1
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Joo SY, Sung K, Lee H. Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity. Bioessays 2024; 46:e2300229. [PMID: 38922965 DOI: 10.1002/bies.202300229] [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: 11/29/2023] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.
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Affiliation(s)
- So Young Joo
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
| | - Keewon Sung
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, South Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
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2
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Jiang J, Sun M, Wang Y, Huang W, Xia L. Deciphering the roles of the HMGB family in cancer: Insights from subcellular localization dynamics. Cytokine Growth Factor Rev 2024; 78:85-104. [PMID: 39019664 DOI: 10.1016/j.cytogfr.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024]
Abstract
The high-mobility group box (HMGB) family consists of four DNA-binding proteins that regulate chromatin structure and function. In addition to their intracellular functions, recent studies have revealed their involvement as extracellular damage-associated molecular patterns (DAMPs), contributing to immune responses and tumor development. The HMGB family promotes tumorigenesis by modulating multiple processes including proliferation, metabolic reprogramming, metastasis, immune evasion, and drug resistance. Due to the predominant focus on HMGB1 in the literature, little is known about the remaining members of this family. This review summarizes the structural, distributional, as well as functional similarities and distinctions among members of the HMGB family, followed by a comprehensive exploration of their roles in tumor development. We emphasize the distributional and functional hierarchy of the HMGB family at both the organizational and subcellular levels, with a focus on their relationship with the tumor immune microenvironment (TIME), aiming to prospect potential strategies for anticancer therapy.
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Affiliation(s)
- Junqing Jiang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China
| | - Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China; State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi' an 710032, China.
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3
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Zhang R, Yang L, Xiao X, Liu H. Dissipative Particle Dynamics Simulation of Protein Folding in Explicit and Implicit Solvents: Coarse-Grained Model for Atomic Resolution. J Chem Theory Comput 2024. [PMID: 39053012 DOI: 10.1021/acs.jctc.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Advancements have been made to dissipative particle dynamics (DPD), a robust coarse-grained (CG) simulation method, to study the folded structures of four miniproteins (1L2Y, 1WN8, 1YRF, and 2I9M) in explicit and implicit solvents. In this endeavor, we aim to establish model parametrization and enhance computational efficiency. Unlike traditional CG models that use empirical force parameters, ex-force parameters (r0(ex), a ~ , δd, δp) of DPD particles constructed for specific research purposes can be obtained from atomistic molecular dynamics simulations. On the other hand, im-force parameters (r0(im), c, σ) can be derived from ex-DPD simulations, according to the underlying thermodynamic theory. Based on a mapping scheme proposed for the modeling of amino acids, all-atom proteins can be converted into a CG model. Both ex-/im-DPDs are then carried out to investigate the folding pathways of the four mini-proteins. Structural analysis of the RMSDs shows that the im-simulated proteins have greater structural similarity to native proteins than the ex-simulated ones. The constructed CG models achieve a resolution of Angstrom (Å), a level normally associated with atomic models. Additionally, speed tests reveal that im-DPD accelerates the simulation process and significantly improves simulation efficiency.
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Affiliation(s)
- Ruzhuang Zhang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Hainan University, Haikou City, Hainan Province 570228, PR China
| | - Li Yang
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, PR China
| | - Xingqing Xiao
- Department of Chemistry, School of Chemistry and Chemical Engineering, Hainan University, Haikou City, Hainan Province 570228, PR China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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4
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Wang X, Holthauzen LMF, Paz-Villatoro JM, Bien KG, Yu B, Iwahara J. Phosphorylation by Protein Kinase C Weakens DNA-Binding Affinity and Folding Stability of the HMGB1 Protein. Biochemistry 2024; 63:1718-1722. [PMID: 38916994 PMCID: PMC11282465 DOI: 10.1021/acs.biochem.4c00194] [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] [Indexed: 06/27/2024]
Abstract
The HMGB1 protein typically serves as a DNA chaperone that assists DNA-repair enzymes and transcription factors but can translocate from the nucleus to the cytoplasm or even to extracellular space upon some cellular stimuli. One of the factors that triggers the translocation of HMGB1 is its phosphorylation near a nuclear localization sequence by protein kinase C (PKC), although the exact modification sites on HMGB1 remain ambiguous. In this study, using spectroscopic methods, we investigated the HMGB1 phosphorylation and its impact on the molecular properties of the HMGB1 protein. Our nuclear magnetic resonance (NMR) data on the full-length HMGB1 protein showed that PKC specifically phosphorylates the A-box domain, one of the DNA binding domains of HMGB1. Phosphorylation of S46 and S53 was particularly efficient. Over a longer reaction time, PKC phosphorylated some additional residues within the HMGB1 A-box domain. Our fluorescence-based binding assays showed that the phosphorylation significantly reduces the binding affinity of HMGB1 for DNA. Based on the crystal structures of HMGB1-DNA complexes, this effect can be ascribed to electrostatic repulsion between the negatively charged phosphate groups at the S46 side chain and DNA backbone. Our data also showed that the phosphorylation destabilizes the folding of the A-box domain. Thus, phosphorylation by PKC weakens the DNA-binding affinity and folding stability of HMGB1.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Luis Marcelo F. Holthauzen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Jonathan M Paz-Villatoro
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Karina G. Bien
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
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5
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Merlino F, Marzano S, Zizza P, D’Aria F, Grasso N, Carachino A, Iachettini S, Biroccio A, Fonzo SD, Grieco P, Randazzo A, Amato J, Pagano B. Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity. Nucleic Acids Res 2024; 52:6748-6762. [PMID: 38828773 PMCID: PMC11229374 DOI: 10.1093/nar/gkae471] [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: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Noncanonical nucleic acid structures, particularly G-quadruplexes, have garnered significant attention as potential therapeutic targets in cancer treatment. Here, the recognition of G-quadruplex DNA by peptides derived from the Rap1 protein is explored, with the aim of developing novel peptide-based G-quadruplex ligands with enhanced selectivity and anticancer activity. Biophysical techniques were employed to assess the interaction of a peptide derived from the G-quadruplex-binding domain of the protein with various biologically relevant G-quadruplex structures. Through alanine scanning mutagenesis, key amino acids crucial for G-quadruplex recognition were identified, leading to the discovery of two peptides with improved G-quadruplex-binding properties. However, despite their in vitro efficacy, these peptides showed limited cell penetration and anticancer activity. To overcome this challenge, cell-penetrating peptide (CPP)-conjugated derivatives were designed, some of which exhibited significant cytotoxic effects on cancer cells. Interestingly, selected CPP-conjugated peptides exerted potent anticancer activity across various tumour types via a G-quadruplex-dependent mechanism. These findings underscore the potential of peptide-based G-quadruplex ligands in cancer therapy and pave the way for the development of novel therapeutic strategies targeting these DNA structures.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Alice Carachino
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Sara Iachettini
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste 34149, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
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6
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Liu Y, Song D, Li S, Guo Z, Zheng P. Click Chemistry-Based Force Spectroscopy Revealed Enhanced Binding Dynamics of Phosphorylated HMGB1 to Cisplatin-DNA. J Am Chem Soc 2024; 146:13126-13132. [PMID: 38696488 DOI: 10.1021/jacs.4c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Cisplatin, a cornerstone in cancer chemotherapy, is known for its DNA-binding capacity and forms lesions that lead to cancer cell death. However, the repair of these lesions compromises cisplatin's effectiveness. This study investigates how phosphorylation of HMGB1, a nuclear protein, modifies its binding to cisplatin-modified DNA (CP-DNA) and thus protects it from repair. Despite numerous methods for detecting protein-DNA interactions, quantitative approaches for understanding their molecular mechanism remain limited. Here, we applied click chemistry-based single-molecule force spectroscopy, achieving high-precision quantification of the interaction between phosphorylated HMGB1 and CP-DNA. This method utilizes a synergy of click chemistry and enzymatic ligation for precise DNA-protein immobilization and interaction in the system. Our results revealed that HMGB1 binds to CP-DNA with a significantly high rupture force of ∼130 pN, stronger than most natural DNA-protein interactions and varying across different DNA sequences. Moreover, Ser14 is identified as the key phosphorylation site, enhancing the interaction's kinetic stability by 35-fold. This increase in stability is attributed to additional hydrogen bonding suggested by molecular dynamics (MD) simulations. Our findings not only reveal the important role of phosphorylated HMGB1 in potentially improving cisplatin's therapeutic efficacy but also provide a precise method for quantifying protein-DNA interactions.
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Affiliation(s)
- Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Senmiao Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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7
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Napolitano E, Criscuolo A, Riccardi C, Esposito CL, Catuogno S, Coppola G, Roviello GN, Montesarchio D, Musumeci D. Directing in Vitro Selection towards G-quadruplex-forming Aptamers to Inhibit HMGB1 Pathological Activity. Angew Chem Int Ed Engl 2024; 63:e202319828. [PMID: 38358301 DOI: 10.1002/anie.202319828] [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: 01/12/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
In the search for novel, effective inhibitors of High-Mobility Group Box1 (HMGB1)-a protein involved in various inflammatory and autoimmune diseases as well as in cancer-we herein discovered a set of anti-HMGB1 G-quadruplex(G4)-forming aptamers by using an in vitro selection procedure applied to a doped library of guanine-rich oligonucleotides. The selected DNA sequences were then studied in a pseudo-physiological buffer mimicking the extracellular medium, where HMGB1 exerts its pathological activity, using spectroscopic, electrophoretic, and chromatographic techniques. All the oligonucleotides proved to fold into monomeric G4s and in some cases also dimeric species, stable at physiological temperature. Remarkably, the protein preferentially recognized the sequences forming dimeric parallel G4 structures, as evidenced by a properly designed chemiluminescent binding assay which also highlighted a good selectivity of these aptamers for HMGB1. Moreover, all aptamers showed anti-HMGB1 activity, inhibiting protein-induced cell migration. The acquired data allowed identifying L12 as the best anti-HMGB1 aptamer, featured by high thermal and enzymatic stability, no toxicity at least up to 5 μM concentration on healthy cells, along with potent anti-HMGB1 activity (IC50 ca. 28 nM) and good binding affinity for the protein, thus indicating it as a very promising lead candidate for in vivo studies.
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Affiliation(s)
- Ettore Napolitano
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Andrea Criscuolo
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Carla L Esposito
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Silvia Catuogno
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Gabriele Coppola
- Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), National Research Council (CNR), Via Sergio Pansini 5, 80131, Napoli, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), 80145, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, 80126, Napoli, Italy
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), 80145, Napoli, Italy
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8
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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9
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Zhu Z, Li S, Yin X, Sun K, Song J, Ren W, Gao L, Zhi K. Review: Protein O-GlcNAcylation regulates DNA damage response: A novel target for cancer therapy. Int J Biol Macromol 2024; 264:130351. [PMID: 38403231 DOI: 10.1016/j.ijbiomac.2024.130351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DNA damage response (DDR) safeguards the stable genetic information inheritance by orchestrating a complex protein network in response to DNA damage. However, this mechanism can often hamper the effectiveness of radiotherapy and DNA-damaging chemotherapy in destroying tumor cells, causing cancer resistance. Inhibiting DDR can significantly improve tumor cell sensitivity to radiotherapy and DNA-damaging chemotherapy. Thus, DDR can be a potential target for cancer treatment. Post-translational modifications (PTMs) of DDR-associated proteins profoundly affect their activity and function by covalently attaching new functional groups. O-GlcNAcylation (O-linked-N-acetylglucosaminylation) is an emerging PTM associated with adding and removing O-linked N-acetylglucosamine to serine and threonine residues of proteins. It acts as a dual sensor for nutrients and stress in the cell and is sensitive to DNA damage. However, the explanation behind the specific role of O-GlcNAcylation in the DDR remains remains to be elucidated. To illustrate the complex relationship between O-GlcNAcylation and DDR, this review systematically describes the role of O-GlcNAcylation in DNA repair, cell cycle, and chromatin. We also discuss the defects of current strategies for targeting O-GlcNAcylation-regulated DDR in cancer therapy and suggest potential directions to address them.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaopeng Yin
- Department of Oral and Maxillofacial Surgery, Central Laboratory of Jinan Stamotological Hospital, Jinan Key Laboratory of Oral Tissue Regeneration, Jinan 250001, Shandong Province, China
| | - Kai Sun
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Jianzhong Song
- Department of Oral and Maxilloafacial Surgery, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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10
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Russo C, Russomanno P, D'Amore VM, Alfano AI, Santoro F, Guzelj S, Gobec M, Amato J, Pagano B, Marinelli L, Carotenuto A, Tron GC, Di Leva FS, Jakopin Ž, Brancaccio D, Giustiniano M. Discovery of 2,3-Diaminoindole Derivatives as a Novel Class of NOD Antagonists. J Med Chem 2024; 67:3004-3017. [PMID: 38301029 DOI: 10.1021/acs.jmedchem.3c02094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
NOD1 and NOD2 are members of the pattern recognition receptors involved in the innate immune response. Overactivation of NOD1 is implicated in inflammatory disorders, multiple sclerosis, and cancer cell metastases. NOD1 antagonists would represent valuable pharmacological tools to gain further insight into protein roles, potentially leading to new therapeutic strategies. We herein report the expansion of the chemical space of NOD1 antagonists via a multicomponent synthetic approach affording a novel chemotype, namely, 2,3-diaminoindoles. These efforts resulted in compound 37, endowed with low micromolar affinity toward NOD1. Importantly, a proof-of-evidence of direct binding to NOD1 of Noditinib-1 and derivative 37 is provided here for the first time. Additionally, the combination of computational studies and NMR-based displacement assays enabled the characterization of the binding modality of 37 to NOD1, thus providing key unprecedented knowledge for the design of potent and selective NOD1 antagonists.
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Affiliation(s)
- Camilla Russo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Antonella Ilenia Alfano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Federica Santoro
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Samo Guzelj
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Gian Cesare Tron
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, Novara 28100, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
| | - Mariateresa Giustiniano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, Naples 80131, Italy
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11
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Peng R, Zuo S, Li X, Huang Y, Chen S, Zou X, Long H, Chen M, Yang Y, Yuan H, Zhao Q, Guo B, Liu L. Investigating HMGB1 as a potential serum biomarker for early diabetic nephropathy monitoring by quantitative proteomics. iScience 2024; 27:108834. [PMID: 38303703 PMCID: PMC10830865 DOI: 10.1016/j.isci.2024.108834] [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: 09/01/2023] [Revised: 12/01/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
Current diagnostic methods for diabetic nephropathy (DN) lack precision, especially in early stages and monitoring progression. This study aims to find potential biomarkers for DN progression and evaluate their accuracy. Using serum samples from healthy controls (NC), diabetic patients (DM), early-medium stage DN (DN-EM), and late-stage DN (DN-L), researchers employed quantitative proteomics and Mfuzz clustering analysis revealed 15 proteins showing increased expression during DN progression, hinting at their biomarker potential. Combining Mfuzz clustering with weighted gene co-expression network analysis (WGCNA) highlighted five candidates (HMGB1, CD44, FBLN1, PTPRG, and ADAMTSL4). HMGB1 emerged as a promising biomarker, closely correlated with renal function changes. Experimental validation supported HMGB1's upregulation under high glucose conditions, reinforcing its potential as an early detection biomarker for DN. This research advances DN understanding and identifies five potential biomarkers, notably HMGB1, as a promising early monitoring target. These findings set the stage for future clinical diagnostic applications in DN.
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Affiliation(s)
- Rui Peng
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Siyang Zuo
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Xia Li
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- Center for Clinical Medical Research, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Yun Huang
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Siyu Chen
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Xue Zou
- Center for Clinical Medical Research, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Hehua Long
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Min Chen
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Yuan Yang
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Huixiong Yuan
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Qingqing Zhao
- Center for Clinical Medical Research, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Bing Guo
- Department of Pathophysiology, Guizhou Medical University, Guiyang 550025, China
- Laboratory of Pathogenesis Research, Drug Prevention and Treatment of Major Diseases, Guizhou Medical University, Guiyang 550025, China
| | - Lirong Liu
- Center for Clinical Laboratories, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China
- Guizhou Precision Medicine Institute, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
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12
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Grasso N, Graziano R, Marzano S, D'Aria F, Merlino F, Grieco P, Randazzo A, Pagano B, Amato J. Unveiling the interaction between DNA G-quadruplexes and RG-rich peptides. Int J Biol Macromol 2023; 253:126749. [PMID: 37689293 DOI: 10.1016/j.ijbiomac.2023.126749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
G-quadruplexes are non-canonical DNA secondary structures formed within guanine-rich strands that play important roles in various biological processes, including gene regulation, telomere maintenance and DNA replication. The biological functions and formation of these DNA structures are strictly controlled by several proteins that bind and stabilize or resolve them. Many G-quadruplex-binding proteins feature an arginine and glycine-rich motif known as the RGG or RG-rich motif. Although this motif plays a crucial role in the recognition of such non-canonical structures, their interaction is still poorly understood. Here, we employed a combination of several biophysical techniques to provide valuable insights into the interaction between a peptide containing an RGG motif shared by numerous human G-quadruplex-binding proteins (NIQI) and various biologically relevant G-quadruplex DNA structures with different topologies. We also shed light on the key amino acids involved in the binding process. Our findings contribute to lay the basis for the development of a new class of peptide-based G-quadruplex ligands as an alternative to small molecules. These ligands may serve as valid tools for interfering in DNA-protein interactions, with potential therapeutic applications.
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Affiliation(s)
- Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Raffaele Graziano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
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13
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Yang Q, Li M, Hou Y, He H, Sun S. High-mobility group box 1 emerges as a therapeutic target for asthma. Immun Inflamm Dis 2023; 11:e1124. [PMID: 38156383 PMCID: PMC10739362 DOI: 10.1002/iid3.1124] [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: 08/01/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
High-mobility group box 1 (HMGB1) is a highly conserved nonhistone nuclear protein found in the calf thymus and participates in a variety of intracellular processes such as DNA transcription, replication and repair. In the cytoplasm, HMGB1 promotes mitochondrial autophagy and is involved in in cellular stress response. Once released into the extracellular, HMGB1 becomes an inflammatory factor that triggers inflammatory responses and a variety of immune responses. In addition, HMGB1 binding with the corresponding receptor can activate the downstream substrate to carry out several biological effects. Meanwhile, HMGB1 is involved in various signaling pathways, such as the HMGB1/RAGE pathway, HMGB1/NF-κB pathway, and HMGB1/JAK/STAT pathway, which ultimately promote inflammation. Moreover, HMGB1 may be involved in the pathogenesis of asthma by regulating downstream signaling pathways through corresponding receptors and mediates a number of signaling pathways in asthma, such as HMGB1/TLR4/NF-κB, HMGB1/RAGE, HMGB1/TGF-β, and so forth. Accordingly, HMGB1 emerges as a therapeutic target for asthma.
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Affiliation(s)
- Qianni Yang
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
- 2021 Class 2 of AnesthesiologyKunming Medical UniversityKunmingChina
| | - Min Li
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Yunjiao Hou
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Huilin He
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Shibo Sun
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
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14
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Hu Q, Wang R, Zhang J, Xue Q, Ding B. Tumor-associated neutrophils upregulate PANoptosis to foster an immunosuppressive microenvironment of non-small cell lung cancer. Cancer Immunol Immunother 2023; 72:4293-4308. [PMID: 37907644 DOI: 10.1007/s00262-023-03564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Tumor microenvironment (TME) cells orchestrate an immunosuppressive milieu that supports cancer cell proliferation. Tumor-associated neutrophils (TANs) have gained attention as inflammation biomarkers. However, the role of heterogeneous TAN populations in TME immune tolerance and their clinical potential remain unclear. Herein, we used public database to conduct single-cell transcriptomic analysis of 81 patients with non-small cell lung cancer (NSCLC) to elucidate TAN phenotypes linked to unfavorable clinical outcomes. We identified a pro-tumoral TAN cluster characterized by elevated HMGB1 expression, which could potentially engage with the TME through HMGB1-TIM-3 interaction. GATA2 was the transcription factor that drove HMGB1 expression in this pro-tumoral TAN subcluster. Further in vivo experiments confirmed the recruitment of HMGB1-positive TANs to the tumor lesion. Dual-luciferase reporter assays consolidated that the transcription factor GATA2 mediated HMGB1 expression by binding to its promoter region. Moreover, surgical NSCLC specimens verified the putative association between HMGB1-positive TAN and the pathological grades of primary tumors. Overall, this report revealed a pro-tumoral TAN cluster with HMGB1 overexpression that potentially dampen anti-tumoral immunity and contributed to immune evasion via the GATA2/HMGB1/TIM-3 axis. Moreover, this report suggests that this specific phenotype of TAN could serve as an indicator to clinical outcomes and immunotherapy effects for NSCLC.
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Affiliation(s)
- Qin Hu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226000, People's Republic of China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226000, China
| | - Runtian Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Jiaxin Zhang
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226000, People's Republic of China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226000, China
| | - Qun Xue
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226000, People's Republic of China.
| | - Bo Ding
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226000, People's Republic of China.
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15
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Serrano-León IM, Prieto P, Aguilar M. Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding. BMC Genomics 2023; 24:642. [PMID: 37884878 PMCID: PMC10601145 DOI: 10.1186/s12864-023-09738-y] [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: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Barley (Hordeum vulgare) is one of the most popular cereal crops globally. Although it is a diploid species, (2n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.
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Affiliation(s)
- I M Serrano-León
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain
| | - P Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain.
| | - M Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 3ª Planta, Córdoba, Spain
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16
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Chen R, Zou J, Kang R, Tang D. The Redox Protein High-Mobility Group Box 1 in Cell Death and Cancer. Antioxid Redox Signal 2023; 39:569-590. [PMID: 36999916 DOI: 10.1089/ars.2023.0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Significance: As a redox-sensitive protein, high-mobility group box 1 (HMGB1) is implicated in regulating stress responses to oxidative damage and cell death, which are closely related to the pathology of inflammatory diseases, including cancer. Recent Advances: HMGB1 is a nonhistone nuclear protein that acts as a deoxyribonucleic acid chaperone to control chromosomal structure and function. HMGB1 can also be released into the extracellular space and function as a damage-associated molecular pattern protein during cell death, including during apoptosis, necrosis, necroptosis, pyroptosis, ferroptosis, alkaliptosis, and cuproptosis. Once released, HMGB1 binds to membrane receptors to shape immune and metabolic responses. In addition to subcellular localization, the function and activity of HMGB1 also depend on its redox state and protein posttranslational modifications. Abnormal HMGB1 plays a dual role in tumorigenesis and anticancer therapy (e.g., chemotherapy, radiation therapy, and immunotherapy) depending on the tumor types and stages. Critical Issues: A comprehensive understanding of the role of HMGB1 in cellular redox homeostasis is important for deciphering normal cellular functions and pathological manifestations. In this review, we discuss compartmental-defined roles of HMGB1 in regulating cell death and cancer. Understanding these advances may help us develop potential HMGB1-targeting drugs or approaches to treat oxidative stress-related diseases or pathological conditions. Future Directions: Further studies are required to dissect the mechanism by which HMGB1 maintains redox homeostasis under different stress conditions. A multidisciplinary effort is also required to evaluate the potential applications of precisely targeting the HMGB1 pathway in human health and disease. Antioxid. Redox Signal. 39, 569-590.
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Affiliation(s)
- Ruochan Chen
- Hunan Key Laboratory of Viral Hepatitis; Central South University, Changsha, China
- Department of Infectious Diseases; Xiangya Hospital, Central South University, Changsha, China
| | - Ju Zou
- Hunan Key Laboratory of Viral Hepatitis; Central South University, Changsha, China
- Department of Infectious Diseases; Xiangya Hospital, Central South University, Changsha, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
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17
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De Piante E, D'Aria F, Napolitano LMR, Amato J, Pirrello S, Onesti S, Giancola C. Exploring the G-quadruplex binding and unwinding activity of the bacterial FeS helicase DinG. Sci Rep 2023; 13:12610. [PMID: 37537265 PMCID: PMC10400533 DOI: 10.1038/s41598-023-39675-5] [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: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Despite numerous reports on the interactions of G-quadruplexes (G4s) with helicases, systematic analysis addressing the selectivity and specificity of each helicase towards a variety of G4 topologies are scarce. Among the helicases able to unwind G4s are those containing an iron-sulphur (FeS) cluster, including both the bacterial DinG (found in E. coli and several pathogenic bacteria) and the medically important eukaryotic homologues (XPD, FancJ, DDX11 and RTEL1). We carried out a detailed study of the interactions between the E. coli DinG and a variety of G4s, by employing physicochemical and biochemical methodologies. A series of G4-rich sequences from different genomic locations (promoter and telomeric regions), able to form unimolecular G4 structures with diverse topologies, were analyzed (c-KIT1, KRAS, c-MYC, BCL2, Tel23, T30695, Zic1). DinG binds to most of the investigated G4s with little discrimination, while it exhibits a clear degree of unwinding specificity towards different G4 topologies. Whereas previous reports suggested that DinG was active only on bimolecular G4s, here we show that it is also able to bind to and resolve the more physiologically relevant unimolecular G4s. In addition, when the G4 structures were stabilized by ligands (Pyridostatin, PhenDC3, BRACO-19 or Netropsin), the DinG unwinding activity decreased and in most cases was abolished, with a pattern that is not simply explained by a change in binding affinity. Overall, these results have important implications for the biochemistry of helicases, strongly suggesting that when analysing the G4 unwinding property of an enzyme, it is necessary to investigate a variety of G4 substrates.
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Affiliation(s)
- Elisa De Piante
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Trieste, Italy
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Luisa M R Napolitano
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Trieste, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Simone Pirrello
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Trieste, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A, 34149, Trieste, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy.
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18
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Wang X, Bigman LS, Greenblatt HM, Yu B, Levy Y, Iwahara J. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res 2023; 51:4701-4712. [PMID: 36774964 PMCID: PMC10250230 DOI: 10.1093/nar/gkad045] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/14/2023] Open
Abstract
In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions (IDRs) with large negative charge, some of which involve a consecutive sequence of aspartate (D) or glutamate (E) residues. We refer to them as D/E repeats. The functional role of D/E repeats is not well understood, though some of them are known to cause autoinhibition through intramolecular electrostatic interaction with functional domains. In this work, we investigated the impacts of D/E repeats on the target DNA search kinetics for the high-mobility group box 1 (HMGB1) protein and the artificial protein constructs of the Antp homeodomain fused with D/E repeats of varied lengths. Our experimental data showed that D/E repeats of particular lengths can accelerate the target association in the overwhelming presence of non-functional high-affinity ligands ('decoys'). Our coarse-grained molecular dynamics (CGMD) simulations showed that the autoinhibited proteins can bind to DNA and transition into the uninhibited complex with DNA through an electrostatically driven induced-fit process. In conjunction with the CGMD simulations, our kinetic model can explain how D/E repeats can accelerate the target association process in the presence of decoys. This study illuminates an unprecedented role of the negatively charged IDRs in the target search process.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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D'Amico F, Graziano R, D'Aria F, Russomanno P, Di Fonzo S, Amato J, Pagano B. Cytosine epigenetic modifications and conformational changes in G-quadruplex DNA: An ultraviolet resonance Raman spectroscopy study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122901. [PMID: 37244027 DOI: 10.1016/j.saa.2023.122901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
Epigenetic modifications of DNA are known to play important regulatory roles in biological systems, especially in regulation of gene expression, and are associated with many types of human diseases, including cancer. Alternative DNA secondary structures, such as G-quadruplexes, can also influence gene transcription, thus suggesting that such structures may represent a distinctive layer of epigenetic information. G-quadruplex structures and DNA epigenetic modifications often go side by side, and recent evidence reveals that cytosine modifications within loops of G-quadruplexes can play a role in modulating their stability and structural polymorphism. Therefore, the development and validation of experimental techniques that can easily and reliably analyse G-quadruplex structures are highly desirable. In the present study, we propose to exploit the advantages of UV resonance Raman (UVRR) spectroscopy to investigate cytosine epigenetic modifications along with conformational changes in G-quadruplex-forming DNA. Our findings show that clear and specific spectral changes occur when there is a change in a G-quadruplex structure. Moreover, UVRR spectral analysis can indirectly distinguish the spectral variations occurring because of modifications in the guanine glycosidic conformations, as well as detect changes in the loops induced by H-bond formation or hydration of nitrogenous bases. The results further underscore the utility of UVRR spectroscopy for G-quadruplex structure elucidation under biologically relevant solution conditions.
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Affiliation(s)
- Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste I-34149, Italy
| | - Raffaele Graziano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste I-34149, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
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20
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Tian Y, Chen R, Su Z. HMGB1 is a Potential and Challenging Therapeutic Target for Parkinson's Disease. Cell Mol Neurobiol 2023; 43:47-58. [PMID: 34797463 DOI: 10.1007/s10571-021-01170-8] [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: 07/14/2021] [Accepted: 11/14/2021] [Indexed: 01/07/2023]
Abstract
Parkinson's disease (PD) is one of the most common degenerative diseases of the human nervous system and has a wide range of serious impacts on human health and quality of life. Recently, research targeting high mobility group box 1 (HMGB1) in PD has emerged, and a variety of laboratory methods for inhibiting HMGB1 have achieved good results to a certain extent. However, given that HMGB1 undergoes a variety of intracellular modifications and three different forms of extracellular redox, the possible roles of these forms in PD are likely to be different. General inhibition of all forms of HMGB1 is obviously not ideal and has become one of the biggest obstacles in the clinical application of targeting HMGB1. In this review, pure mechanistic research of HMGB1 and in vivo research targeting HMGB1 were combined, the effects of HMGB1 on neurons and immune cell responses in PD are discussed in detail, and the problems that need to be focused on in the future are addressed.
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Affiliation(s)
- Yu Tian
- International Genome Center, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.,Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Rong Chen
- International Genome Center, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.,Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Zhaoliang Su
- International Genome Center, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China. .,Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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21
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Du X, Zhang X, Dong J, Zou N, Guo D, Yao W, Wang X, Li S, Song C, Yan K, Shen W, Zhu S. Irradiation-induced exosomal HMGB1 to confer radioresistance via the PI3K/AKT/FOXO3A signaling pathway in ESCC. J Transl Med 2022; 20:507. [PMID: 36335371 PMCID: PMC9636677 DOI: 10.1186/s12967-022-03720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Background Radioresistance is a major cause of treatment failure in esophageal squamous cell carcinoma (ESCC) radiotherapy, and the underlying mechanisms of radioresistance are still unclear. Irradiation (IR) stimulates changes in tumor-derived exosome contents, which can be taken up by recipient cells, playing an important role in the proliferation, cell cycle and apoptosis of recipient cells. This study investigated the effect of IR-induced exosomal high mobility group box 1 (HMGB1) on radioresistance in ESCC cells. Methods Plasma exosomes were isolated from 21 ESCC patients and 24 healthy volunteers, and the expression of HMGB1 was examined. Then, the therapeutic effect of radiotherapy was analyzed according to the different expression levels of plasma exosomal HMGB1 in ESCC patients. The uptake of exosomes by recipient cells was verified by immunofluorescence staining, and the localization of exosomes and HMGB1 in cells before and after IR was evaluated. The effects of IR-induced exosomes on cell proliferation, invasion, apoptosis, cell cycle distribution and radioresistance after HMGB1 knockdown were verified. Moreover, western blotting was used to measure changes in the expression of cyclin B1, CDK1, Bax, Bcl2, phosphorylated histone H2AX and the PI3K/AKT/FOXO3A pathway in the HMGB1-knockdown exosome group and the negative control group. Results The expression of HMGB1 in ESCC plasma exosomes was significantly increased compared with that in healthy volunteers, and high expression of HMGB1 in plasma exosomes was associated with radioresistance (P = 0.016). IR-induced the release of exosomal HMGB1 and promoted proliferation and radioresistance in recipient cells, with a sensitization enhancement ratio (SER) of 0.906 and 0.919, respectively. In addition, IR-induced exosomal HMGB1 promotes G2/M phase arrest by regulating the proteins cyclin B1 and CDK1, cooperating with the proteins Bax and Bcl2 to reduce the apoptosis rate through the PI3K/AKT/FOXO3A signaling pathway, and participated in IR-induced DNA damage repair through γH2AX. Conclusion These findings indicate that high expression of plasma exosomal HMGB1 is associated with an adverse radiotherapy response. IR-induced exosomal HMGB1 enhances the radioresistance of ESCC cells.
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22
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Iachettini S, Ciccarone F, Maresca C, D' Angelo C, Petti E, Di Vito S, Ciriolo MR, Zizza P, Biroccio A. The telomeric protein TERF2/TRF2 impairs HMGB1-driven autophagy. Autophagy 2022:1-12. [PMID: 36310382 DOI: 10.1080/15548627.2022.2138687] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023] Open
Abstract
TERF2/TRF2 is a pleiotropic telomeric protein that plays a crucial role in tumor formation and progression through several telomere-dependent and -independent mechanisms. Here, we uncovered a novel function for this protein in regulating the macroautophagic/autophagic process upon different stimuli. By using both biochemical and cell biology approaches, we found that TERF2 binds to the non-histone chromatin-associated protein HMGB1, and this interaction is functional to the nuclear/cytoplasmic protein localization. Specifically, silencing of TERF2 alters the redox status of the cells, further exacerbated upon EBSS nutrient starvation, promoting the cytosolic translocation and the autophagic activity of HMGB1. Conversely, overexpression of wild-type TERF2, but not the mutant unable to bind HMGB1, negatively affects the cytosolic translocation of HMGB1, counteracting the stimulatory effect of EBSS starvation. Moreover, genetic depletion of HMGB1 or treatment with inflachromene, a specific inhibitor of its cytosolic translocation, completely abolished the pro-autophagic activity of TERF2 silencing. In conclusion, our data highlighted a novel mechanism through which TERF2 modulates the autophagic process, thus demonstrating the key role of the telomeric protein in regulating a process that is fundamental, under both physiological and pathological conditions, in defining the fate of the cells.Abbreviations: ALs: autolysosomes; ALT: alternative lengthening of telomeres; ATG: autophagy related; ATM: ATM serine/threonine kinase; CQ: Chloroquine; DCFDA: 2',7'-dichlorofluorescein diacetate; DDR: DNA damage response; DHE: dihydroethidium; EBSS: Earle's balanced salt solution; FACS: fluorescence-activated cell sorting; GFP: green fluorescent protein; EGFP: enhanced green fluorescent protein; GSH: reduced glutathione; GSSG: oxidized glutathione; HMGB1: high mobility group box 1; ICM: inflachromene; IF: immunofluorescence; IP: immunoprecipitation; NAC: N-acetyl-L-cysteine; NHEJ: non-homologous end joining; PLA: proximity ligation assay; RFP: red fluorescent protein; ROS: reactive oxygen species; TIF: telomere-induced foci; TERF2/TRF2: telomeric repeat binding factor 2.
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Affiliation(s)
- Sara Iachettini
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Fabio Ciccarone
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Biochemistry of aging section, IRCCS San Raffaele Roma, Rome, Italy
| | - Carmen Maresca
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Carmen D' Angelo
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Eleonora Petti
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Serena Di Vito
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Rosa Ciriolo
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Biochemistry of aging section, IRCCS San Raffaele Roma, Rome, Italy
| | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Annamaria Biroccio
- Translational Oncology Research Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
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Wang X, Mayorga-Flores M, Bien KG, Bailey AO, Iwahara J. DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem 2022; 298:102577. [DOI: 10.1016/j.jbc.2022.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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24
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [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: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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25
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Vincenzi M, Anna Mercurio F, Di Natale C, Palumbo R, Pirone L, La Manna S, Marasco D, Maria Pedone E, Leone M. Targeting Ship2-Sam with peptide ligands: Novel insights from a multidisciplinary approach. Bioorg Chem 2022; 122:105680. [DOI: 10.1016/j.bioorg.2022.105680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
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26
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Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules 2022; 12:biom12050648. [PMID: 35625576 PMCID: PMC9138358 DOI: 10.3390/biom12050648] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.
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27
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Edwards-Smallbone J, Jensen AL, Roberts LE, Totañes FIG, Hart SR, Merrick CJ. Plasmodium falciparum GBP2 Is a Telomere-Associated Protein That Binds to G-Quadruplex DNA and RNA. Front Cell Infect Microbiol 2022; 12:782537. [PMID: 35273922 PMCID: PMC8902816 DOI: 10.3389/fcimb.2022.782537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023] Open
Abstract
In the early-diverging protozoan parasite Plasmodium, few telomere-binding proteins have been identified and several are unique. Plasmodium telomeres, like those of most eukaryotes, contain guanine-rich repeats that can form G-quadruplex structures. In model systems, quadruplex-binding drugs can disrupt telomere maintenance and some quadruplex-binding drugs are potent anti-plasmodial agents. Therefore, telomere-interacting and quadruplex-interacting proteins may offer new targets for anti-malarial therapy. Here, we report that P. falciparum GBP2 is such a protein. It was identified via 'Proteomics of Isolated Chromatin fragments', applied here for the first time in Plasmodium. In vitro, PfGBP2 binds specifically to G-rich telomere repeats in quadruplex form and it can also bind to G-rich RNA. In vivo, PfGBP2 partially colocalises with the known telomeric protein HP1 but is also found in the cytoplasm, probably due to its affinity for RNA. Consistently, its interactome includes numerous RNA-associated proteins. PfGBP2 is evidently a multifunctional DNA/RNA-binding factor in Plasmodium.
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Affiliation(s)
- James Edwards-Smallbone
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, United Kingdom
| | - Anders L. Jensen
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Lydia E. Roberts
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | | | - Sarah R. Hart
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Staffordshire, United Kingdom
| | - Catherine J. Merrick
- Department of Pathology, Cambridge University, Cambridge, United Kingdom,*Correspondence: Catherine J. Merrick,
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28
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Ceschi S, Berselli M, Cozzaglio M, Giantin M, Toppo S, Spolaore B, Sissi C. Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters. Nucleic Acids Res 2022; 50:1370-1381. [PMID: 35100428 PMCID: PMC8860586 DOI: 10.1093/nar/gkab1274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) structures that can form at guanine-rich genomic sites, including telomeres and gene promoters, are actively involved in genome maintenance, replication, and transcription, through finely tuned interactions with protein networks. In the present study, we identified the intermediate filament protein Vimentin as a binder with nanomolar affinity for those G-rich sequences that give rise to at least two adjacent G4 units, named G4 repeats. This interaction is supported by the N-terminal domains of soluble Vimentin tetramers. The selectivity of Vimentin for G4 repeats versus individual G4s provides an unprecedented result. Based on GO enrichment analysis performed on genes having putative G4 repeats within their core promoters, we suggest that Vimentin recruitment at these sites may contribute to the regulation of gene expression during cell development and migration, possibly by reshaping the local higher-order genome topology, as already reported for lamin B.
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Affiliation(s)
- Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Michele Berselli
- Department of Molecular Medicine, University of Padova, Padova 35131, Italy
| | - Marta Cozzaglio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Stefano Toppo
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
- Department of Molecular Medicine, University of Padova, Padova 35131, Italy
| | - Barbara Spolaore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
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29
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Jia S, He D, Liang X, Cheng P, Liu J, Chen M, Wang C, Zhang H, Meng C. Corilagin induces apoptosis and inhibits autophagy of HL‑60 cells by regulating miR‑451/HMGB1 axis. Mol Med Rep 2021; 25:34. [PMID: 34850958 PMCID: PMC8669704 DOI: 10.3892/mmr.2021.12550] [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: 12/31/2020] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Corilagin is the primary active component of the Euphorbia phyllanthus plant and has significant anti-cancer properties. However, the biological effects and mechanisms of corilagin on acute myeloid leukemia (AML) have not been clarified. The Cell Counting Kit-8 and Carboxyfluorescein Diacetate Succinimidyl Ester assay results showed that corilagin significantly inhibited proliferation of the AML cell line HL-60 in a time- and dose-dependent manner. Western blotting and flow cytometry analysis were performed to determine the levels of apoptosis in HL-60 cells. The protein levels of cleaved caspase-3 and Bak were upregulated, while Bcl-xl was downregulated in cells treated with corilagin. The percentage of early- and late-stage apoptotic cells increased following corilagin treatment in a dose-dependent manner, indicating that the intrinsic mitochondrial apoptosis pathway was activated by corilagin. Simultaneously, western blotting and immunofluorescence results revealed that autophagy was suppressed; this was accompanied by a decrease in light chain 3-II (LC3-II) conversion and autophagosomes. MicroRNA (miRNA/miR) profile analysis showed that corilagin elevated the expression of the tumor suppressor miR-451, while the mRNA and protein levels of high mobility group protein B1 (HMGB1), the target of miR-451, decreased following exposure to corilagin. Knockdown of miR-451 decreased the downregulation of HMGB1 caused by corilagin, indicating negative regulation of HMGB1 by miR-451 during corilagin treatment. Furthermore, knockdown of miR-451 also attenuated corilagin-induced proliferation inhibition of HL-60 cells, implying that miR-451 was essential for the proliferation inhibitory effect of corilagin. In conclusion, these results indicated that corilagin induced apoptosis and inhibited autophagy in HL-60 cells by regulating the miR-451/HMGB1 axis, and corilagin may be a novel therapeutic drug for the treatment of AML.
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Affiliation(s)
- Shu Jia
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Dongye He
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Xiao Liang
- Department of Spine Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Panpan Cheng
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Jilan Liu
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Mingtai Chen
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Cuiling Wang
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Hao Zhang
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Chunyang Meng
- Department of Spine Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
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30
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Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules 2021; 11:biom11101451. [PMID: 34680084 PMCID: PMC8533419 DOI: 10.3390/biom11101451] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023] Open
Abstract
High Mobility Group Box (HMGB) proteins are small architectural DNA binding proteins that regulate multiple genomic processes such as DNA damage repair, nucleosome sliding, telomere homeostasis, and transcription. In doing so they control both normal cellular functions and impact a myriad of disease states, including cancers and autoimmune diseases. HMGB proteins bind to DNA and nucleosomes to modulate the local chromatin environment, which facilitates the binding of regulatory protein factors to the genome and modulates higher order chromosomal organization. Numerous studies over the years have characterized the structure and function of interactions between HMGB proteins and DNA, both biochemically and inside cells, providing valuable mechanistic insight as well as evidence these interactions influence pathological processes. This review highlights recent studies supporting the roles of HMGB1 and HMGB2 in global organization of the genome, as well as roles in transcriptional regulation and telomere maintenance via interactions with G-quadruplex structures. Moreover, emerging models for how HMGB proteins function as RNA binding proteins are presented. Nuclear HMGB proteins have broad regulatory potential to impact numerous aspects of cellular metabolism in normal and disease states.
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31
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Wang X, Greenblatt HM, Bigman LS, Yu B, Pletka CC, Levy Y, Iwahara J. Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions. J Mol Biol 2021; 433:167122. [PMID: 34181980 DOI: 10.1016/j.jmb.2021.167122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/03/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Abstract
Highly negatively charged segments containing only aspartate or glutamate residues ("D/E repeats") are found in many eukaryotic proteins. For example, the C-terminal 30 residues of the HMGB1 protein are entirely D/E repeats. Using nuclear magnetic resonance (NMR), fluorescence, and computational approaches, we investigated how the D/E repeats causes the autoinhibition of HMGB1 against its specific binding to cisplatin-modified DNA. By varying ionic strength in a wide range (40-900 mM), we were able to shift the conformational equilibrium between the autoinhibited and uninhibited states toward either of them to the full extent. This allowed us to determine the macroscopic and microscopic equilibrium constants for the HMGB1 autoinhibition at various ionic strengths. At a macroscopic level, a model involving the autoinhibited and uninhibited states can explain the salt concentration-dependent binding affinity data. Our data at a microscopic level show that the D/E repeats and other parts of HMGB1 undergo electrostatic fuzzy interactions, each of which is weaker than expected from the macroscopic autoinhibitory effect. This discrepancy suggests that the multivalent nature of the fuzzy interactions enables strong autoinhibition at a macroscopic level despite the relatively weak intramolecular interaction at each site. Both experimental and computational data suggest that the D/E repeats interact preferentially with other intrinsically disordered regions (IDRs) of HMGB1. We also found that mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition. This study illuminates a functional role of the fuzzy interactions of D/E repeats.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA.
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32
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Xu J, Jiang R, He H, Ma C, Tang Z. Recent advances on G-quadruplex for biosensing, bioimaging and cancer therapy. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116257] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Paul R, Dutta D, Das T, Debnath M, Dash J. G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells. Chemistry 2021; 27:8590-8599. [PMID: 33851760 DOI: 10.1002/chem.202100907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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Lan J, Luo H, Wu R, Wang J, Zhou B, Zhang Y, Jiang Y, Xu J. Internalization of HMGB1 (High Mobility Group Box 1) Promotes Angiogenesis in Endothelial Cells. Arterioscler Thromb Vasc Biol 2020; 40:2922-2940. [PMID: 32998518 DOI: 10.1161/atvbaha.120.315151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE In patients with peripheral artery disease, blockages in arterioles <1 mm cannot be treated surgically, and there are currently few effective medicines. Studies have shown that inflammation in ischemic tissue is related to injury recovery and angiogenesis, but insufficient attention has been paid to this area. Studies have suggested that HMGB1 (high mobility group protein 1), which is released by ischemic tissue, promotes angiogenesis, but the mechanism is not entirely clear. In this study, we tested the internalization of HMGB1 in endothelial cells and investigated a novel proangiogenic pathway. Approach and Results: Using green fluorescent protein-tagged HMGB1 to stimulate endothelial cells, we demonstrated HMGB1 internalization via dynamin and RAGE (receptor for advanced glycation end products)-dependent signaling. Using a fluorescence assay, we detected internalized protein fusion to lysosomes, followed by activation of CatB (cathepsin B) and CatL (cathepsin L). The latter promoted the release of VEGF (vascular endothelial growth factor)-A and endoglin and upregulated the capacities of cell migration, proliferation, and tube formation in endothelial cells. We identified that the cytokine-induced fragment-a key functional domain in HMGB1-mediates the internalization and angiogenic function of HMGB1. We further confirmed that HMGB1 internalization also occurs in vivo in endothelial cells and promotes angiogenesis in mouse femoral artery ligation. CONCLUSIONS In this study, we identified a novel pathway of HMGB1 internalization-induced angiogenesis in endothelial cells. This finding sheds light on the regulatory role of inflammatory factors in angiogenesis through cell internalization and opens a new door to understand the relationship between inflammation and angiogenesis in ischemic diseases.
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Affiliation(s)
- Jiaoli Lan
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Haihua Luo
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Rong Wu
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Biying Zhou
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yun Zhang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Jia Xu
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failured Research, Department of Pathophysiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
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36
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Amato J, Mashima T, Kamatari YO, Kuwata K, Novellino E, Randazzo A, Giancola C, Katahira M, Pagano B. Improved Anti-Prion Nucleic Acid Aptamers by Incorporation of Chemical Modifications. Nucleic Acid Ther 2020; 30:414-421. [PMID: 32991255 DOI: 10.1089/nat.2020.0899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nucleic acid aptamers are innovative and promising candidates to block the hallmark event in the prion diseases, that is the conversion of prion protein (PrP) into an abnormal form; however, they need chemical modifications for effective therapeutic activity. This communication reports on the development and biophysical characterization of a small library of chemically modified G-quadruplex-forming aptamers targeting the cellular PrP and the evaluation of their anti-prion activity. The results show the possibility of enhancing anti-prion aptamer properties through straightforward modifications.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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37
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Masai H, Tanaka T. G-quadruplex DNA and RNA: Their roles in regulation of DNA replication and other biological functions. Biochem Biophys Res Commun 2020; 531:25-38. [PMID: 32826060 DOI: 10.1016/j.bbrc.2020.05.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/19/2022]
Abstract
G-quadruplex is one of the best-studied non-B type DNA that is now known to be prevalently present in the genomes of almost all the biological species. Recent studies reveal roles of G-quadruplex (G4) structures in various nucleic acids and chromosome transactions. In this short article, we will first describe recent findings on the roles of G4 in regulation of DNA replication. G4 is involved in regulation of spatio-temporal regulation of DNA replication through interaction with a specific binding protein, Rif1. This regulation is at least partially mediated by generation of specific chromatin architecture through Rif1-G4 interactions. We will also describe recent studies showing the potential roles of G4 in initiation of DNA replication. Next, we will present showcases of highly diversified roles of DNA G4 and RNA G4 in regulation of nucleic acid and chromosome functions. Finally, we will discuss how the formation of cellular G4 could be regulated.
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Affiliation(s)
- Hisao Masai
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Taku Tanaka
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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38
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics. Sci Rep 2020; 10:3176. [PMID: 32081872 PMCID: PMC7035250 DOI: 10.1038/s41598-020-59774-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
An increasingly comprehension of the folding intermediate states of DNA G-quadruplexes (G4s) is currently an important scientific challenge, especially for the human telomeric (h-tel) G4s-forming sequences, characterized by a highly polymorphic nature. Despite the G-triplex conformation was proposed as one of the possible folding intermediates for the antiparallel and hybrid h-tel G4s, for the parallel h-tel topology with an all-anti guanine orientation, a vertical strand-slippage involving the G-triplets was proposed in previous works through microseconds-long standard molecular dynamics simulations (MDs). Here, in order to get further insights into the vertical strand-slippage and the folding intermediate states of the parallel h-tel G4s, we have carried out a Well-Tempered Metadynamics simulation (WT-MetaD), which allowed us to retrieve an ensemble of six G4s having two/G-tetrad conformations derived by the G-triplets vertical slippage. The insights highlighted in this work are aimed at rationalizing the mechanistic characterisation of the parallel h-tel G4 folding process.
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40
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Wang XH, Zhang SY, Shi M, Xu XP. HMGB1 Promotes the Proliferation and Metastasis of Lung Cancer by Activating the Wnt/β-Catenin Pathway. Technol Cancer Res Treat 2020; 19:1533033820948054. [PMID: 32815451 PMCID: PMC7444109 DOI: 10.1177/1533033820948054] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/19/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
The aim of this study was to investigate the role of high mobility group protein-1 (HMGB1) in the proliferation and migration of lung cancer cells. CCK-8 assays and colony formation assays were used to evaluate the effect of HMGB1 regulation on cancer cell viability and colony formation. Trans-well assays and wound healing assays were also performed. Our data showed that HMGB1 is upregulated in clinical lung cancer tissues compared with non-cancer tissues, and it is differentially expressed in lung cancer cell lines. The knockdown of HMGB1 in A549 lung cancer cells significantly reduced cell proliferation, viability and motility. In contrast, overexpression of HMGB1 in lung cancer H1299 cells significantly increased cell viability and motility. Western blotting showed that HMGB1 could promote epithelial-mesenchymal transition. The Wnt/β-catenin pathway was activated after overexpression of HMGB1 in H1299 cells, while it was inactivated by knocking down HMGB1 in A549 cells. These data suggest that HMGB1 promotes the proliferation and migration of lung cancer cells in vitro. The carcinogenic behavior of HMGB1 can be achieved by activating the Wnt/β-catenin pathway.
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Affiliation(s)
- Xiao-hui Wang
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Shu-ying Zhang
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Mei Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiao-peng Xu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
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G-Quadruplex Binders Induce Immunogenic Cell Death Markers in Aggressive Breast Cancer Cells. Cancers (Basel) 2019; 11:cancers11111797. [PMID: 31731707 PMCID: PMC6895816 DOI: 10.3390/cancers11111797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background: DNA G-quadruplex (G4) structures represent potential anti-cancer targets. In this study, we compared the effect of two G4-targeting compounds, C066-3108 and the gold standard BRACO-19. Methods: In breast and prostate cancer cells, cytotoxicity induced by both molecules was measured by a sulforhodamine B assay. In breast cancer cells, cycle, apoptosis, the formation of G4 structures, calreticulin and high mobility group box 1 (HMGB1), as well as T cell activation, were analyzed by flow cytometry and adenosine triphosphate (ATP) by luminescence. Results: Both ligands inhibited cell survival and induced DNA damage. In MCF-7 cells, G4 ligands increased the subG0/G1 phase of the cell cycle inducing apoptosis and reduced intracellular ATP. In untreated MCF-7 cells, we observed a slight presence of G4 structures associated with the G2/M phase. In MDA-MB231 cells, G4 ligands decreased the G1 and enhanced the G2/M phase. We observed a decrease of intracellular ATP, calreticulin cell surface exposure and an increase of HMGB1, accompanied by T cell activation. Both compounds induced G4 structure formation in the subG0/G1 phase. Conclusions: Our data report similar effects for both compounds and the first evidence that G4 ligands induce the release of danger signals associated with immunogenic cell death and induction of T cell activation.
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