tissue-specific Notch regulation involving phosphorylation of CSL transcription factors within the DNA-binding domain. Earlier we found that a phospho-mimetic mutation of the Drosophila CSL ortholog Suppressor of Hairless [Su(H)] at Ser269 impedes DNA-binding. By genome-engineering, we now introduced phospho-specific Su(H) mutants at the endogenous Su(H) locus, encoding either a phospho-deficient [Su(H) S269A ] or a phospho-mimetic [Su(H) S269D ] isoform. Su(H) S269D mutants were defective of Notch activity in all analyzed tissues, consistent with impaired DNA-binding. In contrast, the phospho-deficient Su(H) S269A mutant did not generally augment Notch activity, but rather specifically in several aspects of blood cell development. Unexpectedly, this process was independent of the corepressor Hairless acting otherwise as a general Notch antagonist in Drosophila. This finding is in agreement with a novel mode of Notch regulation by posttranslational modification of Su(H) in the context of hematopoiesis. Importantly, our studies of the mammalian CSL ortholog (RBPJ/CBF1) emphasize a potential conservation of this regulatory mechanism: phospho-mimetic RBPJ S221D was dysfunctional in both the fly as well as two human cell culture models, whereas phospho-deficient RBPJ S221A rather gained activity during fly hematopoiesis. Thus, dynamic phosphorylation of CSL-proteins within the DNA-binding domain provides a novel means to fine-tune Notch signal transduction in a context-dependent manner.
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Affiliation(s)
- Lisa Frankenreiter
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Bernd M Gahr
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Hannes Schmid
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Mirjam Zimmermann
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Sebastian Deichsel
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Philipp Hoffmeister
- Department of Internal Medicine 1, Center for Internal Medicine, University Medical Center Ulm, Ulm, Germany
| | | | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig University of Giessen, Giessen, Germany
| | - Franz Oswald
- Department of Internal Medicine 1, Center for Internal Medicine, University Medical Center Ulm, Ulm, Germany
| | - Anja C Nagel
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
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19
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Transcription Factor RBPJ as a Molecular Switch in Regulating the Notch Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1287:9-30. [PMID: 33034023 DOI: 10.1007/978-3-030-55031-8_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Notch signal transduction cascade requires cell-to-cell contact and results in the proteolytic processing of the Notch receptor and subsequent assembly of a transcriptional coactivator complex containing the Notch intracellular domain (NICD) and transcription factor RBPJ. In the absence of a Notch signal, RBPJ remains at Notch target genes and dampens transcriptional output. Like in other signaling pathways, RBPJ is able to switch from activation to repression by associating with corepressor complexes containing several chromatin-modifying enzymes. Here, we focus on the recent advances concerning RBPJ-corepressor functions, especially in regard to chromatin regulation. We put this into the context of one of the best-studied model systems for Notch, blood cell development. Alterations in the RBPJ-corepressor functions can contribute to the development of leukemia, especially in the case of acute myeloid leukemia (AML). The versatile role of transcription factor RBPJ in regulating pivotal target genes like c-MYC and HES1 may contribute to the better understanding of the development of leukemia.
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20
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Crow JJ, Albig AR. Notch family members follow stringent requirements for intracellular domain dimerization at sequence-paired sites. PLoS One 2020; 15:e0234101. [PMID: 33232323 PMCID: PMC7685452 DOI: 10.1371/journal.pone.0234101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
Notch signaling is essential for multicellular life, regulating core functions such as cellular identity, differentiation, and fate. These processes require highly sensitive systems to avoid going awry, and one such regulatory mechanism is through Notch intracellular domain dimerization. Select Notch target genes contain sequence-paired sites (SPS); motifs in which two Notch transcriptional activation complexes can bind and interact through Notch's ankyrin domain, resulting in enhanced transcriptional activation. This mechanism has been mostly studied through Notch1, and to date, the abilities of the other Notch family members have been left unexplored. Through the utilization of minimalized, SPS-driven luciferase assays, we were able to test the functional capacity of Notch dimers. Here we show that the Notch 2 and 3 NICDs also exhibit dimerization-induced signaling, following the same stringent requirements as seen with Notch1. Furthermore, our data suggested that Notch4 may also exhibit dimerization-induced signaling, although the amino acids required for Notch4 NICD dimerization appear to be different than those required for Notch 1, 2, and 3 NICD dimerization. Interestingly, we identified a mechanical difference between canonical and cryptic SPSs, leading to differences in their dimerization-induced regulation. Finally, we profiled the Notch family members' SPS gap distance preferences and found that they all prefer a 16-nucleotide gap, with little room for variation. In summary, this work highlights the potent and highly specific nature of Notch dimerization and refines the scope of this regulatory function.
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MESH Headings
- Animals
- Base Sequence
- Basic Helix-Loop-Helix Transcription Factors/genetics
- HEK293 Cells
- Humans
- Mice
- Mutagenesis
- Promoter Regions, Genetic
- Protein Binding
- Protein Domains
- Protein Multimerization
- Receptor, Notch2/chemistry
- Receptor, Notch2/genetics
- Receptor, Notch2/metabolism
- Receptor, Notch3/chemistry
- Receptor, Notch3/genetics
- Receptor, Notch3/metabolism
- Receptor, Notch4/chemistry
- Receptor, Notch4/genetics
- Receptor, Notch4/metabolism
- Receptors, Notch/chemistry
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Signal Transduction
- Transcriptional Activation
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Affiliation(s)
- Jacob J. Crow
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, United States of America
| | - Allan R. Albig
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, United States of America
- Department of Biological Sciences, Boise State University, Boise, ID, United States of America
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21
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Kobia FM, Preusse K, Dai Q, Weaver N, Hass MR, Chaturvedi P, Stein SJ, Pear WS, Yuan Z, Kovall RA, Kuang Y, Eafergen N, Sprinzak D, Gebelein B, Brunskill EW, Kopan R. Notch dimerization and gene dosage are important for normal heart development, intestinal stem cell maintenance, and splenic marginal zone B-cell homeostasis during mite infestation. PLoS Biol 2020; 18:e3000850. [PMID: 33017398 PMCID: PMC7561103 DOI: 10.1371/journal.pbio.3000850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/15/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Cooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence-paired sites (SPS) located near many Notch-regulated genes. Although most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromised viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% dextran sulfate sodium (DSS). The most striking phenotypes-gender imbalance and splenic marginal zone B-cell lymphoma-emerged in combination with gene dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis and is consistent with Notch-dependent anti-parasite immune responses being compromised in Notch dimer-deficient animals.
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Affiliation(s)
- Francis M. Kobia
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kristina Preusse
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Quanhui Dai
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Nicholas Weaver
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew R. Hass
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Praneet Chaturvedi
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sarah J. Stein
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Yi Kuang
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Natanel Eafergen
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Eric W. Brunskill
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
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22
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Pan L, Lemieux ME, Thomas T, Rogers JM, Lipper CH, Lee W, Johnson C, Sholl LM, South AP, Marto JA, Adelmant GO, Blacklow SC, Aster JC. IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation. eLife 2020; 9:e58081. [PMID: 32936072 PMCID: PMC7529455 DOI: 10.7554/elife.58081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Notch signaling regulates squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is tumor suppressive. Here, we show that conditional activation of Notch in squamous cells activates a context-specific gene expression program through lineage-specific regulatory elements. Among direct Notch target genes are multiple DNA damage response genes, including IER5, which we show is required for Notch-induced differentiation of squamous carcinoma cells and TERT-immortalized keratinocytes. IER5 is epistatic to PPP2R2A, a gene that encodes the PP2A B55α subunit, which we show interacts with IER5 in cells and in purified systems. Thus, Notch and DNA-damage response pathways converge in squamous cells on common genes that promote differentiation, which may serve to eliminate damaged cells from the proliferative pool. We further propose that crosstalk involving Notch and PP2A enables tuning and integration of Notch signaling with other pathways that regulate squamous differentiation.
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Affiliation(s)
- Li Pan
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | | | - Tom Thomas
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Julia M Rogers
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Winston Lee
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Carl Johnson
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Jarrod A Marto
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
- Departmentof Oncologic Pathology and Blais Proteomics Center, Dana FarberCancer Institute, HarvardMedical SchoolBostonUnited States
| | - Guillaume O Adelmant
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
- Departmentof Oncologic Pathology and Blais Proteomics Center, Dana FarberCancer Institute, HarvardMedical SchoolBostonUnited States
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Jon C Aster
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical SchoolBostonUnited States
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23
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Abstract
Notch pathway signaling is implicated in several human cancers. Aberrant activation and mutations of Notch signaling components are linked to tumor initiation, maintenance, and resistance to cancer therapy. Several strategies, such as monoclonal antibodies against Notch ligands and receptors, as well as small-molecule γ-secretase inhibitors (GSIs), have been developed to interfere with Notch receptor activation at proximal points in the pathway. However, the use of drug-like small molecules to target the downstream mediators of Notch signaling, the Notch transcription activation complex, remains largely unexplored. Here, we report the discovery of an orally active small-molecule inhibitor (termed CB-103) of the Notch transcription activation complex. We show that CB-103 inhibits Notch signaling in primary human T cell acute lymphoblastic leukemia and other Notch-dependent human tumor cell lines, and concomitantly induces cell cycle arrest and apoptosis, thereby impairing proliferation, including in GSI-resistant human tumor cell lines with chromosomal translocations and rearrangements in Notch genes. CB-103 produces Notch loss-of-function phenotypes in flies and mice and inhibits the growth of human breast cancer and leukemia xenografts, notably without causing the dose-limiting intestinal toxicity associated with other Notch inhibitors. Thus, we describe a pharmacological strategy that interferes with Notch signaling by disrupting the Notch transcription complex and shows therapeutic potential for treating Notch-driven cancers.
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24
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Mukherjee M, Ratnayake I, Janga M, Fogarty E, Scheidt S, Grassmeyer J, deRiso J, Chandrasekar I, Ahrenkiel P, Kopan R, Surendran K. Notch signaling regulates Akap12 expression and primary cilia length during renal tubule morphogenesis. FASEB J 2020; 34:9512-9530. [PMID: 32474964 DOI: 10.1096/fj.201902358rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022]
Abstract
Alagille syndrome patients present with loss of function mutations in either JAG1 or NOTCH2. About 40%-50% of patients have kidney abnormalities, and frequently display multicystic, dysplastic kidneys. Additionally, gain-of-function mutations in NOTCH2 are associated with cystic kidneys in Hajdu-Cheney syndrome patients. How perturbations in Notch signaling cause renal tubular cysts remains unclear. Here, we have determined that reduced Notch signaling mediated transcription by ectopic expression of dominant-negative mastermind-like (dnMaml) peptide in the nephrogenic epithelia from after the s-shaped body formation and in the developing collecting ducts results in proximal tubular and collecting duct cysts, respectively. An acute inhibition of Notch signaling for two days during kidney development is sufficient to disrupt tubule formation, and significantly increases Akap12 expression. Ectopic expression of Akap12 in renal epithelia results in abnormally long primary cilia similar to that observed in Notch-signaling-deficient epithelia. Both loss of Notch signaling and elevated Akap12 expression disrupt the ability of renal epithelial cells to form spherical structures with a single lumen when grown embedded in matrix. Interestingly, Akap12 can inhibit Notch signaling mediated transcription, which likely explains how both loss of Notch signaling and ectopic expression of Akap12 result in similar renal epithelial abnormalities. We conclude that Notch signaling regulates Akap12 expression while also ensuring normal primary cilia length and renal epithelial morphogenesis, and suggest that one aspect of diseases associated with defective Notch signaling, such as Alagille syndrome, maybe mechanistically related to ciliopathies.
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Affiliation(s)
- Malini Mukherjee
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Ishara Ratnayake
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines and Technology, Rapid City, SD, USA
| | - Madhusudhana Janga
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Eric Fogarty
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Shania Scheidt
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | | | - Jennifer deRiso
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Indra Chandrasekar
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA.,Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Phil Ahrenkiel
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines and Technology, Rapid City, SD, USA
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kameswaran Surendran
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
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25
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Kuang Y, Golan O, Preusse K, Cain B, Christensen CJ, Salomone J, Campbell I, Okwubido-Williams FV, Hass MR, Yuan Z, Eafergan N, Moberg KH, Kovall RA, Kopan R, Sprinzak D, Gebelein B. Enhancer architecture sensitizes cell specific responses to Notch gene dose via a bind and discard mechanism. eLife 2020; 9:53659. [PMID: 32297857 PMCID: PMC7213981 DOI: 10.7554/elife.53659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/15/2020] [Indexed: 11/13/2022] Open
Abstract
Notch pathway haploinsufficiency can cause severe developmental syndromes with highly variable penetrance. Currently, we have a limited mechanistic understanding of phenotype variability due to gene dosage. Here, we unexpectedly found that inserting an enhancer containing pioneer transcription factor sites coupled to Notch dimer sites can induce a subset of Notch haploinsufficiency phenotypes in Drosophila with wild type Notch gene dose. Using Drosophila genetics, we show that this enhancer induces Notch phenotypes in a Cdk8-dependent, transcription-independent manner. We further combined mathematical modeling with quantitative trait and expression analysis to build a model that describes how changes in Notch signal production versus degradation differentially impact cellular outcomes that require long versus short signal duration. Altogether, these findings support a 'bind and discard' mechanism in which enhancers with specific binding sites promote rapid Cdk8-dependent Notch turnover, and thereby reduce Notch-dependent transcription at other loci and sensitize tissues to gene dose based upon signal duration.
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Affiliation(s)
- Yi Kuang
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, United States
| | - Ohad Golan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Kristina Preusse
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, United States
| | - Collin J Christensen
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, United States.,Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Ian Campbell
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, United States
| | | | - Matthew R Hass
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Nathanel Eafergan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, United States
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, United States
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States
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26
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Yamamoto S. Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila. Dev Growth Differ 2020; 62:15-34. [PMID: 31943162 DOI: 10.1111/dgd.12640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022]
Abstract
Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.,Department of Neuroscience, BCM, Houston, TX, USA.,Program in Developmental Biology, BCM, Houston, TX, USA.,Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
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27
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Falo-Sanjuan J, Bray SJ. Decoding the Notch signal. Dev Growth Differ 2019; 62:4-14. [PMID: 31886523 DOI: 10.1111/dgd.12644] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 01/04/2023]
Abstract
Notch signalling controls many key cellular processes which differ according to the context where the pathway is deployed due to the transcriptional activation of specific sets of genes. The pathway is unusual in its lack of amplification, also raising the question of how it can efficiently activate transcription with limited amounts of nuclear activity. Here, we focus on mechanisms that enable Notch to produce appropriate transcriptional responses and speculate on models that could explain the current gaps in knowledge.
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Affiliation(s)
- Julia Falo-Sanjuan
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
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28
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Jarrett SM, Seegar TCM, Andrews M, Adelmant G, Marto JA, Aster JC, Blacklow SC. Extension of the Notch intracellular domain ankyrin repeat stack by NRARP promotes feedback inhibition of Notch signaling. Sci Signal 2019; 12:12/606/eaay2369. [PMID: 31690634 DOI: 10.1126/scisignal.aay2369] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Canonical Notch signaling relies on regulated proteolysis of the receptor Notch to generate a nuclear effector that induces the transcription of Notch-responsive genes. In higher organisms, one Notch-responsive gene that is activated in many different cell types encodes the Notch-regulated ankyrin repeat protein (NRARP), which acts as a negative feedback regulator of Notch responses. Here, we showed that NRARP inhibited the growth of Notch-dependent T cell acute lymphoblastic leukemia (T-ALL) cell lines and bound directly to the core Notch transcriptional activation complex (NTC), requiring both the transcription factor RBPJ and the Notch intracellular domain (NICD), but not Mastermind-like proteins or DNA. The crystal structure of an NRARP-NICD1-RBPJ-DNA complex, determined to 3.75 Å resolution, revealed that the assembly of NRARP-NICD1-RBPJ complexes relied on simultaneous engagement of RBPJ and NICD1, with the three ankyrin repeats of NRARP extending the Notch1 ankyrin repeat stack. Mutations at the NRARP-NICD1 interface disrupted entry of the proteins into NTCs and abrogated feedback inhibition in Notch signaling assays in cultured cells. Forced expression of NRARP reduced the abundance of NICD in cells, suggesting that NRARP may promote the degradation of NICD. These studies establish the structural basis for NTC engagement by NRARP and provide insights into a critical negative feedback mechanism that regulates Notch signaling.
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Affiliation(s)
- Sanchez M Jarrett
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tom C M Seegar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Andrews
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA.,Department of Oncologic Pathology and Blais Proteomic Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA.,Department of Oncologic Pathology and Blais Proteomic Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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29
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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30
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Abstract
Notch signaling is a form of intercellular communication which plays pivotal roles at various stages in development and disease. Previous findings have hinted that integrins and extracellular matrix may regulate Notch signaling, although a mechanistic basis for this interaction had not been identified. Here, we reveal that the regulation of Notch by integrins and extracellular matrix is carried out by Src family kinases (SFKs) working downstream of integrins. We identify a physical interaction between the SFK member, c-Src, and the Notch intracellular domain (NICD) that is enhanced by β3 integrin and the integrin binding ECM protein, MAGP2. Our results demonstrate that c-Src directly phosphorylates the NICD at specific tyrosine residues and that mutation of these phosphorylation sites increases Notch responsive transcriptional activity. Furthermore, we also find that phosphorylation of the NICD by SFKs attenuates Notch mediated transcription by decreasing recruitment of MAML to the Notch co-transcriptional complex. Finally, we also find that SFK activity decreases NICD half-life. Collectively, our results provide important mechanistic data that underlie the emerging role of Notch as a general sensor and responder to extracellular signals.
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31
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Baron M. Combining genetic and biophysical approaches to probe the structure and function relationships of the notch receptor. Mol Membr Biol 2018; 34:33-49. [PMID: 30246579 DOI: 10.1080/09687688.2018.1503742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Notch is a conserved cell signalling receptor regulating many aspects of development and tissue homeostasis. Notch is activated by ligand-induced proteolytic cleavages that release the Notch intracellular domain, which relocates to the nucleus to regulate gene transcription. Proteolytic activation first requires mechanical force to be applied to the Notch extracellular domain through an endocytic pulling mechanism transmitted through the ligand/receptor interface. This exposes the proteolytic cleavage site allowing the signal to be initiated following removal of the Notch extracellular domain. Ligands can also act, when expressed in the same cell, through non-productive cis-interactions to inhibit Notch activity. Furthermore, ligand selectivity and Notch activation are regulated by numerous post-translational modifications of the extracellular domain. Additional non-canonical trans and cis interactions with other regulatory proteins may modulate alternative mechanisms of Notch activation that depend on endocytic trafficking of the full-length receptor and proteolytic release of the intracellular domain from endo-lysosomal surface. Mutations of Notch, located in different regions of the protein, are associated with a spectrum of different loss and gain of function phenotypes and offer the possibility to dissect distinct regulatory interactions and mechanisms, particularly when combined with detailed structural analysis of Notch in complex with various regulatory partners.
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Affiliation(s)
- Martin Baron
- a School of Biological Sciences , University of Manchester , Manchester , UK
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32
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Miesfeld JB, Moon MS, Riesenberg AN, Contreras AN, Kovall RA, Brown NL. Rbpj direct regulation of Atoh7 transcription in the embryonic mouse retina. Sci Rep 2018; 8:10195. [PMID: 29977079 PMCID: PMC6033939 DOI: 10.1038/s41598-018-28420-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/22/2018] [Indexed: 12/24/2022] Open
Abstract
In vertebrate retinal progenitor cells, the proneural factor Atoh7 exhibits a dynamic tissue and cellular expression pattern. Although the resulting Atoh7 retinal lineage contains all seven major cell types, only retinal ganglion cells require Atoh7 for proper differentiation. Such specificity necessitates complex regulation of Atoh7 transcription during retina development. The Notch signaling pathway is an evolutionarily conserved suppressor of proneural bHLH factor expression. Previous in vivo mouse genetic studies established the cell autonomous suppression of Atoh7 transcription by Notch1, Rbpj and Hes1. Here we identify four CSL binding sites within the Atoh7 proximal regulatory region and demonstrate Rbpj protein interaction at these sequences by in vitro electromobility shift, calorimetry and luciferase assays and, in vivo via colocalization and chromatin immunoprecipitation. We found that Rbpj simultaneously represses Atoh7 transcription using both Notch-dependent and –independent pathways.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA
| | - Myung-Soon Moon
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Amy N Riesenberg
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Ashley N Contreras
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati School of Medicine, Cincinnati, OH, 45267, USA.,Department of Biology, University of Cincinnati Blue Ash College, Cincinnati, OH, 45236, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati School of Medicine, Cincinnati, OH, 45267, USA
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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33
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Fontaine FR, Goodall S, Prokop JW, Howard CB, Moustaqil M, Kumble S, Rasicci DT, Osborne GW, Gambin Y, Sierecki E, Jones ML, Zuegg J, Mahler S, Francois M. Functional domain analysis of SOX18 transcription factor using a single-chain variable fragment-based approach. MAbs 2018; 10:596-606. [PMID: 29648920 PMCID: PMC5972640 DOI: 10.1080/19420862.2018.1451288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibodies are routinely used to study the activity of transcription factors, using various in vitro and in vivo approaches such as electrophoretic mobility shift assay, enzyme-linked immunosorbent assay, genome-wide method analysis coupled with next generation sequencing, or mass spectrometry. More recently, a new application for antibodies has emerged as crystallisation scaffolds for difficult to crystallise proteins, such as transcription factors. Only in a few rare cases, antibodies have been used to modulate the activity of transcription factors, and there is a real gap in our knowledge on how to efficiently design antibodies to interfere with transcription. The molecular function of transcription factors is underpinned by complex networks of protein-protein interaction and in theory, setting aside intra-cellular delivery challenges, developing antibody-based approaches to modulate transcription factor activity appears a viable option. Here, we demonstrate that antibodies or an antibody single-chain variable region fragments are powerful molecular tools to unravel complex protein-DNA and protein-protein binding mechanisms. In this study, we focus on the molecular mode of action of the transcription factor SOX18, a key modulator of endothelial cell fate during development, as well as an attractive target in certain pathophysiological conditions such as solid cancer metastasis. The engineered antibody we designed inhibits SOX18 transcriptional activity, by interfering specifically with an 8-amino-acid motif in the C-terminal region directly adjacent to α-Helix 3 of SOX18 HMG domain, thereby disrupting protein-protein interaction. This new approach establishes a framework to guide the study of transcription factors interactomes using antibodies as molecular handles.
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Affiliation(s)
- Frank R Fontaine
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Stephen Goodall
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia
| | - Jeremy W Prokop
- c HudsonAlpha Institute for Biotechnology , Huntsville AL , USA.,d Department of Pediatrics and Human Development , Michigan State University , East Lansing , MI , USA
| | - Christopher B Howard
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Mehdi Moustaqil
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Sumukh Kumble
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | | | - Geoffrey W Osborne
- e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Yann Gambin
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Emma Sierecki
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Martina L Jones
- e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Johannes Zuegg
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Stephen Mahler
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Mathias Francois
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
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34
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Bray SJ, Gomez-Lamarca M. Notch after cleavage. Curr Opin Cell Biol 2018; 51:103-109. [DOI: 10.1016/j.ceb.2017.12.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/13/2017] [Indexed: 01/13/2023]
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35
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Gomez-Lamarca MJ, Falo-Sanjuan J, Stojnic R, Abdul Rehman S, Muresan L, Jones ML, Pillidge Z, Cerda-Moya G, Yuan Z, Baloul S, Valenti P, Bystricky K, Payre F, O'Holleran K, Kovall R, Bray SJ. Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics. Dev Cell 2018; 44:611-623.e7. [PMID: 29478922 PMCID: PMC5855320 DOI: 10.1016/j.devcel.2018.01.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/27/2017] [Accepted: 01/23/2018] [Indexed: 12/27/2022]
Abstract
A key feature of Notch signaling is that it directs immediate changes in transcription via the DNA-binding factor CSL, switching it from repression to activation. How Notch generates both a sensitive and accurate response-in the absence of any amplification step-remains to be elucidated. To address this question, we developed real-time analysis of CSL dynamics including single-molecule tracking in vivo. In Notch-OFF nuclei, a small proportion of CSL molecules transiently binds DNA, while in Notch-ON conditions CSL recruitment increases dramatically at target loci, where complexes have longer dwell times conferred by the Notch co-activator Mastermind. Surprisingly, recruitment of CSL-related corepressors also increases in Notch-ON conditions, revealing that Notch induces cooperative or "assisted" loading by promoting local increase in chromatin accessibility. Thus, in vivo Notch activity triggers changes in CSL dwell times and chromatin accessibility, which we propose confer sensitivity to small input changes and facilitate timely shut-down.
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Affiliation(s)
- Maria J Gomez-Lamarca
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Julia Falo-Sanjuan
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Robert Stojnic
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Sohaib Abdul Rehman
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Matthew L Jones
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Zoe Pillidge
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Gustavo Cerda-Moya
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Zhenyu Yuan
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267-0524, USA
| | - Sarah Baloul
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Phillippe Valenti
- Centre de Biologie du Développement/UMR5547, CBI (Centre de Biologie Intégrative) University of Toulouse/CNRS, 118 Rte de Narbonne, 31062 Toulouse, France
| | - Kerstin Bystricky
- LBME/UMR5099, CBI (Centre de Biologie Intégrative) University of Toulouse/CNRS, 118 Rte de Narbonne, 31062 Toulouse, France
| | - Francois Payre
- Centre de Biologie du Développement/UMR5547, CBI (Centre de Biologie Intégrative) University of Toulouse/CNRS, 118 Rte de Narbonne, 31062 Toulouse, France
| | - Kevin O'Holleran
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Rhett Kovall
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267-0524, USA
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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CSL-Associated Corepressor and Coactivator Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:279-295. [PMID: 30030832 DOI: 10.1007/978-3-319-89512-3_14] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The highly conserved Notch signal transduction pathway orchestrates fundamental cellular processes including, differentiation, proliferation, and apoptosis during embryonic development and in the adult organism. Dysregulated Notch signaling underlies the etiology of a variety of human diseases, such as certain types of cancers, developmental disorders and cardiovascular disease. Ligand binding induces proteolytic cleavage of the Notch receptor and nuclear translocation of the Notch intracellular domain (NICD), which forms a ternary complex with the transcription factor CSL and the coactivator MAML to upregulate transcription of Notch target genes. The DNA-binding protein CSL is the centrepiece of transcriptional regulation in the Notch pathway, acting as a molecular hub for interactions with either corepressors or coactivators to repress or activate, respectively, transcription. Here we review previous structure-function studies of CSL-associated coregulator complexes and discuss the molecular insights gleaned from this research. We discuss the functional consequences of both activating and repressing binding partners using the same interaction platforms on CSL. We also emphasize that although there has been a significant uptick in structural information over the past decade, it is still under debate how the molecular switch from repression to activation mediated by CSL occurs at Notch target genes and whether it will be possible to manipulate these transcription complexes therapeutically in the future.
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D'Souza W, Saranath D. OMICS, Oral Cancer Molecular Landscapes, and Clinical Practice. ACTA ACUST UNITED AC 2017; 21:689-703. [DOI: 10.1089/omi.2017.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wendy D'Souza
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai, India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai, India
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38
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Vasconcelos FF, Sessa A, Laranjeira C, Raposo AASF, Teixeira V, Hagey DW, Tomaz DM, Muhr J, Broccoli V, Castro DS. MyT1 Counteracts the Neural Progenitor Program to Promote Vertebrate Neurogenesis. Cell Rep 2017; 17:469-483. [PMID: 27705795 PMCID: PMC5067283 DOI: 10.1016/j.celrep.2016.09.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/12/2016] [Accepted: 09/09/2016] [Indexed: 11/30/2022] Open
Abstract
The generation of neurons from neural stem cells requires large-scale changes in gene expression that are controlled to a large extent by proneural transcription factors, such as Ascl1. While recent studies have characterized the differentiation genes activated by proneural factors, less is known on the mechanisms that suppress progenitor cell identity. Here, we show that Ascl1 induces the transcription factor MyT1 while promoting neuronal differentiation. We combined functional studies of MyT1 during neurogenesis with the characterization of its transcriptional program. MyT1 binding is associated with repression of gene transcription in neural progenitor cells. It promotes neuronal differentiation by counteracting the inhibitory activity of Notch signaling at multiple levels, targeting the Notch1 receptor and many of its downstream targets. These include regulators of the neural progenitor program, such as Hes1, Sox2, Id3, and Olig1. Thus, Ascl1 suppresses Notch signaling cell-autonomously via MyT1, coupling neuronal differentiation with repression of the progenitor fate. MyT1 promotes neurogenesis downstream Ascl1 MyT1 represses Notch1 receptor and many of its downstream target genes MyT1 represses Hes1 expression by direct DNA binding and competition with RBPJ Ascl1 suppresses Notch signaling cell-autonomously while promoting differentiation
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Affiliation(s)
| | - Alessandro Sessa
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | | | - Vera Teixeira
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Daniel W Hagey
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Diogo M Tomaz
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jonas Muhr
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
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Siebel C, Lendahl U. Notch Signaling in Development, Tissue Homeostasis, and Disease. Physiol Rev 2017; 97:1235-1294. [PMID: 28794168 DOI: 10.1152/physrev.00005.2017] [Citation(s) in RCA: 598] [Impact Index Per Article: 85.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/19/2017] [Accepted: 05/26/2017] [Indexed: 02/07/2023] Open
Abstract
Notch signaling is an evolutionarily highly conserved signaling mechanism, but in contrast to signaling pathways such as Wnt, Sonic Hedgehog, and BMP/TGF-β, Notch signaling occurs via cell-cell communication, where transmembrane ligands on one cell activate transmembrane receptors on a juxtaposed cell. Originally discovered through mutations in Drosophila more than 100 yr ago, and with the first Notch gene cloned more than 30 yr ago, we are still gaining new insights into the broad effects of Notch signaling in organisms across the metazoan spectrum and its requirement for normal development of most organs in the body. In this review, we provide an overview of the Notch signaling mechanism at the molecular level and discuss how the pathway, which is architecturally quite simple, is able to engage in the control of cell fates in a broad variety of cell types. We discuss the current understanding of how Notch signaling can become derailed, either by direct mutations or by aberrant regulation, and the expanding spectrum of diseases and cancers that is a consequence of Notch dysregulation. Finally, we explore the emerging field of Notch in the control of tissue homeostasis, with examples from skin, liver, lung, intestine, and the vasculature.
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Affiliation(s)
- Chris Siebel
- Department of Discovery Oncology, Genentech Inc., DNA Way, South San Francisco, California; and Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Urban Lendahl
- Department of Discovery Oncology, Genentech Inc., DNA Way, South San Francisco, California; and Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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40
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The Canonical Notch Signaling Pathway: Structural and Biochemical Insights into Shape, Sugar, and Force. Dev Cell 2017; 41:228-241. [PMID: 28486129 DOI: 10.1016/j.devcel.2017.04.001] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/04/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023]
Abstract
The Notch signaling pathway relies on a proteolytic cascade to release its transcriptionally active intracellular domain, on force to unfold a protective domain and permit proteolysis, on extracellular domain glycosylation to tune the forces exerted by endocytosed ligands, and on a motley crew of nuclear proteins, chromatin modifiers, ubiquitin ligases, and a few kinases to regulate activity and half-life. Herein we provide a review of recent molecular insights into how Notch signals are triggered and how cell shape affects these events, and we use the new insights to illuminate a few perplexing observations.
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41
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Vasconcelos FF, Castro DS. Coordinating neuronal differentiation with repression of the progenitor program: Role of the transcription factor MyT1. NEUROGENESIS 2017. [DOI: 10.1080/23262133.2017.1329683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Severson E, Arnett KL, Wang H, Zang C, Taing L, Liu H, Pear WS, Shirley Liu X, Blacklow SC, Aster JC. Genome-wide identification and characterization of Notch transcription complex-binding sequence-paired sites in leukemia cells. Sci Signal 2017; 10:10/477/eaag1598. [PMID: 28465412 DOI: 10.1126/scisignal.aag1598] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Notch transcription complexes (NTCs) drive target gene expression by binding to two distinct types of genomic response elements, NTC monomer-binding sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and have been linked to the Notch responsiveness of a few genes. To assess the overall contribution of SPSs to Notch-dependent gene regulation, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay and applied insights from these in vitro studies to Notch-"addicted" T cell acute lymphoblastic leukemia (T-ALL) cells. We found that SPSs contributed to the regulation of about a third of direct Notch target genes. Although originally described in promoters, SPSs are present mainly in long-range enhancers, including an enhancer containing a newly described SPS that regulates HES5 expression. Our work provides a general method for identifying SPSs in genome-wide data sets and highlights the widespread role of NTC dimerization in Notch-transformed leukemia cells.
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Affiliation(s)
- Eric Severson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kelly L Arnett
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hongfang Wang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02114, USA
| | - Len Taing
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02114, USA
| | - Hudan Liu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Institute of Medicine and Engineering, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Institute of Medicine and Engineering, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02114, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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43
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Tindemans I, Peeters MJW, Hendriks RW. Notch Signaling in T Helper Cell Subsets: Instructor or Unbiased Amplifier? Front Immunol 2017; 8:419. [PMID: 28458667 PMCID: PMC5394483 DOI: 10.3389/fimmu.2017.00419] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/24/2017] [Indexed: 11/16/2022] Open
Abstract
For protection against pathogens, it is essential that naïve CD4+ T cells differentiate into specific effector T helper (Th) cell subsets following activation by antigen presented by dendritic cells (DCs). Next to T cell receptor and cytokine signals, membrane-bound Notch ligands have an important role in orchestrating Th cell differentiation. Several studies provided evidence that DC activation is accompanied by surface expression of Notch ligands. Intriguingly, DCs that express the delta-like or Jagged Notch ligands gain the capacity to instruct Th1 or Th2 cell polarization, respectively. However, in contrast to this model it has also been hypothesized that Notch signaling acts as a general amplifier of Th cell responses rather than an instructive director of specific T cell fates. In this alternative model, Notch enhances proliferation, cytokine production, and anti-apoptotic signals or promotes co-stimulatory signals in T cells. An instructive role for Notch ligand expressing DCs in the induction of Th cell differentiation is further challenged by evidence for the involvement of Notch signaling in differentiation of Th9, Th17, regulatory T cells, and follicular Th cells. In this review, we will discuss the two opposing models, referred to as the “instructive” and the “unbiased amplifier” model. We highlight both the function of different Notch receptors on CD4+ T cells and the impact of Notch ligands on antigen-presenting cells.
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Affiliation(s)
- Irma Tindemans
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, Netherlands
| | | | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, Netherlands
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44
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Fundamental Pathways in Breast Cancer 4: Signaling to Chromatin in Breast Development. Breast Cancer 2017. [DOI: 10.1007/978-3-319-48848-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Aster JC, Pear WS, Blacklow SC. The Varied Roles of Notch in Cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 12:245-275. [PMID: 27959635 DOI: 10.1146/annurev-pathol-052016-100127] [Citation(s) in RCA: 466] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Notch receptors influence cellular behavior by participating in a seemingly simple signaling pathway, but outcomes produced by Notch signaling are remarkably varied depending on signal dose and cell context. Here, after briefly reviewing new insights into physiologic mechanisms of Notch signaling in healthy tissues and defects in Notch signaling that contribute to congenital disorders and viral infection, we discuss the varied roles of Notch in cancer, focusing on cell autonomous activities that may be either oncogenic or tumor suppressive.
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Affiliation(s)
- Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115;
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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46
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47
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Abstract
Peptide-based drug discovery has experienced a remarkable resurgence within the past decade due to the emerging class of inhibitors known as stapled peptides. Stapled peptides are therapeutic protein mimetics that have been locked within a specific conformational structure by hydrocarbon stapling. These peptides are highly important in selectively impairing disease-relevant protein–protein interactions and exhibit significant pharmacokinetic advantages over other forms of therapeutics in terms of affinity, specificity, size, synthetic accessibility and resistance to proteolytic degradation. A series of stapled peptides are currently in development, and the potential successes of these peptides, either as single-agent treatments or as combinational treatments with other therapeutic modalities, could potentially change the landscape of protein therapeutic development. Here, we provide examples of successful discovery efforts to illustrate the research strategies of stapled peptides in drug design and development.
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48
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Abstract
Notch signaling is iteratively used throughout development to maintain stem cell potential or in other instances allow differentiation. The central transcription factor in Notch signaling is CBF-1/RBP-J, Su(H), Lag-1 (CSL)—Su(H) in Drosophila—which functions as a molecular switch between transcriptional activation and repression. Su(H) represses transcription by forming a complex with the corepressor Hairless (H). The Su(H)-repressor complex not only competes with the Notch intracellular domain (NICD) but also configures the local chromatin landscape. In this issue, Yuan and colleagues determined the structure of the Su(H)/H complex, showing that a major conformational change within Su(H) explains why the binding of NICD and H is mutually exclusive. This Primer examines recent research that reveals the structural rearrangements that determine whether the Notch pathway transcription factor CSL/Su(H) activates or represses transcription.
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Affiliation(s)
- Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
- * E-mail:
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm, Germany
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49
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Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster. PLoS Biol 2016; 14:e1002509. [PMID: 27404588 PMCID: PMC4942083 DOI: 10.1371/journal.pbio.1002509] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/10/2016] [Indexed: 11/25/2022] Open
Abstract
Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila, the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo. The transcription factor CSL regulates gene expression in response to Notch pathway signaling. The X-ray structure of the complex between the fruit fly version of CSL, Su(H), and its antagonist, Hairless, reveals a novel binding mode and unanticipated structural plasticity. Notch signaling is a form of cell-to-cell communication, in which extracellular receptor-ligand interactions ultimately result in changes in gene expression. The Notch pathway is highly conserved from the model organism Drosophila melanogaster to humans. When mutations occur within Notch pathway components, this often leads to human disease, such as certain types of cancers and birth defects. Transcription of Notch target genes is regulated by the transcription factor CSL (for CBF1/RBP-J in mammals, Su(H) in Drosophila, and Lag-1 in Caenorhabditis elegans). CSL functions as both a transcriptional activator and repressor by forming complexes with coactivator and corepressor proteins, respectively. Here we determine the high-resolution X-ray structure of Su(H) (the fly CSL ortholog) in complex with the corepressor Hairless, which is the major antagonist of Notch signaling in Drosophila. The structure unexpectedly reveals that Hairless binding results in a dramatic conformational change in Su(H). In parallel, we designed mutations in Su(H) and Hairless based on our structure and showed that these mutants are defective in complex formation in vitro and display functional deficiencies in in vivo assays. Taken together, our work provides significant molecular insights into how CSL functions as a transcriptional repressor in the Notch pathway.
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50
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Kim SH, Hahm ER, Arlotti JA, Samanta SK, Moura MB, Thorne SH, Shuai Y, Anderson CJ, White AG, Lokshin A, Lee J, Singh SV. Withaferin A inhibits in vivo growth of breast cancer cells accelerated by Notch2 knockdown. Breast Cancer Res Treat 2016; 157:41-54. [PMID: 27097807 DOI: 10.1007/s10549-016-3795-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/09/2016] [Indexed: 12/31/2022]
Abstract
The present study offers novel insights into the molecular circuitry of accelerated in vivo tumor growth by Notch2 knockdown in triple-negative breast cancer (TNBC) cells. Therapeutic vulnerability of Notch2-altered growth to a small molecule (withaferin A, WA) is also demonstrated. MDA-MB-231 and SUM159 cells were used for the xenograft studies. A variety of technologies were deployed to elucidate the mechanisms underlying tumor growth augmentation by Notch2 knockdown and its reversal by WA, including Fluorescence Molecular Tomography for measurement of tumor angiogenesis in live mice, Seahorse Flux analyzer for ex vivo measurement of tumor metabolism, proteomics, and Luminex-based cytokine profiling. Stable knockdown of Notch2 resulted in accelerated in vivo tumor growth in both cells reflected by tumor volume and/or latency. For example, the wet tumor weight from mice bearing Notch2 knockdown MDA-MB-231 cells was about 7.1-fold higher compared with control (P < 0.0001). Accelerated tumor growth by Notch2 knockdown was highly sensitive to inhibition by a promising steroidal lactone (WA) derived from a medicinal plant. Molecular underpinnings for tumor growth intensification by Notch2 knockdown included compensatory increase in Notch1 activation, increased cellular proliferation and/or angiogenesis, and increased plasma or tumor levels of growth stimulatory cytokines. WA administration reversed many of these effects providing explanation for its remarkable anti-cancer efficacy. Notch2 functions as a tumor growth suppressor in TNBC and WA offers a novel therapeutic strategy for restoring this function.
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Affiliation(s)
- Su-Hyeong Kim
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Eun-Ryeong Hahm
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Julie A Arlotti
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Suman K Samanta
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michelle B Moura
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephen H Thorne
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yongli Shuai
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carolyn J Anderson
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alexander G White
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anna Lokshin
- 2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joomin Lee
- Department of Food and Nutrition, Chosun University, Gwangju, Korea
| | - Shivendra V Singh
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,2.32A Hillman Cancer Center Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.
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