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Jelinska C, Kannan S, Frosi Y, Ramlan SR, Winnerdy F, Lakshminarayanan R, Johannes CW, Brown CJ, Phan AT, Rhodes D, Verma CS. Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein. RSC Chem Biol 2023; 4:1096-1110. [PMID: 38033728 PMCID: PMC10685803 DOI: 10.1039/d3cb00149k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 12/02/2023] Open
Abstract
DAXX (Death Domain Associated Protein 6) is frequently upregulated in various common cancers, and its suppression has been linked to reduced tumor progression. Consequently, DAXX has gained significant interest as a therapeutic target in such cancers. DAXX is known to function in several critical biological pathways including chromatin remodelling, transcription regulation, and DNA repair. Leveraging structural information, we have designed and developed a novel set of stapled/stitched peptides that specifically target a surface on the N-terminal helical bundle domain of DAXX. This surface serves as the anchor point for binding to multiple interaction partners, such as Rassf1C, p53, Mdm2, and ATRX, as well as for the auto-regulation of the DAXX N-terminal SUMO interaction motif (SIM). Our experiments demonstrate that these peptides effectively bind to and inhibit DAXX with a higher affinity than the known interaction partners. Furthermore, these peptides release the auto-inhibited SIM, enabling it to interact with SUMO-1. Importantly, we have developed stitched peptides that can enter cells, maintaining their intracellular concentrations at nanomolar levels even after 24 hours, without causing any membrane perturbation. Collectively, our findings suggest that these stitched peptides not only serve as valuable tools for probing the molecular interactions of DAXX but also hold potential as precursors to the development of therapeutic interventions.
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Affiliation(s)
- Clare Jelinska
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | | | - Yuri Frosi
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Siti Radhiah Ramlan
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Fernaldo Winnerdy
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
| | - Rajamani Lakshminarayanan
- Ocular Infections and Anti-Microbials Research Group, Singapore Eye Research Institute, The Academia, 20 College Road Singapore 169856 Singapore
- Department of Pharmacy, National University of Singapore Singapore 117543 Singapore
- Academic Clinical Program in Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School 169857 Singapore
| | - Charles W Johannes
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Christopher J Brown
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Anh-Tuan Phan
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Physical and Mathematical Sciences. 21 Nanyang link 637371 Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | - Chandra S Verma
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- Bioinformatics institute (A*STAR), 30 Biopolis Street, Matrix Level 07-01 138671 Singapore
- Department of Biological Sciences, National University of Singapore Block S3 #05-01 16 Science Drive 4 117558 Singapore
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Aguilera P, López-Contreras AJ. ATRX, a guardian of chromatin. Trends Genet 2023; 39:505-519. [PMID: 36894374 DOI: 10.1016/j.tig.2023.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 03/09/2023]
Abstract
ATRX (alpha-thalassemia mental retardation X-linked) is one of the most frequently mutated tumor suppressor genes in human cancers, especially in glioma, and recent findings indicate roles for ATRX in key molecular pathways, such as the regulation of chromatin state, gene expression, and DNA damage repair, placing ATRX as a central player in the maintenance of genome stability and function. This has led to new perspectives about the functional role of ATRX and its relationship with cancer. Here, we provide an overview of ATRX interactions and molecular functions and discuss the consequences of its impairment, including alternative lengthening of telomeres and therapeutic vulnerabilities that may be exploited in cancer cells.
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Affiliation(s)
- Paula Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain.
| | - Andrés J López-Contreras
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain.
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Scherer M, Read C, Neusser G, Kranz C, Kuderna AK, Müller R, Full F, Woerz S, Reichel A, Schilling EM, Walther P, Stamminger T. Dual signaling via interferon and DNA damage response elicits entrapment by giant PML nuclear bodies. eLife 2022; 11:73006. [PMID: 35319461 PMCID: PMC8975554 DOI: 10.7554/elife.73006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
PML nuclear bodies (PML-NBs) are dynamic interchromosomal macromolecular complexes implicated in epigenetic regulation as well as antiviral defense. During herpesvirus infection, PML-NBs induce epigenetic silencing of viral genomes, however, this defense is antagonized by viral regulatory proteins such as IE1 of human cytomegalovirus (HCMV). Here, we show that PML-NBs undergo a drastic rearrangement into highly enlarged PML cages upon infection with IE1-deficient HCMV. Importantly, our results demonstrate that dual signaling by interferon and DNA damage response is required to elicit giant PML-NBs. DNA labeling revealed that invading HCMV genomes are entrapped inside PML-NBs and remain stably associated with PML cages in a transcriptionally repressed state. Intriguingly, by correlative light and transmission electron microscopy (EM), we observed that PML cages also entrap newly assembled viral capsids demonstrating a second defense layer in cells with incomplete first line response. Further characterization by 3D EM showed that hundreds of viral capsids are tightly packed into several layers of fibrous PML. Overall, our data indicate that giant PML-NBs arise via combined interferon and DNA damage signaling which triggers entrapment of both nucleic acids and proteinaceous components. This represents a multilayered defense strategy to act in a cytoprotective manner and to combat viral infections.
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Affiliation(s)
- Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Clarissa Read
- Central Facility for Electron Microscopy, ULM University, Ulm, Germany
| | - Gregor Neusser
- Institute of Analytical and Bioanalytical Chemistry, ULM University, Ulm, Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, ULM University, Ulm, Germany
| | - Anna K Kuderna
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Regina Müller
- Institute of Clinical and Molecular Virology, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Florian Full
- Institute of Clinical and Molecular Virology, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sonja Woerz
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Anna Reichel
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, ULM University, Ulm, Germany
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Wen T, Chen QY. Dynamic Activity of Histone H3-Specific Chaperone Complexes in Oncogenesis. Front Oncol 2022; 11:806974. [PMID: 35087762 PMCID: PMC8786718 DOI: 10.3389/fonc.2021.806974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Canonical histone H3.1 and variant H3.3 deposit at different sites of the chromatin via distinct histone chaperones. Histone H3.1 relies on chaperone CAF-1 to mediate replication-dependent nucleosome assembly during S-phase, while H3.3 variant is regulated and incorporated into the chromatin in a replication-independent manner through HIRA and DAXX/ATRX. Current literature suggests that dysregulated expression of histone chaperones may be implicated in tumor progression. Notably, ectopic expression of CAF-1 can promote a switch between canonical H3.1 and H3 variants in the chromatin, impair the chromatic state, lead to chromosome instability, and impact gene transcription, potentially contributing to carcinogenesis. This review focuses on the chaperone proteins of H3.1 and H3.3, including structure, regulation, as well as their oncogenic and tumor suppressive functions in tumorigenesis.
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Affiliation(s)
- Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
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Probing the Protein-Protein Interaction Between the ATRX ADD Domain and the Histone H3 Tail. Molecules 2020; 25:molecules25071500. [PMID: 32218364 PMCID: PMC7181051 DOI: 10.3390/molecules25071500] [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: 02/19/2020] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022] Open
Abstract
While loss-of-function mutations in the ATRX gene have been implicated as a driving force for a variety of pediatric brain tumors, as well as pancreatic neuroendocrine tumors, the role of ATRX in gene regulation and oncogenic development is not well-characterized. The ADD domain of ATRX (ATRXADD) localizes the protein to chromatin by specifically binding to the histone H3 tail. This domain is also a primary region that is mutated in these cancers. The overall goal of our studies was to utilize a variety of techniques (experimental and computational) to probe the H3:ATRXADD protein-protein interaction (PPI). We developed two biochemical assays that can be utilized to study the interaction. These assays were utilized to experimentally validate and expand upon our previous computational results. We demonstrated that the three anchor points in the H3 tail (A1, K4, and K9) are all essential for high affinity binding and that disruption of more than one contact region will be required to develop a small molecule that disrupts the PPI. Our approach in this study could be applied to other domains of ATRX, as well as PPIs between other distinct proteins.
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Mahmud I, Liao D. DAXX in cancer: phenomena, processes, mechanisms and regulation. Nucleic Acids Res 2019; 47:7734-7752. [PMID: 31350900 PMCID: PMC6735914 DOI: 10.1093/nar/gkz634] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ATRX). DAXX's central region folds with the H3.3/H4 dimer, providing a H3.3-specific chaperoning function. DAXX has two functionally critical SUMO-interacting motifs. These modules are connected by disordered regions. DAXX's structural features provide a framework for deciphering how DAXX mechanistically imparts its functions and how its activity is regulated. DAXX modulates transcription through binding to transcription factors, epigenetic modifiers, and chromatin remodelers. DAXX's localization in the PML nuclear bodies also plays roles in transcriptional regulation. DAXX-regulated genes are likely important effectors of its biological functions. Deposition of H3.3 and its interactions with epigenetic modifiers are likely key events for DAXX to regulate transcription, DNA repair, and viral infection. Interactions between DAXX and its partners directly impact apoptosis and cell signaling. DAXX's activity is regulated by posttranslational modifications and ubiquitin-dependent degradation. Notably, the tumor suppressor SPOP promotes DAXX degradation in phase-separated droplets. We summarize here our current understanding of DAXX's complex functions with a focus on how it promotes oncogenesis.
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Affiliation(s)
- Iqbal Mahmud
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
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